Evolution of protein domain architectures.
暂无分享,去创建一个
[1] Erich Bornberg-Bauer,et al. Rapid similarity search of proteins using alignments of domain arrangements , 2014, Bioinform..
[2] Erich Bornberg-Bauer,et al. DoMosaics: software for domain arrangement visualization and domain-centric analysis of proteins , 2014, Bioinform..
[3] E. Birney,et al. Pfam: the protein families database , 2013, Nucleic Acids Res..
[4] Ming-Jing Hwang,et al. The architectural design of networks of protein domain architectures , 2013, Biology Letters.
[5] Ramanathan Sowdhamini,et al. An alignment-free domain architecture similarity search (ADASS) algorithm for inferring homology between multi-domain proteins , 2013, Bioinformation.
[6] Macarena Toll-Riera,et al. Emergence of novel domains in proteins , 2013, BMC Evolutionary Biology.
[7] Christian M. Zmasek,et al. This Déjà Vu Feeling—Analysis of Multidomain Protein Evolution in Eukaryotic Genomes , 2012, PLoS Comput. Biol..
[8] F. Rentzsch,et al. Repeated Evolution of Identical Domain Architecture in Metazoan Netrin Domain-Containing Proteins , 2012, Genome biology and evolution.
[9] Gary Stacey,et al. Evolutionary dynamics of protein domain architecture in plants , 2012, BMC Evolutionary Biology.
[10] Erich Bornberg-Bauer,et al. Dynamics and Adaptive Benefits of Protein Domain Emergence and Arrangements during Plant Genome Evolution , 2012, Genome biology and evolution.
[11] Erich Bornberg-Bauer,et al. The Dynamics and Evolutionary Potential of Domain Loss and Emergence , 2011, Molecular biology and evolution.
[12] Manolis Kellis,et al. Evolution at the Subgene Level: Domain Rearrangements in the Drosophila Phylogeny , 2011, Molecular biology and evolution.
[13] L. Patthy,et al. Reassessing Domain Architecture Evolution of Metazoan Proteins: The Contribution of Different Evolutionary Mechanisms , 2011, Genes.
[14] L. Patthy,et al. Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Errors Caused by Confusing Paralogs and Epaktologs , 2011, Genes.
[15] E. Szarka,et al. Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors , 2011, Genes.
[16] Roded Sharan,et al. Evolution of domain promiscuity in eukaryotic genomes--a perspective from the inferred ancestral domain architectures. , 2011, Molecular bioSystems.
[17] W. Heyer,et al. Regulation of homologous recombination in eukaryotes. , 2010, Annual review of genetics.
[18] Arndt von Haeseler,et al. FACT: Functional annotation transfer between proteins with similar feature architectures , 2010, BMC Bioinformatics.
[19] Alex Bateman,et al. Quantifying the mechanisms of domain gain in animal proteins , 2010, Genome Biology.
[20] E. Bornberg-Bauer,et al. How do new proteins arise? , 2010, Current opinion in structural biology.
[21] Oliver Eulenstein,et al. Inferring Evolutionary Scenarios for Protein Domain Compositions , 2010, ISBRA.
[22] Philip E. Bourne,et al. The Evolutionary History of Protein Domains Viewed by Species Phylogeny , 2009, PloS one.
[23] Doheon Lee,et al. Protein comparison at the domain architecture level , 2009, BMC Bioinformatics.
[24] R. Farías-Rodríguez,et al. Homologous recombination and dynamics of rhizobial genomes. , 2009, Research in microbiology.
[25] Christine A. Orengo,et al. Gene3D: merging structure and function for a Thousand genomes , 2009, Nucleic Acids Res..
[26] Baris E. Suzek,et al. The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..
[27] M. Batzer,et al. The impact of retrotransposons on human genome evolution , 2009, Nature Reviews Genetics.
[28] A. Buzdin,et al. Retroelements and their impact on genome evolution and functioning , 2009, Cellular and Molecular Life Sciences.
[29] A. Bateman,et al. The evolution of protein domain families. , 2009, Biochemical Society transactions.
