{"id":"https://openalex.org/W4406259813","doi":"https://doi.org/10.1109/bibm62325.2024.10822868","title":"Inferring Gene Regulatory Network Based on scATAC-seq Data with Gene Perturbation","display_name":"Inferring Gene Regulatory Network Based on scATAC-seq Data with Gene Perturbation","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406259813","doi":"https://doi.org/10.1109/bibm62325.2024.10822868"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822868","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822868","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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/A5029048058","display_name":"Wei Shao","orcid":null},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wei Shao","raw_affiliation_strings":["Nankai University,College of Software,Tianjin,China"],"affiliations":[{"raw_affiliation_string":"Nankai University,College of Software,Tianjin,China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073173967","display_name":"Yuti Liu","orcid":"https://orcid.org/0000-0002-2935-7105"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuti Liu","raw_affiliation_strings":["Nankai University,College of Software,Tianjin,China"],"affiliations":[{"raw_affiliation_string":"Nankai University,College of Software,Tianjin,China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100321554","display_name":"Shuang Zhang","orcid":"https://orcid.org/0000-0002-1425-0639"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuang Zhang","raw_affiliation_strings":["Nankai University,College of Software,Tianjin,China"],"affiliations":[{"raw_affiliation_string":"Nankai University,College of Software,Tianjin,China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100443500","display_name":"Shuang Chen","orcid":"https://orcid.org/0000-0002-4448-6378"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuang Chen","raw_affiliation_strings":["Nankai University,College of Software,Tianjin,China"],"affiliations":[{"raw_affiliation_string":"Nankai University,College of Software,Tianjin,China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100393711","display_name":"Qiao Liu","orcid":"https://orcid.org/0000-0002-9781-3360"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qiao Liu","raw_affiliation_strings":["Stanford University,Department of Statistics,Stanford,USA"],"affiliations":[{"raw_affiliation_string":"Stanford University,Department of Statistics,Stanford,USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056271944","display_name":"Jianyu Zhou","orcid":"https://orcid.org/0000-0001-5175-9437"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianyu Zhou","raw_affiliation_strings":["Nankai University,College of Software,Tianjin,China"],"affiliations":[{"raw_affiliation_string":"Nankai University,College of Software,Tianjin,China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077808955","display_name":"Wanwen Zeng","orcid":"https://orcid.org/0000-0003-3426-0890"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wanwen Zeng","raw_affiliation_strings":["Stanford University,Department of Statistics,Stanford,USA"],"affiliations":[{"raw_affiliation_string":"Stanford University,Department of Statistics,Stanford,USA","institution_ids":["https://openalex.org/I97018004"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5029048058"],"corresponding_institution_ids":["https://openalex.org/I205237279"],"apc_list":null,"apc_paid":null,"fwci":0.2501,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.61173976,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"451","last_page":"456"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9779999852180481,"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":0.9779999852180481,"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":0.9742000102996826,"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":0.9724000096321106,"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/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6404968500137329},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5083290934562683},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5031735301017761},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.41706836223602295},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2788766026496887},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2639220356941223},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.25533750653266907}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6404968500137329},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5083290934562683},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5031735301017761},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.41706836223602295},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2788766026496887},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2639220356941223},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.25533750653266907}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822868","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822868","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5600000023841858,"id":"https://metadata.un.org/sdg/13","display_name":"Climate action"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1984689597","https://openalex.org/W2062029454","https://openalex.org/W2332016763","https://openalex.org/W2616922646","https://openalex.org/W2782454362","https://openalex.org/W2794480084","https://openalex.org/W2901292166","https://openalex.org/W2950195808","https://openalex.org/W2952535935","https://openalex.org/W3097075523","https://openalex.org/W3161116336","https://openalex.org/W3186348651","https://openalex.org/W3204674240","https://openalex.org/W3210860076","https://openalex.org/W4223557148","https://openalex.org/W4290672942","https://openalex.org/W4297265143","https://openalex.org/W4319591822","https://openalex.org/W4378212544","https://openalex.org/W4385492234","https://openalex.org/W4387955539","https://openalex.org/W4389178830"],"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],"regulatory":[1,61,124],"networks":[2],"(GRNs)":[3],"are":[4],"critical":[5],"blueprints":[6],"for":[7,159,165],"understanding":[8,166],"gene":[9,45,72,167],"regulation":[10,73,168],"and":[11,57,69,97,108,145],"the":[12,23,66,103,114,122,135,152],"intricate":[13],"interactions":[14],"that":[15,83,118],"drive":[16],"biological":[17,171],"processes.":[18],"Recent":[19],"advances":[20,102],"have":[21],"highlighted":[22],"potential":[24],"of":[25,60,71,116],"single-cell":[26],"ATAC-seq":[27],"(scATAC-seq)":[28],"data":[29,92],"in":[30,44,53,64,139,169],"GRN":[31,160],"inference,":[32,161],"offering":[33],"unprecedented":[34],"insights":[35],"into":[36],"how":[37],"chromatin":[38,110],"accessibility":[39,111],"plays":[40],"an":[41],"important":[42],"part":[43],"regulation.":[46],"However,":[47],"existing":[48],"methods":[49],"often":[50],"fall":[51],"short":[52],"providing":[54,155],"a":[55,80,156],"quantitative":[56],"holistic":[58],"depiction":[59],"relationships,":[62],"particularly":[63],"capturing":[65],"strength,":[67],"direction,":[68],"type":[70],"simultaneously.":[74],"In":[75],"this":[76],"paper,":[77],"we":[78,133],"present":[79],"novel":[81],"approach":[82],"addresses":[84],"these":[85],"limitations":[86],"by":[87,105,154],"leveraging":[88],"genetically":[89],"perturbed":[90],"scATAC-seq":[91],"to":[93,151],"infer":[94],"more":[95,119],"comprehensive":[96],"accurate":[98],"GRNs.":[99],"Our":[100],"method":[101],"field":[104,153],"integrating":[106],"pre-":[107],"post-perturbation":[109],"data,":[112],"enabling":[113],"construction":[115],"GRNs":[117,141],"accurately":[120],"reflect":[121],"dynamic":[123],"landscape.":[125],"Through":[126],"rigorous":[127],"evaluation":[128],"on":[129],"seven":[130],"real":[131],"datasets,":[132],"demonstrate":[134],"method\u2019s":[136],"superior":[137],"performance":[138],"reconstructing":[140],"with":[142,162],"enhanced":[143],"precision":[144],"interpretability.":[146],"This":[147],"work":[148],"significantly":[149],"contributes":[150],"robust":[157],"framework":[158],"broad":[163],"implications":[164],"complex":[170],"systems.":[172]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}