{"id":"https://openalex.org/W4318896523","doi":"https://doi.org/10.1093/bioinformatics/btad071","title":"WMDS.net: a network control framework for identifying key players in transcriptome programs","display_name":"WMDS.net: a network control framework for identifying key players in transcriptome programs","publication_year":2023,"publication_date":"2023-02-01","ids":{"openalex":"https://openalex.org/W4318896523","doi":"https://doi.org/10.1093/bioinformatics/btad071","pmid":"https://pubmed.ncbi.nlm.nih.gov/36727489"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad071","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad071","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad071/49172503/btad071.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad071/49172503/btad071.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003733739","display_name":"Xiang Cheng","orcid":"https://orcid.org/0000-0001-5315-9830"},"institutions":[{"id":"https://openalex.org/I4210137217","display_name":"Women's Hospital, School of Medicine, Zhejiang University","ror":"https://ror.org/042t7yh44","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210137217"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiang Cheng","raw_affiliation_strings":["Department of Gynecologic Oncology, Women\u2019s Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine , Hangzhou 310006, China","Institute of Bioinformatics, Zhejiang University , Hangzhou 310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Gynecologic Oncology, Women\u2019s Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine , Hangzhou 310006, China","institution_ids":["https://openalex.org/I4210137217"]},{"raw_affiliation_string":"Institute of Bioinformatics, Zhejiang University , Hangzhou 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101145757","display_name":"Md Amanullah","orcid":null},"institutions":[{"id":"https://openalex.org/I2802390878","display_name":"Sir Run Run Shaw Hospital","ror":"https://ror.org/00ka6rp58","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802390878"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Md Amanullah","raw_affiliation_strings":["Department of Respiratory Medicine, Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine , Hangzhou 310016, China","Institute of Bioinformatics, Zhejiang University , Hangzhou 310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Respiratory Medicine, Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine , Hangzhou 310016, China","institution_ids":["https://openalex.org/I2802390878","https://openalex.org/I76130692"]},{"raw_affiliation_string":"Institute of Bioinformatics, Zhejiang University , Hangzhou 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079669609","display_name":"Weigang Liu","orcid":"https://orcid.org/0000-0001-9800-2263"},"institutions":[{"id":"https://openalex.org/I2802390878","display_name":"Sir Run Run Shaw Hospital","ror":"https://ror.org/00ka6rp58","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802390878"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weigang Liu","raw_affiliation_strings":["Department of Respiratory Medicine, Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine , Hangzhou 310016, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Respiratory Medicine, Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine , Hangzhou 310016, China","institution_ids":["https://openalex.org/I2802390878","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100330444","display_name":"Yi Liu","orcid":"https://orcid.org/0000-0001-7135-0030"},"institutions":[{"id":"https://openalex.org/I2802390878","display_name":"Sir Run Run Shaw Hospital","ror":"https://ror.org/00ka6rp58","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802390878"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Liu","raw_affiliation_strings":["Department of Respiratory Medicine, Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine , Hangzhou 310016, China","Institute of Bioinformatics, Zhejiang University , Hangzhou 310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Respiratory Medicine, Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine , Hangzhou 310016, China","institution_ids":["https://openalex.org/I2802390878","https://openalex.org/I76130692"]},{"raw_affiliation_string":"Institute of Bioinformatics, Zhejiang University , Hangzhou 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101848102","display_name":"Xiaoqing Pan","orcid":"https://orcid.org/0000-0002-3559-5337"},"institutions":[{"id":"https://openalex.org/I21945476","display_name":"Shanghai Normal University","ror":"https://ror.org/01cxqmw89","country_code":"CN","type":"education","lineage":["https://openalex.org/I21945476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoqing Pan","raw_affiliation_strings":["Department of Mathematics, Shanghai Normal University , Xuhui 200234, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Shanghai Normal University , Xuhui 200234, China","institution_ids":["https://openalex.org/I21945476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078977000","display_name":"Honghe Zhang","orcid":"https://orcid.org/0000-0001-5954-2857"},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Honghe Zhang","raw_affiliation_strings":["Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences, Zhejiang University School of Medicine , Hangzhou 310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Sciences, Zhejiang University School of Medicine , Hangzhou 310058, China","institution_ids":["https://openalex.org/I200296433","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056079345","display_name":"Haiming Xu","orcid":"https://orcid.org/0000-0002-0675-4087"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haiming Xu","raw_affiliation_strings":["Institute of Bioinformatics, Zhejiang University , Hangzhou 310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Bioinformatics, Zhejiang University , Hangzhou 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100714943","display_name":"Pengyuan Liu","orcid":"https://orcid.org/0000-0002-8386-8416"},"institutions":[{"id":"https://openalex.org/I204308271","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244","country_code":"US","type":"education","lineage":["https://openalex.org/I204308271"]},{"id":"https://openalex.org/I4210137217","display_name":"Women's Hospital, School of Medicine, Zhejiang University","ror":"https://ror.org/042t7yh44","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210137217"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Pengyuan Liu","raw_affiliation_strings":["Cancer Center, Zhejiang University , Hangzhou 310029, China","Department of Gynecologic Oncology, Women\u2019s Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine , Hangzhou 310006, China","Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin , Milwaukee, WI 53226, USA"],"raw_orcid":"https://orcid.org/0000-0002-8386-8416","affiliations":[{"raw_affiliation_string":"Cancer Center, Zhejiang University , Hangzhou 310029, China","institution_ids":["https://openalex.org/I76130692"]},{"raw_affiliation_string":"Department of Gynecologic Oncology, Women\u2019s Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine , Hangzhou 310006, China","institution_ids":["https://openalex.org/I4210137217"]},{"raw_affiliation_string":"Department of Physiology, Center of Systems Molecular Medicine, Medical College of Wisconsin , Milwaukee, WI 53226, USA","institution_ids":["https://openalex.org/I204308271"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100627527","display_name":"Yan L\u00fc","orcid":"https://orcid.org/0000-0002-5004-4656"},"institutions":[{"id":"https://openalex.org/I4210137217","display_name":"Women's Hospital, School of Medicine, Zhejiang