{"id":"https://openalex.org/W2091622633","doi":"https://doi.org/10.1109/bibe.2012.6399735","title":"sCoIn: A scoring algorithm based on complex interactions for reverse engineering regulatory networks","display_name":"sCoIn: A scoring algorithm based on complex interactions for reverse engineering regulatory networks","publication_year":2012,"publication_date":"2012-11-01","ids":{"openalex":"https://openalex.org/W2091622633","doi":"https://doi.org/10.1109/bibe.2012.6399735","mag":"2091622633"},"language":"en","primary_location":{"id":"doi:10.1109/bibe.2012.6399735","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2012.6399735","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 12th International Conference on Bioinformatics &amp; Bioengineering (BIBE)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082760446","display_name":"Vijender Chaitankar","orcid":null},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Vijender Chaitankar","raw_affiliation_strings":["Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA","[Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA]"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA","institution_ids":["https://openalex.org/I184840846"]},{"raw_affiliation_string":"[Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA]","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080886331","display_name":"Preetam Ghosh","orcid":"https://orcid.org/0000-0003-3880-5886"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Preetam Ghosh","raw_affiliation_strings":["Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA","[Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA]"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA","institution_ids":["https://openalex.org/I184840846"]},{"raw_affiliation_string":"[Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA]","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041782519","display_name":"Mohamed O. Elasri","orcid":"https://orcid.org/0000-0003-0312-2292"},"institutions":[{"id":"https://openalex.org/I44854399","display_name":"University of Southern Mississippi","ror":"https://ror.org/0270vfa57","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I44854399"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohamed O. Elasri","raw_affiliation_strings":["Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, USA","[Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, USA]"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, USA","institution_ids":["https://openalex.org/I44854399"]},{"raw_affiliation_string":"[Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, USA]","institution_ids":["https://openalex.org/I44854399"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004367115","display_name":"Kurt A. Gust","orcid":"https://orcid.org/0000-0002-7244-3762"},"institutions":[{"id":"https://openalex.org/I1304082316","display_name":"United States Department of the Army","ror":"https://ror.org/035w1gb98","country_code":"US","type":"government","lineage":["https://openalex.org/I1304082316","https://openalex.org/I1330347796"]},{"id":"https://openalex.org/I4210141313","display_name":"Geotechnical and Structures Laboratory","ror":"https://ror.org/04cyj6y78","country_code":"US","type":"facility","lineage":["https://openalex.org/I1304082316","https://openalex.org/I1306490931","https://openalex.org/I1330347796","https://openalex.org/I4210141313","https://openalex.org/I87303767"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kurt A. Gust","raw_affiliation_strings":["E.R.D.C, Environmental Laboratory, Vicksburg, MS, USA","Environmental Laboratory, E.R.D.C, U.S. Army, Vicksburg, MS, USA"],"affiliations":[{"raw_affiliation_string":"E.R.D.C, Environmental Laboratory, Vicksburg, MS, USA","institution_ids":["https://openalex.org/I4210141313"]},{"raw_affiliation_string":"Environmental Laboratory, E.R.D.C, U.S. Army, Vicksburg, MS, USA","institution_ids":["https://openalex.org/I1304082316"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075371599","display_name":"Edward J. Perkins","orcid":"https://orcid.org/0000-0003-1693-7714"},"institutions":[{"id":"https://openalex.org/I1304082316","display_name":"United States Department of the Army","ror":"https://ror.org/035w1gb98","country_code":"US","type":"government","lineage":["https://openalex.org/I1304082316","https://openalex.org/I1330347796"]},{"id":"https://openalex.org/I4210141313","display_name":"Geotechnical and Structures Laboratory","ror":"https://ror.org/04cyj6y78","country_code":"US","type":"facility","lineage":["https://openalex.org/I1304082316","https://openalex.org/I1306490931","https://openalex.org/I1330347796","https://openalex.org/I4210141313","https://openalex.org/I87303767"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edward J. Perkins","raw_affiliation_strings":["E.R.D.C, Environmental Laboratory, Vicksburg, MS, USA","Environmental Laboratory, E.R.D.C, U.S. Army, Vicksburg, MS, USA"],"affiliations":[{"raw_affiliation_string":"E.R.D.C, Environmental Laboratory, Vicksburg, MS, USA","institution_ids":["https://openalex.org/I4210141313"]},{"raw_affiliation_string":"Environmental Laboratory, E.R.D.C, U.S. Army, Vicksburg, MS, USA","institution_ids":["https://openalex.org/I1304082316"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5082760446"],"corresponding_institution_ids":["https://openalex.org/I184840846"],"apc_list":null,"apc_paid":null,"fwci":0.394,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.61819057,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"298","issue":null,"first_page":"572","last_page":"577"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9987999796867371,"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":0.9987000226974487,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7156489491462708},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6761418581008911},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5752753019332886},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.54656583070755},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.5319851636886597},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.504806399345398},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5032243132591248},{"id":"https://openalex.org/keywords/complex-network","display_name":"Complex