{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,30]],"date-time":"2025-10-30T22:37:32Z","timestamp":1761863852383},"reference-count":58,"publisher":"Elsevier","isbn-type":[{"type":"print","value":"9780128114322"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019]]},"DOI":"10.1016\/b978-0-12-809633-8.20170-2","type":"book-chapter","created":{"date-parts":[[2018,5,24]],"date-time":"2018-05-24T17:58:43Z","timestamp":1527184723000},"page":"932-937","source":"Crossref","is-referenced-by-count":2,"title":["Network-Based Analysis of Host-Pathogen Interactions"],"prefix":"10.1016","author":[{"given":"Lokesh P.","family":"Tripathi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yi-An","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kenji","family":"Mizuguchi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eiji","family":"Morita","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/B978-0-12-809633-8.20170-2_bib1","doi-asserted-by":"crossref","first-page":"baw103","DOI":"10.1093\/database\/baw103","article-title":"HPIDB 2.0: A curated database for host\u2013pathogen interactions","volume":"2016","author":"Ammari","year":"2016","journal-title":"Database"},{"issue":"7164","key":"10.1016\/B978-0-12-809633-8.20170-2_bib2","doi-asserted-by":"crossref","first-page":"827","DOI":"10.1038\/nature06247","article-title":"Manipulation of host-cell pathways by bacterial pathogens","volume":"449","author":"Bhavsar","year":"2007","journal-title":"Nature"},{"key":"10.1016\/B978-0-12-809633-8.20170-2_bib3","doi-asserted-by":"crossref","first-page":"1557","DOI":"10.3389\/fmicb.2017.01557","article-title":"Protein-protein interactions in virus-host systems","volume":"8","author":"Brito","year":"2017","journal-title":"Front. Microbiol."},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20170-2_bib4","first-page":"135","article-title":"Automation of yeast two-hybrid screening","volume":"1","author":"Buckholz","year":"1999","journal-title":"J. Mol. Microbiol. Biotechnol."},{"issue":"12","key":"10.1016\/B978-0-12-809633-8.20170-2_bib5","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1038\/nmeth968","article-title":"An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells","volume":"3","author":"Burckstummer","year":"2006","journal-title":"Nat. Methods"},{"issue":"Database issue","key":"10.1016\/B978-0-12-809633-8.20170-2_bib6","doi-asserted-by":"crossref","first-page":"D588","DOI":"10.1093\/nar\/gku830","article-title":"VirusMentha: A new resource for virus-host protein interactions","volume":"43","author":"Calderone","year":"2015","journal-title":"Nucleic Acids Res."},{"issue":"18","key":"10.1016\/B978-0-12-809633-8.20170-2_bib7","doi-asserted-by":"crossref","first-page":"7606","DOI":"10.1073\/pnas.0702332104","article-title":"Epstein-Barr virus and virus human protein interaction maps","volume":"104","author":"Calderwood","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/B978-0-12-809633-8.20170-2_bib8","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1038\/msb.2008.66","article-title":"Hepatitis C virus infection protein network","volume":"4","author":"de Chassey","year":"2008","journal-title":"Mol. Syst. Biol."},{"issue":"7","key":"10.1016\/B978-0-12-809633-8.20170-2_bib9","doi-asserted-by":"crossref","first-page":"e1003440","DOI":"10.1371\/journal.ppat.1003440","article-title":"The interactomes of influenza virus NS1 and NS2 proteins identify new host factors and provide insights for ADAR1 playing a supportive role in virus replication","volume":"9","author":"de Chassey","year":"2013","journal-title":"PLOS Pathog."},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20170-2_bib10","doi-asserted-by":"crossref","first-page":"938","DOI":"10.1038\/embor.2013.130","article-title":"Structure homology and interaction redundancy for discovering virus-host protein interactions","volume":"14","author":"de Chassey","year":"2013","journal-title":"EMBO Rep."