Functional and evolutionary implications of gene orthology
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[1] Salvador Capella-Gutiérrez,et al. PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions , 2010, Nucleic Acids Res..
[2] D. Penny,et al. The modern molecular clock , 2003, Nature Reviews Genetics.
[3] G. Theißen. Birth, life and death of developmental control genes: new challenges for the homology concept. , 2005 .
[4] Günter Theißen,et al. Birth, life and death of developmental control genes: New challenges for the homology concept , 2008, Theory in Biosciences.
[5] A. Sali,et al. Evolutionary constraints on structural similarity in orthologs and paralogs , 2009, Protein science : a publication of the Protein Society.
[6] Predrag Radivojac,et al. Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals , 2011, PLoS Comput. Biol..
[7] E. Sonnhammer,et al. Evolution of protein domain architectures. , 2012, Methods in molecular biology.
[8] Geoffrey I. Webb,et al. Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs , 2011, Nucleic acids research.
[9] Eugene V. Koonin,et al. A Tight Link between Orthologs and Bidirectional Best Hits in Bacterial and Archaeal Genomes , 2012, Genome biology and evolution.
[10] Julien Roux,et al. An ontology to clarify homology-related concepts. , 2010, Trends in genetics : TIG.
[11] W. Fitch. Distinguishing homologous from analogous proteins. , 1970, Systematic zoology.
[12] Javier Herrero,et al. Toward community standards in the quest for orthologs , 2012, Bioinform..
[13] M. Robinson‐Rechavi,et al. How confident can we be that orthologs are similar, but paralogs differ? , 2009, Trends in genetics : TIG.
[14] Sourav Bandyopadhyay,et al. Systematic identification of functional orthologs based on protein network comparison. , 2006, Genome research.
[15] T. Gabaldón. Large-scale assignment of orthology: back to phylogenetics? , 2008, Genome Biology.
[16] Christian E. V. Storm,et al. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. , 2001, Journal of molecular biology.
[17] Christophe Dessimoz,et al. Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs , 2012, PLoS Comput. Biol..
[18] E. Koonin. Orthologs, paralogs, and evolutionary genomics. , 2005, Annual review of genetics.
[19] B. Labedan,et al. The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species. , 2008, Biochimie.
[20] Steven Maere,et al. The gain and loss of genes during 600 million years of vertebrate evolution , 2006, Genome Biology.
[21] B. Hartmann,et al. Decrypting the genome's alternative messages. , 2009, Current opinion in cell biology.
[22] T. Casci. Functional genomics: Degrees of similarity , 2011, Nature Reviews Genetics.
[23] S. Baldauf,et al. Phylogeny for the faint of heart: a tutorial. , 2003, Trends in genetics : TIG.
[24] P. Bork,et al. Measuring genome evolution. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[25] B. Snel,et al. Genome trees and the nature of genome evolution. , 2005, Annual review of microbiology.
[26] Joaquín Dopazo,et al. Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication , 2011, Briefings Bioinform..
[27] E. Koonin,et al. The Impact of Comparative Genomics on Our Understanding of Evolution , 2000, Cell.
[28] Judith A. Blake,et al. On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report , 2012, PLoS Comput. Biol..
[29] Malay Kumar Basu,et al. Domain mobility in proteins: functional and evolutionary implications , 2008, Briefings Bioinform..
[30] Jodie J. Yin,et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes , 2004, Genome Biology.
[31] D. Botstein,et al. Orthology and functional conservation in eukaryotes. , 2007, Annual review of genetics.
[32] T. Gabaldón,et al. Phylogenetic Analyses Uncover a Novel Clade of Transferrin in Nonmammalian Vertebrates , 2012, Molecular biology and evolution.
[33] Bonnie Berger,et al. Global alignment of multiple protein interaction networks with application to functional orthology detection , 2008, Proceedings of the National Academy of Sciences.
[34] Xiaoshu Chen,et al. The Ortholog Conjecture Is Untestable by the Current Gene Ontology but Is Supported by RNA Sequencing Data , 2012, PLoS Comput. Biol..
[35] Gapped BLAST and PSI-BLAST: A new , 1997 .
[36] Vincent J. Lynch,et al. Resurrecting the Role of Transcription Factor Change in Developmental Evolution , 2008, Evolution; international journal of organic evolution.
[37] Christophe Dessimoz,et al. Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods , 2009, PLoS Comput. Biol..
[38] W. Fitch. Homology a personal view on some of the problems. , 2000, Trends in genetics : TIG.
[39] P. Bork,et al. Orthology prediction methods: A quality assessment using curated protein families , 2011, BioEssays : news and reviews in molecular, cellular and developmental biology.
[40] E. Koonin,et al. Orthology, paralogy and proposed classification for paralog subtypes. , 2002, Trends in genetics : TIG.
[41] L. Koski,et al. The Closest BLAST Hit Is Often Not the Nearest Neighbor , 2001, Journal of Molecular Evolution.
[42] Erik L. L. Sonnhammer,et al. Domain architecture conservation in orthologs , 2011, BMC Bioinformatics.
[43] Kimmen Sjölander,et al. Ortholog identification in the presence of domain architecture rearrangement , 2011, Briefings Bioinform..
[44] Michael Y. Galperin,et al. Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution , 2010, Biology Direct.
[45] T. Traut,et al. A minimal gene set for cellular life derived by comparison of complete bacterial genomes , 1998 .
[46] E. Koonin. Orthologs, Paralogs, and Evolutionary Genomics 1 , 2005 .
[47] Boris G. Mirkin,et al. Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell , 2005, Nucleic acids research.
[48] Sudhir Kumar,et al. Molecular clocks: four decades of evolution , 2005, Nature Reviews Genetics.
[49] M. Huynen,et al. Benchmarking ortholog identification methods using functional genomics data , 2006, Genome Biology.
[50] S. Pongor,et al. The quest for orthologs: finding the corresponding gene across genomes. , 2008, Trends in genetics : TIG.
[51] ECOLI SODF,et al. Analogous Enzymes : Independent Inventions in Enzyme Evolution , 1998 .
[52] D. Lipman,et al. A genomic perspective on protein families. , 1997, Science.
[53] Albert J. Vilella,et al. Joining forces in the quest for orthologs , 2009, Genome Biology.
[54] Arcady R. Mushegian,et al. Computational methods for Gene Orthology inference , 2011, Briefings Bioinform..
[55] Jaime Huerta-Cepas,et al. Assigning duplication events to relative temporal scales in genome-wide studies , 2011, Bioinform..
[56] Manuel Irimia,et al. Alternative splicing: decoding an expansive regulatory layer. , 2012, Current opinion in cell biology.
[57] Eugene V. Koonin,et al. Comparative genomics, minimal gene-sets and the last universal common ancestor , 2003, Nature Reviews Microbiology.
[58] Eugene V. Koonin. Obituary: Walter Fitch and the orthology paradigm , 2011, Briefings Bioinform..
[59] C. Ouzounis. Orthology: another terminology muddle. , 1999, Trends in genetics : TIG.