{"id":"https://openalex.org/W4389932368","doi":"https://doi.org/10.1093/bib/bbad380","title":"CoRegNet: unraveling gene co-regulation networks from public RNA-Seq repositories using a beta-binomial statistical model","display_name":"CoRegNet: unraveling gene co-regulation networks from public RNA-Seq repositories using a beta-binomial statistical model","publication_year":2023,"publication_date":"2023-10-12","ids":{"openalex":"https://openalex.org/W4389932368","doi":"https://doi.org/10.1093/bib/bbad380","pmid":"https://pubmed.ncbi.nlm.nih.gov/38113079"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad380","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad380","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad380/54586448/bbad380.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad380/54586448/bbad380.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100753585","display_name":"Jiasheng Wang","orcid":"https://orcid.org/0000-0001-8477-7092"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I4210117334","display_name":"Neurological Research Institute","ror":"https://ror.org/02ea83075","country_code":"US","type":"other","lineage":["https://openalex.org/I4210117334"]},{"id":"https://openalex.org/I4210147586","display_name":"Texas Children's Hospital","ror":"https://ror.org/05cz92x43","country_code":"US","type":"funder","lineage":["https://openalex.org/I4210147586"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiasheng Wang","raw_affiliation_strings":["Department of Pediatrics, Baylor College of Medicine , Houston, TX 77030 , USA","Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine , Houston, TX, 77030 , USA","Jan and Dan Duncan Neurological Research Institute at Texas Children\u2019s Hospital , Houston, TX 77030 , USA","Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, Baylor College of Medicine , Houston, TX 77030 , USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine , Houston, TX, 77030 , USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Jan and Dan Duncan Neurological Research Institute at Texas Children\u2019s Hospital , Houston, TX 77030 , USA","institution_ids":["https://openalex.org/I4210117334","https://openalex.org/I4210147586"]},{"raw_affiliation_string":"Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016453515","display_name":"Ying\u2010Wooi Wan","orcid":"https://orcid.org/0000-0002-4354-7482"},"institutions":[{"id":"https://openalex.org/I1344073410","display_name":"Howard Hughes Medical Institute","ror":"https://ror.org/006w34k90","country_code":"US","type":"facility","lineage":["https://openalex.org/I1344073410"]},{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I4210117334","display_name":"Neurological Research Institute","ror":"https://ror.org/02ea83075","country_code":"US","type":"other","lineage":["https://openalex.org/I4210117334"]},{"id":"https://openalex.org/I4210147586","display_name":"Texas Children's Hospital","ror":"https://ror.org/05cz92x43","country_code":"US","type":"funder","lineage":["https://openalex.org/I4210147586"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ying-Wooi Wan","raw_affiliation_strings":["Department of Molecular and Human Genetics , Baylor College of Medicine, , Houston, TX 77030 , USA","Howard Hughes Medical Institute , Baylor College of Medicine, , Houston, TX 77030 , USA","Jan and Dan Duncan Neurological Research Institute at Texas Children\u2019s Hospital , Houston, TX 77030 , USA","Department of Molecular and Human Genetics, Baylor College of Medicine, Howard Hughes Medical Institute, Houston, TX 77030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Human Genetics , Baylor College of Medicine, , Houston, TX 77030 , USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Howard Hughes Medical Institute , Baylor College of Medicine, , Houston, TX 77030 , USA","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I181547552"]},{"raw_affiliation_string":"Jan and Dan Duncan Neurological Research Institute at Texas Children\u2019s Hospital , Houston, TX 77030 , USA","institution_ids":["https://openalex.org/I4210117334","https://openalex.org/I4210147586"]},{"raw_affiliation_string":"Department of Molecular and Human Genetics, Baylor College of Medicine, Howard Hughes Medical Institute, Houston, TX 77030, USA","institution_ids":["https://openalex.org/I1344073410","https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075934899","display_name":"Rami Al\u2010Ouran","orcid":null},"institutions":[{"id":"https://openalex.org/I100086675","display_name":"Al-Hussein Bin Talal University","ror":"https://ror.org/019dkd780","country_code":"JO","type":"education","lineage":["https://openalex.org/I100086675"]},{"id":"https://openalex.org/I4405260986","display_name":"Al Hussein Technical University","ror":"https://ror.org/04jvdr241","country_code":"JO","type":"education","lineage":["https://openalex.org/I4405260986"]}],"countries":["JO"],"is_corresponding":false,"raw_author_name":"Rami Al-Ouran","raw_affiliation_strings":["Al Hussein Technical University , Amman , Jordan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Al Hussein Technical University , Amman , Jordan","institution_ids":["https://openalex.org/I100086675","https://openalex.org/I4405260986"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101188388","display_name":"Meichen Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I4210117334","display_name":"Neurological Research Institute","ror":"https://ror.org/02ea83075","country_code":"US","type":"other","lineage":["https://openalex.org/I4210117334"]},{"id":"https://openalex.org/I4210147586","display_name":"Texas Children's