{"id":"https://openalex.org/W2048922348","doi":"https://doi.org/10.1186/1471-2105-12-82","title":"Motif-guided sparse decomposition of gene expression data for regulatory module identification","display_name":"Motif-guided sparse decomposition of gene expression data for regulatory module identification","publication_year":2011,"publication_date":"2011-03-22","ids":{"openalex":"https://openalex.org/W2048922348","doi":"https://doi.org/10.1186/1471-2105-12-82","mag":"2048922348","pmid":"https://pubmed.ncbi.nlm.nih.gov/21426557"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-82","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-82","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-82","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/10.1186/1471-2105-12-82","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100766852","display_name":"Ting Gong","orcid":"https://orcid.org/0000-0003-4844-0227"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ting Gong","raw_affiliation_strings":["Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA","[Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA 22203, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"[Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, USA]","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101536121","display_name":"Jianhua Xuan","orcid":"https://orcid.org/0000-0001-7256-1374"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jianhua Xuan","raw_affiliation_strings":["Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, 22203, USA","Virginia Polytechnic Institute And State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, 22203, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Virginia Polytechnic Institute And State University","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100379195","display_name":"Li Chen","orcid":"https://orcid.org/0000-0001-9372-5606"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Li Chen","raw_affiliation_strings":["Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, 22203, USA","[Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, USA]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, 22203, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"[Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, USA]","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032949456","display_name":"Rebecca B. Riggins","orcid":"https://orcid.org/0000-0002-1555-4431"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rebecca B Riggins","raw_affiliation_strings":["Lombardi Comprehensive Cancer Center and Department of Oncology, Physiology and Biophysics, Georgetown University, Washington, DC, 20057, USA","GEORGETOWN UNIVERSITY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lombardi Comprehensive Cancer Center and Department of Oncology, Physiology and Biophysics, Georgetown University, Washington, DC, 20057, USA","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"]},{"raw_affiliation_string":"GEORGETOWN UNIVERSITY","institution_ids":["https://openalex.org/I184565670"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074947237","display_name":"Huai Li","orcid":"https://orcid.org/0000-0001-7129-6660"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I4210136897","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210136897"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Huai Li","raw_affiliation_strings":["Bioinformatics Unit, RRB, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA","National Institutes of Health"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Unit, RRB, National Institute on Aging, National Institutes of Health, Baltimore, MD, 21224, USA","institution_ids":["https://openalex.org/I1299303238","https://openalex.org/I4210136897"]},{"raw_affiliation_string":"National Institutes of Health","institution_ids":["https://openalex.org/I1299303238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086088688","display_name":"Eric P. Hoffman","orcid":"https://orcid.org/0000-0001-6470-5139"},"institutions":[{"id":"https://openalex.org/I1336742384","display_name":"Children's National","ror":"https://ror.org/03wa2q724","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1336742384"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric P Hoffman","raw_affiliation_strings":["Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC, 20010, USA","Children\u00bfs National Medical Center"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center for Genetic Medicine, Children's National Medical Center, Washington, DC, 20010, USA","institution_ids":["https://openalex.org/I1336742384"]},{"raw_affiliation_string":"Children\u00bfs National Medical Center","institution_ids":["https://openalex.org/I1336742384"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011322600","display_name":"Robert Clarke","orcid":"https://orcid.org/0000-0002-9278-0854"},"institutions":[{"id":"https://openalex.org/I184565670","display_name":"Georgetown University","ror":"https://ror.org/05vzafd60","country_code":"US","type":"education","lineage":["https://openalex.org/I184565670"]},{"id":"https://openalex.org/I2799903593","display_name":"Georgetown University Medical Center","ror":"https://ror.org/00hjz7x27","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799903593"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Clarke","raw_affiliation_strings":["Lombardi Comprehensive Cancer Center and Department of Oncology, Physiology and Biophysics, Georgetown University, Washington, DC, 20057, USA","GEORGETOWN UNIVERSITY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lombardi Comprehensive Cancer Center and Department of Oncology, Physiology and Biophysics, Georgetown University, Washington, DC, 20057, USA","institution_ids":["https://openalex.org/I184565670","https://openalex.org/I2799903593"]},{"raw_affiliation_string":"GEORGETOWN UNIVERSITY","institution_ids":["https://openalex.org/I184565670"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100666595","display_name":"Yue Wang","orcid":"https://orcid.org/0000-0001-5918-7525"},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yue Wang","raw_affiliation_strings":["Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, 22203, USA","Virginia Polytechnic Institute And State University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bradley Department of Electrical and Computer Engineering, Virginia Tech, Arlington, VA, 22203, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Virginia Polytechnic Institute And State