{"id":"https://openalex.org/W1560366047","doi":"https://doi.org/10.1186/1471-2105-7-218","title":"XcisClique: analysis of regulatory bicliques","display_name":"XcisClique: analysis of regulatory bicliques","publication_year":2006,"publication_date":"2006-04-21","ids":{"openalex":"https://openalex.org/W1560366047","doi":"https://doi.org/10.1186/1471-2105-7-218","mag":"1560366047","pmid":"https://pubmed.ncbi.nlm.nih.gov/16630346"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-218","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-218","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-218","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/10.1186/1471-2105-7-218","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110021900","display_name":"Amrita Pati","orcid":null},"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":"Amrita Pati","raw_affiliation_strings":["Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. apati@vt.edu","Department of Computer Science, Virginia Polytechnic Institute & State University, Blacksburg, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA. apati@vt.edu","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Computer Science, Virginia Polytechnic Institute & State University, Blacksburg, USA#TAB#","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079316116","display_name":"Cecilia V\u00e1squez-Robinet","orcid":"https://orcid.org/0000-0002-5166-0477"},"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":"Cecilia Vasquez-Robinet","raw_affiliation_strings":["Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA","Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057291575","display_name":"Lenwood S. Heath","orcid":"https://orcid.org/0000-0003-1608-431X"},"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":"Lenwood S Heath","raw_affiliation_strings":["Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA","Department of Computer Science, Virginia Polytechnic Institute & State University, Blacksburg, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Computer Science, Virginia Polytechnic Institute & State University, Blacksburg, USA#TAB#","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043746493","display_name":"Ruth Grene","orcid":"https://orcid.org/0000-0001-8205-6232"},"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":"Ruth Grene","raw_affiliation_strings":["Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA","Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Plant Pathology, Physiology, and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073142937","display_name":"T. M. Murali","orcid":"https://orcid.org/0000-0003-3688-4672"},"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":"TM Murali","raw_affiliation_strings":["Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA","Department of Computer Science, Virginia Polytechnic Institute & State University, Blacksburg, USA#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Department of Computer Science, Virginia Polytechnic Institute & State University, Blacksburg, USA#TAB#","institution_ids":["https://openalex.org/I859038795"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5057291575"],"corresponding_institution_ids":["https://openalex.org/I859038795"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":0.7618,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.670484,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"7","issue":"1","first_page":"218","last_page":"218"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.5533000230789185,"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":0.5533000230789185,"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/T10184","display_name":"Plant Molecular Biology Research","score":0.35370001196861267,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11468","display_name":"Genetic Mapping and Diversity in Plants and Animals","score":0.009499999694526196,"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/gene","display_name":"Gene","score":0.6459428071975708},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6041010618209839},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5406112670898438},{"id":"https://openalex.org/keywords/statistic","display_name":"Statistic","score":0.5064598321914673},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5023758411407471},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5016100406646729},{"id":"https://openalex.org/keywords/bipartite-graph","display_name":"Bipartite graph","score":0.4898790717124939},{"id":"https://openalex.org/keywords/complete-bipartite-graph","display_name":"Complete bipartite graph","score":0.48290181159973145},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.440510630607605},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.4365929365158081},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4002264142036438},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.3331448435783386},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.20476987957954407},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20158395171165466}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6459428071975708},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6041010618209839},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5406112670898438},{"id":"https://openalex.org/C89128539","wikidata":"https://www.wikidata.org/wiki/Q1949963","display_name":"Statistic","level":2,"score":0.5064598321914673},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5023758411407471},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5016100406646729},{"id":"https://openalex.org/C197657726","wikidata":"https://www.wikidata.org/wiki/Q174733","display_name":"Bipartite graph","level":3,"score":0.4898790717124939},{"id":"https://openalex.org/C134119311","wikidata":"https://www.wikidata.org/wiki/Q913598","display_name":"Complete bipartite graph","level":4,"score":0.48290181159973145},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.440510630607605},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.4365929365158081},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4002264142036438},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.3331448435783386},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.20476987957954407},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20158395171165466},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002874","descriptor_name":"Chromosome Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D050436","descriptor_name":"Regulatory