{"id":"https://openalex.org/W4415830212","doi":"https://doi.org/10.1093/bioinformatics/btaf598","title":"Reconstructing gene network structure and dynamics from single cell data","display_name":"Reconstructing gene network structure and dynamics from single cell data","publication_year":2025,"publication_date":"2025-10-28","ids":{"openalex":"https://openalex.org/W4415830212","doi":"https://doi.org/10.1093/bioinformatics/btaf598","pmid":"https://pubmed.ncbi.nlm.nih.gov/41183100"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf598","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf598","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btaf598","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100352685","display_name":"Feng Chen","orcid":"https://orcid.org/0000-0002-1162-1684"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feng Chen","raw_affiliation_strings":["Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai 200433,","Shanghai Center for Mathematical Sciences, Fudan University , Shanghai 200438,","Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, 200438, China","Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai 200433,","institution_ids":["https://openalex.org/I4210164150"]},{"raw_affiliation_string":"Shanghai Center for Mathematical Sciences, Fudan University , Shanghai 200438,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, 200438, China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210164150"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088679847","display_name":"Chunhe Li","orcid":"https://orcid.org/0000-0002-9127-3930"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chunhe Li","raw_affiliation_strings":["Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai 200433,","School of Mathematical Sciences, Shanghai Key Laboratory for Contemporary Applied Mathematics and MOE Frontiers Center for Brain Science, Fudan University , Shanghai 200433,","Shanghai Center for Mathematical Sciences, Fudan University , Shanghai 200438,","Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China","School of Mathematical Sciences, Shanghai Key Laboratory for Contemporary Applied Mathematics and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China"],"raw_orcid":"https://orcid.org/0000-0002-9127-3930","affiliations":[{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University , Shanghai 200433,","institution_ids":["https://openalex.org/I4210164150"]},{"raw_affiliation_string":"School of Mathematical Sciences, Shanghai Key Laboratory for Contemporary Applied Mathematics and MOE Frontiers Center for Brain Science, Fudan University , Shanghai 200433,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai Center for Mathematical Sciences, Fudan University , Shanghai 200438,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4210164150"]},{"raw_affiliation_string":"School of Mathematical Sciences, Shanghai Key Laboratory for Contemporary Applied Mathematics and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China","institution_ids":["https://openalex.org/I24943067"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.8435,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.74432882,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"41","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9632999897003174,"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":0.9632999897003174,"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":0.018799999728798866,"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":0.011599999852478504,"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/source-code","display_name":"Source code","score":0.6388000249862671},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5709999799728394},{"id":"https://openalex.org/keywords/dynamics","display_name":"Dynamics (music)","score":0.5055000185966492},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4325999915599823},{"id":"https://openalex.org/keywords/network-structure","display_name":"Network structure","score":0.41359999775886536},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.3517000079154968},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.29089999198913574}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6858999729156494},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6388000249862671},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5709999799728394},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.5055000185966492},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4325999915599823},{"id":"https://openalex.org/C2988224531","wikidata":"https://www.wikidata.org/wiki/Q20830730","display_name":"Network structure","level":2,"score":0.41359999775886536},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4018000066280365},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3709999918937683},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3537999987602234},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.353300005197525},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.3517000079154968},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3303000032901764},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.29089999198913574},{"id":"https://openalex.org/C123757187","wikidata":"https://www.wikidata.org/wiki/Q9195957","display_name":"Network dynamics","level":2,"score":0.2906999886035919},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.2838999927043915},{"id":"https://openalex.org/C34947359","wikidata":"https://www.wikidata.org/wiki/Q665189","display_name":"Complex