{"id":"https://openalex.org/W4297457819","doi":"https://doi.org/10.1093/bib/bbac424","title":"dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data","display_name":"dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data","publication_year":2022,"publication_date":"2022-09-03","ids":{"openalex":"https://openalex.org/W4297457819","doi":"https://doi.org/10.1093/bib/bbac424","pmid":"https://pubmed.ncbi.nlm.nih.gov/36168811"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac424","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac424","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5067212646","display_name":"Yu Xu","orcid":"https://orcid.org/0009-0005-4873-1659"},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yu Xu","raw_affiliation_strings":["Department of Computer Science, Hong Kong Baptist University , Kowloon Tong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hong Kong Baptist University , Kowloon Tong, Hong Kong","institution_ids":["https://openalex.org/I141568987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100685931","display_name":"Jiaxing Chen","orcid":"https://orcid.org/0000-0001-5795-6722"},"institutions":[{"id":"https://openalex.org/I12615008","display_name":"Beijing Normal-Hong Kong Baptist University","ror":"https://ror.org/04snvc712","country_code":"CN","type":"education","lineage":["https://openalex.org/I12615008"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiaxing Chen","raw_affiliation_strings":["Computer Science and Technology, Division of Science and Technology, BNU-HKBU United International College , Jintong Road, 519087, Zhuhai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science and Technology, Division of Science and Technology, BNU-HKBU United International College , Jintong Road, 519087, Zhuhai, China","institution_ids":["https://openalex.org/I12615008"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112127369","display_name":"Aiping Lyu","orcid":null},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Aiping Lyu","raw_affiliation_strings":["School of Chinese Medicine, Hong Kong Baptist University , Kowloon Tong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Chinese Medicine, Hong Kong Baptist University , Kowloon Tong, Hong Kong","institution_ids":["https://openalex.org/I141568987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022791783","display_name":"William K. Cheung","orcid":"https://orcid.org/0000-0002-7428-2050"},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"William K Cheung","raw_affiliation_strings":["Department of Computer Science, Hong Kong Baptist University , Kowloon Tong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hong Kong Baptist University , Kowloon Tong, Hong Kong","institution_ids":["https://openalex.org/I141568987"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100388624","display_name":"Lu Zhang","orcid":"https://orcid.org/0000-0002-2794-7371"},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Lu Zhang","raw_affiliation_strings":["Department of Computer Science, Hong Kong Baptist University , Kowloon Tong, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hong Kong Baptist University , Kowloon Tong, Hong Kong","institution_ids":["https://openalex.org/I141568987"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5022791783","https://openalex.org/A5100388624","https://openalex.org/A5112127369"],"corresponding_institution_ids":["https://openalex.org/I141568987"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.5109,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.8249908,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"23","issue":"6","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":0.9998000264167786,"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":0.9998000264167786,"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":0.9976000189781189,"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":0.9932000041007996,"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/computer-science","display_name":"Computer science","score":0.6911709308624268},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5769979953765869},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.565345823764801},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.49561774730682373},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.47823160886764526},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4772201180458069},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4377545118331909},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4346103370189667},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.42690154910087585},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3955671191215515},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36694592237472534},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3593830466270447},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2111322283744812},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1502724587917328}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6911709308624268},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5769979953765869},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.565345823764801},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.49561774730682373},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.47823160886764526},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4772201180458069},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4377545118331909},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4346103370189667},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.42690154910087585},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3955671191215515},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36694592237472534},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3593830466270447},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2111322283744812},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1502724587917328},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","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},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac424","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac424","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36168811","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36168811","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2303175871","display_name":null,"funder_award_id":"2019A1515011046","funder_id":"https://openalex.org/F4320337111","funder_display_name":"Basic