{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,10]],"date-time":"2024-07-10T11:36:58Z","timestamp":1720611418568},"reference-count":52,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2015,6,1]],"date-time":"2015-06-01T00:00:00Z","timestamp":1433116800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"funder":[{"name":"Pablo de Olavide University"}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Computational Biology and Chemistry"],"published-print":{"date-parts":[[2015,6]]},"DOI":"10.1016\/j.compbiolchem.2015.03.002","type":"journal-article","created":{"date-parts":[[2015,5,4]],"date-time":"2015-05-04T18:15:36Z","timestamp":1430763336000},"page":"142-151","update-policy":"http:\/\/dx.doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":12,"special_numbering":"C","title":["Gene network coherence based on prior knowledge using direct and indirect relationships"],"prefix":"10.1016","volume":"56","author":[{"ORCID":"http:\/\/orcid.org\/0000-0001-7376-5790","authenticated-orcid":false,"given":"Francisco","family":"G\u00f3mez-Vela","sequence":"first","affiliation":[]},{"given":"Jos\u00e9 Antonio","family":"Lagares","sequence":"additional","affiliation":[]},{"given":"Norberto","family":"D\u00edaz-D\u00edaz","sequence":"additional","affiliation":[]}],"member":"78","reference":[{"issue":"5","key":"10.1016\/j.compbiolchem.2015.03.002_bib0005","doi-asserted-by":"crossref","first-page":"558","DOI":"10.1504\/IJDMB.2011.043033","article-title":"CarGene: characterisation of set of genes based on metabolic pathway analysis","volume":"5","author":"Aguilar-Ruiz","year":"2011","journal-title":"Int. J. Data Min. Bioinform."},{"issue":"1","key":"10.1016\/j.compbiolchem.2015.03.002_bib0010","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/1742-4682-8-39","article-title":"Construction of gene regulatory networks using biclustering and Bayesian networks","volume":"8","author":"Alakwaa","year":"2011","journal-title":"Theor. Biol. Med. Model."},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0015","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1186\/1471-2105-13-226","article-title":"Network enrichment analysis: extension of gene-set enrichment analysis to gene networks","volume":"13","author":"Alexeyenko","year":"2012","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0020","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.aml.2011.06.008","article-title":"Speeding up the Floyd\u2013Warshall algorithm for the cycled shortest path problem","volume":"25","author":"Asghar Ainia","year":"2012","journal-title":"Appl. Math. Lett."},{"issue":"1","key":"10.1016\/j.compbiolchem.2015.03.002_bib0025","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":"10.1016\/j.compbiolchem.2015.03.002_bib0030","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.jmb.2006.04.029","article-title":"Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast","volume":"360","author":"Balaji","year":"2006","journal-title":"J. Mol. Biol."},{"issue":"7","key":"10.1016\/j.compbiolchem.2015.03.002_bib0035","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1093\/bioinformatics\/btl003","article-title":"Inference of gene regulatory networks and compound mode of action from time course gene expression profiles","volume":"22","author":"Bansal","year":"2006","journal-title":"Bioinformatics"},{"issue":"22","key":"10.1016\/j.compbiolchem.2015.03.002_bib0040","doi-asserted-by":"crossref","first-page":"3043","DOI":"10.1093\/bioinformatics\/btp498","article-title":"Next generation software for functional trend analysis","volume":"25","author":"Berriz","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0045","doi-asserted-by":"crossref","first-page":"S85","DOI":"10.1098\/rsif.2008.0132.focus","article-title":"Boolean network models of cellular regulation: prospects and limitations","volume":"5","author":"Bornholdt","year":"2008","journal-title":"J. R. Soc. Interface"},{"issue":"Database issue","key":"10.1016\/j.compbiolchem.2015.03.002_bib0050","first-page":"D637","article-title":"The BioGRID Interaction Database: 2008 update","volume":"36","author":"Breitkreutz","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0055","doi-asserted-by":"crossref","first-page":"2706","DOI":"10.1093\/bioinformatics\/bti388","article-title":"Inferring genetic regulatory logic from expression data","volume":"21","author":"Bulashevska","year":"2005","journal-title":"Bioinformatics"},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0060","first-page":"418","article-title":"Mutual information relevance networks: functional genomic clustering using pairwise entropy measurements","author":"Butte","year":"2000","journal-title":"Pac. Symp. Biocomput."