Arrangements in the modular evolution of proteins.

[1]  E. Bornberg-Bauer,et al.  The Crohn’s disease susceptibility gene DLG5 as a member of the CARD interaction network , 2008, Journal of Molecular Medicine.

[2]  E. Sonnhammer,et al.  Domain tree-based analysis of protein architecture evolution. , 2008, Molecular biology and evolution.

[3]  A. Elofsson,et al.  Quantification of the elevated rate of domain rearrangements in metazoa. , 2007, Journal of molecular biology.

[4]  Rotem Sorek,et al.  The birth of new exons: mechanisms and evolutionary consequences. , 2007, RNA.

[5]  Erich Bornberg-Bauer,et al.  Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN) , 2007, Bioinform..

[6]  K. Nishikawa,et al.  A tree of life based on protein domain organizations. , 2007, Molecular biology and evolution.

[7]  Benjamin J. Raphael,et al.  The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families , 2007, PLoS biology.

[8]  Jessica H. Fong,et al.  Modeling the evolution of protein domain architectures using maximum parsimony. , 2007, Journal of molecular biology.

[9]  K. H. Wolfe,et al.  Not born equal: increased rate asymmetry in relocated and retrotransposed rodent gene duplicates. , 2006, Molecular biology and evolution.

[10]  G. Caetano-Anollés,et al.  Global phylogeny determined by the combination of protein domains in proteomes. , 2006, Molecular biology and evolution.

[11]  Cyrus Chothia,et al.  The SUPERFAMILY database in 2007: families and functions , 2006, Nucleic Acids Res..

[12]  Yu-Dong Cai,et al.  Automatic transcription factor classifier based on functional domain composition. , 2006, Biochemical and biophysical research communications.

[13]  Gabrielle A. Reeves,et al.  Structural diversity of domain superfamilies in the CATH database. , 2006, Journal of molecular biology.

[14]  Arne Elofsson,et al.  Expansion of Protein Domain Repeats , 2006, PLoS Comput. Biol..

[15]  A. Elofsson,et al.  What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? , 2006, Genome Biology.

[16]  Pierre Brézellec,et al.  Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins , 2006, Bioinform..

[17]  Eugene V Koonin,et al.  Comparative genomics and structural biology of the molecular innovations of eukaryotes. , 2006, Current opinion in structural biology.

[18]  Ting Chen,et al.  An integrated approach to the prediction of domain-domain interactions , 2006, BMC Bioinformatics.

[19]  E. Bornberg-Bauer,et al.  Domain deletions and substitutions in the modular protein evolution , 2006, The FEBS journal.

[20]  David A. Lee,et al.  Exploiting protein structure data to explore the evolution of protein function and biological complexity , 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

[21]  Ignacio Marín,et al.  Comparative genomics and protein domain graph analyses link ubiquitination and RNA metabolism. , 2006, Journal of molecular biology.

[22]  Robert D. Finn,et al.  Pfam: clans, web tools and services , 2005, Nucleic Acids Res..

[23]  J. Bennetzen,et al.  Transposable elements, gene creation and genome rearrangement in flowering plants. , 2005, Current opinion in genetics & development.

[24]  A. Elofsson,et al.  Domain rearrangements in protein evolution. , 2005, Journal of molecular biology.

[25]  Fran Lewitter,et al.  Intragenic tandem repeats generate functional variability , 2005, Nature Genetics.

[26]  A. Wagner Robustness and Evolvability in Living Systems , 2005 .

[27]  N. Sakabe,et al.  Signs of Ancient and Modern Exon-Shuffling Are Correlated to the Distribution of Ancient and Modern Domains Along Proteins , 2005, Journal of Molecular Evolution.

[28]  C. Orengo,et al.  Protein families and their evolution-a structural perspective. , 2005, Annual review of biochemistry.

[29]  Jianzhi Zhang,et al.  Gene Complexity and Gene Duplicability , 2005, Current Biology.

[30]  J. Risler,et al.  Identification of genomic features using microsyntenies of domains: domain teams. , 2005, Genome research.

[31]  Julian Gough,et al.  Convergent evolution of domain architectures (is rare) , 2005, Bioinform..

[32]  D. Liberles,et al.  Subfunctionalization of duplicated genes as a transition state to neofunctionalization , 2005, BMC Evolutionary Biology.

[33]  A. Elofsson,et al.  Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. , 2005, Journal of molecular biology.

[34]  Eric J. Deeds,et al.  Prokaryotic phylogenies inferred from protein structural domains. , 2005, Genome research.

[35]  S. Teichmann,et al.  The relationship between domain duplication and recombination. , 2005, Journal of molecular biology.

[36]  S. Teichmann,et al.  The evolution of domain arrangements in proteins and interaction networks , 2005, Cellular and Molecular Life Sciences CMLS.

