{"id":"https://openalex.org/W4318754682","doi":"https://doi.org/10.1093/bib/bbad011","title":"Unsupervised construction of gene regulatory network based on single-cell multi-omics data of colorectal cancer","display_name":"Unsupervised construction of gene regulatory network based on single-cell multi-omics data of colorectal cancer","publication_year":2023,"publication_date":"2023-02-01","ids":{"openalex":"https://openalex.org/W4318754682","doi":"https://doi.org/10.1093/bib/bbad011","pmid":"https://pubmed.ncbi.nlm.nih.gov/36723605"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad011","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad011","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/A5085717026","display_name":"Lingyu Cui","orcid":"https://orcid.org/0000-0003-4221-8430"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lingyu Cui","raw_affiliation_strings":["College of Life Science, Northeast Forestry University , Harbin, 150040 , China"],"raw_orcid":"https://orcid.org/0000-0003-4221-8430","affiliations":[{"raw_affiliation_string":"College of Life Science, Northeast Forestry University , Harbin, 150040 , China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100427008","display_name":"Hongfei Li","orcid":"https://orcid.org/0000-0003-4104-3966"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongfei Li","raw_affiliation_strings":["College of Life Science, Northeast Forestry University , Harbin, 150040 , China"],"raw_orcid":"https://orcid.org/0000-0003-4104-3966","affiliations":[{"raw_affiliation_string":"College of Life Science, Northeast Forestry University , Harbin, 150040 , China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089694665","display_name":"Jilong Bian","orcid":"https://orcid.org/0000-0001-5336-8763"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jilong Bian","raw_affiliation_strings":["College of Information and Computer Engineering, Northeast Forestry University , Harbin, 150040 , China"],"raw_orcid":"https://orcid.org/0000-0001-5336-8763","affiliations":[{"raw_affiliation_string":"College of Information and Computer Engineering, Northeast Forestry University , Harbin, 150040 , China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100649978","display_name":"Guohua Wang","orcid":"https://orcid.org/0000-0001-7381-2374"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guohua Wang","raw_affiliation_strings":["College of Information and Computer Engineering, Northeast Forestry University , Harbin, 150040 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information and Computer Engineering, Northeast Forestry University , Harbin, 150040 , China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051771989","display_name":"Yingjian Liang","orcid":"https://orcid.org/0000-0002-5905-2820"},"institutions":[{"id":"https://openalex.org/I156144747","display_name":"Harbin Medical University","ror":"https://ror.org/05jscf583","country_code":"CN","type":"education","lineage":["https://openalex.org/I156144747"]},{"id":"https://openalex.org/I4210156501","display_name":"First Affiliated Hospital of Harbin Medical University","ror":"https://ror.org/05vy2sc54","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210156501"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yingjian Liang","raw_affiliation_strings":["Department of General Surgery, the First Affiliated Hospital of Harbin Medical University , Harbin, 150007 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of General Surgery, the First Affiliated Hospital of Harbin Medical University , Harbin, 150007 , China","institution_ids":["https://openalex.org/I156144747","https://openalex.org/I4210156501"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5051771989","https://openalex.org/A5100649978"],"corresponding_institution_ids":["https://openalex.org/I156144747","https://openalex.org/I4210156501","https://openalex.org/I47689461"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.1466,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.7763598,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"24","issue":"2","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":0.9987999796867371,"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":0.9987999796867371,"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":0.9939000010490417,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9929999709129333,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/colorectal-cancer","display_name":"Colorectal cancer","score":0.6647925972938538},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5747101902961731},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5144734382629395},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.47823184728622437},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45785582065582275},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.44859400391578674},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2864099144935608},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2257164716720581},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18477410078048706}],"concepts":[{"id":"https://openalex.org/C526805850","wikidata":"https://www.wikidata.org/wiki/Q188874","display_name":"Colorectal