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Integrated multi-omics analyses identify anti-viral host factors and pathways controlling SARS-CoV-2 infection.
Hou J, Wei Y, Zou J, Jaffery R, Sun L, Liang S, Zheng N, Guerrero AM, Egan NA, Bohat R, Chen S, Zheng C, Mao X, Yi SS, Chen K, McGrail DJ, Sahni N, Shi PY, Chen Y, Xie X, Peng W. Hou J, et al. Among authors: chen k, chen s, chen y. Nat Commun. 2024 Jan 2;15(1):109. doi: 10.1038/s41467-023-44175-1. Nat Commun. 2024. PMID: 38168026 Free PMC article.
An integrated map of structural variation in 2,504 human genomes.
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium; Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. Sudmant PH, et al. Among authors: chen j, chen k. Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394. Nature. 2015. PMID: 26432246 Free PMC article.
Systematic Functional Annotation of Somatic Mutations in Cancer.
Ng PK, Li J, Jeong KJ, Shao S, Chen H, Tsang YH, Sengupta S, Wang Z, Bhavana VH, Tran R, Soewito S, Minussi DC, Moreno D, Kong K, Dogruluk T, Lu H, Gao J, Tokheim C, Zhou DC, Johnson AM, Zeng J, Ip CKM, Ju Z, Wester M, Yu S, Li Y, Vellano CP, Schultz N, Karchin R, Ding L, Lu Y, Cheung LWT, Chen K, Shaw KR, Meric-Bernstam F, Scott KL, Yi S, Sahni N, Liang H, Mills GB. Ng PK, et al. Among authors: chen k, chen h. Cancer Cell. 2018 Mar 12;33(3):450-462.e10. doi: 10.1016/j.ccell.2018.01.021. Cancer Cell. 2018. PMID: 29533785 Free PMC article.
In vivo screening identifies GATAD2B as a metastasis driver in KRAS-driven lung cancer.
Grzeskowiak CL, Kundu ST, Mo X, Ivanov AA, Zagorodna O, Lu H, Chapple RH, Tsang YH, Moreno D, Mosqueda M, Eterovic K, Fradette JJ, Ahmad S, Chen F, Chong Z, Chen K, Creighton CJ, Fu H, Mills GB, Gibbons DL, Scott KL. Grzeskowiak CL, et al. Among authors: chen k, chen f. Nat Commun. 2018 Jul 16;9(1):2732. doi: 10.1038/s41467-018-04572-3. Nat Commun. 2018. PMID: 30013058 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.
High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A; PCAWG Transcriptome Working Group; PCAWG Structural Variation Working Group; Creighton CJ; PCAWG Consortium. Zhang Y, et al. Nat Commun. 2020 Feb 5;11(1):736. doi: 10.1038/s41467-019-13885-w. Nat Commun. 2020. PMID: 32024823 Free PMC article.
Integrative pathway enrichment analysis of multivariate omics data.
Paczkowska M, Barenboim J, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC; PCAWG Drivers and Functional Interpretation Working Group; Reimand J; PCAWG Consortium. Paczkowska M, et al. Nat Commun. 2020 Feb 5;11(1):735. doi: 10.1038/s41467-019-13983-9. Nat Commun. 2020. PMID: 32024846 Free PMC article.
Pathway and network analysis of more than 2500 whole cancer genomes.
Reyna MA, Haan D, Paczkowska M, Verbeke LPC, Vazquez M, Kahraman A, Pulido-Tamayo S, Barenboim J, Wadi L, Dhingra P, Shrestha R, Getz G, Lawrence MS, Pedersen JS, Rubin MA, Wheeler DA, Brunak S, Izarzugaza JMG, Khurana E, Marchal K, von Mering C, Sahinalp SC, Valencia A; PCAWG Drivers and Functional Interpretation Working Group; Reimand J, Stuart JM, Raphael BJ; PCAWG Consortium. Reyna MA, et al. Nat Commun. 2020 Feb 5;11(1):729. doi: 10.1038/s41467-020-14367-0. Nat Commun. 2020. PMID: 32024854 Free PMC article.
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