{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T02:29:15Z","timestamp":1767925755092,"version":"3.49.0"},"reference-count":66,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2015,3,4]],"date-time":"2015-03-04T00:00:00Z","timestamp":1425427200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004088","type":"journal-article","created":{"date-parts":[[2015,3,4]],"date-time":"2015-03-04T19:00:41Z","timestamp":1425495641000},"page":"e1004088","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":29,"title":["Mining Host-Pathogen Protein Interactions to Characterize Burkholderia mallei Infectivity Mechanisms"],"prefix":"10.1371","volume":"11","author":[{"given":"Vesna","family":"Memi\u0161evi\u0107","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nela","family":"Zavaljevski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Seesandra V.","family":"Rajagopala","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Keehwan","family":"Kwon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rembert","family":"Pieper","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"DeShazer","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jaques","family":"Reifman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anders","family":"Wallqvist","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2015,3,4]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1586\/eri.10.4","article-title":"Present and future therapeutic strategies for melioidosis and glanders","volume":"8","author":"DM Estes","year":"2010","journal-title":"Expert Rev Anti Infect Ther"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"170","DOI":"10.3389\/fmicb.2011.00170","article-title":"Strategies for intracellular survival of <italic>Burkholderia pseudomallei<\/italic>","volume":"2","author":"EM Allwood","year":"2011","journal-title":"Front Microbiol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1146\/annurev.micro.112408.134030","article-title":"Molecular insights into <italic>Burkholderia pseudomallei<\/italic> and <italic>Burkholderia mallei<\/italic> pathogenesis","volume":"64","author":"EE Galyov","year":"2010","journal-title":"Annu Rev Microbiol"},{"key":"ref4","first-page":"151","article-title":"Autotransporters and their role in the virulence of <italic>Burkholderia pseudomallei<\/italic> and <italic>Burkholderia mallei<\/italic>","volume":"2","author":"NR Lazar Adler","year":"2011","journal-title":"Front Microbiol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1093\/gbe\/evq003","article-title":"Continuing evolution of <italic>Burkholderia mallei<\/italic> through genome reduction and large-scale rearrangements","volume":"2","author":"L Losada","year":"2010","journal-title":"Genome Biol Evol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"14246","DOI":"10.1073\/pnas.0403306101","article-title":"Structural flexibility in the <italic>Burkholderia mallei<\/italic> genome","volume":"101","author":"WC Nierman","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1466","DOI":"10.1111\/j.1365-2958.2007.05734.x","article-title":"Type VI secretion is a major virulence determinant in <italic>Burkholderia mallei<\/italic>","volume":"64","author":"MA Schell","year":"2007","journal-title":"Mol Microbiol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"3036","DOI":"10.1074\/mcp.M113.029041","article-title":"Novel <italic>Burkholderia mallei<\/italic> virulence factors linked to specific host-pathogen protein interactions","volume":"12","author":"V Memi\u0161evi\u0107","year":"2013","journal-title":"Mol Cell Proteomics"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"46","DOI":"10.3389\/fmicb.2012.00046","article-title":"Infection strategies of bacterial and viral pathogens through pathogen-human protein-protein interactions","volume":"3","author":"S Durmus Tekir","year":"2012","journal-title":"Front Microbiol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"e32","DOI":"10.1371\/journal.ppat.0040032","article-title":"The landscape of human proteins interacting with viruses and other pathogens","volume":"4","author":"MD Dyer","year":"2008","journal-title":"PLOS Pathog"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"e12089","DOI":"10.1371\/journal.pone.0012089","article-title":"The human-bacterial pathogen protein interaction networks of <italic>Bacillus anthracis<\/italic>, <italic>Francisella tularensis<\/italic>, and <italic>Yersinia pestis<\/italic>","volume":"5","author":"MD Dyer","year":"2010","journal-title":"PLOS ONE"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1002\/prca.201100083","article-title":"The current <italic>Salmonella<\/italic>-host interactome","volume":"6","author":"S Schleker","year":"2012","journal-title":"Proteomics Clin Appl"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"4413","DOI":"10.1128\/IAI.05622-11","article-title":"Insight into bacterial virulence mechanisms against host immune