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Spatially resolved transcriptomics of high-grade serous ovarian carcinoma.
Stur E, Corvigno S, Xu M, Chen K, Tan Y, Lee S, Liu J, Ricco E, Kraushaar D, Castro P, Zhang J, Sood AK. Stur E, et al. Among authors: chen k. iScience. 2022 Feb 14;25(3):103923. doi: 10.1016/j.isci.2022.103923. eCollection 2022 Mar 18. iScience. 2022. PMID: 35252817 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.
Sequential Therapy with PARP and WEE1 Inhibitors Minimizes Toxicity while Maintaining Efficacy.
Fang Y, McGrail DJ, Sun C, Labrie M, Chen X, Zhang D, Ju Z, Vellano CP, Lu Y, Li Y, Jeong KJ, Ding Z, Liang J, Wang SW, Dai H, Lee S, Sahni N, Mercado-Uribe I, Kim TB, Chen K, Lin SY, Peng G, Westin SN, Liu J, O'Connor MJ, Yap TA, Mills GB. Fang Y, et al. Among authors: chen k, chen x. Cancer Cell. 2019 Jun 10;35(6):851-867.e7. doi: 10.1016/j.ccell.2019.05.001. Cancer Cell. 2019. PMID: 31185210 Free PMC article.
Adaptive responses in a PARP inhibitor window of opportunity trial illustrate limited functional interlesional heterogeneity and potential combination therapy options.
Labrie M, Kim TB, Ju Z, Lee S, Zhao W, Fang Y, Lu Y, Chen K, Ramirez P, Frumovitz M, Meyer L, Fleming ND, Sood AK, Coleman RL, Mills GB, Westin SN. Labrie M, et al. Among authors: chen k. Oncotarget. 2019 May 28;10(37):3533-3546. doi: 10.18632/oncotarget.26947. eCollection 2019 May 28. Oncotarget. 2019. PMID: 31191824 Free PMC article.
Molecular Correlates of Venous Thromboembolism (VTE) in Ovarian Cancer.
Glassman D, Bateman NW, Lee S, Zhao L, Yao J, Tan Y, Ivan C, Rangel KM, Zhang J, Conrads KA, Hood BL, Abulez T, Futreal PA, Fleming ND, Afshar-Kharghan V, Maxwell GL, Conrads TP, Chen K, Sood AK. Glassman D, et al. Among authors: chen k. Cancers (Basel). 2022 Mar 15;14(6):1496. doi: 10.3390/cancers14061496. Cancers (Basel). 2022. PMID: 35326647 Free PMC article.
Single-nucleotide variant calling in single-cell sequencing data with Monopogen.
Dou J, Tan Y, Kock KH, Wang J, Cheng X, Tan LM, Han KY, Hon CC, Park WY, Shin JW, Jin H, Wang Y, Chen H, Ding L, Prabhakar S, Navin N, Chen R, Chen K. Dou J, et al. Among authors: chen k, chen r, chen h. Nat Biotechnol. 2024 May;42(5):803-812. doi: 10.1038/s41587-023-01873-x. Epub 2023 Aug 17. Nat Biotechnol. 2024. PMID: 37592035 Free PMC article.
Variants with a low allele frequency detected in genomic DNA affect the accuracy of mutation detection in cell-free DNA by next-generation sequencing.
Wang JF, Pu X, Zhang X, Chen K, Xi Y, Wang J, Mao X, Zhang J, Heymach JV, Antonoff MB, Hofstetter WL, Mehran RJ, Rice DC, Roth JA, Sepesi B, Swisher SG, Vaporciyan AA, Walsh GL, Meng QH, Shaw KR, Eterovic AK, Fang B. Wang JF, et al. Among authors: chen k. Cancer. 2018 Mar 1;124(5):1061-1069. doi: 10.1002/cncr.31152. Epub 2017 Nov 27. Cancer. 2018. PMID: 29178133 Free PMC article.
Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S; MC3 Working Group; PCAWG novel somatic mutation calling methods working group; Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L; PCAWG Consortium. Bailey MH, et al. Nat Commun. 2020 Sep 21;11(1):4748. doi: 10.1038/s41467-020-18151-y. Nat Commun. 2020. PMID: 32958763 Free PMC article.
Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.
Bailey MH, Meyerson WU, Dursi LJ, Wang LB, Dong G, Liang WW, Weerasinghe A, Li S, Li Y, Kelso S; MC3 Working Group; PCAWG novel somatic mutation calling methods working group; Saksena G, Ellrott K, Wendl MC, Wheeler DA, Getz G, Simpson JT, Gerstein MB, Ding L; PCAWG Consortium. Bailey MH, et al. Nat Commun. 2020 Nov 30;11(1):6232. doi: 10.1038/s41467-020-20128-w. Nat Commun. 2020. PMID: 33257764 Free PMC article.
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.
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