},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0065","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1186\/1471-2105-11-228","article-title":"Learning gene regulatory networks from only positive and unlabeled data","volume":"11","author":"Cerulo","year":"2010","journal-title":"BMC Bioinform."},{"issue":"Database issue","key":"10.1016\/j.compbiolchem.2015.03.002_bib0070","doi-asserted-by":"crossref","first-page":"D816","DOI":"10.1093\/nar\/gks1158","article-title":"The BioGRID interaction database: 2013 update.","volume":"41","author":"Chatr-Aryamontri","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0075","doi-asserted-by":"crossref","first-page":"D700","DOI":"10.1093\/nar\/gkr1029","article-title":"Saccharomyces genome database: the genomics resource of budding yeast","volume":"40","author":"Cherry","year":"2012","journal-title":"Nucleic acids Res."},{"issue":"Suppl. 5","key":"10.1016\/j.compbiolchem.2015.03.002_bib0080","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/1471-2105-8-S5-S4","article-title":"A stochastic differential equation model for transcriptional regulatory networks","volume":"8","author":"Climescu-Haulica","year":"2007","journal-title":"BMC Bioinform."},{"issue":"5964","key":"10.1016\/j.compbiolchem.2015.03.002_bib0085","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1126\/science.1180823","article-title":"The genetic landscape of a cell","volume":"327","author":"Costanzo","year":"2010","journal-title":"Science"},{"issue":"1","key":"10.1016\/j.compbiolchem.2015.03.002_bib0090","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1186\/1471-2105-6-204","article-title":"Tandem machine learning for the identification of genes regulated by transcription factors","volume":"6","author":"Dinakarpandian","year":"2005","journal-title":"BMC Bioinform."},{"issue":"6","key":"10.1016\/j.compbiolchem.2015.03.002_bib0095","doi-asserted-by":"crossref","first-page":"351","DOI":"10.2174\/138920207783406505","article-title":"Validation of inference procedures for gene regulatory networks","volume":"8","author":"Dougherty","year":"2007","journal-title":"Curr. Genomics"},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0100","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1093\/bib\/bbq078","article-title":"Validation of gene regulatory networks: scientific and inferential","volume":"12","author":"Dougherty","year":"2012","journal-title":"Brief. Bioinform."},{"issue":"2","key":"10.1016\/j.compbiolchem.2015.03.002_bib0105","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.tig.2005.12.005","article-title":"Reliability and reproducibility issues in DNA microarray measurements","volume":"22","author":"Draghici","year":"2006","journal-title":"Trends Genet."},{"issue":"Suppl. 2","key":"10.1016\/j.compbiolchem.2015.03.002_bib0110","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1186\/1471-2105-14-S2-S7","article-title":"Discovery and analysis of consistent active sub-networks in cancers","volume":"14","author":"Gaire","year":"2013","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0115","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1186\/1471-2105-12-123","article-title":"Discovering time-lagged rules from microarray data using gene profile classifiers","author":"Gallo","year":"2011","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0120","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1186\/1471-2105-11-95","article-title":"A statistical framework for differential network analysis from microarray data","volume":"11","author":"Gill","year":"2010","journal-title":"BMC Bioinform."},{"issue":"1","key":"10.1016\/j.compbiolchem.2015.03.002_bib0125","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.biosystems.2008.12.004","article-title":"Gene regulatory network inference: data integration in dynamic models \u2013 a review","volume":"96","author":"Hecker","year":"2009","journal-title":"Biosystems"},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0130","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1186\/1471-2105-13-262","article-title":"Cluster-based assessment of protein\u2013protein interaction confidence","volume":"13","author":"Kamburov","year":"2012","journal-title":"BMC Bioinform."