Computational methods for Gene Orthology inference
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Arcady R. Mushegian | Eugene V. Koonin | Yuri I. Wolf | David M. Kristensen | E. Koonin | Y. Wolf | A. Mushegian | D. Kristensen
[1] J A Eisen,et al. Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. , 1998, Genome research.
[2] D. P. Wall,et al. Detecting putative orthologs , 2003, Bioinform..
[3] Ting-Wen Chen,et al. DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection , 2010, BMC Bioinformatics.
[4] A. Hughes,et al. Differential loss of ancestral gene families as a source of genomic divergence in animals , 2004, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[5] Peer Bork,et al. Consistency of genome‐based methods in measuring Metazoan evolution , 2005, FEBS letters.
[6] W. Doolittle,et al. Lateral gene transfer and the origins of prokaryotic groups. , 2003, Annual review of genetics.
[7] E. Koonin,et al. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world , 2008, Nucleic acids research.
[8] Gaston H. Gonnet,et al. Algorithm of OMA for large-scale orthology inference , 2008, BMC Bioinformatics.
[9] Tal Dagan,et al. Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution , 2008, Proceedings of the National Academy of Sciences.
[10] Lavanya Kannan,et al. A low-polynomial algorithm for assembling clusters of orthologous groups from intergenomic symmetric best matches , 2010, Bioinform..
[11] Leonid Peshkin,et al. Roundup: a multi-genome repository of orthologs and evolutionary distances , 2006, Bioinform..
[12] Sean R. Eddy,et al. RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs , 2002, BMC Bioinformatics.
[13] W. Fitch. Homology a personal view on some of the problems. , 2000, Trends in genetics : TIG.
[14] J. Townsend,et al. Horizontal gene transfer, genome innovation and evolution , 2005, Nature Reviews Microbiology.
[15] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[16] Michael Schroeder,et al. Equivalent binding sites reveal convergently evolved interaction motifs , 2006, Bioinform..
[17] Christine Sacerdot,et al. Insertion of Horizontally Transferred Genes within Conserved Syntenic Regions of Yeast Genomes , 2009, PloS one.
[18] Michael Y. Galperin,et al. Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution , 2010, Biology Direct.
[19] A. Sali,et al. Evolutionary constraints on structural similarity in orthologs and paralogs , 2009, Protein science : a publication of the Protein Society.
[20] Ning Ma,et al. BLAST+: architecture and applications , 2009, BMC Bioinformatics.
[21] Bonnie Berger,et al. IsoBase: a database of functionally related proteins across PPI networks , 2010, Nucleic Acids Res..
[22] Amos Bairoch,et al. The ENZYME database in 2000 , 2000, Nucleic Acids Res..
[23] Christophe Perin,et al. Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants , 2008, BMC Genomics.
[24] Eugene V Koonin,et al. Connected gene neighborhoods in prokaryotic genomes. , 2002, Nucleic acids research.
[25] R. Overbeek,et al. The use of gene clusters to infer functional coupling. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[26] Erik L. L. Sonnhammer,et al. Automated ortholog inference from phylogenetic trees and calculation of orthology reliability , 2002, Bioinform..
[27] Kris Popendorf,et al. Accurate identification of orthologous segments among multiple genomes , 2009, Bioinform..
[28] Albert J. Vilella,et al. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. , 2009, Genome research.
[29] Erik L. L. Sonnhammer,et al. Inparanoid: a comprehensive database of eukaryotic orthologs , 2004, Nucleic Acids Res..
[30] T. Gabaldón. Large-scale assignment of orthology: back to phylogenetics? , 2008, Genome Biology.
[31] Gaston H. Gonnet,et al. OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements , 2005, Comparative Genomics.
[32] Ilya B. Muchnik,et al. A Biologically Consistent Model for Comparing Molecular Phylogenies , 1995, J. Comput. Biol..
[33] Paramvir S. Dehal,et al. Two Rounds of Whole Genome Duplication in the Ancestral Vertebrate , 2005, PLoS biology.
[34] G. Petsko. My worries are no longer behind me , 2007, Genome Biology.
[35] Matthew W. Hahn,et al. Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution , 2007, Genome Biology.
[36] P. Albert,et al. A Cautionary Note on the Robustness of Latent Class Models for Estimating Diagnostic Error without a Gold Standard , 2004, Biometrics.
[37] D. Lipman,et al. A genomic perspective on protein families. , 1997, Science.
[38] Natalya Yutin,et al. Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution , 2009, Virology Journal.
[39] Christophe Dessimoz,et al. Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods , 2009, PLoS Comput. Biol..
[40] 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..
[41] Michael Y. Galperin,et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes , 2001, Nucleic Acids Res..
[42] Matthew R. Laird,et al. Improving the specificity of high-throughput ortholog prediction , 2006, BMC Bioinformatics.
[43] Leo Goodstadt,et al. Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human , 2006, PLoS Comput. Biol..
[44] M. Lynch,et al. The altered evolutionary trajectories of gene duplicates. , 2004, Trends in genetics : TIG.
