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183 results
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Streaming fragment assignment for real-time analysis of sequencing experiments.
Roberts A, Pachter L. Roberts A, et al. Among authors: pachter l. Nat Methods. 2013 Jan;10(1):71-3. doi: 10.1038/nmeth.2251. Epub 2012 Nov 18. Nat Methods. 2013. PMID: 23160280 Free PMC article.
VISTA : visualizing global DNA sequence alignments of arbitrary length.
Mayor C, Brudno M, Schwartz JR, Poliakov A, Rubin EM, Frazer KA, Pachter LS, Dubchak I. Mayor C, et al. Among authors: pachter ls. Bioinformatics. 2000 Nov;16(11):1046-7. doi: 10.1093/bioinformatics/16.11.1046. Bioinformatics. 2000. PMID: 11159318
rVista for comparative sequence-based discovery of functional transcription factor binding sites.
Loots GG, Ovcharenko I, Pachter L, Dubchak I, Rubin EM. Loots GG, et al. Among authors: pachter l. Genome Res. 2002 May;12(5):832-9. doi: 10.1101/gr.225502. Genome Res. 2002. PMID: 11997350 Free PMC article.
Applications of generalized pair hidden Markov models to alignment and gene finding problems.
Pachter L, Alexandersson M, Cawley S. Pachter L, et al. J Comput Biol. 2002;9(2):389-99. doi: 10.1089/10665270252935520. J Comput Biol. 2002. PMID: 12015888
Initial sequencing and comparative analysis of the mouse genome.
Mouse Genome Sequencing Consortium, Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES. Mouse Genome Sequencing Consortium, et al. Among authors: pachter l. Nature. 2002 Dec 5;420(6915):520-62. doi: 10.1038/nature01262. Nature. 2002. PMID: 12466850
Strategies and tools for whole-genome alignments.
Couronne O, Poliakov A, Bray N, Ishkhanov T, Ryaboy D, Rubin E, Pachter L, Dubchak I. Couronne O, et al. Among authors: pachter l. Genome Res. 2003 Jan;13(1):73-80. doi: 10.1101/gr.762503. Genome Res. 2003. PMID: 12529308 Free PMC article.
SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model.
Alexandersson M, Cawley S, Pachter L. Alexandersson M, et al. Among authors: pachter l. Genome Res. 2003 Mar;13(3):496-502. doi: 10.1101/gr.424203. Genome Res. 2003. PMID: 12618381 Free PMC article.
Multiple-sequence functional annotation and the generalized hidden Markov phylogeny.
McAuliffe JD, Pachter L, Jordan MI. McAuliffe JD, et al. Among authors: pachter l. Bioinformatics. 2004 Aug 12;20(12):1850-60. doi: 10.1093/bioinformatics/bth153. Epub 2004 Feb 26. Bioinformatics. 2004. PMID: 14988105
Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat.
Dewey C, Wu JQ, Cawley S, Alexandersson M, Gibbs R, Pachter L. Dewey C, et al. Among authors: pachter l. Genome Res. 2004 Apr;14(4):661-4. doi: 10.1101/gr.1939804. Genome Res. 2004. PMID: 15060007 Free PMC article.
Visualization of multiple genome annotations and alignments with the K-BROWSER.
Chakrabarti K, Pachter L. Chakrabarti K, et al. Among authors: pachter l. Genome Res. 2004 Apr;14(4):716-20. doi: 10.1101/gr.1957004. Genome Res. 2004. PMID: 15060015 Free PMC article.
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