and Applied Basic Research Foundation of Guangdong Province"},{"id":"https://openalex.org/G6966040288","display_name":null,"funder_award_id":"2021A1515012226","funder_id":"https://openalex.org/F4320337111","funder_display_name":"Basic and Applied Basic Research Foundation of Guangdong Province"}],"funders":[{"id":"https://openalex.org/F4320337111","display_name":"Basic and Applied Basic Research Foundation of Guangdong Province","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1175879704","https://openalex.org/W1686810756","https://openalex.org/W1967320885","https://openalex.org/W2001903569","https://openalex.org/W2020541351","https://openalex.org/W2034784092","https://openalex.org/W2044525257","https://openalex.org/W2044899905","https://openalex.org/W2057978375","https://openalex.org/W2071547624","https://openalex.org/W2077026063","https://openalex.org/W2089468765","https://openalex.org/W2103017472","https://openalex.org/W2111384508","https://openalex.org/W2122342005","https://openalex.org/W2133254377","https://openalex.org/W2135937351","https://openalex.org/W2150926065","https://openalex.org/W2165009258","https://openalex.org/W2171808845","https://openalex.org/W2177615447","https://openalex.org/W2316095770","https://openalex.org/W2511896561","https://openalex.org/W2534008312","https://openalex.org/W2560266832","https://openalex.org/W2561884319","https://openalex.org/W2577490495","https://openalex.org/W2786672974","https://openalex.org/W2792581694","https://openalex.org/W2802291136","https://openalex.org/W2803928488","https://openalex.org/W2898321887","https://openalex.org/W2900099657","https://openalex.org/W2916020270","https://openalex.org/W2951850020","https://openalex.org/W2952535935","https://openalex.org/W2963806890","https://openalex.org/W2997280954","https://openalex.org/W3045186844","https://openalex.org/W3112600195","https://openalex.org/W3127330229","https://openalex.org/W3156304677","https://openalex.org/W3174608384","https://openalex.org/W3193795275","https://openalex.org/W6637373629","https://openalex.org/W6685630543","https://openalex.org/W6728202225","https://openalex.org/W6748816842","https://openalex.org/W6790017628"],"related_works":["https://openalex.org/W2169501356","https://openalex.org/W1994539334","https://openalex.org/W4241525120","https://openalex.org/W2909382709","https://openalex.org/W2156615630","https://openalex.org/W2125934144","https://openalex.org/W2945498457","https://openalex.org/W2952396239","https://openalex.org/W3003223963","https://openalex.org/W3108101741"],"abstract_inverted_index":{"Time-course":[0],"single-cell":[1],"RNA":[2],"sequencing":[3],"(scRNA-seq)":[4],"data":[5,50,54],"have":[6],"been":[7],"widely":[8],"used":[9],"to":[10,29,43,86,121,189,205],"explore":[11],"dynamic":[12],"changes":[13],"in":[14,175],"gene":[15,32,48,100,143,191],"expression":[16,49,97,144],"of":[17,75,98,109,117],"transcription":[18],"factors":[19],"(TFs)":[20],"and":[21,105,114,140,160,179,193],"their":[22],"target":[23,111],"genes.":[24,209],"This":[25],"information":[26,65],"is":[27],"useful":[28],"reconstruct":[30,87,122],"cell-type-specific":[31],"regulatory":[33],"networks":[34],"(GRNs).":[35],"However,":[36],"the":[37,64,73,95,107,110,115,118,132,142,172,181,201,207],"existing":[38],"tools":[39,203],"are":[40],"commonly":[41],"designed":[42],"analyze":[44],"either":[45],"time-course":[46,90,125,163],"bulk":[47],"or":[51],"static":[52],"scRNA-seq":[53,76,91,126,164],"via":[55],"pseudo-time":[56],"cell":[57],"ordering.":[58],"A":[59],"few":[60],"methods":[61,156,174],"successfully":[62],"utilize":[63],"from":[66,124],"multiple":[67],"time":[68],"points":[69],"while":[70],"also":[71,186],"considering":[72,137,206],"characteristics":[74],"data.":[77,92,127,165],"We":[78,149,185],"proposed":[79],"dynDeepDRIM,":[80],"a":[81,99],"novel":[82],"deep":[83],"learning":[84],"model":[85,141],"GRNs":[88,123],"using":[89,146],"It":[93],"represents":[94],"joint":[96],"pair":[101,113],"as":[102],"an":[103],"image":[104,108],"utilizes":[106],"TF-gene":[112,134,177],"ones":[116],"potential":[119],"neighbors":[120],"dynDeepDRIM":[128,151,166,188],"can":[129],"effectively":[130],"remove":[131],"transitive":[133],"interactions":[135,178],"by":[136],"neighborhood":[138],"context":[139],"dynamics":[145],"high-dimensional":[147],"tensors.":[148],"compared":[150],"with":[152],"six":[153],"GRN":[154],"reconstruction":[155],"on":[157],"both":[158],"simulation":[159],"four":[161],"real":[162],"achieved":[167,196],"substantially":[168],"better":[169,198],"performance":[170,199],"than":[171,200],"other":[173,202],"inferring":[176],"eliminated":[180],"false":[182],"positives":[183],"effectively.":[184],"applied":[187],"annotate":[190],"functions":[192],"found":[194],"it":[195],"evidently":[197],"due":[204],"neighbor":[208]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}