{"id":"https://openalex.org/W3186348651","doi":"https://doi.org/10.1038/s43588-021-00099-8","title":"Modeling gene regulatory networks using neural network architectures","display_name":"Modeling gene regulatory networks using neural network architectures","publication_year":2021,"publication_date":"2021-07-22","ids":{"openalex":"https://openalex.org/W3186348651","doi":"https://doi.org/10.1038/s43588-021-00099-8","mag":"3186348651","pmid":"https://pubmed.ncbi.nlm.nih.gov/38217125"},"language":"en","primary_location":{"id":"doi:10.1038/s43588-021-00099-8","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-021-00099-8","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5020686848","display_name":"Hantao Shu","orcid":"https://orcid.org/0000-0002-7306-5644"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hantao Shu","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0002-7306-5644","affiliations":[{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068072367","display_name":"Jingtian Zhou","orcid":"https://orcid.org/0000-0003-2060-1922"},"institutions":[{"id":"https://openalex.org/I1307098950","display_name":"Salk Institute for Biological Studies","ror":"https://ror.org/03xez1567","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1307098950"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jingtian Zhou","raw_affiliation_strings":["Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA","Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA","institution_ids":["https://openalex.org/I1307098950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072095533","display_name":"Qiuyu Lian","orcid":"https://orcid.org/0000-0002-5279-1989"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiuyu Lian","raw_affiliation_strings":["Department of Automation, Shanghai Jiao Tong University, Shanghai, China","UM-SJTU Joint Institute, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Automation, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"UM-SJTU Joint Institute, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100452600","display_name":"Han Li","orcid":null},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Han Li","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0002-7380-6174","affiliations":[{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067578751","display_name":"Dan Zhao","orcid":"https://orcid.org/0000-0003-0195-6031"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dan Zhao","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0003-0195-6031","affiliations":[{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009826239","display_name":"Jianyang Zeng","orcid":null},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianyang Zeng","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China. zengjy321@mail.tsinghua.edu.cn","Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0003-0950-7716","affiliations":[{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China. zengjy321@mail.tsinghua.edu.cn","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074269040","display_name":"Jianzhu Ma","orcid":"https://orcid.org/0000-0002-8236-6609"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210100255","display_name":"Beijing Academy of Artificial Intelligence","ror":"https://ror.org/016a74861","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210100255"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianzhu Ma","raw_affiliation_strings":["Institute for Artificial Intelligence, Peking University, Beijing, China. majianzhu@pku.edu.cn","Institute for Artificial Intelligence, Peking University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0002-8236-6609","affiliations":[{"raw_affiliation_string":"Institute for Artificial Intelligence, Peking University, Beijing, China. majianzhu@pku.edu.cn","institution_ids":["https://openalex.org/I4210100255"]},{"raw_affiliation_string":"Institute for Artificial Intelligence, Peking University, Beijing, China","institution_ids":["https://openalex.org/I4210100255","https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5074269040"],"corresponding_institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210100255"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":null,"fwci":9.6086,"has_fulltext":false,"cited_by_count":206,"citation_normalized_percentile":{"value":0.98924178,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"1","issue":"7","first_page":"491","last_page":"501"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9995999932289124,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9951000213623047,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/encode","display_name":"ENCODE","score":0.7020014524459839},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6883002519607544},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6463978886604309},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6247327327728271},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5809762477874756},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5634148120880127},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4920327365398407},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.48975253105163574},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.47702571749687195},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.43083593249320984},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35308897495269775},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24238666892051697},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1608184278011322},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11291837692260742},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09199517965316772}],"concepts":[{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.7020014524459839},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6883002519607544},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6463978886604309},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6247327327728271},