{"id":"https://openalex.org/W2075823265","doi":"https://doi.org/10.1145/2688909","title":"Constrained Community-Based Gene Regulatory Network Inference","display_name":"Constrained Community-Based Gene Regulatory Network Inference","publication_year":2015,"publication_date":"2015-02-17","ids":{"openalex":"https://openalex.org/W2075823265","doi":"https://doi.org/10.1145/2688909","mag":"2075823265"},"language":"en","primary_location":{"id":"doi:10.1145/2688909","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2688909","pdf_url":null,"source":{"id":"https://openalex.org/S38703467","display_name":"ACM Transactions on Modeling and Computer Simulation","issn_l":"1049-3301","issn":["1049-3301","1558-1195"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Modeling and Computer Simulation","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://dl.acm.org/citation.cfm?doid=2688909","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052534316","display_name":"Ferdinando Fioretto","orcid":"https://orcid.org/0000-0002-1381-6776"},"institutions":[{"id":"https://openalex.org/I10052268","display_name":"New Mexico State University","ror":"https://ror.org/00hpz7z43","country_code":"US","type":"education","lineage":["https://openalex.org/I10052268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ferdinando Fioretto","raw_affiliation_strings":["New Mexico State University & University of Udine, Las Cruces, NM"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"New Mexico State University & University of Udine, Las Cruces, NM","institution_ids":["https://openalex.org/I10052268"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064407367","display_name":"Agostino Dovier","orcid":"https://orcid.org/0000-0003-2052-8593"},"institutions":[{"id":"https://openalex.org/I129043915","display_name":"University of Udine","ror":"https://ror.org/05ht0mh31","country_code":"IT","type":"education","lineage":["https://openalex.org/I129043915"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Agostino Dovier","raw_affiliation_strings":["University of Udine, Italy","(University of Udine, Italy)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Udine, Italy","institution_ids":["https://openalex.org/I129043915"]},{"raw_affiliation_string":"(University of Udine, Italy)","institution_ids":["https://openalex.org/I129043915"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024528910","display_name":"Enrico Pontelli","orcid":"https://orcid.org/0000-0002-7753-1737"},"institutions":[{"id":"https://openalex.org/I10052268","display_name":"New Mexico State University","ror":"https://ror.org/00hpz7z43","country_code":"US","type":"education","lineage":["https://openalex.org/I10052268"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Enrico Pontelli","raw_affiliation_strings":["New Mexico State University, Las Cruces, NM","New Mexico State University, Las Cruces, NM;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"New Mexico State University, Las Cruces, NM","institution_ids":["https://openalex.org/I10052268"]},{"raw_affiliation_string":"New Mexico State University, Las Cruces, NM;","institution_ids":["https://openalex.org/I10052268"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4434,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.6525944,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"25","issue":"2","first_page":"1","last_page":"26"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9987000226974487,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9987000226974487,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9977999925613403,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9933000206947327,"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/inference","display_name":"Inference","score":0.7477982044219971},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.698292076587677},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.6938010454177856},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5947245955467224},{"id":"https://openalex.org/keywords/constraint-programming","display_name":"Constraint programming","score":0.5842090845108032},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5054924488067627},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4190279543399811},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.41303688287734985},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3696754574775696},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3565070629119873},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.3187825083732605},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.20734649896621704},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1426074504852295},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11980536580085754},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10195550322532654},{"id":"https://openalex.org/keywords/stochastic-programming","display_name":"Stochastic programming","score":0.09676596522331238}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7477982044219971},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.698292076587677},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.6938010454177856},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5947245955467224},{"id":"https://openalex.org/C173404611","wikidata":"https://www.wikidata.org/wiki/Q528588","display_name":"Constraint programming","level":3,"score":0.5842090845108032},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5054924488067627},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4190279543399811},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.41303688287734985},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3696754574775696},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3565070629119873},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.3187825083732605},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.20734649896621704},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1426074504852295},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11980536580085754},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10195550322532654},{"id":"https://openalex.org/C137631369","wikidata":"https://www.wikidata.org/wiki/Q7617831","display_name":"Stochastic