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Windshield splatter analysis with the Galaxy metagenomic pipeline.
Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung WY, Taylor J, Nekrutenko A; Galaxy Team. Kosakovsky Pond S, et al. Among authors: nekrutenko a. Genome Res. 2009 Nov;19(11):2144-53. doi: 10.1101/gr.094508.109. Epub 2009 Oct 9. Genome Res. 2009. PMID: 19819906 Free PMC article.
ETOPE: Evolutionary test of predicted exons.
Nekrutenko A, Chung WY, Li WH. Nekrutenko A, et al. Nucleic Acids Res. 2003 Jul 1;31(13):3564-7. doi: 10.1093/nar/gkg597. Nucleic Acids Res. 2003. PMID: 12824366 Free PMC article.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Gibbs RA, Weinstock GM, Metzker ML, Muzny DM, Sodergren EJ, Scherer S, Scott G, Steffen D, Worley KC, Burch PE, Okwuonu G, Hines S, Lewis L, DeRamo C, Delgado O, Dugan-Rocha S, Miner G, Morgan M, Hawes A, Gill R, Celera, Holt RA, Adams MD, Amanatides PG, Baden-Tillson H, Barnstead M, Chin S, Evans CA, Ferriera S, Fosler C, Glodek A, Gu Z, Jennings D, Kraft CL, Nguyen T, Pfannkoch CM, Sitter C, Sutton GG, Venter JC, Woodage T, Smith D, Lee HM, Gustafson E, Cahill P, Kana A, Doucette-Stamm L, Weinstock K, Fechtel K, Weiss RB, Dunn DM, Green ED, Blakesley RW, Bouffard GG, De Jong PJ, Osoegawa K, Zhu B, Marra M, Schein J, Bosdet I, Fjell C, Jones S, Krzywinski M, Mathewson C, Siddiqui A, Wye N, McPherson J, Zhao S, Fraser CM, Shetty J, Shatsman S, Geer K, Chen Y, Abramzon S, Nierman WC, Havlak PH, Chen R, Durbin KJ, Simons R, Ren Y, Song XZ, Li B, Liu Y, Qin X, Cawley S, Worley KC, Cooney AJ, D'Souza LM, Martin K, Wu JQ, Gonzalez-Garay ML, Jackson AR, Kalafus KJ, McLeod MP, Milosavljevic A, Virk D, Volkov A, Wheeler DA, Zhang Z, Bailey JA, Eichler EE, Tuzun E, Birney E, Mongin E, Ureta-Vidal A, Woodwark C, Zdobnov E, Bork P, Suyama M, Torrents D, Alexandersson M, Trask BJ, Young JM, H… See abstract for full author list ➔ Gibbs RA, et al. Among authors: nekrutenko a. Nature. 2004 Apr 1;428(6982):493-521. doi: 10.1038/nature02426. Nature. 2004. PMID: 15057822
Galaxy: a platform for interactive large-scale genome analysis.
Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. Giardine B, et al. Among authors: nekrutenko a. Genome Res. 2005 Oct;15(10):1451-5. doi: 10.1101/gr.4086505. Epub 2005 Sep 16. Genome Res. 2005. PMID: 16169926 Free PMC article.
A first look at ARFome: dual-coding genes in mammalian genomes.
Chung WY, Wadhawan S, Szklarczyk R, Pond SK, Nekrutenko A. Chung WY, et al. Among authors: nekrutenko a. PLoS Comput Biol. 2007 May;3(5):e91. doi: 10.1371/journal.pcbi.0030091. PLoS Comput Biol. 2007. PMID: 17511511 Free PMC article.
28-way vertebrate alignment and conservation track in the UCSC Genome Browser.
Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ. Miller W, et al. Among authors: nekrutenko a. Genome Res. 2007 Dec;17(12):1797-808. doi: 10.1101/gr.6761107. Epub 2007 Nov 5. Genome Res. 2007. PMID: 17984227 Free PMC article.
Using galaxy to perform large-scale interactive data analyses.
Taylor J, Schenck I, Blankenberg D, Nekrutenko A. Taylor J, et al. Among authors: nekrutenko a. Curr Protoc Bioinformatics. 2007 Sep;Chapter 10:Unit 10.5. doi: 10.1002/0471250953.bi1005s19. Curr Protoc Bioinformatics. 2007. PMID: 18428782 Free PMC article.
103 results