network","level":2,"score":0.28290000557899475},{"id":"https://openalex.org/C2992708514","wikidata":"https://www.wikidata.org/wiki/Q48968323","display_name":"Quantitative biology","level":2,"score":0.27390000224113464},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26930001378059387},{"id":"https://openalex.org/C104122410","wikidata":"https://www.wikidata.org/wiki/Q1416406","display_name":"Network model","level":2,"score":0.2687999904155731},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.2581999897956848},{"id":"https://openalex.org/C2983685735","wikidata":"https://www.wikidata.org/wiki/Q5227355","display_name":"Data source","level":2,"score":0.25540000200271606}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058750","descriptor_name":"Epithelial-Mesenchymal Transition","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D058750","descriptor_name":"Epithelial-Mesenchymal Transition","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf598","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf598","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41183100","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41183100","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:11411701","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12603361","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf598","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf598","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3519221078","display_name":null,"funder_award_id":"2019YFA0709502","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G996845878","display_name":null,"funder_award_id":"12171102","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"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W1494413412","https://openalex.org/W1845430499","https://openalex.org/W1923318030","https://openalex.org/W1951049964","https://openalex.org/W1970070519","https://openalex.org/W1986944049","https://openalex.org/W2002189052","https://openalex.org/W2012095617","https://openalex.org/W2026614436","https://openalex.org/W2031285837","https://openalex.org/W2035824523","https://openalex.org/W2056658264","https://openalex.org/W2065746091","https://openalex.org/W2075040103","https://openalex.org/W2076513103","https://openalex.org/W2081746825","https://openalex.org/W2100790213","https://openalex.org/W2107575419","https://openalex.org/W2121438179","https://openalex.org/W2123973944","https://openalex.org/W2132555912","https://openalex.org/W2140514146","https://openalex.org/W2145444336","https://openalex.org/W2149573463","https://openalex.org/W2162143298","https://openalex.org/W2235572757","https://openalex.org/W2517592377","https://openalex.org/W2735632796","https://openalex.org/W2739335964","https://openalex.org/W2791493111","https://openalex.org/W2799898775","https://openalex.org/W2901292166","https://openalex.org/W2903622309","https://openalex.org/W2916837967","https://openalex.org/W2951068818","https://openalex.org/W2971378659","https://openalex.org/W2973361953","https://openalex.org/W2979519501","https://openalex.org/W2987046671","https://openalex.org/W2989985381","https://openalex.org/W3017209066","https://openalex.org/W3021400239","https://openalex.org/W3029681104","https://openalex.org/W3096828292","https://openalex.org/W3136949212","https://openalex.org/W3159699835","https://openalex.org/W3182302426","https://openalex.org/W3196981277","https://openalex.org/W3201535265","https://openalex.org/W4207078846","https://openalex.org/W4292363360","https://openalex.org/W4295529460","https://openalex.org/W4308132330","https://openalex.org/W4313250874","https://openalex.org/W4321376284","https://openalex.org/W4362731285","https://openalex.org/W4388323202"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Biological":[1],"functions":[2],"are":[3],"governed":[4],"by":[5],"gene":[6],"regulatory":[7,120],"networks":[8],"(GRNs).":[9],"Accurately":[10],"inferring":[11],"GRNs":[12],"from":[13,104],"high-dimensional":[14],"and":[15,32,46,76,86,118],"noisy":[16],"single-cell":[17,105],"data":[18],"remains":[19],"a":[20,56],"major":[21],"challenge":[22],"in":[23],"systems":[24],"biology.":[25],"Conventional":[26],"approaches":[27],"often":[28],"struggle":[29],"with":[30,68],"robustness":[31],"interpretability,":[33],"particularly":[34,92],"when":[35],"applied":[36],"to":[37,89,109],"complex":[38,47],"biological":[39],"processes":[40],"such":[41],"as":[42],"cell":[43],"fate":[44],"decisions":[45],"diseases.":[48],"RESULTS:":[49],"In":[50],"this":[51],"study,":[52],"we":[53,113],"propose":[54],"GGANO,":[55],"hybrid":[57],"framework":[58],"that":[59,81],"integrates":[60],"Gaussian":[61],"Graphical":[62],"Models":[63],"for":[64,73],"conditional":[65],"independence":[66],"learning":[67],"Neural":[69],"Ordinary":[70],"Differential":[71],"Equations":[72],"dynamic":[74],"modeling":[75],"inference.":[77],"Benchmark":[78],"analyzes":[79],"show":[80],"GGANO":[82,97,108],"achieves":[83],"superior":[84],"accuracy":[85],"stability":[87],"compared":[88],"existing":[90],"methods,":[91],"under":[93],"high-noise":[94],"conditions.":[95],"Furthermore,":[96],"enables":[98],"the":[99,110],"inference":[100],"of":[101],"stochastic":[102],"dynamics":[103],"data.":[106],"Applying":[107],"EMT":[111,123],"datasets,":[112],"uncover":[114],"intermediate":[115],"cellular":[116],"states":[117],"key":[119],"genes":[121],"driving":[122],"progression.":[124],"AVAILABILITY":[125],"AND":[126],"IMPLEMENTATION:":[127],"The":[128],"source":[129],"code":[130],"is":[131],"available":[132],"at":[133],"GitHub:":[134],"https://github.com/ChenFeng87/GGANO.":[135]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-11-04T00:00:00"}
