{"id":"https://openalex.org/W4410808041","doi":"https://doi.org/10.1007/s10462-025-11257-z","title":"A review of methods for gene regulatory networks reconstruction and analysis","display_name":"A review of methods for gene regulatory networks reconstruction and analysis","publication_year":2025,"publication_date":"2025-05-29","ids":{"openalex":"https://openalex.org/W4410808041","doi":"https://doi.org/10.1007/s10462-025-11257-z"},"language":"en","primary_location":{"id":"doi:10.1007/s10462-025-11257-z","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10462-025-11257-z","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10462-025-11257-z.pdf","source":{"id":"https://openalex.org/S122814990","display_name":"Artificial Intelligence Review","issn_l":"0269-2821","issn":["0269-2821","1573-7462"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Artificial Intelligence Review","raw_type":"journal-article"},"type":"review","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10462-025-11257-z.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054280154","display_name":"Sher Ali","orcid":null},"institutions":[{"id":"https://openalex.org/I501048437","display_name":"Al-Muthanna University","ror":"https://ror.org/03877wr45","country_code":"IQ","type":"education","lineage":["https://openalex.org/I501048437"]},{"id":"https://openalex.org/I166455938","display_name":"University of Babylon","ror":"https://ror.org/0170edc15","country_code":"IQ","type":"education","lineage":["https://openalex.org/I166455938"]}],"countries":["IQ"],"is_corresponding":true,"raw_author_name":"Sura I. Mohammed Ali","raw_affiliation_strings":["Department of Mathematics and Computer Application, Collage of Science, Al-Muthanna Universit, Sumaway, Iraq","Department of Software, College of Information Technology, University of Babylon, Babylon, Iraq"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Application, Collage of Science, Al-Muthanna Universit, Sumaway, Iraq","institution_ids":["https://openalex.org/I501048437"]},{"raw_affiliation_string":"Department of Software, College of Information Technology, University of Babylon, Babylon, Iraq","institution_ids":["https://openalex.org/I166455938"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083863927","display_name":"Sura Z. Al-Rashid","orcid":"https://orcid.org/0000-0003-1561-0066"},"institutions":[{"id":"https://openalex.org/I166455938","display_name":"University of Babylon","ror":"https://ror.org/0170edc15","country_code":"IQ","type":"education","lineage":["https://openalex.org/I166455938"]}],"countries":["IQ"],"is_corresponding":false,"raw_author_name":"Sura Zaki Alrashid","raw_affiliation_strings":["Department of Software, College of Information Technology, University of Babylon, Babylon, Iraq"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Software, College of Information Technology, University of Babylon, Babylon, Iraq","institution_ids":["https://openalex.org/I166455938"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5054280154"],"corresponding_institution_ids":["https://openalex.org/I166455938","https://openalex.org/I501048437"],"apc_list":{"value":2490,"currency":"EUR","value_usd":3090},"apc_paid":{"value":2490,"currency":"EUR","value_usd":3090},"fwci":11.6443,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.98929108,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"58","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9984999895095825,"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":0.9984999895095825,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9966999888420105,"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":0.9879999756813049,"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":0.6857184767723083},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5562072396278381},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41010022163391113},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.262811541557312},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1756051778793335},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15000289678573608},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09952571988105774}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6857184767723083},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5562072396278381},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41010022163391113},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.262811541557312},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1756051778793335},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15000289678573608},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09952571988105774}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s10462-025-11257-z","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10462-025-11257-z","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10462-025-11257-z.pdf","source":{"id":"https://openalex.org/S122814990","display_name":"Artificial Intelligence Review","issn_l":"0269-2821","issn":["0269-2821","1573-7462"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Artificial