{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T06:58:48Z","timestamp":1763017128739},"reference-count":52,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2011,7,28]],"date-time":"2011-07-28T00:00:00Z","timestamp":1311811200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1002110","type":"journal-article","created":{"date-parts":[[2011,7,28]],"date-time":"2011-07-28T20:50:22Z","timestamp":1311886222000},"page":"e1002110","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":10,"title":["Bayesian Inference for Genomic Data Integration Reduces Misclassification Rate in Predicting Protein-Protein Interactions"],"prefix":"10.1371","volume":"7","author":[{"given":"Chuanhua","family":"Xing","sequence":"first","affiliation":[]},{"given":"David B.","family":"Dunson","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2011,7,28]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1038\/nbt0108-69","article-title":"Protein-protein interaction networks and biology \u2013 what's the connection?","volume":"26","author":"L Hakes","year":"2008","journal-title":"Nat Biotechnol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1517\/14622416.2.3.195","article-title":"Shifting paradigms in gene-mapping methodology for complex traits.","volume":"2","author":"P Sham","year":"2001","journal-title":"Pharmacogenomics"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/nbt.1522","article-title":"Dynamic modularity in protein interaction networks predicts breast cancer outcome.","volume":"27","author":"IW Taylor","year":"2009","journal-title":"Nat Biotechnol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1253","DOI":"10.1038\/nbt1017","article-title":"Systems biology in drug discovery.","volume":"22","author":"EC Butcher","year":"2004","journal-title":"Nat Biotechnol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/S1535-6108(03)00050-3","article-title":"Identification of genotype-selective antitumor agents using synthetic lethal chemical screening in engineered human tumor cells.","volume":"3","author":"S Dolma","year":"2003","journal-title":"Cancer Cell"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1215","DOI":"10.1038\/nbt1004-1215","article-title":"The impact of systems approaches on biological problems in drug discovery.","volume":"22","author":"L Hood","year":"2004","journal-title":"Nat Biotechnol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1038\/nbt1007-1110","article-title":"Network pharmacology.","volume":"25","author":"AL Hopkins","year":"2007","journal-title":"Nat Biotechnol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1038\/nbt1338","article-title":"Drug-target network.","volume":"25","author":"MA Yildirim","year":"2007","journal-title":"Nat Biotechnol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"1971","DOI":"10.1101\/gr.206701","article-title":"Is there a bias in proteome research?","volume":"11","author":"R Mrowka","year":"2001","journal-title":"Genome Res"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"399","DOI":"10.1038\/nature750","article-title":"Comparative assessment of large-scale data sets of proteinprotein interactions.","volume":"417","author":"C von Mering","year":"2002","journal-title":"Nature"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1126\/science.1158684","article-title":"High Quality Binary Protein Interaction Map of the Yeast Interactome Network.","volume":"322","author":"H Yu","year":"2008","journal-title":"Science"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1093\/bioinformatics\/btn640","article-title":"Precision and recall estimates for two-hybrid screens.","volume":"25","author":"H Huang","year":"2009","journal-title":"Bioinformatics,"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/nrg1768","article-title":"Literature mining for the biologist: from information retrieval to biological discovery.","volume":"7","author":"LJ Jensen","year":"2006","journal-title":"Nat Rev Genet"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"3604","DOI":"10.1093\/bioinformatics\/bth451","article-title":"Discovering patterns to extract protein-protein interactions from full texts.","volume":"20","author":"M Huang","year":"2004","journal-title":"Bioinformatics"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"645","DOI":"10.1093\/bioinformatics\/bti597","article-title":"Extraction of regulatory gene\/protein networks from Medline.","volume":"22","author":"J Saric","year":"2006","journal-title":"Bioinformatics"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"W411","DOI":"10.1093\/nar\/gkn281","article-title":"PIE: an online prediction system for protein-protein interactions from text.","volume":"36","author":"S Kim","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"2151","DOI":"10.1093\/bioinformatics\/btl281","article-title":"Combination of text-mining algorithms increases the performance.","volume":"22","author":"R Malik","year":"2006","journal-title":"Bioinformatics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"1536","DOI":"10.1093\/bioinformatics\/btp245","article-title":"Bayesian inference of protein-protein interactions from biological literature.","volume":"25","author":"R Chowdhary","year":"2009","journal-title":"Bioinformatics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"2026","DOI":"10.1126\/science.1092645","article-title":"Structure-based assembly of protein complexes in yeast.","volume":"302","author":"P Aloy","year":"2004","journal-title":"Science"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1038\/47056","article-title":"Protein interaction maps for complete genomes based on gene fusion events.","volume":"402","author":"AJ Enright","year":"1999","journal-title":"Nature"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/S0022-2836(02)01038-0","article-title":"Co-evolutionary analysis reveals insights into protein-protein interactions.","volume":"324","author":"CS Goh","year":"2002","journal-title":"J Mol Biol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1126\/science.1087361","article-title":"A Bayesian networks approach for predicting protein\u2013protein interactions from genomic data.","volume":"302","author":"R Jansen","year":"2003","journal-title":"Science"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1146","DOI":"10.1101\/gr.1145203","article-title":"Multimeric threading-based prediction of protein-protein interactions on a genomic scale: Application to the Saccharomyces cerevisiae proteome.","volume":"13","author":"L Lu","year":"2003","journal-title":"Genome Res"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"357363","DOI":"10.1093\/bioinformatics\/17.4.359","article-title":"Mining literature for protein-protein interactions.","volume":"17","author":"EM Marcotte","year":"2001","journal-title":"Bioinformatics"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1093\/protein\/14.9.609","article-title":"Similarity of phylogenetic trees as indicator of protein-protein interaction.","volume":"14","author":"F Pazos","year":"2001","journal-title":"Protein