Inflamed immune phenotype predicts favorable clinical outcomes of immune checkpoint inhibitor therapy across multiple cancer types. Shen, J., Choi, Y. L., Lee, T., Kim, H., Chae, Y. K., Dulken, B. W., Bogdan, S., Huang, M., Fisher, G. A., Park, S., Lee, S. H., Hwang, J. E., Chung, J. H., Kim, L., Song, H., Pereira, S., Shin, S., Lim, Y., Ahn, C. H., Kim, S., Oum, C., Kim, S., Park, G., Song, S., Jung, W., Kim, S., Bang, Y. J., Mok, T. S., Ali, S. M., Ock, C. Y. J Immunother Cancer. 2024 Feb 14;12(2):e008339. doi: 10.1136/jitc-2023-008339. PMID: 38355279; PMCID: PMC10868175.

Generation of synthetic whole-slide image tiles of tumours from RNA-sequencing data via cascaded diffusion models. Carrillo-Perez F, Pizurica M, Zheng Y, Nandi TN, Madduri R, Shen J, Gevaert O. Nat Biomed Eng. 2024 Mar 21. doi: 10.1038/s41551-024-01193-8. Epub ahead of print. PMID: 38514775.

A pathologist-AI collaboration framework for enhancing diagnostic accuracies and efficiencies. Huang Z, Yang E, Shen J, Gratzinger D, Eyerer F, Liang B, Nirschl J, Bingham D, Dussaq AM, Kunder C, Rojansky R, Gilbert A, Chang-Graham AL, Howitt BE, Liu Y, Ryan EE, Tenney TB, Zhang X, Folkins A, Fox EJ, Montine KS, Montine TJ, Zou J. Nat Biomed Eng. 2024 Jun 19. doi: 10.1038/s41551-024-01223-5. Epub ahead of print. PMID: 38898173.

Prediction of immunotherapy response using mutations to cancer protein assemblies. Kong J, Zhao X, Singhal A, Park S, Bachelder R, Shen J, Zhang H, Moon J, Ahn C, Ock CY, Carter H, Ideker T. Sci Adv. 2024 Sep 20;10(38):eado9746. doi: 10.1126/sciadv.ado9746. Epub 2024 Sep 20. PMID: 39303028; PMCID: PMC11414719.

Multiomic analysis of familial adenomatous polyposis reveals molecular pathways associated with early tumorigenesis. Esplin ED, Hanson C, Wu S, Horning AM, Barapour N, Nevins SA, Jiang L, Contrepois K, Lee H, Guha TK, Hu Z, Laquindanum R, Mills MA, Chaib H, Chiu R, Jian R, Chan J, Ellenberger M, Becker WR, Bahmani B, Khan A, Michael B, Weimer AK, Esplin DG, Shen J, Lancaster S, Monte E, Karathanos TV, Ladabaum U, Longacre TA, Kundaje A, Curtis C, Greenleaf WJ, Ford JM, Snyder MP. Nat Cancer. 2024 Nov;5(11):1737-1753. doi: 10.1038/s43018-024-00831-z. Epub 2024 Oct 30. PMID: 39478120; PMCID: PMC11584401.

Prediction of immunochemotherapy response for diffuse large B-cell lymphoma using artificial intelligence digital pathology. Lee JH, Song GY, Lee J, Kang SR, Moon KM, Choi YD, Shen J, Noh MG, Yang DH. J Pathol Clin Res. 2024 May;10(3):e12370. doi: 10.1002/2056-4538.12370. PMID: 38584594; PMCID: PMC10999948.

Spatially Segregated Macrophage Populations Predict Distinct Outcomes in Colon Cancer. Matusiak M, Hickey JW, van IJzendoorn DGP, Lu G, Kidziński L, Zhu S, Colburg DRC, Luca B, Phillips DJ, Brubaker SW, Charville GW, Shen J, Loh KM, Okwan-Duodu DK, Nolan GP, Newman AM, West RB, van de Rijn M. Cancer Discov. 2024 Aug 2;14(8):1418-1439. doi: 10.1158/2159-8290.CD-23-1300. PMID: 38552005; PMCID: PMC11294822.

Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis. Zhu Y, Lee H, White S, Weimer AK, Monte E, Horning A, Nevins SA, Esplin ED, Paul K, Krieger G, Shipony Z, Chiu R, Laquindanum R, Karathanos TV, Chua MWY, Mills M, Ladabaum U, Longacre T, Shen J, Jaimovich A, Lipson D, Kundaje A, Greenleaf WJ, Curtis C, Ford JM, Snyder MP. Nat Cancer. 2024 Nov;5(11):1697-1712. doi: 10.1038/s43018-024-00823-z. Epub 2024 Oct 30. PMID: 39478119; PMCID: PMC11584406.

Computational pathology in 2030: a Delphi study forecasting the role of AI in pathology within the next decade. Berbís MA, McClintock DS, Bychkov A, Van der Laak J, Pantanowitz L, Lennerz JK, Cheng JY, Delahunt B, Egevad L, Eloy C, Farris AB 3rd, Fraggetta F, García Del Moral R, Hartman DJ, Herrmann MD, Hollemans E, Iczkowski KA, Karsan A, Kriegsmann M, Salama ME, Sinard JH, Tuthill JM, Williams B, Casado-Sánchez C, Sánchez-Turrión V, Luna A, Aneiros-Fernández J, Shen J. EBioMedicine. 2023 Feb;88:104427. doi: 10.1016/j.ebiom.2022.104427. Epub 2023 Jan 4. PMID: 36603288; PMCID: PMC9823157.

Deep learning-based phenotyping reclassifies combined hepatocellular-cholangiocarcinoma. Calderaro J, Ghaffari Laleh N, Zeng Q, Maille P, Favre L, Pujals A, Klein C, Bazille C, Heij LR, Uguen A, Luedde T, Di Tommaso L, Beaufrère A, Chatain A, Gastineau D, Nguyen CT, Nguyen-Canh H, Thi KN, Gnemmi V, Graham RP, Charlotte F, Wendum D, Vij M, Allende DS, Aucejo F, Diaz A, Rivière B, Herrero A, Evert K, Calvisi DF, Augustin J, Leow WQ, Leung HHW, Boleslawski E, Rela M, François A, Cha AW, Forner A, Reig M, Allaire M, Scatton O, Chatelain D, Boulagnon-Rombi C, Sturm N, Menahem B, Frouin E, Tougeron D, Tournigand C, Kempf E, Kim H, Ningarhari M, Michalak-Provost S, Gopal P, Brustia R, Vibert E, Schulze K, Rüther DF, Weidemann SA, Rhaiem R, Pawlotsky JM, Zhang X, Luciani A, Mulé S, Laurent A, Amaddeo G, Regnault H, De Martin E, Sempoux C, Navale P, Westerhoff M, Lo RC, Bednarsch J, Gouw A, Guettier C, Lequoy M, Harada K, Sripongpun P, Wetwittayaklang P, Loménie N, Tantipisit J, Kaewdech A, Shen J, Paradis V, Caruso S, Kather JN. Nat Commun. 2023 Dec 14;14(1):8290. doi: 10.1038/s41467-023-43749-3. PMID: 38092727; PMCID: PMC10719304.

Predicting lymph node metastasis from primary tumor histology and clinicopathologic factors in colorectal cancer using deep learning. Krogue JD, Azizi S, Tan F, Flament-Auvigne I, Brown T, Plass M, Reihs R, Müller H, Zatloukal K, Richeson P, Corrado GS, Peng LH, Mermel CH, Liu Y, Chen PC, Gombar S, Montine T, Shen J, Steiner DF, Wulczyn E. Commun Med (Lond). 2023 Apr 24;3(1):59. doi: 10.1038/s43856-023-00282-0. PMID: 37095223; PMCID: PMC10125969.

Synthetic whole-slide image tile generation with gene expression profile-infused deep generative models. Carrillo-Perez F, Pizurica M, Ozawa MG, Vogel H, West RB, Kong CS, Herrera LJ, Shen J, Gevaert O. Cell Rep Methods. 2023 Jul 19;3(8):100534. doi: 10.1016/j.crmeth.2023.100534. PMID: 37671024; PMCID: PMC10475789.

