Network analysis of S. aureus response to ramoplanin reveals modules for virulence factors and resistance mechanisms and characteristic novel genes.

[1]  D. Raoult,et al.  A Toxin-Antitoxin Module of Salmonella Promotes Virulence in Mice , 2013, PLoS pathogens.

[2]  Yan Zhang,et al.  PATRIC, the bacterial bioinformatics database and analysis resource , 2013, Nucleic Acids Res..

[3]  Jing-quan Li,et al.  Artemisinin rewires the protein interaction network in cancer cells: network analysis, pathway identification, and target prediction. , 2013, Molecular bioSystems.

[4]  W. Chan,et al.  Attenuating Staphylococcus aureus Virulence Gene Regulation: A Medicinal Chemistry Perspective , 2013, Journal of medicinal chemistry.

[5]  Damian Szklarczyk,et al.  STRING v9.1: protein-protein interaction networks, with increased coverage and integration , 2012, Nucleic Acids Res..

[6]  Narmada Thanki,et al.  CDD: conserved domains and protein three-dimensional structure , 2012, Nucleic Acids Res..

[7]  Evgeny M. Zdobnov,et al.  OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs , 2012, Nucleic Acids Res..

[8]  A. Delprato Topological and Functional Properties of the Small GTPases Protein Interaction Network , 2012, PloS one.

[9]  P. François,et al.  Global Analysis of the Staphylococcus aureus Response to Mupirocin , 2011, Antimicrobial Agents and Chemotherapy.

[10]  K. Burnside,et al.  Aspects of eukaryotic-like signaling in Gram-positive cocci: a focus on virulence. , 2011, Future microbiology.

[11]  Geoffrey J. Barton,et al.  Global network analysis of drug tolerance, mode of action and virulence in methicillin-resistant S. aureus , 2011, BMC Systems Biology.

[12]  D. Missiakas,et al.  EsaD, a Secretion Factor for the Ess Pathway in Staphylococcus aureus , 2011, Journal of bacteriology.

[13]  Narmada Thanki,et al.  CDD: a Conserved Domain Database for the functional annotation of proteins , 2010, Nucleic Acids Res..

[14]  Dennis B. Troup,et al.  NCBI GEO: archive for functional genomics data sets—10 years on , 2010, Nucleic Acids Res..

[15]  Damian Szklarczyk,et al.  The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored , 2010, Nucleic Acids Res..

[16]  S. Welkos,et al.  Role of Purine Biosynthesis in Bacillus anthracis Pathogenesis and Virulence , 2010, Infection and Immunity.

[17]  A. Greenough,et al.  Generation of ramoplanin-resistant Staphylococcus aureus. , 2010, FEMS microbiology letters.

[18]  Chuan He,et al.  Golden Pigment Production and Virulence Gene Expression Are Affected by Metabolisms in Staphylococcus aureus , 2010, Journal of bacteriology.

[19]  Susumu Goto,et al.  KEGG for representation and analysis of molecular networks involving diseases and drugs , 2009, Nucleic Acids Res..

[20]  D. Missiakas,et al.  Staphylococcus aureus synthesizes adenosine to escape host immune responses , 2009, The Journal of experimental medicine.

[21]  C. Laudanna,et al.  Analyzing biological network parameters with CentiScaPe , 2009, Bioinform..

[22]  Henry F. Chambers,et al.  Waves of resistance: Staphylococcus aureus in the antibiotic era , 2009, Nature Reviews Microbiology.

[23]  Xuanzhe Liu,et al.  Role of phosphoglucosamine mutase on virulence properties of Streptococcus mutans. , 2009, Oral microbiology and immunology.

[24]  B. Sharma-Kuinkel,et al.  The Staphylococcus aureus LytSR Two-Component Regulatory System Affects Biofilm Formation , 2009, Journal of bacteriology.

[25]  M. Inouye,et al.  Staphylococcus aureus MazF Specifically Cleaves a Pentad Sequence, UACAU, Which Is Unusually Abundant in the mRNA for Pathogenic Adhesive Factor SraP , 2009, Journal of bacteriology.

[26]  David Warde-Farley,et al.  Dynamic modularity in protein interaction networks predicts breast cancer outcome , 2009, Nature Biotechnology.

[27]  Tatiana A. Tatusova,et al.  The National Center for Biotechnology Information's Protein Clusters Database , 2008, Nucleic Acids Res..

[28]  Fidel Ramírez,et al.  Computing topological parameters of biological networks , 2008, Bioinform..

[29]  A. Sonenshein,et al.  Staphylococcus aureus CodY Negatively Regulates Virulence Gene Expression , 2007, Journal of bacteriology.

[30]  V. Nagarajan,et al.  SAMMD: Staphylococcus aureus Microarray Meta-Database , 2007, BMC Genomics.

[31]  S. Fuchs,et al.  Anaerobic Gene Expression in Staphylococcus aureus , 2007, Journal of bacteriology.

[32]  D. Boger,et al.  The mechanism of action of ramoplanin and enduracidin. , 2006, Molecular bioSystems.

[33]  K. Kurokawa,et al.  Novel DNA binding protein SarZ contributes to virulence in Staphylococcus aureus , 2006, Molecular microbiology.