[45] François-Joseph Lapointe,et al. Harvesting evolutionary signals in a forest of prokaryotic gene trees. , 2011, Molecular biology and evolution.
[46] Christian E. V. Storm,et al. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. , 2001, Journal of molecular biology.
[47] Kevin P. Byrne,et al. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. , 2005, Genome research.
[48] Peer Bork,et al. Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. , 2005, Genome research.
[49] Serita M. Nelesen,et al. Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees , 2009, Science.
[50] Jaime Mora,et al. argC Orthologs from Rhizobiales Show Diverse Profiles of Transcriptional Efficiency and Functionality in Sinorhizobium meliloti , 2010, Journal of bacteriology.
[51] Nevin D. Young,et al. OrthoParaMap: Distinguishing orthologs from paralogs by integrating comparative genome data and gene phylogenies , 2003, BMC Bioinformatics.
[52] E. Koonin,et al. Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea , 2007, Biology Direct.
[53] Michael Y. Galperin,et al. Functional genomics and enzyme evolution , 2004, Genetica.
[54] C. Randal Linder,et al. Multiple sequence alignment: a major challenge to large-scale phylogenetics , 2011, PLoS currents.
[55] Inna Dubchak,et al. Trends in Prokaryotic Evolution Revealed by Comparison of Closely Related Bacterial and Archaeal Genomes , 2008, Journal of bacteriology.
[56] Rodrigo Lopez,et al. WU-Blast2 server at the European Bioinformatics Institute , 2003, Nucleic Acids Res..
[57] Erik L. L. Sonnhammer,et al. InParanoid 7: new algorithms and tools for eukaryotic orthology analysis , 2009, Nucleic Acids Res..
[58] Avi Pfeffer,et al. Automatic genome-wide reconstruction of phylogenetic gene trees , 2007, ISMB/ECCB.
[59] Michael Y. Galperin,et al. The cyanobacterial genome core and the origin of photosynthesis , 2006, Proceedings of the National Academy of Sciences.
[60] P. Bork,et al. Quantification of insect genome divergence. , 2007, Trends in genetics : TIG.
[61] E. Koonin,et al. Horizontal gene transfer in prokaryotes: quantification and classification. , 2001, Annual review of microbiology.
[62] Olivier Poch,et al. A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives , 2011, PloS one.
[63] Guy Perrière,et al. Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases , 2005, Bioinform..
[64] S. Dongen. Graph clustering by flow simulation , 2000 .
[65] S. Pongor,et al. The quest for orthologs: finding the corresponding gene across genomes. , 2008, Trends in genetics : TIG.
[66] A. Elofsson,et al. Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. , 2005, Journal of molecular biology.
[67] R. Page,et al. From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. , 1997, Molecular phylogenetics and evolution.
[68] Dr. Susumu Ohno. Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.
[69] N. King,et al. The unicellular ancestry of animal development. , 2004, Developmental cell.
[70] E. Koonin,et al. The Tree and Net Components of Prokaryote Evolution , 2010, Genome biology and evolution.
[71] Katherine H. Huang,et al. Comparative genomics of the lactic acid bacteria , 2006, Proceedings of the National Academy of Sciences.
[72] B. Birren,et al. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae , 2004, Nature.
[73] Eugene V Koonin,et al. Evolution of genome architecture. , 2009, The international journal of biochemistry & cell biology.
[74] Laurent Duret,et al. Differential retention of metabolic genes following whole-genome duplication. , 2009, Molecular biology and evolution.
[75] Vasant Honavar,et al. Detection of gene orthology from gene co-expression and protein interaction networks , 2010, BMC Bioinformatics.
[76] E. Koonin,et al. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[77] W. Fitch. Distinguishing homologous from analogous proteins. , 1970, Systematic zoology.
[78] Christian von Mering,et al. eggNOG: automated construction and annotation of orthologous groups of genes , 2007, Nucleic Acids Res..
[79] Boris G. Mirkin,et al. Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell , 2005, Nucleic acids research.
[80] Eugene V Koonin,et al. The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages , 2009, Proceedings of the National Academy of Sciences.
[81] Maureen A. O’Malley,et al. Prokaryotic evolution and the tree of life are two different things , 2009, Biology Direct.
[82] Gregory D. Schuler,et al. Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.
[83] Lorraine Olendzenski,et al. Evolution of Genes and Organisms , 2009, Annals of the New York Academy of Sciences.
[84] Eugene V. Koonin,et al. Constraints and plasticity in genome and molecular-phenome evolution , 2010, Nature Reviews Genetics.
[85] Kimmen Sjölander,et al. Phylogenomic inference of protein molecular function: advances and challenges , 2004, Bioinform..
[86] P. Bork,et al. Non-orthologous gene displacement. , 1996, Trends in genetics : TIG.
[87] O. Gascuel,et al. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.
[88] Erik L. L. Sonnhammer,et al. OrthoGUI: graphical presentation of Orthostrapper results , 2002, Bioinform..
