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Items: 1 to 20 of 37

1.

Reranking candidate gene models with cross-species comparison for improved gene prediction.

Liu Q, Crammer K, Pereira FC, Roos DS.

BMC Bioinformatics. 2008 Oct 14;9:433. doi: 10.1186/1471-2105-9-433.

2.

Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species.

Keller O, Odronitz F, Stanke M, Kollmar M, Waack S.

BMC Bioinformatics. 2008 Jun 13;9:278. doi: 10.1186/1471-2105-9-278.

3.

Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction.

Liu Q, Mackey AJ, Roos DS, Pereira FC.

Bioinformatics. 2008 Mar 1;24(5):597-605. doi: 10.1093/bioinformatics/btn004. Epub 2008 Jan 10.

PMID:
18187439
4.

Improving the specificity of exon prediction using comparative genomics.

Wu J.

BMC Genomics. 2008 Sep 16;9 Suppl 2:S13. doi: 10.1186/1471-2164-9-S2-S13.

5.

Assembling genes from predicted exons in linear time with dynamic programming.

Guigó R.

J Comput Biol. 1998 Winter;5(4):681-702.

PMID:
10072084
6.

Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies.

Teber ET, Liu JY, Ballouz S, Fatkin D, Wouters MA.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S69. doi: 10.1186/1471-2105-10-S1-S69.

7.

Self-alignments to detect mutually exclusive exon usage.

Stephan M, Möller F, Wiehe T, Kleffe J.

In Silico Biol. 2007;7(6):613-21.

PMID:
18467774
8.

Gene expression trends and protein features effectively complement each other in gene function prediction.

Wabnik K, Hvidsten TR, Kedzierska A, Van Leene J, De Jaeger G, Beemster GT, Komorowski J, Kuiper MT.

Bioinformatics. 2009 Feb 1;25(3):322-30. doi: 10.1093/bioinformatics/btn625. Epub 2008 Dec 2.

PMID:
19050035
9.

Conrad: gene prediction using conditional random fields.

DeCaprio D, Vinson JP, Pearson MD, Montgomery P, Doherty M, Galagan JE.

Genome Res. 2007 Sep;17(9):1389-98. Epub 2007 Aug 9.

10.

Similar selective factors affect both between-gene and between-exon divergence in Drosophila.

Haerty W, Golding B.

Mol Biol Evol. 2009 Apr;26(4):859-66. doi: 10.1093/molbev/msp006. Epub 2009 Jan 15.

PMID:
19150804
11.

Detecting conserved coding genomic regions through signal processing of nucleotide substitution patterns.

Ré M, Pavesi G.

Artif Intell Med. 2009 Feb-Mar;45(2-3):117-23. doi: 10.1016/j.artmed.2008.07.015. Epub 2008 Sep 21.

PMID:
18809300
12.

CLEAN: CLustering Enrichment ANalysis.

Freudenberg JM, Joshi VK, Hu Z, Medvedovic M.

BMC Bioinformatics. 2009 Jul 29;10:234. doi: 10.1186/1471-2105-10-234.

13.

DIGIT: a novel gene finding program by combining gene-finders.

Yada T, Takagi T, Totoki Y, Sakaki Y, Takaeda Y.

Pac Symp Biocomput. 2003:375-87.

14.

Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome.

Severing EI, van Dijk AD, Stiekema WJ, van Ham RC.

BMC Genomics. 2009 Apr 9;10:154. doi: 10.1186/1471-2164-10-154.

15.

Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets.

Hazelett DJ, Lakeland DL, Weiss JB.

Bioinformatics. 2009 Jul 1;25(13):1617-24. doi: 10.1093/bioinformatics/btp282. Epub 2009 Apr 28.

16.

HaMStR: profile hidden markov model based search for orthologs in ESTs.

Ebersberger I, Strauss S, von Haeseler A.

BMC Evol Biol. 2009 Jul 8;9:157. doi: 10.1186/1471-2148-9-157.

17.

Combining multisource information through functional-annotation-based weighting: gene function prediction in yeast.

Ray SS, Bandyopadhyay S, Pal SK.

IEEE Trans Biomed Eng. 2009 Feb;56(2):229-36. doi: 10.1109/TBME.2008.2005955. Epub 2008 Sep 30.

PMID:
19272921
18.

Gene structure prediction by linguistic methods.

Dong S, Searls DB.

Genomics. 1994 Oct;23(3):540-51.

PMID:
7851881
19.

Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

He X, Ling X, Sinha S.

PLoS Comput Biol. 2009 Mar;5(3):e1000299. doi: 10.1371/journal.pcbi.1000299. Epub 2009 Mar 13.

20.

MoccaDB - an integrative database for functional, comparative and diversity studies in the Rubiaceae family.

Plechakova O, Tranchant-Dubreuil C, Benedet F, Couderc M, Tinaut A, Viader V, De Block P, Hamon P, Campa C, de Kochko A, Hamon S, Poncet V.

BMC Plant Biol. 2009 Sep 29;9:123. doi: 10.1186/1471-2229-9-123.

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