{"id":"https://openalex.org/W2161732139","doi":"https://doi.org/10.1186/1471-2105-7-280","title":"Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks","display_name":"Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks","publication_year":2006,"publication_date":"2006-06-02","ids":{"openalex":"https://openalex.org/W2161732139","doi":"https://doi.org/10.1186/1471-2105-7-280","mag":"2161732139","pmid":"https://pubmed.ncbi.nlm.nih.gov/16749936"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-280","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-280","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-280","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-280","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087598092","display_name":"David J. Reiss","orcid":"https://orcid.org/0000-0001-5392-3034"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David J Reiss","raw_affiliation_strings":["Institute for Systems Biology, 1441 N, 34th St, Seattle, WA 98103-8904, USA. dreiss@systemsbiology.org","Institute for Systems Biology, 1441 N. 34th St, Seattle, WA, 98103-8904, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, 1441 N, 34th St, Seattle, WA 98103-8904, USA. dreiss@systemsbiology.org","institution_ids":["https://openalex.org/I3148997608"]},{"raw_affiliation_string":"Institute for Systems Biology, 1441 N. 34th St, Seattle, WA, 98103-8904, USA","institution_ids":["https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005287667","display_name":"Nitin S. Baliga","orcid":"https://orcid.org/0000-0001-9157-5974"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nitin S Baliga","raw_affiliation_strings":["Institute for Systems Biology, 1441 N. 34th St, Seattle, WA, 98103-8904, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Systems Biology, 1441 N. 34th St, Seattle, WA, 98103-8904, USA","institution_ids":["https://openalex.org/I3148997608"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055203249","display_name":"Richard Bonneau","orcid":"https://orcid.org/0000-0003-4354-7906"},"institutions":[{"id":"https://openalex.org/I57206974","display_name":"New York University","ror":"https://ror.org/0190ak572","country_code":"US","type":"education","lineage":["https://openalex.org/I57206974"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Richard Bonneau","raw_affiliation_strings":["Dept. of Biology, Dept. of Computer Science, New York University, New York, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept. of Biology, Dept. of Computer Science, New York University, New York, USA","institution_ids":["https://openalex.org/I57206974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5005287667","https://openalex.org/A5055203249"],"corresponding_institution_ids":["https://openalex.org/I3148997608","https://openalex.org/I57206974"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":8.1376,"has_fulltext":true,"cited_by_count":260,"citation_normalized_percentile":{"value":0.9846349,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"7","issue":"1","first_page":"280","last_page":"280"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.29089999198913574,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.29089999198913574,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.19099999964237213,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.16200000047683716,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6785746812820435},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6394366025924683},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6337664723396301},{"id":"https://openalex.org/keywords/biclustering","display_name":"Biclustering","score":0.6234415769577026},{"id":"https://openalex.org/keywords/regulon","display_name":"Regulon","score":0.5933303833007812},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5748907923698425},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.49899935722351074},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.46469753980636597},{"id":"https://openalex.org/keywords/decipher","display_name":"DECIPHER","score":0.45704442262649536},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.44284379482269287},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4426388442516327},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.28285539150238037},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2286105751991272},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.20667004585266113},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.11644533276557922},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.11194610595703125}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6785746812820435},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6394366025924683},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6337664723396301},{"id":"https://openalex.org/C144817290","wikidata":"https://www.wikidata.org/wiki/Q2976575","display_name":"Biclustering","level":5,"score":0.6234415769577026},{"id":"https://openalex.org/C62361671","wikidata":"https://www.wikidata.org/wiki/Q1754612","display_name":"Regulon","level":4,"score":0.5933303833007812},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5748907923698425},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.49899935722351074},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.46469753980636597},{"id":"https://openalex.org/C164614171","wikidata":"https://www.wikidata.org/wiki/Q5204775","display_name":"DECIPHER","level":2,"score":0.45704442262649536},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.44284379482269287},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4426388442516327},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.28285539150238037},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2286105751991272},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.20667004585266113},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.11644533276557922},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11194610595703125},{"id":"https://openalex.org/C33704608","wikidata":"https://www.wikidata.org/wiki/Q5014717","display_name":"CURE