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Single-cell dissection of intratumoral heterogeneity and lineage diversity in metastatic gastric adenocarcinoma.
Wang R, Dang M, Harada K, Han G, Wang F, Pool Pizzi M, Zhao M, Tatlonghari G, Zhang S, Hao D, Lu Y, Zhao S, Badgwell BD, Blum Murphy M, Shanbhag N, Estrella JS, Roy-Chowdhuri S, Abdelhakeem AAF, Wang Y, Peng G, Hanash S, Calin GA, Song X, Chu Y, Zhang J, Li M, Chen K, Lazar AJ, Futreal A, Song S, Ajani JA, Wang L. Wang R, et al. Among authors: chen k. Nat Med. 2021 Jan;27(1):141-151. doi: 10.1038/s41591-020-1125-8. Epub 2021 Jan 4. Nat Med. 2021. PMID: 33398161 Free PMC article.
Clonal evolution in breast cancer revealed by single nucleus genome sequencing.
Wang Y, Waters J, Leung ML, Unruh A, Roh W, Shi X, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Zhao R, Michor F, Meric-Bernstam F, Navin NE. Wang Y, et al. Among authors: chen k. Nature. 2014 Aug 14;512(7513):155-60. doi: 10.1038/nature13600. Epub 2014 Jul 30. Nature. 2014. PMID: 25079324 Free PMC article.
Gene mutations in primary tumors and corresponding patient-derived xenografts derived from non-small cell lung cancer.
Hao C, Wang L, Peng S, Cao M, Li H, Hu J, Huang X, Liu W, Zhang H, Wu S, Pataer A, Heymach JV, Eterovic AK, Zhang Q, Shaw KR, Chen K, Futreal A, Wang M, Hofstetter W, Mehran R, Rice D, Roth JA, Sepesi B, Swisher SG, Vaporciyan A, Walsh GL, Johnson FM, Fang B. Hao C, et al. Among authors: chen k. Cancer Lett. 2015 Feb 1;357(1):179-185. doi: 10.1016/j.canlet.2014.11.024. Epub 2014 Nov 18. Cancer Lett. 2015. PMID: 25444907 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.
Monovar: single-nucleotide variant detection in single cells.
Zafar H, Wang Y, Nakhleh L, Navin N, Chen K. Zafar H, et al. Among authors: chen k. Nat Methods. 2016 Jun;13(6):505-7. doi: 10.1038/nmeth.3835. Epub 2016 Apr 18. Nat Methods. 2016. PMID: 27088313 Free PMC article.
Genotyping tumor clones from single-cell data.
Navin NE, Chen K. Navin NE, et al. Among authors: chen k. Nat Methods. 2016 Jun 29;13(7):555-6. doi: 10.1038/nmeth.3903. Nat Methods. 2016. PMID: 27355792 No abstract available.
Novel algorithmic approach predicts tumor mutation load and correlates with immunotherapy clinical outcomes using a defined gene mutation set.
Roszik J, Haydu LE, Hess KR, Oba J, Joon AY, Siroy AE, Karpinets TV, Stingo FC, Baladandayuthapani V, Tetzlaff MT, Wargo JA, Chen K, Forget MA, Haymaker CL, Chen JQ, Meric-Bernstam F, Eterovic AK, Shaw KR, Mills GB, Gershenwald JE, Radvanyi LG, Hwu P, Futreal PA, Gibbons DL, Lazar AJ, Bernatchez C, Davies MA, Woodman SE. Roszik J, et al. Among authors: chen k, chen jq. BMC Med. 2016 Oct 25;14(1):168. doi: 10.1186/s12916-016-0705-4. BMC Med. 2016. PMID: 27776519 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.
Comprehensive Characterization of Cancer Driver Genes and Mutations.
Bailey MH, Tokheim C, Porta-Pardo E, Sengupta S, Bertrand D, Weerasinghe A, Colaprico A, Wendl MC, Kim J, Reardon B, Ng PK, Jeong KJ, Cao S, Wang Z, Gao J, Gao Q, Wang F, Liu EM, Mularoni L, Rubio-Perez C, Nagarajan N, Cortés-Ciriano I, Zhou DC, Liang WW, Hess JM, Yellapantula VD, Tamborero D, Gonzalez-Perez A, Suphavilai C, Ko JY, Khurana E, Park PJ, Van Allen EM, Liang H; MC3 Working Group; Cancer Genome Atlas Research Network; Lawrence MS, Godzik A, Lopez-Bigas N, Stuart J, Wheeler D, Getz G, Chen K, Lazar AJ, Mills GB, Karchin R, Ding L. Bailey MH, et al. Among authors: chen k. Cell. 2018 Apr 5;173(2):371-385.e18. doi: 10.1016/j.cell.2018.02.060. Cell. 2018. PMID: 29625053 Free PMC article.
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. 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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