{"id":"https://openalex.org/W7164750895","doi":"https://doi.org/10.1093/bib/bbag300","title":"A unified framework for selecting and evaluating cell-type-specific gene co-expressions in single-cell data","display_name":"A unified framework for selecting and evaluating cell-type-specific gene co-expressions in single-cell data","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7164750895","doi":"https://doi.org/10.1093/bib/bbag300","pmid":"https://pubmed.ncbi.nlm.nih.gov/42289047"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag300","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag300","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":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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"gold","oa_url":"https://doi.org/10.1093/bib/bbag300","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063372161","display_name":"Xinning Shan","orcid":"https://orcid.org/0000-0001-6270-0094"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xinning Shan","raw_affiliation_strings":["Department of Biostatistics, Yale University , New Haven, CT 06511 ,"],"raw_orcid":"https://orcid.org/0000-0001-6270-0094","affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Yale University , New Haven, CT 06511 ,","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033771420","display_name":"Yingxin Lin","orcid":"https://orcid.org/0000-0002-4299-7326"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yingxin Lin","raw_affiliation_strings":["Department of Biostatistics, Yale University , New Haven, CT 06511 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Yale University , New Haven, CT 06511 ,","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074828414","display_name":"Hongyu Zhao","orcid":"https://orcid.org/0000-0003-1195-9607"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hongyu Zhao","raw_affiliation_strings":["Department of Biostatistics, Yale University , New Haven, CT 06511 ,"],"raw_orcid":"https://orcid.org/0000-0003-1195-9607","affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Yale University , New Haven, CT 06511 ,","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5074828414"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.64318552,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"3","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":0.9843000173568726,"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":0.9843000173568726,"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":0.009499999694526196,"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/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.00139999995008111,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.739799976348877},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.7160999774932861},{"id":"https://openalex.org/keywords/correlation","display_name":"Correlation","score":0.5788999795913696},{"id":"https://openalex.org/keywords/estimation","display_name":"Estimation","score":0.5437999963760376},{"id":"https://openalex.org/keywords/ground-truth","display_name":"Ground truth","score":0.4569999873638153},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.44449999928474426}],"concepts":[{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.739799976348877},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.71670001745224},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7160999774932861},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.5788999795913696},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5515000224113464},{"id":"https://openalex.org/C96250715","wikidata":"https://www.wikidata.org/wiki/Q965330","display_name":"Estimation","level":2,"score":0.5437999963760376},{"id":"https://openalex.org/C146849305","wikidata":"https://www.wikidata.org/wiki/Q370766","display_name":"Ground truth","level":2,"score":0.4569999873638153},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.44449999928474426},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4255000054836273},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4034999907016754},{"id":"https://openalex.org/C2776207758","wikidata":"https://www.wikidata.org/wiki/Q5303302","display_name":"Downstream (manufacturing)","level":2,"score":0.4027999937534332},{"id":"https://openalex.org/C112789634","wikidata":"https://www.wikidata.org/wiki/Q18207010","display_name":"False positives and false negatives","level":3,"score":0.37770000100135803},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.35109999775886536},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2897000014781952},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2775999903678894},{"id":"https://openalex.org/C2780009758","wikidata":"https://www.wikidata.org/wiki/Q6804172","display_name":"Measure (data warehouse)","level":2,"score":0.2542000114917755},{"id":"https://openalex.org/C66882249","wikidata":"https://www.wikidata.org/wiki/Q169336","display_name":"Homogeneous","level":2,"score":0.25279998779296875}],"mesh":[{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","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":"D019295","descriptor_name":"Computational