Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae

[1]  P. Woo,et al.  Complete Genome Sequence of the Veterinary Pathogen Staphylococcus pseudintermedius Strain HKU10-03, Isolated in a Case of Canine Pyoderma , 2011, Journal of bacteriology.

[2]  I. M. Gould VRSA-doomsday superbug or damp squib? , 2010, The Lancet. Infectious diseases.

[3]  F. Hildebrand,et al.  Evidence of Selection upon Genomic GC-Content in Bacteria , 2010, PLoS genetics.

[4]  S. Dragacci,et al.  How Should Staphylococcal Food Poisoning Outbreaks Be Characterized? , 2010, Toxins.

[5]  F. DeLeo,et al.  Mobile genetic elements of Staphylococcus aureus , 2010, Cellular and Molecular Life Sciences.

[6]  Mary Ann Robinson,et al.  Identification of a Novel Staphylococcus aureus Two-Component Leukotoxin Using Cell Surface Proteomics , 2010, PloS one.

[7]  Jeet Sukumaran,et al.  DendroPy: a Python library for phylogenetic computing , 2010, Bioinform..

[8]  Jason Hinds,et al.  Evolutionary Genomics of Staphylococcus aureus Reveals Insights into the Origin and Molecular Basis of Ruminant Host Adaptation , 2010, Genome biology and evolution.

[9]  G. Archer,et al.  Roles of CcrA and CcrB in Excision and Integration of Staphylococcal Cassette Chromosome mec, a Staphylococcus aureus Genomic Island , 2010, Journal of bacteriology.

[10]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[11]  A. Friedrich,et al.  Emergence of methicillin-resistant Staphylococcus aureus (MRSA) in different animal species. , 2010, International journal of medical microbiology : IJMM.

[12]  P. Woo,et al.  Complete Genome Sequence of Staphylococcus lugdunensis Strain HKU09-01 , 2010, Journal of bacteriology.

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

[14]  Erin Beck,et al.  The comprehensive microbial resource , 2000, Nucleic Acids Res..

[15]  A. Rambaut,et al.  Recent human-to-poultry host jump, adaptation, and pandemic spread of Staphylococcus aureus , 2009, Proceedings of the National Academy of Sciences.

[16]  Martin Wiedmann,et al.  Genome wide evolutionary analyses reveal serotype specific patterns of positive selection in selected Salmonella serotypes , 2009, BMC Evolutionary Biology.

[17]  Masahira Hattori,et al.  Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli , 2009, Proceedings of the National Academy of Sciences.

[18]  V. Nizet,et al.  Staphylococcus aureus Panton-Valentine Leukocidin Contributes to Inflammation and Muscle Tissue Injury , 2009, PloS one.

[19]  Tristan Lefébure,et al.  Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter. , 2009, Genome research.

[20]  C. Wolz,et al.  Diversity of Prophages in Dominant Staphylococcus aureus Clonal Lineages , 2009, Journal of bacteriology.

[21]  I. Uchiyama,et al.  Complete Genome Sequence of Macrococcus caseolyticus Strain JSCS5402, Reflecting the Ancestral Genome of the Human-Pathogenic Staphylococci , 2008, Journal of bacteriology.

[22]  Tetsuya Hayashi,et al.  Complete Genome Sequence and Comparative Genome Analysis of Enteropathogenic Escherichia coli O127:H6 Strain E2348/69 , 2008, Journal of bacteriology.

[23]  G. Węgrzyn,et al.  Staphylococcus aureus as an infectious agent: overview of biochemistry and molecular genetics of its pathogenicity. , 2009, Acta biochimica Polonica.

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

[25]  S. Schuster,et al.  Genome Analysis of the Meat Starter Culture Bacterium Staphylococcus carnosus TM300 , 2008, Applied and Environmental Microbiology.

[26]  M. Bischoff,et al.  CcpA Mediates the Catabolite Repression of tst in Staphylococcus aureus , 2008, Infection and Immunity.