[34]  L. Martínez-Martínez,et al.  Evaluation of differential gene expression in susceptible and resistant clinical isolates of Klebsiella pneumoniae by DNA microarray analysis. , 2006, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[35]  M. S. Barbagelata,et al.  Attenuation and Persistence of and Ability To Induce Protective Immunity to a Staphylococcus aureus aroA Mutant in Mice , 2006, Infection and Immunity.

[36]  Anne Kümmel,et al.  In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network. , 2005, Biotechnology and bioengineering.

[37]  M. Marsili,et al.  Scale-free networks with an exponent less than two. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[38]  I. Boneca,et al.  The role of peptidoglycan in pathogenesis. , 2005, Current opinion in microbiology.

[39]  D. Missiakas,et al.  EsxA and EsxB are secreted by an ESAT-6-like system that is required for the pathogenesis of Staphylococcus aureus infections. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[40]  Christoph Freiberg,et al.  The impact of transcriptome and proteome analyses on antibiotic drug discovery. , 2004, Current opinion in microbiology.

[41]  H. Monteil,et al.  Regulation of virulence determinants in Staphylococcus aureus: complexity and applications. , 2004, FEMS microbiology reviews.

[42]  A. Barabasi,et al.  Functional and topological characterization of protein interaction networks , 2004, Proteomics.

[43]  Z. Oltvai,et al.  Network biology: understanding the cell's functional organization , 2004, Nature Reviews Genetics.

[44]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[45]  Young Ran Kim,et al.  Characterization and Pathogenic Significance of Vibrio vulnificus Antigens Preferentially Expressed in Septicemic Patients , 2003, Infection and Immunity.

[46]  V. Singh,et al.  Genome-wide transcriptional profiling of the response of Staphylococcus aureus to cell-wall-active antibiotics reveals a cell-wall-stress stimulon. , 2003, Microbiology.

[47]  H. Mori,et al.  Two‐component system VraSR positively modulates the regulation of cell‐wall biosynthesis pathway in Staphylococcus aureus , 2003, Molecular microbiology.

[48]  E. Mongodin,et al.  Microarray Transcription Analysis of Clinical Staphylococcus aureus Isolates Resistant to Vancomycin , 2003, Journal of bacteriology.

[49]  R. Novick Autoinduction and signal transduction in the regulation of staphylococcal virulence , 2003, Molecular microbiology.

[50]  Fan Chung Graham,et al.  Duplication Models for Biological Networks , 2002, J. Comput. Biol..

[51]  R. Zagursky,et al.  Transcription Profiling-Based Identification ofStaphylococcus aureus Genes Regulated by the agrand/or sarA Loci , 2001, Journal of bacteriology.

[52]  Christine Brun,et al.  In silico prediction of protein-protein interactions in human macrophages , 2001, BMC Research Notes.

[53]  A. Krogh,et al.  Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. , 2001, Journal of molecular biology.

[54]  S. Levy,et al.  Differential Expression of over 60 Chromosomal Genes in Escherichia coli by Constitutive Expression of MarA , 2000, Journal of bacteriology.

[55]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[56]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[57]  W. Witte,et al.  Antibiotic resistance in gram-positive bacteria: epidemiological aspects. , 1999, The Journal of antimicrobial chemotherapy.

[58]  D. Simon,et al.  Large-Scale Identification of Virulence Genes fromStreptococcus pneumoniae , 1998, Infection and Immunity.

[59]  I. Kullik,et al.  Sequence of the putative alanine racemase operon in Staphylococcus aureus: insertional interruption of this operon reduces D-alanine substitution of lipoteichoic acid and autolysis. , 1998, Gene.

[60]  Duncan J. Watts,et al.  Collective dynamics of ‘small-world’ networks , 1998, Nature.

[61]  C. Hackbarth,et al.  blaI and blaR1 regulate beta-lactamase and PBP 2a production in methicillin-resistant Staphylococcus aureus , 1993, Antimicrobial Agents and Chemotherapy.

[62]  B. Stocker,et al.  Effect of different purine auxotrophic mutations on mouse-virulence of a Vi-positive strain of Salmonella dublin and of two strains of Salmonella typhimurium. , 1987, Microbial pathogenesis.

[63]  F. Parenti,et al.  A-16686, a new antibiotic from Actinoplanes. I. Fermentation, isolation and preliminary physico-chemical characteristics. , 1984, The Journal of antibiotics.

[64]  R. Brubaker Interconversion of Purine Mononucleotides in Pasteurella pestis , 1970, Infection and immunity.

[65]  S. Horvath,et al.  A General Framework for Weighted Gene Co-Expression Network Analysis , 2005, Statistical applications in genetics and molecular biology.

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

[67]  Hiroyuki Aburatani,et al.  Topological and functional discovery in a gene coexpression meta-network of gastric cancer. , 2006, Cancer research.

[68]  Gary D Bader,et al.  An automated method for finding molecular complexes in large protein interaction networks , 2003, BMC Bioinformatics.

[69]  R. Kruger,et al.  Chemistry and biology of the ramoplanin family of peptide antibiotics. , 2002, Biopolymers.

[70]  E. Brunskill,et al.  Identification and Molecular Characterization of a Putative Regulatory Locus That Affects Autolysis in Staphylococcus aureus , 2022 .

[71]  BIOINFORMATICS ORIGINAL PAPER , 2022 .