Literature – Online Learning Portal

LIBRARY

Click the tabs below to explore a few of our most popular applications for our suite of HALO products.

CUSTOMER PUBLICATIONS

Indica Labs’ customers perform quantitative image analysis on research areas as diverse as immuno-oncology, toxicology, metabolism, and neuroscience. Check out the latest publications from our customers with HALO image analysis software! Click the navigation bar to sort according to Application, Journal, HALO Module, and more.

Title	Authors	Year	Journal	Application	HALO Modules	Product
Stem cellderived CAR T cells traffic to HIV reservoirs in macaques	Barber-Axthelm IM, Barber-Axthelm V, Sze KY, Zhen A, Suryawanshi GW, Chen ISY, Zack JA, Kitchen SG, Kiem H-P, Peterson CW	2021	JCI Insight	Immunology, Infectious Disease	Area Quantification	HALO
IL-1-driven stromal-neutrophil interaction in deep ulcers defines a pathotype of therapy non-responsive inflammatory bowel disease	Friedrich M, Pohin M, Jackson MA, Korsunsky I, Bullers S, Rue-Albrecht K, Christoforidou Z, Sathananthan D, Ravindran R, Peres RS, Sharpe H, Wei K, Watts GFM, Mann EH, Geremia A, Thomas T, Attar M, Oxford IBD Cohort Investigators, Roche Fibroblast Network Consortium, McCuaig S, Thomas L, Collantes E, Uhlig HH, Sansom S, Easton A, Raychaudhuri S, Travis SP, Powrie FM	2021	bioRxiv	Immunology	Cytonuclear	HALO
Highly Fermentable Fiber Alters Fecal Microbiota and Mitigates Swine Dysentery Induced by Brachyspira hyodysenteriae	Helm ET, Gabler NK, Burrough ER	2021	Animals	Infectious Disease	Cytonuclear	HALO
Vascular endothelial ERp72 is involved in the inflammatory response in a rat model of skeletal muscle injury	Khalaf NB, Al-Mehatab D, Fathallah DM	2021	Medicine Reports	Immunology	Cytonuclear	HALO
Lipid Source and Peroxidation Status Alter Immune Cell Recruitment in Broiler Chicken Ileum	Fries-Craft KA, Meyer MM, Lindblom SC, Kerr BJ, Bobeck EA	2021	The Journal of Nutrition	Immunology	ISH/FISH	HALO
Frontotemporal lobar degeneration proteinopathies have disparate microscopic patterns of white and grey matter pathology	Giannini LAA, Peterson C, Ohm D, Xie SX, McMillan CT, Raskovsky K, Massimo L, Suh E, Van Deerlin VM, Wolk DA, Trojanowski JQ, Lee EB, Grossman M, Irwin DJ	2021	Acta Neuropathologica Communications	Neuroscience	Area Quantification	HALO
Fasting reverses drug-resistance in hepatocellular carcinoma through p53-dependent metabolic synergism	Krstic J, Reinisch I, Schindlmaier K, Galhuber M, Berger N, Kupper N, Moyschewitz E, Auer M, Michenthaler H, Nössing C, Depaoli MR, Ramadani-Muja J, Stryeck S, Pichler M, Rinner B, Deutsch AJA, Reinisch A, Madl T, Chiozzi RZ, Heck AJR, Huch M, Malli R, Prokesch A	2021	bioRxiv	Oncology	Classifier, Cytonuclear	HALO
Recruitment of KRAS downstream target ARL4C to membrane protrusions accelerates pancreatic cancer cell invasion	Harada A, Matsumoto S, Yasumizu Y, Akama T, Eguchi H, Kikuchi A	2021	bioRxiv	Oncology	Area Quantification	HALO
Potential role of M2 TAMs around lymphatic vessels during lymphatic invasion in papillary thyroid carcinoma	Kabasawa T, Ohe R, Aung NY, Urano Y, Kitaoka T, Tamazawa N, Utsunomiya A, Yamakawa M	2021	Scientific Reports	Oncology	Area Quantification	HALO
Amylin deposition activates HIF1? and 6-phosphofructo-2-kinase/fructose-2, 6-biphosphatase 3 (PFKFB3) signaling in failing hearts of non-human primates	Liu M, Li N, Qu C, Gao Y, Wu L, Hu LG	2021	Communications Biology	Metabolism	Area Quantification, Cytonuclear	HALO
BMP pathway antagonism by Grem1 regulates epithelial cell fate in intestinal regeneration	Koppens MAJ, Davis H, Valbuena GN, Mulholland EJ, Nasreddin N, Colombe M, Antanaviciute A, Biswas S, Friedrich M, Lee L, Oxford IBD cohort investigators, Wang LM, Koelzer VH, East JE, Simmons A, Winton DJ, Leedham SJ	2021	bioRxiv	Gastroenterology	Area Quantification	HALO
A distinct repertoire of cancer-associated fibroblasts is enriched in cribriform prostate cancer	Hesterberg AB, Rios BL, Wolf EM, Tubbs C, Wong HY, Schaffer KR, Lotan TL, Giannico GA, Gordetsky JB, Hurley PJ	2021	Journal of Pathology:Clinical Research	Oncology	Classifier, ISH/FISH	HALO
Dystrophic microglia are associated with neurodegenerative disease and not healthy aging in the human brain	Shahidehpour RK, Higdon RE, Crawford NG, Neltner JH, Ighodaro ET, Patel E, Price D, Nelson PT, Bachstetter AD	2021	Neurobiology of Aging	Neuroscience	Area Quantification	HALO
Inhibition of Hedgehog signaling alters fibroblast composition in pancreatic cancer	Steele NG, Biffi G, Kemp SB, Zhang Y, Drouillard D, Syu L-J, Hao Y, Oni TE, Brosnan E, Elyada E, Doshi A, Hansma C, Espinoza C, Abbas A, The S, Irizarry-Negron VM, Halbrook CJ, Franks N, Hoffman M, Brown KL, Carpenter ES, Nwosu ZC, Johnson C, Lima F, Anderson MA, Park Y, Crawford HC, Lyssiotis CA, Frankel TF, Rao A, Bednar F, Dlugosz AA, Preall J, Tuveson DA, Allen B, di Magliano MP	2021	Clinical Cancer Research	Oncology	Area Quantification	HALO
Locally confined IFN? production by CD4+ T cells provides niches for murine cytomegalovirus 4 replication in the salivary gland	Oderbolz J, Zangger N, Zimmerman L, Sandu I, Starruß J, Graw F, Oxenius A	2021	bioRxiv		Classifier, Spatial Analysis, Highplex FL	HALO
Kaiso (ZBTB33) subcellular partitioning functionally links LC3A/B, the tumor microenvironment, and breast cancer survival	Singhal SK, Byun JS, Park S, Yan T, Yancey R, Caban A, Hernandez SG, Hewitt SM, Boisvert H, Hennek S, Bobrow M, Ahmed SU, White J, Yates C, Aukerman A, Vanguri R, Bareja R, Lenci R, Farré PL, De Siervi A, Nápoles AM, Vohra N, Gardner K	2021	Communications Biology	Oncology	Cytonuclear, TMA	HALO
Deep Learning-Based Annotation Transfer between Molecular Imaging Modalities: An Automated Workflow for Multimodal Data Integration	Race AM, Sutton D, Hamm G, Maglennon G, Morton JP, Strittmatter N, Campbell A, Sansom OJ, Wang Y, Barry ST, Takáts Z, Goodwin RJA, Bunch J	2021	Analytical Chemistry	Oncology		HALO AI
Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma	Bakouny Z, Braun DA, Shukla SA, Pan W, Gao X, Hou Y, Flaifel A, Tang S, Bosma-Moody A, He MX, Vokes N, Nyman J, Xie W, Nassar AH, Alaiwi SA, Flippot R, Bouchard G, Steinharter JA, Nuzzo PV, Ficial M, SantAngelo M, Forman J, Berchuck JE, Dudani S, Bi K, Park J, Camp S, Sticco-Ivins M, Hirsch L, Baca SC, Wind-Rotolo M, Ross-Macdonald P, Sun M, Mary Lee G-SM, Chang SL, Wei XX, McGregor BA, Harshman LC, Genovese G, Ellis L, Pomerantz M, Hirsch MS, Freedman ML, Atkins MB, Wu CJ, Ho TH, Linehan WM, McDermott DF, Heng DYC, Viswanathan SR, Signoretti S, Van Allen EM, Choueiri TK	2021	Nature Communications	Oncology	Highplex FL	HALO
IgA transcytosis and antigen recognition govern ovarian cancer immunity	Biswas S, Mandal G, Payne KK, Anadon CM, Gatenbee CD, Chaurio RA, Costich TL, Moran C, Harro CM, Rigolizzo KE, Mine JA, Trillo-Tinoco J, Sasamoto N, Terry KL, Marchion D, Buras A, Wenham RM, Yu X, Townsend MK, Tworoger SS, Rodriguez CR, Anderson AR, Conejo-Garcia JR	2021	Nature	Immuno-oncology	Highplex FL	HALO
Characterization of Macrophages and Osteoclasts in the Osteosarcoma Tumor Microenvironment at Diagnosis: New Perspective for Osteosarcoma Treatment?	Gomez-Brouchet A, Gilhodes J, Van Acker N, Brion R, Bouvier C, Assemat P, Gaspar N, Aubert S, Guinebretiere J-M, Marie B, Larousserie F, Entz-Werlé N, de Pinieux G, Mascard E, Gouin F, Brousset P, Tabone M-D, Jimenez M, Le Deley M-C, Blay J-Y, Brugieres L , Piperno-Neumann S, Rédini F	2021	Cancers	Immuno-oncology	Highplex FL	HALO
CD30+OX40+ Treg is associated with improved overall survival in colorectal cancer	Lam JH, Hong M, Koo S-L, Chua CWL, Lim KL, Wee F, Wan WK, Leow WQ, Yeo JG, Tan IBH, Yeong J, Lim TKH, Lim TS	2021	Cancer Immunology, Immunotherapy	Immuno-oncology	Highplex FL	HALO
Sustained Helicobacter pylori infection accelerates gastric dysplasia in a mouse model	OBrien VP, Koehne AL, Dubrulle J, Rodriguez AE, Leverich CK, Kong VP, Campbell JS, Pierce RH, Goldenring JR, Choi E, Salama NR	2021	Life Science Alliance	Immuno-oncology	Highplex FL	HALO
A feasibility study of combined epigenetic and vaccine therapy in advanced colorectal cancer with pharmacodynamic endpoint	Bever KM, Thomas DL, Zhang J, Rivera EAD, Rosner GL, Zhu Q, Nauroth JM, Christmas B, Thompson ED, Anders RA, Judkins C, Liu M, Jaffee EM, Ahuja N, Zheng L, Azad NS	2021	Clinical Epigenetics	Oncology	Immune, Membrane	HALO
CD8+ T cells fail to limit SIV reactivation following ART withdrawal until after viral amplification	Okoye AA, Duell DD, Fukazawa Y, Varco-Merth B, Marenco A, Behrens H, Chaunzwa TM, Selseth AN, Gilbride RM, Shao J, Edlefsen PT, Geleziunas R, Pinkevych M, Davenport MP, Busman-Sahay K, Nekorchuk MD, Park H, Smedley JV, Axthelm MK, Estes JD, Hansen SG, Keele BF, Lifson JD, Picker LJ	2021	The Journal of Clinical Investigation	Immunology, Infectious Disease	ISH/FISH	HALO, HALO AI
The effect of cyfluthrin on testis inhibin B in rats and the intervention of Lycium barbarum polysaccharide	Guo X, Xie Y-X, Guo C, Wei J-L, Yang H-F	2021	Molecular & Cellular Toxicology	Toxicology	Multiplex IHC	HALO
Cooperative targeting of immunotherapy-resistant melanoma and lung cancer by an AXL-targeting antibody-drug conjugate and immune checkpoint blockade	Boshuizen J, Pencheva N, Krijgsman O, Altimari DD, Castro PG, de Bruijn B, Ligtenberg MA, den Heuvel EG, Vredevoogd DW, Song J-Y, Visser N, Apriamashvili G, Janmaat ML, Plantinga TS, Franken P, Houtkamp M, Lingnau A, Jure-Kunkel M, Peeper DS	2021	Cancer Research	Immuno-oncology		HALO
ATP-binding cassette transporters restrict drug delivery and efficacy against brain tumors even when blood-brain barrier integrity is lost	de Gooijer MC, Kemper EM, Buil LCM, Citirikkaya CH, Buckle T, Beijnen JH, van Tellingen O	2021	Cell Reports Medicine	Oncology		HALO
The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancer	Najumudeen AK, Ceteci F, Fey SK, Hamm G, Steven RT, Hall H, Nikula CJ, Dexter A, Murta T, Race AM, Sumpton D, Vlahov N, Gay DM, Knight JRP, Jackstadt R, Leach JDG, Ridgway RA, Johnson ER, Nixon C, Hedley A, Gilroy K, Clark W, Malla SB, Dunne PD, Rodriguez-Blanco G, Critchlow SE, Mrowinska A, Malviya G, Solovyev D, Brown G, Lewis DY, Mackay GM, Strathdee D, Tardito S, Gottlieb E, CRUK Rosetta Grand Challenge Consortium, Takats Z, Barry ST, Goodwin RJA, Bunch J, Bushell M, Campbell AD, Sansom OJ	2021	Nature Genetics	Oncology		HALO
Single-cell analysis shows that adipose tissue of persons with both HIV and diabetes is enriched for clonal, cytotoxic, and CMV-specific CD4+ T cells	Wanjalla CN, McDonnell WY, Ram R, Chopra A, Gangula R, Leary S, Mashayekhi M, Simmons JD, Warren CM, Bailin S, Gabriel CL, Cuo L, Furch BD, Lima MC, Woodward BO, Hannah L, Pilkinton MA, Fuller DT, Kawai K, Virmani R, Finn AV, Hasty AH, Mallal SA, Kalams SA, Koethe JR	2021	Cell Reports Medicine	Immunology, Metabolism		HALO
Acute Respiratory Distress in Aged, SARS-CoV-2 Infected African Green Monkeys but not Rhesus Macaques	Blair RV, Vaccari M, Doyle-Meyers LA, Roy CJ, Russell-Lodrigue K, Fahlberg M, Monjure CJ, Beddingfield B, Plante KS, Plante JA, Weaver SC, Qin X, Midkiff CC, Lehmicke G, Golden N, Threeton B, Penney T, Allers C, Barnes MB, Pattison M, Datta PK, Maness NJ, Birnbaum A, Fischer T, Bohm RP, Rappaport J	2020	The American Journal of Pathology	Infectious Disease	Classifier	HALO
Association of COVID-19 inflammation with activation of the C5aC5aR1 axis	Carvelli J, Demaria O, Vely F, Batista L, Benmansour NC, Fares J, Carpentier S, Thibult M-L, Morel A, Andre P, Represa A, Piperoglou C, Cordier PY, Le Dault E, Guervilly C, Simone P, Gainnier M, Morel Y, Ebbo M, Schleinitz N, Vivier E	2020	Nature	Immunology	Cytonuclear	HALO
Impact of Preanalytical Factors During Histology Processing on Section Suitability for Digital Image Analysis	Chlipala EA, Butters M, Brous M, Fortin JS, Archuletta R, Copeland K, Bolon B	2020	Toxicologic Pathology	Toxicology	Area Quantification, Cytonuclear	HALO
Tumor vessel normalization, immuno-stimulatory reprogramming, and improved survival in glioblastoma with combined inhibition of PD-1, angiopoietin-2, and VEGF	Di Tacchio M, Macas J, Weissenberger J, Sommer K, Bähr O, Steinbach JP, Senft C, Seifert V, Glas M, Herrlinger U, Krex D, Meinhardt M, Weyerbrock A, Timmer M, Goldbrunner R, Deckert M, Scheel AH, Büttner R, Grauer OM, Schittenhelm J, Tabatabai G, Harter PN, Guenther S, Devraj K, Plate KH, Reiss Y	2020	Cancer Immunology Research	Oncology, Immuno-oncology	Classifier, Cytonuclear	HALO
Immune cell landscaping reveals a protective role for regulatory T cells during kidney injury and fibrosis	do Valle Duraes F, Lafont A, Biebel M, Martin K, Darribat K, Cuttat R, Waldt A, Naumann U, Wieczorek G, Gaulis S, Pfister S, Mertz KD, Li J, Roma G, Warncke M	2020	JCI Insight	Immunology	Area Quantification, Cytonuclear	HALO
The prevalence and prognostic significance of estrogen receptor beta expression in non-small cell lung cancer	Enwere EK, Dean ML, Li H, D'Silva A, Bebb DG	2020	Translational Lung Cancer Research	Oncology	Cytonuclear, TMA	HALO
Dendritic Cell Paucity Leads to Dysfunctional Immune Surveillance in Pancreatic Cancer	Hedge S, Krisnawan VE, Herzog BH, Zuo C, Breden MA, Knolhoff BL, Hogg GD, Tang JP, Baer JM, Mpoy C, Lee KB, Alexander KA, Rogers BE, Murphy KM, Hawkins WG, Fields RC, DeSelm CJ, Schwarz JK, DeNardo DG	2020	Cancer Cell	Oncology, Immuno-oncology	Area Quantification, Cytonuclear, Immune	HALO
Periconceptional exposure to lopinavir, but not darunavir, impairs decidualization: a potential mechanism leading to poor birth outcomes in HIV-positive pregnancies	Kala S, Dunk C, Acosta S, Serghides L	2020	Human Reproduction	Infectious Disease	Cytonuclear	HALO
Three-dimensional culture models mimic colon cancer heterogeneity induced by different microenvironments	Kawai S, Yamazaki M, Shibuya K, Yamazaki M, Fujji E, Nakano K, Suzuki M	2020	Scientific Reports	Oncology	Cytonuclear	HALO
Epithelial-mesenchymal transition of absorptive enterocytes and depletion of Peyer's patch M cells after PEDV infection	Chen Y-M, Helm ET, Groeltz-Thrush, Gabler NK, Burrough ER	2020	Virology	Immunology	Area Quantification	HALO
Imaging breast cancer using hyperpolarized carbon-13 MRI	Gallagher FA, Woitek R, McLean MA, Gill AB, Garcia RM, Provenzano E, Riemer F, Kaggie J, Chhabra A, Ursprung S, Grist JT, Daniels CJ, Zaccagna F, Laurent M-C, Locke M, Hilborne S, Frary A, Torheim T, Boursnell C, Schiller A, Patterson I, Slough R, Carmo B, Kane J, Biggs H, Harrison E, Deen SS, Patterson A, Lanz T, Kingsbury Z, Ross M, Basu B, Baird R, Lomas DJ, Sala E, Wason J, Rueda OM, Chin S-F, Wilkinson IB, Graves MJ, Abraham JE, Gilbert FJ, Caldas C, Brindle KM	2020	Proceedings of the National Academy of Sciences	Oncology	Area Quantification	HALO
Conformation-selective tau monoclonal antibodies inhibit tau pathology in primary neurons and a mouse model of Alzheimers disease	Gibbons GS, Kim S-J, Wu Q, Riddle DM, Leight SN, Changolkar L, Xu H, Meymand ES, O'Reilly M, Zhang B, Brunden KR, Trojanowski JQ, Lee VMY	2020	Molecular Neurodegeneration	Neuroscience	Area Quantification	HALO
TGF?-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblasts	Grauel AL, Nguyen B, Ruddy D, Laszewski T, Schwartz S, Chang J, Chen J, Piquet M, Pelletier M, Yan Z, Kirkpatrick ND, Wu J, deWeck A, Riester M, Hims M, Geyer FC, Wagner J, MacIsaac K, Deeds J, Diwanji R, Jayaraman P, Yu Y, Simmons Q, Weng S, Raza A, Minie B, Dostalek M, Chikkegowda P, Ruda V, Iartchouk O, Chen N, Thierry R, Zhou J, Pruteanu-Malinici I, Fabre C, Engelman JA, Dranoff G, Cremasco V	2020	Nature Communications	Oncology	Area Quantification	HALO
Ex-vivo delivery of monoclonal antibody (Rituximab) to treat human donor lungs prior to transplantation	Ku TJY, Ribeiero RVP, Ferreira VH, Galasso M, Keshavjee S, Kumar D, Cypel M, Humar A	2020	EBioMedicine	Other	Classifier, Cytonuclear	HALO
Transmission of tauopathy strains is independent of their isoform composition	He Z, McBride JD, Zu, Changolkar L, Kim S, Zhang B, Narasimhan S, Gibbons GS, Kozak M, Schellenberg GD, Trrojanowski JQ, Lee VM-Y	2020	Nature Communications	Neuroscience	Area Quantification	HALO
Human cardiac fibroblasts expressing VCAM1 improve heart function in postinfarct heart failure rat models by stimulating lymphangiogenesis	Iwamiya T, Segnard B-D, Matsuoka Y, Imamura T	2020	PLOS One	Myology	Area Quantification	HALO
Environmental contaminant ammonia triggers epithelial-to-mesenchymal transition-mediated jejunal fibrosis with the disassembly of epithelial cell-cell contacts in chicken	Jing H, Wang S, Wang Y, Shen N, Gao X-J	2020	ScienceTotalEnvrt	Toxicology	Area Quantification	HALO
Cholinergic receptors on intestine cells of Ascaris suum and activation of nAChRs by levamisole	McHugh M, Williams P, Verma S, Powell-Coffman JA, Robertson AP, Martin RJ	2020	International Journal for Parasitology: Drugs and Drug Resistance	Gastroenterology, Infectious Disease	Area Quantification	HALO
Adult onset pan-neuronal human tau tubulin kinase 1 expression causes severe cerebellar neurodegeneration in mice	McMillan P, Wheeler J, Gatlin RE, Taylor L, Strovas T, Baum M, Bird TD, Latimer C, Keene CD, Kraemer BC, Liachko NF	2020	Acta Neuropathologica Communications	Neuroscience	Area Quantification	HALO
Spatial immune profiling of the colorectal tumor microenvironment predicts good outcome in stage II patients	Nearchou IP, Gwyther BM, Georgiakakis ECT, Gavriel CG, Kajiwara Y, Ueno H, Harrison DJ, Caie PD	2020	Digital Medicine	Immuno-oncology	Classifier, Area Quantification, Spatial Analysis	HALO
11? hydroxysteroid dehydrogenase 1: a new marker for predicting response to immune-checkpoint blockade therapy in non-small-cell lung carcinoma	Saito R, Miki Y, Abe T, Miyauchi E, Abe J, Nanamiya R, Inoue C, Sato I, Sasano H	2020	British Journal of Cancer	Immuno-oncology	Area Quantification	HALO
Clinicopathological significance of endoplasmic reticulum stress proteins in ovarian carcinoma	Samanta S, Tamura S, Dubeau L, Mhawech-Fauceglia P, Miyagi Y, Kato H, Lieberman R, Buckanovich RJ, Lin YG, Neamati N	2020	Scientific Reports	Oncology	Area Quantification	HALO
Prognostic value of tumor-inltrating immune cells in primary colorectal cancer and metastases	Martin SZ, Tagscherer KE, Deckert S, Horst D, Moehler M, Lang H, Roth W	2020	*Pre-Print	Immuno-oncology	Classifier, Cytonuclear	HALO
Implementation of PD-L1 22C3 IHC pharmDxTM in Cell Block Preparations of Lung Cancer: Concordance with Surgical Resections and Technical Validation of CytoLyt® Prefixation	Lou SK, Ko HM, Kinoshita T, MacDonald S, Weiss J, Czarnecka-Kujawa K, Boerner SL, Yasufuku K, Tsao M-S, Schwock J	2020	Acta Cytologica	Oncology	Classifier, Membrane	HALO
Immuno-Interface Score to Predict Outcome in Colorectal Cancer Independent of Microsatellite Instability Status	Nestarenkaite A, Fadhil W, Ramusson A, Susanti S, Hadjimichael E, Laurinaviciene A, Ilyas M, Laurinavicius A	2020	Cancers	Immuno-oncology	Classifier, Multiplex IHC	HALO
Assessment of associations between clinical and immune microenvironmental factors and tumor mutation burden in resected nonsmall cell lung cancer by applying machine learning to whole-slide images	Ono A, Terada Y, Kawata T, Serizawa M, Isaka M, Kawabata T, Imai T, Mori K, Muramatsu K, Hayashi I, Kenmotsu H, Oshima K, Urakami K, Nagashima T, Kusuhara M, Akiyama Y, Sugino T, Ohde Y, Yamaguchi K, Takahashi T T	2020	Cancer Medicine		Classifier, Multiplex IHC, Serial Section	HALO
Prevalence of CD8+ cytotoxic lymphocytes in human neoplasms	Blessin NC, Spriestersbach P, Li W, Mandelkow T, Dum D, Simon R, Hube-Magg C, Lutz F, Viehweger F, Lennartz M, Fraune C, Nickelsen V, Fehrle W, Göbel C, Weidemann S, Clauditz T, Lebok P, Möller K, Steurer S, Izbicki JR, Sauter G, Minner S, Jacobsen F, Luebke AM, Büscheck F, Höflmayer D, Wilczak W, Burandt E, Hinsch A	2020	Cellular Oncology	Oncology, Immuno-oncology	Membrane, TMA	HALO
Persistence of adoptively transferred T cells with a kinetically engineered IL-2 receptor agonist	Parisi G, Saco JD, Salazar FB, Tsoi J, Krystofinski P, Puig-Saus C, Zhang R, Zhou J, Cheung-Lau GC, Garcia AJ, Grasso CS, Tavaré R, Hu-Lieskovan S, Mackay S, Zalevsky J, Bernatchez C, Diab A, Wu AM , Comin-Anduix B, Charych D, Ribas A	2020	Nature Communications	Oncology, Immuno-oncology	Cytonuclear	HALO
Mechanical regulation of glycolysis via cytoskeleton architecture	Park JS, Burckhardt CJ, Lazcano R, Solis LM, Isogai T, Li L, Chen CS, Gao B, Minna JD, Bachoo R, DeBerardinis RJ, Danuser G	2020	Nature	Oncology	Classifier, Cytonuclear, TMA	HALO
Naproxen chemoprevention promotes immune activation in Lynch syndrome colorectal mucosa	Reyes-Uribe L, Wu W, Gelincik O, Bommi PV, Francisco-Cruz A, Solis LM, Lynch PM, Lim R, Stoffel EM, Kanth P, Samadder NJ, Mork ME, Taggart MW, Milne GL, Marnett LJ, Vornik L, Liu DD, Revuelta M, Chang K, You YN, Kopelovich L, Wistuba II, Lee JJ, Sei S, Shoemaker RH, Szabo E, Richmond E, Umar A, Perloff M, Brown PH, Lipkin SM, Vilar E	2020	Gut	Oncology	Classifier, Cytonuclear	HALO
p53 is associated with high-risk and pinpoints TP53 missense mutations in mantle cell lymphoma	Rodrigues JM, Hassan M, Freiburghaus C, Eskelund CW, Geisler C, Raty R, Kolstad A, Sundstrom C, Glimelius I, Gronbaek K, Kwiecinska A, Porwit A, Jerkeman M, Ek S	2020	British Journal of Haematology	Oncology	Classifier, Cytonuclear	HALO
RUNX1 is a driver of renal cell carcinoma correlating with clinical outcome	Rooney N, Mason SM, McDonald L, Däbritz HM, Campbell KJ, Hedley A, Howard S, Athineos D, Nixon C, Clark W, Leach JDG, Samsom OJ, Edwards J, Cameron ER, Blyth K	2020	Cancer Research	Oncology	Cytonuclear	HALO
Analytical Performance of an Immunoprofiling Assay Based on RNA Models	Schillebeeckx I, Armstrong JR, Forys JT, Hiken J, Earls J, Flanagan KC, Cui T, Glasscock JI, Messina DN, Duncavage EJ	2020	The Journal of Molecular Diagnostics	Immunology	Cytonuclear	HALO
Prognostic significance of mesothelin expression in colorectal cancer disclosed by area-specific four-point tissue microarrays	Shiraishi T, Shinto E, Nearchou IP, Tsuda H, Kajiwara Y, Einama T, Caie PD, Kishi Y, Ueno H	2020	Vichows Archiv	Oncology	Cytonuclear, TMA	HALO AI
Prognostic and Predictive Value of Tumor-infiltrating Leukocytes and of Immune Checkpoint Molecules PD1 and PDL1 in Clear Cell Renal Cell Carcinoma	Stenzel PJ, Schindeldecker M, Teagscherer KE, Foersch S, Herpel E, Hohenfellner M, Hatiboglu G, Alt J, Thomas C, Haferkamp A, Roth W, Macher-Goeppinger S	2020	Translational Oncology	Oncology, Immuno-oncology	Classifier, Cytonuclear, TMA	HALO
Linking epigenetic signature and metabolic phenotype in IDH mutant and IDH wildtype diffuse glioma	Buran Y, Filipski K, Bernatz S, Baumgarten P, Roller B, Zinke J, Zeiner PS, Ilina E, Senft C, Ronellenfitsch MW, Plate KH, Bähr O, Hattingen E, Steinbach JP, Mittelbron M, Harter PN	2020	Neuropathology and Applied Neurobiology	Neuroscience	Multiplex IHC, TMA	HALO
O 6-Methylguanine DNA Methyltransferase and Glucose Transporter 2 in Foregut and Hindgut Gastrointestinal Neuroendocrine Neoplasms	Watanbe H, Yamazaki Y, Fujishima F, Izxumi K, Imamura M, Hijioka S, Toriyama K, Yatabe Y, Kudo A, Motoi F, Unno M, Sasano H	2020	BMC Cancer	Oncology	Cytonuclear	HALO
SLFN11 informs on standard of care and novel treatments in a wide range of cancer models	Winkler C, Armenia J, Jones GN, Tobalina L, Sale MJ, Petreus T, Baird T, Serra V, Wang AT, Lau A, Garnett MJ, Jaaks P, Coker EA, Pierce AJ, O'Connor MJ, Leo E	2020	British Journal of Cancer	Oncology	Classifier, Cytonuclear	HALO
Lung Expression of Human ACE2 Sensitizes the Mouse to SARS-CoV-2 Infection	Han K, Blair RV, Iwanaga N, Liu F, Russell-Lodrigue KE, Qin Z, Midkiff CC, Golden NA, Doyle-Meyers LA, Kabir ME, Chandler KE, Cutrera KL, Ren M, Monjure CJ, Lehmicke G, Fischer T, Beddingfield B, Wanek AG, Birnbaum A, Maness NJ, Roy CJ, Datta PK, Rappaport J, Kolls JK, Qin X	2020	American Journal of Respiratory Cell and Molecular Biology	Infectious Disease		HALO AI
Human ileal organoid model recapitulates clinical incidence of diarrhea associated with small molecule drugs	Belair DG, Visconti RJ, Hong M, Marella M, Peters MF, Scott CW, Kolaja KL	2020	Toxicology in Vitro	Toxicology	Highplex FL	HALO
Multiomic analysis and immunoprofiling reveal distinct subtypes of human angiosarcoma	Chan JY, Lim JQ, Yeong J, Ravi V, Guan P, Boot A, Tay TKY, Selvarajan S, Nasir NDM, Loh JH, Ong CK, Huang D, Tan J, Li Z, Ng CC-Y, Tan TT, Masuzawa M, Sung KW-K, Farid M, Quek RHH, Tan NC, Teo MCC, Rozen SG, Tan P, Fotreal A, The BT, Soo KC	2020	The Journal of Clinical Investigation	Immuno-oncology	Highplex FL	HALO
Tumoral PD-1hiCD8+ 1 T cells are partially exhausted and 2 predict favorable outcome in triple-negative breast cancer	Guo L, Cao C, Goswami S, Huang X, Ma L, Guo Y, Yang B, Li T, Chi Y, Zhang X, Wu J	2020	Clinical Science	Immuno-oncology	Highplex FL	HALO
CXCR4+ cells are increased in lung tissue of patients with idiopathic pulmonary fibrosis	Jaffar J, Griffiths K, Oveissi S, Duan M, Foley M, Glaspole I, Symons K, Organ L, Westfall G	2020	Respiratory Research	Fibrosis	Highplex FL	HALO
Rova-T enhances the anti-tumor activity of anti-PD1 in a murine model of small cell lung cancer with endogenous Dll3 expression	Vitorino P, Chuang C-H, Iannello Z, Zhao X, Anderson W, Ferrando R, Zhang Z, Madhavan S, Karsunky H, Saunders LR	2020	Translational Oncology	Immuno-oncology	Highplex FL	HALO
Safety, immunogenicity, and clinical efficacy of durvalumab in combination with folate receptor alpha vaccine TPIV200 in patients with advanced ovarian cancer: a phase II trial	Zamarin D, Walderich S, Holland A, Zhou Q, Iasonos AE, Torrisi JM, Merghoub T, Chesebrough LF, Mcdonnell AS, Gallagher JM, Li Y, Hollmann TJ, Grisham RN, Erskine CL, Block MS, Knutson KL, O'Cearbhaill RE, Aghajanian C, Konner JA	2020	Journal for ImmunoTherapy of Cancer	Immuno-oncology	Highplex FL	HALO
Trajectory and Functional Analysis of PD-1high CD4+CD8+ T Cells in Hepatocellular Carcinoma by Single-Cell Cytometry and Transcriptome Sequencing	Zheng B, Wang D, Qiu X, Luo G, Wu T, Yang S, Li Z, Zhu Y, Wang S, Wu R, Sui C, Gu Z, Shen S, Jeong S, Wu Z, Gu J, Wang H, Chen L	2020	Advanced Science	Immuno-oncology	Highplex FL	HALO
Pulmonary Mycobacterium tuberculosis control associates with CXCR3- and CCR6-expressing antigen-specific Th1 and Th17 cell recruitment	Shanmugasundaram U, Bucsan AN, Ganatra SR, Ibegbu C, Quezada M, Blair RV, Alvarez X, Velu V, Kaushal D, Rengarajan J	2020	JCI Insight	Infectious Disease	Highplex FL	HALO AI
A first-in-human, phase 1, dose-escalation study of ABBV-176, an antibody-drug conjugate targeting the prolactin receptor, in patients with advanced solid tumors	Lemech C, Woodward N, Chan N, Mortimer J, Naumovski L, Nuthalapati S, Tong B, Jiang F, Ansell P, Ratajczak CK, Sachdev J	2020	Investigational New Drugs	Oncology	ISH/FISH	HALO
Gene expression of prostaglandin EP4 receptor in three canine carcinomas	Musser ML, Viall AK, Phillips RL, Hostetter JM, Johannes CM	2020	BMC Veterinary Research	Oncology	ISH/FISH	HALO
Cholecystokinin-1 receptor agonist induced pathological findings in the exocrine pancreas of non-human primates	Nyborg NCB, Kirk RK, de Boer AS, Andersen DW, Bugge A, Wulff BS, Thorup I, Clausen TR	2020	Toxicology & Applied Pharmacology	Metabolism	ISH/FISH	HALO
NPY mediates the rapid feeding and glucose metabolism regulatory functions of AgRP neurons	Ruud LE, Pereira MMA, de Solis AJ, Fenselau H, Bruning JC	2020	Nature Communications	Metabolism	ISH/FISH	HALO
Age-determined expression of priming protease TMPRSS2 and localization of SARS-CoV-2 infection in the lung epithelium	Schuler BA, Habermann AC, Plosa EJ, Taylor CJ, Jetter C, Kapp ME, Benjamin JT, Gullerman P, Nichols DS, Braunstein LZ, Hackett A, Koval M, Guttentag SH, Blackwell TS, Webber SA, Banovich NE, Kropski JA, Sucre JMS	2020	The Journal of Clincial Invesitgation	Infectious Disease	ISH/FISH	HALO
STAT3 inhibition with galiellalactone efectively targets the prostate cancer stem?like cell population	Canesin G, Maggio V, Palominos M, Stiehm A, Contreras HR, Castellon EA, Morote J, Paciucci R, Maitland NJ, Bjartell A, Hellsten R	2020	Scientific Reports	Oncology	Membrane	HALO
Genetic alterations and expression characteristics of ARID1A impact tumor immune contexture and survival in early-onset gastric cancer	Zou J, Qin W, Wang L, Wang Y, Shen J, Xiong W, Yu S, Song S, Ajani JA, Lin S-Y, Mills GB, Yuan X, Chen J, Peng G	2020	American Journal of Cancer Research	Immuno-oncology	Spatial Analysis, Highplex FL	HALO
Computational image analysis of T-cell infiltrates in resectable gastric cancer: association with survival and molecular subtypes	Challoner BR, von Loga K, Woolston A, Griffiths B, Sivamanoharan N, Semiannikova M, Newey A, Barber LJ, Mansfield D, Hewitt LC, Saito Y, Davarzani N, Starling N, Melcher A, Grabsch HI, Gerlinger M	2020	JNCI: Journal of the National Cancer Institute	Immuno-oncology	Multiplex IHC	HALO
Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection	Desai N, Neyaz A, Szabolcs A, Shih AR, Chen JH, Thapar V, Nieman LT, Solovyov A, Mehta A, Lieb DJ, Kulkarni AS, Jaicks C, Pinto CJ, Juric D, Chebib I, Colvin RB, Kim AY, Monroe R, Warren SE, Danaher P, Reeves JW, Gong J, Rueckert EH, Greenbaum BD, Hacohen N, Lagana SM, Rivera MN, Sholl LM, Stone JR, Ting DT, Deshpande V	2020	medRxiv	Infectious Disease	Multiplex IHC	HALO
An Antibody Targeting ICOS Increases Intratumoral Cytotoxic to Regulatory T-cell Ratio and Induces Tumor Regression	Sainson RCA, Thotakura AK, Kosmac M, Borhis G, Parveen N, Kimber R, Carvalho J, Henderson SJ, Pryke KL, Okell T, O'Leary S, Ball S, Van Krinks C, Gamand L, Taggart E, Pring EJ, Ali H, Craig H, Wong VWY, Liang Q, Rowlands RJ, Lecointre M, Campbell J, Kirby I, Melvin D, Germaschewski V, Oelmann E, Quaratino S, McCourt M	2020	Cancer Immunology Research	Immuno-oncology	Multiplex IHC	HALO
Immunogradient Indicators for Antitumor Response Assessment by Automated Tumor-Stroma Interface Zone Detection	Rasmusson A, Zilenaite D, Nestarenkaite A, Augulis R, Laurinaviciene A, Ostapenko V, Poskus T, Laurinavicius A	2020	The American Journal of Pathology		Multiplex IHC	HALO AI
Neoadjuvant immunotherapy leads to pathological responses in MMR-proficient and MMR-deficient early-stage colon cancers	Chalabi M, Fanchi LF, Dijkstra KK, Van den Berg JG, Aalbers AG, Sikorska K, Lopez-Yurda M, Grootscholten C, Beets GL, Snaebjornsson P, Maas M, Mertz J, Veninga V, Bounova G, Broeks A, Beets-Tan RG, de Wijkerslooth TR, van Lent AU, Marsman HA, Nuijten E, Kok NF, Kuiper M, Verbeek WH, Kok M, Van Leerdam ME, Schumacher TN, Voest EE, Haanen JB	2020	Nature Medicine	Immuno-oncology	Multiplex IHC, Serial Section	HALO
MCL1 inhibition is effective against a subset of small-cell lung cancer with high MCL1 and low BCL-XL expression	Yasuda Y, Ozasa H, Kim YH, Yamazoe M, Ajimizu H, Funazo TY, Nomizo T, Tsuji T, Yoshida H, Sakamori Y, Najajima N, Menju T, Yoshizawa A, Date H, Hirai T	2020	Cell Death & Disease	Oncology, Immuno-oncology	Cytonuclear	HALO
Inhibition of myostatin prevents microgravity-induced loss of skeletal muscle mass and strength	Smith RC, Cramer MS, Mitchell PJ, Lucchesi J, Ortega AM, Livingston EW, Ballard D, Zhang L, Hanson J, Barton K, Berens S, Credille KM, Bateman TA, Ferguson VL, Ma YL, Stodieck LS	2020	PLOS One	Myology	Muscle Fiber	HALO
Photoacoustic imaging biomarkers for monitoring biophysical changes during nanobubble-mediated radiation treatment	Hysi E, Fadhel MN, Wang Y, Sebastian JA, Giles A, Czarnota GJ, Exner AA, Kolios MC	2020	Photoacoustics	Other	Classifier, Area Quantification, Object Colocalization	HALO
Single-cell analysis of germinal-center B cells informs on lymphoma cell of origin and outcome	Holmes AB, Corinaldesi C, Shen Q, Kumar R, Compagno N, Wang Z, Nitzan M, Grunstein E, Pasqualucci L, Dalla-Favera R, Basso K	2020	Journal of Experimental Medicine	Oncology	Registration	HALO
Artificial intelligence as the next step towards precision pathology	Acs B, Rantalainen M, Hartman J	2020	Journal of Internal Medicine	Review		HALO
Ngly1?/? rats develop neurodegenerative phenotypes and pathological abnormalities in their peripheral and central nervous systems	Asahina M, Fujinawa R, Nakamura S, Yokoyama K, Tozawa R, Suzuki T	2020	Human Molecular Genetics			HALO
Consumptive coagulopathy of severe yellow fever occurs independently of hepatocellular tropism and massive hepatic injury	Baileya AL, Kanga L-I, Zanellab LGFdABD, Silveirab CGT, Hod Y-H, Foquete L, Biale G, McCunef BT, Duarte-Netog AN, Thomash A, Rauéh H-P, Byrnesa K, Kallasd EG, Slifkah MK, Diamond MS	2020	Proceedings of the National Academy of Sciences	Infectious Disease		HALO
?-Synuclein modulates tau spreading in mouse brains	Bassil F, Meymand ES, Brown HJ, Xu H, Cox TO, Pattabhiraman S, Maghames CM, Wu Q, Zhang B, Trojanowski JQ, Lee VM-Y	2020	Journal of Experimental Medicine	Neuroscience		HALO
Ad26 vaccine protects against SARS-CoV-2 severe clinical disease in hamsters	Tostanoski LH, Wegmann F, Martinot AJ, Loos C, McMahan K, Mercado NB, Yu J, Chan CN, Bondoc S, Starke CE, Nekorchuk M, Busman-Sahay K, Piedra-Mora C, Wrijil LM, Ducat S, Custers J, Atyeo C, Fischinger S, Burke JS, Feldman J, Hauser BM, Caradonna TM, Bondzie EA, Dagotto G, Gebre MS, Jacob-Dolan C, Lin Z, Mahrokhian SH, Nampanya F, Nityanandam R, Pessaint L, Porto M, ALi V, Benetiene D, Tevi K, Andersen H, Lewis MG, Schmidt AG, Lauffenburger DA, Alter G, Estes JD, Schuitemaker H, Zahn R, Barouch DH	2020	Nature Medicine	Infectious Disease	Area Quantification, Multiplex IHC	HALO
Prognostic relevance of programmed cell death protein 1/programmed death-ligand 1 pathway in thymic malignancies with combined immunohistochemical and biomolecular approach	Berardi R, Goteri G, Brunelli A, Pagliaretta S, Paolucci V, Caramanti M, Rinaldi S, Refai M, Pompili C, Morgese F, Torniai, Marcantognini, Ricci G, Mazzanti P, Onofri A, Bianchi F, Sabbatini A, Cascinu S	2020	Expert Opinion on Therapeutic Targets	Oncology		HALO
Liraglutide treatment improves endothelial function in the Ldlr?/? mouse model of atherosclerosis and affects genes involved in vascular remodelling and inflammation	Bjørnholm KD, Skovsted GF, Mitgaard-Thomsen A, Rakipovski G, Tveden-Nyborg P, Lykkesfeldt J, Povlsen GK	2020	Basic & Clinical Pharmacology & Toxicology	Immunology, Toxicology		HALO
Microglial-associated responses to comorbid amyloid pathology and hyperhomocysteinemia in an aged knock-in mouse model of Alzheimerís disease	Braun DJ, Dimayuga E, Morganti JM, Van Eldik LJ	2020	Journal of Neuroinflammation	Neuroscience		HALO
Glucagon Receptor Inhibition Reduces Hyperammonemia and Lethality in Male Mice with Urea Cycle Disorder	Cavino K, Sung B, Su Q, Na E, Kim J, Cheng X, Gromada J, Okamoto H	2020	Endocrinology	Metabolism		HALO
Immune parameters associated with survival in metaplastic breast cancer	Chao X, Liu L, Sun P, Yang X, Li M, Luo R, Huang Y, He J, Yun J	2020	Breast Cancer Research	Immuno-oncology		HALO
Alterations in Intestinal Innate Mucosal Immunity of Weaned Pigs During Porcine Epidemic Diarrhea Virus Infection	Chen Y-M, Helm ET, Gabler N, Hostetter JM, Burrough ER	2020	Veterinary Pathology	Infectious Disease		HALO
Expression of the Autoantigen Topoisomerase-1 is Enriched in the Lung Tissues of Patients With Autoimmune Interstitial Lung Disease: A Case Control Study	Cottrell TR, Askin F, Halushka MK, Casciola-Rosen L, McMahan ZH	2020	ACR Open Reumatology	Immunology		HALO
Growth Factor Receptor Expression in Oropharyngeal Squamous Cell Cancer: Her14 and c-Met in Conjunction with the Clinical Features and Human Papillomavirus (p16) Status	Deuss E, Gößwein D, Gül D, Zimmer S, Foersch S, Eger CS, Limburg I, Stauber RH, Künzel J	2020	Cancers	Oncology		HALO
Formoterol, a ?2-adrenoreceptor agonist, induces mitochondrial biogenesis and promotes cognitive recovery after traumatic brain injury	Vekaria HJ, Hubbard WB, Scholpa NE, Spry ML, Gooch JL, Prince SJ, Schnellmann Sullivan PG	2020	Neurobiology of Disease	Neuroscience	Area Quantification	HALO
Deep Brain Stimulation of the Medial Septal Nucleus Induces Expression of a Virally Delivered Reporter Gene in Dentate Gyrus	Fomenko A, Lee DJ, McKinnon C, Lee EJ, de Snoo ML, Gondard E, Neudorfer C, Hamani C, Lozano AM, Kalia LV, Kalia SK	2020	Frontiers of Neuroscience	Neuroscience		HALO
The membrane protein sortilin can be targeted to inhibit pancreatic cancer cell invasion	Gao F, Griffin N, Faulkner S, Li X, King SJ, Jobling P, Denham JW, Jiang CC, Hondermarck H	2020	The American Journal of Pathology	Oncology		HALO
Neoadjuvant PD-L1 plus CTLA-4 blockade in patients with cisplatin-ineligible operable high-risk urothelial carcinoma	Gao J, Navai N, Alhalabi O, Siefker-Radtke A, Campbell MT, Tidwell RS, Guo CC, Kamat AM, Matin SF, Araujo CJ, Shah AY, Msaouel P, Corn P, Wang J, Papadopoulos JN, Yadav SS, Blando JM, Duan F, Basu S, Liu W, Shen Y, Macaluso MD, Wang Y, Chen J, Zhang J, Futreal A, Dinney C, Allison JP, Goswami S, Sharma P	2020	Nature Medicine	Toxicology		HALO
Intratumoral heterogeneity of the tumor cells based on in situ cortisol excess in cortisol-producing adenomas; An association among morphometry, genotype and cellular senescence	Gao X, Yamazaki Y, Tezuka Y, Pieroni J, Ishii K, Atsumi N, Ono Y, Omata K, Morimoto R, Nakamura Y, Satoh F, Sasano H	2020	The Journal of Steroid Biochemistry and Molecular Biology	Oncology		HALO
Nicotinic Receptor Subunit Distribution in Auditory Cortex: Impact of Aging on Receptor Number and Function	Ghimire M, Cai R, Ling L, Hackett TA, Caspary DM	2020	Journal of Neuroscience	Neuroscience		HALO
Acute brain inflammation, white matter oxidative stress, and myelin deficiency in a model of neonatal intraventricular hemorrhage	Goulding DS, Vogel RC, Gensel JC, Morganti JM, Stromberg AJ, Miller BA	2020	Journal of Neuroscience	Immunology, Neuroscience		HALO
Neonatal hydrocephalus leads to white matter neuroinflammation and injury in the corpus callosum of Ccdc39 hydrocephalic mice	Goulding DS, Vogel RC, Pandya CD, Shula C, Gensel JC, Mangano FT, Goto J, Miller BA	2020	Journal of Neurosurgery	Immunology, Neuroscience		HALO
Quantification of Viral and Host Biomarkers in the Liver of Rhesus Macaques: a Longitudinal Study of Zaire Ebolavirus strain Kikwit (EBOV/Kik)	Greenberg AR, Huber BR, Liu DX, Logue JP, Hischak AMW, Hart RJ, Abbott M, Isic N, Hisada YM, Mackman N, Bennet RS, Hensley LE, Connor JH, Crossland NA	2020	The American Journal of Pathology			HALO
Clinicopathological significance of nerves in esophageal cancer	Griffin N, Rowe CW, Gao F, Jobling P, Wills V, Walker MM, Faulkner S, Hondermarck H	2020	The American Journal of Pathology	Oncology		HALO
The human IL-15 superagonist N-803 promotes migration of virus-specific CD8+ T and NK cells to B cell follicles but does not reverse latency in ART-suppressed, SHIV-infected macaques	Webb GM, Molden J, Bushman-Sahay K, Abdulhaqq S, Wu HL, Weber WC, Bateman KB, Reed JS, Northrup M, Maier N,Tanaka S, Gao L, Davey B, Carpenter BL, Axthelm MK, Stanton JJ, Smedley J, Greene JM, Safrit JT, Estes JD, Skinner PJ, Sacha JB	2020	PLOS Pathogens	Infectious Disease	Cytonuclear, ISH/FISH	HALO
Neonatal therapy with PF543, a sphingosine kinase 1 inhibitor, ameliorates hyperoxia-indused airway remodeling in a murine model of bronchopulmonary dysplasia	Ha AW, Sudhadevi T, Ebenezeer DL, Fu P, Berdyshev EV, Ackerman SJ, Natarajan V, Harijith A	2020	American Journal of Physiology	Other		HALO
Investigating Radiotherapy Response in a Novel Syngeneic Model of Prostate Cancer	Haughey CM, Mukherjee D, Steele RE, Popple A, Dura-Perez L, Pickard A, Patel M, Jain S, Mullan PB, Williams R, Oliveira P, Buckley NE, Honeychurch J, McDade SS, Illidge T, Mills IG, Eddie SL	2020	Cancers	Oncology		HALO
Intratumoral interleukin-12 mRNA therapy promotes TH1 transformation of the tumor microenvironment	Hewitt SL, Bailey D, Zielinski J, Apte A, Musenge F, Karp R, Burke S, Garcon F, Mishra A, Gurumurthy S, Watkins A, Arnold K, Moynihan J, Clancy-Thompson E, Mulgrew K, Adjei G, Deschler K, Potz D, Moody G, Leinster DA, Novick S, Sulikowski M, Bagnall CJ, Martin P, Lapointe J-M, Si H, Morehouse CA, Sedic M, Wilkinson RW, Herbst R, Frederick JP, Luheshi N	2020	Clinical Cancer Research	Immuno-oncology		HALO
IFN-III is selectively produced by cDC1 and predicts good clinical outcome in breast cancer	Hubert M, Gobbini E, Couillault C, Manh T-PV, Doffin A-C, Berthet J, Rodriguez C, Ollion V, Kielbassa J, Sajous C, Treilleux I, Tredan O, Dubois B, Dalod M, Bendriss-Vermare N, Caux C, Valladeau-Guilemond J	2020	Immunology			HALO
PNOCARC Neurons Promote Hyperphagia and Obesity upon High-Fat-Diet Feeding	Jais A, Paeger L, Sotelo-Hitschfeld T, Bremser S, Prinzensteiner M, Klemm P, Mykytiuk V, Widdershooven PJM, Vesting AJ, Grzelka K, Minere M, Cremer AL, Xu J, Korotkova T, Lowell BB, Zeilhofer HU, Backes H, Fenselau H, Wunderlich FT, Kloppenburg P, Bruning JC	2020	Neuron	Neuroscience		HALO
Tutorial: guidance for quantitative confocal miscroscopy	Jonkman J, Brown CM, Wright GD, Anderesion KI, North AJ	2020	Nature Protocols			HALO
Omental macrophages secrete chemokine ligands that promote ovarian cancer colonization of the omentum via CCR1	Krishnan V, Tallapragada S, Schaar B, Kamat K, Chanana AM, Zhang Y, Patel S, Parkash V, Rinker-Schaeffer C, Folkins AK, Rankin EB, Dorigo O	2020	Communications Biology	Oncology		HALO
A drug-induced hypotensive challenge to verify catheter-based radiofrequency renal denervation in an obese hypertensive swine model	Lauder L, Moon LB, Pipenhagen CA, Ewen S, Fish JM, Virmani R, Jensen JA, Böhm M, Mahfoud F	2020	Clinical Research in Cardiology	Myology		HALO
The identification and functional analysis of CD8+PD-1+CD161+ T cells in hepatocellular carcinoma	Li Z, Zheng B, Qiu X, Wu R, Wu T, Yang S, Zhu Y, Wu X, Wang S, Gu Z, Shen S, Wu M, Wang H, Chen L	2020	Percision Oncology	Immuno-oncology		HALO
The diagnostic and prognostic value of UBE2T in intrahepatic cholangiocarcinoma	Yu H, Wang H, Dong W, Cao Z-Y, Li R, Yang C, Cong W-M, Dong H, Jin G-Z	2020	Peer J	Oncology	Cytonuclear	HALO
Degradation of the Tumor Suppressor PDCD4 Is Impaired by the Suppression of p62/SQSTM1 and Autophagy	Manirujjaman M, Ozaki I, Murata Y, Guo J, Xia J, Nishioka K, Perveen R, Takashashi H, Anzai K, Matsuhashi S	2020	Cells	Oncology		HALO
Robust and persistent reactivation of SIV and HIV by N-803 and depletion of CD8+ cells	McBrien JB, Mavigner M, Li LF, Smith SA, White E, Tharp GK, Walum H, Busman-Suhay K, Aguilera-Sandoval CR, Thayer WO, Spagnuolo RA, Kovarova M, Wahl A, Cervasi B, Margolis DM, Vanderford TH, Carnathan DG, Paiardini M, Lifson JD, Lee JH, Safrit JT, Bosinger SE, Estes JD, Derdeyn CA, Garcia JV, Kulpa DA, Chahroudi A, Silvestri G	2020	Nature			HALO
Early-onset impairment of the ubiquitin-proteasome system in dopaminergic neurons caused by ?-synucleinn	McKinnon C, De Snoo ML, Gondard E, Neudorfer C, Chau H, Ngana SG, O'Hara DM, Brotchie JM , Koprich JB, Lozano AM, Kalia LV, Kalia SK	2020	Acta Neuropathologica Communications	Neuroscience		HALO
A Dedicated Evolutionarily Conserved Molecular Network Licenses Differentiated Cells to Return to the Cell Cycle	Miao Z-F, Lewis MA, Cho CJ, Adkins-Threats M, Park D, Brown JW, Sun J-X, Burclaff JR, Kennedy S, Lu J, Mahar M, Vietor I, Huber LA, Davidson NO, Cavalli V, Rubin DC, Wang Z-N, Mills JC	2020	Developmental Cell			HALO
The Unfolded Protein Response Mediator PERK Governs Myeloid Cell-Driven Immunosuppression in Tumors through Inhibition of STING Signaling	Mohamed E, Sierra RA, Trillo-Tinoco J, Cao Y, Innamarato P, Payne KK, Pulido M, Mandula J, Zhang S, Thevenot P, Biswas S, Abdalla SK, Costich TL, Hanggi K, Anadon CM, Flores ER, Haura EB, Mehrotra, Pilon-Thomas S, Ruffel B, Munn DH, Cubillos-Ruiz JR, Conejo-Garcia JR, Rodriguez PC	2020	Immunity	Immuno-oncology		HALO
CD137 agonist-based combination immunotherapy enhances activated, effector memory T cells and prolongs survival in pancreatic adenocarcinoma	Muth ST, Saung MT, Blair AB, Henderson MG, Thomass DL II, Xheng L	2020	Cancer Letters	Immuno-oncology		HALO
Immunohistochemical scoring of CD38 in the tumor microenvironment predicts responsiveness to anti-PD-1/PD-L1 immunotherapy in hepatocellular carcinoma	Ng HHM, Lee RY, Goh S, Tay ISY, Lim X, Lee B, Chew V, Li H, Tan B, Lim S, Lim JCT, Au B, Loh JJH, Saraf S, Connolly JE, Loh T, Leow WQ, Lee JJX, Toh HC, Malavasi F, Lee SY, Chow P, Newell EW, Choo SP, Tai D, Yeong J, Lim TKH	2020	Journal for ImmunoTherapy of Cancer	Immuno-oncology		HALO
Features of increased malignancy in eosinophilic clear cell renal cell carcinoma	Nilsson H, Lindgren D, Axelson H, Brueffer C, Saal LH, Lundgren J, Johansson ME	2020	Journal of Pathology	Immuno-oncology		HALO
Antitumor Activity of Eribulin After Fulvestrant Plus CDK4/6 Inhibitor in Breast Cancer Patient-derived Xenograft Models	Niwa Y, Asano M, Nakagawa T, France D, Semba T, Funahashi Y	2020	Anticancer Research	Oncology		HALO
A Fas-4-1BB fusion protein converts a death to a pro-survival signal and enhances T cell therapy	Oda SK, Andereson KG, Ravikumar P, Bonson P, Garcia NM, Jenkins CM, Zhuang S, Daman A, Chiu EY, Bates BM, Greenberg PD	2020	Journal of Experimental Medicine	Immuno-oncology		HALO
The Arp2/3 complex is crucial for colonisation of the mouse skin by melanoblasts	Papalazarou V, Swaminathan K, Jaber-Hijaz Fi, Spence H, Lahmann I, Nixon C, Salmeron-Sanchez M, Arnold H-H, Rottner K, Machesky LM	2020	Development	Review		HALO
Incomplete Freunds adjuvant reduces arginase and enhances Th1 dominance, TLR signaling and CD40 ligand expression in the vaccine site microenvironment	Pollack KE, Meneveau MO, Melssen MM, Lynch KT, Koeppel AF, Young SJ, Turner S, Kumar P, Sol-Church K, Mauldin IS, Slingfluff CL	2020	Journal for ImmunoTherapy of Cancer	Immuno-oncology		HALO
Senescence, Necrosis, and Apoptosis Govern Circulating Cell-free DNA Release Kinetics	Rostami A, Lambie M, Yu CW, Stambolic V, Waldron JN, Bratman SV	2020	Cell Reports	Toxicology		HALO
Discoidin Domain Receptor 1 (DDR1) is Necessary for Tissue Homeostasis in Pancreatic Injury and Pathogenesis of Pancreatic Ductal Adenocarcinoman	Ruggeri JM, Franco-Barraza J, Sohail A, Zhang Y, Long D, di Magliano MP, Cukierman E, Fridman R, Crawford HC	2020	The American Journal of Pathology	Oncology, Immunology		HALO
Natural killer cells in the human lung tumor microenvironment display immune inhibitory functions	Russick J, Joubert P-E, Gillard-Bocquet M, Torset C, Meylan M, Petitprez F, Dragon-Durey M-A, Marmier S, Varthaman A, Josseaume N, Germain C, Jérémy Goc J, Dieu-Nosjean M-C, Validire P, Fournel L, Zitvogel L, Bindea G, Lupo A, Damotte D, Alifano M, Cremer I	2020	Journal for ImmunoTherapy of Cancer	Immuno-oncology		HALO
A potent peptide-steroid conjugate accumulates in cartilage and reverses arthritis without evidence of systemic corticosteroid exposure	Sanger MLC, Girard EJ, Hopping G, Yin C, Pakiam F, Brusniak M-Y, Nguyen E, Ruff R, Gewe MM, Byrnes-Blake K, Nairn NW, Miller DM, Mehlin C, Strand AD, Mhyre AJ, Correnti CE, Strong RK, Simon JA, Olson JM	2020	Science Translational Medicine	Immunology		HALO
Intratumoral Combinatorial Administration of CD1c (BDCA-1) + Myeloid Dendritic Cells Plus Ipilimumab and Avelumab in Combination with Intravenous Low-Dose Nivolumab in Patients with Advanced Solid Tumors: A Phase IB Clinical Trial	Schwarze JK, Awada G, Cras L, Tijtgat J, Forsyth R, Dufait I, Tuyaerts S, Riet VI, Neyns B	2020	Vaccines	Immuno-oncology		HALO
IL6/STAT3 Signaling Hijacks Estrogen Receptor ? Enhancers to Drive Breast Cancer Metastasis	Siersbæk R, Scabia V, Nagarajan S, Chernukhin I, Papachristou EK, Broome R, Johnston SJ, Joosten SEP, Green AR, Kumar S, Jones J, Omarjee S, Alvarez-Fernandez R, Glont S, Aitken SJ, Kishore K, Cheeseman D, Rakha EA, D'Santos C, Zwart W, Ruseel A, Brisken C, Carroll JS	2020	Cancer Cell	Oncology		HALO
GSTO1?1 is an upstream suppressor of M2 macrophage skewing and HIF?1??induced eosinophilic airway inflammation/a>	Sokulsky LA, Goggins B, Sherwin S, Eyeers F, Kaiko GE, Board PG, Keely S, Yang M, Foster PS	2020	Clinical & Experimental Allergy	Immunology		HALO
Neoantigen responses, immune correlates, and favorable outcomes after ipilimumab treatment of patients with prostate cancer	Subudhi SK, Vence L, Zhao H, Blando J, Yadav SS, Xiong Q, Reuben A, Aparicio A, Corn PG, Chapin BF, Pisters LL, Troncoso P, Tidwell RS, Thall P, Wu C-J, Zhang J, Logothetis CL, Futreal A, Allison JP, Sharma P	2020	Cancer			HALO
Overview of multiplex immunohistochemistry/immunofluorescence techniques in the era of cancer immunotherapy	Tan WCCT, Nerurkar SN, Cai HY, Ng HHM, Wu D, Wee YTF, Lim JCT, Yeong J, Lim TKH	2020	Cancer Communications	Review		HALO
Association between CD8 and PD?L1 expression and outcomes after radical prostatectomy for localized prostate cancer	Vicier C, Ravi P, Kwak L, Werner L, Huang Y, Evan C, Loda M, Hamid AA, Sweeney CJ	2020	The Prostate	Immuno-oncology		HALO
Insoluble Tau From Human FTDP-17 Cases Exhibit Unique Transmission Properties In Vivo	Weitzman SA, Narasimhan S, He Z, Changolkar L, McBride JD, Zhang B, Schellenberg GD, Trojanowski JQ, Lee VMY	2020	Journal of Neuropathology & Experimental Neurology	Neuroscience		HALO
Engineering functional microvessels in synthetic polyurethane random-pore scaffolds by harnessing perfusion flow	Wright MEE, Yu JK, Jain D, Maeda A, Yeh S-CA, DaCosta RS, Lin CP, Santerre JP	2020	Biomaterials			HALO
Neuronal activity modulates alpha-synuclein aggregation and spreading in organotypic brain slice cultures and in vivo	Wu Q, Shaikh MA, Meymand ES, Zhang B, Luk KC, Trojanowski JO, Lee VM-Y	2020	Acta Neuropathologica	Neuroscience		HALO
*A living biobank of matched pairs of patient-derived xenografts and organoids for cancer pharmacology	Xu X, Wang S, Zhou J, Chen J, Huang Y, Kumari R, Mao B, Zheng M, Wang J, Tu X, An X, Chen X, Zhang L, Tian X, Wang H, Dong X, Bao Z, Guo S, Ouyang X, Shan L, Wang F, Yan X, Li Z, Zhang R, Zhang H, Meiler S, Vries R, Clevers H	2020	*Pre-Print	Oncology		HALO
Safety and clinical activity of PD-L1 blockade in patients with aggressive recurrent respiratory papillomatosis	Allen CT, Lee S, Norberg SM, Kovalovsky D, Ye H, Clavijo PE, Hu-Lieskovan S, Schlegel R, Schlom J, Strauss J, Gulley JL, Trepel J, Hinrichs CS	2019	Journal for ImmunoTherapy of Cancer	Oncology, Immuno-oncology	Cytonuclear	HALO
Cutaneous pharmacologic cAMP induction induces melanization of the skin and improves recovery from ultraviolet injury in melanocortin 1 receptor?intact or heterozygous skin	Bautista R-M, Carter KM, Jarrett SG, Napier D, Wakamatsu K, Ito S, D'Orazio JA	2019	Pigment Cell & Melanoma Research	Dermatology	Area Quantification	HALO
Islet amyloidosis in a child with type 1 diabetes	Beery ML, Jacobsen LM, Atkinson MA, Butler AE, Campbell-Thompson M	2019	Islets	Metabolism	Classifier	HALO
Predicting breast cancer response to neoadjuvant chemotherapy based on tumor vascular features in needle biopsies	Brocato TA, Brown-Glaberman U, Wang Z, Selwyn RG, Wilson CM, Wyckoff EF, Lomo LC, Saline JL, Hooda-Nehra A, Pasqualini R, Arap W, Brinker CJ, Cristini V	2019	JCI Insight	Oncology	Classifier	HALO
Magnetic Resonance Imaging as a Biomarker in Rodent Peripheral Nerve Injury Models Reveals an Age-Related Impairment of Nerve Regeneration	Giorgetti E, Obrecht M, Ronco M, Panesar M, Lambert C, Accart N, Doelemeyer A, Nash M, Bidinosti M, Beckmann N	2019	Scientific Reports	Neuroscience	Classifier	HALO
Unmasking of oestrogen?dependent changes in left ventricular structure and function in aged female rats: a potential model for pre?heart failure with preserved ejection fraction	Bustamante M, Garate?Carrillo A, Ito BR, Garcia R, Carson N, Ceballos G, Ramirez?Sanchez I, Omens J, Villarreal F	2019	The Journal of Physiology	Myology	Area Quantification, Layer Thickness	HALO
MEDI3039, a novel highly potent tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) receptor 2 agonist, causes regression of orthotopic tumors and inhibits outgrowth of metastatic triple-negative breast cancer	Greer YE, Gilbert SF, Gril B, Narwal R, Brooks DLP, Tice DA, Steeg PS, Lipkowitz	2019	Breast Cancer Research	Oncology	Classifier	HALO
Glucose-Dependent Insulinotropic Polypeptide Receptor-Expressing Cells in the Hypothalamus Regulate Food Intake	Adriaenssens AE, Biggs EK, Darwish T, Tadross J, Sukthankar T, Girish M, Polex-Wolf J, Lam BY, Zvetkova I, Pan W, Chiarugi D, Yeo GSH, Blouet C, Gribble FM, Reimann F	2019	Cell Metabolism	Metabolism	ISH/FISH	HALO
Intravital imaging reveals systemic ezrin inhibition impedes cancer cell migration and lymph node metastasis in breast cancer	Ghaffari A, Hoskin V, Turashvili G, Varma S, Mewburn J, Mullins G, Greer PA, Kiefer F, Day AG, Madarnas Y, SenGupta S, Elliott BE	2019	Breast Cancer Research	Oncology	Classifier, Cytonuclear	HALO
Modulation of Microglia by Voluntary Exercise or CSF1R Inhibition Prevents Age-Related Loss of Functional Motor Units	Giorgetti E, Panesar M, Zhang Y, Joller S, Ronco M, Obrecht M, Lambert C, Accart N, Beckmann N, Doelemeyer A, Perrot L, Fruh I, Mueller M, Pierrel E, Summermatter S, Bidinosti M, Shimshek DR, Brachat S, Nash M	2019	Cell Reports	Neuroscience	Classifier, Cytonuclear	HALO
LLRRK2 inhibition does not impart protection from ?-synuclein pathology and neuron death in non-transgenic mice	Henderson MX, Sengupta M, McGeary I, Zhang B, Olufemi MF, Brown H, Trojanowski JQ, Lee VMY	2019	Acta Neuropathologica Communications	Neuroscience	Area Quantification, Cytonuclear	HALO
Tumor Characteristics Associated with Benefit from Pembrolizumab in Advanced Non-Small Cell Lung Cancer	Hu-Lieskovan S, Lisberg A, Zaretsky JM, Grogan TR, Rizvi H, Wells DK, Carroll J, Cummings A, Madrigal J, Jones B, Gukasyan J, Shintaku IP, Slamon D, Dubinett S, Goldman JW, Elashoff D, Hellmann MD, Ribas A, Garon EB	2019	Clinical Cancer Research	Immuno-oncology	Cytonuclear	HALO
Empiric Methods to Account for Pre-analytical Variability in Digital Histopathology in Frontotemporal Lobar Degeneration	Giannini LAA, Xie SX, Peterson C, Zhou C, Lee EB, Wolk DA, Grossman M, Trojanowski JQ, McMillan CT, Irwin DJ	2019	Frontiers in Neuroscience	Neuroscience	Area Quantification, Registration, Figure Maker	HALO
Alterations of the MEK/ERK, BMP, and Wnt/?-catenin pathways detected in the blood of individuals with lymphatic malformations	Kim T, Tafoya E, Chelliah MP, Lekwuttikarn R, Li J, Sarin KY, Teng J	2019	PLOS One	Other	Cytonuclear	HALO
Detection and quantification of Parascaris P-glycoprotein drug transporter expression with a novel mRNA hybridization technique	Chelladurai JJ, Brewer MT	2019	Veterinary Parasitology	Infectious Disease	ISH/FISH	HALO
IL-7-dependent compositional changes within the ?? T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response	Chen H-C, Eling N, Martinez-Jimenez CP, O'Brien LM, Carbonaro V, Marioni JC, Odom DT, de la Roche M	2019	EMBO Reports	Oncology, Immuno-oncology	ISH/FISH	HALO
Assessment of PD-L1 mRNA and protein expression in non-small cell lung cancer, head and neck squamous cell carcinoma and urothelial carcinoma tissue specimens using RNAScope and immunohistochemistry	Duncan DJ, Scott M, Scorer P, Barker C	2019	PLOS One	Oncology, Immuno-oncology	ISH/FISH	HALO
Expression of cholecystokinin by neurons in mouse spinal dorsal horn	Guitierrez-Mecinas M, Bell AM, Shepherd F, Polgar E, Watanabe M, Furuta T, Todd AJ	2019	The Journal of Comparitive Neurology	Neuroscience	ISH/FISH	HALO
Methacrylic Acid Copolymer Coating Enhances Constructive Remodeling of Polypropylene Mesh by Increasing the Vascular Response	Coindre VF, Carleton MM, Sefton MV	2019	Advanced Healthcare Materials	Biomaterials	Area Quantification	HALO
Cognitive and Pathological Influences of Tau Pathology in Lewy Body Disorders	Coughlin DG, Xie SX, Liang M, Williams A, Peterson C, Weintraub D, McMillan CT, Wolk DA, Akhtar RS, Hurtig H, Coslett HB, Hamilton R, Siderowf A, Duda JE, Rascovsky K, Lee EB, Lee VM-Y, Grossman M, Trojanowski JQ, Irwin DJ	2019	Annals of Neurology	Neuroscience	Classifier, Area Quantification	HALO
CCN3/Nephroblastoma Overexpressed Is a Functional Mediator of Prostate Cancer Bone Metastasis That Is Associated with Poor Patient Prognosis	Dankner M, Ouellet V, Communal L, Schmitt E, Perkins D, Annis MG, Barrès V, Caron C, Mes-Masson A-M, Saad F, Siegel PM	2019	The American Journal of Pathology	Oncology	Area Quantification	HALO
Divergent patterns of TDP?43 and tau pathologies in primary progressive aphasia	Giannini LAA, Xie SX, McMillan CT, Liang M, Williams A, Jester C, Rascovsky K, Wolk DA, Ash S, Lee EB, Trojanowski JQ, Grossman M, Irwin DJ	2019	Annals of Neurology	Neuroscience	Area Quantification	HALO
Characterization of novel conformation-selective ?-synuclein antibodies as potential immunotherapeutic agents for Parkinson's disease	Henderson MX, Covell DJ, Chung C-HY, Pitkin RM, Sandler RM, Decker SC, Riddle DM, Zhang B, Gathagan RJ, James MJ, Trojanowski JQ, Brunden KR, Lee VMY, Luk KC	2019	Neurobiology of Disease	Neuroscience	Area Quantification	HALO
Alzheimerís disease tau is a prominent pathology in LRRK2 Parkinsonís disease	Henderson MX, Sengupta M, Trojanowski JQ, Lee VMY	2019	Acta Neuropathologica Communications	Neuroscience	Area Quantification	HALO
Lenvatinib induces death of human hepatocellular carcinoma cellsharboring an activated FGF signaling pathway through inhibition ofFGFReMAPK cascades	Hoshi T, Miyano SW, Watanabe H, Sonobe RMK, Seki Y, Ohta E, Nomoto K, Matsui J, Funahashi Y	2019	Biochemical and Biophysical Research Communications	Oncology	Area Quantification	HALO
Molecular and functional heterogeneity of cancer associated fibroblasts in high-grade serous ovarian cancer	Hussain A, Voisin V, Poon S, Dmytryshyn J ,Richman C, Meens J, Ho VW, Tang KH, Paterson J, Clarke B, Bernardini M, Bader G, Neel B, Ailles L	2019	bioRxiv	Oncology	Classifier, Area Quantification	HALO
Alzheimer Disease Pathology-Associated Polymorphism in a Complex Variable Number of Tandem Repeat Region Within the MUC6 Gene, Near the AP2A2 Gene	Katsumata Y, Fardo DW, Bachstetter AD, Artiushin SC, Wang W-X, Wei A, Brzezinski LJ, Nelson BG, Huang Q, Abner EL, Anderson S, Patel I, Shaw BC, Price DA, Niedowicz DM, Wilcock DW, Jicha GA, Neltner JH, Van Eldik LJ, Estus S, Nelson PT	2019	Journal of Neuropathology & Experimental Neurology	Neuroscience	Area Quantification, Cytonuclear	HALO
IRAK4 mediates colitis-induced tumorigenesis and chemoresistance in colorectal cancer	Li Q, Chen Y, Zhang D, Grossman J, Li L, Khurana N, Jiang H, Grierson PM, Herndon J, DeNardo DG, Challen GA, Liu J, Ruzinova MB, Fields RC, Lim K-H	2019	JCI Insight	Oncology, Immuno-oncology	Area Quantification	HALO
Dysregulated expression but redundant function of the long non-coding RNA HOTAIR in diabetic kidney disease	Majumder S, Hadden MJ, Thieme K, Batchu SN, Niveditha D, Chowdhury S, Yerra VG, Advani SL, Bowskill BB, Liu Y, Vakili H, Alghamdi TA, White KE, Geldenhuys L, Siddiqi FS, Advani A	2019	Diabetologia	Metabolism	Area Quantification	HALO
Targeted drug delivery via caveolae-associated protein PV1 improves lung fibrosis	Marchetti GM, Burwell TJ, Peterson NC, Cann JA, Hanna RN, Li Q, Ongstad EL, Boyd JT, Kennedy MA, Zhao W, Rickert KW, Grimsby JS, DallAcqua WF, Wu H, Tsui P, Borrok MJ, Gupta R	2019	Communications Biology	Fibrosis	Area Quantification	HALO
Persistence of inflammatory phenotype in residual psoriatic plaques in patients on effective biologic therapy: Residual Psoriatic Plaques After Treatment	Mashiko S, Edelmayer RM, Bi Y, Olson LM, Wetter JB, Wang J, Maari C, Proulx ES-C, Kaimal V, Li X, Salte K, Garcet S, Kannan AK, Huang SM, Cao X, Liu Z, Krueger JG, Sarfati M, Bissonnette R, Smith KM	2019	Journal of Investigative Dermatology	Immunology, Dermatology	Area Quantification	HALO
In Situ Temporospatial Characterization of the Glial Response to Prion Infection	Michael AV, Greenlee JJ, Harm TA, Moore SJ, Zhang M, Lind MS, Greenlee MHW, Smith JD	2019	Veterinary Pathology	Immunology, Neuroscience, Infectious Disease	Area Quantification	HALO
Exposure to maternal obesity programs sex differences in pancreatic islets of the offspring in mice	Nicholas LM, Nagao M, Kusinski LC, Fernandez-Twinn DS, Eliasson L, Ozanne SE	2019	Diabetologia	Metabolism	Area Quantification	HALO
Histological characterization of aldosterone-producing adrenocortical adenomas with different somatic mutations	Ono Y, Yamazaki Y, Omata K, Else T, Tomlins SA, Rhayem Y, Williams TA, Reincke M, Carling T, Monticone S, Mulatero P, Beuschlein F, Ito S, Satoh F, Rainey WE, Sasano H	2019	The Journal of Clinical Endocrinology & Metabolism	Oncology	Classifier, Area Quantification	HALO
Epithelial to mesenchymal plasticity and differential response to therapies in pancreatic ductal adenocarcinoma	Porter RL, Magnus NKC, Thapar V, Morris R, Szabolcs A, Neyaz A, Kulkarni AS, Tai E, Chougule A, Hillis A, Golczer G, Guo H, Yamada T, Kurokawa T, Yashaswini C, Ligorio M, Vo KD, Nieman L, Liss AS, Deshpande V, Lawrence MS, Maheswaran S, Fernandez-Del Castillo C, Hong TS, Ryan DP, ODwyer PJ, Drebin JA, Ferrone CR, Haber DA, Ting DT	2019	Proceedings of the National Academy of Sciences	Oncology	Area Quantification	HALO
Multiplexed Immunohistochemistry for Molecular and Immune Profiling in Lung CancerÄîJust About Ready for Prime-Time?	Hofman P, Badoual C, Henderson F, Berland L, Hamila M, Long-Mira E, Lassalle S, Roussel H, Hofman V, Tartour E, Ilié M	2019	Cancers	Oncology, Immuno-oncology, Review	Classifier, Multiplex IHC	HALO
Quantification of histopathological findings using a novel image analysis platform	Horai Y, Mizukawa M, Nishina H, Nishikawa S, Ono Y, Takemoto K, Baba N	2019	Journal of Toxicologic Pathology	Toxicology	Classifier	HALO
