Members of the Quest for Orthologs Consortium, and the OrthoMCL database are funded ,
Overview and comparison of ortholog databases, Drug Discovery Today: Technologies, vol.3, issue.2, pp.137-143, 2006. ,
DOI : 10.1016/j.ddtec.2006.06.002
Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods, PLoS Computational Biology, vol.19, issue.1, p.1000262, 2009. ,
DOI : 10.1371/journal.pcbi.1000262.s018
URL : https://doi.org/10.1371/journal.pcbi.1000262
RNAcentral: A vision for an international database of RNA sequences, RNA, vol.17, issue.11, pp.1941-1946, 2011. ,
DOI : 10.1261/rna.2750811
URL : https://hal.archives-ouvertes.fr/hal-00639172
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees, Briefings in Bioinformatics, vol.12, issue.5, pp.423-435, 2011. ,
DOI : 10.1093/bib/bbr034
URL : https://academic.oup.com/bib/article-pdf/12/5/423/753549/bbr034.pdf
Functional prediction: Identification of protein orthologs and paralogs, Protein Science, vol.121, issue.12, pp.2344-2353, 2000. ,
DOI : 10.1093/oxfordjournals.jbchem.a021573
URL : http://onlinelibrary.wiley.com/doi/10.1110/ps.9.12.2344/pdf
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups, Nucleic Acids Research, vol.34, issue.90001, pp.363-368, 2006. ,
DOI : 10.1093/nar/gkj123
Assessing Performance of Orthology Detection Strategies Applied to Eukaryotic Genomes, PLoS ONE, vol.17, issue.4, p.383, 2007. ,
DOI : 10.1371/journal.pone.0000383.s008
Representative Proteomes: A Stable, Scalable and Unbiased Proteome Set for Sequence Analysis and Functional Annotation, PLoS ONE, vol.55, issue.4, 2011. ,
DOI : 10.1371/journal.pone.0018910.s002
URL : https://doi.org/10.1371/journal.pone.0018910
Phylogenomics and the reconstruction of the tree of life, Nature Reviews Genetics, vol.3, issue.5, pp.361-375, 2005. ,
DOI : 10.1006/mpev.1994.1037
URL : https://hal.archives-ouvertes.fr/halsde-00193293
Editorial: Orthology and applications, Briefings in Bioinformatics, vol.12, issue.5, pp.375-376, 2011. ,
DOI : 10.1093/bib/bbr057
URL : https://academic.oup.com/bib/article-pdf/12/5/375/757139/bbr057.pdf
The what, where, how and why of gene ontology--a primer for bioinformaticians, Briefings in Bioinformatics, vol.12, issue.6, pp.723-735, 2011. ,
DOI : 10.1093/bib/bbr002
HaMStR: Profile hidden markov model based search for orthologs in ESTs, BMC Evolutionary Biology, vol.9, issue.1, p.157, 2009. ,
DOI : 10.1186/1471-2148-9-157
URL : https://bmcevolbiol.biomedcentral.com/track/pdf/10.1186/1471-2148-9-157?site=bmcevolbiol.biomedcentral.com
Distinguishing Homologous from Analogous Proteins, Systematic Zoology, vol.19, issue.2, pp.99-113, 1970. ,
DOI : 10.2307/2412448
Ensembl 2011, Nucleic Acids Research, vol.39, issue.Database, pp.800-806, 2011. ,
DOI : 10.1093/nar/gkq1064
URL : https://academic.oup.com/nar/article-pdf/39/suppl_1/D800/7626802/gkq1064.pdf
Domain architecture conservation in orthologs, BMC Bioinformatics, vol.12, issue.1, p.326, 2011. ,
DOI : 10.1002/pro.143
URL : https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-12-326?site=bmcbioinformatics.biomedcentral.com
Large-scale assignment of orthology: back to phylogenetics?, Genome Biology, vol.9, issue.10, p.235, 2008. ,
DOI : 10.1186/gb-2008-9-10-235
Joining forces in the quest for orthologs, Genome Biology, vol.10, issue.9, p.403, 2009. ,
DOI : 10.1186/gb-2009-10-9-403
Rfam: Wikipedia, clans and the "decimal" release, Nucleic Acids Research, vol.39, issue.Database, pp.141-145, 2011. ,
DOI : 10.1093/nar/gkq1129
URL : https://academic.oup.com/nar/article-pdf/39/suppl_1/D141/7630954/gkq1129.pdf
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium, Briefings in Bioinformatics, vol.12, issue.5, pp.449-462, 2011. ,
DOI : 10.1093/bib/bbr042
miROrtho: computational survey of microRNA genes, Nucleic Acids Research, vol.37, issue.Database, pp.111-117, 2009. ,
DOI : 10.1093/nar/gkn707
URL : https://academic.oup.com/nar/article-pdf/37/suppl_1/D111/3251397/gkn707.pdf
Modeling the percolation of annotation errors in a database of protein sequences, Bioinformatics, vol.18, issue.12, pp.1641-1649, 2002. ,
DOI : 10.1093/bioinformatics/18.12.1641
A Reversible Jump Method for Bayesian Phylogenetic Inference with a Nonhomogeneous Substitution Model, Molecular Biology and Evolution, vol.24, issue.6, pp.1286-1299, 2007. ,