data clustering algorithm","level":4,"score":0.0},{"id":"https://openalex.org/C94641424","wikidata":"https://www.wikidata.org/wiki/Q5172845","display_name":"Correlation clustering","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006217","descriptor_name":"Halobacterium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006217","descriptor_name":"Halobacterium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006217","descriptor_name":"Halobacterium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016480","descriptor_name":"Helicobacter pylori","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-7-280","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-280","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-280","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16749936","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16749936","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:osti.gov:1626322","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1626322","pdf_url":"https://www.osti.gov/servlets/purl/1626322","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:5de70e9ac3ea40cc97de681bca6a6e26","is_oa":false,"landing_page_url":"https://doaj.org/article/5de70e9ac3ea40cc97de681bca6a6e26","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 7, Iss 1, p 280 (2006)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1502140","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1502140","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-280","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-280","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-280","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.550000011920929,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G230815042","display_name":"ITR:  Development of an Integrated Computational and Experimental Approach to Predict Biological Networks in Halobacterium sp","funder_award_id":"0220153","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G455025026","display_name":"QSB: Modeling Predictive Biological Networks in Halobacterium sp.","funder_award_id":"0425825","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5015013786","display_name":"BE/Gen-En:  The Oxygen-stress Response in the Extremophile Halobacterium sp. NRC-1: Systems Analysis and Development of Supplemental High School Instruction Modules","funder_award_id":"0313754","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320875","display_name":"Deutscher Akademischer Austauschdienst","ror":"https://ror.org/039djdh30"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2161732139.pdf","grobid_xml":"https://content.openalex.org/works/W2161732139.grobid-xml"},"referenced_works_count":103,"referenced_works":["https://openalex.org/W1480376833","https://openalex.org/W1493217831","https://openalex.org/W1527927437","https://openalex.org/W1549090124","https://openalex.org/W1554944419","https://openalex.org/W1592870802","https://openalex.org/W1805258884","https://openalex.org/W1812401750","https://openalex.org/W1840933474","https://openalex.org/W1958371615","https://openalex.org/W1990144966","https://openalex.org/W1995117714","https://openalex.org/W2008620264","https://openalex.org/W2008669517","https://openalex.org/W2013416277","https://openalex.org/W2024060531","https://openalex.org/W2025399691","https://openalex.org/W2025474488","https://openalex.org/W2033829365","https://openalex.org/W2038540528","https://openalex.org/W2040853949","https://openalex.org/W2040941311","https://openalex.org/W2041877620","https://openalex.org/W2044482436","https://openalex.org/W2046140008","https://openalex.org/W2053126761","https://openalex.org/W2053906518","https://openalex.org/W2055043387","https://openalex.org/W2057682468","https://openalex.org/W2057885377","https://openalex.org/W2058221907","https://openalex.org/W2058849889","https://openalex.org/W2064787891","https://openalex.org/W2078129874","https://openalex.org/W2080278541","https://openalex.org/W2080498142","https://openalex.org/W2087530874","https://openalex.org/W2096358531","https://openalex.org/W2097396311","https://openalex.org/W2100332892","https://openalex.org/W2101327327","https://openalex.org/W2103453943","https://openalex.org/W2105797070","https://openalex.org/W2105883975","https://openalex.org/W2107233900","https://openalex.org/W2108167744","https://openalex.org/W2108420379","https://openalex.org/W2109501217","https://openalex.org/W2109715166","https://openalex.org/W2111031006","https://openalex.org/W2112811019","https://openalex.org/W2114844197","https://openalex.org/W2117549173","https://openalex.org/W2121905508","https://openalex.org/W2123079633","https://openalex.org/W2123280311","https://openalex.org/W2125508747","https://openalex.org/W2126873530","https://openalex.org/W2126952238","https://openalex.org/W2126991359","https://openalex.org/W2127479124","https://openalex.org/W2129265801","https://openalex.org/W2130