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Repeats in the Cell Surface Proteins of Archaeal and Bacterial Genomes Using Computational Tools","volume":"5","author":"S Adindla","year":"2004","journal-title":"Comp Funct Genomics"},{"issue":"2","key":"ref45","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1073\/pnas.022629899","article-title":"Mutation Rate in Mammalian Genomes","volume":"19","author":"S Kumar","year":"2002","journal-title":"Proc Nat Acd Sci"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"549","DOI":"10.1101\/gr.1925704","article-title":"Comparative Analysis of Amino-Acid Repeats in Rodents and Humans","volume":"14","author":"MM Alb\u00e0","year":"2004","journal-title":"Genome Research"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1283:1287","DOI":"10.1126\/science.1123061","article-title":"Toward Automatic Reconstruction of a Highly Resolved Tree of Life","volume":"311","author":"FD Ciccarelli","year":"2006","journal-title":"Science"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1007\/s10930-009-9201-4","article-title":"Intrinsically Disordered Proteins and Their Environment: Effects of Strong Denaturants, temperature, pH, Counter Ions, Membranes, Binding Partners, Osmolytes, and Macromolecular Crowding","volume":"28","author":"VN Uversky","year":"2009","journal-title":"Protein J"},{"key":"ref49","unstructured":"Graur D, Li WH (2000). Fundamentals of Molecular Evolution, <italic>2nd Ed., Sinauer Assoc., Sunderland, MA<\/italic>."},{"issue":"3","key":"ref50","doi-asserted-by":"crossref","first-page":"427","DOI":"10.2307\/2408092","article-title":"Character change, speciation and higher taxa","volume":"36","author":"S Wright","year":"1982","journal-title":"Evolution"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1038\/nrg1272","article-title":"Network Biology: understanding the cell&apos;s functional organization","volume":"5","author":"AL Barabasi","year":"2004","journal-title":"Nat Rev Genet"},{"issue":"8","key":"ref52","doi-asserted-by":"crossref","first-page":"e1002173","DOI":"10.1371\/journal.pcbi.1002173","article-title":"Are there laws of genome evolution?","volume":"7","author":"E Koonin","year":"2011","journal-title":"PLoS Comp Biol"},{"issue":"6","key":"ref53","doi-asserted-by":"crossref","first-page":"e1002567","DOI":"10.1371\/journal.pcbi.1002567","article-title":"ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin","volume":"8","author":"JA Capra","year":"2012","journal-title":"PLoS Comp Biol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1007\/s10955-011-0229-4","article-title":"Are biological systems poised at criticality?","volume":"144","author":"T Mora","year":"2011","journal-title":"J Stat Phys"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"066119","DOI":"10.1103\/PhysRevE.81.066119","article-title":"Statistical mechanics of letters in words","volume":"81","author":"GJ Stephens","year":"2010","journal-title":"Phy Rev E"},{"key":"ref56","article-title":"Understanding and identifying amino acid repeats","author":"H Luo","year":"2013","journal-title":"Briefings in Bioinformatics"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"R45","DOI":"10.1186\/gb-2006-7-6-r45","article-title":"What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?","volume":"7","author":"D Ekman","year":"2006","journal-title":"Genome Biology"},{"issue":"1","key":"ref58","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.gene.2004.11.023","article-title":"Simple sequence repeats in proteins and their significance for network evolution","volume":"345","author":"JM Hancock","year":"2005","journal-title":"Gene"},{"issue":"12","key":"ref59","doi-asserted-by":"crossref","first-page":"5405","DOI":"10.1073\/pnas.1001705107","article-title":"Maximum entropy models for antibody diversity","volume":"107","author":"T Mora","year":"2010","journal-title":"Proc Nat Acd Sci"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1038\/nature07894","article-title":"Darwin&apos;s bridge between microevolution and macroevolution","volume":"457","author":"DN Reznick","year":"2009","journal-title":"Nature"},{"issue":"7","key":"ref61","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1016\/S0169-5347(01)02187-5","article-title":"Chromosomal rearrangements and speciation","volume":"16","author":"LH Rieseberg","year":"2001","journal-title":"Trends Ecol Evol"},{"issue":"6","key":"ref62","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/S0169-5347(03)00033-8","article-title":"Evolution by gene duplication","volume":"18","author":"J Zhang","year":"2003","journal-title":"Trends Ecol Evol"},{"key":"ref63","first-page":"794:799","article-title":"Parallel evolution by gene duplication in the genomes of two unicellular Fungi","volume":"13","author":"L Austin","year":"2003","journal-title":"Genome Research"},{"key":"ref64","unstructured":"Eldredge N, Gould SJ (1972). Models in Paleobiology. In T.J.M. Schopf (ed), San Francisco: Freeman Cooper and Co., pp:82\u2013115."},{"key":"ref65","first-page":"6","article-title":"The million-year wait for macroevolutionary bursts","volume":"1","author":"JC Uyeda","year":"2011","journal-title":"Proc Nat Acd Sci, early edition"},{"issue":"1","key":"ref66","doi-asserted-by":"crossref","first-page":"41:55","DOI":"10.1111\/j.1475-4983.2006.00613.x","article-title":"Macroevolution and macroecology through deep time","volume":"50","author":"NJ Butterfield","year":"2007","journal-title":"Palaeontology"},{"key":"ref67","doi-asserted-by":"crossref","unstructured":"S. J. Gould (2002). 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