Ex vivo tissue slice culture system to measure drug-response rates of hepatic metastatic colorectal cancer	Martin SZ, Wagner DC, Hörner N, Horst D, Lang H, Tagscherer KE, Roth W	2019	BMC Cancer	Oncology	Classifier, Cytonuclear	HALO
Neutrophil content predicts lymphocyte depletion and anti-PD1 treatment failure in NSCLC	Kargl J, Zhu X, Zhang H, Yang GHY, Friesen TJ, Shipley M, Maeda DY, Zebala JA, McKay-Fleisch J, Meredith G, Mashadi-Hossein A, Baik C, Pierce RH, Redman MW, Thompson JC, Albelda SM, Bolouri H, Houghton AM	2019	JCI Insight	Immuno-oncology	Classifier, Highplex FL	HALO
Precision immunoprofiling by image analysis and artificial intelligence	Koelzer VH, Sirinukunwattana K, Rittscher J, Mertz KD	2019	Vichows Archiv	Review	Classifier, Multiplex IHC, Spatial Analysis	HALO
Machine learning approaches for pathologic diagnosis	Komura D, Ishikawa S	2019	Vichows Archiv	Review	Classifier	HALO AI
MYB-NFIB gene fusions identified in archival adenoid cystic carcinoma tissue employing NanoString analysis: an exploratory study	McIntyre JB, Ko JJ, Siever J, Chan AMY, Simpson RHW, Hao D, Lau HY	2019	Diagnostic Pathology	Oncology	Classifier, Highplex FL	HALO
A Dual Blocker of Endothelin A/B Receptors Mitigates Hypertension but not Renal Dysfunction in a Rat Model of Chronic Kidney Disease and Sleep Apnea	Morales-Loredo H, Jones DT, Barrera A, Mendiola P, Garcia J, Pace CE, Murphy M, Kanagy NL, Gonzalez Bosc LV	2019	Renal Pathology	Metabolism	Classifier, Cytonuclear, Figure Maker	HALO
Detection of Lung Cancer Lymph Node Metastases from Whole-Slide Histopathologic Images Using a Two-Step Deep Learning Approach	Pham HHN, Futakuchi M, Bychkov A, Furukawa T, Kuroda K, Fukuoka J	2019	The American Journal of Pathology	Oncology	Classifier	HALO AI
Imaging Mass Spectrometry and Proteome Analysis of Marek's Disease Virus-Induced Tumors	Pauker VI, Bertzbach LD, Hohmann A, Kheimar A, Teifke JP, Mettenleiter TC, Karger A, Kaufe BB	2019	mSpere	Oncology	Cytonuclear	HALO
TNF-? Contributes to Lymphoid Tissue Disorganization and Germinal Center B Cell Suppression during Intracellular Bacterial Infection	Popescu M, Cabrera-Martinez B, Winslow GM	2019	The Journal of Immunology	Immunology	Cytonuclear	HALO
Characterization of psoriasiform dermatitis induced by systemic injection of interleukin?23 minicircles in mice	Leys L, Wang Y, Paulsboe S, Edelmayer R, Salte K, Wetter J, Namovic M, Phillips L, Dunstan R, Gauvin D, Donnelly-Roberts D, Su Z, Honore P, McGaraughty S	2019	The Journal of Dermatology	Dermatology	Area Quantification, Layer Thickness	HALO
Automated Computational Detection, Quantitation, and Mapping of Mitosis in WholeÄëSlide Images for Clinically Actionable Surgical Pathology Decision Support	Puri M, Hoover S, Hewitt S, Wei B-R, Adissu H, Halsey C, Beck J, Bradley C, Cramer S, Durham A, Esplin D, Frank C, Lyle L, McGill L, Sanchez M, Schaffer P, Traslavina R, Buza E, Yang H, Lee M, Dwyer J, Simpson R	2019	Journal of Pathology Informatics	Oncology	Cytonuclear	HALO
Lamin?B1 is a senescence?associated biomarker in clear?cell renal cell carcinoma	Radspieler M, Schindeldecker M, Stenzel P, Försc S, Tagscherer K, Herpel E, Hohenfellner M, Hatiboglu G, Roth W, Macher?Goeppinger S	2019	Oncology Letters	Oncology	Cytonuclear	HALO
Upper tract urothelial carcinoma has a luminal-papillary T-cell depleted contexture and activated FGFR3 signaling	Robinson BD, Vlachostergios PJ, Bhinder B, Liu W, Li K, Moss TJ, Bareja R, Park K, Tavassoli P, Cyrta J, Tagawa ST, Nanus DM, Beltran H, Molina AM, Khani F, Miguel Mosquera J, Xylinas E, Shariat SF, Scherr DS, Rubin MA, Lerner SP, Matin SF, Elemento O, Faltas BM	2019	Nature Communications	Oncology, Immuno-oncology	Cytonuclear	HALO
IL?36 receptor antagonistic antibodies inhibit inflammatory responses in preclinical models of psoriasiform dermatitis	Su Z, Paulsboe S, Wetter J, Salte K, Kannan A, Mathew S, Horowitz A, Gerstein C, Namovic M, Todorovi? V, Seagal J, Edelmayer RM, Viner M, Rinaldi L, Zhou L, Leys L, Huang S, Wang L, Sadhukhan R, Honore P, McGaraughty S, Scott VE	2019	Experimental Dermatology	Dermatology	Area Quantification, Cytonuclear	HALO
Neurexin 3 transmembrane and soluble isoform expression and splicing haplotype are associated with neuron inflammasome and Alzheimer's disease	Hishimoto A, Pletnikova O, Lang DL, Troncoso JC, Egan JM, Liu Q-R	2019	Alzheimer's Research & Therapy	Neuroscience	ISH/FISH	HALO
IL?1? cleavage by inflammatory caspases of the noncanonical inflammasome controls the senescence?associated secretory phenotype	Wiggins KA, Parry AJ, Cassidy LD, Humphry M, Webster SJ, Goodall JC, Narita M, Clarke MCH	2019	Aging Cell	Immunology	Cytonuclear	HALO
The role of WNT10B in normal prostate gland development and prostate cancer	Madueke I, Hu W-Y, Hu D, Swanson SM, Griend DV, Abern M, Prins GS	2019	The Prostate	Oncology	Multiplex IHC, TMA	HALO
Role of IL-15 Signaling in the Pathogenesis of Simian Immunodeficiency Virus Infection in Rhesus Macaques	Okoye AA, DeGottardi MQ, FukazawaY, Vaidya M, Abana CO, Konfe AL, Fachko DN, Duell DM, He Li H, Lum R, Gao L, Park BS, Skalsky RL, Lewis AD, Axthelm MK, Lifson JD, Wong SW, Picker LJ	2019	The Journal of Immunology	Infectious Disease	Cytonuclear, Figure Maker	HALO
A Deep Learning Convolutional Neural Network Can Recognize Common Patterns of Injury in Gastric Pathology	Martin DR, Hanson JA, Gullapalli RR, Schultz FA, Sethi A, Clark DP	2019	Archives of Pathology and Laboratory Medicine	Gastroenterology		HALO AI
Advanced Prostate Cancer with ATM Loss: PARP and ATR Inhibitors	Neeb A, Herranz N, Arce-Gallego S, Miranda S, Lorenzo Buroni L, Wei Yuan W, Alejandro Athie A, Teresa Casals T, Juliet Carmichael J, Daniel Nava Rodrigues DN, Bora Gurel B, Pasquale Rescigno P, Jan Rekowski J, Jon Welti J, Ruth Riisnaes R, Veronica Gil V, Jian Ning J, Verena Wagner, Irene Casanova-Salas I, Cordoba S, Natalia Castro N, Maria Dolores Fenor de la Maza, George Seed, Khobe Chandran, Ana Ferreira A, Ines Figueiredo I, Claudia Bertan, Diletta Bianchini, Caterina Aversa, Alec Paschalis A, Macarena Gonzalez N, Rafael Morales-Barrera, Cristina Suarez C, Joan Carles J, Amanda Swain A, Adam Sharp A, Jesus Gil, Violeta Serra, Christopher Lord, Suzanne Carreira S, Joaquin Mateo, Johann S. de Bono JS	2019	European Urology	Oncology		HALO AI
Reduction of Global H3K27me3 Enhances HER2/ErbB2 Targeted Therapy	Hirukawa A, Singh S, Wang J, Rennhack JP, Swiatnicki M, Sanguin-Gendreau V, Zuo D, Daldoul K, Lavoie C, Park M, Andrechek ER, Westbrook TF, Harris LN, Varadan V, Smith HW, Muller WJ	2019	Cell Reports	Oncology	Highplex FL	HALO
Macrophage-Derived CXCL9 and CXCL10 Are Required for Antitumor Immune Responses Following Immune Checkpoint Blockade	House IG, Savas P, Lai J, Chen AXY, Oliver AJ, Teo ZL, Todd KL, Henderson MA, Giuffrida L, Petley EV, Sek K, Mardiana S, Gide TN, Quek C, Scolyer RA, Long GV, Wilmott JS, Loi S, Darcy PK, Beavis PA	2019	Clinical Cancer Research	Immuno-oncology	Highplex FL	HALO
A single dose of neoadjuvant PD-1 blockade predicts clinical outcomes in resectable melanoma	Huang AC, Orlowski RJ, Xu X, Mick R, George SM, Yan PK, Manne S, Kraya AA, Wubbenhorst B, Dorfman L, DAndrea K, Wenz BM, Liu S, Chilukuri L, Kozlov A, Carberry M, Giles L, Kier MW, Quagliarello F, McGettigan S, Kreider K, Annamalai L, Zhao Q, Mogg R, Xu W, Blumenschein WM, Yearley JH, Linette GP, Amaravadi RK, Schuchter LM, Herati RS, Bengsch B, Nathanson KL, Farwell MD, Karakousis GC, Wherry EJ, Mitchell TC	2019	Nature Medicine	Oncology, Immuno-oncology	Highplex FL	HALO
CXCR3 enables recruitment and site-specific bystander activation of memory CD8+ T cells	Maurice NJ, McElrath MJ, Andersen-Nissen E, Frahm N, Prlic M	2019	Nature Communications	Immunology	Highplex FL	HALO
Development of resistance to FAK inhibition in pancreatic cancer is linked to stromal depletion	Jiang H, Liu X, Knolhoff BL, Hegde S, Lee KB, Jiang H, Fields RC, Pachter JA, Lim K-H, DeNardo DG	2019	Gut	Oncology	Cytonuclear, ISH/FISH	HALO
Single-Cell Quantification of mRNA Expression in The Human Brain	Jolly S, Lang V, Koelzer VH, Frigerio CS, Magno L, Salinas PC, Whiting P, Palomer E	2019	Scientific Reports	Neuroscience	ISH/FISH	HALO
The Fat Mass and Obesity-Associated Protein (FTO) Regulates Locomotor Responses to Novelty via D2R Medium Spiny Neurons	Ruud J, Alber J, Tokarska A, Engström Ruu L, Nolte H, Biglari N, Lippert R, Lautenschlager Ä, Cie?lak PE, Szumiec ?, Hess ME, Brönneke HS, Krüger M, Nissbrandt H, Korotkova T, Silberberg G, Rodriguez Parkitna J, Brüning J	2019	Cell Reports	Neuroscience, Metabolism	ISH/FISH	HALO
Quantitative digital pathology reveals association of cell-specific PNPLA3 transcription with NAFLD disease activity	Sandhu B, Perez Matos MC, Tran S, Zhong A, Csizmadia E, Kim M, Herman MA, Nasser I, Lai M, Jiang ZG	2019	JHEP Reports	Fibrosis	ISH/FISH	HALO
Alpha-synuclein is a DNA binding protein that modulates DNA repair with implications for Lewy body disorders	Schaser AJ, Osterberg VR, Dent SE, Stackhouse TL, Wakeham CM, Boutros SW, Weston LJ, Owen N, Weissman TA, Luna E, Raber J, Luk KC, McCullough AK, Woltjer RL, Unni VK	2019	Scientific Reports	Neuroscience	ISH/FISH	HALO
Small Molecule IL-36? Antagonist as a Novel Therapeutic Approach for Plaque Psoriasis	Todorovi? V, Su Z, Putman CB, Kakavas SJ, Salte KM, McDonald HA, Wetter JB, Paulsboe SE, Sun Q, Gerstein CE, Medina L, Sielaff B, Sadhukhan R, Stockmann H, Richardson PL, Qiu W, Argiriadi MA, Henry RF, Herold JM, Shotwell JB, McGaraughty SP, Honore P, Gopalakrishnan SM, Sun CC, Scott VE	2019	Scientific Reports	Immunology, Dermatology	ISH/FISH	HALO
Changes in epidermal morphology associated with dandruff	Pople JE, Bhogal RK, Moore AE, Jenkins G	2019	International Journal of Cosmetic Science	Dermatology	Cytonuclear, Layer Thickness	HALO
PD-L1 Expression and Clinical Outcomes to Cabozantinib, Everolimus, and Sunitinib in Patients with Metastatic Renal Cell Carcinoma: Analysis of the Randomized Clinical Trials METEOR and CABOSUN	Flaifel A, Xie W, Braun DA, Ficial M, Bakouny Z, Nassar AH, Jennings RB, Escudier B, George DJ, Motzer RJ, Morris MJ, Powles, Wang E, Huang Y, Freeman GJ, Choueiri TK, Signoretti S	2019	Clinical Cancer Research	Immuno-oncology	Multiplex IHC	HALO
The KDM5A/RBP2 histone demethylase represses NOTCH signaling to sustain neuroendocrine differentiation and promote small cell lung cancer tumorigenesis	Oser MG, Sabet AH, Gao W, Chakraborty AA, Schinzel AC, Jennings RB, Fonseca R, Bonal DM, Booker MA, Flaifel A, Novak JS, Christensen VL, Zhang H, Herbert ZT, Tolstorukov MY, Buss EJ, Wong K-K, Bronson RT, Nguyen Q-D, Signoretti S, Kaelin Jr WG	2019	Genes & Development	Oncology	Multiplex IHC	HALO
Physiologic serum 1,25 dihydroxyvitamin D is inversely associated with prostatic Ki67 staining in a diverse sample of radical prostatectomy patients	Rosenberg A, NetteY OS, Gogana P, Sheikh U, Virgilia M, Macias V, Kajdacsy-Balla A, R Sharifi R, Kittles RA, Murphy AB	2019	Cancer Causes & Control	Oncology	Multiplex IHC	HALO
Nuclear Glycogenolysis Modulates Histone Acetylation in Human Non-Small Cell Lung Cancers	Sun RC, Dukhande VV, Zhou Z, Young LEA, Emanuelle S, Brainson CF, Gentry MS	2019	Cell Metabolism	Oncology	Multiplex IHC	HALO
Inducing and exploiting vulnerabilities for the treatment of liver cancer	Wang C, Vegna S, Jin H, Benedict B, Lieftink C, Ramirez C, de Oliveira RL, Morris B, Gadiot J, Wang W, du Chatinier A, Wang L, Gao D, Evers B, Jin G, Xue Z, Schepers A, Jochems F, Sanchez AM, Mainardi S, te Riele H, Beijersbergen RL, Qin W, Akkari L, Bernards R	2019	Nature	Oncology	Multiplex IHC	HALO
Neoadjuvant anti-PD-1 immunotherapy promotes a survival benefit with intratumoral and systemic immune responses in recurrent glioblastoma	Cloughesy TF, Mochizuki AY, Orpilla JR, Hugo W, Lee AH, Davidson TB, Wang AC, Ellingson BM, Rytlewski JA, Sanders CM, Kawaguchi ES, Du L, Li G, Yong WH, Gaffey SC, Cohen AL, Mellinghoff IK, Lee EQ, Reardon DA, OBrien BJ, Butowski NA, Nghiemphu PL, Clarke JL, Arrillaga-Romany IC, Colman H, Kaley TJ, de Groot JF, Liau LM, Wen PY, Prins RM	2019	Nature Medicine	Oncology, Immuno-oncology	Spatial Analysis, Highplex FL	HALO
PAK4 inhibition improves PD-1 blockade immunotherapy	Abril-Rodriguez G, Torrejon DY, Liu W, Zaretsky JM, Nowick TS, Tsoi J, Puig-Saus C, Baselga-Carretero I, Medina E, Quist MJ, Garcia AJ, Senapedis W, Baloglu E, Kalbasi A, Cheung-Lau G, Berent-Maoz B, Comin-Anduix B, Hu-Lieskovan S, Wang C-Y, Grasso CS, Ribas A	2019	Nature Cancer	Immuno-oncology		HALO
Histological characterization of aldosterone-producing adrenocortical adenomas with different somatic mutations	Acosta-Ruiz A, Gutzeit VA, Skelly MJ, Meadows S, Lee J, Parekh P, Orr AG, Liston C, Pleil KE, Broichhagan J, Levitz J	2019	Neuron	Neuroscience		HALO
Amyloid-Beta (A?) Plaques Promote Seeding and Spreading of Alpha-Synuclein and Tau in a Mouse Model of Lewy Body Disorders with A? Pathology	Bassil F, Brown HJ, Pattabhiraman S, Iwasyk JE, Maghames CM, Meymand ES, Cox TO, Riddle FM, BinZhang N, Trojanowski JQ, Lee VM-Y	2019	Neuron	Neuroscience		HALO
Rabbit monoclonal E?cadherin antibody: A cost?effective alternative to mouse monoclonal antibody in distinguishing ductal carcinoma in situ from lobular carcinoma in situ	Baum JE, Croyle JA, Brodsky VB, Liu Y, Shin SJ	2019	The Breast Journal	Oncology	Cytonuclear	HALO
MAPKAPK2 (MK2) inhibition mediates radiation-induced inflammatory cytokine production and tumor growth in head and neck squamous cell carcinoma	Berggren KL, Cruz SR, Hixon MD, Cowan AT, Keysar SB, Craig S, James J, Barry M, Ozbun MA, Jimeno A, McCance DJ, Beswick EJ, Gan GN	2019	Oncogene	Oncology	Cytonuclear, Figure Maker	HALO
Pre-diagnostic anthropometry, sex, and risk of colorectal cancer according to tumor immune cell composition	Berntsson J, Eberhard J, Nodin B, Leandersson K, Larsson AH, Eberhard J, Jirstrom K	2019	OncoImmunology	Immuno-oncology		HALO
Single cell transcriptomic profiling of large intestinal enteroendocrine cells in mice - Identification of selective stimuli for insulin-like peptide-5 and glucagon-like peptide-1 co-expressing cells	Billing LJ, Larraufie P, Lewis J, Leiter A, Li J, Lam B, Yeo GSH, Goldspink DA, Kay RG, Gribble FM, Reimann F	2019	Molecular Metabolism	Metabolism		HALO
Genetic mutations underlying phenotypic plasticity in basosquamous carcinoma	Chiang A, Tan CZ, Kuonen F, Hodgkinson LM, Chiang F, Cho RJ, South AP, Tang Jean Y, Chang ALS, Rieger KE, Oro AE, Sarin KY	2019	Journal of Investigative Dermatology	Oncology	Cytonuclear	HALO
Kras and Lkb1 mutations synergistically induce intraductal papillary mucinous neoplasm derived from pancreatic duct cells	Collet L, Ghurburrun E, Meyers N, Assi M, Pirlot B, Leclercq IA, Couvelard A, Komuta M, Cros J, Demetter P, Lemaigre FP, Borbath I, Jacquemin P	2019	Gut	Oncology		HALO
Next-generation computational tools for interrogating cancer immunity	Finotello F, Rieder D, Hackl H, Trajanoski Z	2019	Nature Reviews Genetics	Review		HALO
The crosstalk between aldosterone and calcium metabolism in primary aldosteronism: A possible calcium metabolism-associated aberrant neoplastic steroidogenesis in adrenals	Gao X, Yamazaki Y, Tezuka Y, Onodera Y, Ogata H, Omata K, Morimoto R, Nakamura Y, Satoh F, Sasano H	2019	The Journal of Steroid Biochemistry and Molecular Biology	Oncology, Metabolism	Cytonuclear	HALO
Farnesoid X Receptor Agonism, AcetylCoenzyme A Carboxylase Inhibition, and Back Translation of Clinically Observed Endpoints of De Novo Lipogenesis in a Murine NASH Model	Gapp B, Jourdain M, Bringer P, Kueng B, Weber D, Osmont A, Zurbruegg S, Knehr J, Falchetto R, Roma G, Dietrich W, Valdez R, Beckmann N, Nigsch F, Sanyal AJ, Ksiazek I	2019	Hepatology Communications	Metabolism	Cytonuclear	HALO
Open radial artery harvesting better preserves endothelial function compared to the endoscopic approach	Gaudino MF, Lorusso R, Ohmes LB, Narula N, McIntire PJ, Gargiulo A, Bucci MR, Leonard J, Rahouma M, Di Franco A, He GW, Girardi LN, Tranbaugh RF, Di Lorenzo A	2019	Interactive CardioVascular and Thoracic Surgery			HALO
Dynamic changes to lipid mediators support transitions among macrophage subtypes during muscle regeneration	Giannakis N, Sansbury BE, Patsalos A, Hays TT, Riley CO, Han X, Spite M, Nagy L	2019	Nature Immunology	Immunology, Myology	Muscle Fiber	HALO
Evaluation of Peritumoral Fibrosis in Metastatic Colorectal Adenocarcinoma to the Liver Using Digital Image Analysis	Waters KM, Cottrell TR, Besharati S, Zhu Q, Anders RA	2019	American Journal of Clinical Pathology	Oncology	Area Quantification, Partitions (tiles, margins)	HALO
Cross-Platform Comparison of Computer-assisted Image Analysis Quantification of In Situ mRNA Hybridization in Investigative Pathology.	Holzer TR, Hanson JC, Wray EM, Bailey JA, Kennedy KR, Finnegan PR, Nasir A, Credille KM	2019	Applied Immunohistochemistry & Molecular Morpholgy			HALO
Oral tenofovir disoproxil fumarate/emtricitabine for HIV pre-exposure prophylaxis increases expression of type I/III interferon-stimulated factors in the gastrointestinal tract but not in the blood	Hughes SM, Levy CN, Calienes F, Stekler JD, Pandey U, Vojtech L, Berard AR, Birse K, Noel-Romas L, Richardson B, Golden J, Cartwright M, Collier AC, Stevens CE, Curlin ME, Holtz TH, Mugo N, Irungu E, Katabira E, Muwonge T, Lama JR, Baeten JM, Burgener A, Lingappa JR, McElrath MJ, Mackelprang R, McGowan I, Cranston RD, Cameron MJ, Hladik F	2019	bioRxiv	Infectious Disease	Cytonuclear	HALO
Intraintestinal and Parenteral Administration of an Insulin Analogue Leads to Comparable Activation of Signaling Downstream of the Insulin Receptor in the Small Intestine	Hvid H, Kildegaard J, Kristensen K, Porsgaard T, Jørgensen MS, Ballarín-González B, Ahnfelt-Rønne J, Hansen Bo F, Nishimura E	2019	Journal of Diabetes Science and Technology	Metabolism		HALO
Epithelial NOTCH Signaling Rewires the Tumor Microenvironment of Colorectal Cancer to Drive Poor-Prognosis Subtypes and Metastasis	Jackstadt R, van Hooff ST, Leach JD, Cortes-Lavaud X, Lohuis JO, Ridgway RA, Wouters VM, JatinRoper J, Kendall TJ, Roxburgh CS, Horgan PG, Nixon C, Nourse C, Gunzer M, Clark W, Hedley A, Yilmaz OH, Rashid M, Bailey P, Biankin AV, Campbell AD, Adams DJ, Barry ST, Steele CW, Medema JP, Sansom OJ	2019	Cancer Cell	Oncology		HALO
Expression of avian ?-defensin mRNA in the chicken yolk sac	Zhang H, Wong EA	2019	Developmental & Comparative Immunology	Immunology	ISH/FISH	HALO
Lenvatinib plus anti-PD-1 antibody combination treatment activates CD8+ T cells through reduction of tumor-associated macrophage and activation of the interferon pathway	Kato Y, Tabata K, Kimura T, Yachie-Kinoshita A, Ozawa Y, Yamada K, Ito J, Tachino S, Hori Y, Matsuki M, Matsuoka Y, Ghosh S, Kitano H, Nomoto K, Matsui J, Funahashi Y	2019	PLOS One	Immuno-oncology		HALO
Calpain 9 as a therapeutic target in TGF?-induced mesenchymal transition and fibrosis	Kim DH, Beckett JD, Nagpal V, Seman-Senderos MA, Gould Russell A, Creamer TJ, MacFarlane EG, Chen Y, Bedja D, Butcher JT, Mitzner W, Rouf R, Hata S, Warren DS, Dietz HC	2019	Science Translational Medicine	Fibrosis		HALO
Delayed Azithromycin Treatment Improves Recovery After Mouse Spinal Cord Injury	Kopper TJ, McFarlane KE, Bailey WM, Orr MB, Zhang B, Gensel JC	2019	Frontiers in Ceullar Neuroscience	Neuroscience		HALO
Long-Term Persistence of Anti-HIV Broadly Neutralizing Antibody-Secreting Hematopoietic Cells in Humanized Mice	Kuhlmann A-S, Haworth KG, Barber-Axthelm IM, Ironside C, Giese MA, Peterson CW, Kiem H-P	2019	Molecular Therapy	Infectious Disease		HALO
Temporal Analysis of Amylase Expression in Control, Autoantibody Positive, and Type 1 Diabetes Pancreatic Tissues	Kusmartseva I, Beery M, Hiller H, Padilla M, Selman S, Posgai A, Nick HS, Campbell-Thompson M, Schatz DA, Haller MJ, Wasserfall CH, Atkinson MA	2019	Diabetes	Metabolism		HALO
Phosphorylation of connexin 43 at MAPK, PKC or CK1 sites each distinctly alter the kinetics of epidermal wound repair	Lastwika JK, Dunn CA, Solan JL, Lampe PD	2019	Journal of Cell Science			HALO
Active Cushing's Disease is Characterized by Increased Adipose Tissue Macrophage Presence	Lee IT, Atuahene A, Egritag HE, Buettner C, Wang L, Geer EB, Donovan M	2019	The Journal of Clinical Endocrinology & Metabolism	Metabolism		HALO
Impact of a Pre-Operative Exercise Intervention on Breast Cancer Proliferation and Gene Expression: Results from the Pre-Operative Health and Body (PreHAB) Study	Ligibel JA, Dillon D, Giobbie-Hurder A, McTiernan A, Frank E, Cornwell M, Pun M, Campbell N, Dowling RJO, Chang MC, Tolaney S, Chagpar AB, Yung RL, Freedman RA, Dominici LS, Golshan M, Rhei E, Taneja K, Huang Y, Brown M, Winer EP, Jeselsohn R, Irwin ML	2019	Clinical Cancer Research			HALO
A phase 2 study of GVAX colon vaccine with cyclophosphamide and pembrolizumab in patients with mismatch repair proficient advanced colorectal cancer	Yarchoan M, Huang C-Y, Zhu Q, Ferguson AK, Durham JN, Anders RA, Thompson ED, Rozich NS, Thomas DL, Nauroth JM, Rodriguez C, Osipov A, De Jesus-Acosta A, Le DT, Murphy AG, Laheru D, Donehower RC, Jaffee EM, Zheng L, Azad NS	2019	Cancer Medicine	Immuno-oncology	Area Quantification, Partitions (tiles, margins)	HALO
Hotspot enumeration of CD8+ tumor infiltrating lymphocyte using digital image analysis in triple negative breast Cancer yields consistent results	McIntire PJ, Zhong E, Patel A, Khani F, D'Alfonso T, Chen Z, Shin SJ, Ginter PS	2019	Human Pathology	Oncology	Cytonuclear	HALO
Female-biased embryonic death from inflammation induced by genomic instability	McNairn AJ, Chuang C-H, Bloom JC, Wallace MD, Schimenti JC	2019	Nature	Immunology	Cytonuclear	HALO
Imaging CAR T cell therapy with PSMA-targeted positron emission tomography	Minn I, Huss DJ, Ahn H-H, Chinn TM, Park A, Jones J, Brummet M, Rowe SP, Sysa-Shah P, Du Y, Levitsky HI, Pomper MG	2019	Science Advances	Oncology	Cytonuclear	HALO
Reliable identification of prostate cancer using mass spectrometry metabolomic imaging in needle core biopsies	Morse N, Jamaspishvili T, Simon D, Patel PG, Ren KYM, Wang J, Oleschuk R, Kaufmann M, Gooding RJ, Berman DM	2019	Laboratory Invesigations	Oncology		HALO
Efficacy of ruthenium coordination complex-based Rutherrin in a preclinical rat glioblastoma model	Munegowda MA, Fisher C, Molehuis D, Foltz W, Roufaiel M, Bassan J, Nitz M, Mandel A, Lilge L	2019	Neuro-Oncology Advances			HALO
HIF-independent synthetic lethality between CDK4/6 inhibition and VHL loss across species	Nicholson HE, Tariq Z, Housden BE, Jennings RB, Stransky LA, Perrimon N, Signoretti S, Kaelin WG	2019	Cancer Therapy			HALO
Prohibitin is a prognostic marker of relapse and therapeutic target to block chemotherapy resistance in Wilms tumor	Ortiz MV, Ahmed S, Burns M, Henssen AG, Hollmann TJ, MacArthur I, Gunasekera S, Gaewsky L, Bradwin G, Ryan J, Letai A, He Y, Naranjo A, Chi Y-Y, LaQuaglia M, Heaton T, Cifani P, Dome JS, Gadd S, Perlman E, Mullen E, Steen H, Kentsis A	2019	JCI Insight	Oncology	Cytonuclear	HALO
Validation and characterisation of prognostically significant PD-L1+ immune cells in HPV+ oropharyngeal squamous cell carcinoma	Young RJ, Bressel M, Porceddu S, Cernelc J, Savas P, Liu H, Urban D, Thai AA, Cooper C, Fua T, Neeson P, Rischin D, Solomon B	2019	Oral Oncology	Oncology, Infectious Disease	Classifier, Highplex FL	HALO
Human 3D Gastrointestinal Microtissue Barrier Function As a Predictor of Drug-Induced Diarrhea	Peters MF, Landry T, Pin C, Maratea K, Dick C, Wagoner MP, Choy AL, Barthlow H, Snow D, Stevens Z, Armento A, Scott CW, Ayehunie S	2019	Toxicological Sciences	Gastroenterology		HALO
PTEN loss in Gleason grade 7 prostate tumors exhibits intratumoral heterogeneity and is associated with unfavorable pathological features	Picanço-Albuquerque CG, Vidotto T, Pereira CS, Saggioro FP, Jamaspishvili T, Koti M, Berman DM, Squire JA, Reis RB	2019	Applied Cancer Research	Oncology		HALO
Extramammary Paget disease shows differential expression of B7 family members B7-H3, B7-H4, PD-L1, PD-L2 and cancer/testis antigens NY-ESO-1 and MAGE-A	Pourmaleki M, Young JH, Socci ND, Chiang S, Edelweiss M, Li Y, Zhang M, Roshal L, Chi DS, Busam KJ, Mellinghoff IK, Hollmann TJ	2019	Oncotarget			HALO
Impact of TREM2 risk variants on brain region-specific immune activation and plaque microenvironment in Alzheimer's disease patient brain samples	Prokop S, Miller KR, Labra SR, Pitkin RM, Hoxha K, Narasimhan S, Changolkar L, Rosenbloom A, Lee VM-Y, Trojanowski JQ	2019	Acta Neuropathologica	Neuroscience		HALO
Delta-like protein 3 expression and therapeutic targeting in neuroendocrine prostate cancer	Puca L, Gavyert K, Sailer V, Conteduca V, Dardenne E, Sigouros M, Isse K, Kearney M, Vosoughi A, Fernandez L, Pan H, Motanagh S, Hess J, Donoghue AJ, Sboner A, Wang Y, Dittamore R, Rickman D, Nanus DM, Tagawa ST, Elemento O, Mosquera JM, Saunders L, Beltran H	2019	Science Translational Medicine	Oncology		HALO
Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells	Reitman ZJ, Paolella BR, Bergthold G, Pelton K, Becker S, Jones R, Sinai CE, Malkin H, Huang Y, Grimmet L, Herbert ZT, Sun Y, Weatherbee JL, Alberta JA, Daley JF, Rozenblatt-Rosen O, Condurat AL, Qian K, Khadka P, Segal RA, Haas-Kogan D, Filbin MG, Suva ML, Regev A, Stiles CD, Kieran MW, Goumnerova L, Ligon KL, Shalek AK, Bandopadhayay P, Beroukhim R	2019	Nature Communications	Oncology		HALO
Pre-exposure prophylaxis differentially alters circulating and mucosal immune cell activation in herpes simplex virus type 2 seropositive women	Richert-Spuhler LE, Pattacini L, Plews M, Irungu E, Muwonge TR, Katabira E, Mugo N, Meyers AFA, Celum C, Baeten JM, Lingappa JR, Lund JM	2019	AIDS	Infectious Disease		HALO
A MYCGCN2eIF2? negative feedback loop limits protein synthesis to prevent MYC-dependent apoptosis in colorectal cancer	Schmidt S, Gay D, Uthe FW, Denk S, Paauwe M, Matthes N, Diefenbacher ME, Bryson S, Warrander FC, Erhard F, Ade CP, Baluapuri A, Walz S, Jackstadt R, Ford C, Vlachogiannis G, Valeri N, Otto C, Schülein-Völk C, Maurus K, Schmitz W, Knight JRP, Wolf E, Strathdee D, Schulze A, Germer C-T, Rosenwald A, Sansom OJ, Eilers M	2019	Nature Cell Biology	Oncology		HALO
Mobilization of CD8+ T cells via CXCR4 blockade facilitates PD-1 checkpoint therapy in human pancreatic cancer	Seo YD, Jiang X, Sullivan KM, Jalikis FG, Smythe KS, Abbasi A, Vignali M, Park JO, Daniel SK, Pollack SM, Kim TS, Yeung R, Crispe IN, Pierce RH, Robins H, Pillarisetty VG	2019	Clinical Cancer Research	Immuno-oncology		HALO
Targeting glutamate metabolism in melanoma	Singh S, Shah R, Chen S, Filipp FV	2019	arXiv			HALO
Logic-Gated ROR1 Chimeric Antigen Receptor Expression Rescues T Cell-Mediated Toxicity to Normal Tissues and Enables Selective Tumor Targeting	Srivastava S, Salter A, Liggitt D, Yechan-Gunja S, Sarvothama M, Cooper K, Smythe KS, Dudakov JA, Pierce RH, Rader C, Riddell SR	2019	Cancer Cell	Oncology, Immuno-oncology		HALO
Citrullination of fibronectin alters integrin clustering and focal adhesion stability promoting stromal cell invasion	Stefanelli VL, Choudhury S, Hu P, Liu Y, Schwenzer A, Yeh C-R, Chambers DM, Pesson K, Li W, Segura T, Midwood KS, Torres M, Barker TH	2019	Matrix Biology	Oncology, Fibrosis		HALO
A Short Isoform of Coagulation Factor XII mRNA Is Expressed by Neurons in the Human Brainl	Zamolodchikov D, Bai Y, Tang Y, McWhirter JR, Macdonald LE, Alessandri-Haber N	2019	Neuroscience	Neuroscience	Figure Maker	HALO
Automated macrophage counting in DLBCL tissue samples: a ROF filter based approach	Wagner M, Hansel R, Reinke S, Richter J, Altenbuchinger M, Braumann U-D, Spang R, Loffler Mk Klapper W	2019	Biological Proectures Online	Oncology	Object Colocalization	HALO
Impact of pre?therapy glioblastoma multiforme microenvironment on clinical response to autologous CMV?specific T?cell therapy	Walker DG, Shakya R, Morrison B, Neller MA, Matthews KK, Nicholls J, Smith C, Khanna R	2019	Clinical & Translational Immunology	Immuno-oncology	Classifier	HALO
Human pseudoislet system enables detection of differences in G-protein-coupledreceptor signaling pathways between ? and ? cells	Walker JT, Haliyur R, Nelson HA, Ishahak M, Poffenberger G, Aramandla R, Reihsmann C, Luchsinger JR, Saunders DC, Wang P, Garcia-Ocana A, Bottino R, Agarwal A, Powers AC, Brissove M	2019	bioRxiv			HALO
Multiplex Immunofluorescence of Bone Marrow Core Biopsies: Visualizing the Bone Marrow Immune Contexture	Walters DK, Jelinek DF	2019	Journal of Histochemistry & Cytochemistry			HALO
No Evidence of Neurogenesis in Adult Rat Sympathetic Ganglia Following Guanethidine-Induced Neuronal Loss	Walters KM, Boucher M, Boucher GG, Opsahl AC, Mouton PR, Liu C-N, Ritenour CR, Kawabe TT, Pryski HN, Somps CJ	2019	Toxicologic Pathology	Toxicology, Neuroscience		HALO
ATDC is required for the initiation of KRAS-induced pancreatic tumorigenesis	Wang L, Yang H, Zamperone A, Diolaiti D, Palmbos PL, Abel EV, Purohit V, Dolgalev I, Rhim AD, Ljungman M, Hadju CH, Halbrook CJ, Bar-Sagi D, di Magliano MP, Crawford HC, Simeone DM	2019	Genes & Development	Oncology		HALO
Monocytes/Macrophages play a pathogenic role in IL-23 mediated psoriasis-like skin inflammation	Wang Y, Edelmayer R, Wetter J, Salte K, Gauvin D, Leys L, Paulsboe S, Su Z, Weinberg I, Namovic M, Gauld SB, Honore P, Scott VE, McGaraughty S	2019	Scientific Reports	Immunology, Dermatology		HALO
Myeloid Cell-Derived HB-EGF Drives Tissue Recovery After Pancreatitis	Wen H-J, Gao S, Wang Y, Ray M, Magnuson MA, Wright CVE, Di Magliano MP, Frankel TL, Crawford HC	2019	Cellular and Molecular Gastroenterology and Hepatology	Immunology		HALO
Nrf2 represses the onset of type 1 diabetes in non-obese diabetic mice	Yagishita Y, Uruno A, Chartoumpekis DV, Kensler TW, Yamamoto M	2019	The Journal of Endocrinology	Metabolism		HALO
Systemic mRNA Therapy for the Treatment of Fabry Disease: Preclinical Studies in Wild-Type Mice, Fabry Mouse Model, and Wild-Type Non-human Primates	Zhu S, Li S, Escuin-Ordinas H, Dimatteo R, Xia W, Ribas A, Segura T	2019	The American Journal of Human Genetics	Metabolism		HALO
Selective modulation of the androgen receptor AF2 domain rescues degeneration in spinal bulbar muscular atrophy	Badders NM, Korff A, Miranda HC, Vuppala PK, Smith RB, Winborn BJ, Quemin ER, Sopher BL, Dearman J, Messing J, Kim NC, Moore J, Freibaum BD, Kanagaraj AP, Fan B, Tillman H, Chen P-C, Wang Y, Freeman BB, Li Y, Kim HJ, La Spada AR, Taylor JP	2018	Nature Medicine	Myology	Area Quantification	HALO
Anti-NKG2A mAb Is a Checkpoint Inhibitor that Promotes Anti-tumor Immunity by Unleashing Both T and NK Cells	Andre ?P, Denis C, Soulas C, Bourbon-Caillet C, Lopez J, Arnoux T, Ble?ry M, Bonnafous C, Gauthier L, Morel A, Rossi B, Remark R, Breso V, Bonnet E, Habif G, Guia S, Lalanne AI, Hoffmann C, Lantz O, Fayette J, Boyer-Chammard A, Zerbib R, Dodion P, Ghadially H, Jure-Kunkel M, Morel Y, Herbst R, Narni-Mancinelli E, Cohen RB, Vivier E	2018	Cell	Oncology, Immuno-oncology	Area Quantification, Cytonuclear	HALO
Tuning of delta-protocadherin adhesion through combinatorial	Bisogni AJ, Ghazanfar S, Williams EO, Marsh HM, Yang JYH, Lin DM	2018	eLife	Neuroscience	Area Quantification	HALO
RAD51 foci as a functional biomarker of homologous recombination repair and PARP inhibitor resistance in germline BRCA mutated breast cancer	Cruz C, Castroviejo-Bermejo M, Gutiérrez-Enríquez S, Llop-Guevara A, Ibrahim YH, Gris-Oliver A, Bonache S, Morancho B, Bruna A, Rueda OM, Lai Z, Polanska UM, Jones GN,Kristel P, de Bustos L, Guzman M, Rodriguez O, Grueso J, Montalban G, Caratú G, Mancuso F, Fasani R, Jiménez J, Howat WJ, Dougherty B, Vivancos A, Nuciforo P, Serres-Créixams X, Rubio IT, Oaknin A, Cadogan O, Barrett JC, Caldas C, Baselga J, Saura C, Cortés J, Arribas J, Jonkers J, Díez O, OConnor MJ, Balmaña J, SerraV	2018	Annals of Oncology	Oncology	Classifier, Cytonuclear	HALO
The brain-penetrant clinical ATM inhibitor AZD1390 radiosensitizes and improves survival of preclinical brain tumor models	Durant ST, Zheng L, Wang Y, Chen K, Zhang L, Zhang T, Yang Z, Riches L, Trinidad AG, Fok JHL, Hunt T, Pike KG, Wilson J, Smith A, Colclough N, Reddy VP, Sykes A, Janefeldt A, Johnström P, Varnäs K, Takano A, Ling S, Orme J, Stott J, Roberts C, Barrett I, Jones G, Roudier M, Pierce A, Allen J, Kahn J, Sule A, Karlin J, Cronin A, Chapman M, Valerie K, Illingworth R, Pass M	2018	Science Advances	Oncology, Neuroscience	Classifier, Cytonuclear	HALO
High response rate to PD-1 blockade in desmoplastic melanomas	Eroglu Z, Zaretsky JM, Hu-Lieskovan H, Kim DW, Algazi A, Johnson DB, Liniker E, Kong B, Munhoz R, Rapisuwon S, Gherardini PF, Chmielowski B, Wang X, Shintaku IP, Wei C, Sosman JA, Joseph RW, Postow MA, Carlino MS, Hwu W-J, Scolyer RA, Messina J, Cochran AJ, Long GV, Ribas A	2018	Nature	Oncology, Immuno-oncology	Cytonuclear	HALO
Early Stage HER2-Positive Breast Cancers Not Achieving a pCR From Neoadjuvant Trastuzumab- or Pertuzumab-Based Regimens Have an Immunosuppressive Phenotype	Force J, Howie LJ, Abbot SE, Bentley R, Marcom PK, Kimmick G, Westbrook K, Sammons SL, Parks M, Topping DL, Emerson R, Broadwater G, Hyslop T, Blackwell KL, Nair SK	2018	Clinical Breast Cancer	Oncology, Immuno-oncology	Cytonuclear	HALO
Bortezomib prevents cytarabine resistance in MCL, which is characterized by down-regulation of dCK and up-regulation of SPIB resulting in high NF-?B activity	Freiburghaus C, Emruli VK, Johansson A, Eskelund CW, Grønbæk K, Olsson R, Ek F, Jerkeman M, Ek S	2018	BMC Cancer	Oncology	Classifier, Cytonuclear	HALO
The novel ATM inhbitior (AZ31) enhances antitumor activity in patient derived xenografts that are resistant to irinotecan montherapy	Greene J, Nguyen A, Bagby SM, Jones GN, Tai WM, Quackenbush KS, Schreiber A, Messersmith WA, Devaraj KM, Blatchford P, Eckhardt SG, Cadogan EB, Hughes GD, Smith A, Pitts TM, Arcaroli JJ	2018	Oncotarget	Oncology	Classifier, Area Quantification, Cytonuclear	HALO
Cystic fibrosisrelated diabetes is caused by islet loss and inflammation	Hart NJ, Aramandla R, Poffenberger G, Fayolle C, Thames AH, Bautista A, Spigelman AF, Babon JAB, DeNicola ME, Dadi PK, Bush WS, Balamurugan AN, Brissova M, Dai C, Prasad N, Bottino R, Jacobson DA, Drumm ML, Kent SC, MacDonald PE, Powers AC	2018	JHI Insights	Immunology, Metabolism, Fibrosis	Cytonuclear	HALO
Attenuation of diet-induced hypotalamic inflammation following bariatric surgery in female mice	Herrick MK, Favela KM, Simerly RB, Abumrad NN, Bingham NC	2018	Molecular Medicine	Immunology, Neuroscience	Cytonuclear	HALO
pRAD50: a novel and clinically applicable pharmacodynamic biomarker of both ATM and ATR inhibition identified using mass spectrometry and immunohistochemistry	Jones GN, Rooney C, Griffin N, Roudier M, Young LA, Garcia-Trinidad A, Hughes GD, Whiteaker JR, Wilson Z, Odedra R, Zhao L, Ivey RG, Howat WJ, Harrington EA, Carrett JC, Ramos-Montoya A, Lau A, Paulovich AG, Cadogan EB, Pierce AJ	2018	British Journal of Cancer	Oncology	Classifier, Cytonuclear	HALO
Mice harboring the human SLC30A8 R138X loss-of-function mutation have increased insulin secretory capacity	Kleinera S, Gomeza D, Megraa B, Naa E, Bhavsara R, Cavinoa K, Xina Y, Rojasa J, Dominguez-Gutierreza G, Zambrowicza B, Carratb G, Chabosseaub P, Hub M, Murphya AJ, Yancopoulosa GD, Rutterb GA, Gromadaa J	2018	Proceedings of the National Academy of Sciences	Metabolism	Cytonuclear	HALO
TGF? inhibition restores a regenerative response in acute liver injury by suppressing paracrine senescence	Bird TG, Müller M, Boulter L, Vincent DF, Ridgway RA, Elena Lopez-Guadamillas E, Lu W-Y, Jamieson T, Govaere O, Campbell AD, Ferreira-Gonzalez S, Cole AM, Hay T, Simpson KJ, Clark W, Hedley A, Clarke M, Gentaz P, Nixon C, Bryce S, Kiourtis C, Sprangers J, Nibbs RJB, Van Rooijen N, Bartholin L, McGreal SR, Apte U, Barry ST, Iredale JP, Clarke AR, Serrano M, Roskams TA, Sansom OJ, Forbes SJ	2018	Science Translational Medicine	Metabolism	ISH/FISH	HALO
Food Perception Primes Hepatic ER Homeostasis via Melanocortin-Dependent Control of mTOR Activation	Brandt C, Nolte H, Henschke S, Ruud LE, Awazawa M, Morgan DA, Gabel P, Sprenger H-G, Hess ME, Günther S, Langer T, Rahmouni K, Fenselau H, Krüger M, Brüning JC	2018	Cell	Neuroscience, Metabolism	ISH/FISH	HALO
Gene Signature of Proliferating Human Pancreatic ?-Cells	Dominguez Gutierrez G, Xin Y, Okamoto H, Kim J, Lee A-H, Ni M, Adler C, Yancopoulos GD, Murphy AJ, Gromada J	2018	Endocrionology	Metabolism	ISH/FISH	HALO
A phase II study of the dual mTOR inhibitor MLN0128 in patients with metastatic castration resistant prostate cancer	Graham L, Banda K, Torres A, Carver BS, Chen Y, Pisano K, Shelkey G, Curley T, Scher HI, Lotan TL, Hsieh AC, Rathkopf DE	2018	Investigational New Drugs	Oncology	ISH/FISH	HALO
Ultrasensitive automated RNA in situ hybridization for kappa and lambda light chain mRNA detects B-cell clonality in tissue biopsies with performance comparable or superior to flow cytometry	Guo L, Wang Z, Anderson CA, Doolittle E, Kernag S, Cotta CV, Ondrejka SL, Ma X-J, Cook JR	2018	Modern Pathology	Other	Classifier, ISH/FISH	HALO
CD163+ macrophages promote angiogenesis and vascular permeability accompanied by inflammation in atherosclerosis	Guo L, Akahori H, Harari E, Smith SL, Polavarapu R, Karmali V, Otsuka F, Gannon RL, Braumann RE, Dickinson MH, Gupta A, Jenkins AL, Lipinski MJ, Kim J, Chhour P, de Vries PS, Jinnouchi H, Kutys R, Mori H, Kutyna MD, Torii S, Sakamoto A, Choi CU, Cheng Q, Grove M, Mariem A. Sawan MA, Zhang Y, Cao Y, Kolodgie FD, Cormode DP, Arking DE, Boerwinkle E, Morrison AC, Erdmann J, Sotoodehnia N, Virmani R, and Finn AV	2018	The Journal of Clinical Investigation	Immunology	Layer Thickness	HALO
Glucagon contibutes to liver zonation	Cheng X, Kim SK, Okamoto H, Xin Y, Yancopoulos GD, Murphy AJ, Gromada J	2018	Proceedings of the National Academy of Sciences	Metabolism	Area Quantification	HALO
Evaluation of PD-L1 expression on vortex-isolated circulating tumor cells in metastatic lung cancer	Dhar M, Wong J, Che J, Matsumoto M, Grogan T, Elashof D, Garon EB, Goldman JW, Christen ES, Carlo DD, Kulkarni RP	2018	Scientific Reports	Oncology, Immuno-oncology	Area Quantification	HALO
Digital image analysis of Ki67 proliferation index in breast cancer using virtual dual staining on whole tissue sections: clinical validation and inter?platform agreement	Koopman T, Buikema HJ, Hollema H, de Bock GH, van der Vegt B	2018	Breast Cancer Research and Treatment	Oncology	Classifier, Cytonuclear	HALO
The neurotrophic tyrosine kinase receptor TrkA and its ligand NGF are increased in squamous cell carcinomas of the lung	Gao F, Griffin N, Faulkner S, Rowe CW, Williams L, Roselli S, Thorne RF, Ferdoush A, Jobling P, Walker MM, Hondermarck H	2018	Scientific Reports	Oncology	Area Quantification	HALO
Ovarian Tumor Microenvironment Signaling: Convergence on the Rac1 GTPase	Hudson LG, Gillette JM, Kang H, Rivera MR, Wandinger-Ness A	2018	Cancers	Review	Classifier, Cytonuclear, Figure Maker	HALO
A murine glaucoma model induced by rapid in vivo photopolymerization of hyaluronic acid glycidyl methacrylate	Guo C, Qu X, Rangaswamy N, Leehy B, Xiang C, Rice D, Prasanna G	2018	PLOS One	Biomaterials	Area Quantification	HALO
Systemic messenger RNA as an etiological treatment for acute intermittent porphyria	Jiang L, Berraondo P, Jericó D, Guey LT, Sampedro A, Frassetto A, Benenato KE, Burke K, Santamaría E, Alegre M, Pejenaute A, Kalariya M, Butcher W, Park JS, Zhu X, Sabnis S, Kumarasinghe ES, Salerno T, Kenney M, Lukacs CM, Ávila MA, Martini PGV, Fontanellas A	2018	Nature Medicine	Metabolism	Area Quantification	HALO
Tumor Microenvironment in Functional Adrenocortical Adenomas: Immune Cell Infiltration in Cortisol-producing Adrenocortical Adenoma	Kitawaki Y, Nakamura Y, Kubota-Nakayama F, YamazakiY, Miki Y, Hata S, Ise K, Kikuchie K, MorimotoR, Satoh F, Sasano H	2018	Human Pathology	Oncology, Immuno-oncology	Area Quantification	HALO
Up-Regulation of Iba-1 and GFAP in the Acidic Saline Model of Chronic Widespread Musculoskeletal Pain: A Pilot Study Examining the Relationship Between Gliosis and Hyperalgesia	Lambert DM, Kumar U, Hafell UO	2018	Journal of Neuroscience and Neuropharmacology	Neuroscience	Area Quantification, Partitions (tiles, margins)	HALO
Tough Composite Hydrogels with High Loading and Local Release of Biological Drugs	Li J, Weber E, Guth?Gundel S, Schuleit M, Kuttler A, Halleux C, Accart N, Doelemeyer A, Basler A, Tigani B, Wuersch K, Fornaro M, Kneissel M, Stafford A, Freedman BR, Mooney DJ	2018	Advanced Healthcare Materials	Biomaterials	Area Quantification	HALO
Blocking HIF signaling via novel inhibitors of CA9 and APE1/Ref-1 dramatically affects pancreatic cancer cell survival	Logsdon DP, Fenil S, Fabrizio C, Supuran CT, Kamocka M, Jacobsen MH, Sandusky GE, Kelley MR, Fishel ML	2018	Scientific Reports	Oncology	Classifier, Cytonuclear	HALO
Diet-Induced Growth Is Regulated via Acquired Leptin Resistance and Engages a PomcSomatostatin-Growth Hormone Circuit	Lohr H, Hess S, Pereira MMA, Reino P, Leibold S, Schenkel C, Wunderlich CM, Kloppenburg P, Bruning JC, Hammerschmidt M	2018	Cell Reports	Neuroscience, Metabolism	Cytonuclear	HALO
Chronic Intermittent Hypoxia Induces Robust Astrogliosis in an Alzheimer's Disease-Relevant Mouse Model	Macheda T, Roberts K, Lyons DN, Higgins E, Ritter KJ, Lin A-L, Alilain WJ, Bachstetter AD	2018	Neuroscience	Neuroscience	Area Quantification	HALO
Cellular milieu imparts distinct pathological ?-synuclein strains in ?-synucleinopathies	Peng C, Gathagan RJ, Covell DJ, Medellin C, Stieber A, Robinson JL, Zhang B, Pitkin RM, Olufemi MF, Luk KC, Trojanowski JQ, Lee VM-Y	2018	Nature	Neuroscience	Area Quantification	HALO
Differential ?-synuclein expression contributes to selective vulnerability of hippocampal neuron subpopulations to fibril-induced toxicity	Luna E, Decker SC, Riddle DM, Caputo A, Zhang B, Cole T, Caswell C, Xie SX, Lee VMY, Luk KC	2018	Acta Neuopathologica	Neuroscience	Area Quantification, Cytonuclear	HALO
Digital image analysis improves precision of PD?L1 scoring in cutaneous melanoma	Koelzer VH, Gisler A, Hanhart JC, Griss J, Wagner SN, Willi N, Cathomas G, Sachs M, Kempf W, Thommen DS, Mertz KD	2018	Histopathology	Oncology, Immuno-oncology	Classifier, Multiplex IHC	HALO
Lenvatinib inhibits angiogenesis and tumor fibroblast growth factor signaling pathways in human hepatocellular carcinoma models	Matsuki M, Hoshi T, Yamamoto Y, Ikemori-Kawada M, Minoshima Y, Funahashi Y, Matsui J	2018	Cancer Medicine	Oncology	Cytonuclear	HALO
Hot Spot and Whole-Tumor Enumeration of CD8(+) Tumor-Infiltrating Lymphocytes Utilizing Digital Image Analysis Is Prognostic in Triple-Negative Breast Cancer	McIntire PJ, Irshaid L, Liu Y, Chen Z, Menken F, Nowak E, Shin SJ, Ginter PS	2018	Clinical Breast Cancer	Oncology, Immuno-oncology	Cytonuclear, Figure Maker	HALO
Altered dopaminergic regulation of the dorsal striatum is able to induce tic-like movements in juvenile rats	Nespoli E, Rizzo F, Boeckers T, Schulze U, Hengerer B	2018	PLOS One	Neuroscience	Cytonuclear	HALO
Induction of hemangiosarcoma in mice after chronic treatment with S1P-modulator siponimod and its lack of relevance to rat and human	Pognan F, Mahl JA, Papoutsi M, David Ledieu D, Raccuglia M, Theil D, Voytek SB, Devine PJ, Kubek?Luck K, Claudio N, Cordier A, Heier A, Kolly C, Hartmann A, Chibout S-D, Bouchard P, Trendelenburg C	2018	Archives of Toxicology	Toxicology	Classifier, Cytonuclear	HALO
Intermittent Hypoxia Exacerbates Increased Blood Pressure in Rats with Chronic Kidney Disease	Riggs J, Pace C, Ward HH, Gonzalez Bosc L, Rios L, Barrera A, Kanagy NL	2018	American Jornal of Physiology-Renal Physiology	Metabolism	Classifier, Cytonuclear	HALO
Mild Impairment of Mitochondrial OXPHOS Promotes Fatty Acid Utilization in POMC Neurons and Improves Glucose Homeostasis in Obesity	Timper K, Paeger L, Sánchez-Lasheras C, Varela L, Jais A, Nolte H, Vogt MC, Hausen AC, Heilinger C, Evers N, Pospisilik JA, Penninger JM, Taylor EB, Horvath TL, Kloppenburg P, Brüning JC	2018	Cell Repots	Neuroscience, Metabolism	Cytonuclear	HALO
Biomarker Evaluation and Toxic Effects of an Acute Oral and Systemic Fumonisin Exposure of Pigs with a Special Focus on Dietary Fumonisin Esterase Supplementation	Schertz H, Danicke S, Frahm J, Schatzmayr D, Dohnal I, Bichl G, Schwartz-Zimmerman HE, Colicchia S, Breves G, Teifke JP, Kluess J	2018	Toxins	Toxicology	Classifier	HALO
Mutant myocilin impacts sarcomere ultrastructure in mouse gastrocnemius muscle	Lynch JM, Dolman AJ, Guo C, Dolan K, Xiang C, Reda S, Li B, Prasanna G	2018	PLOS One	Gastroenterology, Myology	ISH/FISH	HALO
Breast and pancreatic cancer interrupt IRF8-dependent dendritic cell development to overcome immune surveillance	Meyer MA, Baer JM, Knolhoff BL, Nywening TM, Panni RZ, Su X, Weilbaecher KN, Hawkins WG, Ma C, Fields RC, Linehan DC, Challen GA, Faccio R, Aft RL, DeNardo DG	2018	Nature Communications	Oncology, Immuno-oncology	ISH/FISH	HALO
What is the added value of digital image analysis of HER2 immunohistochemistry in breast cancer in clinical practice? A study with multiple platforms	Koopman T, Buikema HJ, Hollema H, de Bock GH, van der Vegt B	2018	Histopathology	Oncology	Membrane	HALO
Tumor Cell Subtypes Based on the Intracellular Hormonal Activity in KCNJ5-Mutated Aldosterone-Producing Adenoma	Yamazaki Y, Omata K, Tezuka Y, Ono Y, Morimoto R, Adachi Y, Ise K, Nakamura Y, Gomez-Sanchez CE, Shibahara Y, Kitamoto T, Nishikawa T, Ito S, Satoh F, Sasano H	2018	Hypertension	Oncology	Area Quantification, Cytonuclear	HALO
Disease Progression and Pharmacological Intervention in a Nutrient-Deficient Rat Model of Nonalcoholic Steatohepatitis	Tølbøl KS, Stierstorfer B, Rippmann JF, Veidal SS, Rigbolt KTG, Schönberger T, Gillum MP, Hansen HH, Vrang N, Jelsing J, Feigh M, Broermann A	2018	Digestive Diseases and Sciences	Metabolism	Area Quantification	HALO
FOXM1 contributes to treatment failure in acute myeloid leukemia	Khan I, Halasi M, Patel A, Schultz R, Kalakota N, Chen Y-H, Aardsma N, Liu L, Crispino JD, Mahmud N, Frankfurt O, Gartel AL	2018	JCI Insight	Oncology	Multiplex IHC	HALO
A transcriptionally and functionally distinct PD-1+ CD8+ T cell pool with predictive potential in non-small-cell lung cancer treated with PD-1 blockade	Thommen DS, Koelzer VH, Herzig P, Roller A, Trefny M, Dimeloe S, Kiialainen A, Hanhart J, Schil C, Hess C, Prince SS, Wiese M, Lardinois D, Ho P-C, Klein C, Karanikas V, Mertz KD, Schumacher TN, Zippelius A	2018	Nature Medicine	Oncology, Immuno-oncology	Multiplex IHC	HALO
Relationship between mismatch repair immunophenotype and long-term survival in patients with resected periampullary adenocarcinoma	Heby M, Lundgren S, Nodin B, Elebro J, Eberhard J, Jirström K	2018	Journal of Translational Medicine	Oncology, Immuno-oncology	Object Colocalization	HALO
Luminally-polarized mural and vascular remodeling in ileal strictures of Crohn's Disease	Zhang X, Ko HM, Torres J, Panchal HJ, Cai Z, WagneR M, Sands BE, Colombel J-F, Cho J, Taouli B, Harpaz N	2018	Human Pathology	Immunology	Layer Thickness	HALO
Age-related pathology after adenoviral overexpression of the leucine-rich repeat kinase 2 in the mouse striatum	Kritzingerab A, Ferger B, Gillardon F, Stierstorfer B, Birk G, Kochanek S, Ciossek T	2018	Neurobiology of Aging	Neuroscience	Area Quantification, Object Colocalization, Microglia	HALO
Pharmacogenetic neuronal stimulation increases human tau pathology and trans-synaptic spread of tau to distal brain regions in mice	Schultz MK, Gentzel R, Usenovic M, Gretzul C, Ware C, Parmentier-Batteur S, Schachter JB, Zariwala HA	2018	Neurobiology of Disease	Neuroscience	Object Colocalization	HALO
Comparison of Biologic Effect and Particulate Embolization after Femoral Artery Treatment with Three Drug-Coated Balloons in Healthy Swine Model	Torii S, Jinnouchi H, Sakamoto A, Romero ME, Kolodgie FD, Virmani R, Finn AV	2018	Journal of Vascular and Interventional Radiology	Other	Object Colocalization	HALO
Multidimensional, quantitative assessment of PD-1/PD-L1 expression in patients with Merkel cell carcinoma and association with response to pembrolizumab	Giraldo NA, Nguyen P, Engle EL, Kaunitz GJ, Cottrell TR, Berry S, Green B, Soni A, Cuda JD, Stein JE, Sunshine JC, Succaria F, Xu H, Ogurtsova A, Danilova L, Church CD, Miller NJ, Fling S, Lundgren L, Ramchurren N, Yearley JH, Lipson EJ, Cheever M, Anders RA, Nghiem PT, Topalian SL, Taube JM	2018	Journal for ImmunoTherapy of Cancer	Oncology, Immuno-oncology	Spatial Analysis, Serial Section	HALO
A CD3-bispecific molecule targeting P-cadherin demonstrates T cell-mediated regression of established solid tumors in mice	TS Fisher, AT Hooper, J Lucas, TH Clark, AK Rohner, B Peano, MW Elliott, K Tsaparikos, H Wang, J Golas, M Gavriil, N Haddish-Berhane, L Tchistiakova, H-P Gerber, AR Root, C May	2018	Cancer Immunology, Immunotherapy	Oncology, Immuno-oncology	Area Quantification	HALO
Innate Sex Bias of Staphylococcus aureus Skin Infection Is Driven by a-Hemolysin	Castleman MJ, Pokhrel S, Triplett KD, Kusewitt DF, Elmore BO, Joyner JA, Femling JK, Sharma G, Hathaway HJ, Prossnitz ER, Hall PR	2018	The Journal of Immunology	Infectious Disease		HALO
Subclonal evolution of pulmonary adenocarcinomas delineated by spatially distributed somatic mitochondrial mutations	Kazdal D, Harms A, Endris V, Penzel R, Kriegsmann M, Eichhorn F, Muley T, Stenzinger A, Pfarr N, Weichert W, and Warth A	2018	Lung Cancer			HALO
Molecular and immunologic analysis of laryngeal squamous cell carcinoma in smokers and non-smokers	Malm I-J, rooper LM, Bishop JA, Ozgursoy SK, Hillel AT, Akst LM, Best SR	2018	American Journal of Otolaryngology	Oncology, Immuno-oncology		HALO
Class 4 Semaphorins and Plexin-B receptors regulate GABAergic and glutamatergic synapse development in the mammalian hippocampus	McDermott JE, Goldblatt D, Paradis S	2018	Molecular and Cellular Neuroscience	Neuroscience		HALO
Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA	Paulson KG, Voillet V, McAfee MS, Hunter DS, Wagener FD, Perdicchio, Valente WJ, Koelle SJ, Church CD, Vandeven N, Thomas H, Colunga AG, Iyer JG, Yee C, Kulikauskas R, Koelle DM, Pierce RH, Bielas JH, Greenberg PD, Bhatia S, Gottardo R, Nghiem P, Chapuis AG	2018	Nature Communications	Immuno-oncology	Partitions (tiles, margins), Figure Maker	HALO
Digital image analysis supports a nuclear-to-cytoplasmic ratio cutoff value below 0.7 for positive for high-grade urothelial carcinoma and suspicious for high-grade urothelial carcinoma in urine cytology specimens	McIntire PJ, Snow JT, Elsoukkary SS, Soong L, Sweeney J, Robinson BD, Siddiqui MT	2018	Cancer Cytopathology	Oncology		HALO
Ossabaw Pigs With a PCSK9 Gain?of?Function Mutation Develop Accelerated Coronary Atherosclerotic Lesions: A Novel Model for Preclinical Studies	Yuan F, Guo L, Park K-H, Woollard JR, Taek?Geun K, Jiang K, Melkamu T, Zang B, Smith SL, Fahrenkrug SC, Kolodgie FD, Lerman A, Virmani R, Lerman LO, Carlson DF	2018	Journal of the American Heart Association	Myology	Area Quantification	HALO
Accelerated wound healing by injectable star poly(ethylene)-b-poly(propylene sulfide) scaffolds loaded with poorly water-soluble drugs	Zhu X, Yin L, Theisen M, Zhuo J, Siddiqui S, Levy B, Presnyak V, Frassetto A, Milton J, Salerno T, Benenato KE, Milano J, Lynn A, Sabnis S, Burke K, Besin G, Lukacs CM, Guey LT, Finn PF, Martini PGV	2018	Journal of Controlled Release	Biomaterials, Wound Healing	Cytonuclear	HALO
The use of automated Ki67 analysis to predict Oncotype DX risk-of-recurrence categories in early-stage breast cancer	Thakur SS, Li H, Chan AMY, Tudor R, Bigras G, Morris D, Enwere EK	2018	PLOS ONE	Oncology	Cytonuclear, Figure Maker, Partitions (tiles, margins)	HALO
Inhibiting Interleukin 36 Receptor Signaling Reduces Fibrosis in Mice with Chronic Intestinal Inflammation	Scheibe K, Kersten C, Schmied A, Vieth M, Primbs T, Carlé B, Knieling F, Claussen J, Klimowicz AC, Zheng J, Baum P, Meyer S, Schürmann S, Friedrich O, Waldner MJ, Rath T, Wirtz S, Kollias G, Ekici AB, Atreya R, Raymond EL, Mbow ML, Neurath MF, Neufert C	2018	Gastroenterology	Immunology, Fibrosis		HALO
Low and variable tumor reactivity of the intratumoral TCR repertoire in human cancers	Scheper W, Kelderman S, Fanchi LF, Linnemann C, Bendle G, de Rooij MAJ, Hirt C, Mezzadra R, Slagter M, Dijkstra K, Kluin RJC, Snaebjornsson P, Milne K, Nelson BH, Zijlmans H, Kenter G, Voest EE, Haanen JBAG, Schumacher TN	2018	Nature Medicine	Oncology, Immuno-oncology	Cytonuclear	HALO
A suboptimal maternal diet combined with accelerated postnatal growth results in an altered aging profile in the thymus of male rats	Tarry-Adkins JL, Aiken CE, Ashmore TJ, Fernandez-Twinn DS, Chen J-H, Ozanne SE	2018	The FASEB Journal	Neuroscience, Metabolism	Classifier, Vacuole	HALO
A brain-penetrant triazolopyrimidine enhances microtubule-stability, reduces axonal dysfunction and decreases tau pathology in a mouse tauopathy model.	Zhang B, Yao Y, Cornec A-S, Oukoloff K, James MJ, Koivula P, Trojanowski JQ, Smith AB III, Lee VM-Y, Ballatore C, Brunden KR	2018	Molecular Neurodegeneration	Neuroscience	Area Quantification	HALO
GABA promotes ?-cell proliferation, but does not overcome impaired glucose homeostasis associated with diet-induced obesity	Untereiner A, Abdo S, Bhattacharjee A, Gohil H, Pourasgari F, Ibeh N, Lai M, Batchuluun B, Wong A, Khuu N, Liu Y, Rijjal DA, Winegarden N, Virtanen C, Orser BA, Cabrera O, Varga G, Rocheleau J, Dai FF, Wheeler MB	2018	The FASEB Journal	Metabolism	Cytonuclear	HALO
Ki67 reproducibility using digital image analysis: an inter-platform and inter-operator study	Acs B, Pelekanou V, Bai Y, Martinez-Morilla S, Toki M, Leung SCY, Nielsen TO, Rimm DL	2017	Laboratory Invesigations	Oncology	Classifier, Cytonuclear	HALO
Efficacy of injectable praziquantel for elimination of trematode metacercariae in bluegills (Lepomis macrochirus) and quantification of parasite death by propidium iodide staining	Bader C, Chelladurai JJ, Starling DE, Jones DE, Brewer MT	2017	Parasitology Research	Infectious Disease	Area Quantification	HALO
Both brown adipose tissue and skeletal muscle thermogenesis processes are activated during mild to severe cold adaptation in mice	Bal NC, Singh S, Reis FCG, Maurya SK, Pani S, Rowland LA, Periasamy M	2017	Journal of Biological Chemistry	Myology	Area Quantification	HALO
Sex- and Dose-Specific Effects of Maternal Bisphenol A Exposure on Pancreatic Islets of First- and Second-Generation Adult Mice Offspring	Bansal A, Rashid C, Xin F, Li C, Polyak E, Duemler A, van der Meer T, Stefaniak M, Wajid S, Doliba N, Bartolomei MS, Simmons RA	2017	Environmental Health Perspectives	Metabolism	Area Quantification	HALO
The R-enantiomer of ketorolac delays mammary tumor development in mouse mammary tumor virus-polyoma middle T antigen (MMTV-PyMT) mice	AS Peretti, D Dominguez, MM Grimes, HJ Hathaway, ER Prossnitz, MR Rivera, A Wandinger-Ness, D Kusewitt, LG Hudson	2017	The American Journal of Pathology	Oncology	Classifier, Area Quantification, Cytonuclear	HALO
The clinical impact of tumour-infiltrating lymphocytes in colorectal cancer differs by anatomical subsite: A cohort study	Berntsson J, Svensson MC, Leandersson K, Nodin B, Micke P, Larsson AH, Eberhard J, Jirstrom K	2017	International Journal of Cancer	Oncology, Immuno-oncology	Cytonuclear	HALO
Acetate Recapturing by Nuclear Acetyl-CoA Synthetase 2 Prevents Loss of Histone Acetylation during Oxygen and Serum Limitation	Bulusu V, Tumanov S, Michalopoulou E, van den Broek NJ, MacKay G, Nixon C, Dhayade S, Schug ZT, Voorde JV, Blyth K, Gottlieb E, Vazquez A, Kamphorst JJ	2017	Cell Reports	Oncology, Metabolism	Cytonuclear	HALO
Loss of the imprinted, non-coding Snord116 gene cluster in the interval deleted in the Prader Willi syndrome results in murine neuronal and endocrine pancreatic developmental phenotypes	Burnett LC, Hubner G, LeDuc C, Morabito MV, Carli JFM, Leibel RL	2017	Human Moledular Genetics	Metabolism	Cytonuclear	HALO
Identification of the SUMO E3 ligase PIAS1 as a potential survival biomarker in breast cancer	Chanda A, Chan A, Deng L, Kornaga EN, Enwere EK, Morris DG, Bonni S	2017	PLOS One	Oncology	Classifier, Cytonuclear	HALO
Spatial distribution of EGFR and KRAS mutation frequencies correlates with histological growth patterns of lung adenocarcinomas	Dietz S, Harms A, Endris V, Eichhorn, Kriegsmann M, Longuespée R, Stenzinger A, Sültmann H, Warth A, and Kazdal D	2017	International Journal of Cancer	Oncology	Cytonuclear	HALO
Aging African green monkeys manifest transcriptional, pathological, and cognitive hallmarks of human Alzheimer's disease	Cramer PE, Gentzel RC, Tanis KQ, Vardigan J, Wang Y, Connolly B, Manfre P, Lodge K, Renger JJ, Zerbinatti C, Uslaner JM	2017	Neurobiology of Aging	Neuroscience	Object Colocalization	HALO
Retinoic-acid-orphan-receptor-C inhibition suppresses Th17 cells and induces thymic aberrations	Guntermann C, Piaia A, Hamel M-L, Theil D, Rubic-Schneider T, del Rio-Espinola A, Dong L, Billich A, Kaupmann K, Dawson J, Hoegenauer K, Orain D, Hintermann S, Stringer R, Pate DD, Doelemeyer A, Deurinck M, and Schümann J	2017	JCI Insight	Oncology, Immuno-oncology	Area Quantification, Cytonuclear	HALO
Digital image analysis agrees with visual estimates of bone marrow trephine biopsy cellularity	Hagiya AS, Etman A, Siddiqi IN, Cen S, Matcuk Jr GR, Brynes RK, Salama ME	2017	International Journal of Laboratory Hematology	Oncology	Cytonuclear	HALO
Selective imaging of internalized proteopathic ?-synuclein seeds in primary neurons reveals mechanistic insight into transmission of synucleinopathies	Karpowicz RJ, Haney CM, Mihaila TS, Sandler RM, Petersson EJ, and Lee VM-Y	2017	Journal of Biological Chemistry	Neuroscience	Area Quantification, Cytonuclear	HALO
Prevalence of somatic mitochondrial mutations and spatial distribution of mitochondria in non-small cell lung cancer	Kazdal D, Harms A, Endris V, Penzel R, Oliveira C, Kriegsmann M, Longuespee R, Winter H, Schneider MA, Muley T, Pfarr N, Weichert W, Stenzinger A,Warth A	2017	British Journal of Cancer	Oncology	Cytonuclear	HALO
Amino Acid Transporter Slc38a5 Controls Glucagon Receptor Inhibition-Induced Pancreatic ? Cell Hyperplasia in Mice	Kim J, Okamoto H, Huang ZJ, Anguiano G, Chen S, Liu Q, Cavino K, Xin Y, Na E, Hamid R, Lee J, Zambrowicz B, Unger R, Murphy AJ, Xu Y, Yancopoulos GD, Li W, Gromada J	2017	Cell Metabolism	Metabolism	Cytonuclear	HALO
APNG as a prognostic marker in patients with glioblastoma	Fosmark S, Hellwege S, Dahlrot RH, Jensen KL, Derand H, Lohse J, Sørensen MD, Hansen S, Kristensen BW	2017	PLOS One	Oncology	ISH/FISH	HALO
TGF? pathway limits dedifferentiation following WNT and MAPK pathway activation to suppress intestinal tumourigenesis	Cammareri P, Vincent DF, Hodder MC, Ridgway RA, Murgia C, Nobis M, Campbell AD, Varga J, Huels DJ, Subramani C, Prescott KLH, Nixon C, Hedley A, Barry ST, Greten FR, Inman GJ, and Sansom OJ	2017	Cell Death and Differentiation	Oncology	Layer Thickness	HALO
Digital analysis and epigenetic regulation of the signature of rejection in colorectal cancer	Koelzer VH, Sokol L, Zahnd S, Christe L, Dawson H, Berger MD, Inderbitzin D, Zlobec I, Lugli A	2017	OncoImmunology	Oncology	Cytonuclear	HALO
Asymmetry of post-mortem neuropathology in behavioural-variant frontotemporal dementia	DJ Irwin, CT McMillan, SX Xie, K Rascovsky, VM Van Deerlin, HB Coslett, R Hamilton, G Aguirre, EB Lee, VMY Lee, JQ Trojanowski, M Grossman	2017	Brain	Neuroscience	Area Quantification, Partitions (tiles, margins)	HALO
Co-clinical Analysis of a Genetically Engineered Mouse Model and Human Prostate Cancer Reveals Significance of NKX3.1 Expression for Response to 5?-reductase Inhibition	Dutta A, Panja S, Virk RK, Kim JY, Zott R, Cremers S, Golombos DM, Liu D, Mosquera JM, Mostaghel EA, Barbieri CE, Mitrofanova A, Abate-Shen C	2017	European Urology	Oncology	Area Quantification	HALO
Amyloid-? plaques enhance Alzheimer's brain tau-seeded pathologies by facilitating neuritic plaque tau aggregation	He Z, Guo JL, McBride JD, Narasimhan S, Kim H, Changolkar L, Zhang B, Gathagan RJ, Yue C, Dengler C, Stieber A, Nitla M, Coulter DA, Abel T, Brunden KR, Trojanowski JQ, Lee V M-Y	2017	Nature Medicine	Neuroscience	Area Quantification	HALO
An ancestral retroviral protein identified as a therapeutic target in type-1 diabetes	Levet S, Medina J, Joanou J, Demolder A, Queruel N, Réant K, Normand M, Seffals M, Dimier J, Germi R, Piofczyk T, Portoukalian J, Touraine J-L, Perron H	2017	JCI Insight	Immunology, Metabolism	Classifier, Cytonuclear	HALO
Receptor tyrosine kinase expression and phosphorylation in canine nasal carcinoma	Hocker SA, Higginbotham ML, Schermerhorn T, Henningson J	2017	Research in Veterinary Science	Oncology	Area Quantification, Multiplex IHC	HALO
Differential roles of RET isoforms in medullary and papillary thyroid carcinomas	Lian EY, Maritan SM, Cockburn JG, Kasaian K, Crupi MJF, Hurlbut D, Jones SJM, Wiseman SM, Mulligan LM	2017	Endocrine-Related Cancer	Oncology	Cytonuclear	HALO
Ante mortem CSF tau levels correlate with post mortem tau pathology in FTLD	Irwin DJ, Lleó A, Xie SX, McMillan CT, Wolk D, Lee EB, Van Deerlin VM, Shaw LM, Trojanowski JQ, Grossman M	2017	Annals of Neurology	Neuroscience	Area Quantification	HALO
Neutorphils dominate the immune cell composition in non-small cell lung cancer	Kargl J, Busch SE, Yang GHY, Kim K-H, Hanke ML, Metz HE, Hubbard JJ, Lee SM, Madtes DK, McIntosh MW, Houghton AM	2017	Nature Communications	Oncology	Area Quantification	HALO