},{"issue":"3","key":"10.1016\/B978-0-12-809633-8.20170-2_bib11","doi-asserted-by":"crossref","first-page":"e17844","DOI":"10.1371\/journal.pone.0017844","article-title":"TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery","volume":"6","author":"Chen","year":"2011","journal-title":"PLOS ONE"},{"key":"10.1016\/B978-0-12-809633-8.20170-2_bib12","doi-asserted-by":"crossref","DOI":"10.1093\/database\/baw009","article-title":"An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework","volume":"2016","author":"Chen","year":"2016","journal-title":"Database"},{"key":"10.1016\/B978-0-12-809633-8.20170-2_bib13","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/1752-0509-8-24","article-title":"Computational prediction of the human-microbial oral interactome","volume":"8","author":"Coelho","year":"2014","journal-title":"BMC Syst. Biol."},{"issue":"Suppl 7","key":"10.1016\/B978-0-12-809633-8.20170-2_bib14","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1186\/1471-2105-13-S7-S5","article-title":"Prediction of protein-protein interactions between viruses and human by an SVM model","volume":"13","author":"Cui","year":"2012","journal-title":"BMC Bioinform."},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20170-2_bib15","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1002\/hep.25649","article-title":"Proteome and computational analyses reveal new insights into the mechanisms of hepatitis C virus-mediated liver disease posttransplantation","volume":"56","author":"Diamond","year":"2012","journal-title":"Hepatology"},{"issue":"12","key":"10.1016\/B978-0-12-809633-8.20170-2_bib16","doi-asserted-by":"crossref","first-page":"3199","DOI":"10.1039\/c3mb70343f","article-title":"Identification and comparative analysis of hepatitis C virus-host cell protein interactions","volume":"9","author":"Dolan","year":"2013","journal-title":"Mol. Biosyst."},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20170-2_bib17","doi-asserted-by":"crossref","first-page":"1576","DOI":"10.1002\/pmic.201100523","article-title":"Affinity-purification coupled to mass spectrometry: Basic principles and strategies","volume":"12","author":"Dunham","year":"2012","journal-title":"Proteomics"},{"key":"10.1016\/B978-0-12-809633-8.20170-2_bib18","first-page":"235","article-title":"A review on computational systems biology of pathogen-host interactions","volume":"6","author":"Durmus","year":"2015","journal-title":"Front. Microbiol."},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20170-2_bib19","doi-asserted-by":"crossref","first-page":"1357","DOI":"10.1093\/bioinformatics\/btt137","article-title":"PHISTO: Pathogen-host interaction search tool","volume":"29","author":"Durmus","year":"2013","journal-title":"Bioinformatics"},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20170-2_bib20","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1002\/2211-5463.12167","article-title":"Comparative interactomics for virus-human protein-protein interactions: DNA viruses versus RNA viruses","volume":"7","author":"Durmus","year":"2017","journal-title":"FEBS Open Bio"},{"issue":"13","key":"10.1016\/B978-0-12-809633-8.20170-2_bib21","doi-asserted-by":"crossref","first-page":"i159","DOI":"10.1093\/bioinformatics\/btm208","article-title":"Computational prediction of host-pathogen protein-protein interactions","volume":"23","author":"Dyer","year":"2007","journal-title":"Bioinformatics"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20170-2_bib22","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":"Dyer","year":"2008","journal-title":"PLOS Pathog."