Functional and evolutionary implications of gene orthology

[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.