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A community effort to create standards for evaluating tumor subclonal reconstruction.
Salcedo A, Tarabichi M, Espiritu SMG, Deshwar AG, David M, Wilson NM, Dentro S, Wintersinger JA, Liu LY, Ko M, Sivanandan S, Zhang H, Zhu K, Ou Yang TH, Chilton JM, Buchanan A, Lalansingh CM, P'ng C, Anghel CV, Umar I, Lo B, Zou W; DREAM SMC-Het Participants; Simpson JT, Stuart JM, Anastassiou D, Guan Y, Ewing AD, Ellrott K, Wedge DC, Morris Q, Van Loo P, Boutros PC. Salcedo A, et al. Among authors: ou yang th. Nat Biotechnol. 2020 Jan;38(1):97-107. doi: 10.1038/s41587-019-0364-z. Epub 2020 Jan 9. Nat Biotechnol. 2020. PMID: 31919445 Free PMC article.
Biomolecular events in cancer revealed by attractor metagenes.
Cheng WY, Ou Yang TH, Anastassiou D. Cheng WY, et al. Among authors: ou yang th. PLoS Comput Biol. 2013;9(2):e1002920. doi: 10.1371/journal.pcbi.1002920. Epub 2013 Feb 21. PLoS Comput Biol. 2013. PMID: 23468608 Free PMC article.
The Cancer Genome Atlas Pan-Cancer analysis project.
Cancer Genome Atlas Research Network; Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM. Cancer Genome Atlas Research Network, et al. Nat Genet. 2013 Oct;45(10):1113-20. doi: 10.1038/ng.2764. Nat Genet. 2013. PMID: 24071849 Free PMC article.
Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction.
Salcedo A, Tarabichi M, Buchanan A, Espiritu SMG, Zhang H, Zhu K, Ou Yang TH, Leshchiner I, Anastassiou D, Guan Y, Jang GH, Mootor MFE, Haase K, Deshwar AG, Zou W, Umar I, Dentro S, Wintersinger JA, Chiotti K, Demeulemeester J, Jolly C, Sycza L, Ko M; PCAWG Evolution and Heterogeneity Working Group; SMC-Het Participants; Wedge DC, Morris QD, Ellrott K, Van Loo P, Boutros PC. Salcedo A, et al. Among authors: ou yang th. Nat Biotechnol. 2024 Jun 11. doi: 10.1038/s41587-024-02250-y. Online ahead of print. Nat Biotechnol. 2024. PMID: 38862616
The Immune Landscape of Cancer.
Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, Porta-Pardo E, Gao GF, Plaisier CL, Eddy JA, Ziv E, Culhane AC, Paull EO, Sivakumar IKA, Gentles AJ, Malhotra R, Farshidfar F, Colaprico A, Parker JS, Mose LE, Vo NS, Liu J, Liu Y, Rader J, Dhankani V, Reynolds SM, Bowlby R, Califano A, Cherniack AD, Anastassiou D, Bedognetti D, Mokrab Y, Newman AM, Rao A, Chen K, Krasnitz A, Hu H, Malta TM, Noushmehr H, Pedamallu CS, Bullman S, Ojesina AI, Lamb A, Zhou W, Shen H, Choueiri TK, Weinstein JN, Guinney J, Saltz J, Holt RA, Rabkin CS; Cancer Genome Atlas Research Network; Lazar AJ, Serody JS, Demicco EG, Disis ML, Vincent BG, Shmulevich I. Thorsson V, et al. Among authors: ou yang th. Immunity. 2018 Apr 17;48(4):812-830.e14. doi: 10.1016/j.immuni.2018.03.023. Epub 2018 Apr 5. Immunity. 2018. PMID: 29628290 Free PMC article.
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