059379","https://openalex.org/W2130158951","https://openalex.org/W2130687290","https://openalex.org/W2135221645","https://openalex.org/W2135738425","https://openalex.org/W2136107412","https://openalex.org/W2137167578","https://openalex.org/W2137683543","https://openalex.org/W2138907483","https://openalex.org/W2140863273","https://openalex.org/W2141408320","https://openalex.org/W2144544802","https://openalex.org/W2145333821","https://openalex.org/W2146312020","https://openalex.org/W2146856779","https://openalex.org/W2147977520","https://openalex.org/W2151233592","https://openalex.org/W2151763757","https://openalex.org/W2152350018","https://openalex.org/W2155606054","https://openalex.org/W2159482845","https://openalex.org/W2159675211","https://openalex.org/W2159767718","https://openalex.org/W2159883877","https://openalex.org/W2161782181","https://openalex.org/W2162111678","https://openalex.org/W2162142896","https://openalex.org/W2163296727","https://openalex.org/W2165336645","https://openalex.org/W2166898290","https://openalex.org/W2167190345","https://openalex.org/W2169536307","https://openalex.org/W2170809966","https://openalex.org/W2171088586","https://openalex.org/W2510854709","https://openalex.org/W2992848669","https://openalex.org/W4205238219","https://openalex.org/W4252706339","https://openalex.org/W4255855797","https://openalex.org/W4285719527","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W61127607","https://openalex.org/W1984136937","https://openalex.org/W2115350162","https://openalex.org/W1786268878","https://openalex.org/W2794893700","https://openalex.org/W4281651837","https://openalex.org/W4313622135","https://openalex.org/W4362693150","https://openalex.org/W2164421791","https://openalex.org/W1011779"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,218],"learning":[2],"of":[3,23,29,54,61,104,156,169,185,209,269],"global":[4],"genetic":[5],"regulatory":[6,191],"networks":[7],"from":[8],"expression":[9,158],"data":[10,159,200],"is":[11,17,65,101],"a":[12,52,85,266],"severely":[13],"under-constrained":[14],"problem":[15],"that":[16,40,146,278],"aided":[18],"by":[19,27,152,221],"reducing":[20],"the":[21,24,102,125,132,154,165,179,205,238,244],"dimensionality":[22],"search":[25],"space":[26],"means":[28],"clustering":[30,126,274],"genes":[31,46,62,72,249],"into":[32,124],"putatively":[33],"co-regulated":[34,49,149],"groups,":[35],"as":[36,183],"opposed":[37],"to":[38,130,178,188,250],"those":[39],"are":[41,73,116,281],"simply":[42],"co-expressed.":[43],"Be":[44],"cause":[45],"may":[47],"be":[48],"only":[50],"across":[51],"subset":[53],"all":[55,285],"observed":[56],"experimental":[57],"conditions,":[58],"biclustering":[59,155],"(clustering":[60],"and":[63,83,160,215,227,257,276],"conditions)":[64],"more":[66,107,135,282],"appropriate":[67],"than":[68],"standard":[69],"clustering.":[70],"Co-regulated":[71],"also":[74],"often":[75],"functionally":[76],"(physically,":[77],"spatially,":[78],"genetically,":[79],"and/or":[80],"evolutionarily)":[81],"associated,":[82],"such":[84],"priori":[86],"known":[87,225,260],"or":[88,106],"pre-computed":[89],"associations":[90,163],"can":[91,128],"provide":[92],"support":[93],"for":[94,201,232,288],"appropriately":[95],"grouping":[96],"genes.":[97],"One":[98],"important":[99],"association":[100],"presence":[103],"one":[105],"common":[108],"cis-regulatory":[109],"motifs.":[110,171],"In":[111,193],"organisms":[112,203],"where":[113],"these":[114],"motifs":[115],"not":[117],"known,":[118],"their":[119],"de":[120,166],"novo":[121,167],"detection,":[122],"integrated":[123],"algorithm,":[127,144],"help":[129],"guide":[131],"process":[133],"towards":[134],"biologically":[136],"parsimonious":[137,283],"solutions.":[138],"RESULTS:":[139],"We":[140,173,263],"have":[141,174,264],"developed":[142],"an":[143],"cMonkey,":[145],"detects":[147],"putative":[148],"gene":[150,157],"groupings":[151],"integrating":[153],"various":[161],"functional":[162],"with":[164,253,284],"detection":[168],"sequence":[170],"CONCLUSION:":[172],"applied":[175],"this":[176,251],"procedure":[177],"archaeon":[180],"Halobacterium":[181,233],"NRC-1,":[182],"part":[184],"our":[186],"efforts":[187],"decipher":[189],"its":[190,259],"network.":[192],"addition,":[194],"we":[195],"used":[196],"cMonkey":[197,222,270,279],"on":[198],"public":[199],"three":[202],"in":[204,237],"other":[206,273],"two":[207],"domains":[208],"life:":[210],"Helicobacter":[211],"pylori,":[212],"Saccharomyces":[213],"cerevisiae,":[214],"Escherichia":[216],"coli.":[217],"biclusters":[219,280],"detected":[220,258],"both":[223],"recapitulated":[224],"biology":[226],"enabled":[228],"novel":[229],"predictions":[230],"(some":[231],"were":[234],"subsequently":[235],"confirmed":[236],"laboratory).":[239],"For":[240],"example,":[241],"it":[242],"identified":[243],"bacteriorhodopsin":[245],"regulon,":[246],"assigned":[247],"additional":[248],"regulon":[252],"apparently":[254],"unrelated":[255],"function,":[256],"promoter":[261],"motif.":[262],"performed":[265],"thorough":[267],"comparison":[268],"results":[271],"against":[272],"methods,":[275],"find":[277],"available":[286],"evidence":[287],"co-regulation.":[289]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":13},{"year":2018,"cited_by_count":12},{"year":2017,"cited_by_count":15},{"year":2016,"cited_by_count":16},{"year":2015,"cited_by_count":17},{"year":2014,"cited_by_count":15},{"year":2013,"cited_by_count":18},{"year":2012,"cited_by_count":18}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