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5809762477874756},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5634148120880127},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4920327365398407},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.48975253105163574},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.47702571749687195},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.43083593249320984},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35308897495269775},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24238666892051697},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1608184278011322},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11291837692260742},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09199517965316772},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"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/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1038/s43588-021-00099-8","is_oa":false,"landing_page_url":"https://doi.org/10.1038/s43588-021-00099-8","pdf_url":null,"source":{"id":"https://openalex.org/S4210228084","display_name":"Nature Computational Science","issn_l":"2662-8457","issn":["2662-8457"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Computational Science","raw_type":"journal-article"},{"id":"pmid:38217125","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38217125","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":"Nature computational science","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3927232695","display_name":null,"funder_award_id":"61872216","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6429079033","display_name":null,"funder_award_id":"81630103","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7314568505","display_name":null,"funder_award_id":"31900862","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":99,"referenced_works":["https://openalex.org/W1677182931","https://openalex.org/W1795707064","https://openalex.org/W1964963969","https://openalex.org/W1967327758","https://openalex.org/W1979283544","https://openalex.org/W2018934435","https://openalex.org/W2019552331","https://openalex.org/W2023887100","https://openalex.org/W2038859824","https://openalex.org/W2051658465","https://openalex.org/W2059334100","https://openalex.org/W2076513103","https://openalex.org/W2099606984","https://openalex.org/W2102212449","https://openalex.org/W2126750365","https://openalex.org/W2131681506","https://openalex.org/W2132555912","https://openalex.org/W2140258573","https://openalex.org/W2140952049","https://openalex.org/W2152656267","https://openalex.org/W2152692691","https://openalex.org/W2166676212","https://openalex.org/W2175370850","https://openalex.org/W2181788163","https://openalex.org/W2217442075","https://openalex.org/W2259938310","https://openalex.org/W2313470939","https://openalex.org/W2332016763","https://openalex.org/W2342688693","https://openalex.org/W2403934794","https://openalex.org/W2465917013","https://openalex.org/W2509315794","https://openalex.org/W2511896561","https://openalex.org/W2514159238","https://openalex.org/W2515907404","https://openalex.org/W2523369352","https://openalex.org/W2526262591","https://openalex.org/W2552077236","https://openalex.org/W2555892463","https://openalex.org/W2560674852","https://openalex.org/W2600453489","https://openalex.org/W2616922646","https://openalex.org/W2626990934","https://openalex.org/W2741564801","https://openalex.org/W2744040456","https://openalex.org/W2746374269","https://openalex.org/W2753738274","https://openalex.org/W2757234574","https://openalex.org/W2767826728","https://openalex.org/W2784808866","https://openalex.org/W2789254933","https://openalex.org/W2793988528","https://openalex.org/W2800392236","https://openalex.org/W2892055372","https://openalex.org/W2900310474","https://openalex.org/W2900569176","https://openalex.org/W2901292166","https://openalex.org/W2901677030","https://openalex.org/W2902652978","https://openalex.org/W2912321349","https://openalex.org/W2940980190","https://openalex.org/W2944330565","https://openalex.org/W2946746976","https://openalex.org/W2947877009","https://openalex.org/W2948978827","https://openalex.org/W2950976066","https://openalex.org/W2951381561","https://openalex.org/W2951506174","https://openalex.org/W2951850020","https://openalex.org/W2952369555","https://openalex.org/W2952535935","https://openalex.org/W2961943679","https://openalex.org/W2964121744","https://openalex.org/W2964250774","https://openalex.org/W2964315448","https://openalex.org/W2965552103","https://openalex.org/W2968352143","https://openalex.org/W2980495984","https://openalex.org/W2988716798","https://openalex.org/W2997831639","https://openalex.org/W3000350302","https://openalex.org/W3004479572","https://openalex.org/W3006301383","https://openalex.org/W3021272327","https://openalex.org/W3021861803","https://openalex.org/W3037538172","https://openalex.org/W3048433432","https://openalex.org/W3059136655","https://openalex.org/W3087952073","https://openalex.org/W3099768174","https://openalex.org/W3103543904","https://openalex.org/W3122075993","https://openalex.org/W3133082627","https://openalex.org/W4298091299","https://openalex.org/W6641188306","https://openalex.org/W6727463826","https://openalex.org/W6728500052","https://openalex.org/W6912662942","https://openalex.org/W7075682736"],"related_works":["https://openalex.org/W2468279273","https://openalex.org/W2354198838","https://openalex.org/W1989130879","https://openalex.org/W2103419012","https://openalex.org/W2378211422","https://openalex.org/W2950199998","https://openalex.org/W2560421304","https://openalex.org/W2951387065","https://openalex.org/W4385727351","https://openalex.org/W4306798985"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":19},{"year":2025,"cited_by_count":71},{"year":2024,"cited_by_count":53},{"year":2023,"cited_by_count":45},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":4}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}
