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Items: 1 to 20 of 25

1.

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.

Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA; Gene Ontology Consortium.

PLoS Comput Biol. 2012;8(2):e1002386. doi: 10.1371/journal.pcbi.1002386. Epub 2012 Feb 16.

2.

Ensembl 2012.

Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sobral D, Tang YA, Taylor K, Trevanion S, Vandrovcova J, White S, Wilson M, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Harrow J, Herrero J, Hubbard TJ, Parker A, Proctor G, Spudich G, Vogel J, Yates A, Zadissa A, Searle SM.

Nucleic Acids Res. 2012 Jan;40(Database issue):D84-90. doi: 10.1093/nar/gkr991. Epub 2011 Nov 15.

3.

Domain architecture conservation in orthologs.

Forslund K, Pekkari I, Sonnhammer EL.

BMC Bioinformatics. 2011 Aug 5;12:326. doi: 10.1186/1471-2105-12-326.

4.

Testing the ortholog conjecture with comparative functional genomic data from mammals.

Nehrt NL, Clark WT, Radivojac P, Hahn MW.

PLoS Comput Biol. 2011 Jun;7(6):e1002073. doi: 10.1371/journal.pcbi.1002073. Epub 2011 Jun 9.

5.

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.

Huerta-Cepas J, Dopazo J, Huynen MA, Gabaldón T.

Brief Bioinform. 2011 Sep;12(5):442-8. doi: 10.1093/bib/bbr022. Epub 2011 Apr 22.

PMID:
21515902
6.

The what, where, how and why of gene ontology--a primer for bioinformaticians.

du Plessis L, Skunca N, Dessimoz C.

Brief Bioinform. 2011 Nov;12(6):723-35. doi: 10.1093/bib/bbr002. Epub 2011 Feb 17.

7.

OMA 2011: orthology inference among 1000 complete genomes.

Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C.

Nucleic Acids Res. 2011 Jan;39(Database issue):D289-94. doi: 10.1093/nar/gkq1238. Epub 2010 Nov 27.

8.

Orthology confers intron position conservation.

Henricson A, Forslund K, Sonnhammer EL.

BMC Genomics. 2010 Jul 2;11:412. doi: 10.1186/1471-2164-11-412.

9.

Protein subcellular relocalization in the evolution of yeast singleton and duplicate genes.

Qian W, Zhang J.

Genome Biol Evol. 2009 Jul 22;1:198-204. doi: 10.1093/gbe/evp021.

10.

Semantic similarity in biomedical ontologies.

Pesquita C, Faria D, Falcão AO, Lord P, Couto FM.

PLoS Comput Biol. 2009 Jul;5(7):e1000443. doi: 10.1371/journal.pcbi.1000443. Epub 2009 Jul 31. Review.

11.

The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.

Reference Genome Group of the Gene Ontology Consortium.

PLoS Comput Biol. 2009 Jul;5(7):e1000431. doi: 10.1371/journal.pcbi.1000431. Epub 2009 Jul 3.

12.

Evolutionary constraints on structural similarity in orthologs and paralogs.

Peterson ME, Chen F, Saven JG, Roos DS, Babbitt PC, Sali A.

Protein Sci. 2009 Jun;18(6):1306-15. doi: 10.1002/pro.143.

13.

How confident can we be that orthologs are similar, but paralogs differ?

Studer RA, Robinson-Rechavi M.

Trends Genet. 2009 May;25(5):210-6. doi: 10.1016/j.tig.2009.03.004. Epub 2009 Apr 14.

PMID:
19368988
14.

Protein function prediction--the power of multiplicity.

Rentzsch R, Orengo CA.

Trends Biotechnol. 2009 Apr;27(4):210-9. doi: 10.1016/j.tibtech.2009.01.002. Epub 2009 Feb 27. Review.

PMID:
19251332
15.

Phylogenetic and functional assessment of orthologs inference projects and methods.

Altenhoff AM, Dessimoz C.

PLoS Comput Biol. 2009 Jan;5(1):e1000262. doi: 10.1371/journal.pcbi.1000262. Epub 2009 Jan 16.

16.

Algorithm of OMA for large-scale orthology inference.

Roth AC, Gonnet GH, Dessimoz C.

BMC Bioinformatics. 2008 Dec 4;9:518. doi: 10.1186/1471-2105-9-518. Erratum in: BMC Bioinformatics.2009;10. doi:10.1186/1471-2105-10-220.

17.

The GOA database in 2009--an integrated Gene Ontology Annotation resource.

Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R.

Nucleic Acids Res. 2009 Jan;37(Database issue):D396-403. doi: 10.1093/nar/gkn803. Epub 2008 Oct 27.

18.

Quantitative sequence-function relationships in proteins based on gene ontology.

Sangar V, Blankenberg DJ, Altman N, Lesk AM.

BMC Bioinformatics. 2007 Aug 8;8:294.

19.

Ensembl 2007.

Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E.

Nucleic Acids Res. 2007 Jan;35(Database issue):D610-7. Epub 2006 Dec 5.

20.

A new measure for functional similarity of gene products based on Gene Ontology.

Schlicker A, Domingues FS, Rahnenführer J, Lengauer T.

BMC Bioinformatics. 2006 Jun 15;7:302.

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