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A computational approach to distinguish somatic vs. germline origin of genomic alterations from deep sequencing of cancer specimens without a matched normal.
Sun JX, He Y, Sanford E, Montesion M, Frampton GM, Vignot S, Soria JC, Ross JS, Miller VA, Stephens PJ, Lipson D, Yelensky R. Sun JX, et al. Among authors: he y. PLoS Comput Biol. 2018 Feb 7;14(2):e1005965. doi: 10.1371/journal.pcbi.1005965. eCollection 2018 Feb. PLoS Comput Biol. 2018. PMID: 29415044 Free PMC article.
Targeted Next Generation Sequencing Identifies Markers of Response to PD-1 Blockade.
Johnson DB, Frampton GM, Rioth MJ, Yusko E, Xu Y, Guo X, Ennis RC, Fabrizio D, Chalmers ZR, Greenbowe J, Ali SM, Balasubramanian S, Sun JX, He Y, Frederick DT, Puzanov I, Balko JM, Cates JM, Ross JS, Sanders C, Robins H, Shyr Y, Miller VA, Stephens PJ, Sullivan RJ, Sosman JA, Lovly CM. Johnson DB, et al. Among authors: he y. Cancer Immunol Res. 2016 Nov;4(11):959-967. doi: 10.1158/2326-6066.CIR-16-0143. Epub 2016 Sep 26. Cancer Immunol Res. 2016. PMID: 27671167 Free PMC article.
Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden.
Chalmers ZR, Connelly CF, Fabrizio D, Gay L, Ali SM, Ennis R, Schrock A, Campbell B, Shlien A, Chmielecki J, Huang F, He Y, Sun J, Tabori U, Kennedy M, Lieber DS, Roels S, White J, Otto GA, Ross JS, Garraway L, Miller VA, Stephens PJ, Frampton GM. Chalmers ZR, et al. Among authors: he y. Genome Med. 2017 Apr 19;9(1):34. doi: 10.1186/s13073-017-0424-2. Genome Med. 2017. PMID: 28420421 Free PMC article.
Analysis of DNA Damage Response Gene Alterations and Tumor Mutational Burden Across 17,486 Tubular Gastrointestinal Carcinomas: Implications for Therapy.
Parikh AR, He Y, Hong TS, Corcoran RB, Clark JW, Ryan DP, Zou L, Ting DT, Catenacci DV, Chao J, Fakih M, Klempner SJ, Ross JS, Frampton GM, Miller VA, Ali SM, Schrock AB. Parikh AR, et al. Among authors: he y. Oncologist. 2019 Oct;24(10):1340-1347. doi: 10.1634/theoncologist.2019-0034. Epub 2019 Apr 30. Oncologist. 2019. PMID: 31040255 Free PMC article.
Genomic Alterations Observed in Colitis-Associated Cancers Are Distinct From Those Found in Sporadic Colorectal Cancers and Vary by Type of Inflammatory Bowel Disease.
Yaeger R, Shah MA, Miller VA, Kelsen JR, Wang K, Heins ZJ, Ross JS, He Y, Sanford E, Yantiss RK, Balasubramanian S, Stephens PJ, Schultz N, Oren M, Tang L, Kelsen D. Yaeger R, et al. Among authors: he y. Gastroenterology. 2016 Aug;151(2):278-287.e6. doi: 10.1053/j.gastro.2016.04.001. Epub 2016 Apr 8. Gastroenterology. 2016. PMID: 27063727 Free PMC article.
Distinct age-associated molecular profiles in acute myeloid leukemia defined by comprehensive clinical genomic profiling.
Tarlock K, Zhong S, He Y, Ries R, Severson E, Bailey M, Morley S, Balasubramanian S, Erlich R, Lipson D, Otto GA, Vergillo JA, Kolb EA, Ross JS, Mughal T, Stephens PJ, Miller V, Meshinchi S, He J. Tarlock K, et al. Among authors: he y, he j. Oncotarget. 2018 May 29;9(41):26417-26430. doi: 10.18632/oncotarget.25443. eCollection 2018 May 29. Oncotarget. 2018. PMID: 29899868 Free PMC article.
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