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Page 1
A research roadmap for next-generation sequencing informatics.
Altman RB, Prabhu S, Sidow A, Zook JM, Goldfeder R, Litwack D, Ashley E, Asimenos G, Bustamante CD, Donigan K, Giacomini KM, Johansen E, Khuri N, Lee E, Liang XS, Salit M, Serang O, Tezak Z, Wall DP, Mansfield E, Kass-Hout T. Altman RB, et al. Among authors: sidow a. Sci Transl Med. 2016 Apr 20;8(335):335ps10. doi: 10.1126/scitranslmed.aaf7314. Sci Transl Med. 2016. PMID: 27099173 Free PMC article. Review.
svviz: a read viewer for validating structural variants.
Spies N, Zook JM, Salit M, Sidow A. Spies N, et al. Among authors: sidow a. Bioinformatics. 2015 Dec 15;31(24):3994-6. doi: 10.1093/bioinformatics/btv478. Epub 2015 Aug 18. Bioinformatics. 2015. PMID: 26286809
Genome-wide reconstruction of complex structural variants using read clouds.
Spies N, Weng Z, Bishara A, McDaniel J, Catoe D, Zook JM, Salit M, West RB, Batzoglou S, Sidow A. Spies N, et al. Among authors: sidow a. Nat Methods. 2017 Sep;14(9):915-920. doi: 10.1038/nmeth.4366. Epub 2017 Jul 17. Nat Methods. 2017. PMID: 28714986 Free PMC article.
Extensive sequencing of seven human genomes to characterize benchmark reference materials.
Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M. Zook JM, et al. Among authors: sidow a. Sci Data. 2016 Jun 7;3:160025. doi: 10.1038/sdata.2016.25. Sci Data. 2016. PMID: 27271295 Free PMC article.
Distribution and intensity of constraint in mammalian genomic sequence.
Cooper GM, Stone EA, Asimenos G; NISC Comparative Sequencing Program; Green ED, Batzoglou S, Sidow A. Cooper GM, et al. Among authors: sidow a. Genome Res. 2005 Jul;15(7):901-13. doi: 10.1101/gr.3577405. Epub 2005 Jun 17. Genome Res. 2005. PMID: 15965027 Free PMC article.
Inference of tumor phylogenies with improved somatic mutation discovery.
Salari R, Saleh SS, Kashef-Haghighi D, Khavari D, Newburger DE, West RB, Sidow A, Batzoglou S. Salari R, et al. Among authors: sidow a. J Comput Biol. 2013 Nov;20(11):933-44. doi: 10.1089/cmb.2013.0106. J Comput Biol. 2013. PMID: 24195709 Free PMC article.
Genome evolution during progression to breast cancer.
Newburger DE, Kashef-Haghighi D, Weng Z, Salari R, Sweeney RT, Brunner AL, Zhu SX, Guo X, Varma S, Troxell ML, West RB, Batzoglou S, Sidow A. Newburger DE, et al. Among authors: sidow a. Genome Res. 2013 Jul;23(7):1097-108. doi: 10.1101/gr.151670.112. Epub 2013 Apr 8. Genome Res. 2013. PMID: 23568837 Free PMC article.
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.
Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. Landt SG, et al. Among authors: sidow a. Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111. Genome Res. 2012. PMID: 22955991 Free PMC article.
88 results