cancer","level":3,"score":0.6647925972938538},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5747101902961731},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5144734382629395},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.47823184728622437},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45785582065582275},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.44859400391578674},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2864099144935608},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2257164716720581},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18477410078048706}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","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":"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad011","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad011","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:36723605","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36723605","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":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.75}],"awards":[{"id":"https://openalex.org/G1091266728","display_name":"\u57fa\u4e8e\u5dee\u5f02-\u5171\u8868\u8fbe\u7f51\u7edc\u7684\u5355\u7ec6\u80de\u5173\u952e\u57fa\u56e0\u8bc6\u522b\u4e0e\u7ec6\u80de\u5206\u7c7b\u65b9\u6cd5\u7814\u7a76","funder_award_id":"62072095","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3250074440","display_name":null,"funder_award_id":"2572022AW70","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G5125408974","display_name":null,"funder_award_id":"2021YFC2100101","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G870551797","display_name":null,"funder_award_id":"62225109","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"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W65738273","https://openalex.org/W1993418188","https://openalex.org/W2030017878","https://openalex.org/W2068478010","https://openalex.org/W2076513103","https://openalex.org/W2102619694","https://openalex.org/W2108234281","https://openalex.org/W2119180969","https://openalex.org/W2131271579","https://openalex.org/W2137465688","https://openalex.org/W2170551349","https://openalex.org/W2171808845","https://openalex.org/W2175370850","https://openalex.org/W2272984102","https://openalex.org/W2312170576","https://openalex.org/W2616922646","https://openalex.org/W2757234574","https://openalex.org/W2782454362","https://openalex.org/W2903435154","https://openalex.org/W2907514116","https://openalex.org/W2946296908","https://openalex.org/W2954610188","https://openalex.org/W2963210853","https://openalex.org/W2983968250","https://openalex.org/W3038004940","https://openalex.org/W3097582316","https://openalex.org/W3128646645","https://openalex.org/W3165720345","https://openalex.org/W3196689760","https://openalex.org/W4200379876","https://openalex.org/W4206804332","https://openalex.org/W4211038303","https://openalex.org/W4213111299","https://openalex.org/W4213167486","https://openalex.org/W4214854288","https://openalex.org/W4220885858","https://openalex.org/W4224302557","https://openalex.org/W4225845169","https://openalex.org/W4283157828"],"related_works":["https://openalex.org/W2374019147","https://openalex.org/W2015369371","https://openalex.org/W2370262613","https://openalex.org/W4362606997","https://openalex.org/W2172237894","https://openalex.org/W4361825250","https://openalex.org/W4377092742","https://openalex.org/W4229447658","https://openalex.org/W4386462333","https://openalex.org/W2375232943"],"abstract_inverted_index":{"Identifying":[0],"gene":[1,79],"regulatory":[2],"networks":[3],"(GRNs)":[4],"at":[5],"the":[6,18,62,75],"resolution":[7],"of":[8,20,40,83,90],"single":[9],"cells":[10],"has":[11],"long":[12],"been":[13],"a":[14,33],"great":[15],"challenge,":[16],"and":[17,45,53,101,105,116],"advent":[19],"single-cell":[21,41,46],"multi-omics":[22],"data":[23],"provides":[24],"unprecedented":[25],"opportunities":[26],"to":[27,36,60,73,111,118],"construct":[28],"GRNs.":[29],"Here,":[30],"we":[31],"propose":[32],"novel":[34],"strategy":[35,85],"integrate":[37],"omics":[38],"datasets":[39],"ribonucleic":[42],"acid":[43],"sequencing":[44],"Assay":[47],"for":[48],"Transposase-Accessible":[49],"Chromatin":[50],"using":[51,54],"sequencing,":[52],"an":[55],"unsupervised":[56],"learning":[57],"neural":[58],"network":[59],"divide":[61],"samples":[63],"with":[64,96],"high":[65],"copy":[66],"number":[67],"variation":[68],"scores,":[69],"which":[70],"are":[71,93,109,128],"used":[72],"infer":[74],"GRN":[76],"in":[77],"each":[78],"block.":[80],"Accuracy":[81],"validation":[82],"proposed":[84],"shows":[86],"that":[87],"approximately":[88],"80%":[89],"transcription":[91,107],"factors":[92,108],"directly":[94],"associated":[95],"cancer,":[97,99],"colorectal":[98],"malignancy":[100],"disease":[102],"by":[103,120],"TRRUST;":[104],"most":[106],"prone":[110],"produce":[112],"multiple":[113],"transcript":[114],"variants":[115],"lead":[117],"tumorigenesis":[119],"RegNetwork":[121],"database,":[122],"respectively.":[123],"The":[124],"source":[125],"code":[126],"access":[127],"available":[129],"at:":[130],"https://github.com/Cuily-v/Colorectal_cancer.":[131]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-06-06T09:05:17.133730","created_date":"2025-10-10T00:00:00"}