},{"issue":"4","key":"10.1016\/B978-0-12-809633-8.20170-2_bib23","doi-asserted-by":"crossref","first-page":"26","DOI":"10.3390\/proteomes5040026","article-title":"Proteogenomics in aid of host-pathogen interaction studies: A bacterial perspective","volume":"5","author":"Fels","year":"2017","journal-title":"Proteomes"},{"issue":"6230","key":"10.1016\/B978-0-12-809633-8.20170-2_bib24","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/340245a0","article-title":"A novel genetic system to detect protein-protein interactions","volume":"340","author":"Fields","year":"1989","journal-title":"Nature"},{"issue":"26","key":"10.1016\/B978-0-12-809633-8.20170-2_bib25","doi-asserted-by":"crossref","first-page":"10538","DOI":"10.1073\/pnas.1101440108","article-title":"Structural principles within the human-virus protein-protein interaction network","volume":"108","author":"Franzosa","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"10","key":"10.1016\/B978-0-12-809633-8.20170-2_bib26","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1016\/j.tim.2011.07.003","article-title":"Virus-host interactomes and global models of virus-infected cells","volume":"19","author":"Friedel","year":"2011","journal-title":"Trends Microbiol."},{"issue":"Database issue","key":"10.1016\/B978-0-12-809633-8.20170-2_bib27","doi-asserted-by":"crossref","first-page":"D417","DOI":"10.1093\/nar\/gkn708","article-title":"Human immunodeficiency virus type 1, human protein interaction database at NCBI","volume":"37","author":"Fu","year":"2009","journal-title":"Nucleic Acids Res."},{"issue":"Database issue","key":"10.1016\/B978-0-12-809633-8.20170-2_bib28","doi-asserted-by":"crossref","first-page":"D583","DOI":"10.1093\/nar\/gku1121","article-title":"VirHostNet 2.0: Surfing on the web of virus\/host molecular interactions data","volume":"43","author":"Guirimand","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/B978-0-12-809633-8.20170-2_bib29","doi-asserted-by":"crossref","DOI":"10.1093\/bfgp\/elx026","article-title":"Review of computational methods for virus-host protein interaction prediction: A case study on novel Ebola-human interactions","author":"Halder","year":"2017","journal-title":"Brief. Funct. Genomics"},{"issue":"7","key":"10.1016\/B978-0-12-809633-8.20170-2_bib30","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1093\/bioinformatics\/btu763","article-title":"Molecular principles of human virus protein-protein interactions","volume":"31","author":"Halehalli","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/B978-0-12-809633-8.20170-2_bib31","doi-asserted-by":"crossref","first-page":"19486","DOI":"10.1038\/srep19486","article-title":"Prediction and characterization of protein-protein interaction network in Bacillus licheniformis WX-02","volume":"6","author":"Han","year":"2016","journal-title":"Sci. Rep."},{"issue":"7381","key":"10.1016\/B978-0-12-809633-8.20170-2_bib32","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1038\/nature10719","article-title":"Global landscape of HIV-human protein complexes","volume":"481","author":"Jager","year":"2011","journal-title":"Nature"},{"key":"10.1016\/B978-0-12-809633-8.20170-2_bib33","doi-asserted-by":"crossref","first-page":"1386","DOI":"10.3389\/fmicb.2015.01386","article-title":"Literature mining and ontology based analysis of Host-Brucella Gene-Gene Interaction Network","volume":"6","author":"Karadeniz","year":"2015","journal-title":"Front. Microbiol."},{"issue":"18","key":"10.1016\/B978-0-12-809633-8.20170-2_bib34","doi-asserted-by":"crossref","first-page":"i466","DOI":"10.1093\/bioinformatics\/bts375","article-title":"Techniques to cope with missing data in host-pathogen protein interaction prediction","volume":"28","author":"Kshirsagar","year":"2012","journal-title":"Bioinformatics"},{"issue":"13","key":"10.1016\/B978-0-12-809633-8.20170-2_bib35","doi-asserted-by":"crossref","first-page":"i217","DOI":"10.1093\/bioinformatics\/btt245","article-title":"Multitask learning for host-pathogen protein interactions","volume":"29","author":"Kshirsagar","year":"2013","journal-title":"Bioinformatics"},{"issue":"Database issue","key":"10.1016\/B978-0-12-809633-8.20170-2_bib36","doi-asserted-by":"crossref","first-page":"D578","DOI":"10.1093\/nar\/gku903","article-title":"ViRBase: A resource for virus-host ncRNA-associated interactions","volume":"43","author":"Li","year":"2015","journal-title":"Nucleic Acids Res."