[27]  D. Missiakas,et al.  EsaC substrate for the ESAT‐6 secretion pathway and its role in persistent infections of Staphylococcus aureus , 2008, Molecular microbiology.

[28]  O. Schneewind,et al.  Genome Sequence of Staphylococcus aureus Strain Newman and Comparative Analysis of Staphylococcal Genomes: Polymorphism and Evolution of Two Major Pathogenicity Islands , 2007, Journal of bacteriology.

[29]  Masaru Tomita,et al.  Computational Genome Analysis Using The G-language System , 2008 .

[30]  Martin Wiedmann,et al.  Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes , 2008, BMC Evolutionary Biology.

[31]  G. Weinstock,et al.  Subtle genetic changes enhance virulence of methicillin resistant and sensitive Staphylococcus aureus , 2007, BMC Microbiology.

[32]  James M. Musser,et al.  Molecular Correlates of Host Specialization in Staphylococcus aureus , 2007, PloS one.

[33]  H. Yuzawa,et al.  Mutated Response Regulator graR Is Responsible for Phenotypic Conversion of Staphylococcus aureus from Heterogeneous Vancomycin-Intermediate Resistance to Vancomycin-Intermediate Resistance , 2007, Antimicrobial Agents and Chemotherapy.

[34]  Adam Zemla,et al.  MvirDB—a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications , 2006, Nucleic Acids Res..

[35]  Vincent A. Fischetti,et al.  Gram-positive pathogens , 2006 .

[36]  M. Stanhope,et al.  Evolution of the core and pan-genome of Streptococcus: positive selection, recombination, and genome composition , 2007, Genome Biology.

[37]  A. Vankeerberghen,et al.  First Case of Staphylococcus pseudintermedius Infection in a Human , 2006, Journal of Clinical Microbiology.

[38]  Dennis R. Livesay,et al.  Probalign: multiple sequence alignment using partition function posterior probabilities , 2006, Bioinform..

[39]  Masaru Tomita,et al.  G-language System as a platform for large-scale analysis of high-throughput omics data , 2006 .

[40]  Jon R. Armstrong,et al.  Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[41]  G. Sensabaugh,et al.  Complete genome sequence of USA300, an epidemic clone of community-acquired meticillin-resistant Staphylococcus aureus , 2006, The Lancet.

[42]  A. Hanssen,et al.  SCCmec in staphylococci: genes on the move. , 2006, FEMS immunology and medical microbiology.

[43]  D. Kernodle Mechanisms of Resistance to β-Lactam Antibiotics , 2006 .

[44]  P. Bork,et al.  Environments shape the nucleotide composition of genomes , 2005, EMBO reports.

[45]  A. Ankai,et al.  Whole-Genome Sequencing of Staphylococcus haemolyticus Uncovers the Extreme Plasticity of Its Genome and the Evolution of Human-Colonizing Staphylococcal Species , 2005, Journal of bacteriology.

[46]  Naryttza N. Diaz,et al.  The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes , 2005, Nucleic acids research.

[47]  M. Hattori,et al.  Whole genome sequence of Staphylococcus saprophyticus reveals the pathogenesis of uncomplicated urinary tract infection. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[48]  S. Mobashery,et al.  β-Lactam resistance in Staphylococcus aureus: the adaptive resistance of a plastic genome , 2005, Cellular and Molecular Life Sciences.

[49]  R. Pantůček,et al.  Staphylococcus simiae sp. nov., isolated from South American squirrel monkeys. , 2005, International journal of systematic and evolutionary microbiology.

[50]  Peter Dawyndt,et al.  Staphylococcus pseudintermedius sp. nov., a coagulase-positive species from animals. , 2005, International journal of systematic and evolutionary microbiology.

