{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T10:25:02Z","timestamp":1777890302436,"version":"3.51.4"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2016,10,5]],"date-time":"2016-10-05T00:00:00Z","timestamp":1475625600000},"content-version":"vor","delay-in-days":1579,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,7,1]]},"DOI":"10.1093\/nar\/gks553","type":"journal-article","created":{"date-parts":[[2012,6,12]],"date-time":"2012-06-12T01:19:36Z","timestamp":1339463976000},"page":"W147-W151","source":"Crossref","is-referenced-by-count":65,"title":["BIPS: BIANA Interolog Prediction Server. A tool for protein\u2013protein interaction inference"],"prefix":"10.1093","volume":"40","author":[{"given":"Javier","family":"Garcia-Garcia","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sylvia","family":"Schleker","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Judith","family":"Klein-Seetharaman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Baldo","family":"Oliva","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,6,9]]},"reference":[{"key":"key\n\t\t\t\t20170720163801_gks553-B1","doi-asserted-by":"crossref","first-page":"1317","DOI":"10.1038\/nbt1018","article-title":"Ten thousand interactions for the molecular biologist","volume":"22","author":"Aloy","year":"2004","journal-title":"Nat. Biotechnol."},{"key":"key\n\t\t\t\t20170720163801_gks553-B2","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1186\/1471-2105-11-605","article-title":"New insights into protein-protein interaction data lead to increased estimates of the S. cerevisiae interactome size","volume":"11","author":"Sambourg","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170720163801_gks553-B3","first-page":"531","article-title":"Random forest similarity for protein-protein interaction prediction from multiple sources","author":"Qi","year":"2005","journal-title":"Pac. Symp. Biocomput."},{"key":"key\n\t\t\t\t20170720163801_gks553-B4","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1186\/1471-2105-11-562","article-title":"An improved method for scoring protein-protein interactions using semantic similarity within the gene ontology","volume":"11","author":"Jain","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170720163801_gks553-B5","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1101\/gr.1774904","article-title":"Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs","volume":"14","author":"Yu","year":"2004","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B6","doi-asserted-by":"crossref","first-page":"2120","DOI":"10.1101\/gr.205301","article-title":"Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or \u201cinterologs\u201d","volume":"11","author":"Matthews","year":"2001","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B7","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1477-5956-10-2","article-title":"Prediction and characterization of protein-protein interaction networks in swine","volume":"10","author":"Wang","year":"2012","journal-title":"Proteome Sci."},{"key":"key\n\t\t\t\t20170720163801_gks553-B8","doi-asserted-by":"crossref","first-page":"5256","DOI":"10.1002\/pmic.200900262","article-title":"Towards the mammalian interactome: inference of a core mammalian interaction set in mouse","volume":"9","author":"Shin","year":"2009","journal-title":"Proteomics"},{"key":"key\n\t\t\t\t20170720163801_gks553-B9","doi-asserted-by":"crossref","first-page":"991","DOI":"10.1002\/cbdv.201100392","article-title":"Prediction and comparison of Salmonella-human and Salmonella-Arabidopsis interactomes","volume":"9","author":"Schleker","year":"2012","journal-title":"Chem Biodivers"},{"key":"key\n\t\t\t\t20170720163801_gks553-B10","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1016\/j.ijbiomac.2011.01.030","article-title":"Prediction of protein-protein interactions between human host and a pathogen and its application to three pathogenic bacteria","volume":"48","author":"Krishnadev","year":"2011","journal-title":"Int. J. Biol Macromol."},{"key":"key\n\t\t\t\t20170720163801_gks553-B11","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/1752-0509-4-36","article-title":"Building and analyzing protein interactome networks by cross-species comparisons","volume":"4","author":"Wiles","year":"2010","journal-title":"BMC Syst. Biol."},{"key":"key\n\t\t\t\t20170720163801_gks553-B12","doi-asserted-by":"crossref","first-page":"D642","DOI":"10.1093\/nar\/gkn722","article-title":"Michigan molecular interactions r2: from interacting proteins to pathways","volume":"37","author":"Tarcea","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B13","doi-asserted-by":"crossref","first-page":"W369","DOI":"10.1093\/nar\/gkp309","article-title":"PPISearch: a web server for searching homologous protein-protein interactions across multiple species","volume":"37","author":"Chen","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B14","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1186\/1471-2105-12-289","article-title":"Bio::Homology::InterologWalk\u2014a Perl module to build putative protein-protein interaction networks through interolog mapping","volume":"12","author":"Gallone","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170720163801_gks553-B15","doi-asserted-by":"crossref","first-page":"S19","DOI":"10.1186\/1471-2105-7-S5-S19","article-title":"An evaluation of human protein-protein interaction data in the public domain","volume":"7","author":"Mathivanan","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170720163801_gks553-B16","doi-asserted-by":"crossref","first-page":"166","DOI":"10.4172\/jpb.1000023","article-title":"Integration and prediction of PPI using multiple resources from public databases","volume":"1","author":"Aragues","year":"2008","journal-title":"J. Proteomics. Bioinform."