{"id":"https://openalex.org/W4412709826","doi":"https://doi.org/10.1186/s12859-025-06218-w","title":"Time-coexpress: temporal trajectory modeling of dynamic gene co-expression patterns using single-cell transcriptomics data","display_name":"Time-coexpress: temporal trajectory modeling of dynamic gene co-expression patterns using single-cell transcriptomics data","publication_year":2025,"publication_date":"2025-07-29","ids":{"openalex":"https://openalex.org/W4412709826","doi":"https://doi.org/10.1186/s12859-025-06218-w","pmid":"https://pubmed.ncbi.nlm.nih.gov/40731381"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06218-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06218-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06218-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06218-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024033003","display_name":"Shuyi Yang","orcid":"https://orcid.org/0009-0004-1604-8874"},"institutions":[{"id":"https://openalex.org/I155781252","display_name":"University of South Carolina","ror":"https://ror.org/02b6qw903","country_code":"US","type":"education","lineage":["https://openalex.org/I155781252"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shuyi Yang","raw_affiliation_strings":["Department of Statistics, University of South Carolina, Columbia, USA. shuyi@email.sc.edu"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of South Carolina, Columbia, USA. shuyi@email.sc.edu","institution_ids":["https://openalex.org/I155781252"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116037266","display_name":"Anderson Bussing","orcid":"https://orcid.org/0000-0002-0910-1129"},"institutions":[{"id":"https://openalex.org/I155781252","display_name":"University of South Carolina","ror":"https://ror.org/02b6qw903","country_code":"US","type":"education","lineage":["https://openalex.org/I155781252"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anderson Bussing","raw_affiliation_strings":["Department of Statistics, University of South Carolina, Columbia, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of South Carolina, Columbia, USA","institution_ids":["https://openalex.org/I155781252"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026261134","display_name":"Giampiero Marra","orcid":"https://orcid.org/0000-0002-9010-2646"},"institutions":[{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Giampiero Marra","raw_affiliation_strings":["Department of Statistical Science, University College London, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistical Science, University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044927844","display_name":"Michelle L. Brinkmeier","orcid":"https://orcid.org/0000-0001-9505-4682"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michelle L. Brinkmeier","raw_affiliation_strings":["Department of Human Genetics, University of Michigan, Ann Arbor, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Human Genetics, University of Michigan, Ann Arbor, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020938661","display_name":"Sally A. Camper","orcid":"https://orcid.org/0000-0001-8556-3379"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sally A. Camper","raw_affiliation_strings":["Department of Human Genetics, University of Michigan, Ann Arbor, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Human Genetics, University of Michigan, Ann Arbor, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026389380","display_name":"Shannon W. Davis","orcid":"https://orcid.org/0000-0001-7354-5691"},"institutions":[{"id":"https://openalex.org/I155781252","display_name":"University of South Carolina","ror":"https://ror.org/02b6qw903","country_code":"US","type":"education","lineage":["https://openalex.org/I155781252"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shannon W. Davis","raw_affiliation_strings":["Department of Biological Sciences, University of South Carolina, Columbia, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of South Carolina, Columbia, USA","institution_ids":["https://openalex.org/I155781252"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033863599","display_name":"Yen\u2010Yi Ho","orcid":"https://orcid.org/0000-0002-3224-3184"},"institutions":[{"id":"https://openalex.org/I155781252","display_name":"University of South Carolina","ror":"https://ror.org/02b6qw903","country_code":"US","type":"education","lineage":["https://openalex.org/I155781252"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yen-Yi Ho","raw_affiliation_strings":["Department of Statistics, University of South Carolina, Columbia, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of South Carolina, Columbia, USA","institution_ids":["https://openalex.org/I155781252"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.1519,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.78814815,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"26","issue":"1","first_page":"199","last_page":"199"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994000196456909,"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":0.9994000196456909,"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":9.999999747378752e-05,"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":0.0,"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":0.5757387280464172},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5687645673751831},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5270039439201355},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.49621254205703735},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.46679431200027466},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.41544464230537415},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3688356578350067},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3652833104133606},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18862780928611755}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5757387280464172},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5687645673751831},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5270039439201355},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.49621254205703735},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.46679431200027466},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.41544464230537415},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3688356578350067},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3652833104133606},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18862780928611755},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"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},{"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":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06218-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06218-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06218-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40731381","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40731381","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:ca37cf5c2f2b4f3a9061dde2413d4919","is_oa":true,"landing_page_url":"https://doaj.org/article/ca37cf5c2f2b4f3a9061dde2413d4919","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-26 