{"id":"https://openalex.org/W4376224154","doi":"https://doi.org/10.1093/bib/bbad180","title":"P-CSN: single-cell RNA sequencing data analysis by partial cell-specific network","display_name":"P-CSN: single-cell RNA sequencing data analysis by partial cell-specific network","publication_year":2023,"publication_date":"2023-05-01","ids":{"openalex":"https://openalex.org/W4376224154","doi":"https://doi.org/10.1093/bib/bbad180","pmid":"https://pubmed.ncbi.nlm.nih.gov/37170676"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad180","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad180","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/A5101397195","display_name":"Yan Wang","orcid":"https://orcid.org/0000-0002-7882-1015"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Wang","raw_affiliation_strings":["School of Science, Jiangnan University , Wuxi 214122 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Science, Jiangnan University , Wuxi 214122 , China","institution_ids":["https://openalex.org/I111599522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047539619","display_name":"Chenxu Xuan","orcid":null},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chenxu Xuan","raw_affiliation_strings":["School of Science, Jiangnan University , Wuxi 214122 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Science, Jiangnan University , Wuxi 214122 , China","institution_ids":["https://openalex.org/I111599522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103166820","display_name":"Wu HanWen","orcid":null},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hanwen Wu","raw_affiliation_strings":["School of Science, Jiangnan University , Wuxi 214122 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Science, Jiangnan University , Wuxi 214122 , China","institution_ids":["https://openalex.org/I111599522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065836602","display_name":"Bai Zhang","orcid":"https://orcid.org/0000-0002-2234-4176"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bai Zhang","raw_affiliation_strings":["School of Science, Jiangnan University , Wuxi 214122 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Science, Jiangnan University , Wuxi 214122 , China","institution_ids":["https://openalex.org/I111599522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048868382","display_name":"Tao Ding","orcid":"https://orcid.org/0000-0002-7354-0994"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Tao Ding","raw_affiliation_strings":["School of Mathematics Statistics and Physics, Newcastle University , Newcastle upon Tyne NE1 7RU , UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics Statistics and Physics, Newcastle University , Newcastle upon Tyne NE1 7RU , UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5105034310","display_name":"Jie Gao","orcid":"https://orcid.org/0000-0002-2842-1304"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jie Gao","raw_affiliation_strings":["School of Science, Jiangnan University , Wuxi 214122 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Science, Jiangnan University , Wuxi 214122 , China","institution_ids":["https://openalex.org/I111599522"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5105034310"],"corresponding_institution_ids":["https://openalex.org/I111599522"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.163,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.78326253,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"24","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":0.9998999834060669,"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":0.9998999834060669,"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":0.9977999925613403,"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":0.9883999824523926,"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/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6312273740768433},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5647469758987427},{"id":"https://openalex.org/keywords/conditional-independence","display_name":"Conditional independence","score":0.5617579221725464},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5543373227119446},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5109488368034363},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3947274088859558},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3649088740348816},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33298492431640625},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2957882285118103},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27794530987739563}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6312273740768433},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5647469758987427},{"id":"https://openalex.org/C79772020","wikidata":"https://www.wikidata.org/wiki/Q5159264","display_name":"Conditional