Eng"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/S0022-2836(03)00114-1","article-title":"Exploiting the coevolution of interacting proteins to discover interaction specificity.","volume":"327","author":"AK Ramani","year":"2003","journal-title":"J Mol Biol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/79847","article-title":"Prediction of protein interactions: Metabolic enzymes are frequently involved in gene fusion.","volume":"26","author":"S Tsoka","year":"2000","journal-title":"Nature Genetics"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1016\/j.sbi.2004.05.003","article-title":"Protein interaction networks from yeast to human.","volume":"14","author":"P Bork","year":"2004","journal-title":"Curr Opin Struct Biol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"e43","DOI":"10.1371\/journal.pcbi.0030043","article-title":"Deciphering protein-protein interactions. Part II. Computational methods to predict protein and domain interaction partners.","volume":"3","author":"BA Shoemaker","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1016\/S0959-440X(02)00333-0","article-title":"Computational methods for the prediction of protein interactions.","volume":"12","author":"A Valencia","year":"2002","journal-title":"Curr Opin Struct Biol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1186\/1471-2105-5-154","article-title":"Information assessment on predicting protein protein interactions.","volume":"5","author":"N Lin","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/1471-2105-5-38","article-title":"Predicting co-complexed protein pairs using genomic and proteomic data integration.","volume":"5","author":"LV Zhang","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"S6","DOI":"10.1186\/1471-2105-8-S10-S6","article-title":"A mixture of feature experts approach for protein-protein interaction prediction.","volume":"8","author":"Y Qi","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1073\/pnas.97.1.262","article-title":"Knowledge-based analysis of microarray gene expression data by using support vector machines.","volume":"97","author":"MP Brown","year":"2000","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1101\/gr.4573206","article-title":"Computational modeling of the Plasmodium falciparum interactome reveals protein function on a genome-wide scale.","volume":"16","author":"SV Date","year":"2006","journal-title":"Genome Res"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1555","DOI":"10.1126\/science.1099511","article-title":"A probabilistic functional network of yeast genes.","volume":"306","author":"I Lee","year":"2004","journal-title":"Science"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1101\/gr.3610305","article-title":"Assessing the limits of genomic data integration for predicting protein networks.","volume":"15","author":"LJ Lu","year":"2005","journal-title":"Genome Res"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1038\/nbt1103","article-title":"Probabilistic model of the human protein-protein interaction network.","volume":"23","author":"DR Rhodes","year":"2005","journal-title":"Nat Biotechnol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1186\/gb-2006-7-11-120","article-title":"How complete are current yeast and human protein-interaction networks?","volume":"7","author":"GT Hart","year":"2006","journal-title":"Genome Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1186\/1471-2105-8-239","article-title":"Probabilistic prediction and ranking of human protein-protein interactions.","volume":"8","author":"MS Scott","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"8348","DOI":"10.1073\/pnas.0832373100","article-title":"A Bayesian framework for combining heterogeneous data sources for gene function predition (in S. cerevisiae).","volume":"100","author":"OG Troyanskaya","year":"2003","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"D433","DOI":"10.1093\/nar\/gki005","article-title":"STRING: known and predicted protein-protein associations, integrated and transferred across organisms.","volume":"33","author":"C von Mering","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1016\/j.compbiomed.2010.01.002","article-title":"A knowledge-driven probabilistic framework for the prediction of protein-protein interaction networks.","volume":"40","author":"F Browne","year":"2010","journal-title":"Comput Biol Med"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"e7492","DOI":"10.1371\/journal.pone.0007492","article-title":"Accounting for redundancy when integrating gene interaction databases.","volume":"4","author":"A Elefsinioti","year":"2009","journal-title":"PLoS One"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1093\/bioinformatics\/btq044","article-title":"Prediction of human functional genetic networks from heterogeneous data using RVM-based ensemble learning.","volume":"26","author":"CC Wu","year":"2010","journal-title":"Bioinformatics"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1038\/nbt924","article-title":"Gaining confidence in high-throughput protein interaction networks.","volume":"22","author":"JS Bader","year":"2004","journal-title":"Nat Biotechnol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1186\/1471-2105-8-414","article-title":"InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes.","volume":"8","author":"J Sun","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1002\/prot.20865","article-title":"Evaluation of Different Biological Data and Computational Classification Methods for Use in Protein Interaction Prediction.","volume":"63","author":"Y Qi","year":"2006","journal-title":"Proteins"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1093\/bioinformatics\/bti115","article-title":"The MIPS mammalian protein-protein interaction database.","volume":"21","author":"P Pagel","year":"2005","journal-title":"Bioinformatics"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"S21","DOI":"10.1186\/1471-2105-6-S4-S21","article-title":"HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms.","volume":"6","author":"M Persico","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1093\/biomet\/asn043","article-title":"Bayesian nonparametric inference on stochastic ordering.","volume":"95","author":"DB Dunson","year":"2008","journal-title":"Biometrika"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"16173","DOI":"10.1198\/016214501750332758","article-title":"Gibbs sampling methods for stick-breaking priors.","volume":"96","author":"H Ishwaran","year":"2001","journal-title":"J Am Statist Assoc"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002110","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,6,13]],"date-time":"2019-06-13T14:34:02Z","timestamp":1560436442000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1002110"}},"subtitle":[],"editor":[{"given":"Christos A.","family":"Ouzounis","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2011,7,28]]},"references-count":52,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2011,7,28]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1002110","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,7,28]]}}}