TY - JOUR AU - Orengo, C. A. AU - Thornton, J. M. PY - 2005 DA - 2005// TI - Protein families and their evolution - a structural perspective. JO - Annu Rev Biochem VL - 74 UR - https://doi.org/10.1146/annurev.biochem.74.082803.133029 DO - 10.1146/annurev.biochem.74.082803.133029 ID - Orengo2005 ER - TY - BOOK AU - Branden, C. AU - Tooze, J. PY - 1999 DA - 1999// TI - Introduction to Protein Structure PB - Garland CY - New York ID - Branden1999 ER - TY - JOUR AU - Koonin, E. V. AU - Wolf, Y. I. AU - Karev, G. P. PY - 2002 DA - 2002// TI - The structure of the protein universe and genome evolution. JO - Nature VL - 420 UR - https://doi.org/10.1038/nature01256 DO - 10.1038/nature01256 ID - Koonin2002 ER - TY - JOUR AU - Madan Babu, M. AU - Teichmann, S. PY - 2003 DA - 2003// TI - Evolution of transcription factors and the gene regulatory network in Escherichia coli. JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg210 DO - 10.1093/nar/gkg210 ID - Madan Babu2003 ER - TY - JOUR AU - Nye, T. M. AU - Berzuini, C. AU - Gilks, W. R. AU - Babu, M. M. AU - Teichmann, S. A. PY - 2005 DA - 2005// TI - Statistical analysis of domains in interacting protein pairs. JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti086 DO - 10.1093/bioinformatics/bti086 ID - Nye2005 ER - TY - JOUR AU - Carbone, M. N. AU - Arnold, F. H. PY - 2007 DA - 2007// TI - Engineering by homologous recombination: exploring sequence and function within a conserved fold. JO - Curr Opin Struct Biol VL - 17 UR - https://doi.org/10.1016/j.sbi.2007.08.005 DO - 10.1016/j.sbi.2007.08.005 ID - Carbone2007 ER - TY - JOUR AU - Itzkovitz, S. AU - Tlusty, T. AU - Alon, U. PY - 2006 DA - 2006// TI - Coding limits on the number of transcription factors. JO - BMC Genomics VL - 7 UR - https://doi.org/10.1186/1471-2164-7-239 DO - 10.1186/1471-2164-7-239 ID - Itzkovitz2006 ER - TY - JOUR AU - Qian, J. AU - Luscombe, N. M. AU - Gerstein, M. PY - 2001 DA - 2001// TI - Protein family and fold occurrence in genomes: power law behaviour and evolutionary model. JO - J Mol Biol VL - 313 UR - https://doi.org/10.1006/jmbi.2001.5079 DO - 10.1006/jmbi.2001.5079 ID - Qian2001 ER - TY - JOUR AU - Ranea, J. A. AU - Buchan, D. W. AU - Thornton, J. M. AU - Orengo, C. A. PY - 2004 DA - 2004// TI - Evolution of protein superfamilies and bacterial genome size. JO - J Mol Biol VL - 336 UR - https://doi.org/10.1016/j.jmb.2003.12.044 DO - 10.1016/j.jmb.2003.12.044 ID - Ranea2004 ER - TY - JOUR AU - Murzin, A. G. AU - Brenner, S. E. AU - Hubbard, T. AU - Chothia, C. PY - 1995 DA - 1995// TI - SCOP: a structural classification of proteins database for the investigation of sequences and structures. JO - J Mol Biol VL - 247 ID - Murzin1995 ER - TY - JOUR AU - Orengo, C. A. AU - Michie, A. D. AU - Jones, S. AU - Jones, D. T. AU - Swindells, M. B. AU - Thornton, J. M. PY - 1997 DA - 1997// TI - CATH-a hierarchic classification of protein domain structures. JO - Structure VL - 5 UR - https://doi.org/10.1016/S0969-2126(97)00260-8 DO - 10.1016/S0969-2126(97)00260-8 ID - Orengo1997 ER - TY - JOUR AU - Ranea, J. A. AU - Sillero, A. AU - Thornton, J. M. AU - Orengo, C. A. PY - 2006 DA - 2006// TI - Protein superfamily evolution and the last universal common ancestor (LUCA). JO - J Mol Evol VL - 63 UR - https://doi.org/10.1007/s00239-005-0289-7 DO - 10.1007/s00239-005-0289-7 ID - Ranea2006 ER - TY - JOUR AU - Bornberg-Bauer, E. AU - Beaussart, F. AU - Kummerfeld, S. K. AU - Teichmann, S. A. AU - Weiner, J. PY - 2005 DA - 2005// TI - The evolution of domain arrangements in proteins and interaction networks. JO - Cell Mol Life Sci VL - 62 UR - https://doi.org/10.1007/s00018-004-4416-1 DO - 10.1007/s00018-004-4416-1 ID - Bornberg-Bauer2005 ER - TY - JOUR AU - Weiner, J. AU - Beaussart, F. AU - Bornberg-Bauer, E. PY - 2006 DA - 2006// TI - Domain deletions and substitutions in the modular protein evolution. JO - FEBS J VL - 273 UR - https://doi.org/10.1111/j.1742-4658.2006.05220.x DO - 10.1111/j.1742-4658.2006.05220.x ID - Weiner2006 ER - TY - JOUR AU - Huynen, M. A. AU - van Nimwegen, E. PY - 1998 DA - 1998// TI - The frequency distribution of gene family sizes in complete genomes. JO - Mol Biol Evol VL - 15 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025959 DO - 10.1093/oxfordjournals.molbev.a025959 ID - Huynen1998 ER - TY - JOUR AU - Karev, G. P. AU - Wolf, Y. I. AU - Rzhetsky, A. Y. AU - Berezovskaya, F. S. AU - Koonin, E. V. PY - 2002 DA - 2002// TI - Birth and death of protein domains: a simple model of evolution explains power law behavior. JO - BMC Evol Biol VL - 2 UR - https://doi.org/10.1186/1471-2148-2-18 DO - 10.1186/1471-2148-2-18 ID - Karev2002 ER - TY - CHAP AU - Kuznetsov, V. A. ED - Zhang, W. ED - Shmulevich, I. PY - 2002 DA - 2002// TI - Statistics of the numbers of transcripts and protein sequences encoded in the genome. BT - Computational and Statistical Approaches to Genomics PB - Kluwer CY - Boston ID - Kuznetsov2002 ER - TY - JOUR AU - Abeln, S. AU - Deane, C. M. PY - 2005 DA - 2005// TI - Fold usage on genomes and protein fold evolution. JO - Proteins VL - 60 UR - https://doi.org/10.1002/prot.20506 DO - 10.1002/prot.20506 ID - Abeln2005 ER - TY - STD TI - Wilson D, Madera M, Vogel C, Chothia C, Gough J: The SUPERFAMILY database in 2007: families and functions. Nucleic Acids Res. 2007, D308-D313. 35 Database ID - ref19 ER - TY - JOUR AU - Li, H. AU - Tang, C. AU - Wingreen, N. S. PY - 1998 DA - 1998// TI - Are protein folds atypical? JO - Proc Natl Acad Sci USA VL - 95 UR - https://doi.org/10.1073/pnas.95.9.4987 DO - 10.1073/pnas.95.9.4987 ID - Li1998 ER - TY - JOUR AU - Deeds, E. J. AU - Shakhnovich, E. I. PY - 2007 DA - 2007// TI - A structure-centric view of protein evolution, design, and adaptation. JO - Adv Enzymol Relat Areas Mol Biol VL - 75 ID - Deeds2007 ER - TY - CHAP AU - Kamal, M. AU - Luscombe, N. AU - Qian, J. AU - Gerstein, M. ED - Koonin, E. ED - Wolf, Y. ED - Karev, G. PY - 2006 DA - 2006// TI - Analytical evolutionary model for protein fold occurrence in genomes, accounting for the effects of gene duplication, deletion, acquisition and selective pressure. BT - Power Laws, Scale-Free Networks and Genome Biology PB - Spinger CY - New York UR - https://doi.org/10.1007/0-387-33916-7_10 DO - 10.1007/0-387-33916-7_10 ID - Kamal2006 ER - TY - JOUR AU - Durrett, R. AU - Schweinsberg, J. PY - 2005 DA - 2005// TI - Power laws for family sizes in a duplication model. JO - Ann Probab VL - 33 UR - https://doi.org/10.1214/009117905000000369 DO - 10.1214/009117905000000369 ID - Durrett2005 ER - TY - JOUR AU - Karev, G. P. AU - Wolf, Y. I. AU - Koonin, E. V. PY - 2003 DA - 2003// TI - Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve? JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg351 DO - 10.1093/bioinformatics/btg351 ID - Karev2003 ER - TY - JOUR AU - Karev, G. P. AU - Wolf, Y. I. AU - Berezovskaya, F. S. AU - Koonin, E. V. PY - 2004 DA - 2004// TI - Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models. JO - BMC Evol Biol VL - 4 UR - https://doi.org/10.1186/1471-2148-4-32 DO - 10.1186/1471-2148-4-32 ID - Karev2004 ER - TY - JOUR AU - Karev, G. P. AU - Berezovskaya, F. S. AU - Koonin, E. V. PY - 2005 DA - 2005// TI - Modeling genome evolution