response via the <italic>Yersinia pestis<\/italic>-human protein-protein interaction network","volume":"79","author":"H Yang","year":"2011","journal-title":"Infect Immun"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"508","DOI":"10.1016\/j.ymeth.2012.06.011","article-title":"Computational analysis of interactomes: Current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space","volume":"57","author":"R Arnold","year":"2012","journal-title":"Methods"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"i480","DOI":"10.1093\/bioinformatics\/bts376","article-title":"Graphlet-based edge clustering reveals pathogen-interacting proteins","volume":"28","author":"RW Solava","year":"2012","journal-title":"Bioinformatics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"i217","DOI":"10.1093\/bioinformatics\/btt245","article-title":"Multitask learning for host-pathogen protein interactions","volume":"29","author":"M Kshirsagar","year":"2013","journal-title":"Bioinformatics"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"e1002823","DOI":"10.1371\/journal.ppat.1002823","article-title":"Five mechanisms of manipulation by bacterial effectors: A ubiquitous theme","volume":"8","author":"DM Anderson","year":"2012","journal-title":"PLOS Pathog"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1038\/nature06247","article-title":"Manipulation of host-cell pathways by bacterial pathogens","volume":"449","author":"AP Bhavsar","year":"2007","journal-title":"Nature"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1128\/IAI.00985-09","article-title":"<italic>Burkholderia mallei<\/italic> cluster 1 type VI secretion mutants exhibit growth and actin polymerization defects in RAW 264.7 murine macrophages","volume":"78","author":"MN Burtnick","year":"2010","journal-title":"Infect Immun"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"7857","DOI":"10.1128\/JB.187.22.7857-7862.2005","article-title":"Actin-binding proteins from <italic>Burkholderia mallei<\/italic> and <italic>Burkholderia thailandensis<\/italic> can functionally compensate for the actin-based motility defect of a <italic>Burkholderia pseudomallei bimA<\/italic> mutant","volume":"187","author":"JM Stevens","year":"2005","journal-title":"J Bacteriol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"1150","DOI":"10.1128\/IAI.72.2.1150-1154.2004","article-title":"Type III secretion: A virulence factor delivery system essential for the pathogenicity of <italic>Burkholderia mallei<\/italic>","volume":"72","author":"RL Ulrich","year":"2004","journal-title":"Infect Immun"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1186\/1471-2105-15-244","article-title":"DBSecSys: A database of <italic>Burkholderia mallei<\/italic> secretion systems","volume":"15","author":"V Memi\u0161evi\u0107","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: Tool for the unification of biology","volume":"25","author":"M Ashburner","year":"2000","journal-title":"Nat Genet"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1636","DOI":"10.1128\/IAI.01339-08","article-title":"<italic>Burkholderia mallei tssM<\/italic> encodes a putative deubiquitinase that is secreted and expressed inside infected RAW 264.7 murine macrophages","volume":"77","author":"J Shanks","year":"2009","journal-title":"Infect Immun"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/1471-2105-13-79","article-title":"Inferring high-confidence human protein-protein interactions","volume":"13","author":"X Yu","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1042\/bj3450297","article-title":"14\u20133\u20133 isotypes facilitate coupling of protein kinase C-zeta to Raf-1: Negative regulation by 14\u20133\u20133 phosphorylation","volume":"2","author":"PC Van Der Hoeven","year":"2000","journal-title":"Biochem J 345 Pt"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1039\/b900658n","article-title":"Moonlighting proteins\u2014an update","volume":"5","author":"CJ Jeffery","year":"2009","journal-title":"Mol Biosyst"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1002\/iub.491","article-title":"Moonlighting proteins in neurological disorders","volume":"63","author":"J Ovadi","year":"2011","journal-title":"IUBMB Life"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"3476","DOI":"10.1128\/IAI.00179-11","article-title":"Bacterial virulence in the moonlight: Multitasking bacterial moonlighting proteins are virulence determinants in infectious disease","volume":"79","author":"B Henderson","year":"2011","journal-title":"Infect Immun"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"911","DOI":"10.1086\/430799","article-title":"Single-gene disorders: What role could moonlighting enzymes play?","volume":"76","author":"G Sriram","year":"2005","journal-title":"Am J Hum Genet"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/S0163-7258(02)00326-1","article-title":"Regulators of G-protein signalling: Multifunctional proteins