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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. Among authors: boeckmann b. 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.
Big data and other challenges in the quest for orthologs.
Sonnhammer EL, Gabaldón T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C; Quest for Orthologs consortium. Sonnhammer EL, et al. Among authors: boeckmann b. Bioinformatics. 2014 Nov 1;30(21):2993-8. doi: 10.1093/bioinformatics/btu492. Epub 2014 Jul 26. Bioinformatics. 2014. PMID: 25064571 Free PMC article.
Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream.
Boeckmann B, Marcet-Houben M, Rees JA, Forslund K, Huerta-Cepas J, Muffato M, Yilmaz P, Xenarios I, Bork P, Lewis SE, Gabaldón T; Quest for Orthologs Species Tree Working Group. Boeckmann B, et al. Genome Biol Evol. 2015 Jul 1;7(7):1988-99. doi: 10.1093/gbe/evv121. Genome Biol Evol. 2015. PMID: 26133389 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.
Gearing up to handle the mosaic nature of life in the quest for orthologs.
Forslund K, Pereira C, Capella-Gutierrez S, da Silva AS, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT; Quest for Orthologs Consortium; Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S; Quest for Orthologs Consortium. Forslund K, et al. Among authors: boeckmann b. Bioinformatics. 2018 Jan 15;34(2):323-329. doi: 10.1093/bioinformatics/btx542. Bioinformatics. 2018. PMID: 28968857 Free PMC article.
UniProt: the Universal Protein knowledgebase.
Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS. Apweiler R, et al. Among authors: boeckmann b. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D115-9. doi: 10.1093/nar/gkh131. Nucleic Acids Res. 2004. PMID: 14681372 Free PMC article.
The Universal Protein Resource (UniProt).
Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS. Bairoch A, et al. Among authors: boeckmann b. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D154-9. doi: 10.1093/nar/gki070. Nucleic Acids Res. 2005. PMID: 15608167 Free PMC article.
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M. Boeckmann B, et al. Nucleic Acids Res. 2003 Jan 1;31(1):365-70. doi: 10.1093/nar/gkg095. Nucleic Acids Res. 2003. PMID: 12520024 Free PMC article.
31 results