DPP9 enzyme activity controls survival of mouse migratory tongue muscle progenitors and its absence leads to neonatal lethality due to suckling defect	Kim M, Minoux M, Piaia A, Kueng B, Gapp B, Weber D, Haller C, Barbieri S, Namoto K, Lorenz T, Wirsching J, Bassilana F, Dietrich W, Rijli FM, Ksiazek I	2017	Developmental Biology	Myology	Classifier, Area Quantification	HALO
Connexin-43 and aquaporin-4 are markers of ageing-related tau astrogliopathy (ARTAG)-related astroglial response	Kovacs GG, Yousef A, Kaindl S, Lee VM, Trojanowski JQ	2017	Neuropathology and Applied Neurobiology	Neuroscience	Area Quantification	HALO
Angptl4 does not control hyperglucagonemia or ?-cell hyperplasia following glucagon receptor inhibition	Okamoto H, Cavino K, Na E, Krumm E, Kim SY, Stevis PE, Harp J, Murphy AJ, Yancopoulos GD, Gromada J	2017	Proceedings of the National Academy of Sciences	Metabolism	Area Quantification	HALO
Glucagon receptor inhibition normalizes blood glucose in severe insulin-resistant mice	Okamoto H, Kim J, Aglione JP, Lee J, Cavino K, Na E, Rafique A, Kim JH, Harp J, Valenzuela DM, Yancopoulos GD, Murphy AJ, Gromada J	2017	Proceedings of the National Academy of Sciences	Metabolism	Area Quantification	HALO
Cysteinyl leukotriene receptor 1 facilitates tumorigenesis in a mouse model of colitis-associated colon cancer	Osman J, Savari S, Chandrashekar NK, Bellamkonda K, Souglas D, Sjolander A	2017	Oncotarget	Oncology, Immunology	Classifier, Area Quantification	HALO
Plant-based vaccines for oral delivery of type 1 diabetes-related autoantigens: Evaluating oral tolerance mechanisms and disease prevention in NOD mice	Posgai AL, Wasserfall CH, Kwon K-C, Daniell H, Schatz DA, Atkinson MA	2017	Scientific Reports	Metabolism	Area Quantification	HALO
cFOS-SOX9 Axis Reprograms Bone Marrow-Derived Mesenchymal Stem Cells into Chondroblastic Osteosarcoma	He Y, Zhu W, Shin MH, Gary J, Liu C, Dubois W, Hoover SB, Jiang S, Marrogi E, Mock B, Simpson RM, and Huang J	2017	Stem Cell Reports	Oncology	Classifier	HALO
Modulating the therapeutic response of tumours to dietary serine and glycine starvation	Maddocks ODK, Athineos D, Cheung EC, Lee P, Zhang T, van den Broek NJF, Mackay GM, Labuschagne CF, Gay D, Kruiswijk F, Blagih J, Vincent DF, Campbell KJ, Ceteci F, Sansom OJ, Blyth K, Vousden KH	2017	Nature	Oncology	Cytonuclear	HALO
Expression of protein disulfide isomerase family members correlates with tumor progression and patient survival in ovarian cancer	Samanta S, Tamura S, Dubeau L, Mhawech-Fauceglia P, Miyagi Y, Kato H, Lieberman R, Buckanovich RJ, Lin YG, Neamati N	2017	Oncotarget	Oncology	Area Quantification	HALO
Targeting autophagy inhibits melanoma growth by enhancing NK cells infiltration in a CCL5-dependent manner	Mgrditchiana T, Arakeliana T, Paggettia J, Nomana MZ, Virya E, Moussaya E, Van Moera K, Kreisb S, Guerinc C, Buartd S, Roberte C, Borgf C, Vielhg P, Chouaibd S, Berchema G, Janji B	2017	Proceedings of the National Academy of Sciences	Oncology, Immuno-oncology	Cytonuclear	HALO
Weight Pertubation Alters Leptin Signal Transduction in a Region-Specific Manner throughout the Brain	Morabito MV, Ravussin Y, Mueller BR, Skowronski AA, Watanabe K, Foo KS, Lee SX, Lehmann A, Hjorth S, ZeltserLM, LeDuc CA, Leibel RL	2017	PLOS One	Metabolism	Cytonuclear	HALO
A single dose of peripherally infused EGFRvIII-directed CAR T cells mediates antigen loss and induces adaptive resistance in patients with recurrent glioblastoma	ORourke DM, Nasrallah MP, Desai A, Melenhorst JJ, Mansfield K, MorrissetteJJD, Martinez-Lage M, Brem S, Maloney E, Shen A, Isaacs R, Mohan S, Plesa G, Lacey SF, Navenot J-M, Zheng Z, Levine BL, Okada H, June CH, Brogdon JL, Maus MV	2017	Science Translational Medicine	Oncology, Immuno-oncology	Cytonuclear, Multiplex IHC	HALO
The action of ?-hydroxybutyrate on the growth, metabolism and global histone H3 acetylation of spontaneous mouse mammary tumours: evidence of a ?-hydroxybutyrate paradox	Rodrigues LM, Uribe-Lewis S, Madhu B, Honess DJ, Stubbs M, Griffiths JR	2017	Cancer & Metabolism	Oncology, Metabolism	Area Quantification, Cytonuclear	HALO
High levels of tumor-associated neutrophils are associated with improved overall survival in patients with stage II colorectal cancer	RS Berry, M-J Xiong, A Greenbaum, P Mortaji, RA Nofchissey, F Schultz, C Martinez, L Luo, KT Morris, JA Hanson	2017	PLOS One	Oncology, Immuno-oncology	Cytonuclear	HALO
Pathological tau strains from human brains recapitulate the diversity of tauopathies in non-transgenic mouse brain	S Narasimhan, JL Guo, L Changolkar, A Stieber, JD McBride, LV Silva, Z He, B Zhang, RJ Gathagan, JQ Trojanowski, VMY Lee	2017	Journal of Neuroscience	Neuroscience	Cytonuclear	HALO
T-cell Localization, Activation, and Clonal Expansion in Human Pancreatic Ductal Adenocarcinoma	Stromnes IM, Hulbert A, Pierce RH, Greenberg PD, Hingorani SR	2017	Cancer Immunology Research	Oncology, Immuno-oncology	Highplex FL	HALO
Transcriptional mechanisms of resistance to anti-PD-1 therapy	Ascierto ML, Makohon-Moore A, Lipson EJ, Taube JM, McMiller TL, Berger AE, Fan J, Kaunitz GJ, Cottrell TR, Kohutek ZA, Favorov A, Makarov V, Riaz N, Chan TA, Cope L, Hruban RH, Pardoll DM, Taylor BS, Solit DB, Iacobuzio-Donahue CA, Topalian SL	2017	Clinical Cancer Research	Oncology, Immuno-oncology	Immune	HALO
Comparison of branch and distally focused main renal artery denervation using two different radio-frequency systems in a porcine model	Mahfoud F, Pipenhagen CA, Moon LB, Ewen S, Kulenthiran S, Fish JM, Jensen JA, Virmani R, Joner M, Yahagi K, Tsioufis C, Böhm M	2017	International Journal of Cardiology	Myology	Layer Thickness	HALO
Treatment with the WNT5A-mimicking peptide Foxy-5 effictively reduces the metastatic spread of WNT5A-low prostate cancer cells in an orthotopic mouse model	Canesin G, Evans-Axelsson S, Hellsten R, Krzyzanowska A, Prasad CP, Bjartell A, Andersson T	2017	PLOS One	Oncology	Membrane	HALO
Expression of PD-L1 and presence of CD8-positive T cells in pre-treatment specimens of locally advanced cervical cancer	Enwere EK, Kornaga EN, Dean M, Koulis TA, Phan T, Kalantarian M, Köbel M, Ghatage P, Magliocco AM, Lees-Miller DP, Doll CM	2017	Modern Pathology	Oncology, Immuno-oncology	Membrane	HALO
Association of HIV Status With Local Immune Response to Anal Squamous Cell Carcinoma: Implications for Immunotherapy	Yanik EL, Kaunitz GJ, Cottrell TR, Succaria F, McMiller TL, Ascierto ML, Esandrio J, Xu H, Ogurtsova A, Cornish T, Lipson EJ, Topalian SL, Engels EA, Taube JM	2017	JAMA Oncology	Oncology, Immuno-oncology	Cytonuclear	HALO
Chronic Verubecestat Treatment Suppresses Amyloid Accumulation in Advanced Aged Tg2576-A?PPswe Mice Without Inducing Microhemorrhage	Villarreal S, Zhao F, Hyde LA, Holder D, Forest T, Sondey M, Chen X, Sur C, Parker EM, Kennedy ME	2017	Journal of Alzheime's Disease	Neuroscience	Object Colocalization	HALO
In vivo characterization of a new type of biodegradable starch microsphere for transarterial embolization	Sommer CM, Do TD, Schlett CL, Flechsig P, Gockner TL, Kuthning A, Vollherbst DF, Pereira PL, Kauczor HU, Macher-Göppinger S	2017	Journal of Biomaterials Applications	Oncology	Classifier	HALO
A randomized, open-label study of the efficacy and safety of AZD4547 monotherapy versus paclitaxel for the treatment of advanced gastric adenocarcinoma with FGFR2 polysomy or gene amplification	Van Cutsem E, Bang Y-J, Mansoor W, Petty RD, Chao Y, Cunningham D, Ferry DR, N. R. Smith NR, Frewer P, Ratnayake J, Stockman PK, Kilgour E, and Landers D	2017	Annals of Oncology	Oncology	Classifier, ISH/FISH	HALO
Persistence of Pancreatic Insulin mRNA Expression and Proinsulin Protein in Type 1 Diabetes Pancreata	Wasserfall C, Nick HS, Campbell-Thompson M, Beachy D, Haataja L, Kusmartseva I, Posgai A, Beery M, Rhodes C, Bonifacio E, Arvan P, Atkinson M	2017	Cell Metabolism	Metabolism	Area Quantification	HALO
Neuron loss and degeneration in the progression of TDP-43 in frontotemporal lobar degeneration	Yousef A, Robinson JL, Irwin DJ, Byrne MD, Kwong LK, Lee EB, Xu Y, Xie SX, Rennert L, Suh ER, Van Deerlin VM, Grossman M, Lee VM-Y, Trojanowski JQ	2017	Acta Neuropathologica Communications		Area Quantification, Cytonuclear	HALO
Qualitative Comparison Between Carrier-based and Classical Tissue Microarrays	Lisenko K, Leichsenring J, Zgorzelski C, Longuespee R, Casadonte R, Harms A, Kazdal D, Stenzinger A, Warth A, Kriegsmann M	2017	Applied Immunohistochemistry & Molecular Morpholgy			HALO
In situ macrophage phenotypic transition is affected by altered cellular composition prior to acute sterile muscle injury	Patsalos A, Pap A, Varga T, Trencsenyi G, Contreras GA, Garai I, Papp Z, Dezso B, Pintye E, Nagy L	2017	The Journal of Physiology	Myology		HALO
Obstruction of BRAFV600E transcription by complementary PNA oligomers as a means to inhibit BRAF-mutant melanoma growth	Rothman JH, Surriga O, de Stanchina E, Vasudeva SD, Schwartz GK	2017	Cancer Gene Therapy	Oncology		HALO
The integrative clinical impact of tumor-infiltrating T lymphocytes and NK cells in relation to B lymphocyte and plasma cell density in esophageal and gastric adenocarcinoma	Svensson MC, Warfvinge CF, Fristedt R, Hedner C, Borg D, Eberhard J, Micke P, Nodin B, Leandersson K, Jirstrom K	2017	Oncotarget	Immuno-oncology	Object Colocalization	HALO
Control of mitochondrial function and cell growth by the atypical cadherin Fat1	Cao LL, Riascos-Bernal DF, Chinnasamy P, Dunaway CM, Hou R, Pujato MA, O'Rourke BP, Miskolci V, Guo L, Hodgson L, Fiser A, Sibinga NES	2016	Nature	Metabolism	Cytonuclear	HALO
Phosphorylation of calcium/calmodulin-stimulated protein kinase II at T286 enhances invasion and migration of human breast cancer cells	Chi M, Evans, Gilchrist J, Mayhew J, Hoffman A, Pearsall EA, Jankowski H, Brzozowski JS, Skelding KA	2016	Scientific Reports	Oncology	Cytonuclear	HALO
Evidence of ?-Cell Dedifferentiation in Human Type 2 Diabetes	Cinti F, Bouchi R, Kim-Muller JY, Ohmura Y, Sandoval PR, Masini M, Marselli L, Suleiman M, Ratner LE, Marchetti P, Accili D	2016	The Journal of Clinical Endocrinology & Metabolism	Metabolism	Cytonuclear	HALO
Cutaneous wound healing through paradoxical MAPK activation by BRAF inhibitors	Escuin-Ordinas H, Li S, Xie MW, Sun L, Hugo W, Huang RR, Jiao J, Meira de-Faria F, Realegeno S, Krystofinski P, Azhdam A, Komenan SMD, Atefi M, Comin-Anduix B, Pellegrini M, Cochran AJ, Modlin RL, HerschmanHR, Lo RS, McBride WH, Segura T, Ribas A	2016	Nature Communications	Wound Healing	Cytonuclear	HALO
A Phase II Trial of Dovitinib in BCD-Unresponsive Urothelial Carcinoma with FGFR3 Mutations or Over-Expression: Hoosier Cancer Research Network Trial HCRN 12-157	Hahn NH, Bivalacqua TJ, Ross AE, Netto GJ, Baras AS, Park JC, Chapman C, Masterson TA, Koch MO, Bihrle R, Foster RS, Gardner TA, Cheng L, Jones DR, Kyle McElyea K, Sandusky GE, Breen T, Liu Z, Albany C, Moore ML, Loman RA, Reed A, Turner SA, de Abreu FB, Gallagher TL, Tsongalis GJ, Plimack ER, Greenberg RE, Geynisman DM	2016	Clinical Cancer Research	Oncology	Classifier, Cytonuclear	HALO
Mitogen-activated Protein Kinase Kinase Activity Maintains Acinar-to-Ductal Metaplasia and Is Required for Organ Regeneration in Pancreatitis	Halbrook CJ, Wen H-J, Ruggeri JM, Takuchi KK, Zhang Y, di Magliano MP, Crawford HC	2016	Cellular and Molecular Gastroenterology and Hepatology	Immunology, Gastroenterology	Cytonuclear	HALO
Fully automated RNAscope in situ hybridization assays for formalin?fixed paraffin?embedded cells and tissues	Anderson CM, Zhang B, Miller M, Butko E, Wu X, Laver T, Kernag C, Kim J, Luo Y, Lamparski H	2016	Journal of Cellular Biochemistry	Oncology, Gastroenterology, Infectious Disease	ISH/FISH	HALO
A Depot Medroxyprogesterone Acetate Dose That Modes Human Use and Its Effect on Vaginal SHIV Acquisition Risk	Butler K, Ritter JM, Ellis S, Morris MR, Hanson DL, McNicholl JM, Kersh EN	2016	J Acquir Immune Defic Syndr	Infectious Disease	Layer Thickness	HALO
Epigenetic regulation of the thioredoxin-interacting protein (TXNIP) gene by hyperglycemia in kidney	De Marinis Y, Cai M, Bompada P, Atac D, Kotova O, Johansson ME, Garcia-Vaz E, Gomez MF, Laakso M, Groop L	2016	Kidney International	Metabolism	Area Quantification	HALO
ProNGF is a potential diagnostic biomarker for thyroid cancer	Faulkner S, Roselli S, Demont Y, Pundavela J, Choquet G, Leissner P, Oldmeadow C, Attia J, Walker MM, Hondermarck H	2016	Oncotarget	Oncology	Area Quantification	HALO
The Dynamics and Turnover of Tau Aggregates in Cultured Cells: Insights into Therapies for Tauopathies	Guo JL, Buist A, Soares A, Callaerts K, Calafate S, Stevenaert F, Daniels JP, Zoll BE, Crowe A, Brunden KR, Moechars D, Lee VMY	2016	The Journal of Biological Chemistry	Neuroscience	Area Quantification	HALO
Unique pathological tau conformers from Alzheimer's brains transmit tau pathology in nontransgenic mice	Guo JL, Narasimhan S, Changolkar L, He Z, Stieber Z, Zhang B, Gathagan RJ, Iba M, McBride JD, Trojanowski JQ, Lee VMY	2016	Journal of Experimental Medicine	Neuroscience	Area Quantification	HALO
Bimodality of intratumor Ki67 expression is an independent prognostic factor of overall survival in patients with invasive breast carcinoma	Laurinavicius A, Plancoulaine B, Rasmusson A, Besusparis J, Augulis R, Meskauskas R, Herlin P, Laurinaviciene A, Muftah AAA, Miligy I, Aleskandarany M, Rakha EA, Green AR, Ellis IO	2016	Virchows Archiv	Oncology	Classifier, Cytonuclear	HALO
Resistance to Anti-VEGF Therapy Mediated by Autocrine IL6/STAT3 Signaling and Overcome by IL6 Blockade	Eichten A, Su J, Adler AP, Zhang L, Ioffe E, Parveen AA, Yancopoulos GD, Rudge J, Lowy I, Lin HC, MacDonald D, Daly C, Duan X, Thurston G	2016	Cancer Research	Oncology, Immuno-oncology	Cytonuclear, Object Colocalization	HALO
Cerebral Protection During MitraClip Implantation: Initial Experience at 2 Centers	Frerker C, Schlüter M, Sanchez OD, Reith S, Romero ME, Ladich E, Schröder J, Schmidt T, Kreidel F, Joner M	2016	JACC: Cardiovascular Interventions	Myology	Object Colocalization	HALO
Upregulation of Glucose-Regulated Protein 78 in Metastatic Cancer Cells Is Necessary for Lung Metastasis Progression	Lizardo MM, Morrow JJ, Miller TE, Hong ES, Ren L, Mendoza A, Halsey CH, Scacheri PC, Helman LJ, Khanna C	2016	Neoplasia	Oncology	Cytonuclear	HALO
Evaluation of the brain-penetrant microtubule-stabilizing agent, dictyostatin, in the PS19 tau transgenic mouse model of tauopathy	Makani V, Zhang B, Han H, Yao Y, Lassalas P, Lou K, Paterson I, Lee VMY, Trojanowski JQ, Ballatore C, Smith AB, Brunden KR	2016	Acta Neuropatholgica Communications	Neuroscience	Area Quantification	HALO
CNS-accessible inhibitor of glucosylceramide synthase for substrate reduction therapy of neuronopathic Gaucher disease	Marshall J, Sun Y, Bangari DS, Budman E, Park H, Nietupski JB, Allaire A, Cromwell MA, Wang B, Grabowski GA, Leonard JP, Cheng SH	2016	Molecular Therapy	Neuroscience	Area Quantification	HALO
Leptin, BMI, and a Metabolic Gene Expression Signature Associated with Clinical Outcome to VEGF Inhibition in Colorectal Cancer	Pommier AJC, Farren M, Patel B, Wappett M, Michopoulos F, Smith NR, Kendrew J, Frith J, Huby R, Eberlein C, Campbell H, Womack C, Smith PD, Robertson J, Morgan S, Critchlow SE, Barry ST	2016	Cell Metabolism	Oncology, Metabolism, Gastroenterology	Area Quantification	HALO
Intrathecal Administration of AAV/GALC Vectors in 10- 11-Day-Old Twitcher Mice Improves Survival and Is Enhanced by Bone Marrow Transplant	Karmuthil-Melethil S, Marshall MS, Heindel C, Jakubauskas B, Bongarzone ER, Gray SJ	2016	Journal of Neuroscience Research	Neuroscience	Axon	HALO
Tasquinimod modulates tumor-infiltrating myeloid cells and improves the antitumor immune response to PD-L1 blockade in bladder cancer	Nakhlé J, Pierron V, Bauchet A-L, Plas P, Thiongane A, Meyer-Losic F, Schmidlin F	2016	OncoImmunology	Oncology, Immuno-oncology	Cytonuclear	HALO
Primary resistance to PD-1 blockade mediated by JAK1/2 mutations	Shin DS, Zaretsky JM, Escuin-Ordinas H, Garcia-Diaz A, Hu-Lieskovan S, Kalbasi A, Grasso CS, Hugo W, Sandoval S, Torrejon DY, Palaskas N, Rodriguez GA, Parisi G, Azhdam A, Chmielowski B, Cherry G, Seja E, Berent-Maoz B, Shintaku IP, Le DT, Pardol DM, Diaz LA, Tumeh PC, Graeber TG, Lo RS, Comin-Anduix B, Ribas A	2016	Cancer Discovery	Oncology, Immuno-oncology	Cytonuclear	HALO
KS-Detect-Validation of Solar Thermal PCR for the Diagnosis of Kaposi's Sarcoma Using Pseudo-Biopsy Samples	Snodgrass R, Gardner A, Jiang L, Fu C, Cesarman E, Erickson D	2016	PLOS ONE	Oncology	Cytonuclear	HALO
Development of antibody-siRNA conjugate targeted to cardiac and skeletal muscles	Sugo T, Terada M, Oikawa T, Miyata K, Nishimura S, Kenjo E, Ogasawara-Shimizu M, Makita Y, Imaichi S, Murata S, Kentaro Otaka, Kikuchi K, Teratani M, Masuda Y, Kamei T, Takagahara S, Ikeda S, Ohtaki T, Matsumoto H	2016	The Journal of Controlled Release	Myology	Cytonuclear, Muscle Fiber	HALO
Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells	Xin Y, Kim J, Ni M, Wei Y, Okamoto H, Lee J, Adler C, Cavino K, Murphy AJ, Yancopoulos GD, Lin HC, Gromada J	2016	Proceedings of the National Academy of Sciences	Metabolism	Cytonuclear	HALO
Comparison of the methods for measuring the Ki-67 labeling index in adrenocortical carcinoma: manual versus digital image analysis	Yamazaki Y, Nakamura Y, Shibahara Y, Konosu-Fukaya S, Sato N, Kubota-Nakayama F, Oki Y, Baba S, Midorikawa S, Morimoto R, Satoh F, Sasano	2016	Human Pathology	Oncology	Cytonuclear	HALO
Variability in Platelet-Derived Growth Factor Receptor Alpha Antibody Specificity May Impact Clinical Utility of Immunohistochemistry Assays	Holzer TR, Reising LO, Credille KM, Schade AE, Oakley	2016	Journal of Histochemistry & Cytochemistry	Oncology	Cytonuclear, ISH/FISH	HALO
Differential Cytokine Gene Expression in Granulomas from Lungs and Lymph Nodes of Cattle Experimentally Infected with Aerosolized Mycobacterium bovis	Palmer MV, Thacker TC, Waters WR	2016	PLOS One	Infectious Disease	ISH/FISH	HALO
RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes	Xin Y, Kim J, Okamoto H, Ni M, Wei Y, Adler C, Murphy AJ, Yancopoulos GD, Lin C, Gromada J	2016	Endocrinology	Metabolism	Islet	HALO
The Prognostic Impact of NK/NKT Cell Density in Periampullary Adenocarcinoma Differs by Morphological Type and Adjuvant Treatment	Lundgren S, Warfvinge CF, Elebro J, Heby M, Nodin B, Krzyzanowska A, Bjartell A, Leandersson K, Eberhard J, Jirstrom K	2016	PLOS ONE	Oncology, Immuno-oncology	Object Colocalization	HALO
Solid-state NMR structure of a pathogenic fibril of full-length human [alpha]-synuclein	Tuttle MD, Comellas G, Nieuwkoop AJ, Covell DJ, Berthold DA, Kloepper KD, Courtney JM, Kim JK, Barclay AM, Kendall A, Wan W, Stubbs G, Schwieters CD, Lee VMY, George JM, Rienstra CM	2016	Structural & Molecular Biology	Neuroscience	Area Quantification	HALO
RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes	Xin Y, Kim J, Okamoto H, Ni M, Wei Y, Adler C, Murphy AJ, Yancopoulos GD, Lin C, Gromada J	2016	Cell Metabolism	Metabolism	ISH/FISH	HALO
Synergistic targeted inhibition of MEK and dual PI3K/mTOR diminishes viability and inhibits tumor growth of canine melanoma underscoring its utility as a preclinical model for human mucosal melanoma	Wei B-R, Michael HT, Hasley CHC, Peer CJ, Adhikari A, Dwyer JE, Hoover SB, El Meskini R, Kozlov S, Ohler ZW, Figg WD, Merlino G, Simpson RM	2016	Pigment Cell & Melanoma Research	Oncology	Area Quantification	HALO
Mutations Associated with Acquired Resistance to PD-1 Blockade in Melanoma	Zaretsky JM, Garcia-Diaz A, Shin DS, Escuin-Ordinas H, Hugo W, Hu-Lieskovan S, Torrejon DY, Abril-Rodriguez G, Sandoval S, Barthly L, Saco J, Homet Moreno BH, Mezzadra R, Chmielowski B, Ruchalski K, Shintaku IP, Sanchez PJ, Puig-Saus C, Cherry G, Seja E, Kong X, Pang J, Berent-Maoz B, Comin-Anduix B, Graeber TG, Tumeh PC, Schumacher TNM, Lo RS, Ribas A	2016	The New England Journal of Medicine	Oncology, Immuno-oncology	Cytonuclear	HALO
The PDE10A inhibitor MP-10 and haloperidol produce distinct gene expression profiles in the striatum and influence cataleptic behavior in rodents	Gentzel RC, Toolan D, Roberts R, Koser AJ, Kandebo M, Hershey J, Renger JJ, Uslaner J, Smith SM	2015	Neuropharmacology	Neuroscience	Cytonuclear	HALO
Phenotyping of tumor-associated macrophages in colorectal cancer: impact on single cell invasion (tumor budding) and clinicopathological outcome	Koelzer VH, Canonica K, Dawson H, Sokol L, Karamitopoulou-Diamantis E, Lugli A, Zlobec I	2015	OncoImmunology	Oncology, Immuno-oncology, Gastroenterology	Cytonuclear	HALO
G-protein-independent coupling of MC4R to Kir7. 1 in hypothalamic neurons	Ghamari-Langroudi M, Digby GJ, Sebag JA, Millhauser GL, Palomino R, Matthews R, Gillyard T, Panaro BL, Tough IR, Cox HM, Denton JS, Cone RD	2015	Nature	Metabolism	ISH/FISH	HALO
Analysis of putative mucosal SHIV susceptibility factors during repeated DMPA treatments in pigtail macaques	Butler K, Ritter J, Ellis S, Henning TR, Montague J, Zaki S, Garber, McNicholl JM, Kersh EN	2015	Journal of medical primatology	Infectious Disease	Layer Thickness	HALO
Semi-Automated Digital Image Analysis of Pick's Disease and TDP-3 Proteinopathy	Irwin DJ, Byrne MD, McMillan CT, Cooper F, Arnold SE, Lee EB, Van Deerlin VM, Xie SX, Lee VM, Grossman M, Trojanowski JQ	2015	Journal of Histochemistry & Cytochemistry	Neuroscience	Object Colocalization, Layer Thickness	HALO
Myostatin blockade with a fully human monoclonal antibody induces muscle hypertrophy and reverses muscle atrophy in young and aged mice	Latres E, Pangilinan J, Miloscio L, Bauerlein R, Na E, Potocky TB, Huang Y, Eckersdorff M, Rafique A, Mastaitis J, Lin C, Murphy AJ, Yancopoulos GD, Gromada J, Stitt T	2015	Skeletal Muscle	Myology	Muscle Fiber	HALO
Relationship of Estimated SHIV Acquisition Time Points During the Menstrual Cycle and Thinning of Vaginal Epithelial Layers in Pigtail Macaques	Kersh EN, Ritter J, Butler K, Ostergaard SD, Hanson D, Ellis S, Zaki S, McNicholl JM	2015	Sexually Transmitted Diseases	Infectious Disease	Layer Thickness	HALO
Glucagon Receptor Blockade With a Human Antibody Normalizes Blood Glucose in Diabetic Mice and Monkeys	Okamoto H, Cavino K, Na E, Krumm E, Kim SY, Cheng X, Murphy AJ, Yancopoulos GD, Gromada J	2015	Endocrinology	Metabolism	Area Quantification	HALO
Nerve fibers infiltrate the tumor microenvironment and are associated with nerve growth factor production and lymph node invasion in breast cancer	Pundavela J, Roselli S, Faulkner S, Attia J, Scott RJ, Thorne RF, Forbes JF, Bradshaw RA, Walker MM, Jobling P, Hondermarck H	2015	Molecular Oncology	Oncology, Neuroscience	Area Quantification	HALO
Tasquinimod triggers an early change in the polarization of tumor associated macrophages in the tumor microenvironment	Olsson A, Nakhle J, Sundstedt A, Plas P, Bauchet AL, Pierron V, Bruetschy L, Deronic A, Tomgren M, Liberg D, Schmidlin F, Leanderson T	2015	Journal for ImmunoTherapy of Cancer	Oncology, Immuno-oncology	Cytonuclear	HALO
Exacerbated experimental colitis in TNFAIP8-deficient mice	Sun H, Lou Y, Porturas T, Morrissey S, Luo G, Qi J, Ruan Q, Shi S, Chen YH	2015	The Journal of Immunology	Gastroenterology	Cytonuclear	HALO
Combination therapy reverses hyperglycemia in NOD mice with established type 1 diabetes	Xue S, Posgai A, Wasserfall C, Myhr C, Campbell-Thompson M, Mathews CE, Brusko T, Rabinovitch A, Savinov A, Battaglia M, Schatz D, Haller M, Atkinson MA	2015	Diabetes	Metabolism	Cytonuclear	HALO
A combined oral contraceptive affects mucosal SHIV susceptibility factors in a pigtail macaque (Macaca nemestrina) model	Ostergaard DS, Butler K, Ritter JM, Johnson R, Sanders J, Powell N, Lathrop G, Zaki SR, McNicholl JM, Kersh EN	2015	Journal of medical primatology	Infectious Disease	Layer Thickness	HALO
Applicability of digital analysis and imaging technology in neuropathology assessment	Dunn WD, Gearing M, Park Y, Zhang L, Hanfelt J, Glass JD, Gutman DA	2015	Neuropathology			HALO
Islet-1 is essential for pancreatic ?-cell function	Ediger BN, Du A, Liu J, Hunter CS, Walp ER, Schug J, Kaestner KH, Stein R, Stoffers DA, May CL	2014	Diabetes	Metabolism	Cytonuclear	HALO
Characterization of the exocrine pancreas in the male Zucker diabetic fatty rat model of type 2 diabetes mellitus following 3 months of treatment with sitagliptin	Forest T, Holder D, Smith A, Cunningham C, Yao X, Dey M, Frederick C, Prahalada S	2014	Endocrinology	Metabolism	Cytonuclear	HALO
Peripheral androgen receptor gene suppression rescues disease in mouse models of spinal and bulbar muscular atrophy	Lieberman AP, Yu Z, Murray S, Peralta R, Low A, Guo S, Yu XX, Cortes CJ, Bennett CF, Monia BP, La Spada AR, Hung G	2014	Cell Reports	Myology	Muscle Fiber	HALO
ANGPTL8/betatrophin does not control pancreatic beta cell expansion	Gusarova V, Alexa CA, Na E, Stevis PE, Xin Y, Bonner-Weir S, Cohen JC, Hobbs HH, Murphy AJ, Yancopoulos GD, Gromada J	2014	Cell	Metabolism	Area Quantification	HALO
PD-1 blockade induces responses by inhibiting adaptive immune resistance	Tumeh PC, Harview CL, Yearley JH, Shintaku IP, Taylor EJM, Robert L, Chmielowski B, Spasic M, Henry G, Ciobanu V, West AN, Carmona M, Kivork C, Seja E, Cherry G, Gutierrez A, Grogan TR, Mateus C, Tomasic G, Glaspy JA, Emerson RO, Robins H, Pierce RH, Elas	2014	Nature	Oncology, Immuno-oncology	Cytonuclear	HALO
Marked expansion of exocrine and endocrine pancreas with incretin therapy in humans with increased exocrine pancreas dysplasia and potential for glucagon-producing neuroendocrine tumors	Butler AE, Campbell-Thompson M, Gurlo T, Dawson DW, Atkinson M, Butler PC	2013	Diabetes	Oncology, Metabolism	Cytonuclear	HALO
CRISPR-Cas9 gene editing of hepatitis B virusin chronically infected humanized mice	Stone D, Long KR, Loprieno MA, De Silva Feelixge HS, Kenkel EJ, Liley, RM, Rapp S, Roychoudhury P, Nguyen T, Stensland L, Cólon-Thillet R, Klouser LM, Weber ND, Le C, Wagoner J, Goecker EA, Li AZ, Eichholz K, Corey L, Tyrrell DL, Greninger AL, Huang ML, Polyak SJ, Aubert M, Sagartz JE, Jerome KR	2021	Molecular Therapy Methods & Clinical Development	Infectious Disease		HALO Link
Digital Immunophenotyping Predicts Disease Free and Overall Survival in Early Stage Melanoma Patients	De Logu F, Galli F, Nassini R, Ugolini F, Simi S, Cossa M, Miracco C, Gianatti A, De Giorgi V, Rulli E, Cossu A, Massi D, Mandalà M	2021	Cells	Oncology, Immuno-oncology	Multiplex IHC	HALO, HALO Link
Monomeric/dimeric forms of Fgf15/FGF19 show differential activity in hepatocyte proliferation and metabolic function	Williams CM, Calderon JH, Hock E, Jimenez Y, Barringer K, Carbonaro M, Molina-Portela MP, Thurston G, Li Z, Daly C	2021	The FASEB Journal	Metabolism	Cytonuclear	HALO, HALO Link
CD38 in Advanced Prostate Cancers	Guo C, Crespo M, Gurel B, Dolling D, Rekowski J, Sharp A, Petremolo A, Sumanasuriya S, Rodrigues DN, Ferreira A, Pereira R, Figueiredo I, Mehra N, Lambros MBK, Neeb A, Gil V, Seed G, Terstappen L, Alimonti A, Drake CG, Yuan W, de Bono JS	2021	European Urology	Oncology	Classifier, Highplex FL	HALO
Exploring transcriptional regulators Ref-1 and STAT3 as therapeutic targets in malignant peripheral nerve sheath tumours	Gampala S, Shah F, Zhang C, Rhodes SD, Babb O, Grimard M, Wireman RS, Rad E, Calver B, Bai R-Y, Staedtke V, Hulsey EL, Saadatzadeh MR, Pollok KE, Tong Y, Smith AE, Clapp DW, Tee AR, Kelley MR, Fishel ML	2021	British Journal of Cancer	Oncology	Area Quantification, Cytonuclear	HALO
First in class dual MDM2/MDMX inhibitor ALRN-6924 enhances antitumor efficacy of chemotherapy in TP53 wild-type hormone receptor-positive breast cancer models	Pairawan S, Zhao M, Yuca E, Annis A, Evans K, Sutton D, Carvajal L, Ren J-G, Santiago S, Guerlavais, Akcakanat A, Tapia C, Yang F, Bose PSC, Zheng X, Dumbrava EI, Aivado M, Meric-Bernstam F	2021	Breast Cancer Research	Oncology	Cytonuclear	HALO
Influence of tumor-infiltrating immune cells on local control rate, distant metastasis, and survival in patients with soft tissue sarcoma	Smolle MA, Herbsthofer L, Goda M, Granegger B, Brcic I, Bergovec M, Scheipl S, Prietl B, El-Heliebi A, Pichler M, Gerger A, Posch F, Tomberger M, López-García P, Feichtinger J, Baumgartner C, Leithner A, Liegl-Atzwanger B, Szkandera J	2021	OncoImmunology	Immuno-oncology	Highplex FL	HALO
Phenotypic characterization of Adig null mice suggests roles for adipogenin in the regulation of fat mass accrual and leptin secretion	Alvarez-Guaita A, Patel S, Lim K, Haider A, Dong L, Conway OJ, Ma MKL, Chiarugi D, Saudek V, O'Rahilly S, Savage DB	2021	Cell Reports	Metabolism	Vacuole	HALO
Prognostic Impact of CXCR7 and CXCL12 Expression in Patients with Esophageal Adenocarcinoma	Goto M, Shibahara Y, Baciu C, Allison F, Yeung JC, Darling GE, Liu M	2021	Thoracic Oncology	Oncology		HALO
An extended release GLP-1 analogue increases ?-synuclein accumulation in a mouse model of prodromal Parkinson's disease	Bergkvist L, Johnson ME, Mercado G, Steiner JA, Meyerdick L, Schulz E, Madaj Z, Ma J, Becker K, Li Y, Brudin P	2021	Experimental Neurology	Neuroscience	Area Quantification	HALO
Activation of the renal GLP?1R leads to expression of Ren1 in the renal vascular tree	Bjørnholm KD, Ougaard ME, Skovsted GF, Knudsen LB, Pyke C	2021	Endocrinology, Diabetes, & Metabolism	Metabolism	ISH/FISH	HALO
A Method to Pre-Screen Rat Mammary Gland Whole-Mounts Prior To RNAscope	Duderstadt EL, Sanders MA, Samuelson DJ	2021	Journal of Mammary Gland Biology and Neoplasia		ISH/FISH	HALO
Activated Regulatory T-Cells, Dysfunctional and SenescentT-Cells Hinder the Immunity in Pancreatic Cancer	Sivakumar S, Abu-Shah E, Ahern DJ, Arbe-Barnes EH, Jainarayanan AK, Mangal N, Reddy S, Rendek A, Easton A, Kurz E, Silva M, Soonawalla Z, Heij LR, Bashford-Rogers R, Middleton MR, DUstin ML	2021	cancers		Classifier, Multiplex IHC, Spatial Analysis, Highplex FL	HALO
Age-associated expression of p21and p53 during human wound healing	Chia CW, Sherman-Baust CA, Larson SA, Pandey R, Withers R, Karikkineth AC, Zukley LM, Campisi J, Egan JM, Sen R, Ferrucci L	2021	Aging Cell	Dermatology	Area Quantification, ISH/FISH, Multiplex IHC	HALO
Breast adipocyte size associates with ipsilateral invasive breast cancer risk after ductal carcinoma in situ	Almekinders MMM, Schaapveld M, Thijssen B, Visser LL, Bismeijer T, Sanders J, Isnaldi E, Hofland I, Mertz M, Wessels LFA, Broeks A, Hooijberg E, Zwart W, Lips EH, Grand Challenge PRECISION Consortium, Desmedt C, Wesseling J	2021	npj Breast Cancer	Oncology	Vacuole	HALO
COM902, a novel therapeutic antibody targeting TIGIT augments anti-tumor T cell function in combination with PVRIG or PD-1 pathway blockade	Kyle Hansen K, Sandeep Kumar, Kathryn Logronio, Sarah Whelan, Samir Qurashi, Hsin-Yuan Cheng, Andrew Drake, Margaret Tang, Patrick Wall, David Bernados, Ling Leung, Eran Ophir, Zoya Alteber Z, Gady Cojocaru G, Moran Galperin M, Masha Frenkel M, Mark White M, John Hunter J, Spencer C. Liang & Maya F. Kotturi	2021	Cancer Immunology, Immunotherapy	Immuno-oncology		HALO
Conventional and semi-automatic histopathological analysis of tumor cell content for multigene sequencing of lung adenocarcinoma	Kazdal D, Rempel E, Oliveira C, Allgäuer M, Harms A, Singer K, Kohlwes E, Ormanns S, Fink L, Kriegsmann J, Leichsenring M, Kriegsmann K, Stögbauer F, Tavernar L, Leichsenring J, Volckmar A-L, Longuespée R, Winter H, Eichhorn M, Heußel CP, Herth F, Christopoulos P, Reck M, Muley T, Weichert W, Budczies J, Thomas M, Peters S, Warth A, Schirmacher P, Stenzinger A, Kriegsmann M	2021	Translational Lung Cancer Research	Oncology	Classifier, Cytonuclear	HALO
Crotonaldehyde exposure induces liver dysfunction and mitochondrial energy metabolism disorder in rats	Zhang S, Zhang B, Zhang Q, Zhang Z	2021	Toxicology Mechanisms and Methods	Metabolism		HALO
Cytotoxic lymphocytes target characteristic biophysical vulnerabilities in cancer	Bhanot U, MOrris L, Boire A, Hsu KC, Massague J, Huse M, Er EE	2021	Immunity	Immuno-oncology		HALO
Empagliflozin Disrupts a Tnfrsf12a-Mediated Feed Forward Loop That Promotes Left Ventricular Hypertrophy	Yerra VG, Batchu SN, Kabir G, Advani SL, Liu Y, Siddiqi FS, Connelly KA, Advani A	2021	Cardiovascular Drugs and Therapy	Myology		HALO
Genetic Inactivation of Peroxiredoxin-I Impairs the Growth of Human Pancreatic Cancer Cells	Dahou H, Minati M-A, Jacquemin P, Assi M	2021	antioxidants	Oncology	Cytonuclear	HALO
Immune-regulated IDO1-dependent tryptophan metabolism is source of one-carbon units for pancreatic cancer and stellate cells	Newman AC, Falcone M, Uribe AH, Zhang T, Athineos D, Pietzke M, Vazquez A, Blyth K, Maddocks ODK	2021	Molecular Cell	Immuno-oncology	Classifier, ISH/FISH	HALO
Inhibition of STAT3 augments antitumor efficacy of anti-CTLA-4 treatment against prostate cancer	Witt K, Evans-Axelsson S, Lundqvist A, Johansson M, Bjartell A, Hellsten R	2021	Cancer Immunology, Immunotherapy	Immuno-oncology	Area Quantification, Multiplex IHC	HALO
The immune suppressive microenvironment affects efficacy of radio-immunotherapy in brain metastasis	Niesel K, Schulz M, Anthes J, Alekseeva T, Macas J, Salamero-Boix A, Mockl A, Oberwahrenbrock T, Lolies M, Stein S, Plate KH, Reiss Y, Rodel F, Sevenich L	2021	EMBO Molecular Medicine	Immuno-oncology	Spatial Analysis, Highplex FL	HALO
Tracing Lung Cancer Risk Factors Through Mutational Signatures in Never-Smokers	Landi MT, Synnott NC, Rosenbaum J, Zhang T, Zhu B, Shi J, Zhao W, Kebede M, Sang J, Choi J, Mendoza L, Pacheco M, Hicks B, Caporaso NE, Abubakar M, Gordenin DA, Wedge, Alexandrov LB, Rothman N, Lan Q, Garcia-Closas M, Chanock SJ	2021	American Journal of Epidemiology	Oncology		HALO
Tumor cell PD-L1 expression is a strong predictor of unfavorable prognosis in immune checkpoint therapy-naive clear cell renal cell cancer	Möller K, Fraune C, Blessin NC, Lennartz M, Kluth M, Hube-Magg C, Lindhorst L, Dahlem R, Fisch M, Eichenauer T, Riechardt S, Simon R, Sauter G, Büscheck F, Höppner W, Matthies C, Doh O, Krech T, Marx AH, Zecha H, Rink M, Steurer S, Clauditz TS	2021	International Urology and Nephrology	Immuno-oncology	Multiplex IHC, TMA	HALO
Validation of multiplex immunofluorescence and digital image analysis for programmed death-ligand 1 expression and immune cell assessment in non-small cell lung cancer: comparison with conventional immunohistochemistry	Wu J, Mao L, Sun W, Yang X, Wang H, Liu X, Chi K, Xiaozheng H, Lin D	2021	Journal of Clinical Pathology	Immuno-oncology		HALO
VGLUT2 is a determinant of dopamine neuron resilience in a rotenone model of dopamine neurodegeneration	Buck SA, De Miranda BR, Logan RW, Fish KN, Greenamyre JT, Freyberg Z	2021	The Journal of Neuroscience	Neuroscience	ISH/FISH	HALO
Ki-67 Proliferation Index Assessment in Gastroenteropancreatic Neuroendocrine Tumors by Digital Image Analysis With Stringent Case and Hotspot Level Concordance Requirements	Boukhar SA, Gosse MD, Bellizzi AM, Rajan A	2021	American Journal of Clinical Pathology	Oncology		HALO
Global Neurotoxicity: Quantitative Analysis of Rat Brain Toxicity Following Exposure to Trimethyltin	Srivastava A, Liachenko S, Sarkar S, Paule M, Sadovova N, Hanig JP	2021	International Journal of Toxicology	Toxicology		HALO
High estrogen receptor alpha activation confers resistance to estrogen deprivation and is required for therapeutic response to estrogen in breast cancer	Traphagen NA, Hosford SR, Jiang A, Marotti JD, Brauer BL, Demidenko E, Miller TW	2021	Oncogene	Oncology		HALO
In vivo endothelialization and neointimal hyperplasia assessment after rabbit carotid endarterectomy with bovine pericardium	Chen Y, Feng Y, Wang T, Zhang X, Zhang M, Bai X, Li L, Yang K, Ma Y, Zhang Z, Jiao L	2021	Annals of Translational Medicine	Myology	Cytonuclear	HALO
Prognostic role of proliferating CD8+ cytotoxic Tcells in human cancers	Blessin NC, Li W, Mandelkow T, Jansen HL, Yang C, Raedler JB, Simon R, Büscheck F, Dum D, Luebke AM, Hinsch A, Möller K, Menz A, Bernreuther C, Lebok P, Clauditz T, Sauter G, Marx A, Uhlig R, Wilczak W, Minner S, Krech T, Fraune C, Höflmayer D, Burandt E, Steurer S	2021	Cellular Oncology	Immuno-oncology	Highplex FL, TMA	HALO
TNFα secreted by glioma associated macrophages promotes endothelial activation and resistance against anti-angiogenic therapy	Wei Z, Singh O, Ekinci C, Gill J, Li M, Mamatjan Y, Karimi S, Bunda S, Mansouri S, Aldape K, Zadeh G	2021	Acta Neuropathologica Communications	Immunology, Neuroscience	Classifier, Multiplex IHC	HALO
Tumor morphology and location associate with immune cell composition in pleomorphic sarcoma	Wustrack RL, Shao E, Sheridan J, Zimel M, Cho S-J, Horvai AE, Luong D, Kwek SS, Fong L, Okimoto RA	2021	Cancer Immunology, Immunotherapy	Immuno-oncology	Cytonuclear	HALO
Engineered red blood cells as an off-the-shelf allogeneic anti-tumor therapeutic	Zhang X, Lou M, Dastagir SR, Nixon M, Khamhoung A, Schmidt A, Lee A, Subbiah N, McLaughlin DC, Moore CL, Gribble M, Bayhi N, Amin V, Pepi R, Pawar S, Lyford TJ, Soman V, Mellen J, Carpenter CL, Turka LA, Wickham Tj, Chen TF	2021	Nature Communications	Oncology	Object Colocalization, Highplex FL	HALO
Mastocytosis-derived extracellular vesicles deliver miR-23a and miR-30a into pre-osteoblasts and prevent osteoblastogenesis and bone formation	Kim D-K, Bandara G, Cho Y-E, Komarow HD, Donahue DR, Karim B, Baek M-C, Kim HM, Metcalfe DD, Olivera A	2021	Nature Communications		Classifier	HALO
Mitigation of endemic GI-tract pathogen-mediated inflammation through development of multimodal treatment regimen and its impact on SIV acquisition in rhesus macaques	Bochart RM, Busman-Sahay K, Bondoc S, Morrow DW, Ortiz AM, Fennessey CM, Fischer MB, Shiel O, Swanson T, Shriver-Munsch CM, Crang HB, Armantrout KM, Barber-Axthelm AM, Langner C, Moats CR, Labriola CS, MacAllister R, Axthelm MK, Brenchley JM, Keele BF, Estes JD, Hansen SG, Smedley JV	2021	PLOS Pathogens	Infectious Disease	ISH/FISH, Multiplex IHC	HALO
Mucosal IFNγ production and potential role in protection in Escherichia coli O157:H7 vaccinated and challenged cattle	Schaut RG, Palmer MV, Boggiatto PM, Kudva IT, Loving CL, Sharma VK	2021	Scientific Reports	Immunology	ISH/FISH	HALO
Next-Generation Digital Histopathology of the Tumor Microenvironment	Mungenast F, Fernando A, Nica R, Boghiu B, Lungu B, Batra J, Ecker RC	2021	genes	Review		HALO
RIPK1 activation mediates neuroinflammation and disease progression in multiple sclerosis	Zelic M, Pontarelli F, Woodworth L, Zhu C, Mahan A, Ren Y, LaMorte M, Gruber R, Keane A, Loring P, Guo L, Xia T, Zhang B, Orning P, Lien E, Degterev A, Hammond T, Ofengeim D	2021	Cell Reports	Immunology		HALO
Single-cell dissection of cellular components and interactions shaping the tumor immune phenotypes in ovarian cancer	Hornburg M, Desbois M, Lu S, Guan Y, Lo AA, Kaufman S, Elrod A, Lotstein A, DesRochers TM, Munoz-Rodriguez JL, Wang X, Giltnane J, Mayba O, Turley SJ, Bourgon R, Daemen A, Wang Y	2021	Cancer Cell	Immuno-oncology		HALO
Acute inflammatory profiles differ with sex and age after spinal cord injury	Stewart AN, Lowe JL, Glaser EP, Mott CA, Shahidehpour RK, McFarlane KE, Bailey WM, Zhang B, Gensel JC	2021	Journal of Neuroinflammation	Immunology, Neuroscience		HALO
Analysis of genomic and non-genomic signaling of estrogen receptor in PDX models of breast cancer treated with a combination of the PI3K inhibitor alpelisib (BYL719) and fulvestrant	Jacquemetton J, Kassem L, Poulard C, Dahmani A, De Plater L, Montaudon E, Sourd L, Morisset L, El Botty R, Chateau-Joubert S, Vacher S, Bièche I, Treilleux I, Trédan O, Marangoni E, Le Romancer M	2021	Breast Cancer Research	Oncology	Multiplex IHC	HALO
AP-3-dependent targeting of flippase ATP8A1 to lamellar bodies suppresses activation of YAP in alveolar epithelial type 2 cells	Kook S, Wang P, Meng S, Jetter CS, Sucre JMS, Benjamin JT, Gokey JJ, Hanby HA, Jaume A, Goetzl L, Marks MS, Guttentag SH	2021	Proceedings of the National Academy of Sciences	Fibrosis		HALO
Cellular Senescence in Human Aldosterone-Producing Adrenocortical Cells and Related Disorders	Pieroni J, Yamazaki Y, Gao X, Tezuka Y, Ogata H, Omata K, Ono Y, Morimoto R, Nakamura Y, Satoh F, Sasano H	2021	Biomedicines	Metabolism	Cytonuclear	HALO
Functionally distinct POMC-expressing neuron subpopulations in hypothalamus revealed by intersectional targeting	Biglari N, Gaziano I, Schumacher J, Radermacher J, Paeger L, Klemm P, Chen W, Corneliussen S, Wunderlich CM, Sue M, Vollmar S, Klöckener T, Sotelo-Hitschfeld T, Abbasloo A, Edenhofer F, Reimann F, Gribble FM, Fenselau H, Kloppenburg P, Wunderlich FT, Brüning JC	2021	Nature Neuroscience	Neuroscience	ISH/FISH	HALO
SeqStain is an efficient method for multiplexed, spatialomic profiling of human and murine tissues	Rajagopalan A, Venkatesh I, Aslam R, Kirchenbuechler D, Khanna S, Cimbaluk D, Kordower JH, Gupta V	2021	Cell Reports Methods			HALO
Novel insulin sensitizer MSDC-0602K improves insulinemia and fatty liver disease in mice, alone and in combination with liraglutide	Kamm DR, Pyles KD, Sharpe MC, Healy LN, Colca JR, McCommis KS	2021	Journal of Biological Chemistry	Metabolism		HALO
Pathways of immune exclusion in metastatic osteosarcoma are associated with inferior patient outcomes	Ligon JA, Choi W, Cojocaru G, Fu W, Hsiue EH-C, Oke TF, Siegel N, Fong MH, Ladle B, Pratilas CA, Morris CD, Levin A, Rhee DS, Meyer CF, Tam AJ, Blosser R, Thompson ED, Suru A, McConkey D, Housseau F, Anders R, Pardoll DM, Llosa N	2021	Journal for ImmunoTherapy of Cancer	Immuno-oncology	Multiplex IHC	HALO
Predicting nodal metastases in papillary thyroid carcinoma using artificial intelligence	Esce AR, Redemann JP, Sanchez AC, Olson GT, Hanson JA, Argwal S, Boyd NH, Martin DR	2021	The American Journal of Surgery	Oncology		HALO
Toluidine blue staining of murine mast cells and quantitation by a novel, automated image analysis method using whole slide skin images	Raja N, Naikodi S, Govindarajan A, Palanisamy K	2021	Journal of Histotechnology	Immunology	Cytonuclear	HALO
Pancreatic ? cellselective zinc transporter 8 insufficiency accelerates diabetes associated with islet amyloidosis	Xu J, Wijesekara N, Regeenes R, Al Rijjal D, Piro AL, Song Y, Anne Wu A, Bhattacharjee A, Liu Y, Marzban L, Rocheleau JV, Fraser PE, Dai FF, Hu C, Wheeler MB	2021	JCI Insight	Metabolism		HALO
Human Type II Taste Cells Express ACE2 and are Infected by SARS-CoV-2	Doyle M, Ashley Appleton A, Q Liu, Yao Q, Mazucanti C, Egan J	2021	American Journal of Pathology		Cytonuclear	HALO
Oncogenic BRAF, unrestrained by TGF?-receptor signalling, drives right-sided colonic tumorigenesis	Leach J, Vlahov N, Tsantoulis P, et al	2021	Nature Communications	Oncology	ISH/FISH, Highplex FL	HALO
Attenuating CD3 affinity in a PSMAxCD3 bispecific antibody enables killing of prostate tumor cells with reduced cytokine release	Dang K, Castello G, Clarke S, et al.	2021	Journal for Immunotherapy of Cancer	Immuno-oncology	Multiplex IHC	HALO
Heterogeneity in tertiary lymphoid structure B-cells correlates with patient survival in metastatic melanom	Lynch K, Young S, Menaveau M, et al.	2021	Journal for Immunotherapy of Cancer	Immuno-oncology	Highplex FL	HALO
mRNA translation is a therapeutic vulnerability necessary for bladder epithelial transformation	Jana S, Deo R, Hough R, et al.	2021	JCI Insight	Oncology	Multiplex IHC, Highplex FL	HALO
Approaches for Handling Immunopathological and Clinical Data Using Deep Learning Methodology: Multiplex IHC/IF Data as a Paradigm	Goh S, Chua Y, Lee J, Yeong J, Cai Y	2021	Histopathology and Liquid Biopsy	Review		HALO
Tumor necroptosis is correlated with a favorable immune cell signature and programmed death-ligand 1 expression in cholangiocarcinoma	Lomphithak T, Akara-amornthum P, Murakami K, et al.	2021	Scientific Reports	Immuno-oncology	Highplex FL	HALO
Multiparametric Analyses of Hepatocellular Carcinoma Somatic Mouse Models and Their Associated Tumor Microenvironment	Taranto D, Ramirez C, Vegna S, et al.	2021	Current Protocols	Oncology	Multiplex IHC	HALO
Quantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues	Kennedy J, Whiteaker J, Kennedy L, Bosch D, Lerch M, Schoenherr R, Zhao L, Lin C, Chowdhury S, Kilgore M, Allison K, Wang P, Hoofnagle A, Baird G, Paulovich A	2021	Clinical Chemistry	Oncology	Classifier	HALO
Pathological Change and Whole Transcriptome Alternation Caused by ePTFE Implantation in Myocardium	Shan Y, Zhang W, Chen G, Shi Q, Mi Y, Zhang H, Jia B	2021	BioMed Research International	Fibrosis	Area Quantification	HALO
Detection of Lung Cancer from Whole-Slide Histopathologic Images Using Deep Learning Approach	Mishra N, Behera P, Nanda R, Sahoo M	2019	International Journal of Research in Engineering and Sciences	Oncology	Classifier	HALO AI
Q134R: Small chemical compound with NFAT inhibitory properties improves behavioral performance and synapse function in mouse models of amyloid pathology	Sompol P, Gollihue J, Kraner S, Artiushin I, Cloyd R, Chishti E, Koren S, Nation G, Abisambra J, Huzian O, Nagy L, Santha M, Hackler L, Puskas L, Norris C	2021	Aging Cell	Neuroscience	Area Quantification	HALO
Methods to Determine and Analyze the Cellular Spatial Distribution Extracted From Multiplex Immunofluorescence Data to Understand the Tumor Microenvironment	Parra E	2021	Frontiers in Molecular Biosciences	Review		HALO
Mismatch repair-deficient prostate cancer with parenchymal brain metastases treated with immune checkpoint blockade	Sena L, Salles D, Engle E, Zhu Q, Tukachinsky H, Lotan T, Antonarakis E	2021	Molecular Case Studies	Immuno-oncology	Highplex FL	HALO
Lawsonia intracellularis infected enterocytes lack sucrase-isomaltase which contributes to reduced pig digestive capacity	Helm E, Burrough E, Leite, F, Gabler, N	2021	Veterinary Research	Other	ISH/FISH	HALO
Mechanism of Nucleic Acid Sensing in Retinal Pigment Epithelium (RPE): RIG-I Mediates Type I Interferon Response in Human RPE	Schustak J, Twarog M, Wu X, Huang Q, Bao Y	2021	Journal of Immunology Research		Area Quantification, ISH/FISH	HALO
Rejection of benign melanocytic nevi by nevus-resident CD4+ T cells	Schiferle E, Cheon S, Ham S, Son H, Messerschmidt J, Lawrence D, Cohen J, Flaherty K, Moon J, Lian C, Sullivan R, Demehri S	2021	Science Advances	Oncology	Multiplex IHC	HALO
Wound healing with topical BRAF inhibitor therapy in a diabetic model suggests tissue regenerative effects	Escuin-Ordinas H, Liu Y, Hufo W, Dimatteo R, Huang R, Krystofinski P, Azhdam A, Lee J, Comin-Anduix B, Cochran A, Lo R, Segura T, Scumpia P, Ribas A	2021	PLOS ONE	Dermatology	Object Colocalization, Multiplex IHC	HALO
The Goto Kakizaki rat: Impact of age upon changes in cardiac and renal structure, function	Meagher P, Civitarese R, Lee X, Gordon M, Bugyei-Twum A, Desjardins J, Kabir G, Zhang Y, Kosanam H, Visram A, Leong-Poi H, Advani A, Connelly K	2022	PLOS ONE	Myology	Muscle Fiber	HALO
Extensive Three-Dimensional Intratumor Proteomic Heterogeneity Revealed by Multiregion Sampling in High-Grade Serous Ovarian Tumor Specimens	Hunt A, Bateman N, Barakat W, Makohon-Moore S, Hood B, Conrads K, Zhou M, Calvert V, Pierobon M, Loffredo J, Litzi T, Oliver J, Mitchell D, Gist G, Rojas C, Blanton B, Robinson E, Odunsi K, Sood A, Casablanca Y, Darcy K, Schriver C, Petricoin E, Rao U, Maxwell G, Conrads T	2021	iScience		Multiplex IHC	HALO
Dissecting spatial heterogeneity and the immuneevasion mechanism of CTCs by single-cell RNA-seq in hepatocellular carcinoma	Sun Y, Wu L, Liu S, Jiang M, Hu B, Zhou K, Guo W, Xu Y, Zhong Y, Zhou X, Zhang Z, Liu G, Liu S, Shi Y, Ji Y, Du M, Li N, Li G, Zhao Z, Huang X, Xu L, Yu Q, Peng D, Qiu S, Sun H, Dean M, Wang X, Chung W, Dennison A, Zhou J, Hou Y, Fan J, Yang X	2021	Nature Communications	Oncology, Immuno-oncology	Highplex FL	HALO
TMEM229A suppresses non?small cell lung cancer progression via inactivating the ERK pathway	Zhang X, He Y, Jiang Y, Bao Y, Chen Q, Xie D, Yu H, Wang X	2021	Oncology Reports		Multiplex IHC	HALO
Glucocorticoid receptor antagonism promotes apoptosis in solid tumor cells	Greenstein A, Hunt H	2021	Oncotarget		Multiplex IHC	HALO
Anti-tumor effects of RTX-240: an engineered red blood cell expressing 4-1BB ligand and interleukin-15	McArdel S, Dugast A, Hoover M, Bollampalli A, Hong E, Castano Z Leonard S, Pawar S, Mellen J, Muriuki K, McLaughlin D, Bayhi N, Carpenter C, Turka L, Wickham T, Elloul S	2021	Cancer Immunology, Immunotherapy	Immuno-oncology	Highplex FL	HALO
Immune checkpoint blockade in triple negative breast cancer influenced by B cells through myeloid-derived suppressor cells	Vito A, Salem O, El-Sayes N, MacFawn I, Portillo A, Milne K, Harrington D, Ashkar A, Wan Y, Workenhe S, Nelson B, Bruno T, Mossman K	2021	Communications Biology	Immuno-oncology	Cytonuclear	HALO
Computational pathology reveals unique spatial patterns of immune response in H&E images from COVID-19 autopsies: preliminary findings	Corredor G, Toro P, Bera K, Rasmussen D, Viswanathan V, Buzzy C, Fu P, Barton L, Stroberg E, Duval E, Gilmore H, Mukhopadhyay, Madabhushi A	2021	Journal of Medical Imaging	Infectious Disease		HALO Link
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging	Hickey J, Neumann E, Radtke A, Camarillo J, Beuschel R, Albanese A, McDonough E, Hatler J, Wiblin A, Fisher J, Croteau J, Small E, Sood A, Caprioli R, Angelo R Nolan G, Chung K, Hewitt S, Germain R, Spraggins J, Lundberg E, Snyder M, Kelleher N, Saka S	2021	arxiv	Review		HALO
Chemokine-Capturing Wound Contact Layer Rescues Dermal Healing	Schirmer L, Atallah P, Freudenberg U, Werner C	2021	Advanced Science	Dermatology	Highplex FL, Layer Thickness	HALO
Tertiary lymphoid structures critical for prognosis in endometrial cancer patients - a TransPORTEC study	Horeweg N, Workel, H, Loiero D, Church D, Vermij L, Léon-Castillo A, Krog R, de Boer S, Nout R, Powel M, Mileshkin L, MacKay H, Leary A, Singh N, Jürgenliemk-Schulz I, Creutzberg C, Koelzer V, Nijman H, Bosse T, Bruyn M	2021	Research Square		Multiplex IHC, TMA	HALO AI
White adipose tissue autophagy and adipose-liver crosstalk exacerbate nonalcoholic fatty liver disease in mice	Sakane S, Hikita H, Shirai K, Myojin Y, Sasaki Y, Kudo S, Fukumoto K, Mizutani N, Tahata Y, Makino Y, Yamada R, Kodama T, Sakamori R, Tatsumi T, Takehara T	2021	Cellular and Molecular Gasteroenterology and Hepatology	Metabolism		HALO
Neoadjuvant cabozantinib and nivolumab convert locally advanced hepatocellular carcinoma into resectable disease with enhanced antitumor immunity	Ho W, Zhu Q, Durham J, Popovic A, Xavier S, Leatherman J, Mohan A, Mo G, Zhang S, Gross N, Charmsaz S, Lin D, Quong D, Wilt B, Kamel I, Weiss M, Philosophe B, Burkhart R, Burns W, Schubert C, Ejaz A, He J, Deshpande A, Danilova L, Stein-O'Brien G, Sugar E, Laheru D, Anders R, Fertig E, Jaffee, E, Yarchoan M	2021	Nature Cancer	Oncology		HALO
SMAD4 represses FOSL1 expression and pancreatic cancer metastatic colonization	Dai C, Rennhack J, Arnoff T, Thaker M, Younger S, Doench J, Huang A, Yang A, Aguirre A, Wang B, Mun E, O'Connel J, Huang Y, Labella K, Talamas J, Li J, Ilic N, Hwang J, Hong A, Giacomelli A, Gjoerup O, Root D, Hahn W	2021	Cell Reports	Oncology	Area Quantification	HALO
A single-dose mRNA vaccine provides a long-term protection for hACE2 transgenic mice from SARS CoV-2	Huang Q, Ji K, Tian S, Wang F, Huang B, Tong Z, Tan S, Hao J, Wang Q, Tan W, Gao G, Yan J	2021	Nature Communications	Infectious Disease	Multiplex IHC	HALO
Endothelial cell infection and dysfunction, immune activation in severe COVID-19	Qin Z, Liu F, Blair R, Wang C, Yang H, Mudd J, Currey J, Iwanaga N, He J, Mi R, Han K, Midkiff C, Alam M, Aktas B, Heide R, Veazey R, Piedimonte G, Maness N, Ergün S, Mauvais-Jarvis F, Rappaport J, Kolls J, Qin X	2021	Theranostics	Immunology, Infectious Disease	Multiplex IHC, Spatial Analysis	HALO
Histological Studies of the VentricularSubventricular Zone as Neural Stem Cell and Glioma Stem Cell Niche	Brockman A, Mobley B, Rebecca I	2021	Journal of Histochemistry & Cytochemistry	Review		HALO
The deletion of yeaJ gene facilitates Escherichia coli escape from immune recognition	Wang X, Lin X, Wan Z, Wang S, Zuo J, Wang Z, Xu Y, Han X, Miao J	2021	Journal of Bacteriology			HALO
Naproxen chemoprevention promotes immune activation in Lynch syndrome colorectal mucosa	Reyes-Uribe L, Wu Wenhui, Gelincik O, Bommi P, Francisco-Cruz A, Solis L, Lynch P, Lim R, Stoffel E, Kanth P, Samadder N, Mork M, Taggart M, Milne G, Marnett L, Vornik L, Liu D, Revuelta M, Chang K, You Y, Kipelovich L, Wistuba I, Lee J, Sei S, Shoemaker R, Szabo E, Richmond E, Umar A, Perloff M, Brown P, Lipkin S, Vilar E	2020	The BMJ	Oncology, Gastroenterology	Classifier, Cytonuclear	HALO
Repeated porphyrin lipoprotein-based photodynamic therapy controls distant disease in mouse mesothelioma via the abscopal effect	Lou J, Aragaki M, Bernards N, Kinoshita T, Mo J Motooka Y, Ishiwata T, Gregor A, Chee T, Chen Z, Chen J, Kaga K, Wakasa S, Zheng G, Yasufuku K	2021	Nanophotonics	Oncology	Cytonuclear	HALO
Digital pathology in academia: Implementation and impact	Jones-Hall Y	2021	Lab Animal	Review		HALO
GOT1 inhibition promotes pancreatic cancer cell death by ferroptosis	Kremer D, Nelson B, Lin L, Yarosz E Halbrook C, Kerk S, Sajjakulnukit P, Myers A, Thurston G, Hou S, Carpenter E, Andren A, Nwosu Z, Cusmano N, Wisner S, Mbah N, Shan M, Das N, Magnuson B, Little A, Savani M, Ramos J, Gao T, Sastra S, Palermo C, Badgley M, Zhang L, Asara J, McBrayer S, Pasca di Magliano M, Crawford H, Shah Y, Olive K, Lyssiotis C	2021	Nature Communications	Oncology		HALO
A preclinical trial and molecularly-annotated patient cohort identify predictive biomarkers in homologous recombination deficient pancreatic cancer	Wang Y, Park J, Pacis A, Denroche R, Jang G, Zhang A, Cuggia A, Domecq C, Monlong J, Raitses-Gurevich M, Grant R, Borgida A, Holter S, Stossel C, Bu S, Masoomian M, Lungu I, Bartlett J, Wilson J, Gao Z, Riazalhosseini Y, Asselah J, Bouganim N, Cabrera T, Boucher L, Valenti D, Biagi J, Greenwood C, Polak P, Foulkes W, Golan T, O'Kane G, Fischer S, Knox J, Gallinger S, Zogopoulos G	2020	Clinical Cancer Research	Oncology	Classifier, Cytonuclear, Multiplex IHC	HALO
Epigenetic modifications precede molecular alterations and drive human hepatocarcinogenesis	Czauderna C, Poplawski A, O'Roourke C, Castven D, Pérez-Aguilar B, Becker D, Heilmann-Heimbach S, Odenthal M, Amer W, Schmiel M, Drebber U, Binder H, Ridder D, Schindeldecker M, Straub B, Galle P, Andersen J, Thorgeirsson S, Park Y, Marquardt J	2021	JCI Insight	Oncology	Cytonuclear, TMA	HALO
Allostatic hypermetabolic response in PGC1?/? heterozygote mouse despite mitochondrial defects	Rodriguez-Cuenca S, Lelliot C, Campbell M, Peddinti G, Martinuez-Uña M, Ingvorsen C, Dias A, Relat J, Mora S, Hyötyläinen T, Zorzano A, Orei? M, Bjursell M, Bohlooly-Y M, Lindén D, Vidal-Puid A	2021	The FASEB Journal	Metabolism	Vacuole	HALO
Distinct immune signatures in peripheral blood predict chemosensitivity in intrahepatic cholangiocarcinoma patients	Wu T, Yang Y, Zheng B, Shi X, Li W, Ma W, Wang S, Li Z, Zhu Y, Wu J, Wang K, Zhao Y, Wu R, Sui C, Shen S, Wu X, Chen L, Yuan Z, Wang H	2021	Engineering	Oncology, Immunology	Highplex FL	HALO
Constrictive and Hypertrophic Strictures in Ileal Crohns Disease	Liu Q, Zhang X, Ko H, Stocker D, Ellman J, Chen J, Hao Y, Bhardwaj S, Liang Y, Cho J, Colombel J, Taouli B, Harpaz N	2021	Clinical Gastroenterology and Hepatology	Gastroenterology		HALO
The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancer	Najumudeen AK, Ceteci F, Fey SK, Hamm G, Steven RT, Hall H, Nikula CJ, Dexter A, Murta T, Race AM, Sumpton D, Vlahov N, Gay DM, Knight JRP, Jackstadt R, Leach JDG, Ridgway RA, Johnson ER, Nixon C, Hedley A, Gilroy K, Clark W, Malla SB, Dunne PD, Rodriguez-Blanco G, Critchlow SE, Mrowinska A, Malviya G, Solovyev D, Brown G, Lewis DY, Mackay GM, Strathdee D, Tardito S, Gottlieb E, CRUK Rosetta Grand Challenge Consortium, Takats Z, Barry ST, Goodwin RJA, Bunch J, Bushell M, Campbell AD, Sansom OJ	2021	Nature Genetics	Oncology	ISH/FISH	HALO
HIF-independent synthetic lethality between CDK4/6 inhibition and VHL loss across species	Nicholson HE, Tariq Z, Housden BE, Jennings RB, Stransky LA, Perrimon N, Signoretti S, Kaelin WG	2019	Cancer Therapy	Oncology		HALO
Impact of TREM2 risk variants on brain region-specific immune activation and plaque microenvironment in Alzheimer's disease patient brain samples	Prokop S, Miller KR, Labra SR, Pitkin RM, Hoxha K, Narasimhan S, Changolkar L, Rosenbloom A, Lee VM-Y, Trojanowski JQ	2019	Acta Neuropathologica	Neuroscience	Classifier, Area Quantification	HALO
ACT1 is required for murine IL-23-induced psoriasiform inflammation potentially independent of E3 ligase activity	Lipovsky A, Slivka PF, Su Z, Wang Y, Paulsboe S, Wetter J, Namovic MT, Gauvin D, Perron D, Gauld S, McGaragughty S, Goedken ER	2021	Journal of Investigative Dermatology	Immunology	Multiplex IHC	HALO
Robust and persistent reactivation of SIV and HIV by N-803 and depletion of CD8+ cells	McBrien JB, Mavigner M, Li LF, Smith SA, White E, Tharp GK, Walum H, Busman-Suhay K, Aguilera-Sandoval CR, Thayer WO, Spagnuolo RA, Kovarova M, Wahl A, Cervasi B, Margolis DM, Vanderford TH, Carnathan DG, Paiardini M, Lifson JD, Lee JH, Safrit JT, Bosinger SE, Estes JD, Derdeyn CA, Garcia JV, Kulpa DA, Chahroudi A, Silvestri G	2020	Nature	Other	ISH/FISH	HALO
Acute brain inflammation, white matter oxidative stress, and myelin deficiency in a model of neonatal intraventricular hemorrhage	Goulding DS, Vogel RC, Gensel JC, Morganti JM, Stromberg AJ, Miller BA	2020	Journal of Neuroscience	Immunology, Neuroscience	Area Quantification, Object Colocalization	HALO
Pharmacologic modulation of RNA splicing enhances anti-tumor immunity	Lu S, De Neef E, Thomas J, Sabio E, Rousseau B, Gigoux M, Knorr D, Greenbaum B, Elhanti Y, Hogg S, Chow A, Ghosh A, Xie A, Zamarin D, Cui D, Erickson C, Singer M, Cho H, Wang E, Lu B, Durham B, Shah H, Chowell D, Gabel A, Shen Y, Liu J, Jin J, Rhodes M, Taylor R, Molina H, Wolchok J, Merghoub T, Diaz Jr. L, Abdel-Wahab O, Bradley B	2021	Cell	Oncology	Multiplex IHC	HALO
CTLA-4 and PD-1 dual blockade induces SIV reactivation without control of rebound after antiretroviral therapy interruption	Harper J, Gordon S, Chan CN, Wang H, Lindemuth E, Galardi C, Falcinelli SD, Raines SLM, Read JL, Nguyen K, McGary CS, Nekorchuk M, Busman-Sahay K, Schawalder J, King C, Pino M, Micci L, Cervasi B, Jean S, Sanderson A, Johns B, Koblansky AA, Amrine-Madsen H, Lifson J, Margolis DM, Silvestri G, Bar KJ, Favre D, Estes JD, Paiardini	2020	Nature Medicine	Immunology, Infectious Disease	Cytonuclear, ISH/FISH	HALO
Spatially organized multicellular immune hubs in human colorectal cancer	Pelka K, Hofree M, Chen J, Sarkizova S, Pirl J, Jorgji V, Bejnood A, Dionne D, Ge W, Xu K, Chao S, Zollinger D, Lieb D, Reeves J, Fuhrman C, Hoang M, Delorey T, Nguyen L, Waldman J, Klapholz M, Wakiro I, Cohen O, Albers, J, Smillie C, Cuoco M, Wu J, Su M, Yeung J, Vijaykumar B, Magnuson A, Asinovski N, Moll T, Goder-Reise M, Applebaum A, Brais L, DelloStritto L, Denning S, Phillips S, Hill E, Meehan J, Frederick D, Sharova T, Kanodia A, Todres E, Jane-Valbuena J, Biton M, Izar B, Lambden C, Clancy T, Bleday R, Melnitchouk N, Irani J, Kunitake H, Berger D, Srivastava A, Hornick J, Ogino S, Rotem A, Vigneau S, Johnson B, Corcoran R, Sharpe A, Kuchroo V, Ng K, Giannakis M, Nieman L, Boland G, Arguirre A, Anderson A, Rosenblatt-Rosen O, Regev A, Hachohen N	2021	Cell	Oncology	Spatial Analysis, Highplex FL	HALO
Hepatic stellate cells suppress NK cell-sustained breast cancer dormancy	Correia A Guimaraes J, Auf der Maur P, et al.	2021	Nature	Immuno-oncology	Classifier	HALO
Analysis of multispectral imaging with the AstroPath platform informs efficacy of PD-1 blockade	Berry S, Giraldo N, Green B, et al	2021	Science	Immuno-oncology		HALO
Cabozantinib for neurofibromatosis type 1related plexiform neurofibromas: a phase 2 trial	Fisher MJ, Shih C-S, Rhodes SD, Armstrong AE, Wolters PL, Dombi E, Zhang C, Angus SP, Johnson GL, Packer RJ, Allen JC, Ullrich NJ, Goldman S, Gutmann DH, Plotkin SR, Rosser T, Robertson KA, Widemann BC, Smith AE, Bessler WK, He Y, Park S-J, Mund JA, Jiang L, Bijangi-Vishehsaraei K, Robinson CT, Cutter GR, Korf BR, Neurofibromatosis Clinical Trials Consortium, Blakeley JO, Clapp DW	2021	Nature Medicine	Oncology	Area Quantification	HALO
Olaparib and durvalumab in patients with germline BRCA-mutated metastatic breast cancer (MEDIOLA): an open-label, multicentre, phase 1/2, basket study	Domchek SM, Postel-Vinay S, Im S-A, Park YH, Delord J-P, Italiano A, Alexandre J, You B, Bastian S, Krebs MG, Wang D, Waqar SN, Lanasa M, Rhee J, Gao H, Rocher-Ros V, Jones EV, Gulati S, Coenen-Stass A, Kozarewa I, Lai Z, Angell HK, Opincar L, Herbolsheimer P, Kaufman B	2020	The Lancet Oncology	Oncology	Multiplex IHC	HALO
Artificial Intelligence-Based Quantification of Epithelial Proliferation in Mammary Glands of Rats and Oviducts of Göttingen Minipigs	Hvid H, Skydsgaard M, Jensen NK, Vluff BM, Jensen HE, Oleksiewicz MB, Kvist PH	2020	Toxicologic Pathology	Toxicology	Area Quantification	HALO AI
Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma	Braun DA, Hou Y, Bakouny Z, Ficial M, Sant' Angelo M, Forman J, Ross-Macdonald P, Berger AC, Jegede OA, Elagina L, Steinharter J, Sun M, Wind=Rotolo M, Pignon J-C, Cherniack AD, Lichtenstein L, Neuberg D, Catalano P, Freeman GJ, Sharpe AH, McDermott DF, Van Allen EM, Signoretti S, Wu CJ, Shukla SA, Choueiri TK	2020	Nature Medicine	Immuno-oncology	Highplex FL, Partitions (tiles, margins)	HALO
ARID1A influences HDAC1/BRD4 activity, intrinsic proliferative capacity and breast cancer treatment response	Nagarajan S, Rao SV, Sutton J, Cheeseman D, Dunn S, Papachristou EK, Prada J-EG, Couturier D-L, Kumar S, Kishore K, Chilamakuri CSR, Glont E, Goode EA, Brodie C, Guppy N, Natrajan R, Bruna A, Caldas C, Russel A, Siersbaek R, Yusa K, Chernukhin I, Carroll JS	2020	Nature Genetics	Oncology	Multiplex IHC	HALO