[30] N. Brissett,et al. Repairing DNA double-strand breaks by the prokaryotic non-homologous end-joining pathway. , 2009, Biochemical Society transactions.
[31] Cyrus Chothia,et al. Genomic and structural aspects of protein evolution. , 2009, The Biochemical journal.
[32] Sarah A. Teichmann,et al. Protein domain organisation: adding order , 2009, BMC Bioinformatics.
[33] Jeffery P. Demuth,et al. The life and death of gene families , 2009, BioEssays : news and reviews in molecular, cellular and developmental biology.
[34] Malay Kumar Basu,et al. Domain mobility in proteins: functional and evolutionary implications , 2008, Briefings Bioinform..
[35] Cyrus Chothia,et al. SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny , 2008, Nucleic Acids Res..
[36] D. Fusco,et al. Identity and divergence of protein domain architectures after the Yeast Whole Genome Duplication event , 2008, 0811.3389.
[37] Ian Sillitoe,et al. The CATH classification revisited—architectures reviewed and new ways to characterize structural divergence in superfamilies , 2008, Nucleic Acids Res..
[38] Narmada Thanki,et al. CDD: specific functional annotation with the Conserved Domain Database , 2008, Nucleic Acids Res..
[39] Peer Bork,et al. SMART 6: recent updates and new developments , 2008, Nucleic Acids Res..
[40] Robert D. Finn,et al. InterPro: the integrative protein signature database , 2008, Nucleic Acids Res..
[41] Andrew D. Moore,et al. Just how versatile are domains? , 2008, BMC Evolutionary Biology.
[42] Andrew D. Moore,et al. Arrangements in the modular evolution of proteins. , 2008, Trends in biochemical sciences.
[43] E. Koonin,et al. Evolution of protein domain promiscuity in eukaryotes. , 2008, Genome research.
[44] E. Sonnhammer,et al. Domain tree-based analysis of protein architecture evolution. , 2008, Molecular biology and evolution.
[45] Erik L. L. Sonnhammer,et al. PfamAlyzer: domain-centric homology search , 2007, Bioinform..
[46] C. Feschotte,et al. DNA transposons and the evolution of eukaryotic genomes. , 2007, Annual review of genetics.
[47] Tim J. P. Hubbard,et al. Data growth and its impact on the SCOP database: new developments , 2007, Nucleic Acids Res..
[48] A. Elofsson,et al. Quantification of the elevated rate of domain rearrangements in metazoa. , 2007, Journal of molecular biology.
[49] M. Kanehisa,et al. Evolutionary history and functional implications of protein domains and their combinations in eukaryotes , 2007, Genome Biology.
[50] E. E. Schmidt,et al. The origins of polypeptide domains , 2007, BioEssays : news and reviews in molecular, cellular and developmental biology.
[51] Jessica H. Fong,et al. Modeling the evolution of protein domain architectures using maximum parsimony. , 2007, Journal of molecular biology.
[52] C. Orengo,et al. Protein Superfamily Evolution and the Last Universal Common Ancestor (LUCA) , 2006, Journal of Molecular Evolution.
[53] Arne Elofsson,et al. Expansion of Protein Domain Repeats , 2006, PLoS Comput. Biol..
[54] E. Bornberg-Bauer,et al. Domain deletions and substitutions in the modular protein evolution , 2006, The FEBS journal.
[55] E. Bornberg-Bauer,et al. Evolution of circular permutations in multidomain proteins. , 2006, Molecular biology and evolution.
[56] A. Elofsson,et al. Domain rearrangements in protein evolution. , 2005, Journal of molecular biology.
[57] L. Patthy,et al. Modules, multidomain proteins and organismic complexity , 2005, The FEBS journal.
[58] C. Orengo,et al. Protein families and their evolution-a structural perspective. , 2005, Annual review of biochemistry.
[59] Dannie Durand,et al. Graph Theoretical Insights into Evolution of Multidomain Proteins , 2005, RECOMB.
[60] L. Holm,et al. The Pfam protein families database , 2005, Nucleic Acids Res..
[61] Julian Gough,et al. Convergent evolution of domain architectures (is rare) , 2005, Bioinform..