Biology","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":"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":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag300","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag300","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":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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42289047","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42289047","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13265145","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13265145/","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag300","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag300","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":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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3679365667","display_name":null,"funder_award_id":"U24 HG012108","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4323100451","display_name":null,"funder_award_id":"U01 HG013840","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6121916639","display_name":null,"funder_award_id":"R01 GM134005","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"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W2361797231","https://openalex.org/W2783644856","https://openalex.org/W2785509713","https://openalex.org/W2808743742","https://openalex.org/W2929810236","https://openalex.org/W2949086748","https://openalex.org/W2951271761","https://openalex.org/W2952382191","https://openalex.org/W2979835214","https://openalex.org/W2997280954","https://openalex.org/W2997831639","https://openalex.org/W3041062936","https://openalex.org/W3087821509","https://openalex.org/W3108941787","https://openalex.org/W3133413949","https://openalex.org/W3165591717","https://openalex.org/W3180268318","https://openalex.org/W3196992636","https://openalex.org/W3208721686","https://openalex.org/W3217269327","https://openalex.org/W4200416341","https://openalex.org/W4205170489","https://openalex.org/W4220939485","https://openalex.org/W4225981439","https://openalex.org/W4361301386","https://openalex.org/W4366278929","https://openalex.org/W4376134478","https://openalex.org/W4379980212","https://openalex.org/W4385752307","https://openalex.org/W4387142593","https://openalex.org/W4387661643","https://openalex.org/W4409211490"],"related_works":[],"abstract_inverted_index":{"Cell-type-specific":[0],"gene":[1,9,83,110,172,200,217],"co-expression":[2,20,118,143,218],"networks":[3,21,57],"are":[4,67],"widely":[5],"used":[6],"to":[7,17,41,196],"characterize":[8],"relationships.":[10],"Although":[11],"many":[12,34],"methods":[13,145,164],"have":[14,149],"been":[15],"developed":[16],"infer":[18],"such":[19],"from":[22,85],"single-cell":[23,86],"data,":[24,87],"the":[25,64,95,114,162,168,179,212],"lack":[26],"of":[27,29,97,100,117,161,171,216],"consideration":[28],"false":[30,65],"positive":[31],"control":[32],"in":[33],"evaluations":[35],"and":[36,50,112,129,137,176,205,214],"downstream":[37,203],"analyses":[38],"may":[39,58],"lead":[40],"incorrect":[42],"conclusions":[43],"because":[44],"higher":[45,47],"reproducibility,":[46],"functional":[48],"coherence,":[49],"a":[51,131,158,191,207],"larger":[52],"overlap":[53],"with":[54],"known":[55],"biological":[56,186],"not":[59,68,148],"imply":[60],"better":[61],"performance":[62],"if":[63],"positives":[66],"well":[69],"controlled.":[70],"In":[71],"this":[72,123],"study,":[73],"we":[74,127,155],"systematically":[75],"compared":[76],"two":[77],"distinct":[78],"criteria":[79],"for":[80,106,113,142,167,178,194,202,211],"selecting":[81,108],"correlated":[82,199],"pairs":[84,111,173,201],"p-value":[88],"versus":[89],"correlation":[90,101],"strength.":[91],"We":[92],"found":[93],"that":[94,134,146,157],"use":[96],"p-values":[98,141],"instead":[99],"strength":[102],"is":[103],"more":[104,208],"robust":[105],"both":[107],"meaningful":[109],"fair":[115,159],"benchmarking":[116],"estimation":[119,144,163,220],"methods.":[120,221],"To":[121],"make":[122],"approach":[124],"universally":[125],"applicable,":[126],"extended":[128],"validated":[130],"simulation":[132],"method":[133],"can":[135],"efficiently":[136],"reliably":[138],"generate":[139],"empirical":[140],"do":[147],"corresponding":[150],"or":[151],"well-controlled":[152],"p-values.":[153],"Furthermore,":[154],"demonstrated":[156],"comparison":[160,215],"requires":[165],"adjusting":[166],"varying":[169],"number":[170],"they":[174],"identified":[175],"accounting":[177],"inherent":[180],"expression-level":[181],"biases":[182],"within":[183],"ground":[184],"truth":[185],"networks.":[187],"Our":[188],"study":[189,204],"provides":[190],"practical":[192],"guide":[193],"researchers":[195],"select":[197],"reliable":[198],"establishes":[206],"rigorous":[209],"standard":[210],"evaluation":[213],"network":[219]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2026-06-15T00:00:00"}