Preoperative ipilimumab plus nivolumab in locoregionally advanced urothelial cancer: the NABUCCO trial	van Dijk N, Gil-Jimenez A, Silina K, Hendricksen K, Smit LA, de Feijter JM, van Montfoort ML, van Rooijen C, Peters D, Broeks A, van der Poel HG, Bruining A, Lubeck Y, Sikorska K, Boellaard TN, Kvistborg P, Vis DJ, Hooijberg E, Schumacher TN, van den Broek M, Wessels LFA, Blank CU, van Rhijn BW, van der Heijden MS	2020	Nature Medicine	Immuno-oncology	Classifier, Highplex FL	HALO
Immunogenic Chemotherapy Enhances Recruitment of CAR-T Cells to Lung Tumors and Improves Antitumor Efficacy when Combined with Checkpoint Blockade	Srivastava S, Furlan SN, Jaeger-Ruckstuhl CA, Sarvothama M, Berger C, Smythe KS, Garrison SM, Specht JM, Lee SM, Amezquita RA, Voillet V, Muhunthan V, Yechan-Gunja S, Pillai SPS, Rader C, Houghton AM, Pierce RH, Gottardo R, Maloney DG, Riddell SR	2020	Cancer Cell	Immuno-oncology	Multiplex IHC, Highplex FL	HALO
HIV-1-induced cytokines deplete homeostatic innate lymphoid cells and expand TCF7-dependent memory NK cells	Wang Y, Lifschitz L, Gellatly K, Vinton CL, Busman-Sahay K, McCauley S, Vangala P, Kim K, Derr, Jaiswall S, Kucukural A, McDonel P, Hunt PW, Greenough T, Houghton J, Somsouk M, Estes JD, Brenchley JM, Garber M, Deeks SG, Luban J	2020	Nature Immunology	Immunology, Infectious Disease	Area Quantification, Cytonuclear, ISH/FISH	HALO
IL6/STAT3 Signaling Hijacks Estrogen Receptor ? Enhancers to Drive Breast Cancer Metastasis	Siersbæk R, Scabia V, Nagarajan S, Chernukhin I, Papachristou EK, Broome R, Johnston SJ, Joosten SEP, Green AR, Kumar S, Jones J, Omarjee S, Alvarez-Fernandez R, Glont S, Aitken SJ, Kishore K, Cheeseman D, Rakha EA, D'Santos C, Zwart W, Ruseel A, Brisken C, Carroll JS	2020	Cancer Cell	Oncology	Area Quantification, Multiplex IHC	HALO
Multimodal treatment combining cold atmospheric plasma and acidic fibroblast growth factor for multi?tissue regeneration	Tan F, Rui X, Xiang X, Yu Z, Al-Rubeai M	2021	The FASEB Journal	Other	Multiplex IHC	HALO
Promyelocytic leukemia protein promotes the phenotypic switch of smooth muscle cells in atherosclerotic plaques of human coronary arteries	Karle W, Becker S, Stenzel P, Knosalla C, Siegel G, Baum O, Zakrzewicz A, Berkholz J	2021	Clinical Science	Myology	Area Quantification, Object Colocalization	HALO
The Unfolded Protein Response Mediator PERK Governs Myeloid Cell-Driven Immunosuppression in Tumors through Inhibition of STING Signaling	Mohamed E, Sierra RA, Trillo-Tinoco J, Cao Y, Innamarato P, Payne KK, Pulido M, Mandula J, Zhang S, Thevenot P, Biswas S, Abdalla SK, Costich TL, Hanggi K, Anadon CM, Flores ER, Haura EB, Mehrotra, Pilon-Thomas S, Ruffel B, Munn DH, Cubillos-Ruiz JR, Conejo-Garcia JR, Rodriguez PC	2020	Immunity	Immuno-oncology	Highplex FL	HALO
Genomic analysis of Vascular Invasion in Hepatocellular Carcinoma (HCC) Reveals Molecular Drivers and Predictive Biomarkers	Krishnan MS, Rajan KD A, Park J, Arjunan V, Marques FJG, Bermudez A, Girvan OA, Hoang NS, Yin J, Nguyen MH, Kothary N, Pitteri S, Felsher DW, Dhanasekaran R	2020	Hepatology	Oncology	Multiplex IHC, TMA	HALO
Dynamic Hydrogels for Prevention of Post?Operative Peritoneal Adhesions	Stapleton LM, Lucian HJ, Grosskopf AK, Smith AAA, Totherow KP, Woo YJ, Appel EA	2021	Advanced Therapeutics	Biomaterials	Area Quantification	HALO
Efficacy and safety of a 3?in?1 antiaging night facial serum containing melatonin, bakuchiol, and ascorbyl tetraisopalmitate through clinical and histological analysis	Goldberg DJ, Mraz-Robinson D, Granger C	2020	Journal of Cosmetic Dermatology	Dermatology	Area Quantification, Layer Thickness	HALO
ILC2-driven innate immune checkpoint mechanism antagonizes NK cell antimetastatic function in the lung	Schuijs MJ, Png S, Richard AC, Tsyben A, Hamm G, Stockis J, Garcia C, Panaud S, Nicholls A, Ros XR, Su J, Eldridge MD, Riedel A, Serrao EM, Rodewald H-R, Mack M, Shields JD, Cohen ES, McKenzie ANJ, Goodwin RJA, Brindle KM, Marioni JC, Halim TYF	2020	Nature Immunology	Immuno-oncology	Multiplex IHC	HALO
Engineering functional microvessels in synthetic polyurethane random-pore scaffolds by harnessing perfusion flow	Wright MEE, Yu JK, Jain D, Maeda A, Yeh S-CA, DaCosta RS, Lin CP, Santerre JP	2020	Biomaterials	Biomaterials	Area Quantification	HALO
Blockade of the co-inhibitory molecule PD-1 unleashes ILC2-dependent antitumor immunity in melanoma	Jacquelot N, Seillet C, Wang M et al.	2021	Nature Immunology	Immuno-oncology	Classifier, Highplex FL	HALO
Expansion of Immature, Nucleated Red Blood Cells by Transient Low?Dose Methotrexate Immune Tolerance Induction in Mice	Tran JQ, Grover D, Zhang M, Stapels M, Brennan R, Bangari DS, Piepenhagen PA, Roberts E, Olivia P, Zubair F, Vela JL, Richards SM, Joseph AM	2020	Clinical & Experimental Immunology	Immunology	Area quantification	HALO
The InSituPlex® Staining Method for Multiplexed Immunofluorescence Cell Phenotyping and Spatial Profiling of Tumor FFPE Samples	Manesse M, Patel KK, Bobrow M, Downing SR	2020	Biomarkers for Immunotherapy of Cancer	Oncology, Immuno-oncology	Highplex FL	HALO
Highly efficient genome editing in primary human bronchial epithelial cells differentiated at air-liquid interface	Rapiteanu R, Karagyozova T, Zimmerman N, Singh K, Wayne G, Martufi M, Belyaev NN, Hessel EM, Michalovich D, Macarron R, Rowan WC, Cairns WJ, Roger J, Betts J, Beinke S, Maratou K	2020	European Respiratory Journal	Other	Highplex FL	HALO
IBI112, a selective anti-IL23p19 monoclonal antibody, displays high efficacy in IL-23-induced psoriasiform dermatitis	Li L, Wu Z, Qiu X, Wu Y, Kuang Z, Wang L, Sun T, Liu Y, Yi S, Jing H, Zhou S, Chen B, Wu, D, Wu W, Liu J	2020	International Immunopharmacology	Immunology, Dermatology	Classifier, Layer Thickness	HALO
A four-chemokine signature is associated with a T cell-inflamed phenotype in primary and metastatic pancreatic cancer	Romero JM, Grünwald BT, Jang G-H, Bavi PP, Jhaveri A, Masoomian M, Fischer SE, Zhang A, Denroche RE, Lungu IM, De Luca A, Bartlett JMS, Xu J, Li N, Dhaliwal S, Liang S-B, Chadwick D, Vyas F, Bronsert P, Khokha R, McGaha TL, Notta F, Ohashi PS, Done SJ, O'Kane GM, Wilson JM, Knox JJ, Connor A, Wang Y, Zogopoulos G, Gallinger S	2020	Clinical Cancer Research	Oncology	Immune	HALO
A Dedicated Evolutionarily Conserved Molecular Network Licenses Differentiated Cells to Return to the Cell Cycle	Miao Z-F, Lewis MA, Cho CJ, Adkins-Threats M, Park D, Brown JW, Sun J-X, Burclaff JR, Kennedy S, Lu J, Mahar M, Vietor I, Huber LA, Davidson NO, Cavalli V, Rubin DC, Wang Z-N, Mills JC	2020	Developmental Cell	Oncology	Highplex FL	HALO
Mobilization of CD8+ T cells via CXCR4 blockade facilitates PD-1 checkpoint therapy in human pancreatic cancer	Seo YD, Jiang X, Sullivan KM, Jalikis FG, Smythe KS, Abbasi A, Vignali M, Park JO, Daniel SK, Pollack SM, Kim TS, Yeung R, Crispe IN, Pierce RH, Robins H, Pillarisetty VG	2019	Clinical Cancer Research	Immuno-oncology	Cytonuclear	HALO
STAT3 antisense oligonucleotide remodels the suppressive tumor microenvironment to enhance immune activation in combination with anti-PD-L1	Proia T, Singh M, Woessner R, Carnevalli LS, Bommakanti G, Magiera L, Srinivasan SS, Grosskurth SE, Collins M, Womack C, Griffin M, Ye M, Cantin S, Russell DL, Xie M, Hughes AM, Deng N, Mele DA, Fawell SE, Barry ST, Reimer C, Barrett JC, McCoon P	2020	Clinical Cancer Research	Immuno-oncology	Multiplex IHC, Highplex FL	HALO
Imaging Tumor-Infiltrating Lymphocytes in Brain Tumors with [64Cu]Cu-NOTA-anti-CD8-Positron Emission Tomography	Nagle V, Henry K, Hertz C, et al.	2021	Clinical Cancer Research	Immuno-oncology	Multiplex IHC	HALO
Cooperative targeting of immunotherapy-resistant melanoma and lung cancer by an AXL-targeting antibody-drug conjugate and immune checkpoint blockade	Boshuizen J, Pencheva N, Krijgsman O, Altimari DD, Castro PG, de Bruijn B, Ligtenberg MA, den Heuvel EG, Vredevoogd DW, Song J-Y, Visser N, Apriamashvili G, Janmaat ML, Plantinga TS, Franken P, Houtkamp M, Lingnau A, Jure-Kunkel M, Peeper DS	2021	Cancer Research	Immuno-oncology	Multiplex-IHC	HALO
Over-expression of Th2-related molecules in the skin of patients with eosinophilic dermatosis of hematologic malignancy	Maglie R, Ugolini F, De Logu F, Nassini R, Simi S, Nardiello P, Pasqualaini E, Baroini G, Del Bianco E, Massi D, Antiga E	2021	Journal of the American Academy of Dermatology	Oncology, Immuno-oncology	Area Quantification, Multiplex IHC	HALO Link
Temporal Analysis of Amylase Expression in Control, Autoantibody Positive, and Type 1 Diabetes Pancreatic Tissues	Kusmartseva I, Beery M, Hiller H, Padilla M, Selman S, Posgai A, Nick HS, Campbell-Thompson M, Schatz DA, Haller MJ, Wasserfall CH, Atkinson MA	2019	Diabetes	Metabolism	Cytonuclear	HALO
Kras and Lkb1 mutations synergistically induce intraductal papillary mucinous neoplasm derived from pancreatic duct cells	Collet L, Ghurburrun E, Meyers N, Assi M, Pirlot B, Leclercq IA, Couvelard A, Komuta M, Cros J, Demetter P, Lemaigre FP, Borbath I, Jacquemin P	2019	Gut	Oncology	Area Quantification	HALO
Prognostic features of the tumour microenvironment in oesophageal adenocarcinoma	McShane R, Arya S, Stewart A, Caie P, Bates M	2021	Biochimica et Biophysica Acta (BBA) - Reviews on Cancer	Immuno-oncology, Review	Cytonuclear	HALO
Mammalian Retinal Cell Quantification	Muthuswamy A, Chen H, Hu Y, Turner OC, Aina OH	2020	Toxicologic Pathology	Other	Cytonuclear	HALO
Cx43 phosphorylation sites regulate pancreatic cancer metastasis	Solan JL, Hingorani SR, Lampe PD	2021	Oncogene	Oncology	Classifier, Area Quantification	HALO
MAOA-mediated reprogramming of stromal fibroblasts promotes prostate tumorigenesis and cancer stemness	Li J, Pu T, Yin L, Li Q, Liao C-P, Wu BJ	2020	Oncogene	Oncology	Multiplex IHC	HALO
Multimodal In Vivo and Post-mortem Assessments of Tau in Lewy Body Disorders	Coughlin DG, Phillips JS, Roll E, Peterson C, Lobrovich R, Rascovsky K, Ungrady M, Wolk DA, Das S, Weintraub D, Lee EB, Trojanowski JQ, Shaw LM, Vaishnavi S, Siderowf A, Nasrallah IM, Irwin DJ, McMillan CT	2020	Neurobiology of Aging	Neuroscience	Area Quantification	HALO
B7-H3 immune checkpoint expression is a poor prognostic factor in colorectal carcinoma	Lu Z, Zhao Z-X, Cheng P, Huang F, Guan X, Zhang M-G, Chen H-P, Liu Z, Jiang Z, Zheng Z-X, Zou S-M, Wang X-S	2020	Modern Pathology	Immuno-oncology	Multiplex-IHC, TMA	HALO
Chemoradiotherapy efficacy is predicted by intra-tumour CD8+/FoxP3+ double positive T cell density in locally advanced N2 nonsmall-cell lung carcinoma	Boulle G, Velut Y, Mansuet-Lupo A, Gibault L, Blons H, Fournel L, Boni A, Cremer I, Wislez M, Duchatelle V, Tredaniel J, Hammond SA, Herbst R, Alifano M, Giraud P, Damotte D	2020	European Journal of Cancer	Oncology	Highplex FL	HALO
Neonatal hydrocephalus leads to white matter neuroinflammation and injury in the corpus callosum of Ccdc39 hydrocephalic mice	Goulding DS, Vogel RC, Pandya CD, Shula C, Gensel JC, Mangano FT, Goto J, Miller BA	2020	Journal of Neurosurgery	Immunology, Neuroscience	Multiplex IHC, Highplex FL	HALO
The RAC1 target NCKAP1 plays a crucial role in progression of BRAF/PTEN -driven melanoma in mice	Swaminathan K, Campbell A, Papalazarou V, Jaber-Hijazi F, Nixon C, McGhee E, Strathdee D, Sansom OJ, Machesky LM	2020	Journal of Investigative Dermatology	Oncology, Dermatology	Area Quantification, Multiplex IHC	HALO
Intraductal pancreatic cancer is less responsive than cancer in the stroma to neoadjuvant chemotherapy	Fujikura K, Hutchings D, Braxton AM, Zhu Q, Laheru DA, Hruban RH, Thompson ED, Wood LD	2020	Modern Pathology	Oncology	Multiplex IHC	HALO
Phosphorylation of connexin 43 at MAPK, PKC or CK1 sites each distinctly alter the kinetics of epidermal wound repair	Lastwika JK, Dunn CA, Solan JL, Lampe PD	2019	Journal of Cell Science	Dermatology	Cytonuclear	HALO
T-regulatory cells predict clinical outcome in soft tissue sarcoma patients: a clinico-pathological study	Smolle M, Herbsthofer L, Granegger B, Goda M, Brcic I, Bergovec M, Scheipl S, Prietl B, Pichler M, Gerger A, Rossmann C, Riedl J, Tomberger M, López-García P, El-Heliebi A, Leithner A, Liegl-Atzwanger B, Szkandera J	2021	British Journal of Cancer	Oncology	Highplex FL, TMA	HALO
Quantitative digital image analysis of tumor-infiltrating lymphocytes in HER2-positive breast cancer	Abe N, Matsumoto H, Takamatsu R, Tamaki K, Takigami N, Uehara K, Kamada Y, Tamaki N, Motonari T, Unesoko M, Nakada N, Zaha N, Zaha H, Yoshimi N	2019	Vichows Archiv	Oncology	Classifier, Cytonuclear	HALO
RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons	Thomas JD, Polaski JT, Feng Q, De Neef EJ, Hoppe ER, McSharry MV, Pangallo J, Gabel AM, Belleville AE, Watson J, Nkinsi NT, Berger AH, Bradley RK	2020	Nature Genetics	Other	Highplex FL	HALO
Glucagon Receptor Inhibition Reduces Hyperammonemia and Lethality in Male Mice with Urea Cycle Disorder	Cavino K, Sung B, Su Q, Na E, Kim J, Cheng X, Gromada J, Okamoto H	2020	Endocrinology	Metabolism	ISH/FISH, Multiplex IHC	HALO
Characterization of the tumor immune microenvironment in human papillomavirus-positive and -negative head and neck squamous cell carcinomas	Succaria F, Kvistborg P, Stein JE, Engle EL, McMiller TL, Rooper LM, Thompson E, Berger AE, van den Brekel M, Zuur CL, Haanen J, Topalian SL, Taube JM	2020	Cancer Immunology, Immunotherapy	Immuno-oncology	Immune	HALO
Temporospatial Development of Neuropathologic Findings in a Canine Model of Mucopolysaccharidosis IIIB	Harm TA, Hostetter SJ, Nenninger AS, Valentine BN, Ellinwood NM, Smith JD	2020	Veterinary Pathology	Immunology, Neruoscience	Area Quantification, Cytonuclear	HALO
Development of a clinically relevant ovarian cancer model incorporating surgical cytoreduction to evaluate treatment of micro-metastatic disease	Morse CB, Voillet V, Bates BM, Chiu EY, Garcia NM, Gottardo R, Greenberg PD, Anderson KG	2020	Gynecologic Oncology	Oncology	Multiplex IHC	HALO
PIK3CA mutation and CNV status and post-chemoradiotherapy survival in patients with cervical cancer	Martell K, McIntyre JB, Kornaga EN, Chan AMY, Phan T, Kobel M, Enwere EK, Dean ML, Ghatage P, Lees-Miller SP, Doll CM	2020	Gynecologic Oncology	Oncology	Classifier, Highplex FL, TMA	HAO
Tumor Platinum Concentrations and Pathological Responses Following Cisplatin-Containing Chemotherapy in Gastric Cancer Patients	Cao Y, Chang Q, Cabanero M, Zhang W, Hafezi-Bakhtiari S, Hedley D, Darling G, Quereshy F, Jang R, Elimova E, Knox J, Ornatsky O, Serra S, Chen E	2019	Journal of Gastrointestinal Cancer	Oncology	Area Quantification, Cytonuclear	HALO
PLX3397 treatment inhibits constitutive CSF1R-induced oncogenic ERK signaling, reduces tumor growth, and metastatic burden in osteosarcoma	Smeester BA, Slipek NJ, Pomeroy EJ, Laoharawee K, Osum SH, Larsson AT, Williams KB, Stratton N, Yamamoto K, Peterson JJ, Rathe SK, Mills LJ, Hudson WA, Crosby MR, Wang M, Rahramann EP, Moriarity SB, Largaespada DA	2020	Bone	Oncology	Cytonuclear, TMA	HALO
IFN-III is selectively produced by cDC1 and predicts good clinical outcome in breast cancer	Hubert M, Gobbini E, Couillault C, Manh T-PV, Doffin A-C, Berthet J, Rodriguez C, Ollion V, Kielbassa J, Sajous C, Treilleux I, Tredan O, Dubois B, Dalod M, Bendriss-Vermare N, Caux C, Valladeau-Guilemond J	2020	Immunology	Oncology	Highplex FL, Partitions (tiles, margins)	HALO
Using immuno-PET imaging to monitor kinetics of T cell-mediated inflammation and treatment efficiency in a humanized mouse model for GvHD	Pektor S, Schlöder J, Klasen B, Bausbacher N, Wagner D-C, Schreckenberger W, Grabbe S, Jonuleit H, Miederer M	2019	European Journal of Nuclear Medicine and Molecular Imaging	Immunology	Cytonuclear	HALO
Association between CD8 and PD?L1 expression and outcomes after radical prostatectomy for localized prostate cancer	Vicier C, Ravi P, Kwak L, Werner L, Huang Y, Evan C, Loda M, Hamid AA, Sweeney CJ	2020	The Prostate	Immuno-oncology	Classifier, Highplex FL	HALO
?-Synuclein modulates tau spreading in mouse brains	Bassil F, Meymand ES, Brown HJ, Xu H, Cox TO, Pattabhiraman S, Maghames CM, Wu Q, Zhang B, Trojanowski JQ, Lee VM-Y	2020	Journal of Experimental Medicine	Neuroscience	Area Quantification	HALO
A locus coeruleus to dentate gyrus noradrenergic circuit modulates aversive contextual processing	Seo D, Zhang E, Piantadosi S, et al	2021	Neuron	Neuroscience	Area Quantification, Highplex FL	HALO
Clinicopathological significance of nerves in esophageal cancer	Griffin N, Rowe CW, Gao F, Jobling P, Wills V, Walker MM, Faulkner S, Hondermarck H	2020	The American Journal of Pathology	Oncology	Area Quantification	HALO
AST-120 Treatment Alters the Gut Microbiota Composition and Suppresses Hepatic Triglyceride Levels in Obese Mice	Hiraga Y, Kubota T, Katoh, M, et al.	2021	Endocrine Research	Metabolism	Vacuole	HALO
High CD8+ tumour infiltrating lymphocyte density associates with unfavourable prognosis in oesophageal adenocarcinoma following poor response to neo?adjuvant chemoradiotherapy	Koemans WJ, van Dieren JM, van den Berg J, Meijer G, Snaebjornsson P, Chalabi M, Lecot F, Riedl R, Krijgsman O, Hofland I, Broeks A, Voncken FEM, Peppelenbosch MP, Sosef MN, van Sandick JW, Kodach LL	2021	Histopathology	Immuno-oncology	Cytonuclear	HALO
High density of cytotoxic T-lymphocytes is linked to tumoral PD-L1 expression regardless of the mismatch repair status in colorectal cancer	Möller K, Blessin N, Höflmayer D, et al.	2021	Acta Oncologica	Immuno-oncology	Highplex FL	HALO
Discoidin Domain Receptor 1 (DDR1) is Necessary for Tissue Homeostasis in Pancreatic Injury and Pathogenesis of Pancreatic Ductal Adenocarcinoma	Ruggeri JM, Franco-Barraza J, Sohail A, Zhang Y, Long D, di Magliano MP, Cukierman E, Fridman R, Crawford HC	2020	The American Journal of Pathology	Oncology, Immunology	Cytonuclear, Multiplex IHC, Highplex FL	HALO
Chronic stress differentially alters mRNA expression of opioid peptides and receptors in the dorsal hippocampus of female and male rats	Johnson MA, Contoreggi NH, Kogan JF, Bryson M, Rubin BR, Gray JD, Kreek MJ, McEwen BS, Milner TA	2021	The Journal of Comparative Neurology	Neruoscience	ISH/FISH	HALO
Monocyte and macrophage derived myofibroblasts: Is it fate? A review of the current evidence	Vierhout M, Ayoub A, Naiel S, Yazdanshenas P, Revill S, Reihani A, Dvorkin-Gheva A, Shi W, Ask K	2021	Wound Repair and Regeneration	Review	ISH/FISH	HALO
Necroptosis in biliary atresia of the liver	Hashimoto M, Fujishima F, Lomphithak T, Jitkaew S, Nio M, Sasano H	2021	Medical Molecular Morphology	Metabolism	Multiplex IHC	HALO
Intracranial administration of alpha-synuclein fibrils in A30P-synuclein transgenic mice causes robust synucleinopathy and microglial induction	Gentzel R, Toolan D, Jinn S, Schachter J, Ma L, Kahle P, Smith S, Marcus J	2021	Neurobiology of Aging	Neuroscience	Area Quantification	HALO
A comparative study of cirrhosis sub-staging using the Laennec system, Beijing classification, and morphometry	Zhang X, Schiano T, Doyle E, Branch A, Florman S, Fiel M.	2021	Modern Pathology	Metabolism	Classifier, Area Quantification	HALO
Alteration of Colonic Mucin Composition and Cytokine Expression in Acute Swine Dysentery	Lin S J-H, Arruda B, Burrough E	2021	Veterinary Pathology	Immunology	Area Quantification, ISH/FISH	HALO
Selective loss of resident macrophage-derived insulin-like growth factor-1 abolishes adaptive cardiac growth to stress	Zaman R, Hamidzada H, Kantores C, Wong A, Dick S, Wang Y, Momen A, Aronoff L, Lin J, Razani B, Mital S, Billia F, Lavine K, Nejat S, Epelman S	2021	Immunity	Immunology	Highplex FL	HALO
Ki-67 Proliferation Index Assessment in Gastroenteropancreatic Neuroendocrine Tumors by Digital Image Analysis With Stringent Case and Hotspot Level Concordance Requirements	Boukhar SA, Gosse MD, Bellizzi AM, Rajan A	2021	American Journal of Clinical Pathology	Oncology	Cytonuclear	HALO
Establishing standardized immune phenotyping of metastatic melanoma by digital pathology	Sobottka B, Nowak M, Frei A, Haberecker M, Merki S, Tumor Profiler consortium, Levesque M, Dummer R, Moch H, Koelzer V	2021	Laboratory Investigation	Immuno-oncology	Multiplex IHC, Spatial Analysis	HALO AI
Orexin receptors 1 and 2 in serotonergic neurons differentially regulate peripheral glucose metabolism in obesity	Xiao X Yeghiazaryan G, Hess S, Klemm P, Sieben A, Kleinridders A, Morgan D, Wunderlich F. Rahmouni K. Kong D, Scammell T, Lowell B, Kloppenburg P, Brüning J, Hausen A.	2021	Nature Communications	Metabolism	ISH/FISH	HALO
Multiplex Immunohistochemical Phenotyping of T Cells in Primary Prostate Cancer	Ozbek B, Ertunc O, Erickson A, Vidal I, Alexandre C, Guner G, Hicks J, Jones T, Taube J, Sfanos K, Yegnasubramanian S, DeMarzo A	2021	medRxiv	Immuno-oncology	Classifier, Cytonuclear, Highplex FL, Serial Section, Registration	HALO
Simultaneous targeting of TGF-b/PD-L1 synergizes with radiotherapy by reprogramming the tumor microenvironment to overcome immune evasion	Lan Y, Moustaga M, Knoll M, Xu C, Furkel J, Lazorchak A, Yeung T, Hasheminasab S, Jenkins M, Meister S, Yu H, Schlegel J, Marelli B, Tang Z, Qin G, Klein C, Qi J, Zhou C, Locke G, Krunic D, Derner M, Schwager C, Fontana R, Kriegsmann K, Jiang F, Rein K, Kriegsmann M, Debus J, Lo K, Abdollahi A	2021	Cancer Cell	Oncology	Cytonuclear	HALO
SLFN11 captures cancer-immunity interactions associated with platinum sensitivity in high-grade serous ovarian cancer	Winkler C, King M, Berthe J, Ferraioli D, Garuti A, Grillo F, Rodriguez-Canales J, Ferrando L, Chopin N, Ray-Coquard I, Delpuech O, Bedognetti D, Ballestrero A, Leo E, Zoppoli G	2021	JCI Insight	Oncology	Classifier, Cytonuclear	HALO
Three subtypes of lung cancer fibroblasts definedistinct therapeutic paradigms	Hu H, Peotrowska Z, Hare P, Chen H, Mulvey H, Mayfield A, Noeen S, Kattermann K, Greenberg M, Williams A, Riley A, Wilson J, Mao Y, Huang R, Banwait M, Ho J, Crowther G, Hariri L, Sequist L, Benes C, Niederst M, Engelman J	2021	Cancer Cell	Oncology	Cytonuclear, ISH/FISH	HALO
NR4A1 regulates expression of immediate early genes, suppressing replication stress in cancer	Guo H, Golczer G, Wittner B, Langenbucher A, Zachariah M, Dubash T, Hong X, Comaills V, Burr R, Ebright R, Horwitz E, Vuille J, Hajizadeh S, Wiley D, Reeves B, Zhang J, Niederhoffer K, Lu C, Wesley B, Ho U, Nieman L, Toner M, Vasudevan S, Zou L, Mostoslavsky R, Maheswaran S, Lawrence M, Haber D	2021	Molecular Cell	Oncology	Highplex FL	HALO
AG-205 Upregulates Enzymes Involved in Cholesterol Biosynthesis and Steroidogenesis in Human Endometrial Cells Independently of PGRMC1 and Related MAPR Proteins	Thieffry C, Van Wynendaele M, Aynaci A, Maja M, Dupuis C, Loriot A, Marbaix E, Henriet P	2021	Biomolecules	Other	Cytonuclear, Highplex FL	HALO
p53-mediated redox control promotes liver regeneration and maintains liver function in response to CCl4	Humpton T, Hall H, Kiourtis C, Nixon C, Clark W, Hedley A, Shaw R, Bird T, Blyth K, Vousden K	2021	Cell Death & Differentiation	Metabolism	Cytonuclear, Multiplex IHC	HALO
Single-cell RNA transcriptome landscape of hepatocytes and non-parenchymal cells in healthy and NAFLD mouse liver	Su Q, Kim S, Adewale F, Zhou Y, Alder C, Ni M, Wei Y, Burcznski M, Atwal G, Sleeman M, Murphy A, Xin Y, Cheng X	2021	iScience	Metabolism	Area Quantification	HALO
Functional heterogeneity of POMC neurons relies on mTORC1 signaling	Saucisse N, Mazier W, Simon V, Binder E, Catania C, Bellocchio L, Romanov R, Leon S, Matias I, Zizzari P, Quarta C, Cannich A, Meece K, Gonzales D, Clark S, Becker J, Yeo G, Fioramonti X, Merkle F, Wardlaw S, Harkany T, Massa F, Marsicano G, Cota D	2021	Cell Reports	Neuroscience	ISH/FISH	HALO
Atypical chemokine receptor 3 (ACKR3) induces the perturbation of rRNA biogenesis in colonic cells: a novel mechanism of colorectal tumorigenesis	Yang J, Li Y, Pan T, Miao R, Zhang Y, Wu S, Qu X, Cui S	2021	Research Square	Oncology	Area Quantification	HALO
IL-1-driven stromalneutrophil interactions define a subset of patients with inflammatory bowel disease that does not respond to therapies	Friedrich M, Pohin M, Jackson M, Korsunsky I, Bullers S, Rue-Albrecht K, Christoforidou Z, Sathananthan D, Thomas T, Ravindran R, Tandon R, Peres R, Sharpe H, Wei K, Watts G, Mann E, Geremia A, Attar M, Oxford IBD Cohort Investigators, Roche Fibroblast Network Consortium, McCuaig S, Thomas L, Collantes E, Uhlig H, Sansom S, Easton A, Raychaudhuri S, Travis S, Powrie F	2021	Nature Medicine	Gastroenterology	Cytonuclear	HALO
Increased IL-6 expression precedes reliable viral detection in the rhesus macaque brain during acute SIV infection	Gopalakrishnan R, Aid M, Mercado N, Davis C, Malik S, Geiger E, Varner V, Jones R, Bosinger S, Piedra-Mora C, Martinot A, Barouch D, Reeves R, Tan C	2021	JCI Insight	Infectious Disease	Area Quantification	HALO
Combined CTLA-4 and PD-L1 blockade in patients with chemotherapy-naïve metastatic castration-resistant prostate cancer is associated with increased myeloid and neutrophil immune subsets in the bone microenvironment	Subudhi S, Siddiqui B, Aparicio A, Yadav S, Basu S, Chen H, Jindal S, Tidwell R, Varma A, Logothetis C, Allison J, Corn P, Sharma P	2021	Journal for ImmunoTherapy of Cancer	Immuno-oncology	Cytonuclear, Multiplex IHC	HALO
Expression of SARS-CoV-2 Entry Factors in the Pancreas of Normal Organ Donors and Individuals with COVID-19	Kusmartseva I, Wu W, Syed F, Van Der Heide V, Jorgensen M, Joseph P, Tang X, Candelario-Jalil E, Yang C, Nick H, Harbert J, Posgai A, Paulsen J, Lloyd R, Cechin S, Pugliese A, Campbell-Thomson M, Vander Heide R, Evans-Molina C, Homann D, Atkinson M	2020	Cell Metabolism	Infectious Disease	Area Quantification	HALO
Baricitinib Treatment Resolves Lower-Airway Macrophage Inflammation and Neutrophil Recruitment in Sars-Cov-2-Infected Rhesus Macaques	Hoang T, Pino M, Boddapati A, Viox E, Starke C, Upadhyay A, Gumber S, Nekorchuk M, Busman-Sahay K, Strongin Z, Harper J, Tharp G, Pellegrini K, Kirejczyk S, Zandi K, Tao S, Horton T, Beagle E, Mahar E, Lee M, Cohen J, Jean S, Wood J, Connor-Stroud F, Stammen R, Delmas O, Wang S, Cooney K, Sayegh M, Wang L, Filev P, Weiskopf D, Silvestri G, Waggoner J, Piantadosi A, Kasturi S, Al-Shakhshir H, Ribeiro S, Sekaly R, Levit R, Estes J, Vanderfold T, Schinazi R, Bosinger S, Paiardine M	2021	Cell	Infectious Disease	Multiplex IHC	HALO
Diagnostic and prognostic implications of a three-antibody molecular subtyping algorithm for non-muscle invasive bladder cancer	Jackson C, Chen L, Hardy C, Ren K, Visram K, Bratti V, Johnstone J, Sjödahl G, Siemens D, Gooding R, Berman D	2021	The Journal of Pathology: Clinical Research	Oncology	Cytonuclear, TMA	HALO
Transcriptomic Analysis of Healthy and Atopic Dermatitis Samples Reveals the Role of IL-37 in Human Skin	Zhou J, Gemperline D, Turner M, Oldach J, Molignano J, Sims J, Stayrook K	2021	ImmunoHorizons	Dermatology	Area Quantification, Cytonuclear	HALO
Interleukin-33 activates group 2 innate lymphoid cell expansion and modulates endometriosis	Miller J, Lingegowda H, Symons L, Bougie O, Young S, Lessey B, Koti M, Tayade C	2021	JCI Insight	Other	Area Quantification, Cytonuclear	HALO
Development of a novel humanized mouse model for improved evaluation of in vivo anti-cancer effects of anti-PD-1 antibody	Katano I, Hanazawa A, Otsuka I, Yamaguchi T, Mochizuki M, Kawai K, Ito R, Goto M, Kagawa T, Takahashi T	2021	Scientific Reports	Oncology	Cytonuclear, Multiplex IHC	HALO
A comparability study of natural and deglycosylated PD-L1 levels in lung cancer: evidence from immunohistochemical analysis	Mei J, Xu J, Yang X, Gu D, Zhou W, Wang H, Liu C	2021	Molecular Cancer	Oncology	Cytonuclear, Multiplex IHC	HALO
Automated Detection and Classification of Desmoplastic Reaction at the Colorectal Tumour Front Using Deep Learning	Nearchou I, Ueno H, Kajiwara Y, Lillard K, Mochizuki S, Takeuchi K, Harrison D, Caie P	2021	Cancers	Oncology		HALO AI
Mitochondria exert age-divergent effects on recovery from spinal cord injury	Stewart A, McFarlane K, Vekaria H, Bailey W, Slone S, Tranthem L, Zhang B, Patel S, Sullivan P, Gensel J	2021	Experimental Neurology	Neuroscience	Object Colocalization	HALO
Large-Section Histopathology Can Better Indicate the Immune Microenvironment and Predict the Prognosis of Pancreatic Ductal Adenocarcinoma Than Small-Section Histopathology	Ding G, Guo M, Yang Y, Sun C, Wu S, Liu X, Wang J, Jiang H, Liu Y, Zheng J	2021	Frontiers in Oncology	Oncology	Multiplex IHC	HALO
Androgen Receptor Signalling in Macrophages Promotes TREM-1-mediated Cancer Cell Line Migration and Invasion	Cioni B, Zaalberg A, van Beihnum J, Melis M, van Brugsteden J, Muraro M, Hooijberg E, Peters D, Hofland I, Lubeck Y, de Jong J, Sanders J, Vivie J, van der Poel J, Griffioen A, Zwart W, Bergman A	2021	Nature Communications	Oncology	Highplex FL, Partitions (tiles, margins)	HALO
Dysregulation of Innate Lymphoid Cells in Patients with Active Rheumatoid Arthritis and Mice with Collagen-Induced Arthritis	Yang F, Luo X, Zhu W, Li J, Zheng Z, Zhu P	2021	Mediators of Inflammation		Spatial Analysis, Highplex FL	HALO
CD147 antibody specifically and effectively inhibits infection and cytokine storm of SARS-CoV-2 and its variants delta, alpha, beta, and gamma	Geng J, Chen L, Yuan Y, Wang K, Wang Y, Qin C, Wu G, Chen R, Zhang Z, Wei D, Du P, Zhang J, Lin P, Zhang K, Deng Y, Xu K, Liu J, Sun X, Guo T, Yang X, Wu J, Jiang J, Li L, Zhang K, Wang Z, Zhang J, Yan Q, Zhu H, Zheng Z, Miao J, Fu X, Yang F, Chen X, Tang H, Zhang Y, Shi Y, Zhu Y, Pei Z, Huo F, Liang X, Wang Y, Wang Q, Xie W, Li Y, Shi M, Bian H, Zhu P, Chen Z	2021	Signal Transduction and Targeted Therapy	Infectious Disease	Cytonuclear, Multiplex IHC, Highplex FL	HALO
Suppression of insulin-induced gene 1 (INSIG1) function promotes hepatic lipid remodelling and restrains NASH progression	Azzu V, Vacca M, Kamzolas I, Hall Z, Leslie J, Carobbio S, Virtue S, Davies S, Lukasik A, Dale M, Bohlooly-Y M, Acharjee A, Linden D, Bidault G, Petsalaki E, Griffin J, Oakley F, Allison M, Vidal-Puig	2021	Molecular Metabolism	Metabolism	Area Quantification, Cytonuclear, Multiplex IHC	HALO
An endogenous opioid circuit determines state-dependent appetitive behavior	Castro D, Oswell C, Zhang E, Pedersen C, Piantadosi S, Rossi M, Hunker A, Guglin A, Moron J, Zweifel L, Stuber G, Bruchas M	2021	bioRxiv	Neuroscience	Cytonuclear, Highplex FL	HALO
A faithful in vivo model of human macrophages in metastatic melanoma	Voillet V, Berger T, McKenna K, Paulson K, Smythe K, Hunter D, Valente W, Weaver S, Campbell J, Kim T, Byrd D, Bielas J, Pierce R, Chapuis A, Gottardo R, Rongvaux	2021	bioRxiv		Cytonuclear, Multiplex IHC	HALO
Maternal platelets pass interstices of trophoblast columns and are not activated by HLA-G in early human pregnancy	Guettler J, Forstner D, Cvirn G, Maninger S, Brugger B Nonn O, Kupper N, Pritz E, Wernitznig S, Dohr G, Hutter H, Juch H, Isermann B, Kohli S, Gauster M	2021	Journal of Reproductive Immunology	Other	Cytonuclear, Highplex FL	HALO
Absolute copy number fitting from shallow whole genome sequencing data	Sauer C, Eldridge M, Vias M, Hall J, Boyle S, Macintyre G, Bradley T, Markowetz F, Brenton J	2021	bioRxiv	Oncology	Classifier	HALO
E3 ligase-inactivation rewires CBL interactome to elicit oncogenesis by hijacking RTKCBLCIN85 axis	Ahmed S, Buetow L, Gabrielsen M, Lilla S, Sibbet G, Sumpton D, Zanivan S, Hedley A, Clark W, Huang D	2021	Oncogene	Oncology	Cytonuclear, Multiplex IHC	HALO
Detection of EpsteinBarr Virus in Periodontitis: A Review of Methodological Approaches	Tonoyan L, Chevalier M, Vincent-Bungnas S, Marsault R, Doglio A	2021	Mircroorganisms	Review	ISH/FISH, ISH-IHC/FISH-IF	HALO
CYRI-A limits invasive migration through macropinosome formation and integrin uptake regulation	Le A, Yelland T, Paul N, Fort L, Nikolaou S, Ismail S, Machesky L	2021	Journal of Cell Biology	Other	Cytonuclear, Multiplex IHC	HALO
Structure of the helicase core of Werner helicase, a key target in microsatellite instability cancers	Newman J, Gavard A, Lieb S, Ravichandran M, Hauer K, Werni P, Geist L, Bottcher J, Engen J, Rumpel K, Samwer M, Petronczki, Gileadi O	2021	Life Science Alliance	Oncology	Cytonuclear, Highplex FL	HALO
In vitro amplification of pathogenic tau conserves disease-specific bioactive characteristics	Xu H, O'Reilly M, Gibbons G, Changolkar L, McBride J, Riddle D, Zhang B, Stieber A, Nirschl J, Kim S, Hoxha K, Brunden K, Schellenberg G, Trojanowski J, Lee V	2021	Acta Neuropathologica	Neruoscience	Cytonuclear, Multiplex IHC	HALO
Cross-linking of T cell to B cell lymphoma by the T cell bispecific antibody CD20-TCB induces IFN?/CXCL10-dependent peripheral T cell recruitment in humanized murine model	Cremasco F, Menietti E, Speziale D, Sam J, Sammicheli S, Richard M, Varol A, Klein C, Umana P, Bacac M, Colombetti S, Perro M	2021	PLOS ONE	Oncology	Cytonuclear, Multiplex IHC, Highplex FL	HALO
Tissue-resident FOLR2+ macrophages associate with tumor-infiltrating CD8+ T cells and with increased survival of breast cancer patients	Ramos, R, Missolo-Koussou Y, Gerber-Ferder Y, Bromley C, Bugatti M, Nunez N, Tosello J, Richer W, Denizeau J, Sedlik C, Caudana P, Kotsias F, Niborski L, Viel S, Bohec M, Lameiras S, Baulande S, Lesage L, Nicolas A, Mesure D, Vincent-Salomon A, Reyal F, Dutertre C, Ginhoux F, Vimeux L, Donnadieu E, Buttard B, Galon J, Zelenay S, Vermi W, Guermonprez P, Piaggio E, Helft J	2021	bioRxiv	Immuno-oncology	Cytonuclear, Highplex FL, TMA	HALO
CCNE1 amplification is synthetic-lethal with PKMYT1 kinase inhibition	Gallo D, Young J, Fourtounis J, Martino G, Alvarez-Quilon A, Bernier C, Duffy N, Papp R, Roulston A, Stocco R, Szychowski J, Veloso A, Alam H, Baruah P, Fortin A, Bowlan J, Chaudhary N, Desjardins J, Dietrich E, Fournier S, Fugere-Desjardins C, de Rugy T, Leclaire M, Liu B, Melo H, Nicolas O, Singhania A, Szilard R, Tkac J, Yin S, Morris S, Zinda M, Marshall C, Duocher D	2021	bioRxiv	Other	Cytonuclear, Multiplex IHC	HALO
MNK inhibition sensitizes KRAS-mutant colorectal cancer to mTORC1 inhibition by reducing eIF4E phosphorylation and c-MYC expression	Knight J, Alexandrou C, Skalka G, Vlahov N, Pennel K, Officer L, Teodosio A, Kanellos G, Gay D, May-Wilson S, Smith E, Najumudeen A, Gilroy K, Ridgway R, Flanagan D, Smith R, McDonald L, MacKay C, Cheasty A, McArthur K, Stanway E, Leach J, Jackstadt R, Waldron J, Campbell A, Vlachogiannis G, Valeri N, Haigis K, Sonenberg N, Proud C, Jones N, Swarbrick M, McKinnon H, Faller W, LeQuense J, Edwards J, Willis A, Bushell M, Sansom O	2021	Cancer Discovery	Oncology	Cytonuclear, Highplex FL	HALO
Computational modeling of tau pathology spread reveals patterns of regional vulnerability and the impact of a genetic risk factor	Cornblath E, Li H, Changolkar C, Zhang B, Brown H, Gathagan R, Olufemi M, Trojanowski J, Bassett D, Lee V, Henderson M	2021	Science Advances	Neuroscience	Area Quantification	HALO
Tau-tubulin kinase 1 phosphorylates TDP-43 at disease-relevant sites and exacerbates TDP-43 pathology	Tian Y, Wang Y, Jablonski A, Hu Y, Sugam J, Koglin M, Stachel S, Zhou H, Uslaner J, Parmentier-Batteur S	2021	Neurobiology of Disease	Neuroscience	Area Quantification	HALO
Pilot study of Tremelimumab with and without cryoablation in patients with metastatic renal cell carcinoma	Campbell M, Matin S, Tam A, Sheth R, Ahrar K, Tidwell R, Rao P, Karam J, Wood C, Tannir N, Jonasch E, Gao J, Zurita A, Shah A, Jindal S, Duan F, Basu S, Chen H, Espejo A, Allison J, Yadav S, Sharma P	2021	Nature Communications	Oncology	Cytonuclear	HALO
Cancer immune therapy with PD-1-dependent CD137 co-stimulation provides localized tumour killing without systemic toxicity	Qiao Y, Qiu Y, Ding J, Luo N, Wang H, Ling X, Sun J, Wu Z, Wang Y, Liu Y, Guo F, Sun T, Shen W, Zhang M, Wu D, Chen B, Xu W, Wang X	2021	Nature Communications	Immuno-oncology	Cytonuclear, Multiplex IHC	HALO
Small molecule inhibitors of ?-synuclein oligomers identified by targeting early dopamine-mediated motor impairment in C. elegans	Chen K, Menezes K, Rodgers J, )'Hara D, Tran N, Fujisawa K, Ishikura S, Khodaei S, Chau H, Cranston A, Kapadia M, Pawar G, Ping S, Krizus A, Lacoste A, Spangler S, Visanji N, Marras C, Majbour N, El-Agnaf O, Lozano A, Culotti, Suo S, Ryu W, Kalia S, Kalia L	2021	Molecular Neurodegeneration	Neuroscience	Cytonuclear	HALO
Intratumoral Heterogeneity and Immune Response Indicators to Predict Overall Survival in a Retrospective Study of HER2-Borderline (IHC 2+) Breast Cancer Patients	Radziuviene G, Rasmusson A, Augulis R, Grineviciute R, Zilenaite D, Laurinaviciene A, Ostapenko V, Laurinavicius A	2021	Frontiers in Oncology	Immuno-oncology	Membrane, Multiplex IHC	HALO AI
The TRPA1 Channel Amplifies the Oxidative Stress Signal in Melanoma	De Logu F, Monteiro de Araujo D, Ugolini F, Iannone L, Vannucchi M, Portelli F, Landini L, Titiz M, De Giorgi V, Geppetti P, Massi D, Nassini R	2021	Cells		Area Quantification, Multiplex IHC	HALO, HALO Link, HALO AI
CD98-induced CD147 signaling stabilizes the Foxp3 protein to maintain tissue homeostasis	Geng J, Chen R, Yang F, Lin P, Zhu Y, Fu X, Wang K, Feng Z, Wu J, Zhang H, Li Q, Chen Z, Zhu P	2021	Cellular and Molecular Immunology	Immuno-oncology	Cytonuclear, Highplex FL	HALO
Immune Response in Myocardial Injury: In Situ Hybridization and Immunohistochemistry Techniques for SARS-CoV-2 Detection in COVID-19 Autopsies	Chong P, Iqbal J, Yeong J, Aw T, Chan K, Chui P	2021	Frontiers in Molecular Biosciences	Infectious Disease		HALO
STING regulates peripheral nerve regeneration and colony stimulating factor 1 receptor (CSF1R) processing in microglia	Morozzi G, Rothen J, Toussaint G, De Lange K, Westritschnig K, Doelemeyer A, Ueberschlag V, Kahle P, Lambert C, Obrecht M, Beckmann N, Ritter V, Panesar M, Stauffer D, Garnier I, Mueller M, Guerini D, Keller C, Knehr J, Roma G, Bidinosti M, Brachat S, Morvan F, Forano M	2021	iScience	Neuroscience	Cytonuclear	HALO AI
Deleting DNMT3A in CAR T cells prevents exhaustion and enhances antitumor activity	Prinzing B, Zebley C, Petersen C, Fan Y, Anido A, Yi Z, Nguyen P, Houke H, Bell M, Haydar D, Brown C, Boi S, Alli S, Crawford J, Riberdy J, Park J, Zhou S, Velasquez M, DeRenzo C, Lazzarotto C, Tsai S, Vogel P, Pruett-Miller S, Langfitt D, Gottschalk S, Youngblood B, Krenciute G	2021	Science Translational Medicine	Immuno-oncology	Cytonuclear	HALO
Isoform specific anti-TGF? therapy enhances antitumor efficacy in mouse models of cancer	Gupta A, Budhu S, Fitzgerald K, Giese R, Michel A, Holland A, Campesato L, vanSnick J, Uyttenhove C, Ritter G, Wolchok J, Merghoub T	2021	Communications Biology	Oncology	Area Quantification	HALO
Inhibitory effects and mechanisms of the anti-covid-19 traditional Chinese prescription, Keguan-1, on acute lung injury	Bai, Z, Li P, Wen J, Han Y, Cui Y, Zhou Y, Shi Z, Chen S, Li Q, Zhao X, Wang Z, Li R, Guo Y, Zhan X, Xu G, Ding K, Wang J, Xiao X	2021	Journal of Ethnopharmacology	Infectious Disease	Highplex FL	HALO
Soluble guanylate cyclase signalling mediates etoposide resistance in progressing small cell lung cancer	Schenk M, Humprey S, Hossain A, Revill M, Pearsall S, Lallo A, Brown S, Bratt S, Galvin M, Descamps T, Zhou C, Pearce S, Priest L, Greenhalgh M, Chaturvedi A, Kerr A, Blackhall F, Dive C, Frese K	2021	Nature Communications	Oncology	Classifier, Area Quantification	HALO
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging	Hickey J, Neumann E, Radtke A, Camarillo J, Beuschel R, Albanese A McDonough E, Hatler J, Wiblin A, Fisher J, Croteau J, Small E, Sood A, Caprioli R, Angelo R. Nolan G, Chung K, Hewitt S, Germain R, Spraggins J, Lundberg E, Snyder M, Kelleher N, Saka S	2021	Nature Methods	Review		HALO
Alpha-synuclein from patient Lewy bodies exhibits distinct pathological activity that can be propagated in vitro	Marotta N, Ara J, Uemura N, Lougee M, Meymand E, Zhang B, Petersson E, Trojanowski J, Lee V	2021	Acta Neuropathologica Communications	Neuroscience		HALO
Advances in mass cytometry and its applicability to digital pathology in clinical-translational cancer research	Cereceda K, Jorquera R, Villarroel-Espindola, F	2021	Advances in Laboratory Medicine	Review		HALO
Immuno-transcriptomic profiling of extracranial pediatric solid malignancies	Brohl A, Sindiri S, Wei J, Milewski D, Chou H, Song Y, Wen X, Kumar J, Reardon H, Mudunuri U, Collins J, Nagaraj S, Gangalapudi V, Tyagi M, Zhu Y, Masih K, Yohe M, Shern J, Qi Y, Turpin B, Leino D, Iwata S, Andrulis I, Wunder J, Toledo S, Meltzer P, Lau C, Teicher B, Magnan H, Ladanyi M, Khan J	2021	Cell Reports	Oncology		HALO
*Immune cell topography predicts response to PD-1 blockade in cutaneous T cell lymphoma	Phillips D, Matusiak M, Gutierrez BR, Bhate SS, Barlow GL, Jiang S, Demeter J, Smythe KS, Pierce RH, Fling SP, Ramchurren N, Cheever MA, Goltsev Y, West RB, Khodadoust MS, Kim YH, Schürch CM, Nolan GP	2021	Nature Communications	Immuno-oncology		HALO
A single cell atlas reveals distinct immune landscapes in transplant and primary tumors that determine response or resistance to immunotherapy	Wisdom AJ, Mowery YM, Hong CS, Qin X, Zhang D, Himes JE, Chen L, Fradin H, Muise ES, Xu ES, Carpenter DJ, Kent CL, Smythe KS, Williams N, Luo L, Ma Y, Owzar K, Bradley T, Kirsch DG	2020	Nature Communications	Oncology, Immuno-oncology	Cytonuclear	HALO
Spatial Clustering of CD68+ Tumor Associated Macrophages with Tumor Cells is Associated with Worse Overall Survival in Metastatic Clear Cell Renal Cell Carcinoma	Chakiryan NH, Kimmel GJ, Kim Y, Hajiran A, Aydin AM, Zemp L, Katende E, Nguyen J, Lopez-Blanco N, Chahoud J, Spiess PE, Fournier M, Dhillon J, Wang L, Moran-Segura C, El-Kenawi A, Mulé J, Altrock PM, Manley BJ	2021	PLOS ONE	Immuno-oncology	Highplex FL	HALO
A Deep Learning Approach for Tissue Spatial Quantification and Genomic Correlations of Histopathological Images	Lu Z, Zhan X, Wu Y, Chng J, Shao W, Ni D, Han Z, Zhang J, Feng Q, Huang K	2020	Genomics, Proteomics & Bioinformatics	Review		HALO
CD117/c-kit Defines a Prostate CSC-Like Subpopulation Driving Progression and TKI Resistance	Koran S. Harris, Shi L, Foster BM, Mobley ME, Elliott PL, Song CJ, Watabe K, Langefeld CD, Kerr BA	2020	Scientific Reports	Oncology		HALO
Localization of KRAS downstream target ARL4C to invasive pseudopods accelerates pancreatic cancer cell invasion	Harada A, Matsumoto S, Yasumizu Y, Akama T, Eguchi H, Kikuchi A	2021	bioRxiv	Oncology	Area Quantification	HALO
ABCF1 regulates dsDNA-induced immune responses in human airway epithelial cells	Cao QT, Aguiar JA, Tremblay BJ-M, Abbas N, Tiessen N, Revill S, Makhdami N, Ayoub A, Cox G, Ask K, Doxey AC, Hirota JA	2020	Frontiers in Cellular and Infection Microbiology	Immunology		HALO
Accelerated phosphatidylcholine turnover in macrophages promotes adipose tissue inflammation in obesity	Petkevicius K, Virtue S, Bidault G, Jenkins B, Cubuk C, Morgantini C, Aouadi M, Dopazo J, Serlie M, Koulman A, Vidal-Puig A	2019	Elife		Classifier, Vacuole	HALO
Bone Morphogenetic Protein Pathway Antagonism by Grem1 Regulates Epithelial Cell Fate in Intestinal Regeneration	Koppens MAJ, Davis H, Valbuena GN, Mulholland EJ, Nasreddin N, Colombe M, Antanaviciute A, Biswas S, Friedrich M, Lee L, Oxford IBD cohort investigators, Wang LM, Koelzer VH, East JE, Simmons A, Winton DJ, Leedham SJ	2021	Gastroenterology	Gastroenterology	Area Quantification	HALO
Effects of advanced age upon astrocyte-specific responses to acute traumatic brain injury in mice	Early AN, Gorman AA, Van Eldik LJ, Bachstetter AD, Morganti JM	2019	Journal of Neuroinflammation	Neuroscience	Area Quantification	HALO
FK506-binding protein 13 expression is upregulated in interstitial lung disease and correlated with clinical severity: a potentially protective role	Tat V, Ayaub EA, Ayoub A, Vierhout M, Naiel S, Padwal MK, Abed S, Mekhael O, Tandon K, Revill SD, Yousof T, Bellaye PS, Kolb PS, Dvorkin-Gheva A, Naqvi A, Cutz JC , Hambly N, Kato J, Vaughan M, Moss J, Kolb MRJ, Ask K	2019	American Journal of Respiratory Cell and Molecular Biology	Immunology, Fibrosis	Area Quantification, Cytonuclear	HALO
Integrated human pseudoislet system and microfluidic platform demonstrate differences in GPCR signaling in islet cells	Walker JT, Haliyur R, Nelson HA, Ishahak M, Poffenberger G, Aramandla R, Reihsmann C, Luchsinger JR, Saunders DC, Wang P, Garcia-Ocana A, Bottino R, Agarwal A, Powers AC, Brissove M	2019	bioRxiv	Gastroenterology	Cytonuclear	HALO
Detection of engineered T cells in FFPE tissue by multiplex in situ hybridization and immunohistochemistry	Wright JH, Huang L-Y, Weaver S, Archila LD, McAfee MS, Hirayama AV, Chapuis AG, Bleakley M, Rongvaux A, Turtle CJ, Chanthaphavong S, Campbell JS, Pierce RH	2020	Journal of Immunological Methods	Immunology	ISH/FISH, ISH-IHC/FISH-IF	HALO
Mesenchyme-derived IGF2 is a major paracrine regulator of pancreatic growth and function	Hammerle CM, Sandovici I, Brierley GV, Smith NM, Zimmer WE, Zvetkova I, Prosser HM, Sekita Y, Lam BYH, Ma M, Cooper WN, Vidal-Puig A, Ozanne SE, Medina-Gomez G, Constancia M	2020	PLOS Genetics	Toxicology	Area Quantification	HALO AI
Microbial regulation of enteric eosinophils and its impact on tissue remodeling and Th2 immunity	Jimenez-Saiz R, Anipindi VC, Galipeau H, Ellenbogen Y, Chaudhary R, Koenig JF, Gordon ME, Walker TD, Mandur TS, Abed S, Humbles A, Chu DK, Ask K, Verdu EF, Jordana M	2019	Frontiers in Immunology	Immunology, Infectious Disease	Area Quantification	HALO
Distinct fibroblast functional states drive clinical outcomes in ovarian cancer and are regulated by TCF21	Hussain A, Voisin V, Poon S, Dmytryshyn J ,Richman C, Meens J, Ho VW, Tang KH, Paterson J, Clarke B, Bernardini M, Bader G, Neel B, Ailles L	2019	Journal of Experimental Medicine	Oncology	Classifier, Area Quantification	HALO
Transcriptomic analysis links diverse hypothalamic cell types to fibroblast growth factor 1-induced sustained diabetes remission	Bentsen MA, Rausch DM, Mirzadeh Z, Muta K, Scarlett JM, Brown JM, Herranz-Perez V, Baquero AF, Thompson J, Alonge KM, Faber CL, Kaiyala KJ, Bennett C, Pyke C, Ratner C, Egerod KL, Holst B, Meek TH, Kutlu B, Zhang Y, Sparso T, Grove KL, Morton GJ, Kornum BR, Garcia-Verdugo J-M, Secher A, Jorgensen R, Schwartz MW, Pers TH	2020	Nature Communications	Metabolism	ISH/FISH	HALO
PPAR-gamma induced AKT3 expression increases levels of mitochondrial biogenesis driving prostate cancer	Galbraith L, Mui E, Nixon C, Hedley A, Strachan D, MacKay G, Sumpton D, Sansom O, Leung H, Ahmad I	2021	Oncogene	Oncology	ISH/FISH	HALO
Pixelwise H-score: a novel digital image analysis-based metric to quantify membrane biomarker expression from immunohistochemistry images	Ram S, Vizcarra P, Whalen P, Deng S, Painter C, Jackson-Fisher A, Pirie-Shepherd S, Xia X, Powell E	2021	PLOS One	Other	Cytonuclear, Multiplex IHC	HALO
EHF is essential for epidermal and colonic epithelial homeostasis and suppresses Apc-initiated colonic tumorigenesis	Reehorst C, Nightingale R, Luk I, Jenkins L, Koentgen F, Williams D, Darido C, Tan F, Anderton H, Chopin M, Schoffer K, Eissmann M, Buchert M, Mouradov D, Sieber O, Ernst M, Dhillon A, Maridason J	2021	Development	Oncology	Cytonuclear, Highplex FL	HALO
LRPPRC regulates redox homeostasis via the circANKHD1/FOXM1 axis to enhance bladder urothelial carcinoma tumorigenesis	Wei W, Wang N, Deng M, Dong P, Liu J, Xiang Z, Li X, Li Z, Liu Z, Peng Y, Li Z, Jiang L, Yao K, Ye Y, Lu W, Zhang Z, Zhou F, Liu Z, Xie D, Yu C	2021	Redox Biology	Metabolism	Cytonuclear, Multiplex IHC	HALO
A growth factorexpressing macrophage subpopulation orchestrates regenerative inflammation via GDF-15	Patsalos A, Halasz L, Medina-Serpas M, Berger W, Daniel B, Tzerpos P, Kiss M, Nagy G, Fischer C, Simandi Z, Varga T, Nagy L	2021	Journal of Experimental Medicine		Muscle Fiber	HALO
Antiretroviral therapy timing impacts latent tuberculosis infection reactivation in a tuberculosis/simian immunodeficiency virus coinfection model	Sharan R, Ganatra S, Bucsan A, Cole J, Singh D, Alvarez X, Gough M, Alvarez C, Blakley A, Ferdin J, Thippeshappa R, Singh B, Escobedo R, Shivanna V, Dick E, Hall-Ursone S, Khader S, Mehra S, Rengarajan J, Kaushal D	2021	The Journal of Clinical Investigation	Infectious Disease	Cytonuclear, Highplex FL	HALO
Effects of Dietary Pork Fat Cooked Using Different Methods on Glucose and Lipid Metabolism, Liver Inflammation and Gut Microbiota in Rats	Zhu W, Xu Y, Liu J, Chen D, Zhang H, Yang Z, Zhou X	2021	Foods	Metabolism	Area Quantification	HALO
Low immunogenicity of LNP allows repeated administrations of CRISPR-Cas9 mRNA into skeletal muscle in mice	Kenjo E, Hozumi H, Makita Y, Iwabuchi K, Fujimoto N, Matsumoto S, Kimura M, Amano Y, Ifuku M, Naoe Y, Inukai N, Hotta A	2021	Nature Communications	Other	Muscle Fiber	HALO
Comprehensive clinicopathologic study of alpha fetoprotein-expression in a large cohort of patients with hepatocellular carcinoma	Ridder D, Weinmann A, Schindeldecker M, Urbansky L, Berndt K, Gerber T, Lang H, Lotz J, Lackner K, Roth W, Straub B	2021	International Journal of Cancer	Oncology	Cytonuclear, TMA	HALO
Nuclear pore protein NUP210 depletion suppresses metastasis through heterochromatin-mediated disruption of tumor cell mechanical response	Amin R, Shukla A, Zhu J, Kim S, Wang P, Tian S, Tran A, Paul D, Cappell S, Burkett S, Liu H, Lee M, Kruhlak M, Dwyer J, Simpson R, Hager G, Ruan Y, Hunter K	2021	Nature Communications	Oncology	Area Quantification	HALO AI
Inter-organ transmission of hepatocellular senescence induces multi-organ dysfunction through the TGF? signalling pathway	Kiourtis C, Terradas-Terradas M, Gee L, Hsieh Y, Nixon C, Clark W, Shaw R, Hanson P, Sumpton D, Mackay G, May S, Muller M, Najumudeen A, Campbell A, Barry S, Morris C, LeBeau F, Sansom O, Kirschner K, Oakley F, Bird T	2021	Research Square	Other	Area Quantification, Cytonuclear, Multiplex IHC	HALO
Hedgehog-signalling in papillary fibroblasts is essential for hair follicle regeneration during wound healing	Frech S, Forsthuber A, Korosec A, Lipp K, Kozumov V, Lichtenberger B	2021	Journal of Investigative Dermatology	Dermatology	Cytonuclear, Multiplex IHC	HALO
Heterocellular OSM-OSMR signalling reprograms fibroblasts to promote pancreatic cancer growth and metastasis	Lee B, Hogg E, Below C, Kononov A, Blanco-Gomez A, Heider F, Xu J, Hutton C, Zhang X, Scheidt T, Beattie K, Lamarca A, McNamara M, Valle J, Jorgensen C	2021	Nature Communications	Oncology	Classifier, Area Quantification	HALO
Evaluation of Early Markers of Ischemia-reperfusion Injury and Preservation Solutions in a Modified Hindlimb Model of Vascularized Composite Allotransplantation	Rostami S, Xu M, Datta S, Haykal S	2022	Transplantation Direct		Cytonuclear, Multiplex IHC	HALO
B7-1 and programmed cell death-ligand 1 in primary and lymph node metastasis lesions of non-small cell lung carcinoma	Yamada T, Miki Y, Suzuki M, Kondoh O, Saito-Koyama R, Ono K, Okada Y, Sasano H	2021	Cancer Medicine	Oncology	Cytonuclear, Multiplex IHC	HALO
A minimal standardized human bone marrow microphysiological system to assess resident cell behavior during normal and pathological processes	Voeltzel T, Fossard G, Degaud M, Geistlich K, Gadot N, Jeanpierre S, Mikaelian I, Brevet M, Anginot A, Le Bousse-Kerdiles M, Trichet V, Lefort S, Maguer-Satta V	2021	Biomaterials Science	Biomaterials	Area Quantification, Cytonuclear	HALO
Effect of Electroacupuncture at Siguan Acupoints on Expression of BDNF and TrkB Proteins in the Hippocampus of Post-Stroke Depression Rats	Kang Z, Ye H, Chen T, et al.	2021	Journal of Molecular Neuroscience	Neuroscience		HALO
An ex vivo tumor fragment platform to dissect response to PD-1 blockade in cancer	Voabil P, de Bruijn M, Roelofsen L, Hendriks S, Brokamp S, van den Braber M, Broeks A, Sanders J, Herzig P, Zippelius A, Blank C, Hartemink K, Monkhorst K, Haanen J, Schumacher T, Thommen D	2021	Nature Medicine	Immuno-oncology	Classifier, Multiplex IHC,	HALO
Computational pathology reveals unique spatial patterns of immune response in H&E images from COVID-19 autopsies: preliminary findings	Corredor G, Toro P, Bera K, Rasmussen D, Viswanathan V, Buzzy C, Fu P, Barton L, Stroberg E, Duval E, Gilmore H, Mukhopadhyay, Madabhushi A	2021	Journal of Medical Imaging	Infectious Disease		HALO Link
Anti-CD47 antibody administration via cisterna magna in proper dosage can reduce perihematomal cell death following intracerebral hemorrhage in rats	Song Y, Wang H, Li F, Huang Q, Zhang Z	2021	Brain Research Bulletin	Other	Highplex FL	HALO
Investigation of Breast Cancer Microstructure and Microvasculature from Time-Dependent DWI and CEST in Correlation with Histological Biomarkers	Someya Y, Iima M, Imai H, Yoshizawa A, Kataoka M, Isoda H, Le Bihan D, Nakamoto Y	2021	Research Square		Classifier, Multiplex IHC	HALO
Secretory pathway Ca-ATPase2 (SPCA2) gene knockout results in mouse mammary gland changes and a secretory defect	Reinhardt T, Lippolis J, Palmer M	2021	Research Square	Other		HALO
Specificity and off-target effects of AAV8-TBG viral vectors for the manipulation of hepatocellular gene expression in mice	Kiourtis C, Wilczynska A, Nixon C, Clark W, May S, Bird T	2021	Biology Open	Other	Multiplex IHC	HALO
Cross-Platform Comparison of Computer-assisted Image Analysis Quantification of In Situ mRNA Hybridization in Investigative Pathology	Holzer TR, Hanson JC, Wray EM, Bailey JA, Kennedy KR, Finnegan PR, Nasir A, Credille KM	2019	Applied Immunohistochemistry & Molecular Morpholgy	Other	ISH/FISH	HALO
spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data	Creed J, Wilson C, Soupir A, Colin-Leitzinger C, Kimmel G, Ospina O, Chakiryan N, Markowitz J, Peres L, Coghill A, Fridley B	2021	Bioinformatics	Other	Classifier, Cytonuclear, Highplex FL	HALO
Local radiotherapy and E7 RNA-LPX vaccination show enhanced therapeutic efficacy in preclinical models of HPV16+ cancer	Salomon N, Selmi A, Grunwitz C, Kong A, Stanganello E, Neumaier J, Petschenka J, Diken M, Kreiter S, Tureci O, Sahin U, Vascotto F	2021	Cancer Immunology, Immunotherapy	Oncology, Infectious Disease	Highplex FL	HALO
Clinically relevant mitochondrial-targeted therapy improves chronic outcomes after traumatic brain injury	Hubbard W, Spry M, Gooch J, Cloud A, Vekaria H, Burden S, Powell D, Berkowitz B, Geldenhuys W, Harris N, Sullivan P	2021	Brain	Neuroscience	Area Quantification	HALO
Anti-CAIX BB? CAR4/8 T Cells Exhibit Superior Efficacy in a Clear Cell Renal Cell Carcinoma (ccRCC) Mouse Model	Wang Y, Buck A, Grimaud M, Culhane A, Kodangattil S, Razimbaud C, Bonal D, Nguyen Q, Zhu Z, Wei K, O'Donnell M, Huang Y, Signoretti S, Choueiri T, Freeman G, Zhu Q, Marasco	2021	Molecular Therapy: Oncolytics	Oncology	Cytonuclear, Multiplex IHC	HALO
The microglial P2Y6 receptor mediates neuronal loss and memory deficits in neurodegeneration	Puigdellivol M, Milde S, Vilalta A, Cockram T, Allendorf D, Lee J, Dundee J, Pampuscenko K, Borutaite V, Nuthall H, Brelstaff J, Spillantini G, Brown G	2021	Cell Reports	Neuroscience	Area Quantification, Cytonuclear, Multiplex IHC	HALO
Cannabinoid control of gingival immune activation in chronically SIV-infected rhesus macaques involves modulation of the indoleamine-2,3-dioxygenase-1 pathway and salivary microbiome	McDew-White M, Lee E, Alvarez X, Sestak K, Ling B, Byrareddy S, Okeoma C, Mohan M	2022	EBioMedicine	Infectious Disease	Area Quantification, Cytonuclear, Highplex FL	HALO
Neoadjuvant immunotherapy with nivolumab and ipilimumab induces major pathological responses in patients with head and neck squamous cell carcinoma	Vos J, Elbers J, Krijgsman O, Traets J, Qiao X, van der Leun A, Lubeck Y, Seignette I, Smit L, Willems S, van den Brekel M, Dirven R, Karakullukcu B, Karssemakers L, Klop W, Lohuis P, Schreuder W, Smeele L, van der Velden L, Tan I, Onderwater S, Jasperse B, Vogel W, Al-Mamgani A, Keijser A, van der Noort V, Broeks A, Hooijberg E, Peeper D, Schumacher T, Blank C, de Boer J, Haanen J, Zuur C	2021	Nature Communications	Oncology	Classifier, Highplex FL	HALO
ACE2-IgG1 fusions with improved in vitro and in vivo activity against SARS-CoV-2	Iwanaga N, Cooper L, Rong L, Maness N, Beddingfield B, Qin Z, Crabtree J, Tripp R, Yang H, Blair R, Jangra S, Garcia-Sastre A, Schotsaert M, Chandra S, Robinson J, Srivastava A, Rabito F, Qin X, Kolls J	2022	iScience	Infectious Disease	Highplex FL	HALO AI
Tumor MHC Class I Expression Associates with Intralesional Interleukin-2 Response in Melanoma	Pourmaleki M, Jones C, Ariyan C, Zeng Z, Pirun M, Navarrete D, Li Y, Zhang M, Nandakumar S, Campos C, Nadeem S, Klimstra D, Temple-Oberle C, Brenn T, Kipson E, Schenk K, Stein J, Taube J, White M, Traweek R, Wargo J, Kirkwood J, Gasmi B, Goff S, Corwin A, McDonough E, Ginty F, Callahan M, Schietinger A, Socci N, Mellinghoff I, Hollmann T	2022	Cancer Research Immunology	Immuno-oncology	Highplex FL	HALO
Progranulin mediates immune evasion of pancreatic ductal adenocarcinoma through regulation of MHCI expression	Cheung P, Yang J, Fang R, Borgers A, Krengel K, Stoffel A, Althoff K, Yip C, Siu E, Ng L, Lang K, Cham L, Engel D, Soun C, Cima I, Scheffler B, Striefler J, Sinn M, Bahra M, Pelzer U, Oettle H, Markus P, Smeets E, Aarntzen E, Savvatakis K, Liffers S, Lueong S, Neander C, Bazarna A, Zhang X, Paschen A, Crawford H, Chan A, Cheung S, Siveke J	2022	Nature Communications	Oncology	Cytonuclear, Spatial Analysis, Highplex FL	HALO
Tumor cell-derived exosomes deliver TIE2 protein to macrophages to promote angiogenesis in cervical cancer	Du S, Qian J, Tan S, Li W, Liu P, Zhao J, Zeng Y, Xu L, Wang Z, Cai J	2022	Cancer Letters	Oncology	Area Quantification, Cytonuclear, Spatial Analysis, Highplex FL	HALO
Understanding the impact of chemotherapy on the immune landscape of high-grade serous ovarian cancer	Vanguri R, Benhamida J, Young J, Li Y, Zivanovic O, Chi D, Snyder A, Hollmann T, Mager K	2022	Gynecologic Oncology Reports	Oncology	Classifier, Cytonuclear, Highplex FL	HALO
Landscape of cancer-associated fibroblasts identifies the secreted biglycan as a protumor and immunosuppressive factor in triple-negative breast cancer	Zheng S, Zou Y, Tang Y, Yang A, Liang J, Wu L, Tian W, Xiao W, Xie X, Yang L, Xie J, Wei W, Xie X	2022	OncoImmunology	Immuno-oncology	Cytonuclear, Multiplex IHC	HALO
The Tumor Immune Landscape and Architecture of Tertiary Lymphoid Structures in Urothelial Cancer	van Dijk N, Gil-Himenez A, Silina K, van Montfoort M, Einerhand S, Jonkman L, Voskuilen C, Peters D, Sanders J, Lubeck Y, Broeks A, Hooijberg E, Vis D, van den Broek M, Wessels L, van Rhijn B, van der Heijden M	2021	Frontiers in Immunology	Immuno-oncology	Cytonuclear, Spatial Analysis, Highplex FL	HALO AI
Postmortem high-dimensional immune profiling of severe COVID-19 patients reveals distinct patterns of immunosuppression and immunoactivation	Wu H, He P, Ren Y, Xiao S, Wang W, Liu Z, Li H, Wang Z, Zhang D, Cai J, Zhou X, Jiang D, Fei X, Zhao L, Zhang H, Liu Z, Chen R, Li W, Wang C, Zhang S, Qin J, Nasan B, Sun C	2022	Nature Communications	Infectious Disease	Multiplex IHC	HALO
EBV+ tumors exploit tumor cell-intrinsic and -extrinsic mechanisms to produce regulatory T cell-recruiting chemokines CCL17 and CCL22	Jorapur A, Marshall L, Jacobson S, Xu M, Marubayashi S, Zibinsky M, Hu D, Robles O, Jackson J, Baloche V, Busson P, Wustrow D, Brockstedt D, Talay O, Kassner P, Cutler G	2022	PLOS Pathogens	Oncology	ISH/FISH	HALO
AAV9/MFSD8 gene therapy is effective in preclinical models of neuronal ceroid lipofuscinosis type 7 disease	Chen X, Dong T, Hu Y, Shaffo F, Belur N, Mazzulli J, Gray S	2022	The Journal of Clinical Investigation	Neuroscience	Area Quantification, ISH/FISH	HALO
Transcription factor Mesenchyme Homeobox Protein 2 (MEOX2) modulates nociceptor function	Kokotovic T, Lenartowicz E, Langeslag M, Ciotu C, Fell C, Scaramuzza A, Fischer M, Kress M, Penninger J, Nagy V	2022	The FEBS Journal	Neruoscience	Multiplex IHC	HALO
Collaborative workflow between pathologists and deep learning for evaluation of tumor cellularity in lung adenocarcinoma	Sakamoto T, Furukawa T, Pham H, Kuroda K, Tabata K, Kshima Y, Okoshi E, Morimoti S, Bychkov A, Fukuoka J	2022	bioRxiv	Oncology	Cytonuclear, Multiplex IHC	HALO AI
Switching to Regular Diet Partially Resolves Liver Fibrosis Induced by High-Fat, High-Cholesterol Diet in Mice	Farooq M, Hameed H, Dimanchi-Boitrel M, Piquet-Pellorce C, Samson M, Le Seyec J	2022	Nutrients	Metabolism	Area Quantification	HALO
T cell-mediated anti-tumor immunity cooperatively induced by TGF?R1 antagonism and gemcitabine counteracts reformation of the stromal barrier in pancreatic cancer	Li D, Schaub N, Guerin T, Bapiro T, Richards F, Chen V, Talsania K, Kumar P, Gilbert D, Scholmer J, Kim S, Sorber R, Teper Y, Bautista W, Palena C, Ock C, Jodrell D, Pate N, Mehta M, Zhao Y, Kozlov S, Rudloff U	2021	Molecular Cancer Therapeutics	Immuno-oncology	Highplex FL	HALO
Genome Sequence and Experimental Infection of Calves with Bovine Gammaherpesvirus 4 (BoHV-4)	Bauermann F, Falkenberg S, Martins M, Dassanayake R, Neill J, Ridpath J, Silveira S, Palmer M, Buysse A, Mohr A, Flores E, Diel D	2022	Research Square	Infectious Disease, Other	ISH/FISH	HALO
New Fully Automated Preparation of High Apparent Molar Activity 68Ga-FAPI-46 on a Trasis AiO Platform	Da Pieve C, Braga M, Turton D, Valla F, Cakmak P, Plate K, Kramer-Marek G	2022	Molecules	Other	Cytonuclear, Highplex FL	HALO
Retrospective analysis of the efficacy of adjuvant cytokine-induced killer cell immunotherapy combined with chemotherapy in colorectal cancer patients after surgery	Li X, Zhou H, Huang W, Wang X, Meng M, Hou Z, Liao L, Tang W, Xie Y, Wang R, Yu H, Wang L, Zhu H, Wang W, Tan J, Li R	2022	Clinical & Translational Immunology	Oncology	Cytonuclear, Highplex FL	HALO