[62] S. Teichmann,et al. The relationship between domain duplication and recombination. , 2005, Journal of molecular biology.
[63] Walter Willinger,et al. Towards a Theory of Scale-Free Graphs: Definition, Properties, and Implications , 2005, Internet Math..
[64] Sébastien Carrère,et al. The ProDom database of protein domain families: more emphasis on 3D , 2004, Nucleic Acids Res..
[65] Liisa Holm,et al. ADDA: a domain database with global coverage of the protein universe , 2004, Nucleic Acids Res..
[66] A. Grigoriev,et al. Protein domains correlate strongly with exons in multiple eukaryotic genomes--evidence of exon shuffling? , 2004, Trends in genetics : TIG.
[67] Daniel W. A. Buchan,et al. Evolution of protein superfamilies and bacterial genome size. , 2004, Journal of molecular biology.
[68] S. Teichmann,et al. Supra-domains: evolutionary units larger than single protein domains. , 2004, Journal of molecular biology.
[69] L. Patthy. Modular Assembly of Genes and the Evolution of New Functions , 2003, Genetica.
[70] A. van Rijk,et al. Molecular Mechanisms of Exon Shuffling: Illegitimate Recombination , 2003, Genetica.
[71] E. Nimwegen. Scaling Laws in the Functional Content of Genomes , 2003, physics/0307001.
[72] V. Kuznetsov,et al. ANALYSIS OF THE EVOLVING PROTEOMES: PREDICTIONS OF THE NUMBER OF PROTEIN DOMAINS IN NATURE AND THE NUMBER OF GENES IN EUKARYOTIC ORGANISMS , 2002 .
[73] E. Koonin,et al. The structure of the protein universe and genome evolution , 2002, Nature.
[74] E. Koonin,et al. Birth and death of protein domains: A simple model of evolution explains power law behavior , 2002, BMC Evolutionary Biology.
[75] Lewis Y. Geer,et al. CDART: protein homology by domain architecture. , 2002, Genome research.
[76] M. Gerstein,et al. The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties , 2002, Genome Biology.
[77] A. Brivanlou,et al. Signal Transduction and the Control of Gene Expression , 2002, Science.
[78] C. Chothia,et al. The geometry of domain combination in proteins. , 2002, Journal of molecular biology.
[79] M. Gerstein,et al. Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. , 2001, Journal of molecular biology.
[80] Andrey Rzhetsky,et al. Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome , 2001, Bioinform..
[81] S. Wuchty. Scale-free behavior in protein domain networks. , 2001, Molecular biology and evolution.
[82] S. Teichmann,et al. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. , 2001, Journal of molecular biology.
[83] C. DeLisi,et al. Predictions of gene family distributions in microbial genomes: evolution by gene duplication and modification. , 2000, Physical review letters.
[84] Albert,et al. Emergence of scaling in random networks , 1999, Science.
[85] D. Eisenberg,et al. Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.
[86] M. Huynen,et al. The frequency distribution of gene family sizes in complete genomes. , 1998, Molecular biology and evolution.
[87] P Bork,et al. Evolutionarily mobile modules in proteins. , 1993, Scientific American.
[88] J. Farris. Phylogenetic Analysis Under Dollo's Law , 1977 .
[89] J. Rozas,et al. The birth-and-death evolution of multigene families revisited. , 2012, Genome dynamics.
[90] María Martín,et al. The Universal Protein Resource (UniProt) in 2010 , 2010 .
[91] Sarah A Teichmann,et al. Relative rates of gene fusion and fission in multi-domain proteins. , 2005, Trends in genetics : TIG.
[92] S. Teichmann,et al. Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination , 2004, Journal of Structural and Functional Genomics.
[93] Robert D. Finn,et al. The Pfam protein families database , 2004, Nucleic Acids Res..
[94] Cathy H. Wu,et al. UniProt: the Universal Protein knowledgebase , 2004, Nucleic Acids Res..
[95] B. Snel,et al. Genome evolution. Gene fusion versus gene fission. , 2000, Trends in Genetics.
[96] A. Barabasi,et al. Emergence of Scaling in Random Networks , 1999 .