Hospital","ror":"https://ror.org/05cz92x43","country_code":"US","type":"funder","lineage":["https://openalex.org/I4210147586"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Meichen Huang","raw_affiliation_strings":["Department of Neurology, Baylor College of Medicine , Houston, TX 77030 , USA","Jan and Dan Duncan Neurological Research Institute at Texas Children\u2019s Hospital , Houston, TX 77030 , USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurology, Baylor College of Medicine , Houston, TX 77030 , USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Jan and Dan Duncan Neurological Research Institute at Texas Children\u2019s Hospital , Houston, TX 77030 , USA","institution_ids":["https://openalex.org/I4210117334","https://openalex.org/I4210147586"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004947640","display_name":"Zhandong Liu","orcid":"https://orcid.org/0000-0002-7608-0831"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]},{"id":"https://openalex.org/I4210117334","display_name":"Neurological Research Institute","ror":"https://ror.org/02ea83075","country_code":"US","type":"other","lineage":["https://openalex.org/I4210117334"]},{"id":"https://openalex.org/I4210147586","display_name":"Texas Children's Hospital","ror":"https://ror.org/05cz92x43","country_code":"US","type":"funder","lineage":["https://openalex.org/I4210147586"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhandong Liu","raw_affiliation_strings":["Department of Pediatrics, Baylor College of Medicine , Houston, TX 77030 , USA","Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine , Houston, TX, 77030 , USA","Jan and Dan Duncan Neurological Research Institute at Texas Children\u2019s Hospital , Houston, TX 77030 , USA","Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, Baylor College of Medicine , Houston, TX 77030 , USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine , Houston, TX, 77030 , USA","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Jan and Dan Duncan Neurological Research Institute at Texas Children\u2019s Hospital , Houston, TX 77030 , USA","institution_ids":["https://openalex.org/I4210117334","https://openalex.org/I4210147586"]},{"raw_affiliation_string":"Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, 77030, USA","institution_ids":["https://openalex.org/I181547552"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5004947640"],"corresponding_institution_ids":["https://openalex.org/I181547552","https://openalex.org/I4210117334","https://openalex.org/I4210147586"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.2793,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.52136507,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"25","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9997000098228455,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9997000098228455,"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":0.9994000196456909,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9975000023841858,"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/rna-seq","display_name":"RNA-Seq","score":0.645433783531189},{"id":"https://openalex.org/keywords/beta","display_name":"BETA (programming language)","score":0.6166477203369141},{"id":"https://openalex.org/keywords/binomial","display_name":"Binomial (polynomial)","score":0.5800217390060425},{"id":"https://openalex.org/keywords/negative-binomial-distribution","display_name":"Negative binomial distribution","score":0.569750964641571},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5153440833091736},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4980025291442871},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45250946283340454},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29147791862487793},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24258357286453247},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22678399085998535},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2103109061717987},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.20118165016174316},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.18178686499595642},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.0686633288860321}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.645433783531189},{"id":"https://openalex.org/C2776174256","wikidata":"https://www.wikidata.org/wiki/Q830842","display_name":"BETA (programming language)","level":2,"score":0.6166477203369141},{"id":"https://openalex.org/C2781315470","wikidata":"https://www.wikidata.org/wiki/Q193623","display_name":"Binomial (polynomial)","level":2,"score":0.5800217390060425},{"id":"https://openalex.org/C199335787","wikidata":"https://www.wikidata.org/wiki/Q743364","display_name":"Negative binomial distribution","level":3,"score":0.569750964641571},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5153440833091736},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4980025291442871},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45250946283340454},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29147791862487793},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24258357286453247},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22678399085998535},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2103109061717987},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.20118165016174316},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.18178686499595642},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0686633288860321},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"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":"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":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbad380","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad380","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad380/54586448/bbad380.