[89] Tao Jiang,et al. MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement , 2010, BMC Bioinformatics.
[90] P. Bork,et al. Measuring genome evolution. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[91] Albert J. Vilella,et al. Joining forces in the quest for orthologs , 2009, Genome Biology.
[92] W. Doolittle,et al. The practice of classification and the theory of evolution, and what the demise of Charles Darwin's tree of life hypothesis means for both of them , 2009, Philosophical Transactions of the Royal Society B: Biological Sciences.
[93] Darren A. Natale,et al. The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.
[94] Damian Szklarczyk,et al. eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations , 2009, Nucleic Acids Res..
[95] Christian E. V. Storm,et al. Comprehensive analysis of orthologous protein domains using the HOPS database. , 2003, Genome research.
[96] A. Mushegian,et al. Evolutionarily Conserved Orthologous Families in Phages Are Relatively Rare in Their Prokaryotic Hosts , 2011, Journal of bacteriology.
[97] J. Dopazo,et al. The human phylome , 2007, Genome Biology.
[98] Eugene V. Koonin,et al. Comparative genomics, minimal gene-sets and the last universal common ancestor , 2003, Nature Reviews Microbiology.
[99] Teresa M. Przytycka,et al. COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations , 2006, Bioinform..
[100] A. N. Spiridonov,et al. Congruent evolution of different classes of non-coding DNA in prokaryotic genomes. , 2002, Nucleic acids research.
[101] Eugene V Koonin,et al. The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum , 2009, Biology Direct.
[102] Tao Liu,et al. TreeFam: 2008 Update , 2007, Nucleic Acids Res..
[103] E. Rocha,et al. Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes , 2011, PLoS genetics.
[104] L. Koski,et al. The Closest BLAST Hit Is Often Not the Nearest Neighbor , 2001, Journal of Molecular Evolution.
[105] Jianzhi Zhang,et al. Evolutionary conservation of expression profiles between human and mouse orthologous genes. , 2006, Molecular biology and evolution.
[106] E. Myers,et al. Basic local alignment search tool. , 1990, Journal of molecular biology.
[107] M. Huynen,et al. Benchmarking ortholog identification methods using functional genomics data , 2006, Genome Biology.
[108] Paramvir S. Dehal,et al. FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.
[109] Sean R. Eddy,et al. A simple algorithm to infer gene duplication and speciation events on a gene tree , 2001, Bioinform..
[110] C. Hutchison,et al. Gene content phylogeny of herpesviruses. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[111] Olivier Poch,et al. OrthoInspector: comprehensive orthology analysis and visual exploration , 2011, BMC Bioinformatics.
[112] Berend Snel,et al. Orthology prediction at scalable resolution by phylogenetic tree analysis , 2007, BMC Bioinformatics.
[113] Feng Chen,et al. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups , 2005, Nucleic Acids Res..
[114] W. Doolittle,et al. Prokaryotic evolution in light of gene transfer. , 2002, Molecular biology and evolution.
[115] E. Koonin. Orthologs, Paralogs, and Evolutionary Genomics 1 , 2005 .
[116] S. Teichmann,et al. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. , 2001, Journal of molecular biology.
[117] S. Hui,et al. Evaluation of diagnostic tests without gold standards , 1998, Statistical methods in medical research.
[118] I. Muchnik,et al. Ortholog Clustering on a Multipartite Graph , 2005, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[119] M S Waterman,et al. Identification of common molecular subsequences. , 1981, Journal of molecular biology.
[120] Inna Dubchak,et al. ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes , 2008, Nucleic Acids Res..
[121] Tao Jiang,et al. Clustering of Main orthologs for Multiple genomes , 2008, J. Bioinform. Comput. Biol..
[122] M. Suyama,et al. Evolution of prokaryotic gene order: genome rearrangements in closely related species. , 2001, Trends in genetics : TIG.
[123] I. Măndoiu,et al. Identification of mammalian orthologs using local synteny , 2009, BMC Genomics.
[124] C. Stoeckert,et al. OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.
[125] Adam P. Arkin,et al. FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix , 2009, Molecular biology and evolution.
[126] E. Koonin,et al. Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. , 2001, Genome research.
[127] Colin N. Dewey,et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution , 2004, Nature.
[128] Gang Liu,et al. Automatic clustering of orthologs and inparalogs shared by multiple proteomes , 2006, ISMB.
[129] Gaston H. Gonnet,et al. OMA 2011: orthology inference among 1000 complete genomes , 2010, Nucleic Acids Res..
[130] Leszek P. Pryszcz,et al. MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score , 2010, Nucleic acids research.
[131] H Kishino,et al. Freeing phylogenies from artifacts of alignment. , 1992, Molecular biology and evolution.
[132] Kimmen Sjölander,et al. Berkeley PHOG: PhyloFacts orthology group prediction web server , 2009, Nucleic Acids Res..
[133] Hyrum Carroll,et al. Analysis of long branch extraction and long branch shortening , 2010, BMC Genomics.