Fasting improves therapeutic response in hepatocellular carcinoma through p53-dependent metabolic synergism	Krstic J, Reinisch I, Schindlmaier K, Galhuber M, Riahi Z, Berger N, Kupper N, Moyschewitz E, Auer M, Michenthaler H, Nossing C, Repaoli M, Ramadani-Muja J, Usluer S, Stryeck S, Pichler M, Rinner B, Deutsch A, Reinisch A, Madl T, Chiozzi R, Heck A, Huch M, Malli R, Prokesch	2022	Science Advances	Oncology	Classifier	HALO
GPNMB expression identifies TSC1/2/mTOR-associated and MiT family translocation-driven renal neoplasms	Salles D, Asrani K, Woo J, Vidotto T, Liu H, Vidal I, Matoso A, Netto G, Argani P, Lotan T	2022	The Journal of Pathology	Oncology	Membrane	HALO
High-dose rifampin improves bactericidal activity without increased intracerebral inflammation in animal models of tuberculous meningitis	Ruiz-Bedoya C, Mota F, Tucker E, Mahmud F, Reyes-Mantilla M, Erice C, Bahr M, Flavahan K, De Jesus P, Kim J, Foss C, Peloquin C, Hammound D, Ordonez A, Pardo C, Jain S	2022	The Journal of Clinical Investigation	Infectious Disease	Area Quantification	HALO
Evaluation of a PEGylated Fibroblast Growth Factor 21 Variant Using Novel Preclinical Magnetic Resonance Imaging and Magnetic Resonance Elastography in a Mouse Model of Nonalcoholic Steatohepatitis	Tang H, Li J, Zinker B, Boehm S, Mauer A, Rex-Rabe S, Glaser K, Fronheiser M, Bradstreet T, Nakao Y, Petrone T, Pena A, Villano M, Chow P, Malhi H, Charles E, Hayes W, Ehman R, Du S, Yin M	2022	Journal of Magnetic Resonance Imaging	Metabolism	Vacuole	HALO
Therapeutic treatment with the anti-inflammatory drug candidate MW151 may partially reduce memory impairment and normalizes hippocampal metabolic markers in a mouse model of comorbid amyloid and vascular pathology	Braun D, Powell D, McLouth C, Roy S, Watterson D, Van Eldik	2022	PLOS One	Neruoscience	Classifier, Area Quantification	HALO
African-Ancestry Associated Gene Expression Signatures and Pathways in Triple Negative Breast Cancer, a Comparison across Women of African Descent	Martini R, Delpe P, Chu T, Arora K, Lord B, Verma A, Chen Y, Gebregzabher, Oppong J, Adjei E, Jibril A, Awuah B, Bekele M, Abebe E, Kyei I, Aitpillah F, Adinku M, Ankomah K, Osei-Bonsu E, Chitale D, Bensenhaver J, Nathanson S, Jackson L, Jiagge E, Petersen L, Proctor E, Gyan K, Gibbs L, Monojlovic Z, Kittles R, White J, Yates C, Manne U, Gardner K, Mongan N, Cheng E, Ginter P, Hoda S, Elemento O, Robine N, Sboner A, Carpten J, Newman L, Davis M	2022	medRxiv	Oncology	Multiplex IHC, Serial Section	HALO
A selective and orally bioavailable VHL-recruiting PROTAC achieves SMARCA2 degradation in vivo	Kofink C, Trainor N, Mair B, Wrhrle S, Wurm M, Mischerikow N, Bader G, Rumpel K, Gerstberger T, Cui Y, Greb P, Garavel G, Scharnweber M, Fuchs J, Gremel G, Chette P, Hopf S, Budano N, Rinnenthal J, Gmaschitz G, Diers E, McLennan R, Roy M, Whitworth C, Vetma V, Mayer M, Koegl M, Ciulli A, Weinstabl H, Farnaby W	2022	Biological and Medicinal Chemistry		Classifier, Cytonuclear, Multiplex IHC	HALO
Obesity due to Steroid Receptor Coactivator-1 deficiency is associated with endocrine and metabolic abnormalities	Cacciottolo T, Henning E, Keogh J, Lassen P, Lawler K, Bounds R, Ahmed R, Perdikari A, Mendes de Oliverira E, Smith M, Godfrey E, Johnson E, Hodson L, Clement K, van der Klaauw A, Farooqi I	2022	The Journal of Clinical Endocrinology & Metabolism	Metabolism	Vacuole	HALO
Intratumoural spatial distribution of S100B?+?folliculostellate cells is associated with proliferation and expression of FSH and ER? in gonadotroph tumours	Ilie M, Vasiljevic A, Chanal M, Gadot N, Chinezu L, Jouanneau E, Hennino A, Raverot G, Bertolino P	2022	Acta Neuropathologica Communications	Oncology	Cytonuclear, Spatial Analysis	HALO
High-Field Asymmetric Waveform Ion Mobility Spectrometry and Parallel Reaction Monitoring Increases Sensitivity for Clinical Biomarker Quantitation from FormalinFixed, Paraffin-Embedded Tumor Biopsies	Sweet S, Chain D, Yu W, Martin P, Rebelatto M, Chambers A, Cecchi F, Kim Y	2022	bioRxiv	Other		HALO AI
Glioblastoma exosomes influence glial cell hyaluronic acid deposition to promote invasiveness<	Koessinger D, Novo D, Koessinger A, Zerbst D, Moore M, Mitchell L, Neilson M, Stevenson K, Chalmers A, Birch J, Norman J	2022	bioRxiv		Cytonuclear	HALO
The oral drug nitazoxanide restricts SARS-CoV-2 infection and attenuates disease pathogenesis in Syrian hamsters	Miorin L, Mire C, Ranjbar S, Hume A, Huang J, Crossland N, White K, Laporte M, Kehrer T, Haridas V, Moreno E, Nambu A, Jangra S, Cupic A, Dejosez M, Abo K, Tseng A, Werder R, Rathnasinghe R, Mutetwa T, Ramos I, Sainz de Aja J, Garcia de Alba Rivas C, Schotsaert M, Corley R, Falvo J, Fernandez-Sesma A, Kim C, Rossingnol J, Wilson A, Zwaka T, Kotton D, Muhlberger E, Garcia-Sastre A, Goldfeld A	2022	bioRxiv	Infectious Disease	Area Quantification	HALO
Pathogenesis of follicular thymic hyperplasia associated with rheumatoid arthritis	Ohe R, Yang S, Yamashita D, Ichikawa C, Saito A, Kabasawa T, Utsunomiya A, Aung N, Urano Y, Kitaoka T, Suzuki K, Takahara D, Sasaki A, Takakubo Y, Takagi M, Yamakawa M, Futakuchi M	2022	Pathology International	Other	Cytonuclear, Multiplex IHC	HALO
Pancreas resident macrophage-induced fibrosis has divergent roles in pancreas inflammatory injury and PDAC	Baer J, Zuo C, Kang L, Alarcon de la Lastra A, Bocherding N, Knolhoff B, Bogner S, Zhu Y, Lewis M, Zhang N, Kim K, Fields R, Mills J, Ding L, Randolph G, DeNardo D	2022	bioRxiv	Fibrosis	Classifier, Area Quantification, Cytonuclear, Multiplex IHC, Highplex FL, Figure Maker	HALO
Nuclear expression of pSTAT3Tyr705 and pSTAT3Ser727 in the stromal compartment of localized hormone-naïve prostate cancer	Marginean F, Hellsten R, Krzyanowska A, Bjartell A	2022	Pathology - Research and Practice	Oncology	Cytonuclear, Multiplex IHC, TMA	HALO
Extracellular vesicles released after cranial radiation: An insight into an early mechanism of brain injury	Sukati S, Ho J, Chaiswing L, Sompol P, Pandit H, Wei W, Izumi T, Chen Q, Weiss H, Noel T, Bondada S, Butterfield D, St. Cair D	2022	Brain Research	Neuroscience	Area Quantification	HALO
An Fc-inert PD-L1×4-1BB bispecific antibody mediates potent anti-tumor immunity in mice by combining checkpoint inhibition and conditional 4-1BB co-stimulation	Muik A, Altintas I, Gieseke F, Schoedel K, Burm S, Toker A, Salcedo T, Verzijl, Eisel D, Grunwitz C, Kranz L, Vormehr M, Satijn D, Diken M, Kreiter S, Sasser K, Ahmadi T, Tureci O, Breij E, Jure-Kunkel M, Sahin U	2022	OncoImmunology	Immuno-oncology	Area Quantification, Immune, Multiplex IHC	HALO
Eradicating tumor in a recurrent cervical cancer patient with autologous tumorinfiltrating lymphocytes and a modified lymphodepleting regimen	Guo J, Luo N, Ai G, Yang W, Zhu J, Li C, Chen R, Zhang C, Liu S, Jin H, Cheng Z	2022	Journal for ImmunoTherapy of Cancer	Immuno-oncology
e The Association of Cholesterol Uptake and Synthesis with Histology and Genotype in Cortisol-Producing Adenoma (CPA)	Motomura N, Yamazaki Y, Koga D, Harashima S, Gao X, Tezuka Y, Omata K, Ono Y, Morimoto R, Satoh F, Nakamura Y, Kwon G, Choi M, Ito A, Sasano H	2022	International Journal of Molecular Sciences		Area Quantification, Cytonuclear, Membrane	HALO
IgA-dominated humoral immune responses govern patients' outcome in endometrial cancer	Mandal G, Biswas S, Anadon C, Yu X, Gatenbee C, Prabhakaran S, Payne K, Chaurio R, Martin A, Innamarato P, Moran C, Powers J, Harro C, Mine J, Sprenger K, Rigolizzo K, Wang X, Curiel T, Rodriguez P, Anderson A, Saglam O, Conejo-Garcia J	2021	Cancer Research	Immuno-oncology	Classifier, Cytonuclear, Highplex FL	HALO
Tertiary lymphoid structures critical for prognosis in endometrial cancer patients - a TransPORTEC study	Horeweg N, Workel, H, Loiero D, Church D, Vermij L, Léon-Castillo A, Krog R, de Boer S, Nout R, Powel M, Mileshkin L, MacKay H, Leary A, Singh N, Jürgenliemk-Schulz I, Creutzberg C, Koelzer V, Nijman H, Bosse T, Bruyn M	2022	Nature Communications	Oncology	Cytonuclear, Multiplex IHC, TMA	HALO, HALO AI
Genomic and single-cell landscape reveals novel drivers and therapeutic vulnerabilities of transformed cutaneous T-cell lymphoma	Song X, Chang S, Seminario-Vidal L, de Mingo Pulido A, Tordesillas L, Song X, Reed R, Harkins A, Whiddon S, Nguyen J, Segura C, Zhang C, Yoder S, Sayegh Z, Zhao Y, Messina J, Harro C, Zhang X, Conejo-Garcia J, Berglund A, Sokol L, Zhang J, Rodriguez P, Mule J, Futreal A, Tsai K, Chen P	2022	Cancer Discovery	Oncology	Cytonuclear, Highplex FL, TMA	HALO
Collagen-VI expression is negatively mechanosensitive in pancreatic cancer cells and supports the metastatic niche	Papalazarou V, Drew J, Juin A, Spence H, Nixon C, Salmeron-Sanchez M, Machesky L	2022	bioRxiv	Oncology	Area Quantification, Figure Maker	HALO
An immunoPET probe to SARS-CoV-2 reveals early infection of the male genital tract in rhesus macaques	Madden P, Thomas Y, Blair R, Samer S, Doyle M, Midkiff C, Becker M, Arif M, McRaven M, Simons L, Carias A, Martinelli E, Lorenzo-Redondo R, Hultquist J, Villinger F, Veazey R, Hope T	2022	bioRxiv	Infectious Disease		HALO
Transcriptional and DNA Methylation Signatures of Subcutaneous Adipose Tissue and Adipose-Derived Stem Cells in PCOS Women	Divoux A, Erdos E, Whytock K, Osborne T, Smith S	2022	Cells		Area Quantification	HALO
Tumor immune cell clustering and its association with survival in African American women with ovarian cancer	Wilson C, Soupir A, Thapa R, Creed J, Nguyen J, Segura C, Gerke T, Schildkraut J, Peres L, Fridley B	2022	PLOS Computational Biology		Cytonuclear, Highplex FL	HALO
Inhibition of CK2 mitigates Alzheimers tau pathology by preventing NR2B synaptic mislocalization	Marshall C, McBride J, Changolkar L, Riddle D, Trojanowski J, Lee V M-Y	2022	Acta Neuropathologica Communications		Area Quantification	HALO
Immunologic Gene Signature Analysis Correlates Myeloid Cells and M2 Macrophages with Time to Trabectedin Failure in Sarcoma Patients	Schroder B, Zhang Y, Smythe K, Desai P, Thomas A, Viveiros P, Alexiev B, Obeidin F, Chen E, Cranmer L, Wagner M, Jones R, Campbell J, Pierce R, He Q, Pollack S	2022	Cancers	Oncology	Cytonuclear, Highplex FL	HALO
Fatal Neurodissemination and SARS-CoV-2 Tropism in K18-hACE2 Mice Is Only Partially Dependent on hACE2 Expression	Carossino M, Kenney D, O'Connell A, Montarnaro P, Tseng A, Gertje H, Grosz K, Ericsson M, Huber B, Kurnick S, Subramaniam S, Kirkland T, Walker J, Francis K, Klose A, Paragas N, Bosmann M, Saeed M, Balasuriya U, Douam F, Crossland N	2022	Viruses	Infectious Disease	Classifier, Area Quantification, Highplex FL	HALO
Multi-modal molecular imaging maps the correlation between tumor microenvironments and nanomedicine distribution	Strittmatter N, Moss J, Race A, Sutton D, Canales J, Ling S, Wong E, Wilson J, Smith A, Howes C, Bunch J, Barry S, Goodwin R, Ashford M	2022	Theranostics	Immuno-oncology	Highplex FL	HALO, HALO AI
An anti-PD-1GITR-L bispecific agonist induces GITR clustering-mediated T cell activation for cancer immunotherapy	Chan S, Belmar N, Ho S, Rogers B, Stickler M, Graham M, Lee E, Tran N, Zhang D, Gupta P, Sho M, MacDonough T, Woolley A, Kim H, Zhang H, Liu W, Zheng P, Dezso Z, Halliwill K, Ceccarelli M, Rhodes S, Thakur A, Forsyth C, Xiong M, Tan S, Iyer R, Lake M, Digiammarino E, Zhou L, Bigelow L, Longenecker K, Judge R, Liu C, Trumble M, Remis J, Fox M, Cairns B, Akamatsu Y, Hollenbaugh D, Farding F, Alvarez H	2022	Nature Cancer	Immuno-oncology	Area Quantification, Cytonuclear, Highplex FL	HALO
ZEB1 transcription factor promotes immune escape in melanoma	Plaschka M, Benboubker V, Grimont M, Berthet J, Tonon L, Lopez J, Le-Bouar M, Balme B, Tondeau G, de la Fouchardiere A, Larue L, Puisieux A, Grinberg-Bleyer Y, Bendriss-Vermare N, Dubois B, Caux C, Dalle S, Caramel J	2022	Journal for ImmunoTherapy of Cancer	Immuno-oncology	Cytonuclear, Multiplex IHC, Highplex FL	HALO
Malfunction of airway basal stem cells plays a crucial role in pathophysiology of tracheobronchopathia osteoplastica	Hong Y, Shan S, Gu Y, Huang H, Zhang Q, Han Y, Dong Y, Liu Z, Huang M, Ren T	2022	Nature Communications	Other	Cytonuclear, Multiplex IHC	HALO
Deep-Learning-Aided Detection of Mycobacteria in Pathology Specimens Increases the Sensitivity in Early Diagnosis of Pulmonary Tuberculosis Compared with Bacteriology Tests	Zaizen Y, Kanhori Y, Ishijima S, Kitamura Y, Yoon H, Ozasa M, Mukae H, Bychkov A, Hoshino T, Fukuoka J	2022	Diagnostics	Infectious Disease		HALO, HALO AI
Acetyl-CoA-carboxylase 1 (ACC1) plays a critical role in glucagon secretion	Veprik A, Denwood G, Liu D, Bakar R, Morfin V, McHugh K, Tebeka N, Vetterli L, Yonova-Doing E, Gribble F, Reimann F, Hoehn K, Hemsley P, Ahnfelt-Ronne J, Rorsman P, Zhang Q, Wet H, Cantley J	2022	Communications Biology	Metabolism	Cytonuclear, Highplex FL	HALO
Sulforaphane exhibits antiviral activity against pandemic SARS-CoV-2 and seasonal HCoV-OC43 coronaviruses in vitro and in mice	Ordonez A, Bullen C, Villabona-Rueda A, Thompson E, Turner M, Merino V, Yan Y, Kim J, Davis S, Komm O, Powell J, D'Alessio F, Yolken R, Jain S, Jones-Brando L	2022	Communications Biology	Infectious Disease	Area Quantification, Multiplex IHC	HALO
Extracellular matrix proteins regulate NK cell function in peripheral tissues	Bunting M, Vyas M, Requesens M, Langenbucher A, Schiferle E, Manguso R, Lawrence M, Demehri S	2022	Science Advances	Dermatology	Cytonuclear, Highplex FL	HALO
Multiplex Immunohistochemical Phenotyping of T Cells in Primary Prostate Cancer	Ozbek B, Ertunc O, Erickson A, Vidal I, Gomes-Alexandre C, Guner G, Hicks J, Jones T, Taube J, Sfanos K, Yegnasubramanian S, DeMarzo A	2022	The Prostate	Immuno-oncology	Classifier, Cytonuclear, Highplex FL, Serial Section, Registration, Figure Maker, TMA	HALO
Interspatial Distribution of Tumor and Immune Cells in Correlation with PD-L1 in Molecular Subtypes of Gastric Cancers	Dislich B, Mertz K, Gloor B, Langer R	2022	Cancers	Immuno-oncology	Multiplex IHC, Spatial Analysis, Figure Maker	HALO
Adrenal tropism of SARS-CoV-2 and adrenal findings in a post-mortem case series of patients with severe fatal COVID-19	Paul T, Ledderose S, Bartsch H, Sun N, Soliman S, Markl B, Ruf V, Herms J, Stern M, Keppler O, Delbridge C, Muller S, Piontek G, Kimoto Y, Schreiber F, Williams T, Neumann J, Knosel T, Schulz H, Spallek R, Graw M, Kirchner T, Walch A, Rudelius M	2022	Nature Communications	Infectious Disease	Cytonuclear, Highplex FL	HALO
Soluble TREM2 induces microglia dysfunction and brain damage while cleavage-reduced TREM2 shows sustained microglia activation with enhanced remyelination in the cuprizone model	Beckmann N, Neuhaus A, Zurbruegg S, Joller S, Feuerbach D, Doelemeyer A, Schweizer T, Rudin S, Nuemann U, Berth R, Frieauff W, Gasparani F, Shimshek D	2022	Research Square	Neuroscience		HALO
Genome-wide mapping of oncogenic pathways and genetic modifiers of chemotherapy using a high-risk hepatoblastoma genetic model	Fang J, Singh S, Natarajan S, Tillman H, Abuzaid A, Durbin A, Lee H, Wu Q, Steele J, Connelly J, Cheng C, Jin H, Chen W, Fan Y, Pruett-Miller S, Rehg J, Emmons J, Cairo S, Wang R, Glazer E, Murphy A, Chen T, Davidoff A, Easton J, Chen X, Yang J	2022	Research Square	Oncology	Classifier	HALO
Spatially mapping the immune landscape of melanoma using imaging mass cytometry	Moldoveanu D, Ramsay L, Lajoie M, Anderson-Trocme L, Lingrand M, Berry D, Perus L, Wei Y, Moraes C, Alkallas R, Rajkumar S, Zuo D, Dankner M, Xu E, Bertos N, Najafabadi H, Gravel S, Costantino S, Richer M, Lund A, Del Rincon S, Spatz A, Miller W, Jamal R, Lapointe R, Mes-Masson A, Turcotte S, Petrecca K, Dumitra S, Meguerditchian A, Richardson K, Tremblay F, Wang B, Chergui M, Guiot M, Watters K, Stagg J, Quail D, Mihalcioiu C, Meterissian S, Watson I	2022	Science Immunology	Oncology	Highplex FL	HALO
Improved cognitive impairments by silencing DMP1 via enhancing the proliferation of neural progenitor cell in Alzheimer-like mice	Zhao H, Wei J, Du Y, Chen P, Liu X, Liu H	2022	Aging Cell	Neuroscience	Cytonuclear, Highplex FL	HALO
A tumor suppressor role for EZH2 in diffuse midline glioma pathogenesis	Dhar S, Gadd S, Patel P, Vaynshteyn Jm Raju G, Hashizume R, Brat D, Becher O	2022	Acta Neuropathologica Communications	Neuroscience		HALO
Loss of ubiquitin-specific peptidase 18 destabilizes 14-3-3? protein and represses lung cancer metastasis	Chen Z, Zheng L, Chen Y, Liu X, Kawakami M, Mustachi L, Roszik J, Ferry-Galow K, Parchment R, Liu X, Andresson T, Duncan G, Kurie J, Rodriguez-Canales J, Liu X, Dmitrovsky E	2022	Cancer Biology & Therapy	Oncology	Classifier, Cytonuclear	HALO
Ad26.COV2.S prevents upregulation of SARS-CoV-2 induced pathways of inflammation and thrombosis in hamsters and rhesus macaques	Aid M, Vidal S, Piedra-Mora C, Ducat S, Chan C, Bondoc S, Colarusso A, Starke C, Nekorchuk M, Busman-Sahay K, Estes J, Martinot A, Barouch D	2022	PLOS Pathogens	Infectious Disease	Area Quantification, Multiplex IHC	HALO, HALO AI
Clinical tissue biomarker digital image analysis: A review of current applications	Li Z, Bui M, Pantanowitz L	2022	Human Pathology Reports	Review		HALO
Peritumoral TIGIT+CD20+ B cell infiltration indicates poor prognosis but favorable adjuvant chemotherapeutic response in gastric cancer	Liu H, Wu J, Xu X, Wang H, Zhang C, Yin S, He Y	2022	International Immunopharmacology	Oncology	Cytonuclear, Spatial Analysis, Highplex FL	HALO
Subpopulations of cancer-associated fibroblasts link the prognosis and metabolic features of pancreatic ductal adenocarcinoma	Hu B, Wu C, Mao H, Gu H, Dong H, Yan J, Qi Z, Yuan L, Dong Q, Long J	2022	Annals of Translational Medicine	Oncology	Cytonuclear, Highplex FL	HALO
Vertical transmission of attaching and invasive E. coli from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life	Brand M, Proctor A, Hostetter J, Zhou N, Friedberg I, Jergens A, Phillips G, Wannemuehler M	2022	PLOS ONE	Other	ISH/FISH	HALO
Advanced Age and Neurotrauma Diminish Glutathione and Impair Antioxidant Defense after Spinal Cord Injury	Stewart A, Glaser E, Mott C, Bailey W, Sullivan P, Patel S, Gensel J	2022	Journal of Neurotrauma	Neuroscience	Axon	HALO
Humanized mice reveal a macrophage-enriched gene signature defining human lung tissue protection during SARS-CoV-2 infection	Kenney D, O'Connell A, Turcinovic J, Montanaro P, Hekman R, Tamura T, Berneshawi A, Cafiero T, Abdullatif S, Blum B, Goldstein S, Heller B, Gertje H, Bullitt E, Trachtenberg A, Chavez E, Nono E, Morrison C, Tseng A, Sheikh A, Kurnick S, Grosz K, Bosmann M, Ericsson M, Huber B, Saeed M, Balazs A, Francis K, Klose A, Paragas N, Campbell J, Connor J, Emili A, Crossland N, Ploss A, Douam F	2022	Cell Reports	Infectious Disease	Area Quantification, Highplex FL	HALO
A Deep Learning Convolutional Neural Network Can Differentiate Between Helicobacter Pylori Gastritis and Autoimmune Gastritis With Results Comparable to Gastrointestinal Pathologists	Franklin M, Schultz F, Tafoya M, Kerwin A, Broehm C, Fischer E, Gullapalli R, Clark D, Hanson J, Martin D	2022	Archives of Pathology & Laboratory Medicine	Oncology, Gastroenterology		HALO, HALO AI
Interface astrogliosis in contact sport head impacts and military blast exposure	Babcock K, Abdolmohammadi B, Kiernan P, Mahar I, Cherry J, Alvarez V, Goldstein L, Stein T, McKee, Huber B	2022	Acta Neuropathologica Communications	Neruoscience	Area Quantification	HALO
The GBA1 D409V mutation exacerbates synuclein pathology to differing extents in two alpha-synuclein models	Polinski N, Martinez T, Ramboz S, Sasner M, Herberth M, Switzer R, Ahmad S, Pelligrino L, Clark S, Marcus J, Smith S, Dave K, Frasier M	2022	Disease Models & Mechanisms	Neuroscience	Object Colocalization	HALO
Organelle resolved proteomics reveals new chordoma cell surface markers required for proliferation and association with outcome	Khan S, Zuccato J, Ignatchenko V, Singh O, Govindarajan M, Waas M, Gao A, Zadeh G, Kislinger T	2022	Research Square	Oncology	Cytonuclear, Multiplex IHC	HALO
Intraoperative abobotulinumtoxinA alleviates pain after surgery and improves general wellness in a translational animal model	Cornet S, Carre D, Limana L, Castel D, Meilin S, Horn R, Pons L, Evans S, Lezmi S, Kalinichev M	2022	Research Square	Other	Area Quantification, Object Colocalization	HALO
Immune cell subsets in interface cutaneous immune-related adverse events (cirAEs) associated with anti-PD-1 therapy resemble accute graft vs host disease more than licen planus	Cruz G, Kaunitz G, Stein J, Sander I, Hollmann T, Cottrell T, Taube J, Sunshine J	2022	Journal of Cutaneous Pathology	Immunology	Cytonuclear, Multiplex IHC	HALO
Therapeutic impact of BET inhibitor BI 894999 treatment: backtranslation from the clinic	Tontsch-Grunt U, Traexler P, Baum A, Musa H, Marzin K, Wang S, Trapani F, Engelhardt H, Solca F	2022	British Journal of Cancer	Oncology	Classifier, Cytonuclear, Multiplex IHC	HALO
Immune and epithelial determinants of age-related risk and alveolar injury in fatal COVID-19	Chait M, Yilmaz M, Shakil S, Ku A, Dogra P, Connors T, Szabo P, Gray J, Wells S, Kubota M, Matsumoto R, Poon M, Snyder M, Baldwin M, Sims P, Saqi A, Farber D, Weisberg S	2022	JCI Insight	Infectious Disease	Multiplex IHC	HALO
Neuropathology and virus in brain of SARS-CoV-2 infected non-human primates	Rutkai I, Mayer M, Hellmers L, Ning B, Huang Z, Monjure C, Coyne C, Silvestri R, Golden N, Hensley K, Chandler K, Lehmicke G, Bix G, Maness N, Russell-Lodrigue K, Hu T, Roy C, Blair R, Bohm R, Doyle-Meyers L, Rappaport J, Fisher T	2022	Nature Communications	Infectious Disease	Area Quantification	HALO
Increased apoptotic sensitivity of glioblastoma enables therapeutic targeting by BH3-mimetics	Koessinger A, Cloix C, Koessinger D, Heiland D, Bock F, Strathdee K, Kinch K, Martinez-Escardo L, Paul N, Nixon C, Malviya G, Jackson M, Campbell K, Stevenson K, Davis S, Elmasry Y, Ahmed A, O'Prey J, Ichim G, Schnell O, Stewart W, Blyth K, Ryan K, Chalmers A, Norman J, Tait S	2022	Cell Death & Differentiation	Oncology		HALO
SPOP promotes cervical cancer progress by inducing PD-1 move away from PD-L1 in spatial localization	Wu J, Wu Y, Guo Q, Chen S, Wang S, Zhu J, Wu X, Ju X	2022	Research Square	Oncology	Cytonuclear, Spatial Analysis, Highplex FL, TMA	HALO
Hyperpolarized 13C-Pyruvate Metabolism as a Surrogate for Tumor Grade and Poor Outcome in Renal Cell CarcinomaA Proof of Principle Study	Ursprung S, Woitek R, McLean M, Priest A, Crispin-Ortuzar M, Brodie C, Gill A, Gehrung M, Beer L, Riddick A, Field-Rayner J, Grist J, Deen S, Riemer F, Kaggie J, Zaccagna F, Duarte J, Locke M, Frary A, Aho T, Armitage J, Casey R, Mendichovszky I, Welsh S, Barrett T, Graves M, Eisen T, Mitchell T, Warren A, Brindle K, Sala E, Stewart G, Gallagher F	2022	Cancers	Oncology	Area Quantification, Cytonuclear, Multiplex IHC	HALO
A novel soluble epoxide hydrolase vaccine protects murine cardiac muscle against myocardial infarction	Kitsuka T, Shiraki A, Oyama J, Nakagami H, Tanaka A, Node K	2022	Scientific Reports	Other	Figure Maker	HALO, HALO AI
C57BL/6J Mice Are Not Suitable for Modeling Severe SARS-CoV-2 Beta and Gamma Variant Infection	Currey J, Rabito F, Maness N, Blair R, Rappaport J, Qin X, Kolls J, Srivastava A	2022	Viruses	Infectious Disease	Cytonuclear, Multiplex IHC	HALO
Type I interferon regulates proteolysis by macrophages to prevent immunopathology following viral infection	Lee A, Feng E, Chew M, Balint E, Poznanski S, Giles E, Zhang A, Marzok A, Revill S, Vahedi F, Dubey A, Ayaub E, Jimenez-Saiz R, McGrath J, Ritchie T, Jordana M, Jonigk D, Ackermann M, Ask K, Miller M, Richards C, Ashkar A	2022	PLOS Pathogens	Infectious Disease	Area Quantification, Multiplex IHC, TMA	HALO
Dietary Pharmacological Zinc and Copper Enhances Voluntary Feed Intake of Nursery Pigs	DeMille C, Burrough E, Kerr B, Schweer W, Gabler N	2022	Frontiers in Animal Science	Other	Cytonuclear, Multiplex IHC	HALO
Epicardium-derived cells organize through tight junctions to replenish cardiac muscle in salamanders	Eroglu E, Yen C, Witman N, Elewa A, Araus A, Wang H, Szattler T, Umeano C, Sohlmer J, Goedel A, Simon A, Chien K	2022	Nature Cell Biology	Myology	ISH/FISH, ISH-IHC/FISH-IF	HALO
Sotatercept analog suppresses infammation to reverse experimental pulmonary arterial hypertension	Joshi S, Liu J, Bloom T, Atabay E, Kuo T, Lee M, Belecheva E, Spaits M, Grenha R, Maguire M, Frost J, Wang K, Briscoe S, Alaxander M, Herrin B, Castonguay R, Pearsall R, Andre P, Yu P, Kumar R, Li G	2022	Scientific Reports	Other	Layer Thickness	HALO
Spatial transcriptome of a germinal center plasmablastic burst hints at MYD88/CD79B mutants-enriched diffuse large B-cell lymphomas	L'Imperio V, Morello G, Vegliante M, Cancila V, Bertolazzi G, Mazzara S, Belmonte B, Mangogna A, Balzarini P, Corral L, Lopez G, Di Napoli A, Facchetti F, Pagni F, Tripodo C	2022	European Journal of Immunology	Oncology	Cytonuclear, Multiplex IHC	HALO
Single-cell profling of human dura and meningioma reveals cellular meningeal landscape and insights into meningioma immune response	Wang A, Bowman-Kirigin J, Desai R, Kang L, Patel P, Patel B, Khan S, Bender D, Marlin M, Liu J, Osbun J, Leuthardt E, Chicoine M, Dacey Jr R, Zipfel G, Kim A, DeNardo D, Petti A, Dunn G	2022	Genome Medicine	Neuroscience	Area Quantification	HALO
Multi-scale integrative analyses identify THBS2+ cancer-associated fibroblasts as a key orchestrator promoting aggressiveness in early-stage lung adenocarcinoma	Yang H, Sun B, Fan L, Ma W, Xu K, Hall S, Wang Z, Schmid R, Peng R, Marti T, Gao W, Xu J, Yang W, Yao F	2022	Theranostics	Oncology	Cytonuclear, Multiplex IHC	HALO
Automated Cancer Diagnostics via Analysis of Optical and Chemical Images by Deep and Shallow Learning	Isberg O, Giunchiglia V, McKenzie J, Takats Z, Jonasson J, Bodvarsdottir S, Thorsteinsdottir M, Xiang Y	2022	Metabolites	Oncology		HALO, HALO AI
Characterization and Validation of In Vitro and In Vivo Models to Investigate TNF-?-Induced Inflammation in Retinal Diseases	Weigelt C, Zippel N, Fuchs H, Rimpela A, Schonberger T, Stierstorfer B, Bakker R, Redemann N	2022	Translational Vision Science & Technology	Immunology, Other	Area Quantification, Layer Thickness	HALO
Pilot Trial of Arginine Deprivation Plus Nivolumab and Ipilimumab in Patients with Metastatic Uveal Melanoma	Kraehenbuehl L, Holland A, Armstrong E, O'Shea S, Mangarin L, Chekalil S, Johnston A, Bomalaski J, Erinjeri J, Barker C, Francis J, Wolchok J, Merghoub T, Shoushtari A	2022	Cancers	Oncology	Cytonuclear, Highplex FL	HALO
An in vivo accelerated developmental myelination model for testing promyelinating therapeutics	Lariosa-Willingham K, Leunoudakis D, Bragge T, Tolppanen L, Nurmi A, Flanagan M, Gibson J, Wilson D, Stratton J, Lehtimaki K, Miszczuk D	2022	BMC Neuroscience	Neuroscience	Area Quantification	HALO
Nitric oxide favours tumour-promoting inflammation through mitochondria-dependent and -independent actions on macrophages	Drehmer D, Luiz J, Hernandez C, Alves-Filho J, Hussell T, Townsend P, Moncada S	2022	Redox Biology	Oncology	Highplex FL	HALO
Maternal Western-Style Diet Impairs Bone Marrow Development and Drives a Hyperinflammatory Phenotype in Hematopoietic Stem and Progenitor Cells in Fetal Rhesus Macaques	Sureshchandra S, Chan C, Robino J, Parmelee L, Nash M, Wesolowski S, Pietras E, Friedman J, Takahashi D, Shen W, Hennebold J, Goldman D, Packwood W, Lindner J,Roberts C, Burwitz B, Messaoudi I, Varlamov O	2022	bioRxiv	Metabolism	Multiplex IHC	HALO
Preclinical evaluation of FAP?2286 for fbroblast activation protein targeted radionuclide imaging and therapy	Zboralski D, Hoehne A, Bredenbeck A, Schumann A, Nguyen M, Schneider E, Ungewiss J, Paschke M, Haase C, von Hacht J, Kwan T, Lin K, Lenore J, Harding T, Xiao J, Simmons A, Mohan A, Beindorff N, Reineke U, Smerling C, Osterkamp F	2022	European Journal of Nuclear Medicine and Molecular Imaging	Oncology	Cytonuclear, Multiplex IHC	HALO
Different types of reactions to E7386 among colorectal cancer patient?derived organoids and corresponding CAFs	Imai T, Naruse M, Ochiai M, Matsumoto K, Ikeda S, Kani M, Kato Y, Hirayama A, Sogo T, Hori Y, Yokoi A, Ochiai A	2022	Oncology Letters	Oncology	Area Quantification	HALO
Deep Learning Facilitates Distinguishing Histologic Subtypes of Pulmonary Neuroendocrine Tumors on Digital Whole-Slide Images	Ilie M, Benzaquen J, Tourniaire P, Heeke S, Ayache N, Delingette H, Long-Mira E, Lassalle S, Hamila M, Fayada J, Otto J, Cohen C, Gomez-Caro A, Berthet J, Marquette C, Hofman V, Bontoux C, Hofman P	2022	Cancers	Oncology		HALO, HALO AI
Prognostic Integrated Image-Based Immune and Molecular Profiling in Early-Stage Endometrial Cancer	Horeweg N, de Bruyn M, Nout R, Stelloo E, Kedzierska K, Leon-Castillo A, Plat A, Mertz K, Osse M, Jurgenliemk-Schulz I, Lutgens L, Jobsen J, van der Steen-Banasik E, Smit V, Creutzberg C, Bosse T, Nijman H, Koelzer V, Church D	2020	Cancer Immunology Research	Oncology	Cytonuclear, Multiplex IHC, TMA	HALO, HALO AI
Comparing Deep Learning and Immunohistochemistry in Determining the Site of Origin for Well-Differentiated Neuroendocrine Tumors	Redemann J, Schultz F, Martinez C, Harrell M, Clark D, Martin D, Hanson J	2020	Journal of Pathology Informatics	Oncology	Cytonuclear, TMA	HALO, HALO AI
Randomized Controlled Trial of the Gastrin/CCK2 Receptor Antagonist Netazepide in Patients with Barrett's Esophagus	Abrams J, Del Portillo A, Hills C, Compres G, Friedman R, Cheng B, Poneros J, Lightdale C, Del La Rue R, di Pietro M, Fitzgerald R, Sepulveda A, Wang T	2021	Cancer Prevention Research		Cytonuclear, Multiplex IHC	HALO, HALO AI
Myeloid cell-driven nonregenerative pulmonary scarring is conserved in multiple nonhuman primate species regardless of SARS-CoV-2 infection modality	Fears A, Beddingfield B, Chirichella N, Slisarenko N, Kileen S, Redmann R, Goff K, Spencer S, Picou B, Golden N, Bush D, Branco L, Boisen M, Gao H, Montefiori D, Blair R, Doyle-Meyers L, Russel-Lodrigue K, Maness N, Roy C	2021	bioRxiv		Area Quantification, Highplex FL	HALO, HALO AI
Independent Prognostic Value of Intratumoral Heterogeneity and Immune Response Features by Automated Digital Immunohistochemistry Analysis in Early Hormone Receptor-Positive Breast Carcinoma	Zilenaite D, Rasmusson A, Augulis R, Besuparis J, Laurinaviciene A, Plancoulaine B, Ostpenko V, Laurinavicius	2020	Frontiers in Oncology	Oncology	Multiplex IHC, Figure Maker	HALO, HALO AI
Tau isoforms are differentially expressed across the hippocampus in chronic traumatic encephalopathy and Alzheimers disease	Cherry J, Esnault C, Baucom Z, Tripodis Y, Huber B, Alvarez V, Stein T, Dickson D, McKee A	2021	Acta Neuropathologica Communications	Neuroscience		HALO, HALO AI
3UTR-directed, kinase proximal mRNA decay inhibits C/EBP? phosphorylation/activation to suppress senescence in tumor cells	Salotti J, Karim B, Misra S, Hu L, Basu S, Martin N, Luke B, Saylor K, Andresson T, Scheiblin D, Lockett S, Tessarollo L, Johnson P	2022	bioRxiv	Oncology	Classifier, Cytonuclear	HALO, HALO AI
CK2 signaling from TOLLIP-dependent perinuclear endosomes is an essential feature of KRAS mutant cancers	Basu S, Luke B, Karim B, Martin N, Lockett S, Das S, Andresson T, Saylor K, Kozlov S, Bassel L, Esposito D, Johnson P	2022	bioRxiv	Oncology	Area Quantification	HALO, HALO AI
Maternal obesity during pregnancy leads to adipose tissue ER stress in mice via miR-126-mediated reduction in Lunapark	de Almeida-Faria J, Duque-Guimares D, Ong T, Pantaleao L, Carpenter A, Loche E, Kusinki L, Ashmore T, Antrobus R, Bushell M, Fernandez-Twinn, Ozanne S	2021	Diabetologia	Metabolism		HALO, HALO AI
Integrated Analysis Of Immunotherapy Treated Clear Cell Renal Cell Carcinomas: An Exploratory Study	Sobottka B, Nienhold R, Nowak M, Hench J, Haeuptle P, Frank A, Sachs M, Kahraman A, Moch H, Koelzer V, Mertz K	2022	Journal of Immunotherapy	Immuno-oncology	Cytonuclear, Multiplex IHC, Figure Maker	HALO, HALO AI
Excessive immunosuppression by regulatory T cells antagonizes T cell response to schistosome infection in PD-1-deficient mice	Lu L, Li T, Feng X, Liu Z, Liu Y, Chao T, Gu Y, Huang R, Zhang F, He L, Zhou B, Kong E, Liu Z,	2022	PLOS Pathogens	Immunology, Other	Area Quantification	HALO
Orchestrating the Dermal/Epidermal Tissue Ratio during Wound Healing by Controlling the Moisture Content	Tuca A, de Mattos I, Funk M, Winter R, Palackic A, Groeber-Becker F, Kruse D, Kukla F, Lemarchand T, Kamolz L	2022	Biomedicines	Other	Classifier	HALO
Restoring Pro-healing/remodeling- associated M2a/c Macrophages using ON101 Accelerates Diabetic Wound Healing	Lin C, Chen C, Huang W, Chen Y, Chen S, Chou H, Hung C, Chen W, Lu C, Nian S, Chen S, Chang H, Chang V, Liu L, Kuo M, Chang S	2022	JID Innovations	Other	Area Quantification, Cytonuclear	HALO
CD4+ T helper 2 cells suppress breast cancer by inducing terminal differentiation	Boieri M, Malishkevich A, Guennoun R, Marchese E, Kroon S, Trerice K, Awad M, Park J, Iyer S, Kreuzer J, Haas W, Rivera M, Demehri S	2022	Journal of Experimental Medicine	Immuno-oncolgy	Cytonuclear, Highplex FL	HALO
A lncRNA signature associated with tumor immune heterogeneity predicts distant metastasis in locoregionally advanced nasopharyngeal carcinoma	Liang Y, Zhang Y, Tan X, Qiao H, Liu S, Tang L, Mao Y, Chen L, Li W, Zhou G, Zhao Y, Li J, Li Q, Huang S, Gong S, Zheng Z, Li Z, Sun Y, Jiang W, Ma J, Li Y, Liu N	2022	Nature Communications	Immuno-oncology	Classifier, Multiplex IHC, Registration	HALO
Ginkgo Biloba Extract Reduces Cardiac and Brain Inflammation in Rats Fed a HFD and Exposed to Chronic Mental Stress through NF-?B Inhibition	Zhang L, Li G, Tao S, Xia P, Chaudhry N, Kaura S, Stone S, Liu M	2022	Mediators of Inflammation	Immunology	Area Quantification	HALO
Prognostic image-based quantification of CD8CD103 T cell subsets in high-grade serous ovarian cancer patients	Paijens S, Vledder A, Loiero D, Duiker E, Bart J, Hendriks A, Jalving M, Workel H, Hollema H, Werner N, Plat A, Wisman G, Yigit R, Arts H, Kruse A, de Lange N, Koelzer V, Bruyn M, Nijman H	2021	OncoImmunology	Immuno-oncology	Cytonuclear, Multiplex IHC, TMA	HALO, HALO AI
Higher proportions of CD39+ tumorresident cytotoxic T cells predict recurrence-free survival in patients with stage III melanoma treated with adjuvant immunotherapy	Attrill G, Owen C, Ahmed T, Vergara I, Colebatch A, Conway J, Nahar K, Thompson J, da Silva I, Carlino M, Menzies A, Lo S, Palendira U, Scolyer R, Long G, Wilmott J	2022	Journal of Immuno Therapy of Cancer	Immuno-oncology	Cytonuclear, Spatial Analysis, Highplex FL	HALO
TGF?1 Induces Senescence and Attenuated VEGF Production in Retinal Pericytes	Avarmovic D, Archaimbault S, Kemble A, Gruener S, Lazendic M, Westenskow P	2022	Biomedicines	Other	ISH/FISH	HALO
Prenatal di-(2-ethylhexyl_ phthalate exposure induced myocardial cytotoxicity via the regulation of the NRG1-dependent ErbB2/ErbB4-PI3K/AKT signaling pathway in fetal mice	Yu D, Zhu D, Wang X, Li B, Li J, Lu P, Ji Y, Wang X	2022	Ecotoxicology and Environmental Safety	Other	Multiplex IHC	HALO
Satellite repeat RNA expression in epithelial ovarian cancer associates with a tumor immunosuppressive phenotype	Porter R, Sun S, Flores M, Berzolla E, You E, Phillips I, KC N, Desai N, Tai E, Szabolcs A, Lang E, Pankaj A, Raabe M, Thapar V, Xu K, Nieman L, Rabe D, Kolin D, Stover E, Pepin D, Stott S, Deshpande V, Liu J, Solovyov A, Matulonis U, Greenbaum B, Ting D	2022	The Journal of Clinical Investigation	Immuno-oncology	ISH/FISH, ISH-IHC/FISH-IF	HALO
Distinct Encoding of Reward and Aversion by Peptidergic BNST Inputs to the VTA	Soden M, Yee J, Cuevas B, Rastani A, Elum J, Zweifel L	2022	Frontiers in Neural Circuits	Neuroscience	ISH/FISH	HALO
ATG7 is a haploinsufficient repressor of tumor progression and promoter of metastasis	Long J, Kania E, McEwan D, Barthet V, Brucoli M, Ladds M, Nossing C, Ryan K	2022	Proceedings of the National Academy of Sciences	Oncology, Other	Area Quantification	HALO
Effects of Extracorporeal Shockwave Therapy on Functional Recovery and Circulating miR-375 and miR-382-5p after Subacute and Chronic Spinal Cord Contusion Injury in Rats	Ashmwe M, Posa K, Ruhrnossl A, Heinzel J, Heimel P, Mock M, Schadl B, Keibl C, Couillard-Despres S, Redl H, Mittermayr R, Hercher D	2022	Biomedicines	Neuroscience, Other	Classifier, Multiplex IHC	HALO
Baseline and post-treatment biomarkers of resistance to anti-PD-1 therapy in acral and mucosal melanoma: an observational study	Shui I, Liu X, Zhao Q, Kim S, Sun Y, Yearley J, Choudhury T, Webber A, Krepler C, Cristescu R, Lee J	2022	Journal for ImmunoTherapy of Cancer	Immuno-oncology	Cytonuclear, Highplex FL	HALO
Spatial meta-transcriptomics reveal associations of intratumor bacteria burden with lung cancer cells showing a distinct oncogenic signature	Wong-Rolle A, Dong Q, Zhu Y, Divakar P, Hor J, Kedei N, Wong M, Tillo D, Conner E, Rajan A, Schrump D, Jim C, Germain R, Zhao C	2022	Journal for ImmunoTherapy of Cancer	Immuno-oncology	Cytonuclear, Multiplex IHC	HALO
SOX9+ malignant cells define a poor prognosis subtype of Glioma with tumor-associated macrophage recruitment	Yu S, Ma C, Wang H, Yu B, Luan Y, Xia Z	2022	Research Square	Immuno-oncology	Cytonuclear, Multiplex IHC	HALO
Exposure modality influences viral kinetics but not respiratory outcome of COVID-19 in multiple nonhuman primate species	Fears A, Beddingfield B, Chirichella N, Slisarenko N, Kileen S, Redmann R, Goff K, Spencer S, Picou B, Golden N, Midkiff C, Bush D, Branco L, Boisen M, Gao H, Montefiori D, Blair R, Doyle-Meyers L, Russel-Lodrigue K, Maness N, Roy C	2022	PLOS Pathogens	Infectious Disease	Highplex FL	HALO
The combination of gene hyperamplification and PD-L1 expression as a biomarker for the clinical benefit of tislelizumab in gastric/gastroesophageal junction adenocarcinoma	Lu Z, Yang S, Luo X, Shi Y, Lee J, Deva S, Liu T, Chao Y, Zhang Y, Huang R, Xu Y, Shen Z, Shen L	2022	Gastric Cancer	Immuno-oncology	Classifier, Multiplex IHC	HALO
Combined Blockade of GARP:TGF-?1 and PD-1 Increases Infiltration of T Cells and Density of Pericyte-Covered GARP+ Blood Vessels in Mouse MC38 Tumors	Bertrand C, Van Meerbeeck P, de Streel G, Vaherto-Bleeckx N, Benhaddi F, Rouaud L, Noel A, Coulie P, van Baren N, Lucas S	2022	Frontiers of Immunology	Immuno-oncology	Cytonuclear, Object Colocalization	HALO
gp96 Expression in Gliomas and Its Association with Tumor Malignancy and T Cell Infiltrating Level	Li C, Wang Y, Long L, Zhang P, Zhang Y, Ji N	2022	Hindawi Journal of Oncology	Immuno-oncology	Spatial Analysis, Highplex FL, Figure Maker	HALO
Multiplexed immunofluorescence analysis of CAFmarkers, EZH2 and FOXM1 in Gastric Tissue: Associations with Clinicopathological Parameters and Clinical Outcomes	Sun H, Wang X, Wang X, Tan C, Weng W, Zhang M, Ni S, Wang L, Huang D, Sheng W, Xu M	2022	Research Square	Oncology	Cytonuclear, Highplex FL	HALO
Cancer-associated fibroblasts require proline synthesis by PYCR1 for the deposition of pro-tumorigenic extracellular matrix	Kay E, Paterson K, Riero-Domingo C, Sumpton D, Dabritz J, Tardito S, Boldrini C, Hernandez-Fernaud J, Athineos D, Dhayade S, Stepanova E, Gjerga E, Neilson L, Lilla S, Hedley A, Koulouras G, McGregor G, Jamieson C, Johnson R, Park M, Kirschner K, Miller C, Kamphorst J, Loayza-Puch F, Saez-Rodriguez J, Mazzone M, Blyth K, Zagnoni M, Zanivan S	2022	Nature Metabolism	Oncology, Metabolism	Cytonuclear, Multiplex IHC, Highplex FL	HALO
Deep-learning-based classification of desmoplastic reaction on H&E predicts poor prognosis in oesophageal squamous cell carcinoma	Kouzu K, Nearchou I, Kajiwara Y, Tsujimoto H, Lillard K, Kishi Y, Ueno H	2022	Histopathology	Oncology		HALO, HALO AI
Cutaneous Lymphocyte Antigen (CLA) is a potential therapeutic target in Cutaneous T Cell Lymphoma	Peru S, Prochazkova-Carlotti M, Cherrier F, Velazquez J, Richard E, Idrissi Y, Cappellen D, Azzi-Martin L, Pham-Ledard A, Beylot-Barry M, Merlio J, Poglio S	2022	Journal of Investigative Dermatology	Immuno-oncology	Area Quantification	HALO
Loss of EMP1 promotes the metastasis of human bladder cancer cells by promoting migration and conferring resistance to ferroptosis through activation of PPAR gamma signaling	Liu S, Shi J, Wang L, Huang Y, Zhao B, Ding H, Liu Y, Wang W, Chen Z, Yang J	2022	Free Radical Biology and Medicine	Oncology	Area Quantification	HALO
Discovery of a novel ALK/ROS1/FAK inhibitor, APG-2449, in preclinical non-small cell lung cancer and ovarian cancer models	Fang D, Tao R, Wang G, Li Y, Zhang K, Xu C, Zhai G, Wang Q, Wang J, Tang C, Min P, Xiong D, Chen J, Wang S, Yang D, Zhai Y	2022	BMC Cancer	Oncology	Multiplex IHC	HALO
Integrated single-cell analyses decode the developmental landscape of the human fetal spine	Yu H, Tang D, Wu H, Li C, Lu Y, He F, Zhang X, Yang Y, Shi W, Hu W, Zeng Z, Dai W, Ou M, Dai Y	2022	iScience	Other	Highplex FL	HALO
Cell graph neural networks enable the precise prediction of patient survival in gastric cancer	Wang Y, Wang Y, Hu C, Li M, Fan Y, Otter N, Sam I, Gou H, Hu Y, Kwok T, Zalcberg J, Boussioutas A, Daly R, Montufar G, Lio P, Xu D, Webb G, Song J	2022	Precision Oncology	Oncology	Multiplex IHC	HALO
Spartalizumab or placebo in combination with dabrafenib and trametinib in patients with BRAF V600-mutant melanoma: exploratory biomarker analyses from a randomized phase 3 trial (COMBI-i)	Tawbi H, Robert C, Brase J, Gusenleitner D, Gasal E, Garrett J, Savchenko A, Gorgun G, Flaherty K, Ribas A, Dummer R, Schadendorf D, Long G, Nathan P, Ascierto P	2022	Journal for ImmunoTherapy of Cancer	Oncology	Multiplex IHC, Spatial Analysis	HALO
Establishing a multiplex imaging panel to study T cell development in the thymus in mouse	Allam A, Russell S	2022	STAR Protocols	Immunology	Highplex FL	HALO
Developing T cells form an immunological synapse for passage through the ?-selection checkpoint	Allam A, Charnley M, Pham K, Russel S	2022	Journal of Cell Biology	Immunology	Highplex FL	HALO
Sensory neurons display cell-type-specific vulnerability to loss of neuron-glia interactions	Elbaz B, Yang L, Vardy M, Isaac S, Rader B, Kawaguchi R, Traka M, Woolf C, Renthal W, Popko B	2022	Cell Reports	Neuroscience	Axon	HALO
MMO-Net (Multi-Magnification Organ Network): A use case for Organ Identification using Multiple Magnifications in Preclinical Pathology Studies	Serna C, Romero-Palomo F, Arcadu F, Funk J, Schumacher V, Janowczyk A	2022	Journal of Pathology Informatics	Other		HALO
Endothelial cell death after ionizing radiation does not impair vascular structure in mouse tumor models	Kaeppler J, Chen J, Buono M, Vermeer J, Kannan P, Cheng W, Voukantsis D, Thompson J, Hill M, Allen D, Gomes A, Kersemans V, Kinchesh P, Smart S, Buffa F, Nerlov C, Muschel R, Markelc B	2022	EMBO Reports	Oncology	Spatial Analysis, Highplex FL	HALO
Non-canonical EphA2 activation underpins PTEN-mediated metastatic migration and poor clinical outcome in prostate cancer	Sachdeva A, Hart C, Kim K, Tawadros T, Oliveira P, Shanks J, Brown M, Clarke N	2022	British Journal of Cancer	Oncology	Highplex FL	HALO
Approaches to spatially resolving the tumour immune microenvironment of hepatocellular carcinoma	Marsh-Wakefield F, Ferguson A, Liu K, Santhakumar C, McCaughan G, Palendira U	2022	Therapeutic Advances in Medical Oncology	Review	Multiplex IHC, Spatial Analysis, Highplex FL	HALO
Intact HIV proviruses persist in the brain despite viral suppression with ART	Cochrane C, Angelovich T, Byrnes S, Waring E, Guanizo A, Trollope G, Zhou J, Vue J, Senior L, Wanicek E, Eddine J, Gartner M, Jenkins T, Gorry P, Brew B, Lewin S, Estes J, Roche M, Churchill M	2022	Annals of Neurology	Infectious Disease	Multiplex IHC	HALO
Isoniazid and Rifapentine Treatment effectively reduces persistent M. tuberculosis infection 2 in macaque lungs	Sharan R, Ganatra S, Singh D, Cole J, Foreman T, Thippeshappa R, Peloquin C, Shivanna V, Gonzalez O, Day C, Gandhi N, Dick E, Hall-Ursone S, Mehra S, Schlesinger L, Rengarajan J, Kaushal D	2022	Journal of Clinical Investigation	Infectious Disease	Classifier	HALO
Naproxen chemoprevention promotes immune activation in Lynch syndrome colorectal mucosa	Reyes-Uribe L, Wu W, Gelincik O, Bommi PV, Francisco-Cruz A, Solis LM, Lynch PM, Lim R, Stoffel EM, Kanth P, Samadder NJ, Mork ME, Taggart MW, Milne GL, Marnett LJ, Vornik L, Liu DD, Revuelta M, Chang K, You YN, Kopelovich L, Wistuba II, Lee JJ, Sei S, Shoemaker RH, Szabo E, Richmond E, Umar A, Perloff M, Brown PH, Lipkin SM, Vilar E	2020	Gut	Oncology	Classifier, Cytonuclear	HALO
Age-associated expression of p21 and p53 during human wound healing	Chia CW, Sherman-Baust CA, Larson SA, Pandey R, Withers R, Karikkineth AC, Zukley LM, Campisi J, Egan JM, Sen R, Ferrucci L	2021	Aging Cell	Dermatology	Area Quantification, ISH/FISH, Multiplex IHC	HALO
Radioprotective effect of X-ray abdominal FLASH irradiation: Adaptation to oxidative damage and inflammatory response may be benefiting factors	Zhu H, Xie D, Yang Y, Huang S, Gao X, Peng Y, Wang B, Wang J, Xiao D, Wu D, Li C, Li C, Qian C, Deng X	2022	Medical Physics	Oncology, Other	Multiplex IHC	HALO
Genetically engineered microglia-like cells have therapeutic potential for neurodegenerative 2 disease	Plasschaert R, DeAndrade M, Hull F, Nguyen Q, Peterson T, Yan A, Loperfido M, Baricordi C, Barbarossa L, Yoon J, Dogan Y, Unnisa Z, Schindler J, van Til N, Biasco L, Mason C	2021	bioRxiv	Neuroscience	Highplex FL	HALO
NOS2 and COX2 Blockade Limits TNBC Disease Progression and Alters CD8+ T Cell Spatial Orientation and Density	Somasundaram V, Ridnour L, Cheng R, Walke A, Kedei N, Bhattacharyya D, Wink A, Edmondson E, Butcher D, Warner A, Dorsey T, Scheiblin D, Heinz W, Bryant R, Kinders R, Lipkowitz S, Wong S, Pore M, Hewitt S, McVicar D, Anderson S, Chang J, Glynn S, Ambs S, Lockett S, Wink D	2022	bioRxiv	Immuno-oncology	Highplex FL	HALO
Addition of camrelizumab to docetaxel, cisplatin, and radiation therapy in patients with locally advanced esophageal squamous cell carcinoma: a phase 1b study	Zhang W, Yan C, Zhang T, Chen X, Dong J, Zhao J, Han D, Wang J, Zhao G, Cao F, Zhou D, Jiang H, Tang P, Zhao L, Yuan Z, Wang Q, Wang P, Pang Q	2021	OncoImmunology	Oncology	Highplex FL	HALO
Upregulation of C/EBPa Inhibits Suppressive Activity of Myeloid Cells and Potentiates Antitumor Response in Mice and Patients with Cancer	Hashimoto A, Sarker D, Reebye V, Jarvis S, Sodergren M, Kossenkov A, Raulf N, Vasara J, Andrikakou P, Meyer T, Huang K, Plummer R, Chee C, Spalding D, Pai M, Khan S, Pinato D, Sharma R, Basu B, Palmer D, Ma Y, Evans J, Habib R, Martirosyan A, Elasri N Reynaud A, Rossi J, Cobbold M, Habib N, Gabrilovich D	2021	Clinical Cancer Research	Oncology, Immuno-oncology	Multiplex IHC	HALO
Spatial Distribution and Predictive Significance of Dendritic Cells and Macrophages in Esophageal Cancer Treated With Combined Chemoradiotherapy and PD-1 Blockade	Ma X, Guo Z, Wie X, Zhao G, Han D, Zhang T, Chen X Cao F, Dong J, Zhao L, Yuan Z, Wang P, Pang Q, Yan C, Zhang W	2021	Frontiers in Immunology	Oncology	Spatial Analysis, Highplex FL	HALO
Hyperpolarised 13C-MRI identifies the emergence of a glycolytic cell population within intermediate-risk human prostate cancer	Sushentsev N, McLean M, Warren A, Benjamin A, Brodie C, Frary A, Gill A, Jones J, Kaggie J, Lamb B, Locke M, Miller J, Mills I, Priest A, Robb F, Shah N, Schulte R, Graves M, Gnanapragasam V, Brindle K, Barrett T, Gallacher F	2022	Nature Communications	Oncology	ISH/FISH, Membrane, Multiplex IHC	HALO
Antibody-drug conjugate MORAb-202 exhibits long-lasting antitumor efficacy in TNBC PDx models	Furuuchi K, Rybinski K, Fulmer J, Moriyama T, Drozdowski B, Soto A, Fernando S, Wilson K, Milinichik A, Dula M, Tanaka K, Cheng X, Albone E, Uenaka T	2021	Cancer Science	Oncology	Multiplex IHC	HALO
DS-7300a, a DNA Topoisomerase I Inhibitor, DXd-based Antibody-Drug Conjugate 2 Targeting B7-H3 Exerts Potent Antitumor Activities in Preclinical Models	Yamato M, Hasegawa J, Maejima T, Hattori C, Kumagai K, Watanabe A, Nishiya Y, Shibutani T, Aida T, Hayakawa I, Nakada T, Abe Y, Agatsuma T	2022	Molecular Cancer Therapeutics	Oncology	Multiplex IHC	HALO
Prostate cancer androgen receptor activity dictates efficacy of Bipolar Androgen Therapy	Sena L, Kumar R, Sanin D, Thompson E, Rosen D, Dalrymple S, Antony L, Yang Y, Comes-Alexandre C, Hicks J, Jones T, Bowers K, Eskra J, Meyers J, Gupta A, Skaist A, Yegnasubramanian S, Luo J, Brennen W, Kachhap S, Antonarakis E, De Marzo A, Isaacs J, Markowski M, Denmeade S	2022	medRxiv	Oncology	Classifier, Cytonuclear, Multiplex IHC, Registration	HALO
Intraoperative fluorescence imaging with aminolevulinic acid detects grossly occult breast cancer: a phase II randomized controlled trial	Ottolino-Perry K, Shahid A, DeLuca S, Son V, Sukhram M, Meng F, Liu Z, Rapic S, Anantha N, Wang S, Chamma E, Gibson C, Medeiros P, Majeed S, Chu A, Wignall O, Pizzolato A, Rosen C, Teene L, Starr-Dunham D, Kulbatski I, Panzarella T, Done S, Easson A, Leong W, DaCosta R	2021	Breast Cancer Research	Oncology	Classifier, Area Quantification	HALO
Modulation of the Human Pancreatic Ductal Adenocarcinoma Immune Microenvironment by Stereotactic Body Radiotherapy	Mills B, Qiu H, Drage M, Chen C, Mathew J, Garrett-Larsen J, Ye J, Uccello T, Murphy J, Belt B, Lord E, Katz A, Linehan D, Gerber S	2021	Clinical Cancer Research	Oncology	Classifier, Spatial Analysis, Highplex FL	HALO
Senescence-Associated Molecules and Tumor-Immune-Interactions as Prognostic Biomarkers in Colorectal Cancer	Kellers F, Fernandez A, Konykiewitz B, Schindeldecker M, Tagscherer K, Heintz A, Jesinghaus M, Roth W, Foersch S	2022	Frontiers in Medicine	Oncology	Classifier, Multiplex IHC, Spatial Analysis, Registration, TMA	HALO
A survey on artificial intelligence in histopathology image analysis	Abdelsamea M, Zidan U, Senousy Z, Gaber M, Rakha E, Ilyas M	2022	WIREs Data Mining and Knowledge Discovery	Review	Classifier, Cytonuclear, Figure Maker, TMA	HALO
Automated recognition of glomerular lesions in the kidneys of mice by using deep learning	Akatsuka A, Horai Y, Akatsuka A	2022	Journal of Pathology Informatics	Other	Classifier	HALO, HALO AI
Tau Pathology in Chronic Traumatic Encephalopathy is Primarily Neuronal	Butler M, Dixon E, Stein T, Alvarez V, Huber B, Buckland M, McKee A, Cherry J	2022	Journal of Neuropathology & Experimental Neurology	Neuroscience	Multiplex IHC, Spatial Analysis, Highplex FL	HALO, HALO AI
Chemoradiation-induced alteration of programmed death-ligand 1, CD8+ tumor-infiltrating lymphocytes and mucin expression in rectal cancer	Baretti M, Zhu Q, Fu W, Meyer J, Wang H, Anders R, Azad N	2022	Oncotarget	Oncology	Multiplex IHC, Spatial Analysis	HALO
Two independent modes of kidney stone suppression achieved by AIM/CD5L and KIM-1	Matsuura K, Maehara N, Hirota A, Eguchi A, Yasuda K, Taniguchi K, Nishijima A, Matsuhashi N, Shiga Y, Ishii R, Iguchi Y, Tanabe K, Arai S, Miyazaki T	2022	Communications Biology	Other	Area Quantification, Figure Maker	HALO
Dynamic and adaptive cancer stem cell population admixture in colorectal neoplasia	Vasquez E, Nasreddin N, Valbuena G, Mulholland E, Belnoue-Davis H, Eggington H, Schenck R, Wouters V, Wirapati P, Gilroy K, Lannagan R, Flanagan D, Nujumudeen A, Omwenga S, McCorry A, Easton A, Koelzer V, East J, Morton D, Trusolino L, Maughan T, Campbell A, Loughrey M, Dunne P, Tsantoulis P, Juels D, Tejpar S, Sansom O, Leedham S	2022	Cell Stem Cell	Oncology	Highplex FL, Registration	HALO
MYC sensitises cells to apoptosis by driving energetic demand.	Edwards-Hicks J, Su H, Mangolini M, Yoneten K, Wills J, Rodriguez-Blanco G, Young C, Cho K, Barker H, Muir M, Guerrieri A, Li X, White R, Manasterski P, Mandrou E, Wills K, Chen J, Abraham E, Sateri K, Qian B, Bankhead P, Arends M, Gammoh N, von Kriegsheim A, Patti G, Sims A, Acosta J, Brunton V, Kranc K, Christophorou M, Pearce E, Ringshausen I, Finch A	2022	Nature Communications	Oncology, Metabolism	Classifier	HALO
The addition of FAIMS increases targeted proteomics sensitivity from FFPE tumor biopsies	Sweet S, Chain D, Yu W, Martin P, Rebelatto M, Chambers A, Cecchi F, Kim Y	2022	Scientific Reports	Other		HALO, HALO AI
Glycosphingolipids are mediators of cancer plasticity through independent signaling pathways	Cumin C, Huang Y, Rossdam C, Ruoff F, Cespedes S, Liang C, Lombardo F, Coelho R, Rimmer N, Konantz M, Lopez M, Alam S, Schmidt A, Calabrese D, Fedier A, Vlajnic T, Itzstein M, Templin M, Buettner F, Everest-Dass A, Heinzelmann-Schwarz V, Jacob F	2022	Cell reports	Oncology	Classifier, Multiplex IHC	HALO
The Key Molecular Mechanisms of Sini Decoction Plus Ginseng Soup to Rescue Acute Liver Failure: Regulating PPAR? to Reduce Hepatocyte Necroptosis?	He Y, Zhang Y, Zhang J, Hu X	2022	Journal of Inflammation Research	Other	Area Quantification	HALO
Bright-Field Multiplex Immunohistochemistry Assay for Tumor Microenvironment Evaluation in Melanoma Tissues	Ugolini F, Pasqualini E, Simi S, Baroni G, Massi D	2022	Cancers	Other	Multiplex IHC	HALO, HALO Link
Adult re-expression of IRSp53 rescues NMDA receptor function and social behavior in IRSp53-mutant mice	Noh Y, Yook C, Kang J, Lee S, Kim Y, Yang E, Kim H, Kim E	2022	Communications Biology	Neuroscience	ISH/FISH, Figure Maker	HALO
Immune evasion before tumour invasion in early lung squamous carcinogenesis	Mascaux C, Angelova M, Vasaturo A, Beane J, Hijazi K, Anthoine G, Rothe F, Willard-Gallo K, Haller A, Ninane V, Burny A, Sculier J-P, Spira A, Galon J	2019	Nature	Immuno-oncology, Oncology	Multiplex IHC	HALO
Knockdown of ZBTB11 impedes R-loop elimination and increases the sensitivity to cisplatin by inhibiting DDX1 transcription in bladder cancer	Chen L, Liu Z, Tang H, Zhou Z, Chen J, Ma Z, Deng M, Li X, Wu Y, Zheng L, Zhou L, Zheng X, Liu Z	2022	Cell Proliferation	Oncology	Multiplex IHC, Highplex FL, Figure Maker	HALO
LncRNA scaRNA2 bridges DNA end-resection to homologous recombination repair mediated chemoradioresistance	Yang Y, Chen Y, Shen H, Liu T, Cao K, Wan Z, Du Z, Wang H, Yu Y, Ma S, Li B, Zhang W, Cai J, Gao F	2022	Research Square	Oncology	Highplex FL, TMA	HALO
Tumor-infiltrated activated B cells suppress liver metastasis of colorectal cancers	Xu Y, Wei Z, Feng M, Zhu D, Mei S, Wu Z, Feng Q, Chang W, Ji M, Liu C, Zhu Y, Shen L, Yang F, Chen Y, Feng Y, Xu J, Zhu D	2022	Cell Reports	Oncology, Immuno-oncology	Multiplex IHC, Highplex FL	HALO
Tumor immune contexture is a determinant of anti-CD19 CAR T cell efficacy in large B cell lymphoma	Scholler N, Perbost R, Locke F, Jain M, Turcan S, Danan C, Chang E, Neelapu S, Miklos D, Jacobson C, Lekakis L, Lin Y, Ghobadi A, Kim J, Chou J, Plaks V, Wang Z, Xue A, Mattie M, Rossi J, Bot A, Galon J	2022	Nature Medicine	Immuno-oncology	Multiplex IHC, Figure Maker	HALO
Multimodal integration of radiology, pathology and genomics for prediction of response to PD-(L)1 blockade in patients with non-small cell lung cancer	Vanguri R, Luo J, Aukerman A, Egger J, Fong C, Horvat N, Pagano A, Araujo-Filho J, Geneslaw L, Rizvi H, Sosa R, Boehm K, Yang S, Bodd F, Ventura K, Hollmann, T, Ginsberg M, Gao J, MSK MIND Consortium, Hellmann M, Sauter J, Shah S	2022	Nature Cancer	Immuno-oncology		HALO, HALO AI
A Beta-containing bivalent SARS-CoV-2 spike protein vaccine candidate with AS03 elicits durable and broad neutralization of variants including Omicron in macaques and confers protection in hamsters	Berry C, Pavot V, Anosova N, Kishko M, Huang D, Tibbitts T, Raillard A, Gautheron S, Cummings S, Bangari D, Kar S, Atyeo C, Deng Y, Alter G, Gutzeit C, Koutsoukos M, Chicz R, Lecouturier V	2022	Research Square	Infectious Disease	Multiplex IHC	HALO
Combined genetic deletion of GDF15 and FGF21 has modest effects on body weight, hepatic steatosis and insulin resistance in high fat fed mice	Patel S, Haider A, Alvarez-Guaita A, Bidault G, Moustafa J, Guiu-Jurado E, Tadross J, Warner J, Harrison J, Virtue S, Scurria F, Zvetkova I, Bluher M, Small K, O'Rahilly S, Savage D	2022	Molecular Metabolism	Metabolism	Vacuole	HALO
Immune cells in mesothelioma microenvironment simplistic marker of response to nivolumab plus ipilimumab	Disselhorst M, Lubeck Y, van der Noort V, Quispel-Janssen J, Seignette I, Sanders J, Peters D, Hooijberg E, Baas P	2022	Lung Cancer	Oncology	Multiplex IHC, Registration	HALO
In situ mass spectrometry imaging reveals heterogeneous glycogen stores in human normal and cancerous tissues	Young L, Conroy L, Clarke H, Hawkinson T, Bolton K, Sanders W, Chang J, Webb M, Alilain W, Vander Kooi C, Drake R, Andrews D, Badgett T, Wagner L, Allison D, Sun R, Gentry M	2022	EMBO Molecular Medicine	Oncology, Metabolism	Multiplex IHC	HALO
Transcriptional and functional analyses of neoantigen-specific CD4 T cells during a profound response to anti-PD-L1 in metastatic Merkel cell carcinoma	Church C, Pulliam T, Longino N, Park S, Smythe K, Makarov V, Riaz N, Jing L, Amezquita R, Campbell J, Gottardo R, Pierce R, Choi J, Chan T, Koelle D, Nghiem P	2022	Journal for ImmunoTherapy of Cancer	Oncology, Immuno-oncology	Highplex FL	HALO
Modelling aggressive prostate cancers of young men in immune-competent mice, driven by isogenic Trp53 alterations and Pten loss	Mejia-Hernandez J, Keam S, Saleh R, Muntz F, Fox S, Byrne D, Kogan A, Pang L, Huynh J, Litchfield C, Caramia F, Lozano G, He H, You J, Sandhu S, Williams S, Haupt Y, Haupt S	2022	Cell Death & Disease	Oncology	Multiplex IHC, Highplex FL, Figure Maker	HALO
In vivo tumor immune microenvironment phenotypes correlate with inflammation and vasculature to predict immunotherapy response	Sahu A, Kose K, Kraehenbuehl L, Byers C, Holland A, Tembo T, Santella A, Alfonso A, Li M, Cordova M, Gill M, Fox C, Gonzalez S, Kumar P, Wang A, Kurtansky N, Chandrani P, Yin S, Mehta P, Navarrete-Dechent C, Peterson G, King K, Dusza S, Yang N, Liu S, Phillips W, Guitera P, Rossi A, Halpern A, Deng L, Pulitzer M, Marghoob A, Chen C, Merghoub T, Rajadhyaksha M	2022	Nature Communications	Immuno-oncology	Highplex FL, Figure Maker	HALO
Combination of T cell-redirecting bispecific antibody ERY974 and chemotherapy reciprocally enhances efficacy against non-inflamed tumours	Sano Y, Azuma Y, Tsunenari T, Kayukawa Y, Shinozuka J, Fujii E, Amano J, Nishito Y, Maruyama T, Kinoshita Y, Sakamoto Y, Yoshida A, Miyazaki Y, Sato Y, Teramoto-Seida C, Ishiguro T, Tanaka T, Kitazawa T, Endo M	2022	Nature Communications	Immuno-oncology	Immune	HALO
In vivo G-CSF treatment activates the GR-SOCS1 axis to suppress IFN-? secretion by natural killer cells	Zhao X, Peng T, Cao X, Hou Y, Li R, Han T, Fan Z, Zhao M, Chang Y, Chen H, Li C, Huang X	2022	Cell Reports	Immunology	Highplex FL	HALO
Integrated multi-omics analysis of adverse cardiac remodeling and metabolic inflexibility upon ErbB2 and ERR? deficiency	Dufour C, Xia H, B'chir W, Perry M, Kuzmanov U, Gainullina A, Dejgaard K, Scholtes C, Ouellet C, Zuo D, Sanguin-Gendreau V, Guluzian C, Smith H, Muller W, Audet-Walsh E, Sergushichev A, Emili A, Giguere V	2022	Communications Biology	Other	Multiplex IHC	HALO
Phase I/II clinical trial of a helper peptide vaccine plus PD-1 blockade in PD-1 antibody-naïve and PD-1 antibody-experienced patients with melanoma (MEL64)	Vavolizza R, Petroni G, Mauldin I, Chianese-Bullock K, Olson W, Smith K, Dengel L, Haden K, Grosh W, Kaur V, Varhegyi N, Gaughan E, Slingluff C	2022	Journal for ImmunoTherapy of Cancer	Immuno-oncology	Highplex FL	HALO
Unveiling the tumor immune microenvironment of organ-specific melanoma metastatic sites	Conway J, Rawson R, Lo S, Ahmed T, Veregara I, Gide T, Attrill G, Carlino M, Saw R, Thompson J, Spillane A, Shannon K, Shivalingam B, Menzies A, Wilmott J, Long G, Scolyer R, da Silva I	2022	Journal for ImmunoTherapy of Cancer	Oncology	Classifier, Spatial Analysis, Highplex FL	HALO
Effects of hypoxia-preconditioned HucMSCs on neovascularization and follicle survival in frozen/thawed human ovarian cortex transplanted to immunodeficient mice	Cheng J, Ruan X, Li Y, Du J, Jin F, Gu M, Zhou Q, Xu X, Yang Y, Wang H, Mueck A	2022	Stem Cell Research & Therapy	Other	Multiplex IHC	HALO
Intratumoral administration of CD1c (BDCA-1)+ and CD141 (BDCA-3)+ myeloid dendritic cells in combination with talimogene laherparepvec in immune checkpoint blockade refractory advanced melanoma patients: a phase I clinical trial	Schwarze J, Tijtgat J, Awada G, Cras L, Vasaturo A, Bagnall C, Forsyth R, Dufait I, Tuyaerts S, Riet I, Neyns B	2022	Journal for ImmunoTherapy of Cancer	Oncology, Immuno-oncology	Highplex FL	HALO
TIE2-high cervical cancer cells promote tumor angiogenesis by upregulating TIE2 and VEGFR2 in endothelial cells	Tan S, Chen Y, Du S, Li W, Liu P, Zhao J, Yang P, Cai J, Gao R, Wang Z	2022	Translational Oncology	Oncology	Area Quantification, Highplex FL	HALO
Supraphysiologic Testosterone Induces Ferroptosis and Activates Immune Pathways through Nucleophagy in Prostate Cancer	Kumar R, Mendonca J, Owoyemi O, Boyapati K, Thomas N, Kanacharoen S, Coffey M, Topiwala D, Homes C, Ozbek B, Jones T, Rosen M, Dong L, Wiens S, Brennen W, Isaacs J, Marzo A, Markowski M, Antonarakis E, Qian D, Pienta K, Pardoll D, Carducci M, Denmeade S, Kachhap S	2021	Cancer Research	Oncology	Cytonuclear	HALO
Diverse human astrocyte and microglial transcriptional responses to Alzheimers pathology	Smith A, Davey K, Tsartsalis S, Khozoie C, Fancy N, Tang S, Liaptsi E, Weinert M, McGarry A, Muirhead R, Gentleman S, Owen D, Matthews P	2021	Acta Neuropathologica	Neuroscience	Area Quantification, Multiplex IHC, Microglia	HALO
T Cells Limit Accumulation of Aggregate Pathology Following Intrastriatal Injection of ?-Synuclein Fibrils	George S, Tyson T, Rey N, Sheridan R, Peelaerts W, Becker K, Schulz E, Meyerdirk L, Burmeister A, von Linstow C, Steiner J, Galvis M, Ma J, Pospisilik J, Labrie V, Brundin L, Brundin P	2021	Journal of Parkinson's Disease	Immunology, Neuroscience	Microglia	HALO