},{"issue":"1","key":"10.1016\/j.compbiolchem.2015.03.002_bib0135","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"Kegg: Kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0140","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/msb.2010.36","article-title":"Dissecting spatio-temporal protein networks driving human heart development and related disorders","volume":"6","author":"Lage","year":"2010","journal-title":"Mol. Syst. Biol."},{"issue":"10","key":"10.1016\/j.compbiolchem.2015.03.002_bib0145","doi-asserted-by":"crossref","first-page":"e988","DOI":"10.1371\/journal.pone.0000988","article-title":"An improved, bias-reduced probabilistic functional gene network of baker's yeast, Saccharomyces cerevisiae","volume":"2","author":"Lee","year":"2007","journal-title":"PLoS ONE"},{"issue":"9","key":"10.1016\/j.compbiolchem.2015.03.002_bib0150","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1093\/bioinformatics\/btn081","article-title":"Network-constrained regularization and variable selection for analysis of genomic data","volume":"24","author":"Li","year":"2008","journal-title":"Bioinformatics"},{"issue":"Suppl. 13","key":"10.1016\/j.compbiolchem.2015.03.002_bib0155","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/1471-2105-13-S13-S4","article-title":"An effective method for network module extraction from microarray data","volume":"13","author":"Mahanta","year":"2012","journal-title":"BMC Bioinform."},{"issue":"Suppl. 1","key":"10.1016\/j.compbiolchem.2015.03.002_bib0160","doi-asserted-by":"crossref","first-page":"S4","DOI":"10.1186\/gb-2008-9-s1-s4","article-title":"GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function","volume":"9","author":"Mostafavi","year":"2008","journal-title":"Genome Biol."},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0165","series-title":"Genomic Signal Processing and Statistics, 2006 (GENSIPS\u201906)","first-page":"79","article-title":"Elimination of indirect regulatory interactions in gene network inference","author":"Muddana","year":"2006"},{"issue":"Suppl. 1 (Suppl. 17)","key":"10.1016\/j.compbiolchem.2015.03.002_bib0170","doi-asserted-by":"crossref","first-page":"S8","DOI":"10.1186\/1471-2105-13-S17-S8","article-title":"An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds","volume":"13","author":"Nakamura","year":"2012","journal-title":"BMC Bioinform."},{"issue":"8","key":"10.1016\/j.compbiolchem.2015.03.002_bib0175","doi-asserted-by":"crossref","first-page":"e129","DOI":"10.1371\/journal.pcbi.0030129","article-title":"A primer on learning in Bayesian networks for computational biology","volume":"3","author":"Needham","year":"2007","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0180","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1186\/1471-2105-11-517","article-title":"Inferring gene regression networks with model trees","volume":"11","author":"Nepomuceno-Chamorro","year":"2010","journal-title":"BMC Bioinform."},{"issue":"1","key":"10.1016\/j.compbiolchem.2015.03.002_bib0185","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/1756-0381-4-10","article-title":"Using graph theory to analyze biological networks","volume":"4","author":"Pavlopoulos","year":"2011","journal-title":"BioData Min."},{"issue":"6","key":"10.1016\/j.compbiolchem.2015.03.002_bib0190","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1098\/rsfs.2011.0053","article-title":"How to infer gene networks from expression profiles, revisited","volume":"1","author":"Penfold","year":"2011","journal-title":"Interface Focus"},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0195","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1109\/tcbb.2007.1049","article-title":"Inferring adaptive regulation thresholds and association rules from gene expression data through combinatorial optimization learning","volume":"4","author":"Ponzoni","year":"2007","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"issue":"2","key":"10.1016\/j.compbiolchem.2015.03.002_bib0200","doi-asserted-by":"crossref","first-page":"e14598","DOI":"10.1371\/journal.pone.0014598","article-title":"The balance of weak and strong interactions in genetic networks.","volume":"6","author":"Poyatos","year":"2011","journal-title":"PLoS ONE"},{"issue":"Suppl. 7","key":"10.1016\/j.compbiolchem.2015.03.002_bib0205","doi-asserted-by":"crossref","first-page":"S10","DOI":"10.1186\/1471-2105-15-S7-S10","article-title":"Reconstruction of gene co-expression network from microarray data using local expression patterns","volume":"15","author":"Roy","year":"2014","journal-title":"BMC Bioinform."