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38113079","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38113079","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},{"id":"pmh:oai:pubmedcentral.nih.gov:10729864","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10729864","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10729864/pdf/bbad380.pdf","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":"Brief Bioinform","raw_type":"Text"},{"id":"pmh:oai:digitalcommons.library.tmc.edu:baylor_docs-4391","is_oa":false,"landing_page_url":"https://digitalcommons.library.tmc.edu/baylor_docs/3438","pdf_url":null,"source":{"id":"https://openalex.org/S4377196655","display_name":"Digital Commons-TMC (Texas Medical Center)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1337852284","host_organization_name":"Texas Medical Center","host_organization_lineage":["https://openalex.org/I1337852284"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty and Staff Publications","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad380","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad380","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad380/54586448/bbad380.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.4699999988079071,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G345484959","display_name":null,"funder_award_id":"P50 HD103555","funder_id":"https://openalex.org/F4320337611","funder_display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development"},{"id":"https://openalex.org/G8041011128","display_name":null,"funder_award_id":"P50HD103555","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337611","display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","ror":"https://ror.org/04byxyr05"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4389932368.pdf"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1964904043","https://openalex.org/W1966327575","https://openalex.org/W1974423219","https://openalex.org/W1989277387","https://openalex.org/W2018838463","https://openalex.org/W2033582154","https://openalex.org/W2047256610","https://openalex.org/W2061173833","https://openalex.org/W2118258530","https://openalex.org/W2130790725","https://openalex.org/W2131681506","https://openalex.org/W2132982061","https://openalex.org/W2133254377","https://openalex.org/W2146512944","https://openalex.org/W2259632819","https://openalex.org/W2735897797","https://openalex.org/W2761802050","https://openalex.org/W2804802143","https://openalex.org/W2809330972","https://openalex.org/W2889765367","https://openalex.org/W2900569176","https://openalex.org/W2906010089","https://openalex.org/W2941448575","https://openalex.org/W2945183595","https://openalex.org/W2990435446","https://openalex.org/W2996443588","https://openalex.org/W3005531462","https://openalex.org/W3088521497","https://openalex.org/W3099768174","https://openalex.org/W3106811464","https://openalex.org/W4206710640","https://openalex.org/W4231254854","https://openalex.org/W4384692356","https://openalex.org/W6813094581","https://openalex.org/W6854865223"],"related_works":["https://openalex.org/W2323218782","https://openalex.org/W4394426846","https://openalex.org/W4200033037","https://openalex.org/W2404800752","https://openalex.org/W1981276613","https://openalex.org/W4394543623","https://openalex.org/W3213655218","https://openalex.org/W2021262032","https://openalex.org/W4366831151","https://openalex.org/W2052110748"],"abstract_inverted_index":{"Millions":[0],"of":[1,22,24,69,71,75,97,109,116,140],"RNA":[2],"sequencing":[3],"samples":[4],"have":[5],"been":[6],"deposited":[7],"into":[8,30],"public":[9,150],"databases,":[10],"providing":[11],"a":[12,35,51,138,155],"rich":[13],"resource":[14],"for":[15,158],"biological":[16,167],"research.":[17],"These":[18],"datasets":[19],"encompass":[20],"tens":[21,68],"thousands":[23,70],"experiments":[25,43,79],"and":[26,83,125],"offer":[27],"comprehensive":[28],"insights":[29],"human":[31,81],"cellular":[32],"regulation.":[33],"However,":[34],"major":[36],"challenge":[37],"is":[38],"how":[39],"to":[40],"integrate":[41],"these":[42],"that":[44,59,86,111,143],"acquired":[45],"at":[46],"different":[47],"conditions.":[48],"We":[49],"propose":[50],"new":[52,166],"statistical":[53],"tool":[54],"based":[55],"on":[56],"beta-binomial":[57],"distributions":[58],"can":[60],"construct":[61],"robust":[62],"gene":[63,91,141,162],"co-regulation":[64],"network":[65],"(CoRegNet)":[66],"across":[67],"experiments.":[72],"Our":[73],"analysis":[74],"over":[76],"12":[77],"000":[78],"involving":[80],"tissues":[82],"cells":[84],"shows":[85],"CoRegNet":[87,153],"significantly":[88],"outperforms":[89],"existing":[90],"co-expression-based":[92],"methods.":[93],"Although":[94],"the":[95,98,117,122,126,132,145],"majority":[96],"genes":[99,110],"are":[100,112],"linearly":[101],"co-regulated,":[102],"we":[103,136],"did":[104],"discover":[105],"an":[106],"interesting":[107],"set":[108,139],"non-linearly":[113],"co-regulated;":[114],"half":[115,128],"time":[118],"they":[119,129],"change":[120,130],"in":[121,131],"same":[123],"direction":[124],"other":[127],"opposite":[133],"direction.":[134],"Additionally,":[135],"identified":[137],"pairs":[142],"follows":[144],"Simpson's":[146],"paradox.":[147],"By":[148],"utilizing":[149],"domain":[151],"data,":[152],"offers":[154],"powerful":[156],"approach":[157],"identifying":[159],"functionally":[160],"related":[161],"pairs,":[163],"thereby":[164],"revealing":[165],"insights.":[168]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}