Intelligence Review","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1007/s10462-025-11257-z","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10462-025-11257-z","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10462-025-11257-z.pdf","source":{"id":"https://openalex.org/S122814990","display_name":"Artificial Intelligence Review","issn_l":"0269-2821","issn":["0269-2821","1573-7462"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Artificial Intelligence Review","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320329495","display_name":"Al-Muthanna University","ror":"https://ror.org/03877wr45"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410808041.pdf","grobid_xml":"https://content.openalex.org/works/W4410808041.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1816176398","https://openalex.org/W1979104937","https://openalex.org/W1984084871","https://openalex.org/W2062029454","https://openalex.org/W2108675631","https://openalex.org/W2120303002","https://openalex.org/W2129794000","https://openalex.org/W2152054335","https://openalex.org/W2156716434","https://openalex.org/W2340820823","https://openalex.org/W2570516417","https://openalex.org/W2673729825","https://openalex.org/W2769591387","https://openalex.org/W2773499052","https://openalex.org/W2795540478","https://openalex.org/W2944018172","https://openalex.org/W2950742983","https://openalex.org/W2951424836","https://openalex.org/W2969742128","https://openalex.org/W2994421080","https://openalex.org/W2997403971","https://openalex.org/W2998917483","https://openalex.org/W3004773979","https://openalex.org/W3008895300","https://openalex.org/W3009077094","https://openalex.org/W3014321973","https://openalex.org/W3024161231","https://openalex.org/W3024581654","https://openalex.org/W3088462269","https://openalex.org/W3121311454","https://openalex.org/W3130444944","https://openalex.org/W3175392960","https://openalex.org/W3181924398","https://openalex.org/W3182581683","https://openalex.org/W3186348651","https://openalex.org/W4200310615","https://openalex.org/W4206722399","https://openalex.org/W4281929191","https://openalex.org/W4284883273","https://openalex.org/W4288069643","https://openalex.org/W4291954810","https://openalex.org/W4292641461","https://openalex.org/W4306369139","https://openalex.org/W4306398981","https://openalex.org/W4307178962","https://openalex.org/W4308831845","https://openalex.org/W4319295355","https://openalex.org/W4320857528","https://openalex.org/W4323307350","https://openalex.org/W4323310840","https://openalex.org/W4378530717","https://openalex.org/W4382630883","https://openalex.org/W4385835376","https://openalex.org/W4388870182","https://openalex.org/W4390116356"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Gene":[0,127],"regulatory":[1,50],"networks":[2,32],"(GRNs)":[3],"are":[4,141],"one":[5],"of":[6,74,80,102,105,173,192],"the":[7,72,145,174,190],"most":[8],"promising":[9],"techniques":[10,175],"for":[11,91,113,149,178,183],"modeling":[12,55],"and":[13,38,54,77,118,130,162,186],"understanding":[14,191],"biological":[15,116],"processes.":[16,119],"GRNs":[17],"help":[18],"to":[19,126,137,144,188],"understand":[20],"complex":[21,115],"interactions":[22,34],"involving":[23],"genes.":[24],"Regulator":[25],"molecules":[26],"control":[27],"gene":[28,58,81,106,132],"expression":[29,59,82,133],"within":[30],"these":[31],"through":[33],"with":[35],"each":[36],"other":[37,39],"substances":[40],"in":[41,48,57,71,157],"cells.":[42],"They":[43],"play":[44],"a":[45,69,89,110],"crucial":[46],"role":[47],"deciphering":[49],"relationships":[51],"among":[52],"genes":[53],"changes":[56],"under":[60],"various":[61,103],"conditions.":[62],"In":[63],"recent":[64,123],"years,":[65],"there":[66],"has":[67,87],"been":[68],"surge":[70],"generation":[73],"vast":[75],"quantities":[76],"diverse":[78],"varieties":[79],"data.":[83],"This":[84,120,166],"bulk":[85],"production":[86],"created":[88],"demand":[90],"new":[92],"data":[93,134,146],"management":[94],"methods.":[95],"It":[96],"is":[97],"expected":[98],"that":[99],"integrative":[100],"analysis":[101],"types":[104],"information":[107],"will":[108],"provide":[109],"comprehensive":[111],"overview":[112],"researching":[114],"systems":[117],"review":[121,172],"covers":[122],"developments":[124],"related":[125],"Regulatory":[128],"Networks":[129],"associated":[131],"from":[135],"2019":[136],"2023.":[138],"Key":[139],"topics":[140],"presented":[142],"according":[143],"type":[147],"used":[148,156,177],"network":[150,158],"building,":[151],"machine":[152],"learning":[153],"approaches,":[154],"tools":[155],"inference,":[159],"model":[160],"optimization,":[161],"computational":[163],"validation":[164],"techniques.":[165],"paper":[167],"presents":[168],"an":[169],"in-depth":[170],"technical":[171],"currently":[176],"constructing":[179],"GRNs,":[180],"explores":[181],"possibilities":[182],"future":[184],"research,":[185],"aims":[187],"enhance":[189],"GRNs.":[193]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":13}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}
