Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins

[1]  L. Holm,et al.  The Pfam protein families database , 2005, Nucleic Acids Res..

[2]  A. Vinogradov Systemic factors dominate mammal protein evolution , 2010, Proceedings of the Royal Society B: Biological Sciences.

[3]  Gautier Koscielny,et al.  Ensembl’s 10th year , 2009, Nucleic Acids Res..

[4]  Baris E. Suzek,et al.  The Universal Protein Resource (UniProt) in 2010 , 2009, Nucleic Acids Res..

[5]  María Martín,et al.  The Universal Protein Resource (UniProt) in 2010 , 2010 .

[6]  M. Gerstein,et al.  Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity , 2009, BMC Genomics.

[7]  T. Kirkwood,et al.  Metabolic evolution suggests an explanation for the weakness of antioxidant defences in beta-cells , 2009, Mechanisms of Ageing and Development.

[8]  Sébastien Moretti,et al.  Selectome: a database of positive selection , 2008, Nucleic Acids Res..

[9]  Alan F. Scott,et al.  McKusick's Online Mendelian Inheritance in Man (OMIM®) , 2008, Nucleic Acids Res..

[10]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[11]  A. Clark,et al.  Evolutionary constraint and adaptation in the metabolic network of Drosophila. , 2008, Molecular biology and evolution.

[12]  Diethard Tautz,et al.  An Ancient Evolutionary Origin of Genes Associated with Human Genetic Diseases , 2008, Molecular biology and evolution.

[13]  J. Thornton,et al.  Metabolic innovations towards the human lineage , 2008, BMC Evolutionary Biology.

[14]  Ziheng Yang PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[15]  Steven L McKnight,et al.  Restriction of DNA Replication to the Reductive Phase of the Metabolic Cycle Protects Genome Integrity , 2007, Science.

[16]  John M. Hancock,et al.  A kinetic core model of the glucose-stimulated insulin secretion network of pancreatic β cells , 2007, Mammalian Genome.

[17]  Ordering events of biochemical evolution. , 2007, Biochimie.

[18]  Eugene V Koonin,et al.  Origins and impact of constraints in evolution of gene families. , 2006, Genome research.

[19]  Dirk Steinke,et al.  Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates , 2006, BMC Biology.

[20]  R. Mueller Evolutionary rates, divergence dates, and the performance of mitochondrial genes in Bayesian phylogenetic analysis. , 2006, Systematic biology.

[21]  A. Kondrashov,et al.  Role of selection in fixation of gene duplications. , 2006, Journal of theoretical biology.

[22]  T. Pieler,et al.  Forgotten and novel aspects in pancreas development , 2006, Biology of the cell.

[23]  Mark R. Brown,et al.  Signaling and function of insulin-like peptides in insects. , 2006, Annual review of entomology.

[24]  D. Graur,et al.  The "inverse relationship between evolutionary rate and age of mammalian genes" is an artifact of increased genetic distance with rate of evolution and time of divergence. , 2006, Molecular biology and evolution.

[25]  John M. Hancock,et al.  Gene factories, microfunctionalization and the evolution of gene families. , 2005, Trends in genetics : TIG.

[26]  John M. Hancock,et al.  CoGenT++: an extensive and extensible data environment for computational genomics , 2005, Bioinform..

[27]  G. Pesole,et al.  Evolution of nuclearly encoded mitochondrial genes in Metazoa. , 2005, Gene.

[28]  M. Albà,et al.  Inverse relationship between evolutionary rate and age of mammalian genes. , 2005, Molecular biology and evolution.

[29]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2004, Nucleic Acids Res..

[30]  G. Lecointre,et al.  Integrating the universal metabolism into a phylogenetic analysis. , 2004, Molecular biology and evolution.

[31]  Eugene V Koonin,et al.  Duplicated genes evolve slower than singletons despite the initial rate increase , 2004, BMC Evolutionary Biology.

[32]  F. Ashcroft,et al.  Type 2 diabetes mellitus: not quite exciting enough? , 2004, Human molecular genetics.

[33]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[34]  Anton J. Enright,et al.  COmplete GENome Tracking (COGENT): A Flexible Data Environment for Computational Genomics , 2003, Bioinform..

[35]  Sophia Tsoka,et al.  Beyond 100 genomes , 2003, Genome Biology.

[36]  Sophia Tsoka,et al.  The phylogenetic extent of metabolic enzymes and pathways. , 2003, Genome research.

[37]  R. Nusse,et al.  Ablation of Insulin-Producing Neurons in Flies: Growth and Diabetic Phenotypes , 2002, Science.

[38]  R. Garofalo Genetic analysis of insulin signaling in Drosophila , 2002, Trends in Endocrinology & Metabolism.

[39]  E. Koonin,et al.  Selection in the evolution of gene duplications , 2002, Genome Biology.

[40]  A. Force,et al.  The probability of preservation of a newly arisen gene duplicate. , 2001, Genetics.

[41]  M. Lynch,et al.  The evolutionary fate and consequences of duplicate genes. , 2000, Science.

[42]  M. Hüttemann,et al.  Mitochondrial energy metabolism is regulated via nuclear-coded subunits of cytochrome c oxidase. , 2000, Free radical biology & medicine.

[43]  A. Force,et al.  The probability of duplicate gene preservation by subfunctionalization. , 2000, Genetics.

[44]  P. Bork,et al.  Variation and evolution of the citric-acid cycle: a genomic perspective. , 1999, Trends in microbiology.

[45]  D. Eisenberg,et al.  Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[46]  M. Boguski,et al.  Comparative analysis of 1196 orthologous mouse and human full-length mRNA and protein sequences. , 1996, Genome research.

[47]  S Henikoff,et al.  Performance evaluation of amino acid substitution matrices , 1993, Proteins.

[48]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[49]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.