Evolution of protein domain architectures.

[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 .