[37]  R. Doolittle,et al.  Phylogeny determined by protein domain content. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[38]  Boris Hayete,et al.  GOTrees: Predicting GO Associations from Protein Domain Composition Using Decision Trees , 2004, Pacific Symposium on Biocomputing.

[39]  Debasis Dash,et al.  Comparative analysis of protein unfoldedness in human housekeeping and non-housekeeping proteins , 2004, Bioinform..

[40]  A. Grigoriev,et al.  Protein domains correlate strongly with exons in multiple eukaryotic genomes--evidence of exon shuffling? , 2004, Trends in genetics : TIG.

[41]  Matthew Hurles,et al.  Gene Duplication: The Genomic Trade in Spare Parts , 2004, PLoS biology.

[42]  Marcin von Grotthuss,et al.  Detecting distant homology with Meta-BASIC , 2004, Nucleic Acids Res..

[43]  Manyuan Long,et al.  Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species , 2004, Nature Genetics.

[44]  C. Chothia,et al.  Structure, function and evolution of multidomain proteins. , 2004, Current opinion in structural biology.

[45]  Adam Godzik,et al.  Comparative analysis of protein domain organization. , 2004, Genome research.

[46]  S. Teichmann,et al.  Supra-domains: evolutionary units larger than single protein domains. , 2004, Journal of molecular biology.

[47]  Richard W. Lusk,et al.  Organismal complexity, protein complexity, and gene duplicability , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[48]  S. Lovell Are non‐functional, unfolded proteins (‘junk proteins’) common in the genome? , 2003, FEBS letters.

[49]  J. Söding,et al.  More than the sum of their parts: On the evolution of proteins from peptides , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[50]  S. Vucetic,et al.  Flavors of protein disorder , 2003, Proteins.

[51]  L. Patthy Modular Assembly of Genes and the Evolution of New Functions , 2003, Genetica.

[52]  Jianzhi Zhang Evolution by gene duplication: an update , 2003 .

[53]  K. Chou,et al.  Using Functional Domain Composition and Support Vector Machines for Prediction of Protein Subcellular Location* , 2002, The Journal of Biological Chemistry.

[54]  Jérôme Gouzy,et al.  ProDom: Automated Clustering of Homologous Domains , 2002, Briefings Bioinform..

[55]  Christopher J. Oldfield,et al.  Evolutionary Rate Heterogeneity in Proteins with Long Disordered Regions , 2002, Journal of Molecular Evolution.

[56]  Erich Bornberg-Bauer,et al.  Recombinatoric exploration of novel folded structures: A heteropolymer-based model of protein evolutionary landscapes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[57]  S. Wuchty Scale-free behavior in protein domain networks. , 2001, Molecular biology and evolution.

[58]  S. Teichmann,et al.  Domain combinations in archaeal, eubacterial and eukaryotic proteomes. , 2001, Journal of molecular biology.

[59]  L. Tjoelker,et al.  Structural and Functional Definition of the Human Chitinase Chitin-binding Domain* , 2000, The Journal of Biological Chemistry.

[60]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[61]  A. Force,et al.  Preservation of duplicate genes by complementary, degenerative mutations. , 1999, Genetics.

[62]  P. Bork,et al.  Tracing the spread of fibronectin type III domains in bacterial glycohydrolases , 1994, Journal of Molecular Evolution.

[63]  W. Doolittle,et al.  Genes-in-pieces revisited , 1993, Nature.

[64]  L. Patthy Evolution of the proteases of blood coagulation and fibrinolysis by assembly from modules , 1985, Cell.

[65]  A. Mclachlan,et al.  Repeated folding pattern in copper–zinc superoxide dismutase , 1980, Nature.

[66]  W. Gilbert Why genes in pieces? , 1978, Nature.

[67]  J. R. Brown Structural origins of mammalian albumin. , 1976, Federation proceedings.

[68]  Michael G. Rossmann,et al.  Chemical and biological evolution of a nucleotide-binding protein , 1974, Nature.

[69]  Sarah A Teichmann,et al.  Relative rates of gene fusion and fission in multi-domain proteins. , 2005, Trends in genetics : TIG.

[70]  Tim J. P. Hubbard,et al.  SCOP database in 2004: refinements integrate structure and sequence family data , 2004, Nucleic Acids Res..

[71]  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.

[72]  See-Kiong Ng,et al.  InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes , 2003, Nucleic Acids Res..

[73]  John Moult,et al.  A unifold, mesofold, and superfold model of protein fold use , 2002, Proteins.

[74]  C. Ponting,et al.  The natural history of protein domains. , 2002, Annual review of biophysics and biomolecular structure.

[75]  Erich Bornberg-Bauer,et al.  Randomness, Structural Uniqueness, Modularity and Neutral Evolution in Sequence Space of Model Proteins , 2002 .

[76]  S. Eddy Profile hidden Markov models , 1998, Bioinform..

[77]  W. Doolittle,et al.  Molecular evolution. Genes-in-pieces revisited. , 1993, Nature.