University","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5101536121"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.7031,"has_fulltext":true,"cited_by_count":19,"citation_normalized_percentile":{"value":0.83676204,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"12","issue":"1","first_page":"82","last_page":"82"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.5468000173568726,"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":0.5468000173568726,"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/T10885","display_name":"Gene expression and cancer classification","score":0.22830000519752502,"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":0.10949999839067459,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6553299427032471},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6154553890228271},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5681582093238831},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.518117368221283},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5078137516975403},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.496770441532135},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.47449517250061035},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.47339165210723877},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.46972382068634033},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4561270475387573},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.4429605007171631},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.43393999338150024},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3342663645744324},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13227584958076477}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6553299427032471},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6154553890228271},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5681582093238831},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.518117368221283},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5078137516975403},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.496770441532135},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.47449517250061035},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.47339165210723877},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.46972382068634033},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4561270475387573},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.4429605007171631},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.43393999338150024},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3342663645744324},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13227584958076477},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"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":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","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":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-12-82","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-82","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-82","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:21426557","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21426557","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:doaj.org/article:5fd78d5be95443ef95165b99f1fafb86","is_oa":false,"landing_page_url":"https://doaj.org/article/5fd78d5be95443ef95165b99f1fafb86","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 12, Iss 1, p 82 (2011)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2083892","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3072956","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:vtechworks.lib.vt.edu:10919/18810","is_oa":true,"landing_page_url":"http://hdl.handle.net/10919/18810","pdf_url":null,"source":{"id":"https://openalex.org/S4306400248","display_name":"VTechWorks (Virginia Tech)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I859038795","host_organization_name":"Virginia Tech","host_organization_lineage":["https://openalex.org/I859038795"],"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":null,"raw_type":"Article - Refereed"},{"id":"pmh:oai:vtechworks.lib.vt.edu:10919/18811","is_oa":true,"landing_page_url":"http://hdl.handle.net/10919/18811","pdf_url":null,"source":{"id":"https://openalex.org/S4306400248","display_name":"VTechWorks (Virginia Tech)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I859038795","host_organization_name":"Virginia Tech","host_organization_lineage":["https://openalex.org/I859038795"],"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":"","raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-82","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-82","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-82","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":0.75,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1144149631","display_name":null,"funder_award_id":"BC030280","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1153284716","display_name":null,"funder_award_id":"CA139246","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1236271319","display_name":null,"funder_award_id":"R01 NS029525","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G1369073207","display_name":null,"funder_award_id":"CA149147","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2974495216","display_name":null,"funder_award_id":"CA109872","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3025988305","display_name":null,"funder_award_id":"CA096483","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3283202979","display_name":null,"funder_award_id":"EB000830","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3531376913","display_name":null,"funder_award_id":"NS29525","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G403815733","display_name":null,"funder_award_id":"EB000830","funder_id":"https://openalex.org/F4320306078","funder_display_name":"U.S. Department of Defense"},{"id":"https://openalex.org/G4303064284","display_name":null,"funder_award_id":"R01 CA149653","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4716551556","display_name":null,"funder_award_id":"CA149653","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4951317011","display_name":null,"funder_award_id":"CA139246","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G541141811","display_name":null,"funder_award_id":"CA149653","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6138437844","display_name":null,"funder_award_id":"BC030280","funder_id":"https://openalex.org/F4320306078","funder_display_name":"U.S. Department of Defense"},{"id":"https://openalex.org/G6967836897","display_name":null,"funder_award_id":"CA149147","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7695387192","display_name":null,"funder_award_id":"EB000830","funder_id":"https://openalex.org/F4320337363","funder_display_name":"National Institute