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12308957","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12308957","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06218-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06218-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06218-w","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/8","display_name":"Decent work and economic growth","score":0.4399999976158142}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4412709826.pdf"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W1423766661","https://openalex.org/W1507444366","https://openalex.org/W1966327575","https://openalex.org/W1984883254","https://openalex.org/W1998653097","https://openalex.org/W1998963240","https://openalex.org/W2007218422","https://openalex.org/W2018275040","https://openalex.org/W2023194188","https://openalex.org/W2066607611","https://openalex.org/W2106575037","https://openalex.org/W2132555912","https://openalex.org/W2138696716","https://openalex.org/W2139845570","https://openalex.org/W2140308441","https://openalex.org/W2143918377","https://openalex.org/W2151821298","https://openalex.org/W2154065358","https://openalex.org/W2337474841","https://openalex.org/W2373831850","https://openalex.org/W2472502726","https://openalex.org/W2595554554","https://openalex.org/W2885369110","https://openalex.org/W2951799803","https://openalex.org/W2952535935","https://openalex.org/W2963014273","https://openalex.org/W2969718750","https://openalex.org/W3009370296","https://openalex.org/W3032111849","https://openalex.org/W3041345852","https://openalex.org/W3138916222","https://openalex.org/W4221092226","https://openalex.org/W4225981439","https://openalex.org/W4294216483","https://openalex.org/W4297253723","https://openalex.org/W4301014524","https://openalex.org/W4399239786","https://openalex.org/W4400430153","https://openalex.org/W4403479110","https://openalex.org/W4407043969","https://openalex.org/W6842097421"],"related_works":["https://openalex.org/W2052655934","https://openalex.org/W104645380","https://openalex.org/W2027213253","https://openalex.org/W2023641020","https://openalex.org/W2017047508","https://openalex.org/W2165201120","https://openalex.org/W2188530857","https://openalex.org/W2041199873","https://openalex.org/W1971081588","https://openalex.org/W1964194222"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,211],"rapid":[2],"advancement":[3],"of":[4,13,22,162,168,175,219,253],"single-cell":[5],"RNA":[6],"sequencing":[7],"(scRNAseq)":[8],"technology":[9],"provides":[10,119,241],"high-resolution":[11],"views":[12],"transcriptomic":[14],"activity":[15],"within":[16],"individual":[17,27],"cells.":[18],"Most":[19],"routine":[20],"analyses":[21],"scRNAseq":[23,128,163,186,236],"data":[24],"focus":[25],"on":[26],"genes;":[28],"however,":[29],"the":[30,86,120,136,173,176,195,245],"one-gene-at-a-time":[31],"analysis":[32,42,69,161],"is":[33],"likely":[34],"to":[35,55,66,106,122,141],"miss":[36],"meaningful":[37],"genetic":[38],"interactions.":[39],"Gene":[40],"co-expression":[41,68,77,112],"addresses":[43],"this":[44],"limitation":[45],"by":[46],"identifying":[47],"coordinated":[48],"changes":[49,109,148,222,240],"in":[50,53,80,110,127,149,223,235],"gene":[51,67,76,111,143,192,224,254],"expression":[52,155,230],"response":[54],"cellular":[56,114,196,257],"conditions,":[57],"such":[58,130],"as":[59,131],"developmental":[60],"or":[61],"temporal":[62,115,197,233],"trajectories.":[63,116],"Existing":[64],"approaches":[65],"often":[70],"assume":[71],"restrictive":[72],"linear":[73],"relationships.":[74],"However,":[75],"can":[78],"change":[79],"complex,":[81],"non-linear":[82,108,221],"ways,":[83],"which":[84],"suggests":[85],"need":[87],"for":[88],"more":[89,159],"flexible":[90,215],"and":[91,133,153,188,207,216,228,248],"accurate":[92],"methods.":[93],"RESULTS:":[94],"We":[95,179],"propose":[96],"a":[97,158,166,185,250],"copula-based":[98],"framework,":[99],"TIME-CoExpress,":[100],"with":[101],"proper":[102],"data-driven":[103],"smoothing":[104],"functions":[105],"model":[107],"along":[113,194,232],"Our":[117],"method":[118],"flexibility":[121],"incorporate":[123],"characteristics":[124],"commonly":[125],"observed":[126],"data,":[129],"over-dispersion":[132],"zero-inflation,":[134],"into":[135,244],"modeling":[137,142],"framework.":[138],"In":[139],"addition":[140],"co-expression,":[144,225],"TIME-CoExpress":[145],"captures":[146],"dynamic":[147],"gene-level":[150],"zero-inflation":[151,226],"rates":[152],"mean":[154,229],"levels,":[156],"providing":[157],"comprehensive":[160],"data.":[164,237],"Through":[165],"series":[167],"simulation":[169],"analyses,":[170],"we":[171],"evaluated":[172],"performance":[174],"proposed":[177,212],"approach.":[178],"further":[180],"demonstrated":[181],"its":[182],"implementation":[183],"using":[184],"dataset":[187],"identified":[189],"differentially":[190],"co-expressed":[191],"pairs":[193],"trajectory":[198],"during":[199],"pituitary":[200],"embryonic":[201],"development,":[202],"comparing":[203],"[Formula:":[204],"see":[205],"text]":[206],"wild-type":[208],"mice.":[209],"CONCLUSIONS:":[210],"framework":[213],"enables":[214],"robust":[217],"identification":[218],"dynamic,":[220],"rates,":[227],"levels":[231],"trajectories":[234],"Detecting":[238],"these":[239],"deeper":[242],"insights":[243],"biological":[246],"processes":[247],"offers":[249],"better":[251],"understanding":[252],"regulation":[255],"throughout":[256],"development.":[258]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