[51]  Samuel V. Angiuoli,et al.  Insights on Evolution of Virulence and Resistance from the Complete Genome Analysis of an Early Methicillin-Resistant Staphylococcus aureus Strain and a Biofilm-Producing Methicillin-Resistant Staphylococcus epidermidis Strain , 2005, Journal of bacteriology.

[52]  P. Sharp,et al.  Variation in the strength of selected codon usage bias among bacteria , 2005, Nucleic acids research.

[53]  Jun Yu,et al.  VFDB: a reference database for bacterial virulence factors , 2004, Nucleic Acids Res..

[54]  E. Gorovits,et al.  SdrX, a Serine-Aspartate Repeat Protein Expressed by Staphylococcus capitis with Collagen VI Binding Activity , 2004, Infection and Immunity.

[55]  M. P. Cummings PHYLIP (Phylogeny Inference Package) , 2004 .

[56]  Xiao Xue Ma,et al.  Novel Type V Staphylococcal Cassette Chromosome mec Driven by a Novel Cassette Chromosome Recombinase, ccrC , 2004, Antimicrobial Agents and Chemotherapy.

[57]  B. Barrell,et al.  Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[58]  Joakim Bjerketorp,et al.  The von Willebrand factor-binding protein (vWbp) of Staphylococcus aureus is a coagulase. , 2004, FEMS microbiology letters.

[59]  Korbinian Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..

[60]  O. Gascuel,et al.  A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. , 2003, Systematic biology.

[61]  A. Danchin,et al.  Genome‐based analysis of virulence genes in a non‐biofilm‐forming Staphylococcus epidermidis strain (ATCC 12228) , 2003, Molecular microbiology.

[62]  Masaru Tomita,et al.  G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining , 2003, Bioinform..

[63]  Matthew R. Pocock,et al.  The Bioperl toolkit: Perl modules for the life sciences. , 2002, Genome research.

[64]  Hugo Naya,et al.  Aerobiosis Increases the Genomic Guanine Plus Cytosine Content (GC%) in Prokaryotes , 2002, Journal of Molecular Evolution.

[65]  Eduardo P C Rocha,et al.  Base composition bias might result from competition for metabolic resources. , 2002, Trends in genetics : TIG.

[66]  Y. Nagai,et al.  Genome and virulence determinants of high virulence community-acquired MRSA , 2002, The Lancet.

[67]  M. Saier,et al.  Overexpression of the Escherichia coli sugE Gene Confers Resistance to a Narrow Range of Quaternary Ammonium Compounds , 2002, Journal of bacteriology.

[68]  M. Kanehisa,et al.  Whole genome sequencing of meticillin-resistant Staphylococcus aureus , 2001, The Lancet.

[69]  Michael Y. Galperin,et al.  The COG database: new developments in phylogenetic classification of proteins from complete genomes , 2001, Nucleic Acids Res..

[70]  Michael Y. Galperin,et al.  Who's your neighbor? New computational approaches for functional genomics , 2000, Nature Biotechnology.

[71]  S. Dongen Graph clustering by flow simulation , 2000 .

[72]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[73]  A. Ljungh,et al.  Binding of von Willebrand factor by coagulase-negative staphylococci. , 2000, Journal of medical microbiology.

[74]  Michael Y. Galperin,et al.  The COG database: a tool for genome-scale analysis of protein functions and evolution , 2000, Nucleic Acids Res..

[75]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[76]  D. Gatherer,et al.  Nitrogen-fixing aerobic bacteria have higher genomic GC content than non-fixing species within the same genus. , 2004, Hereditas.

[77]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[78]  T. Bannerman,et al.  Update on clinical significance of coagulase-negative staphylococci , 1994, Clinical Microbiology Reviews.

[79]  J. Heesemann [Mechanisms of resistance to beta-lactam antibiotics]. , 1993, Infection.

[80]  D. Livermore Mechanisms of resistance to beta-lactam antibiotics. , 1991, Scandinavian journal of infectious diseases. Supplementum.