},{"issue":"3","key":"10.1016\/B978-0-12-809633-8.20170-2_bib37","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1586\/14789450.2016.1147353","article-title":"Proteomic approaches to uncovering virus-host protein interactions during the progression of viral infection","volume":"13","author":"Lum","year":"2016","journal-title":"Expert Rev. Proteomics"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20170-2_bib38","doi-asserted-by":"crossref","first-page":"350","DOI":"10.2144\/97222pf02","article-title":"Mammalian two-hybrid system: A complementary approach to the yeast two-hybrid system","volume":"22","author":"Luo","year":"1997","journal-title":"Biotechniques"},{"issue":"5","key":"10.1016\/B978-0-12-809633-8.20170-2_bib39","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1016\/j.coviro.2012.09.003","article-title":"Virus-host interactomes \u2013 Antiviral drug discovery","volume":"2","author":"Ma-Lauer","year":"2012","journal-title":"Curr. Opin. Virol."},{"key":"10.1016\/B978-0-12-809633-8.20170-2_bib40","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1007\/978-1-4939-3115-6_12","article-title":"Yeast three-hybrid system for the detection of protein-protein interactions","volume":"1363","author":"Maruta","year":"2016","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20170-2_bib41","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.sbi.2017.02.005","article-title":"Network analysis and in silico prediction of protein-protein interactions with applications in drug discovery","volume":"44","author":"Murakami","year":"2017","journal-title":"Curr. Opin. Struct. Biol."},{"key":"10.1016\/B978-0-12-809633-8.20170-2_bib42","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.mib.2017.07.005","article-title":"Elucidation of host-pathogen protein-protein interactions to uncover mechanisms of host cell rewiring","volume":"39","author":"Nicod","year":"2017","journal-title":"Curr. Opin. Microbiol."},{"key":"10.1016\/B978-0-12-809633-8.20170-2_bib43","doi-asserted-by":"crossref","first-page":"94","DOI":"10.3389\/fmicb.2015.00094","article-title":"Computational approaches for prediction of pathogen-host protein-protein interactions","volume":"6","author":"Nourani","year":"2015","journal-title":"Front. Microbiol."},{"issue":"1","key":"10.1016\/B978-0-12-809633-8.20170-2_bib44","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1759-4499-2-2","article-title":"Construction and analysis of protein-protein interaction networks","volume":"2","author":"Raman","year":"2010","journal-title":"Autom. Exp."},{"issue":"7","key":"10.1016\/B978-0-12-809633-8.20170-2_bib45","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1016\/j.cell.2009.12.018","article-title":"A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection","volume":"139","author":"Shapira","year":"2009","journal-title":"Cell"},{"issue":"7","key":"10.1016\/B978-0-12-809633-8.20170-2_bib46","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1038\/nprot.2010.83","article-title":"Detecting interactions with membrane proteins using a membrane two-hybrid assay in yeast","volume":"5","author":"Snider","year":"2010","journal-title":"Nat. Protoc."},{"issue":"9","key":"10.1016\/B978-0-12-809633-8.20170-2_bib47","doi-asserted-by":"crossref","first-page":"2339","DOI":"10.1016\/j.celrep.2016.07.068","article-title":"Unique requirement for ESCRT factors in flavivirus particle formation on the endoplasmic reticulum","volume":"16","author":"Tabata","year":"2016","journal-title":"Cell Rep."