Elements, Transcriptional","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-7-218","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-218","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-218","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:16630346","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16630346","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:302594","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1513260","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1513260","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1513260","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"},{"id":"pmh:oai:doaj.org/article:1cf87b63982a44f2affacd32c107ea70","is_oa":false,"landing_page_url":"https://doaj.org/article/1cf87b63982a44f2affacd32c107ea70","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 218 (2006)","raw_type":"article"},{"id":"pmh:oai:vtechworks.lib.vt.edu:10919/18951","is_oa":true,"landing_page_url":"http://hdl.handle.net/10919/18951","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"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-218","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-218","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-218","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":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.5899999737739563}],"awards":[{"id":"https://openalex.org/G5699223572","display_name":"ITR: Understanding Stress Resistance Mechanisms in Plants:  Multimodal Models Integrating Experimental Data, Databases, and the Literature","funder_award_id":"0219322","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"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1560366047.pdf","grobid_xml":"https://content.openalex.org/works/W1560366047.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1484413656","https://openalex.org/W1506285740","https://openalex.org/W1692319794","https://openalex.org/W1870378182","https://openalex.org/W1924304903","https://openalex.org/W1933383348","https://openalex.org/W1964895626","https://openalex.org/W1966855142","https://openalex.org/W1971606863","https://openalex.org/W1978173716","https://openalex.org/W1981800986","https://openalex.org/W1999351612","https://openalex.org/W2009475829","https://openalex.org/W2032231928","https://openalex.org/W2032467781","https://openalex.org/W2036215574","https://openalex.org/W2039286232","https://openalex.org/W2070539328","https://openalex.org/W2076248048","https://openalex.org/W2098222328","https://openalex.org/W2100945610","https://openalex.org/W2102240211","https://openalex.org/W2106004801","https://openalex.org/W2106493933","https://openalex.org/W2108818769","https://openalex.org/W2109464129","https://openalex.org/W2111646009","https://openalex.org/W2112318170","https://openalex.org/W2115979107","https://openalex.org/W2119952888","https://openalex.org/W2122221811","https://openalex.org/W2123775704","https://openalex.org/W2124433786","https://openalex.org/W2125508747","https://openalex.org/W2129023473","https://openalex.org/W2130778658","https://openalex.org/W2134307042","https://openalex.org/W2138032440","https://openalex.org/W2141408320","https://openalex.org/W2143246780","https://openalex.org/W2145133452","https://openalex.org/W2157827172","https://openalex.org/W2166559705","https://openalex.org/W2167082201","https://openalex.org/W2169351355","https://openalex.org/W2621043213"],"related_works":["https://openalex.org/W2052655934","https://openalex.org/W3032874291","https://openalex.org/W2122223946","https://openalex.org/W2021297725","https://openalex.org/W2170292930","https://openalex.org/W1986472717","https://openalex.org/W2114454856","https://openalex.org/W2078926220","https://openalex.org/W2035892324","https://openalex.org/W2111172999"],"abstract_inverted_index":{"BACKGROUND:":[0],"Modeling":[1],"of":[2,11,22,30,33,50,63,77,84,145,148,150,164,173,205,207,229,243],"cis-elements":[3,52,120],"or":[4],"regulatory":[5,23,85,239],"motifs":[6,24,152],"in":[7,27,40,53,103,127,153,187,209],"promoter":[8,56],"(upstream)":[9],"regions":[10],"genes":[12,34,78,208],"is":[13,35,57,72,106,142,178],"a":[14,31,38,41,54,75,81,107,128,143,154,179],"challenging":[15],"computational":[16],"problem.":[17],"In":[18],"this":[19,104,183],"work,":[20,105],"set":[21,32,76,83],"simultaneously":[25,88],"present":[26],"the":[28,60,100,146,161,188,227,248],"promoters":[29],"modeled":[36],"as":[37,121,185,201],"biclique":[39,155],"suitably":[42],"defined":[43],"bipartite":[44,129],"graph.":[45],"A":[46,241],"biologically":[47],"meaningful":[48],"co-occurrence":[49],"multiple":[51],"gene":[55,66,92,115,174,196,234],"assessed":[58],"by":[59],"combined":[61],"analysis":[62],"genomic":[64,231],"and":[65,114,132,159,195,212,219,237,255],"expression":[67,93,116,175,235],"data.":[68],"Greater":[69],"statistical":[70,139],"significance":[71],"associated":[73],"with":[74],"that":[79,110,169,198],"shares":[80],"common":[82],"motifs,":[86],"while":[87],"exhibiting":[89],"highly":[90],"correlated":[91],"under":[94],"given":[95],"experimental":[96],"conditions.":[97],"METHODS:":[98],"XcisClique,":[99],"system":[101],"developed":[102],"comprehensive":[108],"infrastructure":[109],"associates":[111],"annotated":[112,230],"genome":[113],"data,":[117,236],"models":[118],"known":[119],"regular":[122],"expressions,":[123],"identifies":[124,192],"maximal":[125],"bicliques":[126,134],"gene-motif":[130],"graph;":[131],"ranks":[133],"based":[135],"on":[136,160],"their":[137],"computed":[138],"significance.":[140],"Significance":[141],"function":[144],"probability":[147],"occurrence":[149],"those":[151],"(a":[156],"hypergeometric":[157],"distribution),":[158],"new":[162,193],"sum":[163],"absolute":[165],"values":[166],"statistic":[167,180],"(SAV)":[168],"uses":[170],"Spearman":[171],"correlations":[172],"vectors.":[176],"SAV":[177],"well-suited":[181],"for":[182],"purpose":[184],"described":[186],"discussion.":[189],"RESULTS:":[190],"XcisClique":[191],"motif":[194,249],"combinations":[197],"might":[199],"indicate":[200],"yet":[202],"unidentified":[203],"involvement":[204],"sets":[206],"biological":[210],"functions":[211],"processes.":[213],"It":[214],"currently":[215],"supports":[216],"Arabidopsis":[217],"thaliana":[218],"can":[220],"be":[221],"adapted":[222],"to":[223],"other":[224],"organisms,":[225],"assuming":[226],"existence":[228],"sequences,":[232],"suitable":[233],"identified":[238],"motifs.":[240],"subset":[242],"Xcis":[244],"Clique":[245],"functionalities,":[246],"including":[247],"visualization":[250],"component":[251],"MotifSee,":[252],"source":[253],"code,":[254],"supplementary":[256],"material":[257],"are":[258],"available":[259],"at":[260],"https://bioinformatics.cs.vt.edu/xcisclique/.":[261]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-23T07:36:19.812096","created_date":"2025-10-10T00:00:00"}