Viral alpha-synuclein knockdown prevents spreading synucleinopathy	Menon S, Kofoed R, Nabbouh F, Xhima K, Al-Fahoum Y, Langman T, Mount H, Shihabuddin L, Sardi S, Fraser P, Watts J, Aubert I, Tandon A	2021	Brain Communication	Neuroscience	Highplex FL	HALO
Neoadjuvant PD-1 blockade induces T cell and cDC1 activation but fails to overcome the immunosuppressive tumor associated macrophages in recurrent glioblastoma	Lee A, Mochizuki A, Reynoso J, Orpilla J, Chow F, Kienzler J, Everson R, Nathanson D, Bensinger S, Liau L, Cloughesy T, Hugo W, Prins R	2021	Nature Communications	Immuno-oncology	Highplex FL	HALO
Haploinsufficiency of the lysosomal sialidase NEU1 results in a model of pleomorphic rhabdomyosarcoma in mice	Machado E, van de Vlekkert D, Sheppard H, Perry S, Downing S, Laxton J, Ashmun R, Finkelstein D, Neale G, Hu H, Harwood F, Koo S, Grosveld G, d'Azzo A	2022	Communications Biology	Oncology	Membrane, Spatial Analysis	HALO
STRIP2 motivates non-small cell lung cancer progression by modulating the TMBIM6 stability through IGF2BP3 dependent	Zhang X, Chen Q, He Y, Shi Q, Yin C, Xie Y, Yu H, Bao Y, Tang C, Dong Z	2022	Research Square	Oncology	Multiplex IHC	HALO
Proliferative tumor infiltrating lymphocytes abundance within microenvironment impact clinical outcome in cutaneous B-cell lymphomas	Menguy S, Prochazkova-Carolotti M, Azzi-Martin L, Ferte T, Bresson-Bepoldin L, Rey C, Vergier B, Merlio J, Beylot-Barry M, Pham-Ledard A	2022	Journal of Investigative Dermatology	Immuno-oncolgy	Classifier, Highplex FL	HALO
Integrated pathological analysis to develop a Gal-9 based immune survival stratification to predict the outcome of lung large cell neuroendocrine carcinoma and its usefulness in immunotherapy	Che Y, Luo Z, Cao Y, Wang J, Xue Q, Sun N, He J	2022	International Journal of Biological Sciences	Oncology	Classifier, Multiplex IHC	HALO
Artificial IntelligenceÐPowered Prediction of ALK Gene Rearrangement in Patients With NonÐSmall-Cell Lung Cancer	Terada Y, Takahashi T, Hayakawa T, Ono A, Kawata T, Isaka M, Muramatsu K, Tone K, Kodama H, Imai T, Notsu A, Mori K, Ohde Y, Nakajima T, Sugino T, Takahashi T	2022	JCO Clinical Cancer Informatics	Oncology		HALO, HALO AI
USP14 promotes tryptophan metabolism and immune suppression by stabilizing IDO1 in colorectal cancer	Shi D, Wu X, Jian Y, Wang J, Huang C, Mo S, Li Y, Li F, Zhang C, Zhang D, Zhang H, Huang H, Chen X, Wang Y, Lin C, Liu G, Song L, Liao W	2022	Nature Communications	Oncology, Dermatology	Cytonuclear, Highplex FL	HALO, HALO AI
Single Cell RNA-Seq Identifies Immune-Related Prognostic Model and Key Signature-SPP1 in Pancreatic Ductal Adenocarcinoma	Chen K, Wang Q, Liu X, Wang F, Ma Y, Zhang S, Shao Z, Yang Y, Tian X	2022	Genes	Oncology	Cytonuclear, Highplex FL	HALO
Dapagliflozin reduces the vulnerability of rats with pulmonary arterial hypertension-induced right heart failure to ventricular arrhythmia by restoring calcium handling	Wu J, Liu T, Shi S, Fan Z, Hiram R, Xiong F, Cui B, Su X, Chang R, Zhang W, Yan M, Tang Y, Huang H, Wu G, Guang C	2022	Cardiovascular Diabetology	Other	Multiplex IHC	HALO
The SGLT2i Dapagliflozin Reduces RV Mass Independent of Changes in RV Pressure Induced by Pulmonary Artery Banding	Connelly K, Wu E, Visram A, Friedberg M, Batchu S, Yeera V, Thai K, Nghiem L, Zhang Y, Kabir G, Desjardins J, Advani A, Gilbert R	2022	Cardiovascular Drugs and Therapy	Other	Area Quantification	HALO
The NALCN channel regulates metastasis and nonmalignant cell dissemination	Rahrmann E, Shorthouse D, Jassim A, Hu L, Ortiz M, Mahler-Araujo B, Vogel P, Paez-Ribes M, Fatemi A, Hannon G, Iyer R, Blundon J, Lourenco F, Kay J, Nazarian R, Hall B, Zakharenko S, Winton D, Zhu L, Gilbertson R	2022	Nature Genetics	Oncology	ISH/FISH, Multiplex IHC	HALO
The proteomic landscape of glioblastoma recurrence reveals novel and targetable immunoregulatory drivers	Tatari N, Khan S, Livingstone J, Zhai K, Mckenna D, Ignatchenko V, Chokshi C, Gwynne W, Singh M, Revill S, Mikolajewicz N, Zhu C, Chan J, Hawkins C, Lu J, Provias J, Ask K, Morrissy S, Brown S, Weiss T, Weller M, Han H, Greenspoon J, Moffat J, Venugopal C, Boutros P	2022	Acta Neuropathologica	Oncology	Multiplex IHC, Figure Maker, TMA	HALO
Relaxin/insulin-like family peptide receptor 4 (Rxfp4) expressing hypothalamic neurons Q8 modulate food intake and preference in mice	Lewis J, Woodward O, Nuzzaci D, Smith C, Adriaenssens A, Billing L, Brighton C, Phillips B, Tadross J, Kinston S, Ciabatti E, Gottgens B, Tripodi M, Mornigold D, Baker D, Gribble F, Reimann F	2022	Molecular Metabolism	Metabolism	ISH/FISH, Highplex FL	HALO
Positron emission tomography imaging of the sodium iodide symporter senses real-time energy stress in vivo	Dzien P, Mackintosh A, Malviya G, Johnson E, Soloviev D, Brown G, Uribe A, Nixon C, Lyons S, Maddocks O, Blyth K, Lewis D	2022	Research Square	Metabolism	Cytonuclear	HALO
Regional epithelial cell diversity in the small intestine of pigs	Wiarda J, Becker S, Sivasankaran S, Loving C,	2022	Journal of Animal Science	Gastroenterology	ISH/FISH, Figure Maker	HALO

Title(click the + for more info)	Authors	Year	Journal	Application	HALO Modules	Product
Stem cellderived CAR T cells traffic to HIV reservoirs in macaques	Barber-Axthelm IM, Barber-Axthelm V, Sze KY, Zhen A, Suryawanshi GW, Chen ISY, Zack JA, Kitchen SG, Kiem H-P, Peterson CW	2021	JCI Insight	Immunology, Infectious Disease	Area Quantification	HALO
IL-1-driven stromal-neutrophil interaction in deep ulcers defines a pathotype of therapy non-responsive inflammatory bowel disease	Friedrich M, Pohin M, Jackson MA, Korsunsky I, Bullers S, Rue-Albrecht K, Christoforidou Z, Sathananthan D, Ravindran R, Peres RS, Sharpe H, Wei K, Watts GFM, Mann EH, Geremia A, Thomas T, Attar M, Oxford IBD Cohort Investigators, Roche Fibroblast Network Consortium, McCuaig S, Thomas L, Collantes E, Uhlig HH, Sansom S, Easton A, Raychaudhuri S, Travis SP, Powrie FM	2021	bioRxiv	Immunology	Cytonuclear	HALO
Highly Fermentable Fiber Alters Fecal Microbiota and Mitigates Swine Dysentery Induced by Brachyspira hyodysenteriae	Helm ET, Gabler NK, Burrough ER	2021	Animals	Infectious Disease	Cytonuclear	HALO
Vascular endothelial ERp72 is involved in the inflammatory response in a rat model of skeletal muscle injury	Khalaf NB, Al-Mehatab D, Fathallah DM	2021	Medicine Reports	Immunology	Cytonuclear	HALO
Lipid Source and Peroxidation Status Alter Immune Cell Recruitment in Broiler Chicken Ileum	Fries-Craft KA, Meyer MM, Lindblom SC, Kerr BJ, Bobeck EA	2021	The Journal of Nutrition	Immunology	ISH/FISH	HALO
Frontotemporal lobar degeneration proteinopathies have disparate microscopic patterns of white and grey matter pathology	Giannini LAA, Peterson C, Ohm D, Xie SX, McMillan CT, Raskovsky K, Massimo L, Suh E, Van Deerlin VM, Wolk DA, Trojanowski JQ, Lee EB, Grossman M, Irwin DJ	2021	Acta Neuropathologica Communications	Neuroscience	Area Quantification	HALO
Fasting reverses drug-resistance in hepatocellular carcinoma through p53-dependent metabolic synergism	Krstic J, Reinisch I, Schindlmaier K, Galhuber M, Berger N, Kupper N, Moyschewitz E, Auer M, Michenthaler H, Nössing C, Depaoli MR, Ramadani-Muja J, Stryeck S, Pichler M, Rinner B, Deutsch AJA, Reinisch A, Madl T, Chiozzi RZ, Heck AJR, Huch M, Malli R, Prokesch A	2021	bioRxiv	Oncology	Classifier, Cytonuclear	HALO
Recruitment of KRAS downstream target ARL4C to membrane protrusions accelerates pancreatic cancer cell invasion	Harada A, Matsumoto S, Yasumizu Y, Akama T, Eguchi H, Kikuchi A	2021	bioRxiv	Oncology	Area Quantification	HALO
Potential role of M2 TAMs around lymphatic vessels during lymphatic invasion in papillary thyroid carcinoma	Kabasawa T, Ohe R, Aung NY, Urano Y, Kitaoka T, Tamazawa N, Utsunomiya A, Yamakawa M	2021	Scientific Reports	Oncology	Area Quantification	HALO
Amylin deposition activates HIF1? and 6-phosphofructo-2-kinase/fructose-2, 6-biphosphatase 3 (PFKFB3) signaling in failing hearts of non-human primates	Liu M, Li N, Qu C, Gao Y, Wu L, Hu LG	2021	Communications Biology	Metabolism	Area Quantification, Cytonuclear	HALO
BMP pathway antagonism by Grem1 regulates epithelial cell fate in intestinal regeneration	Koppens MAJ, Davis H, Valbuena GN, Mulholland EJ, Nasreddin N, Colombe M, Antanaviciute A, Biswas S, Friedrich M, Lee L, Oxford IBD cohort investigators, Wang LM, Koelzer VH, East JE, Simmons A, Winton DJ, Leedham SJ	2021	bioRxiv	Gastroenterology	Area Quantification	HALO
A distinct repertoire of cancer-associated fibroblasts is enriched in cribriform prostate cancer	Hesterberg AB, Rios BL, Wolf EM, Tubbs C, Wong HY, Schaffer KR, Lotan TL, Giannico GA, Gordetsky JB, Hurley PJ	2021	Journal of Pathology:Clinical Research	Oncology	Classifier, ISH/FISH	HALO
Dystrophic microglia are associated with neurodegenerative disease and not healthy aging in the human brain	Shahidehpour RK, Higdon RE, Crawford NG, Neltner JH, Ighodaro ET, Patel E, Price D, Nelson PT, Bachstetter AD	2021	Neurobiology of Aging	Neuroscience	Area Quantification	HALO
Inhibition of Hedgehog signaling alters fibroblast composition in pancreatic cancer	Steele NG, Biffi G, Kemp SB, Zhang Y, Drouillard D, Syu L-J, Hao Y, Oni TE, Brosnan E, Elyada E, Doshi A, Hansma C, Espinoza C, Abbas A, The S, Irizarry-Negron VM, Halbrook CJ, Franks N, Hoffman M, Brown KL, Carpenter ES, Nwosu ZC, Johnson C, Lima F, Anderson MA, Park Y, Crawford HC, Lyssiotis CA, Frankel TF, Rao A, Bednar F, Dlugosz AA, Preall J, Tuveson DA, Allen B, di Magliano MP	2021	Clinical Cancer Research	Oncology	Area Quantification	HALO
Locally confined IFN? production by CD4+ T cells provides niches for murine cytomegalovirus 4 replication in the salivary gland	Oderbolz J, Zangger N, Zimmerman L, Sandu I, Starruß J, Graw F, Oxenius A	2021	bioRxiv		Classifier, Spatial Analysis, Highplex FL	HALO
Kaiso (ZBTB33) subcellular partitioning functionally links LC3A/B, the tumor microenvironment, and breast cancer survival	Singhal SK, Byun JS, Park S, Yan T, Yancey R, Caban A, Hernandez SG, Hewitt SM, Boisvert H, Hennek S, Bobrow M, Ahmed SU, White J, Yates C, Aukerman A, Vanguri R, Bareja R, Lenci R, Farré PL, De Siervi A, Nápoles AM, Vohra N, Gardner K	2021	Communications Biology	Oncology	Cytonuclear, TMA	HALO
Deep Learning-Based Annotation Transfer between Molecular Imaging Modalities: An Automated Workflow for Multimodal Data Integration	Race AM, Sutton D, Hamm G, Maglennon G, Morton JP, Strittmatter N, Campbell A, Sansom OJ, Wang Y, Barry ST, Takáts Z, Goodwin RJA, Bunch J	2021	Analytical Chemistry	Oncology		HALO AI
Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma	Bakouny Z, Braun DA, Shukla SA, Pan W, Gao X, Hou Y, Flaifel A, Tang S, Bosma-Moody A, He MX, Vokes N, Nyman J, Xie W, Nassar AH, Alaiwi SA, Flippot R, Bouchard G, Steinharter JA, Nuzzo PV, Ficial M, SantAngelo M, Forman J, Berchuck JE, Dudani S, Bi K, Park J, Camp S, Sticco-Ivins M, Hirsch L, Baca SC, Wind-Rotolo M, Ross-Macdonald P, Sun M, Mary Lee G-SM, Chang SL, Wei XX, McGregor BA, Harshman LC, Genovese G, Ellis L, Pomerantz M, Hirsch MS, Freedman ML, Atkins MB, Wu CJ, Ho TH, Linehan WM, McDermott DF, Heng DYC, Viswanathan SR, Signoretti S, Van Allen EM, Choueiri TK	2021	Nature Communications	Oncology	Highplex FL	HALO
IgA transcytosis and antigen recognition govern ovarian cancer immunity	Biswas S, Mandal G, Payne KK, Anadon CM, Gatenbee CD, Chaurio RA, Costich TL, Moran C, Harro CM, Rigolizzo KE, Mine JA, Trillo-Tinoco J, Sasamoto N, Terry KL, Marchion D, Buras A, Wenham RM, Yu X, Townsend MK, Tworoger SS, Rodriguez CR, Anderson AR, Conejo-Garcia JR	2021	Nature	Immuno-oncology	Highplex FL	HALO
Characterization of Macrophages and Osteoclasts in the Osteosarcoma Tumor Microenvironment at Diagnosis: New Perspective for Osteosarcoma Treatment?	Gomez-Brouchet A, Gilhodes J, Van Acker N, Brion R, Bouvier C, Assemat P, Gaspar N, Aubert S, Guinebretiere J-M, Marie B, Larousserie F, Entz-Werlé N, de Pinieux G, Mascard E, Gouin F, Brousset P, Tabone M-D, Jimenez M, Le Deley M-C, Blay J-Y, Brugieres L , Piperno-Neumann S, Rédini F	2021	Cancers	Immuno-oncology	Highplex FL	HALO
CD30+OX40+ Treg is associated with improved overall survival in colorectal cancer	Lam JH, Hong M, Koo S-L, Chua CWL, Lim KL, Wee F, Wan WK, Leow WQ, Yeo JG, Tan IBH, Yeong J, Lim TKH, Lim TS	2021	Cancer Immunology, Immunotherapy	Immuno-oncology	Highplex FL	HALO
Sustained Helicobacter pylori infection accelerates gastric dysplasia in a mouse model	OBrien VP, Koehne AL, Dubrulle J, Rodriguez AE, Leverich CK, Kong VP, Campbell JS, Pierce RH, Goldenring JR, Choi E, Salama NR	2021	Life Science Alliance	Immuno-oncology	Highplex FL	HALO
A feasibility study of combined epigenetic and vaccine therapy in advanced colorectal cancer with pharmacodynamic endpoint	Bever KM, Thomas DL, Zhang J, Rivera EAD, Rosner GL, Zhu Q, Nauroth JM, Christmas B, Thompson ED, Anders RA, Judkins C, Liu M, Jaffee EM, Ahuja N, Zheng L, Azad NS	2021	Clinical Epigenetics	Oncology	Immune, Membrane	HALO
CD8+ T cells fail to limit SIV reactivation following ART withdrawal until after viral amplification	Okoye AA, Duell DD, Fukazawa Y, Varco-Merth B, Marenco A, Behrens H, Chaunzwa TM, Selseth AN, Gilbride RM, Shao J, Edlefsen PT, Geleziunas R, Pinkevych M, Davenport MP, Busman-Sahay K, Nekorchuk MD, Park H, Smedley JV, Axthelm MK, Estes JD, Hansen SG, Keele BF, Lifson JD, Picker LJ	2021	The Journal of Clinical Investigation	Immunology, Infectious Disease	ISH/FISH	HALO, HALO AI
The effect of cyfluthrin on testis inhibin B in rats and the intervention of Lycium barbarum polysaccharide	Guo X, Xie Y-X, Guo C, Wei J-L, Yang H-F	2021	Molecular & Cellular Toxicology	Toxicology	Multiplex IHC	HALO
Cooperative targeting of immunotherapy-resistant melanoma and lung cancer by an AXL-targeting antibody-drug conjugate and immune checkpoint blockade	Boshuizen J, Pencheva N, Krijgsman O, Altimari DD, Castro PG, de Bruijn B, Ligtenberg MA, den Heuvel EG, Vredevoogd DW, Song J-Y, Visser N, Apriamashvili G, Janmaat ML, Plantinga TS, Franken P, Houtkamp M, Lingnau A, Jure-Kunkel M, Peeper DS	2021	Cancer Research	Immuno-oncology		HALO
ATP-binding cassette transporters restrict drug delivery and efficacy against brain tumors even when blood-brain barrier integrity is lost	de Gooijer MC, Kemper EM, Buil LCM, Citirikkaya CH, Buckle T, Beijnen JH, van Tellingen O	2021	Cell Reports Medicine	Oncology		HALO
The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancer	Najumudeen AK, Ceteci F, Fey SK, Hamm G, Steven RT, Hall H, Nikula CJ, Dexter A, Murta T, Race AM, Sumpton D, Vlahov N, Gay DM, Knight JRP, Jackstadt R, Leach JDG, Ridgway RA, Johnson ER, Nixon C, Hedley A, Gilroy K, Clark W, Malla SB, Dunne PD, Rodriguez-Blanco G, Critchlow SE, Mrowinska A, Malviya G, Solovyev D, Brown G, Lewis DY, Mackay GM, Strathdee D, Tardito S, Gottlieb E, CRUK Rosetta Grand Challenge Consortium, Takats Z, Barry ST, Goodwin RJA, Bunch J, Bushell M, Campbell AD, Sansom OJ	2021	Nature Genetics	Oncology		HALO
Single-cell analysis shows that adipose tissue of persons with both HIV and diabetes is enriched for clonal, cytotoxic, and CMV-specific CD4+ T cells	Wanjalla CN, McDonnell WY, Ram R, Chopra A, Gangula R, Leary S, Mashayekhi M, Simmons JD, Warren CM, Bailin S, Gabriel CL, Cuo L, Furch BD, Lima MC, Woodward BO, Hannah L, Pilkinton MA, Fuller DT, Kawai K, Virmani R, Finn AV, Hasty AH, Mallal SA, Kalams SA, Koethe JR	2021	Cell Reports Medicine	Immunology, Metabolism		HALO
Acute Respiratory Distress in Aged, SARS-CoV-2 Infected African Green Monkeys but not Rhesus Macaques	Blair RV, Vaccari M, Doyle-Meyers LA, Roy CJ, Russell-Lodrigue K, Fahlberg M, Monjure CJ, Beddingfield B, Plante KS, Plante JA, Weaver SC, Qin X, Midkiff CC, Lehmicke G, Golden N, Threeton B, Penney T, Allers C, Barnes MB, Pattison M, Datta PK, Maness NJ, Birnbaum A, Fischer T, Bohm RP, Rappaport J	2020	The American Journal of Pathology	Infectious Disease	Classifier	HALO
Association of COVID-19 inflammation with activation of the C5aC5aR1 axis	Carvelli J, Demaria O, Vely F, Batista L, Benmansour NC, Fares J, Carpentier S, Thibult M-L, Morel A, Andre P, Represa A, Piperoglou C, Cordier PY, Le Dault E, Guervilly C, Simone P, Gainnier M, Morel Y, Ebbo M, Schleinitz N, Vivier E	2020	Nature	Immunology	Cytonuclear	HALO
Impact of Preanalytical Factors During Histology Processing on Section Suitability for Digital Image Analysis	Chlipala EA, Butters M, Brous M, Fortin JS, Archuletta R, Copeland K, Bolon B	2020	Toxicologic Pathology	Toxicology	Area Quantification, Cytonuclear	HALO
Tumor vessel normalization, immuno-stimulatory reprogramming, and improved survival in glioblastoma with combined inhibition of PD-1, angiopoietin-2, and VEGF	Di Tacchio M, Macas J, Weissenberger J, Sommer K, Bähr O, Steinbach JP, Senft C, Seifert V, Glas M, Herrlinger U, Krex D, Meinhardt M, Weyerbrock A, Timmer M, Goldbrunner R, Deckert M, Scheel AH, Büttner R, Grauer OM, Schittenhelm J, Tabatabai G, Harter PN, Guenther S, Devraj K, Plate KH, Reiss Y	2020	Cancer Immunology Research	Oncology, Immuno-oncology	Classifier, Cytonuclear	HALO
Immune cell landscaping reveals a protective role for regulatory T cells during kidney injury and fibrosis	do Valle Duraes F, Lafont A, Biebel M, Martin K, Darribat K, Cuttat R, Waldt A, Naumann U, Wieczorek G, Gaulis S, Pfister S, Mertz KD, Li J, Roma G, Warncke M	2020	JCI Insight	Immunology	Area Quantification, Cytonuclear	HALO
The prevalence and prognostic significance of estrogen receptor beta expression in non-small cell lung cancer	Enwere EK, Dean ML, Li H, D'Silva A, Bebb DG	2020	Translational Lung Cancer Research	Oncology	Cytonuclear, TMA	HALO
Dendritic Cell Paucity Leads to Dysfunctional Immune Surveillance in Pancreatic Cancer	Hedge S, Krisnawan VE, Herzog BH, Zuo C, Breden MA, Knolhoff BL, Hogg GD, Tang JP, Baer JM, Mpoy C, Lee KB, Alexander KA, Rogers BE, Murphy KM, Hawkins WG, Fields RC, DeSelm CJ, Schwarz JK, DeNardo DG	2020	Cancer Cell	Oncology, Immuno-oncology	Area Quantification, Cytonuclear, Immune	HALO
Periconceptional exposure to lopinavir, but not darunavir, impairs decidualization: a potential mechanism leading to poor birth outcomes in HIV-positive pregnancies	Kala S, Dunk C, Acosta S, Serghides L	2020	Human Reproduction	Infectious Disease	Cytonuclear	HALO
Three-dimensional culture models mimic colon cancer heterogeneity induced by different microenvironments	Kawai S, Yamazaki M, Shibuya K, Yamazaki M, Fujji E, Nakano K, Suzuki M	2020	Scientific Reports	Oncology	Cytonuclear	HALO
Epithelial-mesenchymal transition of absorptive enterocytes and depletion of Peyer's patch M cells after PEDV infection	Chen Y-M, Helm ET, Groeltz-Thrush, Gabler NK, Burrough ER	2020	Virology	Immunology	Area Quantification	HALO
Imaging breast cancer using hyperpolarized carbon-13 MRI	Gallagher FA, Woitek R, McLean MA, Gill AB, Garcia RM, Provenzano E, Riemer F, Kaggie J, Chhabra A, Ursprung S, Grist JT, Daniels CJ, Zaccagna F, Laurent M-C, Locke M, Hilborne S, Frary A, Torheim T, Boursnell C, Schiller A, Patterson I, Slough R, Carmo B, Kane J, Biggs H, Harrison E, Deen SS, Patterson A, Lanz T, Kingsbury Z, Ross M, Basu B, Baird R, Lomas DJ, Sala E, Wason J, Rueda OM, Chin S-F, Wilkinson IB, Graves MJ, Abraham JE, Gilbert FJ, Caldas C, Brindle KM	2020	Proceedings of the National Academy of Sciences	Oncology	Area Quantification	HALO
Conformation-selective tau monoclonal antibodies inhibit tau pathology in primary neurons and a mouse model of Alzheimers disease	Gibbons GS, Kim S-J, Wu Q, Riddle DM, Leight SN, Changolkar L, Xu H, Meymand ES, O'Reilly M, Zhang B, Brunden KR, Trojanowski JQ, Lee VMY	2020	Molecular Neurodegeneration	Neuroscience	Area Quantification	HALO
TGF?-blockade uncovers stromal plasticity in tumors by revealing the existence of a subset of interferon-licensed fibroblasts	Grauel AL, Nguyen B, Ruddy D, Laszewski T, Schwartz S, Chang J, Chen J, Piquet M, Pelletier M, Yan Z, Kirkpatrick ND, Wu J, deWeck A, Riester M, Hims M, Geyer FC, Wagner J, MacIsaac K, Deeds J, Diwanji R, Jayaraman P, Yu Y, Simmons Q, Weng S, Raza A, Minie B, Dostalek M, Chikkegowda P, Ruda V, Iartchouk O, Chen N, Thierry R, Zhou J, Pruteanu-Malinici I, Fabre C, Engelman JA, Dranoff G, Cremasco V	2020	Nature Communications	Oncology	Area Quantification	HALO
Ex-vivo delivery of monoclonal antibody (Rituximab) to treat human donor lungs prior to transplantation	Ku TJY, Ribeiero RVP, Ferreira VH, Galasso M, Keshavjee S, Kumar D, Cypel M, Humar A	2020	EBioMedicine	Other	Classifier, Cytonuclear	HALO
Transmission of tauopathy strains is independent of their isoform composition	He Z, McBride JD, Zu, Changolkar L, Kim S, Zhang B, Narasimhan S, Gibbons GS, Kozak M, Schellenberg GD, Trrojanowski JQ, Lee VM-Y	2020	Nature Communications	Neuroscience	Area Quantification	HALO
Human cardiac fibroblasts expressing VCAM1 improve heart function in postinfarct heart failure rat models by stimulating lymphangiogenesis	Iwamiya T, Segnard B-D, Matsuoka Y, Imamura T	2020	PLOS One	Myology	Area Quantification	HALO
Environmental contaminant ammonia triggers epithelial-to-mesenchymal transition-mediated jejunal fibrosis with the disassembly of epithelial cell-cell contacts in chicken	Jing H, Wang S, Wang Y, Shen N, Gao X-J	2020	ScienceTotalEnvrt	Toxicology	Area Quantification	HALO
Cholinergic receptors on intestine cells of Ascaris suum and activation of nAChRs by levamisole	McHugh M, Williams P, Verma S, Powell-Coffman JA, Robertson AP, Martin RJ	2020	International Journal for Parasitology: Drugs and Drug Resistance	Gastroenterology, Infectious Disease	Area Quantification	HALO
Adult onset pan-neuronal human tau tubulin kinase 1 expression causes severe cerebellar neurodegeneration in mice	McMillan P, Wheeler J, Gatlin RE, Taylor L, Strovas T, Baum M, Bird TD, Latimer C, Keene CD, Kraemer BC, Liachko NF	2020	Acta Neuropathologica Communications	Neuroscience	Area Quantification	HALO
Spatial immune profiling of the colorectal tumor microenvironment predicts good outcome in stage II patients	Nearchou IP, Gwyther BM, Georgiakakis ECT, Gavriel CG, Kajiwara Y, Ueno H, Harrison DJ, Caie PD	2020	Digital Medicine	Immuno-oncology	Classifier, Area Quantification, Spatial Analysis	HALO
11? hydroxysteroid dehydrogenase 1: a new marker for predicting response to immune-checkpoint blockade therapy in non-small-cell lung carcinoma	Saito R, Miki Y, Abe T, Miyauchi E, Abe J, Nanamiya R, Inoue C, Sato I, Sasano H	2020	British Journal of Cancer	Immuno-oncology	Area Quantification	HALO
Clinicopathological significance of endoplasmic reticulum stress proteins in ovarian carcinoma	Samanta S, Tamura S, Dubeau L, Mhawech-Fauceglia P, Miyagi Y, Kato H, Lieberman R, Buckanovich RJ, Lin YG, Neamati N	2020	Scientific Reports	Oncology	Area Quantification	HALO
Prognostic value of tumor-inltrating immune cells in primary colorectal cancer and metastases	Martin SZ, Tagscherer KE, Deckert S, Horst D, Moehler M, Lang H, Roth W	2020	*Pre-Print	Immuno-oncology	Classifier, Cytonuclear	HALO
Implementation of PD-L1 22C3 IHC pharmDxTM in Cell Block Preparations of Lung Cancer: Concordance with Surgical Resections and Technical Validation of CytoLyt® Prefixation	Lou SK, Ko HM, Kinoshita T, MacDonald S, Weiss J, Czarnecka-Kujawa K, Boerner SL, Yasufuku K, Tsao M-S, Schwock J	2020	Acta Cytologica	Oncology	Classifier, Membrane	HALO
Immuno-Interface Score to Predict Outcome in Colorectal Cancer Independent of Microsatellite Instability Status	Nestarenkaite A, Fadhil W, Ramusson A, Susanti S, Hadjimichael E, Laurinaviciene A, Ilyas M, Laurinavicius A	2020	Cancers	Immuno-oncology	Classifier, Multiplex IHC	HALO
Assessment of associations between clinical and immune microenvironmental factors and tumor mutation burden in resected nonsmall cell lung cancer by applying machine learning to whole-slide images	Ono A, Terada Y, Kawata T, Serizawa M, Isaka M, Kawabata T, Imai T, Mori K, Muramatsu K, Hayashi I, Kenmotsu H, Oshima K, Urakami K, Nagashima T, Kusuhara M, Akiyama Y, Sugino T, Ohde Y, Yamaguchi K, Takahashi T T	2020	Cancer Medicine		Classifier, Multiplex IHC, Serial Section	HALO
Prevalence of CD8+ cytotoxic lymphocytes in human neoplasms	Blessin NC, Spriestersbach P, Li W, Mandelkow T, Dum D, Simon R, Hube-Magg C, Lutz F, Viehweger F, Lennartz M, Fraune C, Nickelsen V, Fehrle W, Göbel C, Weidemann S, Clauditz T, Lebok P, Möller K, Steurer S, Izbicki JR, Sauter G, Minner S, Jacobsen F, Luebke AM, Büscheck F, Höflmayer D, Wilczak W, Burandt E, Hinsch A	2020	Cellular Oncology	Oncology, Immuno-oncology	Membrane, TMA	HALO
Persistence of adoptively transferred T cells with a kinetically engineered IL-2 receptor agonist	Parisi G, Saco JD, Salazar FB, Tsoi J, Krystofinski P, Puig-Saus C, Zhang R, Zhou J, Cheung-Lau GC, Garcia AJ, Grasso CS, Tavaré R, Hu-Lieskovan S, Mackay S, Zalevsky J, Bernatchez C, Diab A, Wu AM , Comin-Anduix B, Charych D, Ribas A	2020	Nature Communications	Oncology, Immuno-oncology	Cytonuclear	HALO
Mechanical regulation of glycolysis via cytoskeleton architecture	Park JS, Burckhardt CJ, Lazcano R, Solis LM, Isogai T, Li L, Chen CS, Gao B, Minna JD, Bachoo R, DeBerardinis RJ, Danuser G	2020	Nature	Oncology	Classifier, Cytonuclear, TMA	HALO
Naproxen chemoprevention promotes immune activation in Lynch syndrome colorectal mucosa	Reyes-Uribe L, Wu W, Gelincik O, Bommi PV, Francisco-Cruz A, Solis LM, Lynch PM, Lim R, Stoffel EM, Kanth P, Samadder NJ, Mork ME, Taggart MW, Milne GL, Marnett LJ, Vornik L, Liu DD, Revuelta M, Chang K, You YN, Kopelovich L, Wistuba II, Lee JJ, Sei S, Shoemaker RH, Szabo E, Richmond E, Umar A, Perloff M, Brown PH, Lipkin SM, Vilar E	2020	Gut	Oncology	Classifier, Cytonuclear	HALO
p53 is associated with high-risk and pinpoints TP53 missense mutations in mantle cell lymphoma	Rodrigues JM, Hassan M, Freiburghaus C, Eskelund CW, Geisler C, Raty R, Kolstad A, Sundstrom C, Glimelius I, Gronbaek K, Kwiecinska A, Porwit A, Jerkeman M, Ek S	2020	British Journal of Haematology	Oncology	Classifier, Cytonuclear	HALO
RUNX1 is a driver of renal cell carcinoma correlating with clinical outcome	Rooney N, Mason SM, McDonald L, Däbritz HM, Campbell KJ, Hedley A, Howard S, Athineos D, Nixon C, Clark W, Leach JDG, Samsom OJ, Edwards J, Cameron ER, Blyth K	2020	Cancer Research	Oncology	Cytonuclear	HALO
Analytical Performance of an Immunoprofiling Assay Based on RNA Models	Schillebeeckx I, Armstrong JR, Forys JT, Hiken J, Earls J, Flanagan KC, Cui T, Glasscock JI, Messina DN, Duncavage EJ	2020	The Journal of Molecular Diagnostics	Immunology	Cytonuclear	HALO
Prognostic significance of mesothelin expression in colorectal cancer disclosed by area-specific four-point tissue microarrays	Shiraishi T, Shinto E, Nearchou IP, Tsuda H, Kajiwara Y, Einama T, Caie PD, Kishi Y, Ueno H	2020	Vichows Archiv	Oncology	Cytonuclear, TMA	HALO AI
Prognostic and Predictive Value of Tumor-infiltrating Leukocytes and of Immune Checkpoint Molecules PD1 and PDL1 in Clear Cell Renal Cell Carcinoma	Stenzel PJ, Schindeldecker M, Teagscherer KE, Foersch S, Herpel E, Hohenfellner M, Hatiboglu G, Alt J, Thomas C, Haferkamp A, Roth W, Macher-Goeppinger S	2020	Translational Oncology	Oncology, Immuno-oncology	Classifier, Cytonuclear, TMA	HALO
Linking epigenetic signature and metabolic phenotype in IDH mutant and IDH wildtype diffuse glioma	Buran Y, Filipski K, Bernatz S, Baumgarten P, Roller B, Zinke J, Zeiner PS, Ilina E, Senft C, Ronellenfitsch MW, Plate KH, Bähr O, Hattingen E, Steinbach JP, Mittelbron M, Harter PN	2020	Neuropathology and Applied Neurobiology	Neuroscience	Multiplex IHC, TMA	HALO
O 6-Methylguanine DNA Methyltransferase and Glucose Transporter 2 in Foregut and Hindgut Gastrointestinal Neuroendocrine Neoplasms	Watanbe H, Yamazaki Y, Fujishima F, Izxumi K, Imamura M, Hijioka S, Toriyama K, Yatabe Y, Kudo A, Motoi F, Unno M, Sasano H	2020	BMC Cancer	Oncology	Cytonuclear	HALO
SLFN11 informs on standard of care and novel treatments in a wide range of cancer models	Winkler C, Armenia J, Jones GN, Tobalina L, Sale MJ, Petreus T, Baird T, Serra V, Wang AT, Lau A, Garnett MJ, Jaaks P, Coker EA, Pierce AJ, O'Connor MJ, Leo E	2020	British Journal of Cancer	Oncology	Classifier, Cytonuclear	HALO
Lung Expression of Human ACE2 Sensitizes the Mouse to SARS-CoV-2 Infection	Han K, Blair RV, Iwanaga N, Liu F, Russell-Lodrigue KE, Qin Z, Midkiff CC, Golden NA, Doyle-Meyers LA, Kabir ME, Chandler KE, Cutrera KL, Ren M, Monjure CJ, Lehmicke G, Fischer T, Beddingfield B, Wanek AG, Birnbaum A, Maness NJ, Roy CJ, Datta PK, Rappaport J, Kolls JK, Qin X	2020	American Journal of Respiratory Cell and Molecular Biology	Infectious Disease		HALO AI
Human ileal organoid model recapitulates clinical incidence of diarrhea associated with small molecule drugs	Belair DG, Visconti RJ, Hong M, Marella M, Peters MF, Scott CW, Kolaja KL	2020	Toxicology in Vitro	Toxicology	Highplex FL	HALO
Multiomic analysis and immunoprofiling reveal distinct subtypes of human angiosarcoma	Chan JY, Lim JQ, Yeong J, Ravi V, Guan P, Boot A, Tay TKY, Selvarajan S, Nasir NDM, Loh JH, Ong CK, Huang D, Tan J, Li Z, Ng CC-Y, Tan TT, Masuzawa M, Sung KW-K, Farid M, Quek RHH, Tan NC, Teo MCC, Rozen SG, Tan P, Fotreal A, The BT, Soo KC	2020	The Journal of Clinical Investigation	Immuno-oncology	Highplex FL	HALO
Tumoral PD-1hiCD8+ 1 T cells are partially exhausted and 2 predict favorable outcome in triple-negative breast cancer	Guo L, Cao C, Goswami S, Huang X, Ma L, Guo Y, Yang B, Li T, Chi Y, Zhang X, Wu J	2020	Clinical Science	Immuno-oncology	Highplex FL	HALO
CXCR4+ cells are increased in lung tissue of patients with idiopathic pulmonary fibrosis	Jaffar J, Griffiths K, Oveissi S, Duan M, Foley M, Glaspole I, Symons K, Organ L, Westfall G	2020	Respiratory Research	Fibrosis	Highplex FL	HALO
Rova-T enhances the anti-tumor activity of anti-PD1 in a murine model of small cell lung cancer with endogenous Dll3 expression	Vitorino P, Chuang C-H, Iannello Z, Zhao X, Anderson W, Ferrando R, Zhang Z, Madhavan S, Karsunky H, Saunders LR	2020	Translational Oncology	Immuno-oncology	Highplex FL	HALO
Safety, immunogenicity, and clinical efficacy of durvalumab in combination with folate receptor alpha vaccine TPIV200 in patients with advanced ovarian cancer: a phase II trial	Zamarin D, Walderich S, Holland A, Zhou Q, Iasonos AE, Torrisi JM, Merghoub T, Chesebrough LF, Mcdonnell AS, Gallagher JM, Li Y, Hollmann TJ, Grisham RN, Erskine CL, Block MS, Knutson KL, O'Cearbhaill RE, Aghajanian C, Konner JA	2020	Journal for ImmunoTherapy of Cancer	Immuno-oncology	Highplex FL	HALO
Trajectory and Functional Analysis of PD-1high CD4+CD8+ T Cells in Hepatocellular Carcinoma by Single-Cell Cytometry and Transcriptome Sequencing	Zheng B, Wang D, Qiu X, Luo G, Wu T, Yang S, Li Z, Zhu Y, Wang S, Wu R, Sui C, Gu Z, Shen S, Jeong S, Wu Z, Gu J, Wang H, Chen L	2020	Advanced Science	Immuno-oncology	Highplex FL	HALO
Pulmonary Mycobacterium tuberculosis control associates with CXCR3- and CCR6-expressing antigen-specific Th1 and Th17 cell recruitment	Shanmugasundaram U, Bucsan AN, Ganatra SR, Ibegbu C, Quezada M, Blair RV, Alvarez X, Velu V, Kaushal D, Rengarajan J	2020	JCI Insight	Infectious Disease	Highplex FL	HALO AI
A first-in-human, phase 1, dose-escalation study of ABBV-176, an antibody-drug conjugate targeting the prolactin receptor, in patients with advanced solid tumors	Lemech C, Woodward N, Chan N, Mortimer J, Naumovski L, Nuthalapati S, Tong B, Jiang F, Ansell P, Ratajczak CK, Sachdev J	2020	Investigational New Drugs	Oncology	ISH/FISH	HALO
Gene expression of prostaglandin EP4 receptor in three canine carcinomas	Musser ML, Viall AK, Phillips RL, Hostetter JM, Johannes CM	2020	BMC Veterinary Research	Oncology	ISH/FISH	HALO
Cholecystokinin-1 receptor agonist induced pathological findings in the exocrine pancreas of non-human primates	Nyborg NCB, Kirk RK, de Boer AS, Andersen DW, Bugge A, Wulff BS, Thorup I, Clausen TR	2020	Toxicology & Applied Pharmacology	Metabolism	ISH/FISH	HALO
NPY mediates the rapid feeding and glucose metabolism regulatory functions of AgRP neurons	Ruud LE, Pereira MMA, de Solis AJ, Fenselau H, Bruning JC	2020	Nature Communications	Metabolism	ISH/FISH	HALO
Age-determined expression of priming protease TMPRSS2 and localization of SARS-CoV-2 infection in the lung epithelium	Schuler BA, Habermann AC, Plosa EJ, Taylor CJ, Jetter C, Kapp ME, Benjamin JT, Gullerman P, Nichols DS, Braunstein LZ, Hackett A, Koval M, Guttentag SH, Blackwell TS, Webber SA, Banovich NE, Kropski JA, Sucre JMS	2020	The Journal of Clincial Invesitgation	Infectious Disease	ISH/FISH	HALO
STAT3 inhibition with galiellalactone efectively targets the prostate cancer stem?like cell population	Canesin G, Maggio V, Palominos M, Stiehm A, Contreras HR, Castellon EA, Morote J, Paciucci R, Maitland NJ, Bjartell A, Hellsten R	2020	Scientific Reports	Oncology	Membrane	HALO
Genetic alterations and expression characteristics of ARID1A impact tumor immune contexture and survival in early-onset gastric cancer	Zou J, Qin W, Wang L, Wang Y, Shen J, Xiong W, Yu S, Song S, Ajani JA, Lin S-Y, Mills GB, Yuan X, Chen J, Peng G	2020	American Journal of Cancer Research	Immuno-oncology	Spatial Analysis, Highplex FL	HALO
Computational image analysis of T-cell infiltrates in resectable gastric cancer: association with survival and molecular subtypes	Challoner BR, von Loga K, Woolston A, Griffiths B, Sivamanoharan N, Semiannikova M, Newey A, Barber LJ, Mansfield D, Hewitt LC, Saito Y, Davarzani N, Starling N, Melcher A, Grabsch HI, Gerlinger M	2020	JNCI: Journal of the National Cancer Institute	Immuno-oncology	Multiplex IHC	HALO
Temporal and Spatial Heterogeneity of Host Response to SARS-CoV-2 Pulmonary Infection	Desai N, Neyaz A, Szabolcs A, Shih AR, Chen JH, Thapar V, Nieman LT, Solovyov A, Mehta A, Lieb DJ, Kulkarni AS, Jaicks C, Pinto CJ, Juric D, Chebib I, Colvin RB, Kim AY, Monroe R, Warren SE, Danaher P, Reeves JW, Gong J, Rueckert EH, Greenbaum BD, Hacohen N, Lagana SM, Rivera MN, Sholl LM, Stone JR, Ting DT, Deshpande V	2020	medRxiv	Infectious Disease	Multiplex IHC	HALO
An Antibody Targeting ICOS Increases Intratumoral Cytotoxic to Regulatory T-cell Ratio and Induces Tumor Regression	Sainson RCA, Thotakura AK, Kosmac M, Borhis G, Parveen N, Kimber R, Carvalho J, Henderson SJ, Pryke KL, Okell T, O'Leary S, Ball S, Van Krinks C, Gamand L, Taggart E, Pring EJ, Ali H, Craig H, Wong VWY, Liang Q, Rowlands RJ, Lecointre M, Campbell J, Kirby I, Melvin D, Germaschewski V, Oelmann E, Quaratino S, McCourt M	2020	Cancer Immunology Research	Immuno-oncology	Multiplex IHC	HALO
Immunogradient Indicators for Antitumor Response Assessment by Automated Tumor-Stroma Interface Zone Detection	Rasmusson A, Zilenaite D, Nestarenkaite A, Augulis R, Laurinaviciene A, Ostapenko V, Poskus T, Laurinavicius A	2020	The American Journal of Pathology		Multiplex IHC	HALO AI
Neoadjuvant immunotherapy leads to pathological responses in MMR-proficient and MMR-deficient early-stage colon cancers	Chalabi M, Fanchi LF, Dijkstra KK, Van den Berg JG, Aalbers AG, Sikorska K, Lopez-Yurda M, Grootscholten C, Beets GL, Snaebjornsson P, Maas M, Mertz J, Veninga V, Bounova G, Broeks A, Beets-Tan RG, de Wijkerslooth TR, van Lent AU, Marsman HA, Nuijten E, Kok NF, Kuiper M, Verbeek WH, Kok M, Van Leerdam ME, Schumacher TN, Voest EE, Haanen JB	2020	Nature Medicine	Immuno-oncology	Multiplex IHC, Serial Section	HALO
MCL1 inhibition is effective against a subset of small-cell lung cancer with high MCL1 and low BCL-XL expression	Yasuda Y, Ozasa H, Kim YH, Yamazoe M, Ajimizu H, Funazo TY, Nomizo T, Tsuji T, Yoshida H, Sakamori Y, Najajima N, Menju T, Yoshizawa A, Date H, Hirai T	2020	Cell Death & Disease	Oncology, Immuno-oncology	Cytonuclear	HALO
Inhibition of myostatin prevents microgravity-induced loss of skeletal muscle mass and strength	Smith RC, Cramer MS, Mitchell PJ, Lucchesi J, Ortega AM, Livingston EW, Ballard D, Zhang L, Hanson J, Barton K, Berens S, Credille KM, Bateman TA, Ferguson VL, Ma YL, Stodieck LS	2020	PLOS One	Myology	Muscle Fiber	HALO
Photoacoustic imaging biomarkers for monitoring biophysical changes during nanobubble-mediated radiation treatment	Hysi E, Fadhel MN, Wang Y, Sebastian JA, Giles A, Czarnota GJ, Exner AA, Kolios MC	2020	Photoacoustics	Other	Classifier, Area Quantification, Object Colocalization	HALO
Single-cell analysis of germinal-center B cells informs on lymphoma cell of origin and outcome	Holmes AB, Corinaldesi C, Shen Q, Kumar R, Compagno N, Wang Z, Nitzan M, Grunstein E, Pasqualucci L, Dalla-Favera R, Basso K	2020	Journal of Experimental Medicine	Oncology	Registration	HALO
Artificial intelligence as the next step towards precision pathology	Acs B, Rantalainen M, Hartman J	2020	Journal of Internal Medicine	Review		HALO
Ngly1?/? rats develop neurodegenerative phenotypes and pathological abnormalities in their peripheral and central nervous systems	Asahina M, Fujinawa R, Nakamura S, Yokoyama K, Tozawa R, Suzuki T	2020	Human Molecular Genetics			HALO
Consumptive coagulopathy of severe yellow fever occurs independently of hepatocellular tropism and massive hepatic injury	Baileya AL, Kanga L-I, Zanellab LGFdABD, Silveirab CGT, Hod Y-H, Foquete L, Biale G, McCunef BT, Duarte-Netog AN, Thomash A, Rauéh H-P, Byrnesa K, Kallasd EG, Slifkah MK, Diamond MS	2020	Proceedings of the National Academy of Sciences	Infectious Disease		HALO
?-Synuclein modulates tau spreading in mouse brains	Bassil F, Meymand ES, Brown HJ, Xu H, Cox TO, Pattabhiraman S, Maghames CM, Wu Q, Zhang B, Trojanowski JQ, Lee VM-Y	2020	Journal of Experimental Medicine	Neuroscience		HALO
Ad26 vaccine protects against SARS-CoV-2 severe clinical disease in hamsters	Tostanoski LH, Wegmann F, Martinot AJ, Loos C, McMahan K, Mercado NB, Yu J, Chan CN, Bondoc S, Starke CE, Nekorchuk M, Busman-Sahay K, Piedra-Mora C, Wrijil LM, Ducat S, Custers J, Atyeo C, Fischinger S, Burke JS, Feldman J, Hauser BM, Caradonna TM, Bondzie EA, Dagotto G, Gebre MS, Jacob-Dolan C, Lin Z, Mahrokhian SH, Nampanya F, Nityanandam R, Pessaint L, Porto M, ALi V, Benetiene D, Tevi K, Andersen H, Lewis MG, Schmidt AG, Lauffenburger DA, Alter G, Estes JD, Schuitemaker H, Zahn R, Barouch DH	2020	Nature Medicine	Infectious Disease	Area Quantification, Multiplex IHC	HALO
Prognostic relevance of programmed cell death protein 1/programmed death-ligand 1 pathway in thymic malignancies with combined immunohistochemical and biomolecular approach	Berardi R, Goteri G, Brunelli A, Pagliaretta S, Paolucci V, Caramanti M, Rinaldi S, Refai M, Pompili C, Morgese F, Torniai, Marcantognini, Ricci G, Mazzanti P, Onofri A, Bianchi F, Sabbatini A, Cascinu S	2020	Expert Opinion on Therapeutic Targets	Oncology		HALO
Liraglutide treatment improves endothelial function in the Ldlr?/? mouse model of atherosclerosis and affects genes involved in vascular remodelling and inflammation	Bjørnholm KD, Skovsted GF, Mitgaard-Thomsen A, Rakipovski G, Tveden-Nyborg P, Lykkesfeldt J, Povlsen GK	2020	Basic & Clinical Pharmacology & Toxicology	Immunology, Toxicology		HALO
Microglial-associated responses to comorbid amyloid pathology and hyperhomocysteinemia in an aged knock-in mouse model of Alzheimerís disease	Braun DJ, Dimayuga E, Morganti JM, Van Eldik LJ	2020	Journal of Neuroinflammation	Neuroscience		HALO
Glucagon Receptor Inhibition Reduces Hyperammonemia and Lethality in Male Mice with Urea Cycle Disorder	Cavino K, Sung B, Su Q, Na E, Kim J, Cheng X, Gromada J, Okamoto H	2020	Endocrinology	Metabolism		HALO
Immune parameters associated with survival in metaplastic breast cancer	Chao X, Liu L, Sun P, Yang X, Li M, Luo R, Huang Y, He J, Yun J	2020	Breast Cancer Research	Immuno-oncology		HALO
Alterations in Intestinal Innate Mucosal Immunity of Weaned Pigs During Porcine Epidemic Diarrhea Virus Infection	Chen Y-M, Helm ET, Gabler N, Hostetter JM, Burrough ER	2020	Veterinary Pathology	Infectious Disease		HALO
Expression of the Autoantigen Topoisomerase-1 is Enriched in the Lung Tissues of Patients With Autoimmune Interstitial Lung Disease: A Case Control Study	Cottrell TR, Askin F, Halushka MK, Casciola-Rosen L, McMahan ZH	2020	ACR Open Reumatology	Immunology		HALO
Growth Factor Receptor Expression in Oropharyngeal Squamous Cell Cancer: Her14 and c-Met in Conjunction with the Clinical Features and Human Papillomavirus (p16) Status	Deuss E, Gößwein D, Gül D, Zimmer S, Foersch S, Eger CS, Limburg I, Stauber RH, Künzel J	2020	Cancers	Oncology		HALO
Formoterol, a ?2-adrenoreceptor agonist, induces mitochondrial biogenesis and promotes cognitive recovery after traumatic brain injury	Vekaria HJ, Hubbard WB, Scholpa NE, Spry ML, Gooch JL, Prince SJ, Schnellmann Sullivan PG	2020	Neurobiology of Disease	Neuroscience	Area Quantification	HALO
Deep Brain Stimulation of the Medial Septal Nucleus Induces Expression of a Virally Delivered Reporter Gene in Dentate Gyrus	Fomenko A, Lee DJ, McKinnon C, Lee EJ, de Snoo ML, Gondard E, Neudorfer C, Hamani C, Lozano AM, Kalia LV, Kalia SK	2020	Frontiers of Neuroscience	Neuroscience		HALO
The membrane protein sortilin can be targeted to inhibit pancreatic cancer cell invasion	Gao F, Griffin N, Faulkner S, Li X, King SJ, Jobling P, Denham JW, Jiang CC, Hondermarck H	2020	The American Journal of Pathology	Oncology		HALO
Neoadjuvant PD-L1 plus CTLA-4 blockade in patients with cisplatin-ineligible operable high-risk urothelial carcinoma	Gao J, Navai N, Alhalabi O, Siefker-Radtke A, Campbell MT, Tidwell RS, Guo CC, Kamat AM, Matin SF, Araujo CJ, Shah AY, Msaouel P, Corn P, Wang J, Papadopoulos JN, Yadav SS, Blando JM, Duan F, Basu S, Liu W, Shen Y, Macaluso MD, Wang Y, Chen J, Zhang J, Futreal A, Dinney C, Allison JP, Goswami S, Sharma P	2020	Nature Medicine	Toxicology		HALO
Intratumoral heterogeneity of the tumor cells based on in situ cortisol excess in cortisol-producing adenomas; An association among morphometry, genotype and cellular senescence	Gao X, Yamazaki Y, Tezuka Y, Pieroni J, Ishii K, Atsumi N, Ono Y, Omata K, Morimoto R, Nakamura Y, Satoh F, Sasano H	2020	The Journal of Steroid Biochemistry and Molecular Biology	Oncology		HALO
Nicotinic Receptor Subunit Distribution in Auditory Cortex: Impact of Aging on Receptor Number and Function	Ghimire M, Cai R, Ling L, Hackett TA, Caspary DM	2020	Journal of Neuroscience	Neuroscience		HALO
Acute brain inflammation, white matter oxidative stress, and myelin deficiency in a model of neonatal intraventricular hemorrhage	Goulding DS, Vogel RC, Gensel JC, Morganti JM, Stromberg AJ, Miller BA	2020	Journal of Neuroscience	Immunology, Neuroscience		HALO
Neonatal hydrocephalus leads to white matter neuroinflammation and injury in the corpus callosum of Ccdc39 hydrocephalic mice	Goulding DS, Vogel RC, Pandya CD, Shula C, Gensel JC, Mangano FT, Goto J, Miller BA	2020	Journal of Neurosurgery	Immunology, Neuroscience		HALO
Quantification of Viral and Host Biomarkers in the Liver of Rhesus Macaques: a Longitudinal Study of Zaire Ebolavirus strain Kikwit (EBOV/Kik)	Greenberg AR, Huber BR, Liu DX, Logue JP, Hischak AMW, Hart RJ, Abbott M, Isic N, Hisada YM, Mackman N, Bennet RS, Hensley LE, Connor JH, Crossland NA	2020	The American Journal of Pathology			HALO
Clinicopathological significance of nerves in esophageal cancer	Griffin N, Rowe CW, Gao F, Jobling P, Wills V, Walker MM, Faulkner S, Hondermarck H	2020	The American Journal of Pathology	Oncology		HALO
The human IL-15 superagonist N-803 promotes migration of virus-specific CD8+ T and NK cells to B cell follicles but does not reverse latency in ART-suppressed, SHIV-infected macaques	Webb GM, Molden J, Bushman-Sahay K, Abdulhaqq S, Wu HL, Weber WC, Bateman KB, Reed JS, Northrup M, Maier N,Tanaka S, Gao L, Davey B, Carpenter BL, Axthelm MK, Stanton JJ, Smedley J, Greene JM, Safrit JT, Estes JD, Skinner PJ, Sacha JB	2020	PLOS Pathogens	Infectious Disease	Cytonuclear, ISH/FISH	HALO
Neonatal therapy with PF543, a sphingosine kinase 1 inhibitor, ameliorates hyperoxia-indused airway remodeling in a murine model of bronchopulmonary dysplasia	Ha AW, Sudhadevi T, Ebenezeer DL, Fu P, Berdyshev EV, Ackerman SJ, Natarajan V, Harijith A	2020	American Journal of Physiology	Other		HALO
Investigating Radiotherapy Response in a Novel Syngeneic Model of Prostate Cancer	Haughey CM, Mukherjee D, Steele RE, Popple A, Dura-Perez L, Pickard A, Patel M, Jain S, Mullan PB, Williams R, Oliveira P, Buckley NE, Honeychurch J, McDade SS, Illidge T, Mills IG, Eddie SL	2020	Cancers	Oncology		HALO
Intratumoral interleukin-12 mRNA therapy promotes TH1 transformation of the tumor microenvironment	Hewitt SL, Bailey D, Zielinski J, Apte A, Musenge F, Karp R, Burke S, Garcon F, Mishra A, Gurumurthy S, Watkins A, Arnold K, Moynihan J, Clancy-Thompson E, Mulgrew K, Adjei G, Deschler K, Potz D, Moody G, Leinster DA, Novick S, Sulikowski M, Bagnall CJ, Martin P, Lapointe J-M, Si H, Morehouse CA, Sedic M, Wilkinson RW, Herbst R, Frederick JP, Luheshi N	2020	Clinical Cancer Research	Immuno-oncology		HALO
IFN-III is selectively produced by cDC1 and predicts good clinical outcome in breast cancer	Hubert M, Gobbini E, Couillault C, Manh T-PV, Doffin A-C, Berthet J, Rodriguez C, Ollion V, Kielbassa J, Sajous C, Treilleux I, Tredan O, Dubois B, Dalod M, Bendriss-Vermare N, Caux C, Valladeau-Guilemond J	2020	Immunology			HALO
PNOCARC Neurons Promote Hyperphagia and Obesity upon High-Fat-Diet Feeding	Jais A, Paeger L, Sotelo-Hitschfeld T, Bremser S, Prinzensteiner M, Klemm P, Mykytiuk V, Widdershooven PJM, Vesting AJ, Grzelka K, Minere M, Cremer AL, Xu J, Korotkova T, Lowell BB, Zeilhofer HU, Backes H, Fenselau H, Wunderlich FT, Kloppenburg P, Bruning JC	2020	Neuron	Neuroscience		HALO
Tutorial: guidance for quantitative confocal miscroscopy	Jonkman J, Brown CM, Wright GD, Anderesion KI, North AJ	2020	Nature Protocols			HALO
Omental macrophages secrete chemokine ligands that promote ovarian cancer colonization of the omentum via CCR1	Krishnan V, Tallapragada S, Schaar B, Kamat K, Chanana AM, Zhang Y, Patel S, Parkash V, Rinker-Schaeffer C, Folkins AK, Rankin EB, Dorigo O	2020	Communications Biology	Oncology		HALO
A drug-induced hypotensive challenge to verify catheter-based radiofrequency renal denervation in an obese hypertensive swine model	Lauder L, Moon LB, Pipenhagen CA, Ewen S, Fish JM, Virmani R, Jensen JA, Böhm M, Mahfoud F	2020	Clinical Research in Cardiology	Myology		HALO
The identification and functional analysis of CD8+PD-1+CD161+ T cells in hepatocellular carcinoma	Li Z, Zheng B, Qiu X, Wu R, Wu T, Yang S, Zhu Y, Wu X, Wang S, Gu Z, Shen S, Wu M, Wang H, Chen L	2020	Percision Oncology	Immuno-oncology		HALO
The diagnostic and prognostic value of UBE2T in intrahepatic cholangiocarcinoma	Yu H, Wang H, Dong W, Cao Z-Y, Li R, Yang C, Cong W-M, Dong H, Jin G-Z	2020	Peer J	Oncology	Cytonuclear	HALO
Degradation of the Tumor Suppressor PDCD4 Is Impaired by the Suppression of p62/SQSTM1 and Autophagy	Manirujjaman M, Ozaki I, Murata Y, Guo J, Xia J, Nishioka K, Perveen R, Takashashi H, Anzai K, Matsuhashi S	2020	Cells	Oncology		HALO
Robust and persistent reactivation of SIV and HIV by N-803 and depletion of CD8+ cells	McBrien JB, Mavigner M, Li LF, Smith SA, White E, Tharp GK, Walum H, Busman-Suhay K, Aguilera-Sandoval CR, Thayer WO, Spagnuolo RA, Kovarova M, Wahl A, Cervasi B, Margolis DM, Vanderford TH, Carnathan DG, Paiardini M, Lifson JD, Lee JH, Safrit JT, Bosinger SE, Estes JD, Derdeyn CA, Garcia JV, Kulpa DA, Chahroudi A, Silvestri G	2020	Nature			HALO
Early-onset impairment of the ubiquitin-proteasome system in dopaminergic neurons caused by ?-synucleinn	McKinnon C, De Snoo ML, Gondard E, Neudorfer C, Chau H, Ngana SG, O'Hara DM, Brotchie JM , Koprich JB, Lozano AM, Kalia LV, Kalia SK	2020	Acta Neuropathologica Communications	Neuroscience		HALO
A Dedicated Evolutionarily Conserved Molecular Network Licenses Differentiated Cells to Return to the Cell Cycle	Miao Z-F, Lewis MA, Cho CJ, Adkins-Threats M, Park D, Brown JW, Sun J-X, Burclaff JR, Kennedy S, Lu J, Mahar M, Vietor I, Huber LA, Davidson NO, Cavalli V, Rubin DC, Wang Z-N, Mills JC	2020	Developmental Cell			HALO
The Unfolded Protein Response Mediator PERK Governs Myeloid Cell-Driven Immunosuppression in Tumors through Inhibition of STING Signaling	Mohamed E, Sierra RA, Trillo-Tinoco J, Cao Y, Innamarato P, Payne KK, Pulido M, Mandula J, Zhang S, Thevenot P, Biswas S, Abdalla SK, Costich TL, Hanggi K, Anadon CM, Flores ER, Haura EB, Mehrotra, Pilon-Thomas S, Ruffel B, Munn DH, Cubillos-Ruiz JR, Conejo-Garcia JR, Rodriguez PC	2020	Immunity	Immuno-oncology		HALO
CD137 agonist-based combination immunotherapy enhances activated, effector memory T cells and prolongs survival in pancreatic adenocarcinoma	Muth ST, Saung MT, Blair AB, Henderson MG, Thomass DL II, Xheng L	2020	Cancer Letters	Immuno-oncology		HALO
Immunohistochemical scoring of CD38 in the tumor microenvironment predicts responsiveness to anti-PD-1/PD-L1 immunotherapy in hepatocellular carcinoma	Ng HHM, Lee RY, Goh S, Tay ISY, Lim X, Lee B, Chew V, Li H, Tan B, Lim S, Lim JCT, Au B, Loh JJH, Saraf S, Connolly JE, Loh T, Leow WQ, Lee JJX, Toh HC, Malavasi F, Lee SY, Chow P, Newell EW, Choo SP, Tai D, Yeong J, Lim TKH	2020	Journal for ImmunoTherapy of Cancer	Immuno-oncology		HALO
Features of increased malignancy in eosinophilic clear cell renal cell carcinoma	Nilsson H, Lindgren D, Axelson H, Brueffer C, Saal LH, Lundgren J, Johansson ME	2020	Journal of Pathology	Immuno-oncology		HALO
Antitumor Activity of Eribulin After Fulvestrant Plus CDK4/6 Inhibitor in Breast Cancer Patient-derived Xenograft Models	Niwa Y, Asano M, Nakagawa T, France D, Semba T, Funahashi Y	2020	Anticancer Research	Oncology		HALO
A Fas-4-1BB fusion protein converts a death to a pro-survival signal and enhances T cell therapy	Oda SK, Andereson KG, Ravikumar P, Bonson P, Garcia NM, Jenkins CM, Zhuang S, Daman A, Chiu EY, Bates BM, Greenberg PD	2020	Journal of Experimental Medicine	Immuno-oncology		HALO
The Arp2/3 complex is crucial for colonisation of the mouse skin by melanoblasts	Papalazarou V, Swaminathan K, Jaber-Hijaz Fi, Spence H, Lahmann I, Nixon C, Salmeron-Sanchez M, Arnold H-H, Rottner K, Machesky LM	2020	Development	Review		HALO
Incomplete Freunds adjuvant reduces arginase and enhances Th1 dominance, TLR signaling and CD40 ligand expression in the vaccine site microenvironment	Pollack KE, Meneveau MO, Melssen MM, Lynch KT, Koeppel AF, Young SJ, Turner S, Kumar P, Sol-Church K, Mauldin IS, Slingfluff CL	2020	Journal for ImmunoTherapy of Cancer	Immuno-oncology		HALO
Senescence, Necrosis, and Apoptosis Govern Circulating Cell-free DNA Release Kinetics	Rostami A, Lambie M, Yu CW, Stambolic V, Waldron JN, Bratman SV	2020	Cell Reports	Toxicology		HALO
Discoidin Domain Receptor 1 (DDR1) is Necessary for Tissue Homeostasis in Pancreatic Injury and Pathogenesis of Pancreatic Ductal Adenocarcinoman	Ruggeri JM, Franco-Barraza J, Sohail A, Zhang Y, Long D, di Magliano MP, Cukierman E, Fridman R, Crawford HC	2020	The American Journal of Pathology	Oncology, Immunology		HALO
Natural killer cells in the human lung tumor microenvironment display immune inhibitory functions	Russick J, Joubert P-E, Gillard-Bocquet M, Torset C, Meylan M, Petitprez F, Dragon-Durey M-A, Marmier S, Varthaman A, Josseaume N, Germain C, Jérémy Goc J, Dieu-Nosjean M-C, Validire P, Fournel L, Zitvogel L, Bindea G, Lupo A, Damotte D, Alifano M, Cremer I	2020	Journal for ImmunoTherapy of Cancer	Immuno-oncology		HALO
A potent peptide-steroid conjugate accumulates in cartilage and reverses arthritis without evidence of systemic corticosteroid exposure	Sanger MLC, Girard EJ, Hopping G, Yin C, Pakiam F, Brusniak M-Y, Nguyen E, Ruff R, Gewe MM, Byrnes-Blake K, Nairn NW, Miller DM, Mehlin C, Strand AD, Mhyre AJ, Correnti CE, Strong RK, Simon JA, Olson JM	2020	Science Translational Medicine	Immunology		HALO
Intratumoral Combinatorial Administration of CD1c (BDCA-1) + Myeloid Dendritic Cells Plus Ipilimumab and Avelumab in Combination with Intravenous Low-Dose Nivolumab in Patients with Advanced Solid Tumors: A Phase IB Clinical Trial	Schwarze JK, Awada G, Cras L, Tijtgat J, Forsyth R, Dufait I, Tuyaerts S, Riet VI, Neyns B	2020	Vaccines	Immuno-oncology		HALO
IL6/STAT3 Signaling Hijacks Estrogen Receptor ? Enhancers to Drive Breast Cancer Metastasis	Siersbæk R, Scabia V, Nagarajan S, Chernukhin I, Papachristou EK, Broome R, Johnston SJ, Joosten SEP, Green AR, Kumar S, Jones J, Omarjee S, Alvarez-Fernandez R, Glont S, Aitken SJ, Kishore K, Cheeseman D, Rakha EA, D'Santos C, Zwart W, Ruseel A, Brisken C, Carroll JS	2020	Cancer Cell	Oncology		HALO
GSTO1?1 is an upstream suppressor of M2 macrophage skewing and HIF?1??induced eosinophilic airway inflammation/a>	Sokulsky LA, Goggins B, Sherwin S, Eyeers F, Kaiko GE, Board PG, Keely S, Yang M, Foster PS	2020	Clinical & Experimental Allergy	Immunology		HALO
Neoantigen responses, immune correlates, and favorable outcomes after ipilimumab treatment of patients with prostate cancer	Subudhi SK, Vence L, Zhao H, Blando J, Yadav SS, Xiong Q, Reuben A, Aparicio A, Corn PG, Chapin BF, Pisters LL, Troncoso P, Tidwell RS, Thall P, Wu C-J, Zhang J, Logothetis CL, Futreal A, Allison JP, Sharma P	2020	Cancer			HALO
Overview of multiplex immunohistochemistry/immunofluorescence techniques in the era of cancer immunotherapy	Tan WCCT, Nerurkar SN, Cai HY, Ng HHM, Wu D, Wee YTF, Lim JCT, Yeong J, Lim TKH	2020	Cancer Communications	Review		HALO
Association between CD8 and PD?L1 expression and outcomes after radical prostatectomy for localized prostate cancer	Vicier C, Ravi P, Kwak L, Werner L, Huang Y, Evan C, Loda M, Hamid AA, Sweeney CJ	2020	The Prostate	Immuno-oncology		HALO
Insoluble Tau From Human FTDP-17 Cases Exhibit Unique Transmission Properties In Vivo	Weitzman SA, Narasimhan S, He Z, Changolkar L, McBride JD, Zhang B, Schellenberg GD, Trojanowski JQ, Lee VMY	2020	Journal of Neuropathology & Experimental Neurology	Neuroscience		HALO
Engineering functional microvessels in synthetic polyurethane random-pore scaffolds by harnessing perfusion flow	Wright MEE, Yu JK, Jain D, Maeda A, Yeh S-CA, DaCosta RS, Lin CP, Santerre JP	2020	Biomaterials			HALO
Neuronal activity modulates alpha-synuclein aggregation and spreading in organotypic brain slice cultures and in vivo	Wu Q, Shaikh MA, Meymand ES, Zhang B, Luk KC, Trojanowski JO, Lee VM-Y	2020	Acta Neuropathologica	Neuroscience		HALO
*A living biobank of matched pairs of patient-derived xenografts and organoids for cancer pharmacology	Xu X, Wang S, Zhou J, Chen J, Huang Y, Kumari R, Mao B, Zheng M, Wang J, Tu X, An X, Chen X, Zhang L, Tian X, Wang H, Dong X, Bao Z, Guo S, Ouyang X, Shan L, Wang F, Yan X, Li Z, Zhang R, Zhang H, Meiler S, Vries R, Clevers H	2020	*Pre-Print	Oncology		HALO
Safety and clinical activity of PD-L1 blockade in patients with aggressive recurrent respiratory papillomatosis	Allen CT, Lee S, Norberg SM, Kovalovsky D, Ye H, Clavijo PE, Hu-Lieskovan S, Schlegel R, Schlom J, Strauss J, Gulley JL, Trepel J, Hinrichs CS	2019	Journal for ImmunoTherapy of Cancer	Oncology, Immuno-oncology	Cytonuclear	HALO
Cutaneous pharmacologic cAMP induction induces melanization of the skin and improves recovery from ultraviolet injury in melanocortin 1 receptor?intact or heterozygous skin	Bautista R-M, Carter KM, Jarrett SG, Napier D, Wakamatsu K, Ito S, D'Orazio JA	2019	Pigment Cell & Melanoma Research	Dermatology	Area Quantification	HALO
Islet amyloidosis in a child with type 1 diabetes	Beery ML, Jacobsen LM, Atkinson MA, Butler AE, Campbell-Thompson M	2019	Islets	Metabolism	Classifier	HALO
Predicting breast cancer response to neoadjuvant chemotherapy based on tumor vascular features in needle biopsies	Brocato TA, Brown-Glaberman U, Wang Z, Selwyn RG, Wilson CM, Wyckoff EF, Lomo LC, Saline JL, Hooda-Nehra A, Pasqualini R, Arap W, Brinker CJ, Cristini V	2019	JCI Insight	Oncology	Classifier	HALO
Magnetic Resonance Imaging as a Biomarker in Rodent Peripheral Nerve Injury Models Reveals an Age-Related Impairment of Nerve Regeneration	Giorgetti E, Obrecht M, Ronco M, Panesar M, Lambert C, Accart N, Doelemeyer A, Nash M, Bidinosti M, Beckmann N	2019	Scientific Reports	Neuroscience	Classifier	HALO
Unmasking of oestrogen?dependent changes in left ventricular structure and function in aged female rats: a potential model for pre?heart failure with preserved ejection fraction	Bustamante M, Garate?Carrillo A, Ito BR, Garcia R, Carson N, Ceballos G, Ramirez?Sanchez I, Omens J, Villarreal F	2019	The Journal of Physiology	Myology	Area Quantification, Layer Thickness	HALO
MEDI3039, a novel highly potent tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) receptor 2 agonist, causes regression of orthotopic tumors and inhibits outgrowth of metastatic triple-negative breast cancer	Greer YE, Gilbert SF, Gril B, Narwal R, Brooks DLP, Tice DA, Steeg PS, Lipkowitz	2019	Breast Cancer Research	Oncology	Classifier	HALO
Glucose-Dependent Insulinotropic Polypeptide Receptor-Expressing Cells in the Hypothalamus Regulate Food Intake	Adriaenssens AE, Biggs EK, Darwish T, Tadross J, Sukthankar T, Girish M, Polex-Wolf J, Lam BY, Zvetkova I, Pan W, Chiarugi D, Yeo GSH, Blouet C, Gribble FM, Reimann F	2019	Cell Metabolism	Metabolism	ISH/FISH	HALO
Intravital imaging reveals systemic ezrin inhibition impedes cancer cell migration and lymph node metastasis in breast cancer	Ghaffari A, Hoskin V, Turashvili G, Varma S, Mewburn J, Mullins G, Greer PA, Kiefer F, Day AG, Madarnas Y, SenGupta S, Elliott BE	2019	Breast Cancer Research	Oncology	Classifier, Cytonuclear	HALO
Modulation of Microglia by Voluntary Exercise or CSF1R Inhibition Prevents Age-Related Loss of Functional Motor Units	Giorgetti E, Panesar M, Zhang Y, Joller S, Ronco M, Obrecht M, Lambert C, Accart N, Beckmann N, Doelemeyer A, Perrot L, Fruh I, Mueller M, Pierrel E, Summermatter S, Bidinosti M, Shimshek DR, Brachat S, Nash M	2019	Cell Reports	Neuroscience	Classifier, Cytonuclear	HALO
LLRRK2 inhibition does not impart protection from ?-synuclein pathology and neuron death in non-transgenic mice	Henderson MX, Sengupta M, McGeary I, Zhang B, Olufemi MF, Brown H, Trojanowski JQ, Lee VMY	2019	Acta Neuropathologica Communications	Neuroscience	Area Quantification, Cytonuclear	HALO
Tumor Characteristics Associated with Benefit from Pembrolizumab in Advanced Non-Small Cell Lung Cancer	Hu-Lieskovan S, Lisberg A, Zaretsky JM, Grogan TR, Rizvi H, Wells DK, Carroll J, Cummings A, Madrigal J, Jones B, Gukasyan J, Shintaku IP, Slamon D, Dubinett S, Goldman JW, Elashoff D, Hellmann MD, Ribas A, Garon EB	2019	Clinical Cancer Research	Immuno-oncology	Cytonuclear	HALO
Empiric Methods to Account for Pre-analytical Variability in Digital Histopathology in Frontotemporal Lobar Degeneration	Giannini LAA, Xie SX, Peterson C, Zhou C, Lee EB, Wolk DA, Grossman M, Trojanowski JQ, McMillan CT, Irwin DJ	2019	Frontiers in Neuroscience	Neuroscience	Area Quantification, Registration, Figure Maker	HALO
Alterations of the MEK/ERK, BMP, and Wnt/?-catenin pathways detected in the blood of individuals with lymphatic malformations	Kim T, Tafoya E, Chelliah MP, Lekwuttikarn R, Li J, Sarin KY, Teng J	2019	PLOS One	Other	Cytonuclear	HALO
Detection and quantification of Parascaris P-glycoprotein drug transporter expression with a novel mRNA hybridization technique	Chelladurai JJ, Brewer MT	2019	Veterinary Parasitology	Infectious Disease	ISH/FISH	HALO
IL-7-dependent compositional changes within the ?? T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response	Chen H-C, Eling N, Martinez-Jimenez CP, O'Brien LM, Carbonaro V, Marioni JC, Odom DT, de la Roche M	2019	EMBO Reports	Oncology, Immuno-oncology	ISH/FISH	HALO
Assessment of PD-L1 mRNA and protein expression in non-small cell lung cancer, head and neck squamous cell carcinoma and urothelial carcinoma tissue specimens using RNAScope and immunohistochemistry	Duncan DJ, Scott M, Scorer P, Barker C	2019	PLOS One	Oncology, Immuno-oncology	ISH/FISH	HALO
Expression of cholecystokinin by neurons in mouse spinal dorsal horn	Guitierrez-Mecinas M, Bell AM, Shepherd F, Polgar E, Watanabe M, Furuta T, Todd AJ	2019	The Journal of Comparitive Neurology	Neuroscience	ISH/FISH	HALO
Methacrylic Acid Copolymer Coating Enhances Constructive Remodeling of Polypropylene Mesh by Increasing the Vascular Response	Coindre VF, Carleton MM, Sefton MV	2019	Advanced Healthcare Materials	Biomaterials	Area Quantification	HALO
Cognitive and Pathological Influences of Tau Pathology in Lewy Body Disorders	Coughlin DG, Xie SX, Liang M, Williams A, Peterson C, Weintraub D, McMillan CT, Wolk DA, Akhtar RS, Hurtig H, Coslett HB, Hamilton R, Siderowf A, Duda JE, Rascovsky K, Lee EB, Lee VM-Y, Grossman M, Trojanowski JQ, Irwin DJ	2019	Annals of Neurology	Neuroscience	Classifier, Area Quantification	HALO
CCN3/Nephroblastoma Overexpressed Is a Functional Mediator of Prostate Cancer Bone Metastasis That Is Associated with Poor Patient Prognosis	Dankner M, Ouellet V, Communal L, Schmitt E, Perkins D, Annis MG, Barrès V, Caron C, Mes-Masson A-M, Saad F, Siegel PM	2019	The American Journal of Pathology	Oncology	Area Quantification	HALO
Divergent patterns of TDP?43 and tau pathologies in primary progressive aphasia	Giannini LAA, Xie SX, McMillan CT, Liang M, Williams A, Jester C, Rascovsky K, Wolk DA, Ash S, Lee EB, Trojanowski JQ, Grossman M, Irwin DJ	2019	Annals of Neurology	Neuroscience	Area Quantification	HALO
Characterization of novel conformation-selective ?-synuclein antibodies as potential immunotherapeutic agents for Parkinson's disease	Henderson MX, Covell DJ, Chung C-HY, Pitkin RM, Sandler RM, Decker SC, Riddle DM, Zhang B, Gathagan RJ, James MJ, Trojanowski JQ, Brunden KR, Lee VMY, Luk KC	2019	Neurobiology of Disease	Neuroscience	Area Quantification	HALO