},{"issue":"6","key":"10.1016\/B978-0-12-809633-8.20170-2_bib48","doi-asserted-by":"crossref","first-page":"867","DOI":"10.1093\/bioinformatics\/bts042","article-title":"Literature mining of host-pathogen interactions: Comparing feature-based supervised learning and language-based approaches","volume":"28","author":"Thieu","year":"2012","journal-title":"Bioinformatics"},{"issue":"2","key":"10.1016\/B978-0-12-809633-8.20170-2_bib49","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1083\/jcb.200805092","article-title":"Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes","volume":"183","author":"Trinkle-Mulcahy","year":"2008","journal-title":"J. Cell Biol."},{"issue":"12","key":"10.1016\/B978-0-12-809633-8.20170-2_bib50","doi-asserted-by":"crossref","first-page":"2539","DOI":"10.1039\/c0mb00103a","article-title":"Network based analysis of hepatitis C virus Core and NS4B protein interactions","volume":"6","author":"Tripathi","year":"2010","journal-title":"Mol. Biosyst."},{"issue":"7","key":"10.1016\/B978-0-12-809633-8.20170-2_bib51","doi-asserted-by":"crossref","first-page":"3664","DOI":"10.1021\/pr300121a","article-title":"Proteomic analysis of hepatitis C virus (HCV) core protein transfection and host regulator PA28gamma knockout in HCV pathogenesis: A network-based study","volume":"11","author":"Tripathi","year":"2012","journal-title":"J. Proteome Res."},{"issue":"6","key":"10.1016\/B978-0-12-809633-8.20170-2_bib52","doi-asserted-by":"crossref","first-page":"2537","DOI":"10.1021\/pr3011217","article-title":"Understanding the biological context of NS5A-host interactions in HCV infection: A network-based approach","volume":"12","author":"Tripathi","year":"2013","journal-title":"J. Proteome Res."},{"issue":"5758","key":"10.1016\/B978-0-12-809633-8.20170-2_bib53","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1126\/science.1116804","article-title":"Herpesviral protein networks and their interaction with the human proteome","volume":"311","author":"Uetz","year":"2006","journal-title":"Science"},{"issue":"D1","key":"10.1016\/B978-0-12-809633-8.20170-2_bib54","doi-asserted-by":"crossref","first-page":"D604","DOI":"10.1093\/nar\/gkw1089","article-title":"PHI-base: A new interface and further additions for the multi-species pathogen-host interactions database","volume":"45","author":"Urban","year":"2017","journal-title":"Nucleic Acids Res."},{"issue":"Database issue","key":"10.1016\/B978-0-12-809633-8.20170-2_bib55","doi-asserted-by":"crossref","first-page":"D581","DOI":"10.1093\/nar\/gkt1099","article-title":"PATRIC, the bacterial bioinformatics database and analysis resource","volume":"42","author":"Wattam","year":"2014","journal-title":"Nucleic Acids Res."},{"issue":"7","key":"10.1016\/B978-0-12-809633-8.20170-2_bib56","doi-asserted-by":"crossref","first-page":"R150","DOI":"10.1186\/gb-2007-8-7-r150","article-title":"PHIDIAS: A pathogen-host interaction data integration and analysis system","volume":"8","author":"Xiang","year":"2007","journal-title":"Genome Biol."},{"issue":"3","key":"10.1016\/B978-0-12-809633-8.20170-2_bib57","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.artmed.2010.04.003","article-title":"Document classification for mining host pathogen protein-protein interactions","volume":"49","author":"Yin","year":"2010","journal-title":"Artif. Intell. Med."},{"key":"10.1016\/B978-0-12-809633-8.20170-2_bib58","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1745-6150-9-5","article-title":"Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions","volume":"9","author":"Zhou","year":"2014","journal-title":"Biol. Direct"}],"container-title":["Encyclopedia of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338201702?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:B9780128096338201702?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2019,1,21]],"date-time":"2019-01-21T19:11:06Z","timestamp":1548097866000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/B9780128096338201702"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9780128114322"],"references-count":58,"URL":"https:\/\/doi.org\/10.1016\/b978-0-12-809633-8.20170-2","relation":{},"subject":[],"published":{"date-parts":[[2019]]}}}