{"id":"https://openalex.org/W2995138336","doi":"https://doi.org/10.1109/tcbb.2021.3057241","title":"Reconstruction of Gene Regulatory Networks Using Multiple Datasets","display_name":"Reconstruction of Gene Regulatory Networks Using Multiple Datasets","publication_year":2021,"publication_date":"2021-02-06","ids":{"openalex":"https://openalex.org/W2995138336","doi":"https://doi.org/10.1109/tcbb.2021.3057241","mag":"2995138336","pmid":"https://pubmed.ncbi.nlm.nih.gov/33539303"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3057241","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3057241","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1912.10810","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030084359","display_name":"Mehrzad Saremi","orcid":"https://orcid.org/0000-0002-5340-4784"},"institutions":[{"id":"https://openalex.org/I158248296","display_name":"Amirkabir University of Technology","ror":"https://ror.org/04gzbav43","country_code":"IR","type":"education","lineage":["https://openalex.org/I158248296"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Mehrzad Saremi","raw_affiliation_strings":["Department of Artificial Intelligence, Amirkabir University of Technology, Tehran, Iran","Amirkabir\u00a0University\u00a0of\u00a0Technology"],"raw_orcid":"https://orcid.org/0000-0002-5340-4784","affiliations":[{"raw_affiliation_string":"Department of Artificial Intelligence, Amirkabir University of Technology, Tehran, Iran","institution_ids":["https://openalex.org/I158248296"]},{"raw_affiliation_string":"Amirkabir\u00a0University\u00a0of\u00a0Technology","institution_ids":["https://openalex.org/I158248296"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006999765","display_name":"Maryam Amirmazlaghani","orcid":"https://orcid.org/0000-0001-5956-3797"},"institutions":[{"id":"https://openalex.org/I158248296","display_name":"Amirkabir University of Technology","ror":"https://ror.org/04gzbav43","country_code":"IR","type":"education","lineage":["https://openalex.org/I158248296"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Maryam Amirmazlaghani","raw_affiliation_strings":["Department of Artificial Intelligence, Amirkabir University of Technology, Tehran, Iran","Amirkabir\u00a0University\u00a0of\u00a0Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Artificial Intelligence, Amirkabir University of Technology, Tehran, Iran","institution_ids":["https://openalex.org/I158248296"]},{"raw_affiliation_string":"Amirkabir\u00a0University\u00a0of\u00a0Technology","institution_ids":["https://openalex.org/I158248296"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00167172,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"19","issue":"3","first_page":"1827","last_page":"1839"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.7811999917030334,"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":0.7811999917030334,"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":0.12219999730587006,"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":0.04520000144839287,"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/computer-science","display_name":"Computer science","score":0.7343364953994751},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5852259397506714},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5165787935256958},{"id":"https://openalex.org/keywords/trustworthiness","display_name":"Trustworthiness","score":0.5072207450866699},{"id":"https://openalex.org/keywords/boosting","display_name":"Boosting (machine learning)","score":0.43872085213661194},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.40141555666923523},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3511393964290619},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.32229703664779663}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7343364953994751},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5852259397506714},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5165787935256958},{"id":"https://openalex.org/C153701036","wikidata":"https://www.wikidata.org/wiki/Q659974","display_name":"Trustworthiness","level":2,"score":0.5072207450866699},{"id":"https://openalex.org/C46686674","wikidata":"https://www.wikidata.org/wiki/Q466303","display_name":"Boosting (machine learning)","level":2,"score":0.43872085213661194},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40141555666923523},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3511393964290619},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32229703664779663},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1109/tcbb.2021.3057241","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3057241","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33539303","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33539303","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:arXiv.org:1912.10810","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1912.10810","pdf_url":"https://arxiv.org/pdf/1912.10810","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"mag:2995138336","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1912.10810","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1912.10810","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1912.10810","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1912.10810","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1912.10810","pdf_url":"https://arxiv.org/pdf/1912.10810","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.5400000214576721,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321431","display_name":"Amirkabir University of Technology","ror":"https://ror.org/04gzbav43"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2995138336.pdf","grobid_xml":"https://content.openalex.org/works/W2995138336.