network","score":0.47155141830444336},{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.431551456451416},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4183866083621979},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3695352375507355},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.35904431343078613},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33290040493011475},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3240831196308136},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12728255987167358},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.126562237739563}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7156489491462708},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6761418581008911},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5752753019332886},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.54656583070755},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5319851636886597},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.504806399345398},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5032243132591248},{"id":"https://openalex.org/C34947359","wikidata":"https://www.wikidata.org/wiki/Q665189","display_name":"Complex network","level":2,"score":0.47155141830444336},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.431551456451416},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4183866083621979},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3695352375507355},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.35904431343078613},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33290040493011475},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3240831196308136},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12728255987167358},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.126562237739563},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"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/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"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:10.1109/bibe.2012.6399735","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibe.2012.6399735","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 12th International Conference on Bioinformatics &amp; Bioengineering (BIBE)","raw_type":"proceedings-article"},{"id":"pmh:oai:aquila.usm.edu:fac_pubs-22172","is_oa":false,"landing_page_url":"https://aquila.usm.edu/fac_pubs/20829","pdf_url":null,"source":{"id":"https://openalex.org/S4306402529","display_name":"Aquila Digital Community (University of Southern Mississippi)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I44854399","host_organization_name":"University of Southern Mississippi","host_organization_lineage":["https://openalex.org/I44854399"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Publications","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4099999964237213,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W89551800","https://openalex.org/W195865777","https://openalex.org/W1481919380","https://openalex.org/W1599969036","https://openalex.org/W1635484243","https://openalex.org/W1971224531","https://openalex.org/W2005516743","https://openalex.org/W2017986542","https://openalex.org/W2023348596","https://openalex.org/W2044525257","https://openalex.org/W2045283959","https://openalex.org/W2076513103","https://openalex.org/W2078149659","https://openalex.org/W2082982706","https://openalex.org/W2090554117","https://openalex.org/W2092939357","https://openalex.org/W2098025145","https://openalex.org/W2099111195","https://openalex.org/W2100405637","https://openalex.org/W2126602684","https://openalex.org/W2137965767","https://openalex.org/W2148944713","https://openalex.org/W2150926065","https://openalex.org/W2160533336","https://openalex.org/W2161922735","https://openalex.org/W2163296115","https://openalex.org/W2170704198","https://openalex.org/W2405486631","https://openalex.org/W3099289621","https://openalex.org/W6670026339","https://openalex.org/W6671346601","https://openalex.org/W6673567362","https://openalex.org/W6713639416"],"related_works":["https://openalex.org/W2389214306","https://openalex.org/W2950199998","https://openalex.org/W2560421304","https://openalex.org/W2129331923","https://openalex.org/W2951387065","https://openalex.org/W4385727351","https://openalex.org/W4306798985","https://openalex.org/W4393433587","https://openalex.org/W2734532915","https://openalex.org/W4362637502"],"abstract_inverted_index":{"Structural":[0],"analysis":[1],"over":[2,90],"well":[3],"studied":[4],"transcriptional":[5,57,122],"regulatory":[6,38,58,123],"networks":[7,12,39,59,149,211],"indicates":[8,125],"that":[9,126,185],"these":[10,32],"complex":[11,77,194],"are":[13],"made":[14],"up":[15],"of":[16,19,129,145,156,165,188],"small":[17],"set":[18],"reoccurring":[20],"patterns":[21],"called":[22],"motifs.":[23,82],"While":[24,83],"information":[25,52],"theoretic":[26,53],"approaches":[27,33,54,162],"have":[28],"been":[29],"immensely":[30],"popular,":[31],"rely":[34],"on":[35,111,117,180],"inferring":[36],"the":[37,61,86,118,127,130,160,163,186,189,213],"by":[40],"aggregating":[41],"pair-wise":[42,72,91],"interactions.":[43],"In":[44,159],"this":[45,84],"paper,":[46],"we":[47],"propose":[48],"novel":[49],"structure":[50],"based":[51,93,110],"to":[55,69,104,138,169,209],"infer":[56,210],"from":[60],"microarray":[62],"expression":[63],"data.":[64],"The":[65],"core":[66],"idea":[67],"is":[68,102,133],"go":[70],"beyond":[71],"interactions":[73],"and":[74,100,114,151,175],"consider":[75],"more":[76,193],"structures":[78,166,195,204],"as":[79,142],"found":[80],"in":[81,136],"increases":[85],"network":[87,124,183],"inference":[88],"complexity":[89],"interaction":[92],"approaches,":[94],"it":[95],"achieves":[96],"much":[97],"higher":[98,135,202],"accuracy":[99,128],"yet":[101],"scalable":[103],"genome-level":[105],"inference.":[106],"Detailed":[107],"performance":[108,187],"analyses":[109],"benchmark":[112],"precision":[113],"recall":[115],"metrics":[116],"known":[119],"Escherichia":[120],"coli's":[121],"proposed":[131,161],"algorithms":[132,140],"consistently":[134],"comparison":[137],"popular":[139],"such":[141,201],"context":[143],"likelihood":[144],"relatedness":[146],"(CLR),":[147],"relevance":[148],"(RN)":[150],"GEneNetwork":[152],"Inference":[153],"with":[154],"Ensemble":[155],"trees":[157],"(GENIE3).":[158],"size":[164],"was":[167],"limited":[168],"three":[170],"node":[171,174],"cases":[172],"(any":[173],"its":[176],"two":[177],"parents).":[178],"Analysis":[179],"a":[181],"smaller":[182],"showed":[184],"algorithm":[190],"improved":[191],"when":[192],"were":[196],"considered":[197],"for":[198],"inference,":[199],"although":[200],"level":[203],"may":[205],"be":[206],"computationally":[207],"challenging":[208],"at":[212],"genome":[214],"scale.":[215]},"counts_by_year":[{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
