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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. Calderaro J, et al. Among authors: shen j. Nat Commun. 2023 Dec 14;14(1):8290. doi: 10.1038/s41467-023-43749-3. Nat Commun. 2023. PMID: 38092727 Free PMC article.
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. Kiani A, et al. Among authors: shen j. NPJ Digit Med. 2020 Feb 26;3:23. doi: 10.1038/s41746-020-0232-8. eCollection 2020. NPJ Digit Med. 2020. PMID: 32140566 Free PMC article.
MITI minimum information guidelines for highly multiplexed tissue images.
Schapiro D, Yapp C, Sokolov A, Reynolds SM, Chen YA, Sudar D, Xie Y, Muhlich J, Arias-Camison R, Arena S, Taylor AJ, Nikolov M, Tyler M, Lin JR, Burlingame EA; Human Tumor Atlas Network; Chang YH, Farhi SL, Thorsson V, Venkatamohan N, Drewes JL, Pe'er D, Gutman DA, Herrmann MD, Gehlenborg N, Bankhead P, Roland JT, Herndon JM, Snyder MP, Angelo M, Nolan G, Swedlow JR, Schultz N, Merrick DT, Mazzili SA, Cerami E, Rodig SJ, Santagata S, Sorger PK. Schapiro D, et al. Nat Methods. 2022 Mar;19(3):262-267. doi: 10.1038/s41592-022-01415-4. Nat Methods. 2022. PMID: 35277708 Free PMC article.
Inflamed immune phenotype predicts favorable clinical outcomes of immune checkpoint inhibitor therapy across multiple cancer types.
Shen J, Choi YL, Lee T, Kim H, Chae YK, Dulken BW, Bogdan S, Huang M, Fisher GA, Park S, Lee SH, Hwang JE, Chung JH, Kim L, Song H, Pereira S, Shin S, Lim Y, Ahn CH, Kim S, Oum C, Kim S, Park G, Song S, Jung W, Kim S, Bang YJ, Mok TSK, Ali SM, Ock CY. Shen J, et al. J Immunother Cancer. 2024 Feb 14;12(2):e008339. doi: 10.1136/jitc-2023-008339. J Immunother Cancer. 2024. PMID: 38355279 Free PMC article.
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