},{"key":"key\n\t\t\t\t20170720163801_gks553-B17","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1186\/1471-2105-11-56","article-title":"Biana: a software framework for compiling biological interactions and analyzing networks","volume":"11","author":"Garcia-Garcia","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170720163801_gks553-B18","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":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20170720163801_gks553-B19","doi-asserted-by":"crossref","first-page":"410","DOI":"10.1093\/bioinformatics\/bti011","article-title":"iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions","volume":"21","author":"Finn","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170720163801_gks553-B20","doi-asserted-by":"crossref","first-page":"D718","DOI":"10.1093\/nar\/gkq962","article-title":"3did: identification and classification of domain-based interactions of known three-dimensional structure","volume":"39","author":"Stein","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B21","doi-asserted-by":"crossref","first-page":"W29","DOI":"10.1093\/nar\/gkr367","article-title":"HMMER web server: interactive sequence similarity searching","volume":"39","author":"Finn","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B22","doi-asserted-by":"crossref","first-page":"D449","DOI":"10.1093\/nar\/gkh086","article-title":"The Database of Interacting Proteins: 2004 update","volume":"32","author":"Salwinski","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B23","doi-asserted-by":"crossref","first-page":"D767","DOI":"10.1093\/nar\/gkn892","article-title":"Human Protein Reference Database\u20142009 update","volume":"37","author":"Keshava Prasad","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B24","doi-asserted-by":"crossref","first-page":"D561","DOI":"10.1093\/nar\/gkl958","article-title":"IntAct\u2014open source resource for molecular interaction data","volume":"35","author":"Kerrien","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B25","doi-asserted-by":"crossref","first-page":"D857","DOI":"10.1093\/nar\/gkr930","article-title":"MINT, the molecular interaction database: 2012 update","volume":"40","author":"Licata","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B26","doi-asserted-by":"crossref","first-page":"D436","DOI":"10.1093\/nar\/gkj003","article-title":"MPact: the MIPS protein interaction resource on yeast","volume":"34","author":"Guldener","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B27","doi-asserted-by":"crossref","first-page":"D459","DOI":"10.1093\/nar\/gkj047","article-title":"PHI-base: a new database for pathogen host interactions","volume":"34","author":"Winnenburg","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B28","doi-asserted-by":"crossref","first-page":"D647","DOI":"10.1093\/nar\/gkn799","article-title":"PIG\u2014the pathogen interaction gateway","volume":"37","author":"Driscoll","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B29","doi-asserted-by":"crossref","first-page":"D698","DOI":"10.1093\/nar\/gkq1116","article-title":"The BioGRID Interaction Database: 2011 update","volume":"39","author":"Stark","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B30","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1093\/nar\/gkg056","article-title":"BIND: the Biomolecular Interaction Network Database","volume":"31","author":"Bader","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B31","doi-asserted-by":"crossref","first-page":"D669","DOI":"10.1093\/nar\/gkn739","article-title":"VirusMINT: a viral protein interaction database","volume":"37","author":"Chatr-aryamontri","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B32","doi-asserted-by":"crossref","first-page":"D71","DOI":"10.1093\/nar\/gkr981","article-title":"Reorganizing the protein space at the Universal Protein Resource (UniProt)","volume":"40","author":"UniProt Consortium","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B33","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology. The Gene Ontology Consortium","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t20170720163801_gks553-B34","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1093\/bioinformatics\/btm087","article-title":"A new method to measure the semantic similarity of GO terms","volume":"23","author":"Wang","year":"2007","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170720163801_gks553-B35","doi-asserted-by":"crossref","first-page":"D284","DOI":"10.1093\/nar\/gkr1060","article-title":"eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges","volume":"40","author":"Powell","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B36","doi-asserted-by":"crossref","first-page":"D800","DOI":"10.1093\/nar\/gkq1064","article-title":"Ensembl 2011","volume":"39","author":"Flicek","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B37","first-page":"175","article-title":"A hidden Markov model for predicting transmembrane helices in protein sequences","volume":"6","author":"Sonnhammer","year":"1998","journal-title":"Proc. Int. Conf. Intell. Syst. Mol. Biol."},{"key":"key\n\t\t\t\t20170720163801_gks553-B38","doi-asserted-by":"crossref","first-page":"D540","DOI":"10.1093\/nar\/gkp1026","article-title":"The Negatome database: a reference set of non-interacting protein pairs","volume":"38","author":"Smialowski","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170720163801_gks553-B39","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1126\/science.1203877","article-title":"Evidence for network evolution in an Arabidopsis interactome map","volume":"333","author":"ArabidopsisInteractome Mapping Consortium","year":"2011","journal-title":"Science"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/40\/W1\/W147\/18784611\/gks553.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T10:40:26Z","timestamp":1522665626000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article-lookup\/doi\/10.1093\/nar\/gks553"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,6,9]]},"references-count":39,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2012,6,9]]},"published-print":{"date-parts":[[2012,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gks553","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,6,9]]}}}