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1657934012","https://openalex.org/W1891536063","https://openalex.org/W1893022572","https://openalex.org/W1966716734","https://openalex.org/W1973137995","https://openalex.org/W1986688807","https://openalex.org/W1989075680","https://openalex.org/W2003477935","https://openalex.org/W2022604714","https://openalex.org/W2034662766","https://openalex.org/W2069898971","https://openalex.org/W2070822442","https://openalex.org/W2076513103","https://openalex.org/W2087535060","https://openalex.org/W2106555403","https://openalex.org/W2109384743","https://openalex.org/W2110699703","https://openalex.org/W2112076978","https://openalex.org/W2115664087","https://openalex.org/W2126345910","https://openalex.org/W2137226992","https://openalex.org/W2139997707","https://openalex.org/W2142170851","https://openalex.org/W2144738674","https://openalex.org/W2145073242","https://openalex.org/W2157121418","https://openalex.org/W2163480486","https://openalex.org/W2170704198","https://openalex.org/W2295598076","https://openalex.org/W2408282413","https://openalex.org/W2561175740","https://openalex.org/W2592161069","https://openalex.org/W2786016794","https://openalex.org/W2803928488","https://openalex.org/W2885564894","https://openalex.org/W2899545492","https://openalex.org/W2915583118","https://openalex.org/W3102476541","https://openalex.org/W4297957988","https://openalex.org/W6676769703","https://openalex.org/W6680532697","https://openalex.org/W6681651645"],"related_works":["https://openalex.org/W3128925966","https://openalex.org/W2290190008","https://openalex.org/W3144534434","https://openalex.org/W2034662766","https://openalex.org/W2775083070","https://openalex.org/W3128158089","https://openalex.org/W2188949053","https://openalex.org/W2125510350","https://openalex.org/W2149250260","https://openalex.org/W2364240629","https://openalex.org/W2408001950","https://openalex.org/W3013943034","https://openalex.org/W2035385395","https://openalex.org/W2056837054","https://openalex.org/W2129922540","https://openalex.org/W2112697101","https://openalex.org/W2131301064","https://openalex.org/W2095802318","https://openalex.org/W2527273336","https://openalex.org/W3110700421"],"abstract_inverted_index":{"MOTIVATION:":[0],"Laboratory":[1],"gene":[2,14],"regulatory":[3,15],"data":[4,21,33,61,84,173],"for":[5,44],"a":[6,40,149],"species":[7],"are":[8],"sporadic.":[9],"Despite":[10],"the":[11,27,36,71,74,87,110,113,125,155,163,172],"abundance":[12],"of":[13,32,60,73,112],"network":[16],"algorithms":[17,24,105,123],"that":[18,53,117,148],"employ":[19],"single":[20],"sets,":[22],"few":[23],"can":[25,54,177],"combine":[26],"vast":[28],"but":[29],"disperse":[30],"sources":[31],"and":[34,91,95,99,103,128,139,175],"extract":[35],"potential":[37],"information.":[38],"With":[39],"motivation":[41],"to":[42,108,131],"compensate":[43],"this":[45],"shortage,":[46],"we":[47,146],"developed":[48],"an":[49,64],"algorithm":[50,79],"called":[51],"GENEREF":[52,118],"accumulate":[55],"information":[56],"from":[57,86,180],"multiple":[58],"types":[59],"sets":[62,174],"in":[63],"iterative":[65],"manner,":[66],"with":[67,143,171],"each":[68],"iteration":[69],"boosting":[70],"performance":[72,111],"prediction":[75],"results.":[76],"RESULTS:":[77],"The":[78,167],"is":[80,129,140],"examined":[81],"extensively":[82],"on":[83,124,141,154],"extracted":[85],"quintuple":[88],"DREAM4":[89],"networks":[90,98,127],"DREAM5's":[92],"Escherichia":[93],"coli":[94],"Saccharomyces":[96],"cerevisiae":[97],"sub-networks.":[100],"Many":[101],"single-dataset":[102],"multi-dataset":[104],"were":[106],"compared":[107],"test":[109],"algorithm.":[114],"Results":[115],"show":[116],"surpasses":[119],"non-ensemble":[120],"state-of-the-art":[121],"multi-perturbation":[122],"selected":[126],"competitive":[130],"present":[132],"multiple-dataset":[133],"algorithms.":[134],"Specifically,":[135],"it":[136],"outperforms":[137],"dynGENIE3":[138],"par":[142],"iRafNet.":[144],"Also,":[145],"argued":[147],"scoring":[150],"method":[151],"solely":[152],"based":[153],"AUPR":[156],"criterion":[157],"would":[158],"be":[159,178],"more":[160],"trustworthy":[161],"than":[162],"traditional":[164],"score.":[165],"AVAILABILITY:":[166],"Python":[168],"implementation":[169],"along":[170],"results":[176],"downloaded":[179],"github.com/msaremi/GENEREF.":[181]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
