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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: chen k. Immunity. 2019 Aug 20;51(2):411-412. doi: 10.1016/j.immuni.2019.08.004. Immunity. 2019. PMID: 31433971 Free article. No abstract available.
The somatic genomic landscape of glioblastoma.
Brennan CW, Verhaak RG, McKenna A, Campos B, Noushmehr H, Salama SR, Zheng S, Chakravarty D, Sanborn JZ, Berman SH, Beroukhim R, Bernard B, Wu CJ, Genovese G, Shmulevich I, Barnholtz-Sloan J, Zou L, Vegesna R, Shukla SA, Ciriello G, Yung WK, Zhang W, Sougnez C, Mikkelsen T, Aldape K, Bigner DD, Van Meir EG, Prados M, Sloan A, Black KL, Eschbacher J, Finocchiaro G, Friedman W, Andrews DW, Guha A, Iacocca M, O'Neill BP, Foltz G, Myers J, Weisenberger DJ, Penny R, Kucherlapati R, Perou CM, Hayes DN, Gibbs R, Marra M, Mills GB, Lander E, Spellman P, Wilson R, Sander C, Weinstein J, Meyerson M, Gabriel S, Laird PW, Haussler D, Getz G, Chin L; TCGA Research Network. Brennan CW, et al. Cell. 2013 Oct 10;155(2):462-77. doi: 10.1016/j.cell.2013.09.034. Cell. 2013. PMID: 24120142 Free PMC article.
Bias from removing read duplication in ultra-deep sequencing experiments.
Zhou W, Chen T, Zhao H, Eterovic AK, Meric-Bernstam F, Mills GB, Chen K. Zhou W, et al. Among authors: chen k, chen t. Bioinformatics. 2014 Apr 15;30(8):1073-1080. doi: 10.1093/bioinformatics/btt771. Epub 2014 Jan 2. Bioinformatics. 2014. PMID: 24389657 Free PMC article.
TransVar: a multilevel variant annotator for precision genomics.
Zhou W, Chen T, Chong Z, Rohrdanz MA, Melott JM, Wakefield C, Zeng J, Weinstein JN, Meric-Bernstam F, Mills GB, Chen K. Zhou W, et al. Among authors: chen k, chen t. Nat Methods. 2015 Nov;12(11):1002-3. doi: 10.1038/nmeth.3622. Nat Methods. 2015. PMID: 26513549 Free PMC article. No abstract available.
Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.
Gao Q, Liang WW, Foltz SM, Mutharasu G, Jayasinghe RG, Cao S, Liao WW, Reynolds SM, Wyczalkowski MA, Yao L, Yu L, Sun SQ; Fusion Analysis Working Group; Cancer Genome Atlas Research Network; Chen K, Lazar AJ, Fields RC, Wendl MC, Van Tine BA, Vij R, Chen F, Nykter M, Shmulevich I, Ding L. Gao Q, et al. Among authors: chen k, chen f. Cell Rep. 2018 Apr 3;23(1):227-238.e3. doi: 10.1016/j.celrep.2018.03.050. Cell Rep. 2018. PMID: 29617662 Free PMC article.
Systematic Analysis of Splice-Site-Creating Mutations in Cancer.
Jayasinghe RG, Cao S, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang WW, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ; Cancer Genome Atlas Research Network; Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L. Jayasinghe RG, et al. Among authors: chen k, chen f. Cell Rep. 2018 Apr 3;23(1):270-281.e3. doi: 10.1016/j.celrep.2018.03.052. Cell Rep. 2018. PMID: 29617666 Free PMC article.
Pathogenic Germline Variants in 10,389 Adult Cancers.
Huang KL, Mashl RJ, Wu Y, Ritter DI, Wang J, Oh C, Paczkowska M, Reynolds S, Wyczalkowski MA, Oak N, Scott AD, Krassowski M, Cherniack AD, Houlahan KE, Jayasinghe R, Wang LB, Zhou DC, Liu D, Cao S, Kim YW, Koire A, McMichael JF, Hucthagowder V, Kim TB, Hahn A, Wang C, McLellan MD, Al-Mulla F, Johnson KJ; Cancer Genome Atlas Research Network; Lichtarge O, Boutros PC, Raphael B, Lazar AJ, Zhang W, Wendl MC, Govindan R, Jain S, Wheeler D, Kulkarni S, Dipersio JF, Reimand J, Meric-Bernstam F, Chen K, Shmulevich I, Plon SE, Chen F, Ding L. Huang KL, et al. Among authors: chen k, chen f. Cell. 2018 Apr 5;173(2):355-370.e14. doi: 10.1016/j.cell.2018.03.039. Cell. 2018. PMID: 29625052 Free PMC article.
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