PubMed

Statistical power of phylo-HMM for evolutionarily conserved element detection.

Fan X, Zhu J, Schadt EE, Liu JS.

BMC Bioinformatics. 2007 Oct 5;8:374.PMID: 17919331 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparative annotation of viral genomes with non-conserved gene structure.

de Groot S, Mailund T, Hein J.

Bioinformatics. 2007 May 1;23(9):1080-9. Epub 2007 Mar 6.PMID: 17341494 [PubMed - indexed for MEDLINE]Related articlesFree article

Improving the specificity of high-throughput ortholog prediction.

Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM, Brinkman FS.

BMC Bioinformatics. 2006 May 28;7:270.PMID: 16729895 [PubMed - indexed for MEDLINE]Related articlesFree article

Discovery of regulatory elements in vertebrates through comparative genomics.

Prakash A, Tompa M.

Nat Biotechnol. 2005 Oct;23(10):1249-56.PMID: 16211068 [PubMed - indexed for MEDLINE]Related articles

Using hidden Markov models and observed evolution to annotate viral genomes.

McCauley S, Hein J.

Bioinformatics. 2006 Jun 1;22(11):1308-16. Epub 2006 Apr 13.PMID: 16613911 [PubMed - indexed for MEDLINE]Related articlesFree article

Phylogeny based discovery of regulatory elements.

Gertz J, Fay JC, Cohen BA.

BMC Bioinformatics. 2006 May 22;7:266.PMID: 16716228 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

Chen FC, Chen CJ, Ho JY, Chuang TJ.

BMC Bioinformatics. 2006 Mar 15;7:136.PMID: 16536879 [PubMed - indexed for MEDLINE]Related articlesFree article

Gene finding with a hidden Markov model of genome structure and evolution.

Pedersen JS, Hein J.

Bioinformatics. 2003 Jan 22;19(2):219-27.PMID: 12538242 [PubMed - indexed for MEDLINE]Related articlesFree article

Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation.

Cvijović M, Dalevi D, Bilsland E, Kemp GJ, Sunnerhagen P.

BMC Bioinformatics. 2007 Aug 8;8:295.PMID: 17686169 [PubMed - indexed for MEDLINE]Related articlesFree article

Multiple organism algorithm for finding ultraconserved elements.

Christley S, Lobo NF, Madey G.

BMC Bioinformatics. 2008 Jan 11;9:15.PMID: 18186941 [PubMed - indexed for MEDLINE]Related articlesFree article

Subtree power analysis and species selection for comparative genomics.

McAuliffe JD, Jordan MI, Pachter L.

Proc Natl Acad Sci U S A. 2005 May 31;102(22):7900-5. Epub 2005 May 23.PMID: 15911755 [PubMed - indexed for MEDLINE]Related articlesFree article

Comparative genomics reveals unusually long motifs in mammalian genomes.

Jones NC, Pevzner PA.

Bioinformatics. 2006 Jul 15;22(14):e236-42.PMID: 16873477 [PubMed - indexed for MEDLINE]Related articlesFree article

XRate: a fast prototyping, training and annotation tool for phylo-grammars.

Klosterman PS, Uzilov AV, Bendaña YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I.

BMC Bioinformatics. 2006 Oct 3;7:428.PMID: 17018148 [PubMed - indexed for MEDLINE]Related articlesFree article

Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms.

Sinha AU, Meller J.

BMC Bioinformatics. 2007 Mar 8;8:82.PMID: 17343765 [PubMed - indexed for MEDLINE]Related articlesFree article

Multiple-sequence functional annotation and the generalized hidden Markov phylogeny.

McAuliffe JD, Pachter L, Jordan MI.

Bioinformatics. 2004 Aug 12;20(12):1850-60. Epub 2004 Feb 26.PMID: 14988105 [PubMed - indexed for MEDLINE]Related articlesFree article

GeneSyn: a tool for detecting conserved gene order across genomes.

Pavesi G, Mauri G, Iannelli F, Gissi C, Pesole G.

Bioinformatics. 2004 Jun 12;20(9):1472-4. Epub 2004 Feb 19.PMID: 14976031 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of sequence conservation at nucleotide resolution.

Asthana S, Roytberg M, Stamatoyannopoulos J, Sunyaev S.

PLoS Comput Biol. 2007 Dec;3(12):e254. Epub 2007 Nov 14.PMID: 18166073 [PubMed - indexed for MEDLINE]Related articlesFree article

Automatic generation of gene finders for eukaryotic species.

Munch K, Krogh A.

BMC Bioinformatics. 2006 May 21;7:263.PMID: 16712739 [PubMed - indexed for MEDLINE]Related articlesFree article

Sigma: multiple alignment of weakly-conserved non-coding DNA sequence.

Siddharthan R.

BMC Bioinformatics. 2006 Mar 16;7:143.PMID: 16542424 [PubMed - indexed for MEDLINE]Related articlesFree article

GARD: a genetic algorithm for recombination detection.

Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD.

Bioinformatics. 2006 Dec 15;22(24):3096-8. Epub 2006 Nov 16.PMID: 17110367 [PubMed - indexed for MEDLINE]Related articlesFree article