with a diffusion approximation of a birth-and-death process. JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1202 DO - 10.1093/bioinformatics/bti1202 ID - Karev2005 ER - TY - JOUR AU - Dokholyan, N. V. AU - Shakhnovich, B. AU - Shakhnovich, E. I. PY - 2002 DA - 2002// TI - Expanding protein universe and its origin from the biological Big Bang. JO - Proc Natl Acad Sci USA VL - 99 UR - https://doi.org/10.1073/pnas.202497999 DO - 10.1073/pnas.202497999 ID - Dokholyan2002 ER - TY - JOUR AU - Dokholyan, N. V. PY - 2005 DA - 2005// TI - The architecture of the protein domain universe. JO - Gene VL - 347 UR - https://doi.org/10.1016/j.gene.2004.12.020 DO - 10.1016/j.gene.2004.12.020 ID - Dokholyan2005 ER - TY - BOOK AU - Pitman, J. PY - 2006 DA - 2006// TI - Combinatorial Stochastic Processes PB - Springer-Verlag CY - Berlin ID - Pitman2006 ER - TY - JOUR AU - Pitman, J. AU - Yor, M. PY - 1997 DA - 1997// TI - The two-parameter Poisson-Dirichlet distribution derived from a stable subordinator. JO - Ann Probab VL - 25 UR - https://doi.org/10.1214/aop/1024404422 DO - 10.1214/aop/1024404422 ID - Pitman1997 ER - TY - BOOK AU - Aldous, D. PY - 1985 DA - 1985// TI - Exchangeability and Related Topics PB - Springer CY - Berlin UR - https://doi.org/10.1007/BFb0099421 DO - 10.1007/BFb0099421 ID - Aldous1985 ER - TY - JOUR AU - Kingman, J. PY - 1975 DA - 1975// TI - Random discrete distributions. JO - J Roy Statist Soc B VL - 37 ID - Kingman1975 ER - TY - JOUR AU - Barabasi, A. L. AU - Albert, R. PY - 1999 DA - 1999// TI - Emergence of scaling in random networks. JO - Science VL - 286 UR - https://doi.org/10.1126/science.286.5439.509 DO - 10.1126/science.286.5439.509 ID - Barabasi1999 ER - TY - JOUR AU - Lynch, M. AU - Conery, J. S. PY - 2003 DA - 2003// TI - The origins of genome complexity. JO - Science VL - 302 UR - https://doi.org/10.1126/science.1089370 DO - 10.1126/science.1089370 ID - Lynch2003 ER - TY - JOUR AU - Goldstein, R. A. PY - 2008 DA - 2008// TI - The structure of protein evolution and the evolution of protein structure. JO - Curr Opin Struct Biol VL - 18 UR - https://doi.org/10.1016/j.sbi.2008.01.006 DO - 10.1016/j.sbi.2008.01.006 ID - Goldstein2008 ER - TY - JOUR AU - Jain, R. AU - Rivera, M. C. AU - Lake, J. A. PY - 1999 DA - 1999// TI - Horizontal gene transfer among genomes: the complexity hypothesis. JO - Proc Natl Acad Sci USA VL - 96 UR - https://doi.org/10.1073/pnas.96.7.3801 DO - 10.1073/pnas.96.7.3801 ID - Jain1999 ER - TY - JOUR AU - Aris-Brosou, S. PY - 2005 DA - 2005// TI - Determinants of adaptive evolution at the molecular level: the extended complexity hypothesis. JO - Mol Biol Evol VL - 22 UR - https://doi.org/10.1093/molbev/msi006 DO - 10.1093/molbev/msi006 ID - Aris-Brosou2005 ER - TY - JOUR AU - Lercher, M. J. AU - Pal, C. PY - 2008 DA - 2008// TI - Integration of horizontally transferred genes into regulatory interaction networks takes many million years. JO - Mol Biol Evol VL - 25 UR - https://doi.org/10.1093/molbev/msm283 DO - 10.1093/molbev/msm283 ID - Lercher2008 ER - TY - JOUR AU - Wellner, A. AU - Lurie, M. N. AU - Gophna, U. PY - 2007 DA - 2007// TI - Complexity, connectivity, and duplicability as barriers to lateral gene transfer. JO - Genome Biol VL - 8 UR - https://doi.org/10.1186/gb-2007-8-8-r156 DO - 10.1186/gb-2007-8-8-r156 ID - Wellner2007 ER - TY - JOUR AU - Banavar, J. R. AU - Maritan, A. PY - 2007 DA - 2007// TI - Physics of proteins. JO - Annu Rev Biophys Biomol Struct VL - 36 UR - https://doi.org/10.1146/annurev.biophys.36.040306.132808 DO - 10.1146/annurev.biophys.36.040306.132808 ID - Banavar2007 ER -