Development and Validation of a Machine Learning Model for Detection and Classification of Tertiary Lymphoid Structures in Gastrointestinal Cancers. Li Z, Jiang Y, Li B, Han Z, Shen J, Xia Y, Li R. JAMA Netw Open. 2023 Jan 3;6(1):e2252553. doi: 10.1001/jamanetworkopen.2022.52553. PMID: 36692877; PMCID: PMC10408275.

Relationship between tumor microenvironment (TME)-based histomic TGFβ signature (TGFBs), stromal fibroblast recruitment, and exclusion of immune cells as immunotherapy resistance mechanisms. JPark G, Park J, Shen J, Choi Y, Lee T, Kim H, Chae Y, Lee S, Park S, Chung J, Oum C, Ma M, Seo M, Ock C. Journal of Clinical Oncology 2023 41:16_suppl, 2585-2585

PlexusNet: A neural network architectural concept for medical image classification. Eminaga O, Abbas M, Shen J, Laurie M, Brooks J. D., Liao J, Rubin D. L. Computers in Biology and Medicine. 2023. doi: 10.1016/j.compbiomed.2023.106594

Deep learning model for the prediction of microsatellite instability in colorectal cancer: a diagnostic study. Yamashita R, Long J, Longacre T, Peng L, Berry G, Martin B, Higgins J, Rubin DL, Shen J. Lancet Oncol. 2021 Jan;22(1):132-141. doi: 10.1016/S1470-2045(20)30535-0. PMID: 33387492.

Learning domain-agnostic visual representation for computational pathology using medically-irrelevant style transfer augmentation. Yamashita R, Long J, Banda S, Shen J, Rubin DL. IEEE Transactions on Medical Imaging, 2021 40(12), 3945-3954; doi: 10.1109/TMI.2021.3101985

Deep learning predicts postsurgical recurrence of hepatocellular carcinoma from digital histopathologic images. Yamashita R, Long J, Saleem A, Rubin DL, Shen J. Sci Rep. 2021 Jan 21;11(1):2047. doi: 10.1038/s41598-021-81506-y. PMID: 33479370; PMCID: PMC7820423.

AI-enabled in silico immunohistochemical characterization for Alzheimer's disease. He B, Bukhari S, Fox E, Abid A, Shen J, Kawas C, Corrada M, Montine T, Zou J. Cell Rep Methods. 2022 Mar 28;2(4):100191. doi: 10.1016/j.crmeth.2022.100191. PMID: 35497493; PMCID: PMC9046239.

Impact of a deep learning assistant on the histopathologic classification of liver cancer. Kiani A, Uyumazturk B, Rajpurkar P, Wang A, Gao R, Jones E, Yu Y, Langlotz CP, Ball RL, Montine TJ, Martin BA, Berry GJ, Ozawa MG, Hazard FK, Brown RA, Chen SB, Wood M, Allard LS, Ylagan L, Ng AY, Shen J. NPJ Digit Med. 2020 Feb 26;3:23. doi: 10.1038/s41746-020-0232-8. PMID: 32140566; PMCID: PMC7044422.

Development and Use of Natural Language Processing for Identification of Distant Cancer Recurrence and Sites of Distant Recurrence Using Unstructured Electronic Health Record Data. Karimi YH, Blayney DW, Kurian AW, Shen J, Yamashita R, Rubin D, Banerjee I. JCO Clin Cancer Inform. 2021 Apr;5:469-478. doi: 10.1200/CCI.20.00165. PMID: 33929889; PMCID: PMC8462655.

Deep learning-based sparse whole-slide image analysis for the diagnosis of gastric intestinal metaplasia. Braatz J, Rajpurkar P, Zhang S, Ng AY, Shen J. arXiv preprint arXiv:2201.01449. 2022 Jan 5.; doi: 10.48550/arXiv.2201.01449

Deep learning assistance for the histopathologic diagnosis of Helicobacter pylori. Zhou S, Marklund H, Blaha O, Desai M, Martin B, Bingham D, Berry GJ, Gomulia E, Ng AY, Shen J. Intelligence-Based Medicine. 2020. doi: 10.1016/j.ibmed.2020.100004