Alzheimerís disease tau is a prominent pathology in LRRK2 Parkinsonís disease	Henderson MX, Sengupta M, Trojanowski JQ, Lee VMY	2019	Acta Neuropathologica Communications	Neuroscience	Area Quantification	HALO
Lenvatinib induces death of human hepatocellular carcinoma cellsharboring an activated FGF signaling pathway through inhibition ofFGFReMAPK cascades	Hoshi T, Miyano SW, Watanabe H, Sonobe RMK, Seki Y, Ohta E, Nomoto K, Matsui J, Funahashi Y	2019	Biochemical and Biophysical Research Communications	Oncology	Area Quantification	HALO
Molecular and functional heterogeneity of cancer associated fibroblasts in high-grade serous ovarian cancer	Hussain A, Voisin V, Poon S, Dmytryshyn J ,Richman C, Meens J, Ho VW, Tang KH, Paterson J, Clarke B, Bernardini M, Bader G, Neel B, Ailles L	2019	bioRxiv	Oncology	Classifier, Area Quantification	HALO
Alzheimer Disease Pathology-Associated Polymorphism in a Complex Variable Number of Tandem Repeat Region Within the MUC6 Gene, Near the AP2A2 Gene	Katsumata Y, Fardo DW, Bachstetter AD, Artiushin SC, Wang W-X, Wei A, Brzezinski LJ, Nelson BG, Huang Q, Abner EL, Anderson S, Patel I, Shaw BC, Price DA, Niedowicz DM, Wilcock DW, Jicha GA, Neltner JH, Van Eldik LJ, Estus S, Nelson PT	2019	Journal of Neuropathology & Experimental Neurology	Neuroscience	Area Quantification, Cytonuclear	HALO
IRAK4 mediates colitis-induced tumorigenesis and chemoresistance in colorectal cancer	Li Q, Chen Y, Zhang D, Grossman J, Li L, Khurana N, Jiang H, Grierson PM, Herndon J, DeNardo DG, Challen GA, Liu J, Ruzinova MB, Fields RC, Lim K-H	2019	JCI Insight	Oncology, Immuno-oncology	Area Quantification	HALO
Dysregulated expression but redundant function of the long non-coding RNA HOTAIR in diabetic kidney disease	Majumder S, Hadden MJ, Thieme K, Batchu SN, Niveditha D, Chowdhury S, Yerra VG, Advani SL, Bowskill BB, Liu Y, Vakili H, Alghamdi TA, White KE, Geldenhuys L, Siddiqi FS, Advani A	2019	Diabetologia	Metabolism	Area Quantification	HALO
Targeted drug delivery via caveolae-associated protein PV1 improves lung fibrosis	Marchetti GM, Burwell TJ, Peterson NC, Cann JA, Hanna RN, Li Q, Ongstad EL, Boyd JT, Kennedy MA, Zhao W, Rickert KW, Grimsby JS, DallAcqua WF, Wu H, Tsui P, Borrok MJ, Gupta R	2019	Communications Biology	Fibrosis	Area Quantification	HALO
Persistence of inflammatory phenotype in residual psoriatic plaques in patients on effective biologic therapy: Residual Psoriatic Plaques After Treatment	Mashiko S, Edelmayer RM, Bi Y, Olson LM, Wetter JB, Wang J, Maari C, Proulx ES-C, Kaimal V, Li X, Salte K, Garcet S, Kannan AK, Huang SM, Cao X, Liu Z, Krueger JG, Sarfati M, Bissonnette R, Smith KM	2019	Journal of Investigative Dermatology	Immunology, Dermatology	Area Quantification	HALO
In Situ Temporospatial Characterization of the Glial Response to Prion Infection	Michael AV, Greenlee JJ, Harm TA, Moore SJ, Zhang M, Lind MS, Greenlee MHW, Smith JD	2019	Veterinary Pathology	Immunology, Neuroscience, Infectious Disease	Area Quantification	HALO
Exposure to maternal obesity programs sex differences in pancreatic islets of the offspring in mice	Nicholas LM, Nagao M, Kusinski LC, Fernandez-Twinn DS, Eliasson L, Ozanne SE	2019	Diabetologia	Metabolism	Area Quantification	HALO
Histological characterization of aldosterone-producing adrenocortical adenomas with different somatic mutations	Ono Y, Yamazaki Y, Omata K, Else T, Tomlins SA, Rhayem Y, Williams TA, Reincke M, Carling T, Monticone S, Mulatero P, Beuschlein F, Ito S, Satoh F, Rainey WE, Sasano H	2019	The Journal of Clinical Endocrinology & Metabolism	Oncology	Classifier, Area Quantification	HALO
Epithelial to mesenchymal plasticity and differential response to therapies in pancreatic ductal adenocarcinoma	Porter RL, Magnus NKC, Thapar V, Morris R, Szabolcs A, Neyaz A, Kulkarni AS, Tai E, Chougule A, Hillis A, Golczer G, Guo H, Yamada T, Kurokawa T, Yashaswini C, Ligorio M, Vo KD, Nieman L, Liss AS, Deshpande V, Lawrence MS, Maheswaran S, Fernandez-Del Castillo C, Hong TS, Ryan DP, ODwyer PJ, Drebin JA, Ferrone CR, Haber DA, Ting DT	2019	Proceedings of the National Academy of Sciences	Oncology	Area Quantification	HALO
Multiplexed Immunohistochemistry for Molecular and Immune Profiling in Lung CancerÄîJust About Ready for Prime-Time?	Hofman P, Badoual C, Henderson F, Berland L, Hamila M, Long-Mira E, Lassalle S, Roussel H, Hofman V, Tartour E, Ilié M	2019	Cancers	Oncology, Immuno-oncology, Review	Classifier, Multiplex IHC	HALO
Quantification of histopathological findings using a novel image analysis platform	Horai Y, Mizukawa M, Nishina H, Nishikawa S, Ono Y, Takemoto K, Baba N	2019	Journal of Toxicologic Pathology	Toxicology	Classifier	HALO
Ex vivo tissue slice culture system to measure drug-response rates of hepatic metastatic colorectal cancer	Martin SZ, Wagner DC, Hörner N, Horst D, Lang H, Tagscherer KE, Roth W	2019	BMC Cancer	Oncology	Classifier, Cytonuclear	HALO
Neutrophil content predicts lymphocyte depletion and anti-PD1 treatment failure in NSCLC	Kargl J, Zhu X, Zhang H, Yang GHY, Friesen TJ, Shipley M, Maeda DY, Zebala JA, McKay-Fleisch J, Meredith G, Mashadi-Hossein A, Baik C, Pierce RH, Redman MW, Thompson JC, Albelda SM, Bolouri H, Houghton AM	2019	JCI Insight	Immuno-oncology	Classifier, Highplex FL	HALO
Precision immunoprofiling by image analysis and artificial intelligence	Koelzer VH, Sirinukunwattana K, Rittscher J, Mertz KD	2019	Vichows Archiv	Review	Classifier, Multiplex IHC, Spatial Analysis	HALO
Machine learning approaches for pathologic diagnosis	Komura D, Ishikawa S	2019	Vichows Archiv	Review	Classifier	HALO AI
MYB-NFIB gene fusions identified in archival adenoid cystic carcinoma tissue employing NanoString analysis: an exploratory study	McIntyre JB, Ko JJ, Siever J, Chan AMY, Simpson RHW, Hao D, Lau HY	2019	Diagnostic Pathology	Oncology	Classifier, Highplex FL	HALO
A Dual Blocker of Endothelin A/B Receptors Mitigates Hypertension but not Renal Dysfunction in a Rat Model of Chronic Kidney Disease and Sleep Apnea	Morales-Loredo H, Jones DT, Barrera A, Mendiola P, Garcia J, Pace CE, Murphy M, Kanagy NL, Gonzalez Bosc LV	2019	Renal Pathology	Metabolism	Classifier, Cytonuclear, Figure Maker	HALO
Detection of Lung Cancer Lymph Node Metastases from Whole-Slide Histopathologic Images Using a Two-Step Deep Learning Approach	Pham HHN, Futakuchi M, Bychkov A, Furukawa T, Kuroda K, Fukuoka J	2019	The American Journal of Pathology	Oncology	Classifier	HALO AI
Imaging Mass Spectrometry and Proteome Analysis of Marek's Disease Virus-Induced Tumors	Pauker VI, Bertzbach LD, Hohmann A, Kheimar A, Teifke JP, Mettenleiter TC, Karger A, Kaufe BB	2019	mSpere	Oncology	Cytonuclear	HALO
TNF-? Contributes to Lymphoid Tissue Disorganization and Germinal Center B Cell Suppression during Intracellular Bacterial Infection	Popescu M, Cabrera-Martinez B, Winslow GM	2019	The Journal of Immunology	Immunology	Cytonuclear	HALO
Characterization of psoriasiform dermatitis induced by systemic injection of interleukin?23 minicircles in mice	Leys L, Wang Y, Paulsboe S, Edelmayer R, Salte K, Wetter J, Namovic M, Phillips L, Dunstan R, Gauvin D, Donnelly-Roberts D, Su Z, Honore P, McGaraughty S	2019	The Journal of Dermatology	Dermatology	Area Quantification, Layer Thickness	HALO
Automated Computational Detection, Quantitation, and Mapping of Mitosis in WholeÄëSlide Images for Clinically Actionable Surgical Pathology Decision Support	Puri M, Hoover S, Hewitt S, Wei B-R, Adissu H, Halsey C, Beck J, Bradley C, Cramer S, Durham A, Esplin D, Frank C, Lyle L, McGill L, Sanchez M, Schaffer P, Traslavina R, Buza E, Yang H, Lee M, Dwyer J, Simpson R	2019	Journal of Pathology Informatics	Oncology	Cytonuclear	HALO
Lamin?B1 is a senescence?associated biomarker in clear?cell renal cell carcinoma	Radspieler M, Schindeldecker M, Stenzel P, Försc S, Tagscherer K, Herpel E, Hohenfellner M, Hatiboglu G, Roth W, Macher?Goeppinger S	2019	Oncology Letters	Oncology	Cytonuclear	HALO
Upper tract urothelial carcinoma has a luminal-papillary T-cell depleted contexture and activated FGFR3 signaling	Robinson BD, Vlachostergios PJ, Bhinder B, Liu W, Li K, Moss TJ, Bareja R, Park K, Tavassoli P, Cyrta J, Tagawa ST, Nanus DM, Beltran H, Molina AM, Khani F, Miguel Mosquera J, Xylinas E, Shariat SF, Scherr DS, Rubin MA, Lerner SP, Matin SF, Elemento O, Faltas BM	2019	Nature Communications	Oncology, Immuno-oncology	Cytonuclear	HALO
IL?36 receptor antagonistic antibodies inhibit inflammatory responses in preclinical models of psoriasiform dermatitis	Su Z, Paulsboe S, Wetter J, Salte K, Kannan A, Mathew S, Horowitz A, Gerstein C, Namovic M, Todorovi? V, Seagal J, Edelmayer RM, Viner M, Rinaldi L, Zhou L, Leys L, Huang S, Wang L, Sadhukhan R, Honore P, McGaraughty S, Scott VE	2019	Experimental Dermatology	Dermatology	Area Quantification, Cytonuclear	HALO
Neurexin 3 transmembrane and soluble isoform expression and splicing haplotype are associated with neuron inflammasome and Alzheimer's disease	Hishimoto A, Pletnikova O, Lang DL, Troncoso JC, Egan JM, Liu Q-R	2019	Alzheimer's Research & Therapy	Neuroscience	ISH/FISH	HALO
IL?1? cleavage by inflammatory caspases of the noncanonical inflammasome controls the senescence?associated secretory phenotype	Wiggins KA, Parry AJ, Cassidy LD, Humphry M, Webster SJ, Goodall JC, Narita M, Clarke MCH	2019	Aging Cell	Immunology	Cytonuclear	HALO
The role of WNT10B in normal prostate gland development and prostate cancer	Madueke I, Hu W-Y, Hu D, Swanson SM, Griend DV, Abern M, Prins GS	2019	The Prostate	Oncology	Multiplex IHC, TMA	HALO
Role of IL-15 Signaling in the Pathogenesis of Simian Immunodeficiency Virus Infection in Rhesus Macaques	Okoye AA, DeGottardi MQ, FukazawaY, Vaidya M, Abana CO, Konfe AL, Fachko DN, Duell DM, He Li H, Lum R, Gao L, Park BS, Skalsky RL, Lewis AD, Axthelm MK, Lifson JD, Wong SW, Picker LJ	2019	The Journal of Immunology	Infectious Disease	Cytonuclear, Figure Maker	HALO
A Deep Learning Convolutional Neural Network Can Recognize Common Patterns of Injury in Gastric Pathology	Martin DR, Hanson JA, Gullapalli RR, Schultz FA, Sethi A, Clark DP	2019	Archives of Pathology and Laboratory Medicine	Gastroenterology		HALO AI
Advanced Prostate Cancer with ATM Loss: PARP and ATR Inhibitors	Neeb A, Herranz N, Arce-Gallego S, Miranda S, Lorenzo Buroni L, Wei Yuan W, Alejandro Athie A, Teresa Casals T, Juliet Carmichael J, Daniel Nava Rodrigues DN, Bora Gurel B, Pasquale Rescigno P, Jan Rekowski J, Jon Welti J, Ruth Riisnaes R, Veronica Gil V, Jian Ning J, Verena Wagner, Irene Casanova-Salas I, Cordoba S, Natalia Castro N, Maria Dolores Fenor de la Maza, George Seed, Khobe Chandran, Ana Ferreira A, Ines Figueiredo I, Claudia Bertan, Diletta Bianchini, Caterina Aversa, Alec Paschalis A, Macarena Gonzalez N, Rafael Morales-Barrera, Cristina Suarez C, Joan Carles J, Amanda Swain A, Adam Sharp A, Jesus Gil, Violeta Serra, Christopher Lord, Suzanne Carreira S, Joaquin Mateo, Johann S. de Bono JS	2019	European Urology	Oncology		HALO AI
Reduction of Global H3K27me3 Enhances HER2/ErbB2 Targeted Therapy	Hirukawa A, Singh S, Wang J, Rennhack JP, Swiatnicki M, Sanguin-Gendreau V, Zuo D, Daldoul K, Lavoie C, Park M, Andrechek ER, Westbrook TF, Harris LN, Varadan V, Smith HW, Muller WJ	2019	Cell Reports	Oncology	Highplex FL	HALO
Macrophage-Derived CXCL9 and CXCL10 Are Required for Antitumor Immune Responses Following Immune Checkpoint Blockade	House IG, Savas P, Lai J, Chen AXY, Oliver AJ, Teo ZL, Todd KL, Henderson MA, Giuffrida L, Petley EV, Sek K, Mardiana S, Gide TN, Quek C, Scolyer RA, Long GV, Wilmott JS, Loi S, Darcy PK, Beavis PA	2019	Clinical Cancer Research	Immuno-oncology	Highplex FL	HALO
A single dose of neoadjuvant PD-1 blockade predicts clinical outcomes in resectable melanoma	Huang AC, Orlowski RJ, Xu X, Mick R, George SM, Yan PK, Manne S, Kraya AA, Wubbenhorst B, Dorfman L, DAndrea K, Wenz BM, Liu S, Chilukuri L, Kozlov A, Carberry M, Giles L, Kier MW, Quagliarello F, McGettigan S, Kreider K, Annamalai L, Zhao Q, Mogg R, Xu W, Blumenschein WM, Yearley JH, Linette GP, Amaravadi RK, Schuchter LM, Herati RS, Bengsch B, Nathanson KL, Farwell MD, Karakousis GC, Wherry EJ, Mitchell TC	2019	Nature Medicine	Oncology, Immuno-oncology	Highplex FL	HALO
CXCR3 enables recruitment and site-specific bystander activation of memory CD8+ T cells	Maurice NJ, McElrath MJ, Andersen-Nissen E, Frahm N, Prlic M	2019	Nature Communications	Immunology	Highplex FL	HALO
Development of resistance to FAK inhibition in pancreatic cancer is linked to stromal depletion	Jiang H, Liu X, Knolhoff BL, Hegde S, Lee KB, Jiang H, Fields RC, Pachter JA, Lim K-H, DeNardo DG	2019	Gut	Oncology	Cytonuclear, ISH/FISH	HALO
Single-Cell Quantification of mRNA Expression in The Human Brain	Jolly S, Lang V, Koelzer VH, Frigerio CS, Magno L, Salinas PC, Whiting P, Palomer E	2019	Scientific Reports	Neuroscience	ISH/FISH	HALO
The Fat Mass and Obesity-Associated Protein (FTO) Regulates Locomotor Responses to Novelty via D2R Medium Spiny Neurons	Ruud J, Alber J, Tokarska A, Engström Ruu L, Nolte H, Biglari N, Lippert R, Lautenschlager Ä, Cie?lak PE, Szumiec ?, Hess ME, Brönneke HS, Krüger M, Nissbrandt H, Korotkova T, Silberberg G, Rodriguez Parkitna J, Brüning J	2019	Cell Reports	Neuroscience, Metabolism	ISH/FISH	HALO
Quantitative digital pathology reveals association of cell-specific PNPLA3 transcription with NAFLD disease activity	Sandhu B, Perez Matos MC, Tran S, Zhong A, Csizmadia E, Kim M, Herman MA, Nasser I, Lai M, Jiang ZG	2019	JHEP Reports	Fibrosis	ISH/FISH	HALO
Alpha-synuclein is a DNA binding protein that modulates DNA repair with implications for Lewy body disorders	Schaser AJ, Osterberg VR, Dent SE, Stackhouse TL, Wakeham CM, Boutros SW, Weston LJ, Owen N, Weissman TA, Luna E, Raber J, Luk KC, McCullough AK, Woltjer RL, Unni VK	2019	Scientific Reports	Neuroscience	ISH/FISH	HALO
Small Molecule IL-36? Antagonist as a Novel Therapeutic Approach for Plaque Psoriasis	Todorovi? V, Su Z, Putman CB, Kakavas SJ, Salte KM, McDonald HA, Wetter JB, Paulsboe SE, Sun Q, Gerstein CE, Medina L, Sielaff B, Sadhukhan R, Stockmann H, Richardson PL, Qiu W, Argiriadi MA, Henry RF, Herold JM, Shotwell JB, McGaraughty SP, Honore P, Gopalakrishnan SM, Sun CC, Scott VE	2019	Scientific Reports	Immunology, Dermatology	ISH/FISH	HALO
Changes in epidermal morphology associated with dandruff	Pople JE, Bhogal RK, Moore AE, Jenkins G	2019	International Journal of Cosmetic Science	Dermatology	Cytonuclear, Layer Thickness	HALO
PD-L1 Expression and Clinical Outcomes to Cabozantinib, Everolimus, and Sunitinib in Patients with Metastatic Renal Cell Carcinoma: Analysis of the Randomized Clinical Trials METEOR and CABOSUN	Flaifel A, Xie W, Braun DA, Ficial M, Bakouny Z, Nassar AH, Jennings RB, Escudier B, George DJ, Motzer RJ, Morris MJ, Powles, Wang E, Huang Y, Freeman GJ, Choueiri TK, Signoretti S	2019	Clinical Cancer Research	Immuno-oncology	Multiplex IHC	HALO
The KDM5A/RBP2 histone demethylase represses NOTCH signaling to sustain neuroendocrine differentiation and promote small cell lung cancer tumorigenesis	Oser MG, Sabet AH, Gao W, Chakraborty AA, Schinzel AC, Jennings RB, Fonseca R, Bonal DM, Booker MA, Flaifel A, Novak JS, Christensen VL, Zhang H, Herbert ZT, Tolstorukov MY, Buss EJ, Wong K-K, Bronson RT, Nguyen Q-D, Signoretti S, Kaelin Jr WG	2019	Genes & Development	Oncology	Multiplex IHC	HALO
Physiologic serum 1,25 dihydroxyvitamin D is inversely associated with prostatic Ki67 staining in a diverse sample of radical prostatectomy patients	Rosenberg A, NetteY OS, Gogana P, Sheikh U, Virgilia M, Macias V, Kajdacsy-Balla A, R Sharifi R, Kittles RA, Murphy AB	2019	Cancer Causes & Control	Oncology	Multiplex IHC	HALO
Nuclear Glycogenolysis Modulates Histone Acetylation in Human Non-Small Cell Lung Cancers	Sun RC, Dukhande VV, Zhou Z, Young LEA, Emanuelle S, Brainson CF, Gentry MS	2019	Cell Metabolism	Oncology	Multiplex IHC	HALO
Inducing and exploiting vulnerabilities for the treatment of liver cancer	Wang C, Vegna S, Jin H, Benedict B, Lieftink C, Ramirez C, de Oliveira RL, Morris B, Gadiot J, Wang W, du Chatinier A, Wang L, Gao D, Evers B, Jin G, Xue Z, Schepers A, Jochems F, Sanchez AM, Mainardi S, te Riele H, Beijersbergen RL, Qin W, Akkari L, Bernards R	2019	Nature	Oncology	Multiplex IHC	HALO
Neoadjuvant anti-PD-1 immunotherapy promotes a survival benefit with intratumoral and systemic immune responses in recurrent glioblastoma	Cloughesy TF, Mochizuki AY, Orpilla JR, Hugo W, Lee AH, Davidson TB, Wang AC, Ellingson BM, Rytlewski JA, Sanders CM, Kawaguchi ES, Du L, Li G, Yong WH, Gaffey SC, Cohen AL, Mellinghoff IK, Lee EQ, Reardon DA, OBrien BJ, Butowski NA, Nghiemphu PL, Clarke JL, Arrillaga-Romany IC, Colman H, Kaley TJ, de Groot JF, Liau LM, Wen PY, Prins RM	2019	Nature Medicine	Oncology, Immuno-oncology	Spatial Analysis, Highplex FL	HALO
PAK4 inhibition improves PD-1 blockade immunotherapy	Abril-Rodriguez G, Torrejon DY, Liu W, Zaretsky JM, Nowick TS, Tsoi J, Puig-Saus C, Baselga-Carretero I, Medina E, Quist MJ, Garcia AJ, Senapedis W, Baloglu E, Kalbasi A, Cheung-Lau G, Berent-Maoz B, Comin-Anduix B, Hu-Lieskovan S, Wang C-Y, Grasso CS, Ribas A	2019	Nature Cancer	Immuno-oncology		HALO
Histological characterization of aldosterone-producing adrenocortical adenomas with different somatic mutations	Acosta-Ruiz A, Gutzeit VA, Skelly MJ, Meadows S, Lee J, Parekh P, Orr AG, Liston C, Pleil KE, Broichhagan J, Levitz J	2019	Neuron	Neuroscience		HALO
Amyloid-Beta (A?) Plaques Promote Seeding and Spreading of Alpha-Synuclein and Tau in a Mouse Model of Lewy Body Disorders with A? Pathology	Bassil F, Brown HJ, Pattabhiraman S, Iwasyk JE, Maghames CM, Meymand ES, Cox TO, Riddle FM, BinZhang N, Trojanowski JQ, Lee VM-Y	2019	Neuron	Neuroscience		HALO
Rabbit monoclonal E?cadherin antibody: A cost?effective alternative to mouse monoclonal antibody in distinguishing ductal carcinoma in situ from lobular carcinoma in situ	Baum JE, Croyle JA, Brodsky VB, Liu Y, Shin SJ	2019	The Breast Journal	Oncology	Cytonuclear	HALO
MAPKAPK2 (MK2) inhibition mediates radiation-induced inflammatory cytokine production and tumor growth in head and neck squamous cell carcinoma	Berggren KL, Cruz SR, Hixon MD, Cowan AT, Keysar SB, Craig S, James J, Barry M, Ozbun MA, Jimeno A, McCance DJ, Beswick EJ, Gan GN	2019	Oncogene	Oncology	Cytonuclear, Figure Maker	HALO
Pre-diagnostic anthropometry, sex, and risk of colorectal cancer according to tumor immune cell composition	Berntsson J, Eberhard J, Nodin B, Leandersson K, Larsson AH, Eberhard J, Jirstrom K	2019	OncoImmunology	Immuno-oncology		HALO
Single cell transcriptomic profiling of large intestinal enteroendocrine cells in mice - Identification of selective stimuli for insulin-like peptide-5 and glucagon-like peptide-1 co-expressing cells	Billing LJ, Larraufie P, Lewis J, Leiter A, Li J, Lam B, Yeo GSH, Goldspink DA, Kay RG, Gribble FM, Reimann F	2019	Molecular Metabolism	Metabolism		HALO
Genetic mutations underlying phenotypic plasticity in basosquamous carcinoma	Chiang A, Tan CZ, Kuonen F, Hodgkinson LM, Chiang F, Cho RJ, South AP, Tang Jean Y, Chang ALS, Rieger KE, Oro AE, Sarin KY	2019	Journal of Investigative Dermatology	Oncology	Cytonuclear	HALO
Kras and Lkb1 mutations synergistically induce intraductal papillary mucinous neoplasm derived from pancreatic duct cells	Collet L, Ghurburrun E, Meyers N, Assi M, Pirlot B, Leclercq IA, Couvelard A, Komuta M, Cros J, Demetter P, Lemaigre FP, Borbath I, Jacquemin P	2019	Gut	Oncology		HALO
Next-generation computational tools for interrogating cancer immunity	Finotello F, Rieder D, Hackl H, Trajanoski Z	2019	Nature Reviews Genetics	Review		HALO
The crosstalk between aldosterone and calcium metabolism in primary aldosteronism: A possible calcium metabolism-associated aberrant neoplastic steroidogenesis in adrenals	Gao X, Yamazaki Y, Tezuka Y, Onodera Y, Ogata H, Omata K, Morimoto R, Nakamura Y, Satoh F, Sasano H	2019	The Journal of Steroid Biochemistry and Molecular Biology	Oncology, Metabolism	Cytonuclear	HALO
Farnesoid X Receptor Agonism, AcetylCoenzyme A Carboxylase Inhibition, and Back Translation of Clinically Observed Endpoints of De Novo Lipogenesis in a Murine NASH Model	Gapp B, Jourdain M, Bringer P, Kueng B, Weber D, Osmont A, Zurbruegg S, Knehr J, Falchetto R, Roma G, Dietrich W, Valdez R, Beckmann N, Nigsch F, Sanyal AJ, Ksiazek I	2019	Hepatology Communications	Metabolism	Cytonuclear	HALO
Open radial artery harvesting better preserves endothelial function compared to the endoscopic approach	Gaudino MF, Lorusso R, Ohmes LB, Narula N, McIntire PJ, Gargiulo A, Bucci MR, Leonard J, Rahouma M, Di Franco A, He GW, Girardi LN, Tranbaugh RF, Di Lorenzo A	2019	Interactive CardioVascular and Thoracic Surgery			HALO
Dynamic changes to lipid mediators support transitions among macrophage subtypes during muscle regeneration	Giannakis N, Sansbury BE, Patsalos A, Hays TT, Riley CO, Han X, Spite M, Nagy L	2019	Nature Immunology	Immunology, Myology	Muscle Fiber	HALO
Evaluation of Peritumoral Fibrosis in Metastatic Colorectal Adenocarcinoma to the Liver Using Digital Image Analysis	Waters KM, Cottrell TR, Besharati S, Zhu Q, Anders RA	2019	American Journal of Clinical Pathology	Oncology	Area Quantification, Partitions (tiles, margins)	HALO
Cross-Platform Comparison of Computer-assisted Image Analysis Quantification of In Situ mRNA Hybridization in Investigative Pathology.	Holzer TR, Hanson JC, Wray EM, Bailey JA, Kennedy KR, Finnegan PR, Nasir A, Credille KM	2019	Applied Immunohistochemistry & Molecular Morpholgy			HALO
Oral tenofovir disoproxil fumarate/emtricitabine for HIV pre-exposure prophylaxis increases expression of type I/III interferon-stimulated factors in the gastrointestinal tract but not in the blood	Hughes SM, Levy CN, Calienes F, Stekler JD, Pandey U, Vojtech L, Berard AR, Birse K, Noel-Romas L, Richardson B, Golden J, Cartwright M, Collier AC, Stevens CE, Curlin ME, Holtz TH, Mugo N, Irungu E, Katabira E, Muwonge T, Lama JR, Baeten JM, Burgener A, Lingappa JR, McElrath MJ, Mackelprang R, McGowan I, Cranston RD, Cameron MJ, Hladik F	2019	bioRxiv	Infectious Disease	Cytonuclear	HALO
Intraintestinal and Parenteral Administration of an Insulin Analogue Leads to Comparable Activation of Signaling Downstream of the Insulin Receptor in the Small Intestine	Hvid H, Kildegaard J, Kristensen K, Porsgaard T, Jørgensen MS, Ballarín-González B, Ahnfelt-Rønne J, Hansen Bo F, Nishimura E	2019	Journal of Diabetes Science and Technology	Metabolism		HALO
Epithelial NOTCH Signaling Rewires the Tumor Microenvironment of Colorectal Cancer to Drive Poor-Prognosis Subtypes and Metastasis	Jackstadt R, van Hooff ST, Leach JD, Cortes-Lavaud X, Lohuis JO, Ridgway RA, Wouters VM, JatinRoper J, Kendall TJ, Roxburgh CS, Horgan PG, Nixon C, Nourse C, Gunzer M, Clark W, Hedley A, Yilmaz OH, Rashid M, Bailey P, Biankin AV, Campbell AD, Adams DJ, Barry ST, Steele CW, Medema JP, Sansom OJ	2019	Cancer Cell	Oncology		HALO
Expression of avian ?-defensin mRNA in the chicken yolk sac	Zhang H, Wong EA	2019	Developmental & Comparative Immunology	Immunology	ISH/FISH	HALO
Lenvatinib plus anti-PD-1 antibody combination treatment activates CD8+ T cells through reduction of tumor-associated macrophage and activation of the interferon pathway	Kato Y, Tabata K, Kimura T, Yachie-Kinoshita A, Ozawa Y, Yamada K, Ito J, Tachino S, Hori Y, Matsuki M, Matsuoka Y, Ghosh S, Kitano H, Nomoto K, Matsui J, Funahashi Y	2019	PLOS One	Immuno-oncology		HALO
Calpain 9 as a therapeutic target in TGF?-induced mesenchymal transition and fibrosis	Kim DH, Beckett JD, Nagpal V, Seman-Senderos MA, Gould Russell A, Creamer TJ, MacFarlane EG, Chen Y, Bedja D, Butcher JT, Mitzner W, Rouf R, Hata S, Warren DS, Dietz HC	2019	Science Translational Medicine	Fibrosis		HALO
Delayed Azithromycin Treatment Improves Recovery After Mouse Spinal Cord Injury	Kopper TJ, McFarlane KE, Bailey WM, Orr MB, Zhang B, Gensel JC	2019	Frontiers in Ceullar Neuroscience	Neuroscience		HALO
Long-Term Persistence of Anti-HIV Broadly Neutralizing Antibody-Secreting Hematopoietic Cells in Humanized Mice	Kuhlmann A-S, Haworth KG, Barber-Axthelm IM, Ironside C, Giese MA, Peterson CW, Kiem H-P	2019	Molecular Therapy	Infectious Disease		HALO
Temporal Analysis of Amylase Expression in Control, Autoantibody Positive, and Type 1 Diabetes Pancreatic Tissues	Kusmartseva I, Beery M, Hiller H, Padilla M, Selman S, Posgai A, Nick HS, Campbell-Thompson M, Schatz DA, Haller MJ, Wasserfall CH, Atkinson MA	2019	Diabetes	Metabolism		HALO
Phosphorylation of connexin 43 at MAPK, PKC or CK1 sites each distinctly alter the kinetics of epidermal wound repair	Lastwika JK, Dunn CA, Solan JL, Lampe PD	2019	Journal of Cell Science			HALO
Active Cushing's Disease is Characterized by Increased Adipose Tissue Macrophage Presence	Lee IT, Atuahene A, Egritag HE, Buettner C, Wang L, Geer EB, Donovan M	2019	The Journal of Clinical Endocrinology & Metabolism	Metabolism		HALO
Impact of a Pre-Operative Exercise Intervention on Breast Cancer Proliferation and Gene Expression: Results from the Pre-Operative Health and Body (PreHAB) Study	Ligibel JA, Dillon D, Giobbie-Hurder A, McTiernan A, Frank E, Cornwell M, Pun M, Campbell N, Dowling RJO, Chang MC, Tolaney S, Chagpar AB, Yung RL, Freedman RA, Dominici LS, Golshan M, Rhei E, Taneja K, Huang Y, Brown M, Winer EP, Jeselsohn R, Irwin ML	2019	Clinical Cancer Research			HALO
A phase 2 study of GVAX colon vaccine with cyclophosphamide and pembrolizumab in patients with mismatch repair proficient advanced colorectal cancer	Yarchoan M, Huang C-Y, Zhu Q, Ferguson AK, Durham JN, Anders RA, Thompson ED, Rozich NS, Thomas DL, Nauroth JM, Rodriguez C, Osipov A, De Jesus-Acosta A, Le DT, Murphy AG, Laheru D, Donehower RC, Jaffee EM, Zheng L, Azad NS	2019	Cancer Medicine	Immuno-oncology	Area Quantification, Partitions (tiles, margins)	HALO
Hotspot enumeration of CD8+ tumor infiltrating lymphocyte using digital image analysis in triple negative breast Cancer yields consistent results	McIntire PJ, Zhong E, Patel A, Khani F, D'Alfonso T, Chen Z, Shin SJ, Ginter PS	2019	Human Pathology	Oncology	Cytonuclear	HALO
Female-biased embryonic death from inflammation induced by genomic instability	McNairn AJ, Chuang C-H, Bloom JC, Wallace MD, Schimenti JC	2019	Nature	Immunology	Cytonuclear	HALO
Imaging CAR T cell therapy with PSMA-targeted positron emission tomography	Minn I, Huss DJ, Ahn H-H, Chinn TM, Park A, Jones J, Brummet M, Rowe SP, Sysa-Shah P, Du Y, Levitsky HI, Pomper MG	2019	Science Advances	Oncology	Cytonuclear	HALO
Reliable identification of prostate cancer using mass spectrometry metabolomic imaging in needle core biopsies	Morse N, Jamaspishvili T, Simon D, Patel PG, Ren KYM, Wang J, Oleschuk R, Kaufmann M, Gooding RJ, Berman DM	2019	Laboratory Invesigations	Oncology		HALO
Efficacy of ruthenium coordination complex-based Rutherrin in a preclinical rat glioblastoma model	Munegowda MA, Fisher C, Molehuis D, Foltz W, Roufaiel M, Bassan J, Nitz M, Mandel A, Lilge L	2019	Neuro-Oncology Advances			HALO
HIF-independent synthetic lethality between CDK4/6 inhibition and VHL loss across species	Nicholson HE, Tariq Z, Housden BE, Jennings RB, Stransky LA, Perrimon N, Signoretti S, Kaelin WG	2019	Cancer Therapy			HALO
Prohibitin is a prognostic marker of relapse and therapeutic target to block chemotherapy resistance in Wilms tumor	Ortiz MV, Ahmed S, Burns M, Henssen AG, Hollmann TJ, MacArthur I, Gunasekera S, Gaewsky L, Bradwin G, Ryan J, Letai A, He Y, Naranjo A, Chi Y-Y, LaQuaglia M, Heaton T, Cifani P, Dome JS, Gadd S, Perlman E, Mullen E, Steen H, Kentsis A	2019	JCI Insight	Oncology	Cytonuclear	HALO
Validation and characterisation of prognostically significant PD-L1+ immune cells in HPV+ oropharyngeal squamous cell carcinoma	Young RJ, Bressel M, Porceddu S, Cernelc J, Savas P, Liu H, Urban D, Thai AA, Cooper C, Fua T, Neeson P, Rischin D, Solomon B	2019	Oral Oncology	Oncology, Infectious Disease	Classifier, Highplex FL	HALO
Human 3D Gastrointestinal Microtissue Barrier Function As a Predictor of Drug-Induced Diarrhea	Peters MF, Landry T, Pin C, Maratea K, Dick C, Wagoner MP, Choy AL, Barthlow H, Snow D, Stevens Z, Armento A, Scott CW, Ayehunie S	2019	Toxicological Sciences	Gastroenterology		HALO
PTEN loss in Gleason grade 7 prostate tumors exhibits intratumoral heterogeneity and is associated with unfavorable pathological features	Picanço-Albuquerque CG, Vidotto T, Pereira CS, Saggioro FP, Jamaspishvili T, Koti M, Berman DM, Squire JA, Reis RB	2019	Applied Cancer Research	Oncology		HALO
Extramammary Paget disease shows differential expression of B7 family members B7-H3, B7-H4, PD-L1, PD-L2 and cancer/testis antigens NY-ESO-1 and MAGE-A	Pourmaleki M, Young JH, Socci ND, Chiang S, Edelweiss M, Li Y, Zhang M, Roshal L, Chi DS, Busam KJ, Mellinghoff IK, Hollmann TJ	2019	Oncotarget			HALO
Impact of TREM2 risk variants on brain region-specific immune activation and plaque microenvironment in Alzheimer's disease patient brain samples	Prokop S, Miller KR, Labra SR, Pitkin RM, Hoxha K, Narasimhan S, Changolkar L, Rosenbloom A, Lee VM-Y, Trojanowski JQ	2019	Acta Neuropathologica	Neuroscience		HALO
Delta-like protein 3 expression and therapeutic targeting in neuroendocrine prostate cancer	Puca L, Gavyert K, Sailer V, Conteduca V, Dardenne E, Sigouros M, Isse K, Kearney M, Vosoughi A, Fernandez L, Pan H, Motanagh S, Hess J, Donoghue AJ, Sboner A, Wang Y, Dittamore R, Rickman D, Nanus DM, Tagawa ST, Elemento O, Mosquera JM, Saunders L, Beltran H	2019	Science Translational Medicine	Oncology		HALO
Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells	Reitman ZJ, Paolella BR, Bergthold G, Pelton K, Becker S, Jones R, Sinai CE, Malkin H, Huang Y, Grimmet L, Herbert ZT, Sun Y, Weatherbee JL, Alberta JA, Daley JF, Rozenblatt-Rosen O, Condurat AL, Qian K, Khadka P, Segal RA, Haas-Kogan D, Filbin MG, Suva ML, Regev A, Stiles CD, Kieran MW, Goumnerova L, Ligon KL, Shalek AK, Bandopadhayay P, Beroukhim R	2019	Nature Communications	Oncology		HALO
Pre-exposure prophylaxis differentially alters circulating and mucosal immune cell activation in herpes simplex virus type 2 seropositive women	Richert-Spuhler LE, Pattacini L, Plews M, Irungu E, Muwonge TR, Katabira E, Mugo N, Meyers AFA, Celum C, Baeten JM, Lingappa JR, Lund JM	2019	AIDS	Infectious Disease		HALO
A MYCGCN2eIF2? negative feedback loop limits protein synthesis to prevent MYC-dependent apoptosis in colorectal cancer	Schmidt S, Gay D, Uthe FW, Denk S, Paauwe M, Matthes N, Diefenbacher ME, Bryson S, Warrander FC, Erhard F, Ade CP, Baluapuri A, Walz S, Jackstadt R, Ford C, Vlachogiannis G, Valeri N, Otto C, Schülein-Völk C, Maurus K, Schmitz W, Knight JRP, Wolf E, Strathdee D, Schulze A, Germer C-T, Rosenwald A, Sansom OJ, Eilers M	2019	Nature Cell Biology	Oncology		HALO
Mobilization of CD8+ T cells via CXCR4 blockade facilitates PD-1 checkpoint therapy in human pancreatic cancer	Seo YD, Jiang X, Sullivan KM, Jalikis FG, Smythe KS, Abbasi A, Vignali M, Park JO, Daniel SK, Pollack SM, Kim TS, Yeung R, Crispe IN, Pierce RH, Robins H, Pillarisetty VG	2019	Clinical Cancer Research	Immuno-oncology		HALO
Targeting glutamate metabolism in melanoma	Singh S, Shah R, Chen S, Filipp FV	2019	arXiv			HALO
Logic-Gated ROR1 Chimeric Antigen Receptor Expression Rescues T Cell-Mediated Toxicity to Normal Tissues and Enables Selective Tumor Targeting	Srivastava S, Salter A, Liggitt D, Yechan-Gunja S, Sarvothama M, Cooper K, Smythe KS, Dudakov JA, Pierce RH, Rader C, Riddell SR	2019	Cancer Cell	Oncology, Immuno-oncology		HALO
Citrullination of fibronectin alters integrin clustering and focal adhesion stability promoting stromal cell invasion	Stefanelli VL, Choudhury S, Hu P, Liu Y, Schwenzer A, Yeh C-R, Chambers DM, Pesson K, Li W, Segura T, Midwood KS, Torres M, Barker TH	2019	Matrix Biology	Oncology, Fibrosis		HALO
A Short Isoform of Coagulation Factor XII mRNA Is Expressed by Neurons in the Human Brainl	Zamolodchikov D, Bai Y, Tang Y, McWhirter JR, Macdonald LE, Alessandri-Haber N	2019	Neuroscience	Neuroscience	Figure Maker	HALO
Automated macrophage counting in DLBCL tissue samples: a ROF filter based approach	Wagner M, Hansel R, Reinke S, Richter J, Altenbuchinger M, Braumann U-D, Spang R, Loffler Mk Klapper W	2019	Biological Proectures Online	Oncology	Object Colocalization	HALO
Impact of pre?therapy glioblastoma multiforme microenvironment on clinical response to autologous CMV?specific T?cell therapy	Walker DG, Shakya R, Morrison B, Neller MA, Matthews KK, Nicholls J, Smith C, Khanna R	2019	Clinical & Translational Immunology	Immuno-oncology	Classifier	HALO
Human pseudoislet system enables detection of differences in G-protein-coupledreceptor signaling pathways between ? and ? cells	Walker JT, Haliyur R, Nelson HA, Ishahak M, Poffenberger G, Aramandla R, Reihsmann C, Luchsinger JR, Saunders DC, Wang P, Garcia-Ocana A, Bottino R, Agarwal A, Powers AC, Brissove M	2019	bioRxiv			HALO
Multiplex Immunofluorescence of Bone Marrow Core Biopsies: Visualizing the Bone Marrow Immune Contexture	Walters DK, Jelinek DF	2019	Journal of Histochemistry & Cytochemistry			HALO
No Evidence of Neurogenesis in Adult Rat Sympathetic Ganglia Following Guanethidine-Induced Neuronal Loss	Walters KM, Boucher M, Boucher GG, Opsahl AC, Mouton PR, Liu C-N, Ritenour CR, Kawabe TT, Pryski HN, Somps CJ	2019	Toxicologic Pathology	Toxicology, Neuroscience		HALO
ATDC is required for the initiation of KRAS-induced pancreatic tumorigenesis	Wang L, Yang H, Zamperone A, Diolaiti D, Palmbos PL, Abel EV, Purohit V, Dolgalev I, Rhim AD, Ljungman M, Hadju CH, Halbrook CJ, Bar-Sagi D, di Magliano MP, Crawford HC, Simeone DM	2019	Genes & Development	Oncology		HALO
Monocytes/Macrophages play a pathogenic role in IL-23 mediated psoriasis-like skin inflammation	Wang Y, Edelmayer R, Wetter J, Salte K, Gauvin D, Leys L, Paulsboe S, Su Z, Weinberg I, Namovic M, Gauld SB, Honore P, Scott VE, McGaraughty S	2019	Scientific Reports	Immunology, Dermatology		HALO
Myeloid Cell-Derived HB-EGF Drives Tissue Recovery After Pancreatitis	Wen H-J, Gao S, Wang Y, Ray M, Magnuson MA, Wright CVE, Di Magliano MP, Frankel TL, Crawford HC	2019	Cellular and Molecular Gastroenterology and Hepatology	Immunology		HALO
Nrf2 represses the onset of type 1 diabetes in non-obese diabetic mice	Yagishita Y, Uruno A, Chartoumpekis DV, Kensler TW, Yamamoto M	2019	The Journal of Endocrinology	Metabolism		HALO
Systemic mRNA Therapy for the Treatment of Fabry Disease: Preclinical Studies in Wild-Type Mice, Fabry Mouse Model, and Wild-Type Non-human Primates	Zhu S, Li S, Escuin-Ordinas H, Dimatteo R, Xia W, Ribas A, Segura T	2019	The American Journal of Human Genetics	Metabolism		HALO
Selective modulation of the androgen receptor AF2 domain rescues degeneration in spinal bulbar muscular atrophy	Badders NM, Korff A, Miranda HC, Vuppala PK, Smith RB, Winborn BJ, Quemin ER, Sopher BL, Dearman J, Messing J, Kim NC, Moore J, Freibaum BD, Kanagaraj AP, Fan B, Tillman H, Chen P-C, Wang Y, Freeman BB, Li Y, Kim HJ, La Spada AR, Taylor JP	2018	Nature Medicine	Myology	Area Quantification	HALO
Anti-NKG2A mAb Is a Checkpoint Inhibitor that Promotes Anti-tumor Immunity by Unleashing Both T and NK Cells	Andre ?P, Denis C, Soulas C, Bourbon-Caillet C, Lopez J, Arnoux T, Ble?ry M, Bonnafous C, Gauthier L, Morel A, Rossi B, Remark R, Breso V, Bonnet E, Habif G, Guia S, Lalanne AI, Hoffmann C, Lantz O, Fayette J, Boyer-Chammard A, Zerbib R, Dodion P, Ghadially H, Jure-Kunkel M, Morel Y, Herbst R, Narni-Mancinelli E, Cohen RB, Vivier E	2018	Cell	Oncology, Immuno-oncology	Area Quantification, Cytonuclear	HALO
Tuning of delta-protocadherin adhesion through combinatorial	Bisogni AJ, Ghazanfar S, Williams EO, Marsh HM, Yang JYH, Lin DM	2018	eLife	Neuroscience	Area Quantification	HALO
RAD51 foci as a functional biomarker of homologous recombination repair and PARP inhibitor resistance in germline BRCA mutated breast cancer	Cruz C, Castroviejo-Bermejo M, Gutiérrez-Enríquez S, Llop-Guevara A, Ibrahim YH, Gris-Oliver A, Bonache S, Morancho B, Bruna A, Rueda OM, Lai Z, Polanska UM, Jones GN,Kristel P, de Bustos L, Guzman M, Rodriguez O, Grueso J, Montalban G, Caratú G, Mancuso F, Fasani R, Jiménez J, Howat WJ, Dougherty B, Vivancos A, Nuciforo P, Serres-Créixams X, Rubio IT, Oaknin A, Cadogan O, Barrett JC, Caldas C, Baselga J, Saura C, Cortés J, Arribas J, Jonkers J, Díez O, OConnor MJ, Balmaña J, SerraV	2018	Annals of Oncology	Oncology	Classifier, Cytonuclear	HALO
The brain-penetrant clinical ATM inhibitor AZD1390 radiosensitizes and improves survival of preclinical brain tumor models	Durant ST, Zheng L, Wang Y, Chen K, Zhang L, Zhang T, Yang Z, Riches L, Trinidad AG, Fok JHL, Hunt T, Pike KG, Wilson J, Smith A, Colclough N, Reddy VP, Sykes A, Janefeldt A, Johnström P, Varnäs K, Takano A, Ling S, Orme J, Stott J, Roberts C, Barrett I, Jones G, Roudier M, Pierce A, Allen J, Kahn J, Sule A, Karlin J, Cronin A, Chapman M, Valerie K, Illingworth R, Pass M	2018	Science Advances	Oncology, Neuroscience	Classifier, Cytonuclear	HALO
High response rate to PD-1 blockade in desmoplastic melanomas	Eroglu Z, Zaretsky JM, Hu-Lieskovan H, Kim DW, Algazi A, Johnson DB, Liniker E, Kong B, Munhoz R, Rapisuwon S, Gherardini PF, Chmielowski B, Wang X, Shintaku IP, Wei C, Sosman JA, Joseph RW, Postow MA, Carlino MS, Hwu W-J, Scolyer RA, Messina J, Cochran AJ, Long GV, Ribas A	2018	Nature	Oncology, Immuno-oncology	Cytonuclear	HALO
Early Stage HER2-Positive Breast Cancers Not Achieving a pCR From Neoadjuvant Trastuzumab- or Pertuzumab-Based Regimens Have an Immunosuppressive Phenotype	Force J, Howie LJ, Abbot SE, Bentley R, Marcom PK, Kimmick G, Westbrook K, Sammons SL, Parks M, Topping DL, Emerson R, Broadwater G, Hyslop T, Blackwell KL, Nair SK	2018	Clinical Breast Cancer	Oncology, Immuno-oncology	Cytonuclear	HALO
Bortezomib prevents cytarabine resistance in MCL, which is characterized by down-regulation of dCK and up-regulation of SPIB resulting in high NF-?B activity	Freiburghaus C, Emruli VK, Johansson A, Eskelund CW, Grønbæk K, Olsson R, Ek F, Jerkeman M, Ek S	2018	BMC Cancer	Oncology	Classifier, Cytonuclear	HALO
The novel ATM inhbitior (AZ31) enhances antitumor activity in patient derived xenografts that are resistant to irinotecan montherapy	Greene J, Nguyen A, Bagby SM, Jones GN, Tai WM, Quackenbush KS, Schreiber A, Messersmith WA, Devaraj KM, Blatchford P, Eckhardt SG, Cadogan EB, Hughes GD, Smith A, Pitts TM, Arcaroli JJ	2018	Oncotarget	Oncology	Classifier, Area Quantification, Cytonuclear	HALO
Cystic fibrosisrelated diabetes is caused by islet loss and inflammation	Hart NJ, Aramandla R, Poffenberger G, Fayolle C, Thames AH, Bautista A, Spigelman AF, Babon JAB, DeNicola ME, Dadi PK, Bush WS, Balamurugan AN, Brissova M, Dai C, Prasad N, Bottino R, Jacobson DA, Drumm ML, Kent SC, MacDonald PE, Powers AC	2018	JHI Insights	Immunology, Metabolism, Fibrosis	Cytonuclear	HALO
Attenuation of diet-induced hypotalamic inflammation following bariatric surgery in female mice	Herrick MK, Favela KM, Simerly RB, Abumrad NN, Bingham NC	2018	Molecular Medicine	Immunology, Neuroscience	Cytonuclear	HALO
pRAD50: a novel and clinically applicable pharmacodynamic biomarker of both ATM and ATR inhibition identified using mass spectrometry and immunohistochemistry	Jones GN, Rooney C, Griffin N, Roudier M, Young LA, Garcia-Trinidad A, Hughes GD, Whiteaker JR, Wilson Z, Odedra R, Zhao L, Ivey RG, Howat WJ, Harrington EA, Carrett JC, Ramos-Montoya A, Lau A, Paulovich AG, Cadogan EB, Pierce AJ	2018	British Journal of Cancer	Oncology	Classifier, Cytonuclear	HALO
Mice harboring the human SLC30A8 R138X loss-of-function mutation have increased insulin secretory capacity	Kleinera S, Gomeza D, Megraa B, Naa E, Bhavsara R, Cavinoa K, Xina Y, Rojasa J, Dominguez-Gutierreza G, Zambrowicza B, Carratb G, Chabosseaub P, Hub M, Murphya AJ, Yancopoulosa GD, Rutterb GA, Gromadaa J	2018	Proceedings of the National Academy of Sciences	Metabolism	Cytonuclear	HALO
TGF? inhibition restores a regenerative response in acute liver injury by suppressing paracrine senescence	Bird TG, Müller M, Boulter L, Vincent DF, Ridgway RA, Elena Lopez-Guadamillas E, Lu W-Y, Jamieson T, Govaere O, Campbell AD, Ferreira-Gonzalez S, Cole AM, Hay T, Simpson KJ, Clark W, Hedley A, Clarke M, Gentaz P, Nixon C, Bryce S, Kiourtis C, Sprangers J, Nibbs RJB, Van Rooijen N, Bartholin L, McGreal SR, Apte U, Barry ST, Iredale JP, Clarke AR, Serrano M, Roskams TA, Sansom OJ, Forbes SJ	2018	Science Translational Medicine	Metabolism	ISH/FISH	HALO
Food Perception Primes Hepatic ER Homeostasis via Melanocortin-Dependent Control of mTOR Activation	Brandt C, Nolte H, Henschke S, Ruud LE, Awazawa M, Morgan DA, Gabel P, Sprenger H-G, Hess ME, Günther S, Langer T, Rahmouni K, Fenselau H, Krüger M, Brüning JC	2018	Cell	Neuroscience, Metabolism	ISH/FISH	HALO
Gene Signature of Proliferating Human Pancreatic ?-Cells	Dominguez Gutierrez G, Xin Y, Okamoto H, Kim J, Lee A-H, Ni M, Adler C, Yancopoulos GD, Murphy AJ, Gromada J	2018	Endocrionology	Metabolism	ISH/FISH	HALO
A phase II study of the dual mTOR inhibitor MLN0128 in patients with metastatic castration resistant prostate cancer	Graham L, Banda K, Torres A, Carver BS, Chen Y, Pisano K, Shelkey G, Curley T, Scher HI, Lotan TL, Hsieh AC, Rathkopf DE	2018	Investigational New Drugs	Oncology	ISH/FISH	HALO
Ultrasensitive automated RNA in situ hybridization for kappa and lambda light chain mRNA detects B-cell clonality in tissue biopsies with performance comparable or superior to flow cytometry	Guo L, Wang Z, Anderson CA, Doolittle E, Kernag S, Cotta CV, Ondrejka SL, Ma X-J, Cook JR	2018	Modern Pathology	Other	Classifier, ISH/FISH	HALO
CD163+ macrophages promote angiogenesis and vascular permeability accompanied by inflammation in atherosclerosis	Guo L, Akahori H, Harari E, Smith SL, Polavarapu R, Karmali V, Otsuka F, Gannon RL, Braumann RE, Dickinson MH, Gupta A, Jenkins AL, Lipinski MJ, Kim J, Chhour P, de Vries PS, Jinnouchi H, Kutys R, Mori H, Kutyna MD, Torii S, Sakamoto A, Choi CU, Cheng Q, Grove M, Mariem A. Sawan MA, Zhang Y, Cao Y, Kolodgie FD, Cormode DP, Arking DE, Boerwinkle E, Morrison AC, Erdmann J, Sotoodehnia N, Virmani R, and Finn AV	2018	The Journal of Clinical Investigation	Immunology	Layer Thickness	HALO
Glucagon contibutes to liver zonation	Cheng X, Kim SK, Okamoto H, Xin Y, Yancopoulos GD, Murphy AJ, Gromada J	2018	Proceedings of the National Academy of Sciences	Metabolism	Area Quantification	HALO
Evaluation of PD-L1 expression on vortex-isolated circulating tumor cells in metastatic lung cancer	Dhar M, Wong J, Che J, Matsumoto M, Grogan T, Elashof D, Garon EB, Goldman JW, Christen ES, Carlo DD, Kulkarni RP	2018	Scientific Reports	Oncology, Immuno-oncology	Area Quantification	HALO
Digital image analysis of Ki67 proliferation index in breast cancer using virtual dual staining on whole tissue sections: clinical validation and inter?platform agreement	Koopman T, Buikema HJ, Hollema H, de Bock GH, van der Vegt B	2018	Breast Cancer Research and Treatment	Oncology	Classifier, Cytonuclear	HALO
The neurotrophic tyrosine kinase receptor TrkA and its ligand NGF are increased in squamous cell carcinomas of the lung	Gao F, Griffin N, Faulkner S, Rowe CW, Williams L, Roselli S, Thorne RF, Ferdoush A, Jobling P, Walker MM, Hondermarck H	2018	Scientific Reports	Oncology	Area Quantification	HALO
Ovarian Tumor Microenvironment Signaling: Convergence on the Rac1 GTPase	Hudson LG, Gillette JM, Kang H, Rivera MR, Wandinger-Ness A	2018	Cancers	Review	Classifier, Cytonuclear, Figure Maker	HALO
A murine glaucoma model induced by rapid in vivo photopolymerization of hyaluronic acid glycidyl methacrylate	Guo C, Qu X, Rangaswamy N, Leehy B, Xiang C, Rice D, Prasanna G	2018	PLOS One	Biomaterials	Area Quantification	HALO
Systemic messenger RNA as an etiological treatment for acute intermittent porphyria	Jiang L, Berraondo P, Jericó D, Guey LT, Sampedro A, Frassetto A, Benenato KE, Burke K, Santamaría E, Alegre M, Pejenaute A, Kalariya M, Butcher W, Park JS, Zhu X, Sabnis S, Kumarasinghe ES, Salerno T, Kenney M, Lukacs CM, Ávila MA, Martini PGV, Fontanellas A	2018	Nature Medicine	Metabolism	Area Quantification	HALO
Tumor Microenvironment in Functional Adrenocortical Adenomas: Immune Cell Infiltration in Cortisol-producing Adrenocortical Adenoma	Kitawaki Y, Nakamura Y, Kubota-Nakayama F, YamazakiY, Miki Y, Hata S, Ise K, Kikuchie K, MorimotoR, Satoh F, Sasano H	2018	Human Pathology	Oncology, Immuno-oncology	Area Quantification	HALO
Up-Regulation of Iba-1 and GFAP in the Acidic Saline Model of Chronic Widespread Musculoskeletal Pain: A Pilot Study Examining the Relationship Between Gliosis and Hyperalgesia	Lambert DM, Kumar U, Hafell UO	2018	Journal of Neuroscience and Neuropharmacology	Neuroscience	Area Quantification, Partitions (tiles, margins)	HALO
Tough Composite Hydrogels with High Loading and Local Release of Biological Drugs	Li J, Weber E, Guth?Gundel S, Schuleit M, Kuttler A, Halleux C, Accart N, Doelemeyer A, Basler A, Tigani B, Wuersch K, Fornaro M, Kneissel M, Stafford A, Freedman BR, Mooney DJ	2018	Advanced Healthcare Materials	Biomaterials	Area Quantification	HALO
Blocking HIF signaling via novel inhibitors of CA9 and APE1/Ref-1 dramatically affects pancreatic cancer cell survival	Logsdon DP, Fenil S, Fabrizio C, Supuran CT, Kamocka M, Jacobsen MH, Sandusky GE, Kelley MR, Fishel ML	2018	Scientific Reports	Oncology	Classifier, Cytonuclear	HALO
Diet-Induced Growth Is Regulated via Acquired Leptin Resistance and Engages a PomcSomatostatin-Growth Hormone Circuit	Lohr H, Hess S, Pereira MMA, Reino P, Leibold S, Schenkel C, Wunderlich CM, Kloppenburg P, Bruning JC, Hammerschmidt M	2018	Cell Reports	Neuroscience, Metabolism	Cytonuclear	HALO
Chronic Intermittent Hypoxia Induces Robust Astrogliosis in an Alzheimer's Disease-Relevant Mouse Model	Macheda T, Roberts K, Lyons DN, Higgins E, Ritter KJ, Lin A-L, Alilain WJ, Bachstetter AD	2018	Neuroscience	Neuroscience	Area Quantification	HALO
Cellular milieu imparts distinct pathological ?-synuclein strains in ?-synucleinopathies	Peng C, Gathagan RJ, Covell DJ, Medellin C, Stieber A, Robinson JL, Zhang B, Pitkin RM, Olufemi MF, Luk KC, Trojanowski JQ, Lee VM-Y	2018	Nature	Neuroscience	Area Quantification	HALO
Differential ?-synuclein expression contributes to selective vulnerability of hippocampal neuron subpopulations to fibril-induced toxicity	Luna E, Decker SC, Riddle DM, Caputo A, Zhang B, Cole T, Caswell C, Xie SX, Lee VMY, Luk KC	2018	Acta Neuopathologica	Neuroscience	Area Quantification, Cytonuclear	HALO
Digital image analysis improves precision of PD?L1 scoring in cutaneous melanoma	Koelzer VH, Gisler A, Hanhart JC, Griss J, Wagner SN, Willi N, Cathomas G, Sachs M, Kempf W, Thommen DS, Mertz KD	2018	Histopathology	Oncology, Immuno-oncology	Classifier, Multiplex IHC	HALO
Lenvatinib inhibits angiogenesis and tumor fibroblast growth factor signaling pathways in human hepatocellular carcinoma models	Matsuki M, Hoshi T, Yamamoto Y, Ikemori-Kawada M, Minoshima Y, Funahashi Y, Matsui J	2018	Cancer Medicine	Oncology	Cytonuclear	HALO
Hot Spot and Whole-Tumor Enumeration of CD8(+) Tumor-Infiltrating Lymphocytes Utilizing Digital Image Analysis Is Prognostic in Triple-Negative Breast Cancer	McIntire PJ, Irshaid L, Liu Y, Chen Z, Menken F, Nowak E, Shin SJ, Ginter PS	2018	Clinical Breast Cancer	Oncology, Immuno-oncology	Cytonuclear, Figure Maker	HALO
Altered dopaminergic regulation of the dorsal striatum is able to induce tic-like movements in juvenile rats	Nespoli E, Rizzo F, Boeckers T, Schulze U, Hengerer B	2018	PLOS One	Neuroscience	Cytonuclear	HALO
Induction of hemangiosarcoma in mice after chronic treatment with S1P-modulator siponimod and its lack of relevance to rat and human	Pognan F, Mahl JA, Papoutsi M, David Ledieu D, Raccuglia M, Theil D, Voytek SB, Devine PJ, Kubek?Luck K, Claudio N, Cordier A, Heier A, Kolly C, Hartmann A, Chibout S-D, Bouchard P, Trendelenburg C	2018	Archives of Toxicology	Toxicology	Classifier, Cytonuclear	HALO
Intermittent Hypoxia Exacerbates Increased Blood Pressure in Rats with Chronic Kidney Disease	Riggs J, Pace C, Ward HH, Gonzalez Bosc L, Rios L, Barrera A, Kanagy NL	2018	American Jornal of Physiology-Renal Physiology	Metabolism	Classifier, Cytonuclear	HALO
Mild Impairment of Mitochondrial OXPHOS Promotes Fatty Acid Utilization in POMC Neurons and Improves Glucose Homeostasis in Obesity	Timper K, Paeger L, Sánchez-Lasheras C, Varela L, Jais A, Nolte H, Vogt MC, Hausen AC, Heilinger C, Evers N, Pospisilik JA, Penninger JM, Taylor EB, Horvath TL, Kloppenburg P, Brüning JC	2018	Cell Repots	Neuroscience, Metabolism	Cytonuclear	HALO
Biomarker Evaluation and Toxic Effects of an Acute Oral and Systemic Fumonisin Exposure of Pigs with a Special Focus on Dietary Fumonisin Esterase Supplementation	Schertz H, Danicke S, Frahm J, Schatzmayr D, Dohnal I, Bichl G, Schwartz-Zimmerman HE, Colicchia S, Breves G, Teifke JP, Kluess J	2018	Toxins	Toxicology	Classifier	HALO
Mutant myocilin impacts sarcomere ultrastructure in mouse gastrocnemius muscle	Lynch JM, Dolman AJ, Guo C, Dolan K, Xiang C, Reda S, Li B, Prasanna G	2018	PLOS One	Gastroenterology, Myology	ISH/FISH	HALO
Breast and pancreatic cancer interrupt IRF8-dependent dendritic cell development to overcome immune surveillance	Meyer MA, Baer JM, Knolhoff BL, Nywening TM, Panni RZ, Su X, Weilbaecher KN, Hawkins WG, Ma C, Fields RC, Linehan DC, Challen GA, Faccio R, Aft RL, DeNardo DG	2018	Nature Communications	Oncology, Immuno-oncology	ISH/FISH	HALO
What is the added value of digital image analysis of HER2 immunohistochemistry in breast cancer in clinical practice? A study with multiple platforms	Koopman T, Buikema HJ, Hollema H, de Bock GH, van der Vegt B	2018	Histopathology	Oncology	Membrane	HALO
Tumor Cell Subtypes Based on the Intracellular Hormonal Activity in KCNJ5-Mutated Aldosterone-Producing Adenoma	Yamazaki Y, Omata K, Tezuka Y, Ono Y, Morimoto R, Adachi Y, Ise K, Nakamura Y, Gomez-Sanchez CE, Shibahara Y, Kitamoto T, Nishikawa T, Ito S, Satoh F, Sasano H	2018	Hypertension	Oncology	Area Quantification, Cytonuclear	HALO
Disease Progression and Pharmacological Intervention in a Nutrient-Deficient Rat Model of Nonalcoholic Steatohepatitis	Tølbøl KS, Stierstorfer B, Rippmann JF, Veidal SS, Rigbolt KTG, Schönberger T, Gillum MP, Hansen HH, Vrang N, Jelsing J, Feigh M, Broermann A	2018	Digestive Diseases and Sciences	Metabolism	Area Quantification	HALO
FOXM1 contributes to treatment failure in acute myeloid leukemia	Khan I, Halasi M, Patel A, Schultz R, Kalakota N, Chen Y-H, Aardsma N, Liu L, Crispino JD, Mahmud N, Frankfurt O, Gartel AL	2018	JCI Insight	Oncology	Multiplex IHC	HALO
A transcriptionally and functionally distinct PD-1+ CD8+ T cell pool with predictive potential in non-small-cell lung cancer treated with PD-1 blockade	Thommen DS, Koelzer VH, Herzig P, Roller A, Trefny M, Dimeloe S, Kiialainen A, Hanhart J, Schil C, Hess C, Prince SS, Wiese M, Lardinois D, Ho P-C, Klein C, Karanikas V, Mertz KD, Schumacher TN, Zippelius A	2018	Nature Medicine	Oncology, Immuno-oncology	Multiplex IHC	HALO
Relationship between mismatch repair immunophenotype and long-term survival in patients with resected periampullary adenocarcinoma	Heby M, Lundgren S, Nodin B, Elebro J, Eberhard J, Jirström K	2018	Journal of Translational Medicine	Oncology, Immuno-oncology	Object Colocalization	HALO
Luminally-polarized mural and vascular remodeling in ileal strictures of Crohn's Disease	Zhang X, Ko HM, Torres J, Panchal HJ, Cai Z, WagneR M, Sands BE, Colombel J-F, Cho J, Taouli B, Harpaz N	2018	Human Pathology	Immunology	Layer Thickness	HALO
Age-related pathology after adenoviral overexpression of the leucine-rich repeat kinase 2 in the mouse striatum	Kritzingerab A, Ferger B, Gillardon F, Stierstorfer B, Birk G, Kochanek S, Ciossek T	2018	Neurobiology of Aging	Neuroscience	Area Quantification, Object Colocalization, Microglia	HALO
Pharmacogenetic neuronal stimulation increases human tau pathology and trans-synaptic spread of tau to distal brain regions in mice	Schultz MK, Gentzel R, Usenovic M, Gretzul C, Ware C, Parmentier-Batteur S, Schachter JB, Zariwala HA	2018	Neurobiology of Disease	Neuroscience	Object Colocalization	HALO
Comparison of Biologic Effect and Particulate Embolization after Femoral Artery Treatment with Three Drug-Coated Balloons in Healthy Swine Model	Torii S, Jinnouchi H, Sakamoto A, Romero ME, Kolodgie FD, Virmani R, Finn AV	2018	Journal of Vascular and Interventional Radiology	Other	Object Colocalization	HALO
Multidimensional, quantitative assessment of PD-1/PD-L1 expression in patients with Merkel cell carcinoma and association with response to pembrolizumab	Giraldo NA, Nguyen P, Engle EL, Kaunitz GJ, Cottrell TR, Berry S, Green B, Soni A, Cuda JD, Stein JE, Sunshine JC, Succaria F, Xu H, Ogurtsova A, Danilova L, Church CD, Miller NJ, Fling S, Lundgren L, Ramchurren N, Yearley JH, Lipson EJ, Cheever M, Anders RA, Nghiem PT, Topalian SL, Taube JM	2018	Journal for ImmunoTherapy of Cancer	Oncology, Immuno-oncology	Spatial Analysis, Serial Section	HALO
A CD3-bispecific molecule targeting P-cadherin demonstrates T cell-mediated regression of established solid tumors in mice	TS Fisher, AT Hooper, J Lucas, TH Clark, AK Rohner, B Peano, MW Elliott, K Tsaparikos, H Wang, J Golas, M Gavriil, N Haddish-Berhane, L Tchistiakova, H-P Gerber, AR Root, C May	2018	Cancer Immunology, Immunotherapy	Oncology, Immuno-oncology	Area Quantification	HALO
Innate Sex Bias of Staphylococcus aureus Skin Infection Is Driven by a-Hemolysin	Castleman MJ, Pokhrel S, Triplett KD, Kusewitt DF, Elmore BO, Joyner JA, Femling JK, Sharma G, Hathaway HJ, Prossnitz ER, Hall PR	2018	The Journal of Immunology	Infectious Disease		HALO
Subclonal evolution of pulmonary adenocarcinomas delineated by spatially distributed somatic mitochondrial mutations	Kazdal D, Harms A, Endris V, Penzel R, Kriegsmann M, Eichhorn F, Muley T, Stenzinger A, Pfarr N, Weichert W, and Warth A	2018	Lung Cancer			HALO
Molecular and immunologic analysis of laryngeal squamous cell carcinoma in smokers and non-smokers	Malm I-J, rooper LM, Bishop JA, Ozgursoy SK, Hillel AT, Akst LM, Best SR	2018	American Journal of Otolaryngology	Oncology, Immuno-oncology		HALO
Class 4 Semaphorins and Plexin-B receptors regulate GABAergic and glutamatergic synapse development in the mammalian hippocampus	McDermott JE, Goldblatt D, Paradis S	2018	Molecular and Cellular Neuroscience	Neuroscience		HALO
Acquired cancer resistance to combination immunotherapy from transcriptional loss of class I HLA	Paulson KG, Voillet V, McAfee MS, Hunter DS, Wagener FD, Perdicchio, Valente WJ, Koelle SJ, Church CD, Vandeven N, Thomas H, Colunga AG, Iyer JG, Yee C, Kulikauskas R, Koelle DM, Pierce RH, Bielas JH, Greenberg PD, Bhatia S, Gottardo R, Nghiem P, Chapuis AG	2018	Nature Communications	Immuno-oncology	Partitions (tiles, margins), Figure Maker	HALO
Digital image analysis supports a nuclear-to-cytoplasmic ratio cutoff value below 0.7 for positive for high-grade urothelial carcinoma and suspicious for high-grade urothelial carcinoma in urine cytology specimens	McIntire PJ, Snow JT, Elsoukkary SS, Soong L, Sweeney J, Robinson BD, Siddiqui MT	2018	Cancer Cytopathology	Oncology		HALO
Ossabaw Pigs With a PCSK9 Gain?of?Function Mutation Develop Accelerated Coronary Atherosclerotic Lesions: A Novel Model for Preclinical Studies	Yuan F, Guo L, Park K-H, Woollard JR, Taek?Geun K, Jiang K, Melkamu T, Zang B, Smith SL, Fahrenkrug SC, Kolodgie FD, Lerman A, Virmani R, Lerman LO, Carlson DF	2018	Journal of the American Heart Association	Myology	Area Quantification	HALO
Accelerated wound healing by injectable star poly(ethylene)-b-poly(propylene sulfide) scaffolds loaded with poorly water-soluble drugs	Zhu X, Yin L, Theisen M, Zhuo J, Siddiqui S, Levy B, Presnyak V, Frassetto A, Milton J, Salerno T, Benenato KE, Milano J, Lynn A, Sabnis S, Burke K, Besin G, Lukacs CM, Guey LT, Finn PF, Martini PGV	2018	Journal of Controlled Release	Biomaterials, Wound Healing	Cytonuclear	HALO
The use of automated Ki67 analysis to predict Oncotype DX risk-of-recurrence categories in early-stage breast cancer	Thakur SS, Li H, Chan AMY, Tudor R, Bigras G, Morris D, Enwere EK	2018	PLOS ONE	Oncology	Cytonuclear, Figure Maker, Partitions (tiles, margins)	HALO
Inhibiting Interleukin 36 Receptor Signaling Reduces Fibrosis in Mice with Chronic Intestinal Inflammation	Scheibe K, Kersten C, Schmied A, Vieth M, Primbs T, Carlé B, Knieling F, Claussen J, Klimowicz AC, Zheng J, Baum P, Meyer S, Schürmann S, Friedrich O, Waldner MJ, Rath T, Wirtz S, Kollias G, Ekici AB, Atreya R, Raymond EL, Mbow ML, Neurath MF, Neufert C	2018	Gastroenterology	Immunology, Fibrosis		HALO
Low and variable tumor reactivity of the intratumoral TCR repertoire in human cancers	Scheper W, Kelderman S, Fanchi LF, Linnemann C, Bendle G, de Rooij MAJ, Hirt C, Mezzadra R, Slagter M, Dijkstra K, Kluin RJC, Snaebjornsson P, Milne K, Nelson BH, Zijlmans H, Kenter G, Voest EE, Haanen JBAG, Schumacher TN	2018	Nature Medicine	Oncology, Immuno-oncology	Cytonuclear	HALO
A suboptimal maternal diet combined with accelerated postnatal growth results in an altered aging profile in the thymus of male rats	Tarry-Adkins JL, Aiken CE, Ashmore TJ, Fernandez-Twinn DS, Chen J-H, Ozanne SE	2018	The FASEB Journal	Neuroscience, Metabolism	Classifier, Vacuole	HALO
A brain-penetrant triazolopyrimidine enhances microtubule-stability, reduces axonal dysfunction and decreases tau pathology in a mouse tauopathy model.	Zhang B, Yao Y, Cornec A-S, Oukoloff K, James MJ, Koivula P, Trojanowski JQ, Smith AB III, Lee VM-Y, Ballatore C, Brunden KR	2018	Molecular Neurodegeneration	Neuroscience	Area Quantification	HALO
GABA promotes ?-cell proliferation, but does not overcome impaired glucose homeostasis associated with diet-induced obesity	Untereiner A, Abdo S, Bhattacharjee A, Gohil H, Pourasgari F, Ibeh N, Lai M, Batchuluun B, Wong A, Khuu N, Liu Y, Rijjal DA, Winegarden N, Virtanen C, Orser BA, Cabrera O, Varga G, Rocheleau J, Dai FF, Wheeler MB	2018	The FASEB Journal	Metabolism	Cytonuclear	HALO
Ki67 reproducibility using digital image analysis: an inter-platform and inter-operator study	Acs B, Pelekanou V, Bai Y, Martinez-Morilla S, Toki M, Leung SCY, Nielsen TO, Rimm DL	2017	Laboratory Invesigations	Oncology	Classifier, Cytonuclear	HALO
Efficacy of injectable praziquantel for elimination of trematode metacercariae in bluegills (Lepomis macrochirus) and quantification of parasite death by propidium iodide staining	Bader C, Chelladurai JJ, Starling DE, Jones DE, Brewer MT	2017	Parasitology Research	Infectious Disease	Area Quantification	HALO
Both brown adipose tissue and skeletal muscle thermogenesis processes are activated during mild to severe cold adaptation in mice	Bal NC, Singh S, Reis FCG, Maurya SK, Pani S, Rowland LA, Periasamy M	2017	Journal of Biological Chemistry	Myology	Area Quantification	HALO
Sex- and Dose-Specific Effects of Maternal Bisphenol A Exposure on Pancreatic Islets of First- and Second-Generation Adult Mice Offspring	Bansal A, Rashid C, Xin F, Li C, Polyak E, Duemler A, van der Meer T, Stefaniak M, Wajid S, Doliba N, Bartolomei MS, Simmons RA	2017	Environmental Health Perspectives	Metabolism	Area Quantification	HALO
The R-enantiomer of ketorolac delays mammary tumor development in mouse mammary tumor virus-polyoma middle T antigen (MMTV-PyMT) mice	AS Peretti, D Dominguez, MM Grimes, HJ Hathaway, ER Prossnitz, MR Rivera, A Wandinger-Ness, D Kusewitt, LG Hudson	2017	The American Journal of Pathology	Oncology	Classifier, Area Quantification, Cytonuclear	HALO
The clinical impact of tumour-infiltrating lymphocytes in colorectal cancer differs by anatomical subsite: A cohort study	Berntsson J, Svensson MC, Leandersson K, Nodin B, Micke P, Larsson AH, Eberhard J, Jirstrom K	2017	International Journal of Cancer	Oncology, Immuno-oncology	Cytonuclear	HALO
Acetate Recapturing by Nuclear Acetyl-CoA Synthetase 2 Prevents Loss of Histone Acetylation during Oxygen and Serum Limitation	Bulusu V, Tumanov S, Michalopoulou E, van den Broek NJ, MacKay G, Nixon C, Dhayade S, Schug ZT, Voorde JV, Blyth K, Gottlieb E, Vazquez A, Kamphorst JJ	2017	Cell Reports	Oncology, Metabolism	Cytonuclear	HALO
Loss of the imprinted, non-coding Snord116 gene cluster in the interval deleted in the Prader Willi syndrome results in murine neuronal and endocrine pancreatic developmental phenotypes	Burnett LC, Hubner G, LeDuc C, Morabito MV, Carli JFM, Leibel RL	2017	Human Moledular Genetics	Metabolism	Cytonuclear	HALO
Identification of the SUMO E3 ligase PIAS1 as a potential survival biomarker in breast cancer	Chanda A, Chan A, Deng L, Kornaga EN, Enwere EK, Morris DG, Bonni S	2017	PLOS One	Oncology	Classifier, Cytonuclear	HALO
Spatial distribution of EGFR and KRAS mutation frequencies correlates with histological growth patterns of lung adenocarcinomas	Dietz S, Harms A, Endris V, Eichhorn, Kriegsmann M, Longuespée R, Stenzinger A, Sültmann H, Warth A, and Kazdal D	2017	International Journal of Cancer	Oncology	Cytonuclear	HALO
Aging African green monkeys manifest transcriptional, pathological, and cognitive hallmarks of human Alzheimer's disease	Cramer PE, Gentzel RC, Tanis KQ, Vardigan J, Wang Y, Connolly B, Manfre P, Lodge K, Renger JJ, Zerbinatti C, Uslaner JM	2017	Neurobiology of Aging	Neuroscience	Object Colocalization	HALO