},{"issue":"1","key":"10.1016\/j.compbiolchem.2015.03.002_bib0210","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/1471-2105-13-20","article-title":"Graphite \u2013 a bioconductor package to convert pathway topology to gene network","volume":"13","author":"Sales","year":"2012","journal-title":"BMC Bioinform."},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0215","doi-asserted-by":"crossref","first-page":"2263","DOI":"10.1093\/bioinformatics\/btr373","article-title":"Genenetweaver: in silico benchmark generation and performance profiling of network inference methods","volume":"27","author":"Schaffter","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0220","doi-asserted-by":"crossref","first-page":"R6","DOI":"10.1186\/gb-2003-4-1-r6","article-title":"Towards reconstruction of gene networks from expression data by supervised learning","volume":"4","author":"Soinov","year":"2003","journal-title":"Genome Biol."},{"issue":"12","key":"10.1016\/j.compbiolchem.2015.03.002_bib0225","doi-asserted-by":"crossref","first-page":"3273","DOI":"10.1091\/mbc.9.12.3273","article-title":"Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization","volume":"9","author":"Spellman","year":"1998","journal-title":"Mol. Biol. Cell"},{"issue":"1","key":"10.1016\/j.compbiolchem.2015.03.002_bib0230","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1186\/1471-2105-7-380","article-title":"Validation and functional annotation of expression-based clusters based on gene ontology","volume":"7","author":"Steuer","year":"2006","journal-title":"BMC Bioinform."},{"issue":"1","key":"10.1016\/j.compbiolchem.2015.03.002_bib0235","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/1471-2105-7-43","article-title":"SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms","volume":"7","author":"Van den Bulcke","year":"2006","journal-title":"BMC Bioinform."},{"issue":"Web Server issue","key":"10.1016\/j.compbiolchem.2015.03.002_bib0240","doi-asserted-by":"crossref","first-page":"W214","DOI":"10.1093\/nar\/gkq537","article-title":"The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function","volume":"38","author":"Warde-Farley","year":"2010","journal-title":"Nucleic Acids Res."},{"issue":"12","key":"10.1016\/j.compbiolchem.2015.03.002_bib0245","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1093\/bioinformatics\/btm129","article-title":"A Markov random field model for network-based analysis of genomic data","volume":"23","author":"Wei","year":"2007","journal-title":"Bioinformatics"},{"key":"10.1016\/j.compbiolchem.2015.03.002_bib0250","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1186\/1471-2105-9-472","article-title":"Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data","volume":"9","author":"Xu","year":"2008","journal-title":"BMC Bioinform."},{"issue":"1","key":"10.1016\/j.compbiolchem.2015.03.002_bib0255","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1186\/1471-2105-11-400","article-title":"Intensity dependent estimation of noise in microarrays improves detection of differentially expressed genes","volume":"11","author":"Zeisel","year":"2010","journal-title":"BMC Bioinform."},{"issue":"2","key":"10.1016\/j.compbiolchem.2015.03.002_bib0260","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1109\/TCBB.2007.1067","article-title":"Inferring connectivity of genetic regulatory networks using information-theoretic criteria","volume":"5","author":"Zhao","year":"2008","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."}],"container-title":["Computational Biology and Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927115000481?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1476927115000481?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2020,9,1]],"date-time":"2020-09-01T19:52:55Z","timestamp":1598989975000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1476927115000481"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,6]]},"references-count":52,"alternative-id":["S1476927115000481"],"URL":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2015.03.002","relation":{},"ISSN":["1476-9271"],"issn-type":[{"value":"1476-9271","type":"print"}],"subject":[],"published":{"date-parts":[[2015,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Gene network coherence based on prior knowledge using direct and indirect relationships","name":"articletitle","label":"Article Title"},{"value":"Computational Biology and Chemistry","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.compbiolchem.2015.03.002","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Copyright \u00a9 2015 Elsevier Ltd. All rights reserved.","name":"copyright","label":"Copyright"}]}}