of Biomedical Imaging and Bioengineering"},{"id":"https://openalex.org/G8636808538","display_name":null,"funder_award_id":"CA109872","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320306078","display_name":"U.S. Department of Defense","ror":"https://ror.org/0447fe631"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"},{"id":"https://openalex.org/F4320337363","display_name":"National Institute of Biomedical Imaging and Bioengineering","ror":"https://ror.org/00372qc85"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2048922348.pdf","grobid_xml":"https://content.openalex.org/works/W2048922348.grobid-xml"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W97469372","https://openalex.org/W1517634087","https://openalex.org/W1623768750","https://openalex.org/W1663251599","https://openalex.org/W1851422093","https://openalex.org/W1964321121","https://openalex.org/W1991198967","https://openalex.org/W1992242907","https://openalex.org/W1999470996","https://openalex.org/W2013145602","https://openalex.org/W2013956549","https://openalex.org/W2021880285","https://openalex.org/W2023971898","https://openalex.org/W2051084846","https://openalex.org/W2052412248","https://openalex.org/W2053945283","https://openalex.org/W2058273658","https://openalex.org/W2058906289","https://openalex.org/W2068860273","https://openalex.org/W2069645361","https://openalex.org/W2070476729","https://openalex.org/W2083784140","https://openalex.org/W2094036688","https://openalex.org/W2095517704","https://openalex.org/W2096218546","https://openalex.org/W2096863518","https://openalex.org/W2097090208","https://openalex.org/W2098412979","https://openalex.org/W2099111195","https://openalex.org/W2099254673","https://openalex.org/W2099544459","https://openalex.org/W2101600318","https://openalex.org/W2101995865","https://openalex.org/W2103453943","https://openalex.org/W2103835486","https://openalex.org/W2110065044","https://openalex.org/W2111004422","https://openalex.org/W2111932365","https://openalex.org/W2113613985","https://openalex.org/W2118718620","https://openalex.org/W2119318224","https://openalex.org/W2125310307","https://openalex.org/W2125512776","https://openalex.org/W2126602684","https://openalex.org/W2126715263","https://openalex.org/W2130410032","https://openalex.org/W2131152510","https://openalex.org/W2134001292","https://openalex.org/W2135000328","https://openalex.org/W2135030836","https://openalex.org/W2135187880","https://openalex.org/W2135347957","https://openalex.org/W2135445066","https://openalex.org/W2136787567","https://openalex.org/W2138782161","https://openalex.org/W2144113133","https://openalex.org/W2146999361","https://openalex.org/W2151038079","https://openalex.org/W2151186643","https://openalex.org/W2151945801","https://openalex.org/W2153208554","https://openalex.org/W2155587014","https://openalex.org/W2156933633","https://openalex.org/W2163296727","https://openalex.org/W2165232124","https://openalex.org/W2166106382","https://openalex.org/W2167190345","https://openalex.org/W2168463311","https://openalex.org/W2168783124","https://openalex.org/W2169318796","https://openalex.org/W2170567460","https://openalex.org/W2170728568","https://openalex.org/W2478708596","https://openalex.org/W3151941575"],"related_works":["https://openalex.org/W2069695727","https://openalex.org/W1996185163","https://openalex.org/W2084813257","https://openalex.org/W2045929470","https://openalex.org/W2081127504","https://openalex.org/W2122223946","https://openalex.org/W4233500668","https://openalex.org/W1974145978","https://openalex.org/W1977867163","https://openalex.org/W2393426762"],"abstract_inverted_index":{"BACKGROUND:":[0],"Genes":[1],"work":[2],"coordinately":[3],"as":[4,94],"gene":[5,8,18,22,27,38,43,56,76,81,112,131,177,204,228],"modules":[6,19,78,167,178,206,283],"or":[7],"networks.":[9],"Various":[10],"computational":[11],"approaches":[12],"have":[13,216],"been":[14],"proposed":[15],"to":[16,74,123,139,208],"find":[17],"based":[20],"on":[21,194],"expression":[23,39,82,229],"data;":[24],"for":[25,33,49,160,231,244,266],"example,":[26],"clustering":[28,44,118,242],"is":[29,92,120,136],"a":[30,67,95,116,130,218,239,251,262,276],"popular":[31],"method":[32,119,237,243,259,265],"grouping":[34],"genes":[35,149],"with":[36,180],"similar":[37],"patterns.":[40],"However,":[41],"traditional":[42],"often":[45],"yields":[46],"unsatisfactory":[47],"results":[48,272],"regulatory":[50,77,166,205,232,282],"module":[51,233],"identification":[52],"because":[53],"the":[54,107,110,125,141,147,151,188,191],"resulting":[55],"clusters":[57],"are":[58],"co-expressed":[59],"but":[60],"not":[61],"necessarily":[62],"co-regulated.":[63],"RESULTS:":[64],"We":[65,185,215],"propose":[66],"novel":[68,240],"approach,":[69],"motif-guided":[70,117,223,241,277],"sparse":[71,133,224,263],"decomposition":[72,225,264],"(mSD),":[73],"identify":[75],"by":[79,249],"integrating":[80],"data":[83,199],"and":[84,105,144,170,200,255,287],"DNA":[85],"sequence":[86],"motif":[87],"information.":[88],"The":[89,154,235,257,270],"mSD":[90,155,192,236,258],"approach":[91,156,193],"implemented":[93],"two-step":[96],"algorithm":[97],"comprising":[98],"estimates":[99],"of":[100,109,129,150,190,211,227],"(1)":[101],"transcription":[102,126,152,183,245],"factor":[103,127,246],"activity":[104,128,247],"(2)":[106],"strength":[108,268],"predicted":[111],"regulation":[113,142,267],"event(s).":[114],"Specifically,":[115],"first":[121,158],"developed":[122,217],"estimate":[124,140],"module;":[132],"component":[134],"analysis":[135],"then":[137,186],"applied":[138],"strength,":[143],"so":[145],"predict":[146],"target":[148],"factors.":[153,184],"was":[157],"tested":[159],"its":[161],"improved":[162],"performance":[163],"in":[164,284],"finding":[165,250],"using":[168],"simulated":[169],"real":[171],"yeast":[172,286],"data,":[173,230],"revealing":[174],"functionally":[175],"distinct":[176],"enriched":[179],"biologically":[181],"validated":[182],"demonstrated":[187],"efficacy":[189],"breast":[195,212,288],"cancer":[196,289],"cell":[197],"line":[198],"uncovered":[201],"several":[202],"important":[203],"related":[207],"endocrine":[209],"therapy":[210],"cancer.":[213],"CONCLUSION:":[214],"new":[219],"integrated":[220],"strategy,":[221],"namely":[222],"(mSD)":[226],"identification.":[234],"features":[238],"estimation":[248],"balance":[252],"between":[253],"co-regulation":[254],"co-expression.":[256],"further":[260],"utilizes":[261],"estimation.":[269],"experimental":[271],"show":[273],"that":[274],"such":[275],"strategy":[278],"can":[279],"provide":[280],"context-specific":[281],"both":[285],"studies.":[290]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":6}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}