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An integrative ENCODE resource for cancer genomics.
Zhang J, Lee D, Dhiman V, Jiang P, Xu J, McGillivray P, Yang H, Liu J, Meyerson W, Clarke D, Gu M, Li S, Lou S, Xu J, Lochovsky L, Ung M, Ma L, Yu S, Cao Q, Harmanci A, Yan KK, Sethi A, Gürsoy G, Schoenberg MR, Rozowsky J, Warrell J, Emani P, Yang YT, Galeev T, Kong X, Liu S, Li X, Krishnan J, Feng Y, Rivera-Mulia JC, Adrian J, Broach JR, Bolt M, Moran J, Fitzgerald D, Dileep V, Liu T, Mei S, Sasaki T, Trevilla-Garcia C, Wang S, Wang Y, Zang C, Wang D, Klein RJ, Snyder M, Gilbert DM, Yip K, Cheng C, Yue F, Liu XS, White KP, Gerstein M. Zhang J, et al. Among authors: clarke d. Nat Commun. 2020 Jul 29;11(1):3696. doi: 10.1038/s41467-020-14743-w. Nat Commun. 2020. PMID: 32728046 Free PMC article.
Systematic control of protein interactions for systems biology.
Bhardwaj N, Clarke D, Gerstein M. Bhardwaj N, et al. Among authors: clarke d. Proc Natl Acad Sci U S A. 2011 Dec 20;108(51):20279-80. doi: 10.1073/pnas.1118084109. Epub 2011 Dec 12. Proc Natl Acad Sci U S A. 2011. PMID: 22160691 Free PMC article. No abstract available.
Architecture of the human regulatory network derived from ENCODE data.
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Gerstein MB, et al. Among authors: clarke d. Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245. Nature. 2012. PMID: 22955619 Free PMC article.
Integrative annotation of variants from 1092 humans: application to cancer genomics.
Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM, Lappalainen T, Sboner A, Lochovsky L, Chen J, Harmanci A, Das J, Abyzov A, Balasubramanian S, Beal K, Chakravarty D, Challis D, Chen Y, Clarke D, Clarke L, Cunningham F, Evani US, Flicek P, Fragoza R, Garrison E, Gibbs R, Gümüş ZH, Herrero J, Kitabayashi N, Kong Y, Lage K, Liluashvili V, Lipkin SM, MacArthur DG, Marth G, Muzny D, Pers TH, Ritchie GRS, Rosenfeld JA, Sisu C, Wei X, Wilson M, Xue Y, Yu F; 1000 Genomes Project Consortium; Dermitzakis ET, Yu H, Rubin MA, Tyler-Smith C, Gerstein M. Khurana E, et al. Among authors: clarke l, clarke d. Science. 2013 Oct 4;342(6154):1235587. doi: 10.1126/science.1235587. Science. 2013. PMID: 24092746 Free PMC article.
Reads meet rotamers: structural biology in the age of deep sequencing.
Sethi A, Clarke D, Chen J, Kumar S, Galeev TR, Regan L, Gerstein M. Sethi A, et al. Among authors: clarke d. Curr Opin Struct Biol. 2015 Dec;35:125-34. doi: 10.1016/j.sbi.2015.11.003. Epub 2015 Dec 1. Curr Opin Struct Biol. 2015. PMID: 26658741 Free PMC article. Review.
2,975 results