DOI : 10.1093/molbev/msm046
URL : https://academic.oup.com/mbe/article-pdf/24/6/1286/5786394/msm046.pdf
The Princeton Protein Orthology Database (P-POD): A Comparative Genomics Analysis Tool for Biologists, PLoS ONE, vol.94, issue.8, p.766, 2007. ,
DOI : 10.1371/journal.pone.0000766.t006
Orthology confers intron position conservation, BMC Genomics, vol.11, issue.1, p.412, 2010. ,
DOI : 10.1186/1471-2164-11-412
URL : https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-11-412?site=bmcgenomics.biomedcentral.com
Protein classification and functional assignment, Trends in Biotechnology, vol.16, pp.18-21, 1998. ,
DOI : 10.1016/S0167-7799(98)00131-0
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication, Briefings in Bioinformatics, vol.12, issue.5, pp.442-448, 2011. ,
DOI : 10.1093/bib/bbr022
Benchmarking ortholog identification methods using functional genomics data, Genome Biology, vol.7, issue.4, p.31, 2006. ,
DOI : 10.1186/gb-2006-7-4-r31
Orthologs, Paralogs, and Evolutionary Genomics, Annual Review of Genetics, vol.39, issue.1, pp.309-338, 2005. ,
DOI : 10.1146/annurev.genet.39.073003.114725
Computational methods for Gene Orthology inference, Briefings in Bioinformatics, vol.12, issue.5, pp.379-391, 2011. ,
DOI : 10.1093/bib/bbr030
URL : https://academic.oup.com/bib/article-pdf/12/5/379/751564/bbr030.pdf
Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice, PLANT PHYSIOLOGY, vol.156, issue.3, pp.1316-1330, 2011. ,
DOI : 10.1104/pp.111.177865
A minimal gene set for cellular life derived by comparison of complete bacterial genomes., Proc. Natl Acad. Sci. USA, pp.10268-10273, 1996. ,
DOI : 10.1073/pnas.93.19.10268
Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals, PLoS Computational Biology, vol.21, issue.6, p.1002073, 2011. ,
DOI : 10.1371/journal.pcbi.1002073.s011
URL : https://doi.org/10.1371/journal.pcbi.1002073
A Problem With the Correlation Coefficient as a Measure of Gene Expression Divergence, Genetics, vol.183, issue.4, pp.1597-1600, 2009. ,
DOI : 10.1534/genetics.109.110247
Evolutionary constraints on structural similarity in orthologs and paralogs, Protein Science, vol.33, issue.6, pp.1306-1315, 2009. ,
DOI : 10.1002/pro.143
URL : http://onlinelibrary.wiley.com/doi/10.1002/pro.143/pdf
PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants, The Plant Cell, vol.21, issue.12, pp.3718-3731, 2009. ,
DOI : 10.1105/tpc.109.071506
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score, Nucleic Acids Research, vol.39, issue.5, p.32, 2011. ,
DOI : 10.1093/nar/gkq953
URL : https://academic.oup.com/nar/article-pdf/39/5/e32/16781683/gkq953.pdf
Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade, PLoS ONE, vol.449, issue.4, p.18755, 2011. ,
DOI : 10.1371/journal.pone.0018755.s002
URL : https://doi.org/10.1371/journal.pone.0018755
SeqXML and OrthoXML: standards for sequence and orthology information, Brief. Bioinform, 2011. ,
DOI : 10.1093/bib/bbr025
URL : https://academic.oup.com/bib/article-pdf/12/5/485/751523/bbr025.pdf
Sequence Similarity Network Reveals Common Ancestry of Multidomain Proteins, PLoS Computational Biology, vol.20, issue.5, 2008. ,
DOI : 10.1371/journal.pcbi.1000063.s008
URL : https://doi.org/10.1371/journal.pcbi.1000063
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-2690, 2006. ,
DOI : 10.1093/bioinformatics/btl446
Iterative orthology prediction uncovers new mitochondrial proteins and identifies C12orf62 as the human ortholog of COX14, a protein involved in the assembly of cytochrome c oxidase, Genome Biology, vol.13, issue.2, 2012. ,
DOI : 10.1093/nar/gkq973
A Genomic Perspective on Protein Families, Science, vol.278, issue.5338, pp.631-637, 1997. ,
DOI : 10.1126/science.278.5338.631
Orthology prediction methods: A quality assessment using curated protein families, BioEssays, vol.59, issue.10, pp.769-780, 2011. ,
DOI : 10.1093/sysbio/syq010
URL : http://onlinelibrary.wiley.com/doi/10.1002/bies.201100062/pdf
MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity, Nucleic Acids Research, vol.38, issue.suppl_1, pp.361-365, 2010. ,
DOI : 10.1093/nar/gkp948
URL : https://academic.oup.com/nar/article-pdf/38/suppl_1/D361/11218227/gkp948.pdf