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Page 1
Toil enables reproducible, open source, big biomedical data analyses.
Vivian J, Rao AA, Nothaft FA, Ketchum C, Armstrong J, Novak A, Pfeil J, Narkizian J, Deran AD, Musselman-Brown A, Schmidt H, Amstutz P, Craft B, Goldman M, Rosenbloom K, Cline M, O'Connor B, Hanna M, Birger C, Kent WJ, Patterson DA, Joseph AD, Zhu J, Zaranek S, Getz G, Haussler D, Paten B. Vivian J, et al. Among authors: kent wj. Nat Biotechnol. 2017 Apr 11;35(4):314-316. doi: 10.1038/nbt.3772. Nat Biotechnol. 2017. PMID: 28398314 Free PMC article. No abstract available.
Understanding genome browsing.
Cline MS, Kent WJ. Cline MS, et al. Among authors: kent wj. Nat Biotechnol. 2009 Feb;27(2):153-5. doi: 10.1038/nbt0209-153. Nat Biotechnol. 2009. PMID: 19204697 No abstract available.
The NIH BD2K center for big data in translational genomics.
Paten B, Diekhans M, Druker BJ, Friend S, Guinney J, Gassner N, Guttman M, Kent WJ, Mantey P, Margolin AA, Massie M, Novak AM, Nothaft F, Pachter L, Patterson D, Smuga-Otto M, Stuart JM, Van't Veer L, Wold B, Haussler D. Paten B, et al. Among authors: kent wj. J Am Med Inform Assoc. 2015 Nov;22(6):1143-7. doi: 10.1093/jamia/ocv047. Epub 2015 Jul 13. J Am Med Inform Assoc. 2015. PMID: 26174866 Free PMC article.
Landscape of X chromosome inactivation across human tissues.
Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A; GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI; Biospecimen Collection Source Site—RPCI; Biospecimen Core Resource—VARI; Brain Bank Repository—University of Miami Brain Endowment Bank; Leidos Biomedical—Project Management; ELSI Study; Genome Browser Data Integration &Visualization—EBI; Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz; Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG. Tukiainen T, et al. Nature. 2017 Oct 11;550(7675):244-248. doi: 10.1038/nature24265. Nature. 2017. PMID: 29022598 Free PMC article.
Building a pan-genome reference for a population.
Nguyen N, Hickey G, Zerbino DR, Raney B, Earl D, Armstrong J, Kent WJ, Haussler D, Paten B. Nguyen N, et al. Among authors: kent wj. J Comput Biol. 2015 May;22(5):387-401. doi: 10.1089/cmb.2014.0146. Epub 2015 Jan 7. J Comput Biol. 2015. PMID: 25565268 Free PMC article.
UCSC Data Integrator and Variant Annotation Integrator.
Hinrichs AS, Raney BJ, Speir ML, Rhead B, Casper J, Karolchik D, Kuhn RM, Rosenbloom KR, Zweig AS, Haussler D, Kent WJ. Hinrichs AS, et al. Among authors: kent wj. Bioinformatics. 2016 May 1;32(9):1430-2. doi: 10.1093/bioinformatics/btv766. Epub 2016 Jan 6. Bioinformatics. 2016. PMID: 26740527 Free PMC article.
The UCSC Cancer Genomics Browser: update 2011.
Sanborn JZ, Benz SC, Craft B, Szeto C, Kober KM, Meyer L, Vaske CJ, Goldman M, Smith KE, Kuhn RM, Karolchik D, Kent WJ, Stuart JM, Haussler D, Zhu J. Sanborn JZ, et al. Among authors: kent wj. Nucleic Acids Res. 2011 Jan;39(Database issue):D951-9. doi: 10.1093/nar/gkq1113. Epub 2010 Nov 8. Nucleic Acids Res. 2011. PMID: 21059681 Free PMC article.
Dynamic landscape and regulation of RNA editing in mammals.
Tan MH, Li Q, Shanmugam R, Piskol R, Kohler J, Young AN, Liu KI, Zhang R, Ramaswami G, Ariyoshi K, Gupte A, Keegan LP, George CX, Ramu A, Huang N, Pollina EA, Leeman DS, Rustighi A, Goh YPS; GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI; Biospecimen Collection Source Site—RPCI; Biospecimen Core Resource—VARI; Brain Bank Repository—University of Miami Brain Endowment Bank; Leidos Biomedical—Project Management; ELSI Study; Genome Browser Data Integration &Visualization—EBI; Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz; Chawla A, Del Sal G, Peltz G, Brunet A, Conrad DF, Samuel CE, O'Connell MA, Walkley CR, Nishikura K, Li JB. Tan MH, et al. Nature. 2017 Oct 11;550(7675):249-254. doi: 10.1038/nature24041. Nature. 2017. PMID: 29022589 Free PMC article.
UCSC Genome Browser enters 20th year.
Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ. Lee CM, et al. Among authors: kent wj. Nucleic Acids Res. 2020 Jan 8;48(D1):D756-D761. doi: 10.1093/nar/gkz1012. Nucleic Acids Res. 2020. PMID: 31691824 Free PMC article.
128 results