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308 results
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CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.
Parra G, Bradnam K, Korf I. Parra G, et al. Bioinformatics. 2007 May 1;23(9):1061-7. doi: 10.1093/bioinformatics/btm071. Epub 2007 Mar 1. Bioinformatics. 2007. PMID: 17332020
Assessing the gene space in draft genomes.
Parra G, Bradnam K, Ning Z, Keane T, Korf I. Parra G, et al. Nucleic Acids Res. 2009 Jan;37(1):289-97. doi: 10.1093/nar/gkn916. Epub 2008 Nov 28. Nucleic Acids Res. 2009. PMID: 19042974 Free PMC article.
Sequence and analysis of chromosome 2 of Dictyostelium discoideum.
Glöckner G, Eichinger L, Szafranski K, Pachebat JA, Bankier AT, Dear PH, Lehmann R, Baumgart C, Parra G, Abril JF, Guigó R, Kumpf K, Tunggal B, Cox E, Quail MA, Platzer M, Rosenthal A, Noegel AA; Dictyostelium Genome Sequencing Consortium. Glöckner G, et al. Nature. 2002 Jul 4;418(6893):79-85. doi: 10.1038/nature00847. Nature. 2002. PMID: 12097910
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. Nature. 2002 Dec 5;420(6915):520-62. doi: 10.1038/nature01262. Nature. 2002. PMID: 12466850
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes.
Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sánchez Alvarado A, Yandell M. Cantarel BL, et al. Genome Res. 2008 Jan;18(1):188-96. doi: 10.1101/gr.6743907. Epub 2007 Nov 19. Genome Res. 2008. PMID: 18025269 Free PMC article.
The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences.
Kovach A, Wegrzyn JL, Parra G, Holt C, Bruening GE, Loopstra CA, Hartigan J, Yandell M, Langley CH, Korf I, Neale DB. Kovach A, et al. BMC Genomics. 2010 Jul 7;11:420. doi: 10.1186/1471-2164-11-420. BMC Genomics. 2010. PMID: 20609256 Free PMC article.
Using geneid to identify genes.
Blanco E, Parra G, Guigó R. Blanco E, et al. Curr Protoc Bioinformatics. 2007 Jun;Chapter 4:Unit 4.3. doi: 10.1002/0471250953.bi0403s18. Curr Protoc Bioinformatics. 2007. PMID: 18428791
Gene finding in the chicken genome.
Eyras E, Reymond A, Castelo R, Bye JM, Camara F, Flicek P, Huckle EJ, Parra G, Shteynberg DD, Wyss C, Rogers J, Antonarakis SE, Birney E, Guigo R, Brent MR. Eyras E, et al. BMC Bioinformatics. 2005 May 30;6:131. doi: 10.1186/1471-2105-6-131. BMC Bioinformatics. 2005. PMID: 15924626 Free PMC article.
Gene organization features in A/T-rich organisms.
Szafranski K, Lehmann R, Parra G, Guigo R, Glöckner G. Szafranski K, et al. J Mol Evol. 2005 Jan;60(1):90-8. doi: 10.1007/s00239-004-0201-2. J Mol Evol. 2005. PMID: 15696371
Interestingly, shifts to very high A/T or G/C levels can occur in several distinct branches of the tree of life. The underlying reasons for these shifts therefore may be of different origin. ...
Interestingly, shifts to very high A/T or G/C levels can occur in several distinct branches of the tree of life. The underlying reaso …
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