programming","level":2,"score":0.09676596522331238},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2688909","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2688909","pdf_url":null,"source":{"id":"https://openalex.org/S38703467","display_name":"ACM Transactions on Modeling and Computer Simulation","issn_l":"1049-3301","issn":["1049-3301","1558-1195"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Modeling and Computer Simulation","raw_type":"journal-article"},{"id":"pmh:oai:air.uniud.it:11390/1069108","is_oa":true,"landing_page_url":"http://dl.acm.org/citation.cfm?doid=2688909","pdf_url":null,"source":{"id":"https://openalex.org/S4306401163","display_name":"Institutional Research Information System (University of Udine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I129043915","host_organization_name":"University of Udine","host_organization_lineage":["https://openalex.org/I129043915"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:air.uniud.it:11390/1069108","is_oa":true,"landing_page_url":"http://dl.acm.org/citation.cfm?doid=2688909","pdf_url":null,"source":{"id":"https://openalex.org/S4306401163","display_name":"Institutional Research Information System (University of Udine)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I129043915","host_organization_name":"University of Udine","host_organization_lineage":["https://openalex.org/I129043915"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W18651725","https://openalex.org/W134553548","https://openalex.org/W602980269","https://openalex.org/W1483118642","https://openalex.org/W1506806321","https://openalex.org/W1527927437","https://openalex.org/W1538718565","https://openalex.org/W1554944419","https://openalex.org/W1637197683","https://openalex.org/W1733489975","https://openalex.org/W1892706559","https://openalex.org/W1969008680","https://openalex.org/W1973260612","https://openalex.org/W1978337436","https://openalex.org/W1986688807","https://openalex.org/W2000501190","https://openalex.org/W2008107402","https://openalex.org/W2012731059","https://openalex.org/W2031888594","https://openalex.org/W2035811095","https://openalex.org/W2044525257","https://openalex.org/W2046538693","https://openalex.org/W2050559302","https://openalex.org/W2050653042","https://openalex.org/W2058221907","https://openalex.org/W2061425021","https://openalex.org/W2063978378","https://openalex.org/W2069898971","https://openalex.org/W2094558888","https://openalex.org/W2105527349","https://openalex.org/W2107432340","https://openalex.org/W2109384743","https://openalex.org/W2110699703","https://openalex.org/W2110804558","https://openalex.org/W2115108153","https://openalex.org/W2116290764","https://openalex.org/W2121695897","https://openalex.org/W2125408642","https://openalex.org/W2126669894","https://openalex.org/W2127057035","https://openalex.org/W2127337389","https://openalex.org/W2129265801","https://openalex.org/W2139997707","https://openalex.org/W2142302575","https://openalex.org/W2143076232","https://openalex.org/W2152336513","https://openalex.org/W2153011302","https://openalex.org/W2153316724","https://openalex.org/W2170173760","https://openalex.org/W2170251198","https://openalex.org/W2500402711","https://openalex.org/W2562162676","https://openalex.org/W2787894218","https://openalex.org/W2950638330","https://openalex.org/W3085162807","https://openalex.org/W3099289621","https://openalex.org/W3122241128","https://openalex.org/W4242577767","https://openalex.org/W7084626969"],"related_works":["https://openalex.org/W2158714033","https://openalex.org/W4291309325","https://openalex.org/W2950474130","https://openalex.org/W4313469555","https://openalex.org/W78967844","https://openalex.org/W2737452945","https://openalex.org/W1547011777","https://openalex.org/W1514706798","https://openalex.org/W2949927938","https://openalex.org/W1985899403"],"abstract_inverted_index":{"The":[0,96,132,141],"problem":[1,68,83],"of":[2,11,43,77,81,91,94,111,123,129,138,143],"gene":[3],"regulatory":[4,113],"network":[5,25,104,130],"inference":[6],"is":[7],"a":[8,17,35,53,64],"major":[9],"concern":[10],"systems":[12],"biology.":[13],"In":[14],"recent":[15],"years,":[16],"novel":[18,54],"methodology":[19,55],"has":[20],"gained":[21],"momentum,":[22],"called":[23],"community":[24,103],"approach.":[26],"Community":[27],"networks":[28,114],"integrate":[29,57],"predictions":[30],"from":[31,126],"individual":[32,48],"methods":[33,45],"in":[34,37,150],"\u201cmetapredictor,\u201d":[36],"order":[38],"to":[39,56,100,108,119],"compose":[40],"the":[41,75,82,87,112,121,136],"advantages":[42],"different":[44,92,127],"and":[46,67,89,118],"soften":[47],"limitations.":[49],"This":[50],"article":[51,133],"proposes":[52],"prediction":[58,151],"ensembles":[59],"using":[60],"constraint":[61],"programming":[62,72],",":[63,105],"declarative":[65],"modeling":[66,76],"solving":[69],"paradigm.":[70],"Constraint":[71],"naturally":[73],"allows":[74],"dependencies":[78],"among":[79],"components":[80],"as":[84,101],"constraints,":[85],"facilitating":[86],"integration":[88,122],"use":[90],"forms":[93],"knowledge.":[95],"new":[97],"paradigm,":[98],"referred":[99],"constrained":[102],"uses":[106],"constraints":[107,145],"capture":[109],"properties":[110],"(e.g.,":[115],"topological":[116],"properties)":[117],"guide":[120],"knowledge":[124],"derived":[125],"families":[128],"predictions.":[131],"experimentally":[134],"shows":[135],"potential":[137],"this":[139],"approach:":[140],"addition":[142],"biological":[144],"can":[146],"offer":[147],"significant":[148],"improvements":[149],"accuracy.":[152]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}