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Standardized benchmarking in the quest for orthologs.
Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M; Quest for Orthologs consortium; Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C. Altenhoff AM, et al. Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. Epub 2016 Apr 4. Nat Methods. 2016. PMID: 27043882 Free PMC article.
OMA 2011: orthology inference among 1000 complete genomes.
Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C. Altenhoff AM, et al. Nucleic Acids Res. 2011 Jan;39(Database issue):D289-94. doi: 10.1093/nar/gkq1238. Epub 2010 Nov 27. Nucleic Acids Res. 2011. PMID: 21113020 Free PMC article.
Toward community standards in the quest for orthologs.
Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J; Quest for Orthologs Consortium. Dessimoz C, et al. Bioinformatics. 2012 Mar 15;28(6):900-4. doi: 10.1093/bioinformatics/bts050. Epub 2012 Feb 12. Bioinformatics. 2012. PMID: 22332236 Free PMC article.
Inferring orthology and paralogy.
Altenhoff AM, Dessimoz C. Altenhoff AM, et al. Methods Mol Biol. 2012;855:259-79. doi: 10.1007/978-1-61779-582-4_9. Methods Mol Biol. 2012. PMID: 22407712 Review.
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.
Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S, Bougueleret L, Bucher P, Delorenzi M, Lane L, Le Mercier P, Lisacek F, Michielin O, Palagi PM, Rougemont J, Schwede T, von Mering C, van Nimwegen E, Walther D, Xenarios I, Zavolan M, Zdobnov EM, Zoete V, Appel RD. Stockinger H, et al. Among authors: altenhoff am. Nucleic Acids Res. 2014 Jul;42(Web Server issue):W436-41. doi: 10.1093/nar/gku380. Epub 2014 May 3. Nucleic Acids Res. 2014. PMID: 24792157 Free PMC article.
37 results