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Glocal alignment: finding rearrangements during alignment.
Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S. Brudno M, et al. Among authors: poliakov a. Bioinformatics. 2003;19 Suppl 1:i54-62. doi: 10.1093/bioinformatics/btg1005. Bioinformatics. 2003. PMID: 12855437
Automated whole-genome multiple alignment of rat, mouse, and human.
Brudno M, Poliakov A, Salamov A, Cooper GM, Sidow A, Rubin EM, Solovyev V, Batzoglou S, Dubchak I. Brudno M, et al. Among authors: poliakov a. Genome Res. 2004 Apr;14(4):685-92. doi: 10.1101/gr.2067704. Genome Res. 2004. PMID: 15060011 Free PMC article.
Alignathon: a competitive assessment of whole-genome alignment methods.
Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, Hou M, Herrero J, Kent WJ, Solovyev V, Darling AE, Ma J, Notredame C, Brudno M, Dubchak I, Haussler D, Paten B. Earl D, et al. Among authors: poliakov a. Genome Res. 2014 Dec;24(12):2077-89. doi: 10.1101/gr.174920.114. Epub 2014 Oct 1. Genome Res. 2014. PMID: 25273068 Free PMC article.
VISTA: computational tools for comparative genomics.
Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. Frazer KA, et al. Among authors: poliakov a. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9. doi: 10.1093/nar/gkh458. Nucleic Acids Res. 2004. PMID: 15215394 Free PMC article.
Multiple whole-genome alignments without a reference organism.
Dubchak I, Poliakov A, Kislyuk A, Brudno M. Dubchak I, et al. Among authors: poliakov a. Genome Res. 2009 Apr;19(4):682-9. doi: 10.1101/gr.081778.108. Epub 2009 Jan 28. Genome Res. 2009. PMID: 19176791 Free PMC article.
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: poliakov a. Genome Res. 2003 Jan;13(1):73-80. doi: 10.1101/gr.762503. Genome Res. 2003. PMID: 12529308 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: poliakov a. Nature. 2004 Apr 1;428(6982):493-521. doi: 10.1038/nature02426. Nature. 2004. PMID: 15057822
373 results