with impact on signalling in the cardiovascular system","volume":"97","author":"T Wieland","year":"2003","journal-title":"Pharmacol Ther"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1093\/nar\/27.1.29","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"27","author":"H Ogata","year":"1999","journal-title":"Nucleic Acids Res"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.devcel.2005.06.002","article-title":"Bacteria-host-cell interactions at the plasma membrane: Stories on actin cytoskeleton subversion","volume":"9","author":"K Rottner","year":"2005","journal-title":"Dev Cell"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"M111.012500","DOI":"10.1074\/mcp.M111.012500","article-title":"Categorizing biases in high-confidence high-throughput protein-protein interaction data sets","volume":"10","author":"X Yu","year":"2011","journal-title":"Mol Cell Proteomics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"3525","DOI":"10.1128\/JB.188.10.3525-3534.2006","article-title":"Characterization of the <italic>Yersinia enterocolitica<\/italic> type III secretion ATPase YscN and its regulator, YscL","volume":"188","author":"B Blaylock","year":"2006","journal-title":"J Bacteriol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"4971","DOI":"10.1128\/JB.184.18.4971-4980.2002","article-title":"SpiC is required for translocation of <italic>Salmonella pathogenicity<\/italic> island 2 effectors and secretion of translocon proteins SseB and SseC","volume":"184","author":"JA Freeman","year":"2002","journal-title":"J Bacteriol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"1561","DOI":"10.1128\/jb.176.6.1561-1569.1994","article-title":"YscN, the putative energizer of the <italic>Yersinia<\/italic> Yop secretion machinery","volume":"176","author":"S Woestyn","year":"1994","journal-title":"J Bacteriol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1111\/j.1365-2958.2004.04297.x","article-title":"SsaM and SpiC interact and regulate secretion of <italic>Salmonella<\/italic> pathogenicity island 2 type III secretion system effectors and translocators","volume":"54","author":"XJ Yu","year":"2004","journal-title":"Mol Microbiol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"D545","DOI":"10.1093\/nar\/gks1066","article-title":"Genenames.org: The HGNC resources in 2013","volume":"41","author":"KA Gray","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"D13","DOI":"10.1093\/nar\/gkr1184","article-title":"Database resources of the National Center for Biotechnology Information","volume":"40","author":"EW Sayers","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref41","first-page":"1695","article-title":"The igraph software package for complex network research","author":"G Csardi","year":"2006","journal-title":"InterJournal Complex Systems"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1080\/01621459.1951.10500769","article-title":"The Kolmogorov-Smirnov test for goodness of fit","volume":"46","author":"FJ Massey","year":"1951","journal-title":"J Am Stat Assoc"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"3439","DOI":"10.1093\/bioinformatics\/bti525","article-title":"BioMart and Bioconductor: A powerful link between biological databases and microarray data analysis","volume":"21","author":"S Durinck","year":"2005","journal-title":"Bioinformatics"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.1093\/bioinformatics\/btp167","article-title":"KEGGgraph: A graph approach to KEGG PATHWAY in R and bioconductor","volume":"25","author":"JD Zhang","year":"2009","journal-title":"Bioinformatics"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: A practical and powerful approach to multiple testing","volume":"57","author":"Y Benjamini","year":"1995","journal-title":"J R Statist Soc"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"2619","DOI":"10.1093\/bioinformatics\/btu358","article-title":"DualAligner: A dual alignment-based strategy to align protein interaction networks","volume":"30","author":"BS Seah","year":"2014","journal-title":"Bioinformatics"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1093\/bioinformatics\/btt715","article-title":"NetCoffee: A fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks","volume":"30","author":"J Hu","year":"2014","journal-title":"Bioinformatics"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1093\/bioinformatics\/btt713","article-title":"BEAMS: Backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks","volume":"30","author":"F Alkan","year":"2014","journal-title":"Bioinformatics"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1654","DOI":"10.1093\/bioinformatics\/btt202","article-title":"NETAL: A new graph-based method for global alignment of protein-protein interaction networks","volume":"29","author":"B Neyshabur","year":"2013","journal-title":"Bioinformatics"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1093\/bioinformatics\/btt071","article-title":"SPINAL: Scalable protein interaction network alignment","volume":"29","author":"AE Aladag","year":"2013","journal-title":"Bioinformatics"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.1098\/rsif.2010.0063","article-title":"Topological network alignment uncovers biological function and phylogeny","volume":"7","author":"O Kuchaiev","year":"2010","journal-title":"J R Soc Interface"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"1390","DOI":"10.1093\/bioinformatics\/btr127","article-title":"Integrative network alignment reveals large regions of global network similarity in yeast and human","volume":"27","author":"O Kuchaiev","year":"2011","journal-title":"Bioinformatics"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1039\/c2ib00140c","article-title":"C-GRAAL: Common-neighbors-based global GRAph ALignment of biological networks","volume":"4","author":"V Memi\u0161evi\u0107","year":"2012","journal-title":"Integr Biol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"3105","DOI":"10.1093\/bioinformatics\/bts592","article-title":"Global network alignment using multiscale spectral signatures","volume":"28","author":"R Patro","year":"2012","journal-title":"Bioinformatics"},{"key":"ref55","first-page":"67","article-title":"Identifying evolutionarily conserved protein interaction modules using GraphHopper","author":"C Rivera","year":"2009"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"1974","DOI":"10.1073\/pnas.0409522102","article-title":"Conserved patterns of protein interaction in multiple species","volume":"102","author":"R Sharan","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"257","DOI":"10.4137\/CIN.S680","article-title":"Uncovering biological network function via graphlet degree signatures","volume":"6","author":"T Milenkovi\u0107","year":"2008","journal-title":"Cancer Inform"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"SF Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"ref59","first-page":"241","article-title":"Distribution de la flore alpine dans le bassin des Dranses et dans quelques r\u00e9gions voisines","volume":"37","author":"P Jaccard","year":"1901","journal-title":"Bulletin de la Soci\u00e9t\u00e9 Vaudoise des Sciences Naturelles"},{"key":"ref60","doi-asserted-by":"crossref","unstructured":"Magrane M, Consortium U (2011) UniProt Knowledgebase: A hub of integrated protein data. Database 2011: bar009.","DOI":"10.1093\/database\/bar009"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","article-title":"Cytoscape: A software environment for integrated models of biomolecular interaction networks","volume":"13","author":"P Shannon","year":"2003","journal-title":"Genome Res"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1128\/IAI.73.2.1260-1264.2005","article-title":"A type IV pilin, PilA, contributes to adherence of <italic>Burkholderia pseudomallei<\/italic> and virulence <italic>in vivo<\/italic>","volume":"73","author":"AE Essex-Lopresti","year":"2005","journal-title":"Infect Immun"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"554","DOI":"10.1099\/jmm.0.007724-0","article-title":"<italic>Burkholderia mallei<\/italic> cellular interactions in a respiratory cell model","volume":"58","author":"GC Whitlock","year":"2009","journal-title":"J Med Microbiol"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"2669","DOI":"10.1099\/mic.0.27146-0","article-title":"Attenuated virulence and protective efficacy of a <italic>Burkholderia pseudomallei bsa<\/italic> type III secretion mutant in murine models of melioidosis","volume":"150","author":"MP Stevens","year":"2004","journal-title":"Microbiology"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"6556","DOI":"10.1128\/JB.187.18.6556-6560.2005","article-title":"Multinucleated giant cell formation and apoptosis in infected host cells is mediated by <italic>Burkholderia pseudomallei<\/italic> type III secretion protein BipB","volume":"187","author":"S Suparak","year":"2005","journal-title":"J Bacteriol"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"3576","DOI":"10.1128\/IAI.01262-05","article-title":"Identification of <italic>Burkholderia pseudomallei<\/italic> genes required for the intracellular life cycle and <italic>in vivo<\/italic> virulence","volume":"74","author":"S Pilatz","year":"2006","journal-title":"Infect Immun"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004088","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,7]],"date-time":"2024-06-07T16:30:49Z","timestamp":1717777849000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004088"}},"subtitle":[],"editor":[{"given":"Alice Carolyn","family":"McHardy","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2015,3,4]]},"references-count":66,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2015,3,4]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004088","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,3,4]]}}}