independence","level":2,"score":0.5617579221725464},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5543373227119446},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5109488368034363},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3947274088859558},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3649088740348816},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33298492431640625},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2957882285118103},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27794530987739563}],"mesh":[{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad180","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad180","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:37170676","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37170676","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/G1302938317","display_name":null,"funder_award_id":"11831015","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2514967234","display_name":null,"funder_award_id":"12271216","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1813068103","https://openalex.org/W1979283544","https://openalex.org/W1982900838","https://openalex.org/W1984883254","https://openalex.org/W1993287310","https://openalex.org/W2007439698","https://openalex.org/W2010653277","https://openalex.org/W2056225291","https://openalex.org/W2083620785","https://openalex.org/W2104386599","https://openalex.org/W2111384508","https://openalex.org/W2128120736","https://openalex.org/W2306630387","https://openalex.org/W2307567449","https://openalex.org/W2337819340","https://openalex.org/W2373831850","https://openalex.org/W2511896561","https://openalex.org/W2561394844","https://openalex.org/W2620676965","https://openalex.org/W2725490158","https://openalex.org/W2761971542","https://openalex.org/W2813447943","https://openalex.org/W2906625258","https://openalex.org/W2921554869","https://openalex.org/W2950222828","https://openalex.org/W2961177472","https://openalex.org/W2979981308","https://openalex.org/W3006642983","https://openalex.org/W3032847236","https://openalex.org/W3093659935","https://openalex.org/W3098658004","https://openalex.org/W3135480207","https://openalex.org/W3161508292","https://openalex.org/W4200416341","https://openalex.org/W4311860751","https://openalex.org/W6730767313","https://openalex.org/W6749486397"],"related_works":["https://openalex.org/W2032841337","https://openalex.org/W2950036200","https://openalex.org/W4293775328","https://openalex.org/W2131250617","https://openalex.org/W1595337508","https://openalex.org/W4233034052","https://openalex.org/W3032874291","https://openalex.org/W2005057264","https://openalex.org/W2363156284","https://openalex.org/W2415025170"],"abstract_inverted_index":{"Although":[0],"many":[1],"single-cell":[2,118],"computational":[3],"methods":[4],"proposed":[5,95,124],"use":[6],"gene":[7,17,143],"expression":[8,18],"as":[9],"input,":[10],"recent":[11],"studies":[12],"show":[13],"that":[14],"replacing":[15],"'unstable'":[16],"with":[19,141],"'stable'":[20],"gene-gene":[21,34,184],"associations":[22,45,110,185],"can":[23],"greatly":[24],"improve":[25],"the":[26,43,53,66,89,101,104,116,148,168,171,176,188],"performance":[27,189],"of":[28,46,56,92,103,131,175,181,190],"downstream":[29,191],"analysis.":[30],"To":[31,76],"obtain":[32],"accurate":[33,183],"associations,":[35],"conditional":[36,54],"cell-specific":[37,47,83,152],"network":[38,48,74,84,119,145],"method":[39,49,85,133],"(c-CSN)":[40],"filters":[41],"out":[42],"indirect":[44],"(CSN)":[50],"based":[51,87],"on":[52,88,115,136],"independence":[55,91],"statistics.":[57],"However,":[58],"when":[59],"there":[60,162],"are":[61,134,163],"strong":[62,164],"connections":[63,165],"in":[64,73,96,166],"networks,":[65,153,167],"c-CSN":[67,105],"suffers":[68],"from":[69],"false":[70,172],"negative":[71,173],"problem":[72],"construction.":[75],"overcome":[77],"this":[78,97],"problem,":[79],"a":[80],"new":[81],"partial":[82,90,151],"(p-CSN)":[86],"statistics":[93],"is":[94,122],"paper,":[98],"which":[99],"eliminates":[100],"singularity":[102],"by":[106],"implicitly":[107],"including":[108],"direct":[109],"among":[111],"estimated":[112],"variables.":[113],"Based":[114],"p-CSN,":[117],"entropy":[120],"(scNEntropy)":[121],"further":[123,186],"to":[125,157],"quantify":[126],"cell":[127,156,198,202],"state.":[128],"The":[129,179,194],"superiorities":[130],"our":[132],"verified":[135],"several":[137],"datasets.":[138],"(i)":[139],"Compared":[140],"traditional":[142],"regulatory":[144],"construction":[146],"methods,":[147],"p-CSN":[149,169],"constructs":[150],"namely,":[154],"one":[155,158],"network.":[159],"(ii)":[160],"When":[161],"reduces":[170],"probability":[174],"c-CSN.":[177],"(iii)":[178],"input":[180],"more":[182],"optimizes":[187],"analyses.":[192],"(iv)":[193],"scNEntropy":[195],"effectively":[196],"quantifies":[197],"state":[199],"and":[200],"reconstructs":[201],"pseudo-time.":[203]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}