Retinoic-acid-orphan-receptor-C inhibition suppresses Th17 cells and induces thymic aberrations	Guntermann C, Piaia A, Hamel M-L, Theil D, Rubic-Schneider T, del Rio-Espinola A, Dong L, Billich A, Kaupmann K, Dawson J, Hoegenauer K, Orain D, Hintermann S, Stringer R, Pate DD, Doelemeyer A, Deurinck M, and Schümann J	2017	JCI Insight	Oncology, Immuno-oncology	Area Quantification, Cytonuclear	HALO
Digital image analysis agrees with visual estimates of bone marrow trephine biopsy cellularity	Hagiya AS, Etman A, Siddiqi IN, Cen S, Matcuk Jr GR, Brynes RK, Salama ME	2017	International Journal of Laboratory Hematology	Oncology	Cytonuclear	HALO
Selective imaging of internalized proteopathic ?-synuclein seeds in primary neurons reveals mechanistic insight into transmission of synucleinopathies	Karpowicz RJ, Haney CM, Mihaila TS, Sandler RM, Petersson EJ, and Lee VM-Y	2017	Journal of Biological Chemistry	Neuroscience	Area Quantification, Cytonuclear	HALO
Prevalence of somatic mitochondrial mutations and spatial distribution of mitochondria in non-small cell lung cancer	Kazdal D, Harms A, Endris V, Penzel R, Oliveira C, Kriegsmann M, Longuespee R, Winter H, Schneider MA, Muley T, Pfarr N, Weichert W, Stenzinger A,Warth A	2017	British Journal of Cancer	Oncology	Cytonuclear	HALO
Amino Acid Transporter Slc38a5 Controls Glucagon Receptor Inhibition-Induced Pancreatic ? Cell Hyperplasia in Mice	Kim J, Okamoto H, Huang ZJ, Anguiano G, Chen S, Liu Q, Cavino K, Xin Y, Na E, Hamid R, Lee J, Zambrowicz B, Unger R, Murphy AJ, Xu Y, Yancopoulos GD, Li W, Gromada J	2017	Cell Metabolism	Metabolism	Cytonuclear	HALO
APNG as a prognostic marker in patients with glioblastoma	Fosmark S, Hellwege S, Dahlrot RH, Jensen KL, Derand H, Lohse J, Sørensen MD, Hansen S, Kristensen BW	2017	PLOS One	Oncology	ISH/FISH	HALO
TGF? pathway limits dedifferentiation following WNT and MAPK pathway activation to suppress intestinal tumourigenesis	Cammareri P, Vincent DF, Hodder MC, Ridgway RA, Murgia C, Nobis M, Campbell AD, Varga J, Huels DJ, Subramani C, Prescott KLH, Nixon C, Hedley A, Barry ST, Greten FR, Inman GJ, and Sansom OJ	2017	Cell Death and Differentiation	Oncology	Layer Thickness	HALO
Digital analysis and epigenetic regulation of the signature of rejection in colorectal cancer	Koelzer VH, Sokol L, Zahnd S, Christe L, Dawson H, Berger MD, Inderbitzin D, Zlobec I, Lugli A	2017	OncoImmunology	Oncology	Cytonuclear	HALO
Asymmetry of post-mortem neuropathology in behavioural-variant frontotemporal dementia	DJ Irwin, CT McMillan, SX Xie, K Rascovsky, VM Van Deerlin, HB Coslett, R Hamilton, G Aguirre, EB Lee, VMY Lee, JQ Trojanowski, M Grossman	2017	Brain	Neuroscience	Area Quantification, Partitions (tiles, margins)	HALO
Co-clinical Analysis of a Genetically Engineered Mouse Model and Human Prostate Cancer Reveals Significance of NKX3.1 Expression for Response to 5?-reductase Inhibition	Dutta A, Panja S, Virk RK, Kim JY, Zott R, Cremers S, Golombos DM, Liu D, Mosquera JM, Mostaghel EA, Barbieri CE, Mitrofanova A, Abate-Shen C	2017	European Urology	Oncology	Area Quantification	HALO
Amyloid-? plaques enhance Alzheimer's brain tau-seeded pathologies by facilitating neuritic plaque tau aggregation	He Z, Guo JL, McBride JD, Narasimhan S, Kim H, Changolkar L, Zhang B, Gathagan RJ, Yue C, Dengler C, Stieber A, Nitla M, Coulter DA, Abel T, Brunden KR, Trojanowski JQ, Lee V M-Y	2017	Nature Medicine	Neuroscience	Area Quantification	HALO
An ancestral retroviral protein identified as a therapeutic target in type-1 diabetes	Levet S, Medina J, Joanou J, Demolder A, Queruel N, Réant K, Normand M, Seffals M, Dimier J, Germi R, Piofczyk T, Portoukalian J, Touraine J-L, Perron H	2017	JCI Insight	Immunology, Metabolism	Classifier, Cytonuclear	HALO
Receptor tyrosine kinase expression and phosphorylation in canine nasal carcinoma	Hocker SA, Higginbotham ML, Schermerhorn T, Henningson J	2017	Research in Veterinary Science	Oncology	Area Quantification, Multiplex IHC	HALO
Differential roles of RET isoforms in medullary and papillary thyroid carcinomas	Lian EY, Maritan SM, Cockburn JG, Kasaian K, Crupi MJF, Hurlbut D, Jones SJM, Wiseman SM, Mulligan LM	2017	Endocrine-Related Cancer	Oncology	Cytonuclear	HALO
Ante mortem CSF tau levels correlate with post mortem tau pathology in FTLD	Irwin DJ, Lleó A, Xie SX, McMillan CT, Wolk D, Lee EB, Van Deerlin VM, Shaw LM, Trojanowski JQ, Grossman M	2017	Annals of Neurology	Neuroscience	Area Quantification	HALO
Neutorphils dominate the immune cell composition in non-small cell lung cancer	Kargl J, Busch SE, Yang GHY, Kim K-H, Hanke ML, Metz HE, Hubbard JJ, Lee SM, Madtes DK, McIntosh MW, Houghton AM	2017	Nature Communications	Oncology	Area Quantification	HALO
DPP9 enzyme activity controls survival of mouse migratory tongue muscle progenitors and its absence leads to neonatal lethality due to suckling defect	Kim M, Minoux M, Piaia A, Kueng B, Gapp B, Weber D, Haller C, Barbieri S, Namoto K, Lorenz T, Wirsching J, Bassilana F, Dietrich W, Rijli FM, Ksiazek I	2017	Developmental Biology	Myology	Classifier, Area Quantification	HALO
Connexin-43 and aquaporin-4 are markers of ageing-related tau astrogliopathy (ARTAG)-related astroglial response	Kovacs GG, Yousef A, Kaindl S, Lee VM, Trojanowski JQ	2017	Neuropathology and Applied Neurobiology	Neuroscience	Area Quantification	HALO
Angptl4 does not control hyperglucagonemia or ?-cell hyperplasia following glucagon receptor inhibition	Okamoto H, Cavino K, Na E, Krumm E, Kim SY, Stevis PE, Harp J, Murphy AJ, Yancopoulos GD, Gromada J	2017	Proceedings of the National Academy of Sciences	Metabolism	Area Quantification	HALO
Glucagon receptor inhibition normalizes blood glucose in severe insulin-resistant mice	Okamoto H, Kim J, Aglione JP, Lee J, Cavino K, Na E, Rafique A, Kim JH, Harp J, Valenzuela DM, Yancopoulos GD, Murphy AJ, Gromada J	2017	Proceedings of the National Academy of Sciences	Metabolism	Area Quantification	HALO
Cysteinyl leukotriene receptor 1 facilitates tumorigenesis in a mouse model of colitis-associated colon cancer	Osman J, Savari S, Chandrashekar NK, Bellamkonda K, Souglas D, Sjolander A	2017	Oncotarget	Oncology, Immunology	Classifier, Area Quantification	HALO
Plant-based vaccines for oral delivery of type 1 diabetes-related autoantigens: Evaluating oral tolerance mechanisms and disease prevention in NOD mice	Posgai AL, Wasserfall CH, Kwon K-C, Daniell H, Schatz DA, Atkinson MA	2017	Scientific Reports	Metabolism	Area Quantification	HALO
cFOS-SOX9 Axis Reprograms Bone Marrow-Derived Mesenchymal Stem Cells into Chondroblastic Osteosarcoma	He Y, Zhu W, Shin MH, Gary J, Liu C, Dubois W, Hoover SB, Jiang S, Marrogi E, Mock B, Simpson RM, and Huang J	2017	Stem Cell Reports	Oncology	Classifier	HALO
Modulating the therapeutic response of tumours to dietary serine and glycine starvation	Maddocks ODK, Athineos D, Cheung EC, Lee P, Zhang T, van den Broek NJF, Mackay GM, Labuschagne CF, Gay D, Kruiswijk F, Blagih J, Vincent DF, Campbell KJ, Ceteci F, Sansom OJ, Blyth K, Vousden KH	2017	Nature	Oncology	Cytonuclear	HALO
Expression of protein disulfide isomerase family members correlates with tumor progression and patient survival in ovarian cancer	Samanta S, Tamura S, Dubeau L, Mhawech-Fauceglia P, Miyagi Y, Kato H, Lieberman R, Buckanovich RJ, Lin YG, Neamati N	2017	Oncotarget	Oncology	Area Quantification	HALO
Targeting autophagy inhibits melanoma growth by enhancing NK cells infiltration in a CCL5-dependent manner	Mgrditchiana T, Arakeliana T, Paggettia J, Nomana MZ, Virya E, Moussaya E, Van Moera K, Kreisb S, Guerinc C, Buartd S, Roberte C, Borgf C, Vielhg P, Chouaibd S, Berchema G, Janji B	2017	Proceedings of the National Academy of Sciences	Oncology, Immuno-oncology	Cytonuclear	HALO
Weight Pertubation Alters Leptin Signal Transduction in a Region-Specific Manner throughout the Brain	Morabito MV, Ravussin Y, Mueller BR, Skowronski AA, Watanabe K, Foo KS, Lee SX, Lehmann A, Hjorth S, ZeltserLM, LeDuc CA, Leibel RL	2017	PLOS One	Metabolism	Cytonuclear	HALO
A single dose of peripherally infused EGFRvIII-directed CAR T cells mediates antigen loss and induces adaptive resistance in patients with recurrent glioblastoma	ORourke DM, Nasrallah MP, Desai A, Melenhorst JJ, Mansfield K, MorrissetteJJD, Martinez-Lage M, Brem S, Maloney E, Shen A, Isaacs R, Mohan S, Plesa G, Lacey SF, Navenot J-M, Zheng Z, Levine BL, Okada H, June CH, Brogdon JL, Maus MV	2017	Science Translational Medicine	Oncology, Immuno-oncology	Cytonuclear, Multiplex IHC	HALO
The action of ?-hydroxybutyrate on the growth, metabolism and global histone H3 acetylation of spontaneous mouse mammary tumours: evidence of a ?-hydroxybutyrate paradox	Rodrigues LM, Uribe-Lewis S, Madhu B, Honess DJ, Stubbs M, Griffiths JR	2017	Cancer & Metabolism	Oncology, Metabolism	Area Quantification, Cytonuclear	HALO
High levels of tumor-associated neutrophils are associated with improved overall survival in patients with stage II colorectal cancer	RS Berry, M-J Xiong, A Greenbaum, P Mortaji, RA Nofchissey, F Schultz, C Martinez, L Luo, KT Morris, JA Hanson	2017	PLOS One	Oncology, Immuno-oncology	Cytonuclear	HALO
Pathological tau strains from human brains recapitulate the diversity of tauopathies in non-transgenic mouse brain	S Narasimhan, JL Guo, L Changolkar, A Stieber, JD McBride, LV Silva, Z He, B Zhang, RJ Gathagan, JQ Trojanowski, VMY Lee	2017	Journal of Neuroscience	Neuroscience	Cytonuclear	HALO
T-cell Localization, Activation, and Clonal Expansion in Human Pancreatic Ductal Adenocarcinoma	Stromnes IM, Hulbert A, Pierce RH, Greenberg PD, Hingorani SR	2017	Cancer Immunology Research	Oncology, Immuno-oncology	Highplex FL	HALO
Transcriptional mechanisms of resistance to anti-PD-1 therapy	Ascierto ML, Makohon-Moore A, Lipson EJ, Taube JM, McMiller TL, Berger AE, Fan J, Kaunitz GJ, Cottrell TR, Kohutek ZA, Favorov A, Makarov V, Riaz N, Chan TA, Cope L, Hruban RH, Pardoll DM, Taylor BS, Solit DB, Iacobuzio-Donahue CA, Topalian SL	2017	Clinical Cancer Research	Oncology, Immuno-oncology	Immune	HALO
Comparison of branch and distally focused main renal artery denervation using two different radio-frequency systems in a porcine model	Mahfoud F, Pipenhagen CA, Moon LB, Ewen S, Kulenthiran S, Fish JM, Jensen JA, Virmani R, Joner M, Yahagi K, Tsioufis C, Böhm M	2017	International Journal of Cardiology	Myology	Layer Thickness	HALO
Treatment with the WNT5A-mimicking peptide Foxy-5 effictively reduces the metastatic spread of WNT5A-low prostate cancer cells in an orthotopic mouse model	Canesin G, Evans-Axelsson S, Hellsten R, Krzyzanowska A, Prasad CP, Bjartell A, Andersson T	2017	PLOS One	Oncology	Membrane	HALO
Expression of PD-L1 and presence of CD8-positive T cells in pre-treatment specimens of locally advanced cervical cancer	Enwere EK, Kornaga EN, Dean M, Koulis TA, Phan T, Kalantarian M, Köbel M, Ghatage P, Magliocco AM, Lees-Miller DP, Doll CM	2017	Modern Pathology	Oncology, Immuno-oncology	Membrane	HALO
Association of HIV Status With Local Immune Response to Anal Squamous Cell Carcinoma: Implications for Immunotherapy	Yanik EL, Kaunitz GJ, Cottrell TR, Succaria F, McMiller TL, Ascierto ML, Esandrio J, Xu H, Ogurtsova A, Cornish T, Lipson EJ, Topalian SL, Engels EA, Taube JM	2017	JAMA Oncology	Oncology, Immuno-oncology	Cytonuclear	HALO
Chronic Verubecestat Treatment Suppresses Amyloid Accumulation in Advanced Aged Tg2576-A?PPswe Mice Without Inducing Microhemorrhage	Villarreal S, Zhao F, Hyde LA, Holder D, Forest T, Sondey M, Chen X, Sur C, Parker EM, Kennedy ME	2017	Journal of Alzheime's Disease	Neuroscience	Object Colocalization	HALO
In vivo characterization of a new type of biodegradable starch microsphere for transarterial embolization	Sommer CM, Do TD, Schlett CL, Flechsig P, Gockner TL, Kuthning A, Vollherbst DF, Pereira PL, Kauczor HU, Macher-Göppinger S	2017	Journal of Biomaterials Applications	Oncology	Classifier	HALO
A randomized, open-label study of the efficacy and safety of AZD4547 monotherapy versus paclitaxel for the treatment of advanced gastric adenocarcinoma with FGFR2 polysomy or gene amplification	Van Cutsem E, Bang Y-J, Mansoor W, Petty RD, Chao Y, Cunningham D, Ferry DR, N. R. Smith NR, Frewer P, Ratnayake J, Stockman PK, Kilgour E, and Landers D	2017	Annals of Oncology	Oncology	Classifier, ISH/FISH	HALO
Persistence of Pancreatic Insulin mRNA Expression and Proinsulin Protein in Type 1 Diabetes Pancreata	Wasserfall C, Nick HS, Campbell-Thompson M, Beachy D, Haataja L, Kusmartseva I, Posgai A, Beery M, Rhodes C, Bonifacio E, Arvan P, Atkinson M	2017	Cell Metabolism	Metabolism	Area Quantification	HALO
Neuron loss and degeneration in the progression of TDP-43 in frontotemporal lobar degeneration	Yousef A, Robinson JL, Irwin DJ, Byrne MD, Kwong LK, Lee EB, Xu Y, Xie SX, Rennert L, Suh ER, Van Deerlin VM, Grossman M, Lee VM-Y, Trojanowski JQ	2017	Acta Neuropathologica Communications		Area Quantification, Cytonuclear	HALO
Qualitative Comparison Between Carrier-based and Classical Tissue Microarrays	Lisenko K, Leichsenring J, Zgorzelski C, Longuespee R, Casadonte R, Harms A, Kazdal D, Stenzinger A, Warth A, Kriegsmann M	2017	Applied Immunohistochemistry & Molecular Morpholgy			HALO
In situ macrophage phenotypic transition is affected by altered cellular composition prior to acute sterile muscle injury	Patsalos A, Pap A, Varga T, Trencsenyi G, Contreras GA, Garai I, Papp Z, Dezso B, Pintye E, Nagy L	2017	The Journal of Physiology	Myology		HALO
Obstruction of BRAFV600E transcription by complementary PNA oligomers as a means to inhibit BRAF-mutant melanoma growth	Rothman JH, Surriga O, de Stanchina E, Vasudeva SD, Schwartz GK	2017	Cancer Gene Therapy	Oncology		HALO
The integrative clinical impact of tumor-infiltrating T lymphocytes and NK cells in relation to B lymphocyte and plasma cell density in esophageal and gastric adenocarcinoma	Svensson MC, Warfvinge CF, Fristedt R, Hedner C, Borg D, Eberhard J, Micke P, Nodin B, Leandersson K, Jirstrom K	2017	Oncotarget	Immuno-oncology	Object Colocalization	HALO
Control of mitochondrial function and cell growth by the atypical cadherin Fat1	Cao LL, Riascos-Bernal DF, Chinnasamy P, Dunaway CM, Hou R, Pujato MA, O'Rourke BP, Miskolci V, Guo L, Hodgson L, Fiser A, Sibinga NES	2016	Nature	Metabolism	Cytonuclear	HALO
Phosphorylation of calcium/calmodulin-stimulated protein kinase II at T286 enhances invasion and migration of human breast cancer cells	Chi M, Evans, Gilchrist J, Mayhew J, Hoffman A, Pearsall EA, Jankowski H, Brzozowski JS, Skelding KA	2016	Scientific Reports	Oncology	Cytonuclear	HALO
Evidence of ?-Cell Dedifferentiation in Human Type 2 Diabetes	Cinti F, Bouchi R, Kim-Muller JY, Ohmura Y, Sandoval PR, Masini M, Marselli L, Suleiman M, Ratner LE, Marchetti P, Accili D	2016	The Journal of Clinical Endocrinology & Metabolism	Metabolism	Cytonuclear	HALO
Cutaneous wound healing through paradoxical MAPK activation by BRAF inhibitors	Escuin-Ordinas H, Li S, Xie MW, Sun L, Hugo W, Huang RR, Jiao J, Meira de-Faria F, Realegeno S, Krystofinski P, Azhdam A, Komenan SMD, Atefi M, Comin-Anduix B, Pellegrini M, Cochran AJ, Modlin RL, HerschmanHR, Lo RS, McBride WH, Segura T, Ribas A	2016	Nature Communications	Wound Healing	Cytonuclear	HALO
A Phase II Trial of Dovitinib in BCD-Unresponsive Urothelial Carcinoma with FGFR3 Mutations or Over-Expression: Hoosier Cancer Research Network Trial HCRN 12-157	Hahn NH, Bivalacqua TJ, Ross AE, Netto GJ, Baras AS, Park JC, Chapman C, Masterson TA, Koch MO, Bihrle R, Foster RS, Gardner TA, Cheng L, Jones DR, Kyle McElyea K, Sandusky GE, Breen T, Liu Z, Albany C, Moore ML, Loman RA, Reed A, Turner SA, de Abreu FB, Gallagher TL, Tsongalis GJ, Plimack ER, Greenberg RE, Geynisman DM	2016	Clinical Cancer Research	Oncology	Classifier, Cytonuclear	HALO
Mitogen-activated Protein Kinase Kinase Activity Maintains Acinar-to-Ductal Metaplasia and Is Required for Organ Regeneration in Pancreatitis	Halbrook CJ, Wen H-J, Ruggeri JM, Takuchi KK, Zhang Y, di Magliano MP, Crawford HC	2016	Cellular and Molecular Gastroenterology and Hepatology	Immunology, Gastroenterology	Cytonuclear	HALO
Fully automated RNAscope in situ hybridization assays for formalin?fixed paraffin?embedded cells and tissues	Anderson CM, Zhang B, Miller M, Butko E, Wu X, Laver T, Kernag C, Kim J, Luo Y, Lamparski H	2016	Journal of Cellular Biochemistry	Oncology, Gastroenterology, Infectious Disease	ISH/FISH	HALO
A Depot Medroxyprogesterone Acetate Dose That Modes Human Use and Its Effect on Vaginal SHIV Acquisition Risk	Butler K, Ritter JM, Ellis S, Morris MR, Hanson DL, McNicholl JM, Kersh EN	2016	J Acquir Immune Defic Syndr	Infectious Disease	Layer Thickness	HALO
Epigenetic regulation of the thioredoxin-interacting protein (TXNIP) gene by hyperglycemia in kidney	De Marinis Y, Cai M, Bompada P, Atac D, Kotova O, Johansson ME, Garcia-Vaz E, Gomez MF, Laakso M, Groop L	2016	Kidney International	Metabolism	Area Quantification	HALO
ProNGF is a potential diagnostic biomarker for thyroid cancer	Faulkner S, Roselli S, Demont Y, Pundavela J, Choquet G, Leissner P, Oldmeadow C, Attia J, Walker MM, Hondermarck H	2016	Oncotarget	Oncology	Area Quantification	HALO
The Dynamics and Turnover of Tau Aggregates in Cultured Cells: Insights into Therapies for Tauopathies	Guo JL, Buist A, Soares A, Callaerts K, Calafate S, Stevenaert F, Daniels JP, Zoll BE, Crowe A, Brunden KR, Moechars D, Lee VMY	2016	The Journal of Biological Chemistry	Neuroscience	Area Quantification	HALO
Unique pathological tau conformers from Alzheimer's brains transmit tau pathology in nontransgenic mice	Guo JL, Narasimhan S, Changolkar L, He Z, Stieber Z, Zhang B, Gathagan RJ, Iba M, McBride JD, Trojanowski JQ, Lee VMY	2016	Journal of Experimental Medicine	Neuroscience	Area Quantification	HALO
Bimodality of intratumor Ki67 expression is an independent prognostic factor of overall survival in patients with invasive breast carcinoma	Laurinavicius A, Plancoulaine B, Rasmusson A, Besusparis J, Augulis R, Meskauskas R, Herlin P, Laurinaviciene A, Muftah AAA, Miligy I, Aleskandarany M, Rakha EA, Green AR, Ellis IO	2016	Virchows Archiv	Oncology	Classifier, Cytonuclear	HALO
Resistance to Anti-VEGF Therapy Mediated by Autocrine IL6/STAT3 Signaling and Overcome by IL6 Blockade	Eichten A, Su J, Adler AP, Zhang L, Ioffe E, Parveen AA, Yancopoulos GD, Rudge J, Lowy I, Lin HC, MacDonald D, Daly C, Duan X, Thurston G	2016	Cancer Research	Oncology, Immuno-oncology	Cytonuclear, Object Colocalization	HALO
Cerebral Protection During MitraClip Implantation: Initial Experience at 2 Centers	Frerker C, Schlüter M, Sanchez OD, Reith S, Romero ME, Ladich E, Schröder J, Schmidt T, Kreidel F, Joner M	2016	JACC: Cardiovascular Interventions	Myology	Object Colocalization	HALO
Upregulation of Glucose-Regulated Protein 78 in Metastatic Cancer Cells Is Necessary for Lung Metastasis Progression	Lizardo MM, Morrow JJ, Miller TE, Hong ES, Ren L, Mendoza A, Halsey CH, Scacheri PC, Helman LJ, Khanna C	2016	Neoplasia	Oncology	Cytonuclear	HALO
Evaluation of the brain-penetrant microtubule-stabilizing agent, dictyostatin, in the PS19 tau transgenic mouse model of tauopathy	Makani V, Zhang B, Han H, Yao Y, Lassalas P, Lou K, Paterson I, Lee VMY, Trojanowski JQ, Ballatore C, Smith AB, Brunden KR	2016	Acta Neuropatholgica Communications	Neuroscience	Area Quantification	HALO
CNS-accessible inhibitor of glucosylceramide synthase for substrate reduction therapy of neuronopathic Gaucher disease	Marshall J, Sun Y, Bangari DS, Budman E, Park H, Nietupski JB, Allaire A, Cromwell MA, Wang B, Grabowski GA, Leonard JP, Cheng SH	2016	Molecular Therapy	Neuroscience	Area Quantification	HALO
Leptin, BMI, and a Metabolic Gene Expression Signature Associated with Clinical Outcome to VEGF Inhibition in Colorectal Cancer	Pommier AJC, Farren M, Patel B, Wappett M, Michopoulos F, Smith NR, Kendrew J, Frith J, Huby R, Eberlein C, Campbell H, Womack C, Smith PD, Robertson J, Morgan S, Critchlow SE, Barry ST	2016	Cell Metabolism	Oncology, Metabolism, Gastroenterology	Area Quantification	HALO
Intrathecal Administration of AAV/GALC Vectors in 10- 11-Day-Old Twitcher Mice Improves Survival and Is Enhanced by Bone Marrow Transplant	Karmuthil-Melethil S, Marshall MS, Heindel C, Jakubauskas B, Bongarzone ER, Gray SJ	2016	Journal of Neuroscience Research	Neuroscience	Axon	HALO
Tasquinimod modulates tumor-infiltrating myeloid cells and improves the antitumor immune response to PD-L1 blockade in bladder cancer	Nakhlé J, Pierron V, Bauchet A-L, Plas P, Thiongane A, Meyer-Losic F, Schmidlin F	2016	OncoImmunology	Oncology, Immuno-oncology	Cytonuclear	HALO
Primary resistance to PD-1 blockade mediated by JAK1/2 mutations	Shin DS, Zaretsky JM, Escuin-Ordinas H, Garcia-Diaz A, Hu-Lieskovan S, Kalbasi A, Grasso CS, Hugo W, Sandoval S, Torrejon DY, Palaskas N, Rodriguez GA, Parisi G, Azhdam A, Chmielowski B, Cherry G, Seja E, Berent-Maoz B, Shintaku IP, Le DT, Pardol DM, Diaz LA, Tumeh PC, Graeber TG, Lo RS, Comin-Anduix B, Ribas A	2016	Cancer Discovery	Oncology, Immuno-oncology	Cytonuclear	HALO
KS-Detect-Validation of Solar Thermal PCR for the Diagnosis of Kaposi's Sarcoma Using Pseudo-Biopsy Samples	Snodgrass R, Gardner A, Jiang L, Fu C, Cesarman E, Erickson D	2016	PLOS ONE	Oncology	Cytonuclear	HALO
Development of antibody-siRNA conjugate targeted to cardiac and skeletal muscles	Sugo T, Terada M, Oikawa T, Miyata K, Nishimura S, Kenjo E, Ogasawara-Shimizu M, Makita Y, Imaichi S, Murata S, Kentaro Otaka, Kikuchi K, Teratani M, Masuda Y, Kamei T, Takagahara S, Ikeda S, Ohtaki T, Matsumoto H	2016	The Journal of Controlled Release	Myology	Cytonuclear, Muscle Fiber	HALO
Use of the Fluidigm C1 platform for RNA sequencing of single mouse pancreatic islet cells	Xin Y, Kim J, Ni M, Wei Y, Okamoto H, Lee J, Adler C, Cavino K, Murphy AJ, Yancopoulos GD, Lin HC, Gromada J	2016	Proceedings of the National Academy of Sciences	Metabolism	Cytonuclear	HALO
Comparison of the methods for measuring the Ki-67 labeling index in adrenocortical carcinoma: manual versus digital image analysis	Yamazaki Y, Nakamura Y, Shibahara Y, Konosu-Fukaya S, Sato N, Kubota-Nakayama F, Oki Y, Baba S, Midorikawa S, Morimoto R, Satoh F, Sasano	2016	Human Pathology	Oncology	Cytonuclear	HALO
Variability in Platelet-Derived Growth Factor Receptor Alpha Antibody Specificity May Impact Clinical Utility of Immunohistochemistry Assays	Holzer TR, Reising LO, Credille KM, Schade AE, Oakley	2016	Journal of Histochemistry & Cytochemistry	Oncology	Cytonuclear, ISH/FISH	HALO
Differential Cytokine Gene Expression in Granulomas from Lungs and Lymph Nodes of Cattle Experimentally Infected with Aerosolized Mycobacterium bovis	Palmer MV, Thacker TC, Waters WR	2016	PLOS One	Infectious Disease	ISH/FISH	HALO
RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes	Xin Y, Kim J, Okamoto H, Ni M, Wei Y, Adler C, Murphy AJ, Yancopoulos GD, Lin C, Gromada J	2016	Endocrinology	Metabolism	Islet	HALO
The Prognostic Impact of NK/NKT Cell Density in Periampullary Adenocarcinoma Differs by Morphological Type and Adjuvant Treatment	Lundgren S, Warfvinge CF, Elebro J, Heby M, Nodin B, Krzyzanowska A, Bjartell A, Leandersson K, Eberhard J, Jirstrom K	2016	PLOS ONE	Oncology, Immuno-oncology	Object Colocalization	HALO
Solid-state NMR structure of a pathogenic fibril of full-length human [alpha]-synuclein	Tuttle MD, Comellas G, Nieuwkoop AJ, Covell DJ, Berthold DA, Kloepper KD, Courtney JM, Kim JK, Barclay AM, Kendall A, Wan W, Stubbs G, Schwieters CD, Lee VMY, George JM, Rienstra CM	2016	Structural & Molecular Biology	Neuroscience	Area Quantification	HALO
RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes	Xin Y, Kim J, Okamoto H, Ni M, Wei Y, Adler C, Murphy AJ, Yancopoulos GD, Lin C, Gromada J	2016	Cell Metabolism	Metabolism	ISH/FISH	HALO
Synergistic targeted inhibition of MEK and dual PI3K/mTOR diminishes viability and inhibits tumor growth of canine melanoma underscoring its utility as a preclinical model for human mucosal melanoma	Wei B-R, Michael HT, Hasley CHC, Peer CJ, Adhikari A, Dwyer JE, Hoover SB, El Meskini R, Kozlov S, Ohler ZW, Figg WD, Merlino G, Simpson RM	2016	Pigment Cell & Melanoma Research	Oncology	Area Quantification	HALO
Mutations Associated with Acquired Resistance to PD-1 Blockade in Melanoma	Zaretsky JM, Garcia-Diaz A, Shin DS, Escuin-Ordinas H, Hugo W, Hu-Lieskovan S, Torrejon DY, Abril-Rodriguez G, Sandoval S, Barthly L, Saco J, Homet Moreno BH, Mezzadra R, Chmielowski B, Ruchalski K, Shintaku IP, Sanchez PJ, Puig-Saus C, Cherry G, Seja E, Kong X, Pang J, Berent-Maoz B, Comin-Anduix B, Graeber TG, Tumeh PC, Schumacher TNM, Lo RS, Ribas A	2016	The New England Journal of Medicine	Oncology, Immuno-oncology	Cytonuclear	HALO
The PDE10A inhibitor MP-10 and haloperidol produce distinct gene expression profiles in the striatum and influence cataleptic behavior in rodents	Gentzel RC, Toolan D, Roberts R, Koser AJ, Kandebo M, Hershey J, Renger JJ, Uslaner J, Smith SM	2015	Neuropharmacology	Neuroscience	Cytonuclear	HALO
Phenotyping of tumor-associated macrophages in colorectal cancer: impact on single cell invasion (tumor budding) and clinicopathological outcome	Koelzer VH, Canonica K, Dawson H, Sokol L, Karamitopoulou-Diamantis E, Lugli A, Zlobec I	2015	OncoImmunology	Oncology, Immuno-oncology, Gastroenterology	Cytonuclear	HALO
G-protein-independent coupling of MC4R to Kir7. 1 in hypothalamic neurons	Ghamari-Langroudi M, Digby GJ, Sebag JA, Millhauser GL, Palomino R, Matthews R, Gillyard T, Panaro BL, Tough IR, Cox HM, Denton JS, Cone RD	2015	Nature	Metabolism	ISH/FISH	HALO
Analysis of putative mucosal SHIV susceptibility factors during repeated DMPA treatments in pigtail macaques	Butler K, Ritter J, Ellis S, Henning TR, Montague J, Zaki S, Garber, McNicholl JM, Kersh EN	2015	Journal of medical primatology	Infectious Disease	Layer Thickness	HALO
Semi-Automated Digital Image Analysis of Pick's Disease and TDP-3 Proteinopathy	Irwin DJ, Byrne MD, McMillan CT, Cooper F, Arnold SE, Lee EB, Van Deerlin VM, Xie SX, Lee VM, Grossman M, Trojanowski JQ	2015	Journal of Histochemistry & Cytochemistry	Neuroscience	Object Colocalization, Layer Thickness	HALO
Myostatin blockade with a fully human monoclonal antibody induces muscle hypertrophy and reverses muscle atrophy in young and aged mice	Latres E, Pangilinan J, Miloscio L, Bauerlein R, Na E, Potocky TB, Huang Y, Eckersdorff M, Rafique A, Mastaitis J, Lin C, Murphy AJ, Yancopoulos GD, Gromada J, Stitt T	2015	Skeletal Muscle	Myology	Muscle Fiber	HALO
Relationship of Estimated SHIV Acquisition Time Points During the Menstrual Cycle and Thinning of Vaginal Epithelial Layers in Pigtail Macaques	Kersh EN, Ritter J, Butler K, Ostergaard SD, Hanson D, Ellis S, Zaki S, McNicholl JM	2015	Sexually Transmitted Diseases	Infectious Disease	Layer Thickness	HALO
Glucagon Receptor Blockade With a Human Antibody Normalizes Blood Glucose in Diabetic Mice and Monkeys	Okamoto H, Cavino K, Na E, Krumm E, Kim SY, Cheng X, Murphy AJ, Yancopoulos GD, Gromada J	2015	Endocrinology	Metabolism	Area Quantification	HALO
Nerve fibers infiltrate the tumor microenvironment and are associated with nerve growth factor production and lymph node invasion in breast cancer	Pundavela J, Roselli S, Faulkner S, Attia J, Scott RJ, Thorne RF, Forbes JF, Bradshaw RA, Walker MM, Jobling P, Hondermarck H	2015	Molecular Oncology	Oncology, Neuroscience	Area Quantification	HALO
Tasquinimod triggers an early change in the polarization of tumor associated macrophages in the tumor microenvironment	Olsson A, Nakhle J, Sundstedt A, Plas P, Bauchet AL, Pierron V, Bruetschy L, Deronic A, Tomgren M, Liberg D, Schmidlin F, Leanderson T	2015	Journal for ImmunoTherapy of Cancer	Oncology, Immuno-oncology	Cytonuclear	HALO
Exacerbated experimental colitis in TNFAIP8-deficient mice	Sun H, Lou Y, Porturas T, Morrissey S, Luo G, Qi J, Ruan Q, Shi S, Chen YH	2015	The Journal of Immunology	Gastroenterology	Cytonuclear	HALO
Combination therapy reverses hyperglycemia in NOD mice with established type 1 diabetes	Xue S, Posgai A, Wasserfall C, Myhr C, Campbell-Thompson M, Mathews CE, Brusko T, Rabinovitch A, Savinov A, Battaglia M, Schatz D, Haller M, Atkinson MA	2015	Diabetes	Metabolism	Cytonuclear	HALO
A combined oral contraceptive affects mucosal SHIV susceptibility factors in a pigtail macaque (Macaca nemestrina) model	Ostergaard DS, Butler K, Ritter JM, Johnson R, Sanders J, Powell N, Lathrop G, Zaki SR, McNicholl JM, Kersh EN	2015	Journal of medical primatology	Infectious Disease	Layer Thickness	HALO
Applicability of digital analysis and imaging technology in neuropathology assessment	Dunn WD, Gearing M, Park Y, Zhang L, Hanfelt J, Glass JD, Gutman DA	2015	Neuropathology			HALO
Islet-1 is essential for pancreatic ?-cell function	Ediger BN, Du A, Liu J, Hunter CS, Walp ER, Schug J, Kaestner KH, Stein R, Stoffers DA, May CL	2014	Diabetes	Metabolism	Cytonuclear	HALO
Characterization of the exocrine pancreas in the male Zucker diabetic fatty rat model of type 2 diabetes mellitus following 3 months of treatment with sitagliptin	Forest T, Holder D, Smith A, Cunningham C, Yao X, Dey M, Frederick C, Prahalada S	2014	Endocrinology	Metabolism	Cytonuclear	HALO
Peripheral androgen receptor gene suppression rescues disease in mouse models of spinal and bulbar muscular atrophy	Lieberman AP, Yu Z, Murray S, Peralta R, Low A, Guo S, Yu XX, Cortes CJ, Bennett CF, Monia BP, La Spada AR, Hung G	2014	Cell Reports	Myology	Muscle Fiber	HALO
ANGPTL8/betatrophin does not control pancreatic beta cell expansion	Gusarova V, Alexa CA, Na E, Stevis PE, Xin Y, Bonner-Weir S, Cohen JC, Hobbs HH, Murphy AJ, Yancopoulos GD, Gromada J	2014	Cell	Metabolism	Area Quantification	HALO
PD-1 blockade induces responses by inhibiting adaptive immune resistance	Tumeh PC, Harview CL, Yearley JH, Shintaku IP, Taylor EJM, Robert L, Chmielowski B, Spasic M, Henry G, Ciobanu V, West AN, Carmona M, Kivork C, Seja E, Cherry G, Gutierrez A, Grogan TR, Mateus C, Tomasic G, Glaspy JA, Emerson RO, Robins H, Pierce RH, Elas	2014	Nature	Oncology, Immuno-oncology	Cytonuclear	HALO
Marked expansion of exocrine and endocrine pancreas with incretin therapy in humans with increased exocrine pancreas dysplasia and potential for glucagon-producing neuroendocrine tumors	Butler AE, Campbell-Thompson M, Gurlo T, Dawson DW, Atkinson M, Butler PC	2013	Diabetes	Oncology, Metabolism	Cytonuclear	HALO
CRISPR-Cas9 gene editing of hepatitis B virusin chronically infected humanized mice	Stone D, Long KR, Loprieno MA, De Silva Feelixge HS, Kenkel EJ, Liley, RM, Rapp S, Roychoudhury P, Nguyen T, Stensland L, Cólon-Thillet R, Klouser LM, Weber ND, Le C, Wagoner J, Goecker EA, Li AZ, Eichholz K, Corey L, Tyrrell DL, Greninger AL, Huang ML, Polyak SJ, Aubert M, Sagartz JE, Jerome KR	2021	Molecular Therapy Methods & Clinical Development	Infectious Disease		HALO Link
Digital Immunophenotyping Predicts Disease Free and Overall Survival in Early Stage Melanoma Patients	De Logu F, Galli F, Nassini R, Ugolini F, Simi S, Cossa M, Miracco C, Gianatti A, De Giorgi V, Rulli E, Cossu A, Massi D, Mandalà M	2021	Cells	Oncology, Immuno-oncology	Multiplex IHC	HALO, HALO Link
Monomeric/dimeric forms of Fgf15/FGF19 show differential activity in hepatocyte proliferation and metabolic function	Williams CM, Calderon JH, Hock E, Jimenez Y, Barringer K, Carbonaro M, Molina-Portela MP, Thurston G, Li Z, Daly C	2021	The FASEB Journal	Metabolism	Cytonuclear	HALO, HALO Link
CD38 in Advanced Prostate Cancers	Guo C, Crespo M, Gurel B, Dolling D, Rekowski J, Sharp A, Petremolo A, Sumanasuriya S, Rodrigues DN, Ferreira A, Pereira R, Figueiredo I, Mehra N, Lambros MBK, Neeb A, Gil V, Seed G, Terstappen L, Alimonti A, Drake CG, Yuan W, de Bono JS	2021	European Urology	Oncology	Classifier, Highplex FL	HALO
Exploring transcriptional regulators Ref-1 and STAT3 as therapeutic targets in malignant peripheral nerve sheath tumours	Gampala S, Shah F, Zhang C, Rhodes SD, Babb O, Grimard M, Wireman RS, Rad E, Calver B, Bai R-Y, Staedtke V, Hulsey EL, Saadatzadeh MR, Pollok KE, Tong Y, Smith AE, Clapp DW, Tee AR, Kelley MR, Fishel ML	2021	British Journal of Cancer	Oncology	Area Quantification, Cytonuclear	HALO
First in class dual MDM2/MDMX inhibitor ALRN-6924 enhances antitumor efficacy of chemotherapy in TP53 wild-type hormone receptor-positive breast cancer models	Pairawan S, Zhao M, Yuca E, Annis A, Evans K, Sutton D, Carvajal L, Ren J-G, Santiago S, Guerlavais, Akcakanat A, Tapia C, Yang F, Bose PSC, Zheng X, Dumbrava EI, Aivado M, Meric-Bernstam F	2021	Breast Cancer Research	Oncology	Cytonuclear	HALO
Influence of tumor-infiltrating immune cells on local control rate, distant metastasis, and survival in patients with soft tissue sarcoma	Smolle MA, Herbsthofer L, Goda M, Granegger B, Brcic I, Bergovec M, Scheipl S, Prietl B, El-Heliebi A, Pichler M, Gerger A, Posch F, Tomberger M, López-García P, Feichtinger J, Baumgartner C, Leithner A, Liegl-Atzwanger B, Szkandera J	2021	OncoImmunology	Immuno-oncology	Highplex FL	HALO
Phenotypic characterization of Adig null mice suggests roles for adipogenin in the regulation of fat mass accrual and leptin secretion	Alvarez-Guaita A, Patel S, Lim K, Haider A, Dong L, Conway OJ, Ma MKL, Chiarugi D, Saudek V, O'Rahilly S, Savage DB	2021	Cell Reports	Metabolism	Vacuole	HALO
Prognostic Impact of CXCR7 and CXCL12 Expression in Patients with Esophageal Adenocarcinoma	Goto M, Shibahara Y, Baciu C, Allison F, Yeung JC, Darling GE, Liu M	2021	Thoracic Oncology	Oncology		HALO
An extended release GLP-1 analogue increases ?-synuclein accumulation in a mouse model of prodromal Parkinson's disease	Bergkvist L, Johnson ME, Mercado G, Steiner JA, Meyerdick L, Schulz E, Madaj Z, Ma J, Becker K, Li Y, Brudin P	2021	Experimental Neurology	Neuroscience	Area Quantification	HALO
Activation of the renal GLP?1R leads to expression of Ren1 in the renal vascular tree	Bjørnholm KD, Ougaard ME, Skovsted GF, Knudsen LB, Pyke C	2021	Endocrinology, Diabetes, & Metabolism	Metabolism	ISH/FISH	HALO
A Method to Pre-Screen Rat Mammary Gland Whole-Mounts Prior To RNAscope	Duderstadt EL, Sanders MA, Samuelson DJ	2021	Journal of Mammary Gland Biology and Neoplasia		ISH/FISH	HALO
Activated Regulatory T-Cells, Dysfunctional and SenescentT-Cells Hinder the Immunity in Pancreatic Cancer	Sivakumar S, Abu-Shah E, Ahern DJ, Arbe-Barnes EH, Jainarayanan AK, Mangal N, Reddy S, Rendek A, Easton A, Kurz E, Silva M, Soonawalla Z, Heij LR, Bashford-Rogers R, Middleton MR, DUstin ML	2021	cancers		Classifier, Multiplex IHC, Spatial Analysis, Highplex FL	HALO
Age-associated expression of p21and p53 during human wound healing	Chia CW, Sherman-Baust CA, Larson SA, Pandey R, Withers R, Karikkineth AC, Zukley LM, Campisi J, Egan JM, Sen R, Ferrucci L	2021	Aging Cell	Dermatology	Area Quantification, ISH/FISH, Multiplex IHC	HALO
Breast adipocyte size associates with ipsilateral invasive breast cancer risk after ductal carcinoma in situ	Almekinders MMM, Schaapveld M, Thijssen B, Visser LL, Bismeijer T, Sanders J, Isnaldi E, Hofland I, Mertz M, Wessels LFA, Broeks A, Hooijberg E, Zwart W, Lips EH, Grand Challenge PRECISION Consortium, Desmedt C, Wesseling J	2021	npj Breast Cancer	Oncology	Vacuole	HALO
COM902, a novel therapeutic antibody targeting TIGIT augments anti-tumor T cell function in combination with PVRIG or PD-1 pathway blockade	Kyle Hansen K, Sandeep Kumar, Kathryn Logronio, Sarah Whelan, Samir Qurashi, Hsin-Yuan Cheng, Andrew Drake, Margaret Tang, Patrick Wall, David Bernados, Ling Leung, Eran Ophir, Zoya Alteber Z, Gady Cojocaru G, Moran Galperin M, Masha Frenkel M, Mark White M, John Hunter J, Spencer C. Liang & Maya F. Kotturi	2021	Cancer Immunology, Immunotherapy	Immuno-oncology		HALO
Conventional and semi-automatic histopathological analysis of tumor cell content for multigene sequencing of lung adenocarcinoma	Kazdal D, Rempel E, Oliveira C, Allgäuer M, Harms A, Singer K, Kohlwes E, Ormanns S, Fink L, Kriegsmann J, Leichsenring M, Kriegsmann K, Stögbauer F, Tavernar L, Leichsenring J, Volckmar A-L, Longuespée R, Winter H, Eichhorn M, Heußel CP, Herth F, Christopoulos P, Reck M, Muley T, Weichert W, Budczies J, Thomas M, Peters S, Warth A, Schirmacher P, Stenzinger A, Kriegsmann M	2021	Translational Lung Cancer Research	Oncology	Classifier, Cytonuclear	HALO
Crotonaldehyde exposure induces liver dysfunction and mitochondrial energy metabolism disorder in rats	Zhang S, Zhang B, Zhang Q, Zhang Z	2021	Toxicology Mechanisms and Methods	Metabolism		HALO
Cytotoxic lymphocytes target characteristic biophysical vulnerabilities in cancer	Bhanot U, MOrris L, Boire A, Hsu KC, Massague J, Huse M, Er EE	2021	Immunity	Immuno-oncology		HALO
Empagliflozin Disrupts a Tnfrsf12a-Mediated Feed Forward Loop That Promotes Left Ventricular Hypertrophy	Yerra VG, Batchu SN, Kabir G, Advani SL, Liu Y, Siddiqi FS, Connelly KA, Advani A	2021	Cardiovascular Drugs and Therapy	Myology		HALO
Genetic Inactivation of Peroxiredoxin-I Impairs the Growth of Human Pancreatic Cancer Cells	Dahou H, Minati M-A, Jacquemin P, Assi M	2021	antioxidants	Oncology	Cytonuclear	HALO
Immune-regulated IDO1-dependent tryptophan metabolism is source of one-carbon units for pancreatic cancer and stellate cells	Newman AC, Falcone M, Uribe AH, Zhang T, Athineos D, Pietzke M, Vazquez A, Blyth K, Maddocks ODK	2021	Molecular Cell	Immuno-oncology	Classifier, ISH/FISH	HALO
Inhibition of STAT3 augments antitumor efficacy of anti-CTLA-4 treatment against prostate cancer	Witt K, Evans-Axelsson S, Lundqvist A, Johansson M, Bjartell A, Hellsten R	2021	Cancer Immunology, Immunotherapy	Immuno-oncology	Area Quantification, Multiplex IHC	HALO
The immune suppressive microenvironment affects efficacy of radio-immunotherapy in brain metastasis	Niesel K, Schulz M, Anthes J, Alekseeva T, Macas J, Salamero-Boix A, Mockl A, Oberwahrenbrock T, Lolies M, Stein S, Plate KH, Reiss Y, Rodel F, Sevenich L	2021	EMBO Molecular Medicine	Immuno-oncology	Spatial Analysis, Highplex FL	HALO
Tracing Lung Cancer Risk Factors Through Mutational Signatures in Never-Smokers	Landi MT, Synnott NC, Rosenbaum J, Zhang T, Zhu B, Shi J, Zhao W, Kebede M, Sang J, Choi J, Mendoza L, Pacheco M, Hicks B, Caporaso NE, Abubakar M, Gordenin DA, Wedge, Alexandrov LB, Rothman N, Lan Q, Garcia-Closas M, Chanock SJ	2021	American Journal of Epidemiology	Oncology		HALO
Tumor cell PD-L1 expression is a strong predictor of unfavorable prognosis in immune checkpoint therapy-naive clear cell renal cell cancer	Möller K, Fraune C, Blessin NC, Lennartz M, Kluth M, Hube-Magg C, Lindhorst L, Dahlem R, Fisch M, Eichenauer T, Riechardt S, Simon R, Sauter G, Büscheck F, Höppner W, Matthies C, Doh O, Krech T, Marx AH, Zecha H, Rink M, Steurer S, Clauditz TS	2021	International Urology and Nephrology	Immuno-oncology	Multiplex IHC, TMA	HALO
Validation of multiplex immunofluorescence and digital image analysis for programmed death-ligand 1 expression and immune cell assessment in non-small cell lung cancer: comparison with conventional immunohistochemistry	Wu J, Mao L, Sun W, Yang X, Wang H, Liu X, Chi K, Xiaozheng H, Lin D	2021	Journal of Clinical Pathology	Immuno-oncology		HALO
VGLUT2 is a determinant of dopamine neuron resilience in a rotenone model of dopamine neurodegeneration	Buck SA, De Miranda BR, Logan RW, Fish KN, Greenamyre JT, Freyberg Z	2021	The Journal of Neuroscience	Neuroscience	ISH/FISH	HALO
Ki-67 Proliferation Index Assessment in Gastroenteropancreatic Neuroendocrine Tumors by Digital Image Analysis With Stringent Case and Hotspot Level Concordance Requirements	Boukhar SA, Gosse MD, Bellizzi AM, Rajan A	2021	American Journal of Clinical Pathology	Oncology		HALO
Global Neurotoxicity: Quantitative Analysis of Rat Brain Toxicity Following Exposure to Trimethyltin	Srivastava A, Liachenko S, Sarkar S, Paule M, Sadovova N, Hanig JP	2021	International Journal of Toxicology	Toxicology		HALO
High estrogen receptor alpha activation confers resistance to estrogen deprivation and is required for therapeutic response to estrogen in breast cancer	Traphagen NA, Hosford SR, Jiang A, Marotti JD, Brauer BL, Demidenko E, Miller TW	2021	Oncogene	Oncology		HALO
In vivo endothelialization and neointimal hyperplasia assessment after rabbit carotid endarterectomy with bovine pericardium	Chen Y, Feng Y, Wang T, Zhang X, Zhang M, Bai X, Li L, Yang K, Ma Y, Zhang Z, Jiao L	2021	Annals of Translational Medicine	Myology	Cytonuclear	HALO
Prognostic role of proliferating CD8+ cytotoxic Tcells in human cancers	Blessin NC, Li W, Mandelkow T, Jansen HL, Yang C, Raedler JB, Simon R, Büscheck F, Dum D, Luebke AM, Hinsch A, Möller K, Menz A, Bernreuther C, Lebok P, Clauditz T, Sauter G, Marx A, Uhlig R, Wilczak W, Minner S, Krech T, Fraune C, Höflmayer D, Burandt E, Steurer S	2021	Cellular Oncology	Immuno-oncology	Highplex FL, TMA	HALO
TNFα secreted by glioma associated macrophages promotes endothelial activation and resistance against anti-angiogenic therapy	Wei Z, Singh O, Ekinci C, Gill J, Li M, Mamatjan Y, Karimi S, Bunda S, Mansouri S, Aldape K, Zadeh G	2021	Acta Neuropathologica Communications	Immunology, Neuroscience	Classifier, Multiplex IHC	HALO
Tumor morphology and location associate with immune cell composition in pleomorphic sarcoma	Wustrack RL, Shao E, Sheridan J, Zimel M, Cho S-J, Horvai AE, Luong D, Kwek SS, Fong L, Okimoto RA	2021	Cancer Immunology, Immunotherapy	Immuno-oncology	Cytonuclear	HALO
Engineered red blood cells as an off-the-shelf allogeneic anti-tumor therapeutic	Zhang X, Lou M, Dastagir SR, Nixon M, Khamhoung A, Schmidt A, Lee A, Subbiah N, McLaughlin DC, Moore CL, Gribble M, Bayhi N, Amin V, Pepi R, Pawar S, Lyford TJ, Soman V, Mellen J, Carpenter CL, Turka LA, Wickham Tj, Chen TF	2021	Nature Communications	Oncology	Object Colocalization, Highplex FL	HALO
Mastocytosis-derived extracellular vesicles deliver miR-23a and miR-30a into pre-osteoblasts and prevent osteoblastogenesis and bone formation	Kim D-K, Bandara G, Cho Y-E, Komarow HD, Donahue DR, Karim B, Baek M-C, Kim HM, Metcalfe DD, Olivera A	2021	Nature Communications		Classifier	HALO
Mitigation of endemic GI-tract pathogen-mediated inflammation through development of multimodal treatment regimen and its impact on SIV acquisition in rhesus macaques	Bochart RM, Busman-Sahay K, Bondoc S, Morrow DW, Ortiz AM, Fennessey CM, Fischer MB, Shiel O, Swanson T, Shriver-Munsch CM, Crang HB, Armantrout KM, Barber-Axthelm AM, Langner C, Moats CR, Labriola CS, MacAllister R, Axthelm MK, Brenchley JM, Keele BF, Estes JD, Hansen SG, Smedley JV	2021	PLOS Pathogens	Infectious Disease	ISH/FISH, Multiplex IHC	HALO
Mucosal IFNγ production and potential role in protection in Escherichia coli O157:H7 vaccinated and challenged cattle	Schaut RG, Palmer MV, Boggiatto PM, Kudva IT, Loving CL, Sharma VK	2021	Scientific Reports	Immunology	ISH/FISH	HALO
Next-Generation Digital Histopathology of the Tumor Microenvironment	Mungenast F, Fernando A, Nica R, Boghiu B, Lungu B, Batra J, Ecker RC	2021	genes	Review		HALO
RIPK1 activation mediates neuroinflammation and disease progression in multiple sclerosis	Zelic M, Pontarelli F, Woodworth L, Zhu C, Mahan A, Ren Y, LaMorte M, Gruber R, Keane A, Loring P, Guo L, Xia T, Zhang B, Orning P, Lien E, Degterev A, Hammond T, Ofengeim D	2021	Cell Reports	Immunology		HALO
Single-cell dissection of cellular components and interactions shaping the tumor immune phenotypes in ovarian cancer	Hornburg M, Desbois M, Lu S, Guan Y, Lo AA, Kaufman S, Elrod A, Lotstein A, DesRochers TM, Munoz-Rodriguez JL, Wang X, Giltnane J, Mayba O, Turley SJ, Bourgon R, Daemen A, Wang Y	2021	Cancer Cell	Immuno-oncology		HALO
Acute inflammatory profiles differ with sex and age after spinal cord injury	Stewart AN, Lowe JL, Glaser EP, Mott CA, Shahidehpour RK, McFarlane KE, Bailey WM, Zhang B, Gensel JC	2021	Journal of Neuroinflammation	Immunology, Neuroscience		HALO
Analysis of genomic and non-genomic signaling of estrogen receptor in PDX models of breast cancer treated with a combination of the PI3K inhibitor alpelisib (BYL719) and fulvestrant	Jacquemetton J, Kassem L, Poulard C, Dahmani A, De Plater L, Montaudon E, Sourd L, Morisset L, El Botty R, Chateau-Joubert S, Vacher S, Bièche I, Treilleux I, Trédan O, Marangoni E, Le Romancer M	2021	Breast Cancer Research	Oncology	Multiplex IHC	HALO
AP-3-dependent targeting of flippase ATP8A1 to lamellar bodies suppresses activation of YAP in alveolar epithelial type 2 cells	Kook S, Wang P, Meng S, Jetter CS, Sucre JMS, Benjamin JT, Gokey JJ, Hanby HA, Jaume A, Goetzl L, Marks MS, Guttentag SH	2021	Proceedings of the National Academy of Sciences	Fibrosis		HALO
Cellular Senescence in Human Aldosterone-Producing Adrenocortical Cells and Related Disorders	Pieroni J, Yamazaki Y, Gao X, Tezuka Y, Ogata H, Omata K, Ono Y, Morimoto R, Nakamura Y, Satoh F, Sasano H	2021	Biomedicines	Metabolism	Cytonuclear	HALO
Functionally distinct POMC-expressing neuron subpopulations in hypothalamus revealed by intersectional targeting	Biglari N, Gaziano I, Schumacher J, Radermacher J, Paeger L, Klemm P, Chen W, Corneliussen S, Wunderlich CM, Sue M, Vollmar S, Klöckener T, Sotelo-Hitschfeld T, Abbasloo A, Edenhofer F, Reimann F, Gribble FM, Fenselau H, Kloppenburg P, Wunderlich FT, Brüning JC	2021	Nature Neuroscience	Neuroscience	ISH/FISH	HALO
SeqStain is an efficient method for multiplexed, spatialomic profiling of human and murine tissues	Rajagopalan A, Venkatesh I, Aslam R, Kirchenbuechler D, Khanna S, Cimbaluk D, Kordower JH, Gupta V	2021	Cell Reports Methods			HALO
Novel insulin sensitizer MSDC-0602K improves insulinemia and fatty liver disease in mice, alone and in combination with liraglutide	Kamm DR, Pyles KD, Sharpe MC, Healy LN, Colca JR, McCommis KS	2021	Journal of Biological Chemistry	Metabolism		HALO
Pathways of immune exclusion in metastatic osteosarcoma are associated with inferior patient outcomes	Ligon JA, Choi W, Cojocaru G, Fu W, Hsiue EH-C, Oke TF, Siegel N, Fong MH, Ladle B, Pratilas CA, Morris CD, Levin A, Rhee DS, Meyer CF, Tam AJ, Blosser R, Thompson ED, Suru A, McConkey D, Housseau F, Anders R, Pardoll DM, Llosa N	2021	Journal for ImmunoTherapy of Cancer	Immuno-oncology	Multiplex IHC	HALO
Predicting nodal metastases in papillary thyroid carcinoma using artificial intelligence	Esce AR, Redemann JP, Sanchez AC, Olson GT, Hanson JA, Argwal S, Boyd NH, Martin DR	2021	The American Journal of Surgery	Oncology		HALO
Toluidine blue staining of murine mast cells and quantitation by a novel, automated image analysis method using whole slide skin images	Raja N, Naikodi S, Govindarajan A, Palanisamy K	2021	Journal of Histotechnology	Immunology	Cytonuclear	HALO
Pancreatic ? cellselective zinc transporter 8 insufficiency accelerates diabetes associated with islet amyloidosis	Xu J, Wijesekara N, Regeenes R, Al Rijjal D, Piro AL, Song Y, Anne Wu A, Bhattacharjee A, Liu Y, Marzban L, Rocheleau JV, Fraser PE, Dai FF, Hu C, Wheeler MB	2021	JCI Insight	Metabolism		HALO
Human Type II Taste Cells Express ACE2 and are Infected by SARS-CoV-2	Doyle M, Ashley Appleton A, Q Liu, Yao Q, Mazucanti C, Egan J	2021	American Journal of Pathology		Cytonuclear	HALO
Oncogenic BRAF, unrestrained by TGF?-receptor signalling, drives right-sided colonic tumorigenesis	Leach J, Vlahov N, Tsantoulis P, et al	2021	Nature Communications	Oncology	ISH/FISH, Highplex FL	HALO
Attenuating CD3 affinity in a PSMAxCD3 bispecific antibody enables killing of prostate tumor cells with reduced cytokine release	Dang K, Castello G, Clarke S, et al.	2021	Journal for Immunotherapy of Cancer	Immuno-oncology	Multiplex IHC	HALO
Heterogeneity in tertiary lymphoid structure B-cells correlates with patient survival in metastatic melanom	Lynch K, Young S, Menaveau M, et al.	2021	Journal for Immunotherapy of Cancer	Immuno-oncology	Highplex FL	HALO
mRNA translation is a therapeutic vulnerability necessary for bladder epithelial transformation	Jana S, Deo R, Hough R, et al.	2021	JCI Insight	Oncology	Multiplex IHC, Highplex FL	HALO
Approaches for Handling Immunopathological and Clinical Data Using Deep Learning Methodology: Multiplex IHC/IF Data as a Paradigm	Goh S, Chua Y, Lee J, Yeong J, Cai Y	2021	Histopathology and Liquid Biopsy	Review		HALO
Tumor necroptosis is correlated with a favorable immune cell signature and programmed death-ligand 1 expression in cholangiocarcinoma	Lomphithak T, Akara-amornthum P, Murakami K, et al.	2021	Scientific Reports	Immuno-oncology	Highplex FL	HALO
Multiparametric Analyses of Hepatocellular Carcinoma Somatic Mouse Models and Their Associated Tumor Microenvironment	Taranto D, Ramirez C, Vegna S, et al.	2021	Current Protocols	Oncology	Multiplex IHC	HALO
Quantification of Human Epidermal Growth Factor Receptor 2 by Immunopeptide Enrichment and Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded and Frozen Breast Cancer Tissues	Kennedy J, Whiteaker J, Kennedy L, Bosch D, Lerch M, Schoenherr R, Zhao L, Lin C, Chowdhury S, Kilgore M, Allison K, Wang P, Hoofnagle A, Baird G, Paulovich A	2021	Clinical Chemistry	Oncology	Classifier	HALO
Pathological Change and Whole Transcriptome Alternation Caused by ePTFE Implantation in Myocardium	Shan Y, Zhang W, Chen G, Shi Q, Mi Y, Zhang H, Jia B	2021	BioMed Research International	Fibrosis	Area Quantification	HALO
Detection of Lung Cancer from Whole-Slide Histopathologic Images Using Deep Learning Approach	Mishra N, Behera P, Nanda R, Sahoo M	2019	International Journal of Research in Engineering and Sciences	Oncology	Classifier	HALO AI
Q134R: Small chemical compound with NFAT inhibitory properties improves behavioral performance and synapse function in mouse models of amyloid pathology	Sompol P, Gollihue J, Kraner S, Artiushin I, Cloyd R, Chishti E, Koren S, Nation G, Abisambra J, Huzian O, Nagy L, Santha M, Hackler L, Puskas L, Norris C	2021	Aging Cell	Neuroscience	Area Quantification	HALO
Methods to Determine and Analyze the Cellular Spatial Distribution Extracted From Multiplex Immunofluorescence Data to Understand the Tumor Microenvironment	Parra E	2021	Frontiers in Molecular Biosciences	Review		HALO
Mismatch repair-deficient prostate cancer with parenchymal brain metastases treated with immune checkpoint blockade	Sena L, Salles D, Engle E, Zhu Q, Tukachinsky H, Lotan T, Antonarakis E	2021	Molecular Case Studies	Immuno-oncology	Highplex FL	HALO
Lawsonia intracellularis infected enterocytes lack sucrase-isomaltase which contributes to reduced pig digestive capacity	Helm E, Burrough E, Leite, F, Gabler, N	2021	Veterinary Research	Other	ISH/FISH	HALO
Mechanism of Nucleic Acid Sensing in Retinal Pigment Epithelium (RPE): RIG-I Mediates Type I Interferon Response in Human RPE	Schustak J, Twarog M, Wu X, Huang Q, Bao Y	2021	Journal of Immunology Research		Area Quantification, ISH/FISH	HALO
Rejection of benign melanocytic nevi by nevus-resident CD4+ T cells	Schiferle E, Cheon S, Ham S, Son H, Messerschmidt J, Lawrence D, Cohen J, Flaherty K, Moon J, Lian C, Sullivan R, Demehri S	2021	Science Advances	Oncology	Multiplex IHC	HALO
Wound healing with topical BRAF inhibitor therapy in a diabetic model suggests tissue regenerative effects	Escuin-Ordinas H, Liu Y, Hufo W, Dimatteo R, Huang R, Krystofinski P, Azhdam A, Lee J, Comin-Anduix B, Cochran A, Lo R, Segura T, Scumpia P, Ribas A	2021	PLOS ONE	Dermatology	Object Colocalization, Multiplex IHC	HALO
The Goto Kakizaki rat: Impact of age upon changes in cardiac and renal structure, function	Meagher P, Civitarese R, Lee X, Gordon M, Bugyei-Twum A, Desjardins J, Kabir G, Zhang Y, Kosanam H, Visram A, Leong-Poi H, Advani A, Connelly K	2022	PLOS ONE	Myology	Muscle Fiber	HALO
Extensive Three-Dimensional Intratumor Proteomic Heterogeneity Revealed by Multiregion Sampling in High-Grade Serous Ovarian Tumor Specimens	Hunt A, Bateman N, Barakat W, Makohon-Moore S, Hood B, Conrads K, Zhou M, Calvert V, Pierobon M, Loffredo J, Litzi T, Oliver J, Mitchell D, Gist G, Rojas C, Blanton B, Robinson E, Odunsi K, Sood A, Casablanca Y, Darcy K, Schriver C, Petricoin E, Rao U, Maxwell G, Conrads T	2021	iScience		Multiplex IHC	HALO
Dissecting spatial heterogeneity and the immuneevasion mechanism of CTCs by single-cell RNA-seq in hepatocellular carcinoma	Sun Y, Wu L, Liu S, Jiang M, Hu B, Zhou K, Guo W, Xu Y, Zhong Y, Zhou X, Zhang Z, Liu G, Liu S, Shi Y, Ji Y, Du M, Li N, Li G, Zhao Z, Huang X, Xu L, Yu Q, Peng D, Qiu S, Sun H, Dean M, Wang X, Chung W, Dennison A, Zhou J, Hou Y, Fan J, Yang X	2021	Nature Communications	Oncology, Immuno-oncology	Highplex FL	HALO
TMEM229A suppresses non?small cell lung cancer progression via inactivating the ERK pathway	Zhang X, He Y, Jiang Y, Bao Y, Chen Q, Xie D, Yu H, Wang X	2021	Oncology Reports		Multiplex IHC	HALO
Glucocorticoid receptor antagonism promotes apoptosis in solid tumor cells	Greenstein A, Hunt H	2021	Oncotarget		Multiplex IHC	HALO
Anti-tumor effects of RTX-240: an engineered red blood cell expressing 4-1BB ligand and interleukin-15	McArdel S, Dugast A, Hoover M, Bollampalli A, Hong E, Castano Z Leonard S, Pawar S, Mellen J, Muriuki K, McLaughlin D, Bayhi N, Carpenter C, Turka L, Wickham T, Elloul S	2021	Cancer Immunology, Immunotherapy	Immuno-oncology	Highplex FL	HALO
Immune checkpoint blockade in triple negative breast cancer influenced by B cells through myeloid-derived suppressor cells	Vito A, Salem O, El-Sayes N, MacFawn I, Portillo A, Milne K, Harrington D, Ashkar A, Wan Y, Workenhe S, Nelson B, Bruno T, Mossman K	2021	Communications Biology	Immuno-oncology	Cytonuclear	HALO
Computational pathology reveals unique spatial patterns of immune response in H&E images from COVID-19 autopsies: preliminary findings	Corredor G, Toro P, Bera K, Rasmussen D, Viswanathan V, Buzzy C, Fu P, Barton L, Stroberg E, Duval E, Gilmore H, Mukhopadhyay, Madabhushi A	2021	Journal of Medical Imaging	Infectious Disease		HALO Link
Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging	Hickey J, Neumann E, Radtke A, Camarillo J, Beuschel R, Albanese A, McDonough E, Hatler J, Wiblin A, Fisher J, Croteau J, Small E, Sood A, Caprioli R, Angelo R Nolan G, Chung K, Hewitt S, Germain R, Spraggins J, Lundberg E, Snyder M, Kelleher N, Saka S	2021	arxiv	Review		HALO
Chemokine-Capturing Wound Contact Layer Rescues Dermal Healing	Schirmer L, Atallah P, Freudenberg U, Werner C	2021	Advanced Science	Dermatology	Highplex FL, Layer Thickness	HALO
Tertiary lymphoid structures critical for prognosis in endometrial cancer patients - a TransPORTEC study	Horeweg N, Workel, H, Loiero D, Church D, Vermij L, Léon-Castillo A, Krog R, de Boer S, Nout R, Powel M, Mileshkin L, MacKay H, Leary A, Singh N, Jürgenliemk-Schulz I, Creutzberg C, Koelzer V, Nijman H, Bosse T, Bruyn M	2021	Research Square		Multiplex IHC, TMA	HALO AI
White adipose tissue autophagy and adipose-liver crosstalk exacerbate nonalcoholic fatty liver disease in mice	Sakane S, Hikita H, Shirai K, Myojin Y, Sasaki Y, Kudo S, Fukumoto K, Mizutani N, Tahata Y, Makino Y, Yamada R, Kodama T, Sakamori R, Tatsumi T, Takehara T	2021	Cellular and Molecular Gasteroenterology and Hepatology	Metabolism		HALO
Neoadjuvant cabozantinib and nivolumab convert locally advanced hepatocellular carcinoma into resectable disease with enhanced antitumor immunity	Ho W, Zhu Q, Durham J, Popovic A, Xavier S, Leatherman J, Mohan A, Mo G, Zhang S, Gross N, Charmsaz S, Lin D, Quong D, Wilt B, Kamel I, Weiss M, Philosophe B, Burkhart R, Burns W, Schubert C, Ejaz A, He J, Deshpande A, Danilova L, Stein-O'Brien G, Sugar E, Laheru D, Anders R, Fertig E, Jaffee, E, Yarchoan M	2021	Nature Cancer	Oncology		HALO
SMAD4 represses FOSL1 expression and pancreatic cancer metastatic colonization	Dai C, Rennhack J, Arnoff T, Thaker M, Younger S, Doench J, Huang A, Yang A, Aguirre A, Wang B, Mun E, O'Connel J, Huang Y, Labella K, Talamas J, Li J, Ilic N, Hwang J, Hong A, Giacomelli A, Gjoerup O, Root D, Hahn W	2021	Cell Reports	Oncology	Area Quantification	HALO
A single-dose mRNA vaccine provides a long-term protection for hACE2 transgenic mice from SARS CoV-2	Huang Q, Ji K, Tian S, Wang F, Huang B, Tong Z, Tan S, Hao J, Wang Q, Tan W, Gao G, Yan J	2021	Nature Communications	Infectious Disease	Multiplex IHC	HALO
Endothelial cell infection and dysfunction, immune activation in severe COVID-19	Qin Z, Liu F, Blair R, Wang C, Yang H, Mudd J, Currey J, Iwanaga N, He J, Mi R, Han K, Midkiff C, Alam M, Aktas B, Heide R, Veazey R, Piedimonte G, Maness N, Ergün S, Mauvais-Jarvis F, Rappaport J, Kolls J, Qin X	2021	Theranostics	Immunology, Infectious Disease	Multiplex IHC, Spatial Analysis	HALO
Histological Studies of the VentricularSubventricular Zone as Neural Stem Cell and Glioma Stem Cell Niche	Brockman A, Mobley B, Rebecca I	2021	Journal of Histochemistry & Cytochemistry	Review		HALO
The deletion of yeaJ gene facilitates Escherichia coli escape from immune recognition	Wang X, Lin X, Wan Z, Wang S, Zuo J, Wang Z, Xu Y, Han X, Miao J	2021	Journal of Bacteriology			HALO
Naproxen chemoprevention promotes immune activation in Lynch syndrome colorectal mucosa	Reyes-Uribe L, Wu Wenhui, Gelincik O, Bommi P, Francisco-Cruz A, Solis L, Lynch P, Lim R, Stoffel E, Kanth P, Samadder N, Mork M, Taggart M, Milne G, Marnett L, Vornik L, Liu D, Revuelta M, Chang K, You Y, Kipelovich L, Wistuba I, Lee J, Sei S, Shoemaker R, Szabo E, Richmond E, Umar A, Perloff M, Brown P, Lipkin S, Vilar E	2020	The BMJ	Oncology, Gastroenterology	Classifier, Cytonuclear	HALO
Repeated porphyrin lipoprotein-based photodynamic therapy controls distant disease in mouse mesothelioma via the abscopal effect	Lou J, Aragaki M, Bernards N, Kinoshita T, Mo J Motooka Y, Ishiwata T, Gregor A, Chee T, Chen Z, Chen J, Kaga K, Wakasa S, Zheng G, Yasufuku K	2021	Nanophotonics	Oncology	Cytonuclear	HALO
Digital pathology in academia: Implementation and impact	Jones-Hall Y	2021	Lab Animal	Review		HALO
GOT1 inhibition promotes pancreatic cancer cell death by ferroptosis	Kremer D, Nelson B, Lin L, Yarosz E Halbrook C, Kerk S, Sajjakulnukit P, Myers A, Thurston G, Hou S, Carpenter E, Andren A, Nwosu Z, Cusmano N, Wisner S, Mbah N, Shan M, Das N, Magnuson B, Little A, Savani M, Ramos J, Gao T, Sastra S, Palermo C, Badgley M, Zhang L, Asara J, McBrayer S, Pasca di Magliano M, Crawford H, Shah Y, Olive K, Lyssiotis C	2021	Nature Communications	Oncology		HALO
A preclinical trial and molecularly-annotated patient cohort identify predictive biomarkers in homologous recombination deficient pancreatic cancer	Wang Y, Park J, Pacis A, Denroche R, Jang G, Zhang A, Cuggia A, Domecq C, Monlong J, Raitses-Gurevich M, Grant R, Borgida A, Holter S, Stossel C, Bu S, Masoomian M, Lungu I, Bartlett J, Wilson J, Gao Z, Riazalhosseini Y, Asselah J, Bouganim N, Cabrera T, Boucher L, Valenti D, Biagi J, Greenwood C, Polak P, Foulkes W, Golan T, O'Kane G, Fischer S, Knox J, Gallinger S, Zogopoulos G	2020	Clinical Cancer Research	Oncology	Classifier, Cytonuclear, Multiplex IHC	HALO
Epigenetic modifications precede molecular alterations and drive human hepatocarcinogenesis	Czauderna C, Poplawski A, O'Roourke C, Castven D, Pérez-Aguilar B, Becker D, Heilmann-Heimbach S, Odenthal M, Amer W, Schmiel M, Drebber U, Binder H, Ridder D, Schindeldecker M, Straub B, Galle P, Andersen J, Thorgeirsson S, Park Y, Marquardt J	2021	JCI Insight	Oncology	Cytonuclear, TMA	HALO
Allostatic hypermetabolic response in PGC1?/? heterozygote mouse despite mitochondrial defects	Rodriguez-Cuenca S, Lelliot C, Campbell M, Peddinti G, Martinuez-Uña M, Ingvorsen C, Dias A, Relat J, Mora S, Hyötyläinen T, Zorzano A, Orei? M, Bjursell M, Bohlooly-Y M, Lindén D, Vidal-Puid A	2021	The FASEB Journal	Metabolism	Vacuole	HALO
Distinct immune signatures in peripheral blood predict chemosensitivity in intrahepatic cholangiocarcinoma patients	Wu T, Yang Y, Zheng B, Shi X, Li W, Ma W, Wang S, Li Z, Zhu Y, Wu J, Wang K, Zhao Y, Wu R, Sui C, Shen S, Wu X, Chen L, Yuan Z, Wang H	2021	Engineering	Oncology, Immunology	Highplex FL	HALO
Constrictive and Hypertrophic Strictures in Ileal Crohns Disease	Liu Q, Zhang X, Ko H, Stocker D, Ellman J, Chen J, Hao Y, Bhardwaj S, Liang Y, Cho J, Colombel J, Taouli B, Harpaz N	2021	Clinical Gastroenterology and Hepatology	Gastroenterology		HALO
The amino acid transporter SLC7A5 is required for efficient growth of KRAS-mutant colorectal cancer	Najumudeen AK, Ceteci F, Fey SK, Hamm G, Steven RT, Hall H, Nikula CJ, Dexter A, Murta T, Race AM, Sumpton D, Vlahov N, Gay DM, Knight JRP, Jackstadt R, Leach JDG, Ridgway RA, Johnson ER, Nixon C, Hedley A, Gilroy K, Clark W, Malla SB, Dunne PD, Rodriguez-Blanco G, Critchlow SE, Mrowinska A, Malviya G, Solovyev D, Brown G, Lewis DY, Mackay GM, Strathdee D, Tardito S, Gottlieb E, CRUK Rosetta Grand Challenge Consortium, Takats Z, Barry ST, Goodwin RJA, Bunch J, Bushell M, Campbell AD, Sansom OJ	2021	Nature Genetics	Oncology	ISH/FISH	HALO
HIF-independent synthetic lethality between CDK4/6 inhibition and VHL loss across species	Nicholson HE, Tariq Z, Housden BE, Jennings RB, Stransky LA, Perrimon N, Signoretti S, Kaelin WG	2019	Cancer Therapy	Oncology		HALO
Impact of TREM2 risk variants on brain region-specific immune activation and plaque microenvironment in Alzheimer's disease patient brain samples	Prokop S, Miller KR, Labra SR, Pitkin RM, Hoxha K, Narasimhan S, Changolkar L, Rosenbloom A, Lee VM-Y, Trojanowski JQ	2019	Acta Neuropathologica	Neuroscience	Classifier, Area Quantification	HALO
ACT1 is required for murine IL-23-induced psoriasiform inflammation potentially independent of E3 ligase activity	Lipovsky A, Slivka PF, Su Z, Wang Y, Paulsboe S, Wetter J, Namovic MT

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