University","ror":"https://ror.org/042t7yh44","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210137217"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yan Lu","raw_affiliation_strings":["Cancer Center, Zhejiang University , Hangzhou 310029, China","Department of Gynecologic Oncology, Women\u2019s Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine , Hangzhou 310006, China","Institute of Bioinformatics, Zhejiang University , Hangzhou 310058, China"],"raw_orcid":"https://orcid.org/0000-0002-5004-4656","affiliations":[{"raw_affiliation_string":"Cancer Center, Zhejiang University , Hangzhou 310029, China","institution_ids":["https://openalex.org/I76130692"]},{"raw_affiliation_string":"Department of Gynecologic Oncology, Women\u2019s Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine , Hangzhou 310006, China","institution_ids":["https://openalex.org/I4210137217"]},{"raw_affiliation_string":"Institute of Bioinformatics, Zhejiang University , Hangzhou 310058, China","institution_ids":["https://openalex.org/I76130692"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100627527","https://openalex.org/A5100714943"],"corresponding_institution_ids":["https://openalex.org/I204308271","https://openalex.org/I4210137217","https://openalex.org/I76130692"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.5311,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.90362685,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"39","issue":"2","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":0.6280999779701233,"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":0.6280999779701233,"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":0.2515999972820282,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.05050000175833702,"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/controllability","display_name":"Controllability","score":0.6039721965789795},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5970403552055359},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5379074215888977},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.5251507759094238},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.5100541710853577},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44074803590774536},{"id":"https://openalex.org/keywords/complex-network","display_name":"Complex network","score":0.41596490144729614},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.34808528423309326},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3139938712120056},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22319084405899048},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1628163456916809},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10582193732261658}],"concepts":[{"id":"https://openalex.org/C48209547","wikidata":"https://www.wikidata.org/wiki/Q1331104","display_name":"Controllability","level":2,"score":0.6039721965789795},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5970403552055359},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5379074215888977},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.5251507759094238},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5100541710853577},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44074803590774536},{"id":"https://openalex.org/C34947359","wikidata":"https://www.wikidata.org/wiki/Q665189","display_name":"Complex network","level":2,"score":0.41596490144729614},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34808528423309326},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3139938712120056},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22319084405899048},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1628163456916809},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10582193732261658},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","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":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","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":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad071","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad071","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad071/49172503/btad071.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36727489","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36727489","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9925106","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9925106","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9925106/pdf/btad071.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad071","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad071","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad071/49172503/btad071.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.41999998688697815,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G2037655703","display_name":null,"funder_award_id":"P01 HL149620","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G3005146028","display_name":null,"funder_award_id":"92253203","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4699867024","display_name":null,"funder_award_id":"81871864","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4708576552","display_name":null,"funder_award_id":"LZ20H160001","funder_id":"https://openalex.org/F4320338464","funder_display_name":"Natural Science Foundation of Zhejiang Province"},{"id":"https://openalex.org/G4736470801","display_name":null,"funder_award_id":"HL149620","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6623863905","display_name":null,"funder_award_id":"82072857","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/F4320322927","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320338464","display_name":"Natural Science Foundation of Zhejiang Province","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4318896523.pdf"},"referenced_works_count":70,"referenced_works":["https://openalex.org/W1493071618","https://openalex.org/W1559830894","https://openalex.org/W1965055200","https://openalex.org/W1965856472","https://openalex.org/W1966327575","https://openalex.org/W1984675437","https://openalex.org/W1996442028","https://openalex.org/W1998767819","https://openalex.org/W2008618993","https://openalex.org/W2008620264","https://openalex.org/W2009394950","https://openalex.org/W2009720434","https://openalex.org/W2011039300","https://openalex.org/W2022883176","https://openalex.org/W2023568503","https://openalex.org/W2028133290","https://openalex.org/W2037954058","https://openalex.org/W2044433401","https://openalex.org/W2056254608","https://openalex.org/W2058553784","https://openalex.org/W2059300459","https://openalex.org/W2060705109","https://openalex.org/W2062533676","https://openalex.org/W2076486071","https://openalex.org/W2088544963","https://openalex.org/W2095334215","https://openalex.org/W2096358531","https://openalex.org/W2096460732","https://openalex.org/W2096766502","https://openalex.org/W2101420429","https://openalex.org/W2109363337","https://openalex.org/W2112609377","https://openalex.org/W2118089467","https://openalex.org/W2123227225","https://openalex.org/W2125987139","https://openalex.org/W2127616922","https://openalex.org/W2129973040","https://openalex.org/W2136541538","https://openalex.org/W2139227366","https://openalex.org/W2144940507","https://openalex.org/W2145702571","https://openalex.org/W2147566730","https://openalex.org/W2149082178","https://openalex.org/W2152176732","https://openalex.org/W2156695919","https://openalex.org/W2158529347","https://openalex.org/W2159987716","https://openalex.org/W2161409973","https://openalex.org/W2167202160","https://openalex.org/W2174955952","https://openalex.org/W2192915867","https://openalex.org/W2215244420","https://openalex.org/W2347110697","https://openalex.org/W2508622936","https://openalex.org/W2783397995","https://openalex.org/W2784142616","https://openalex.org/W2891939069","https://openalex.org/W2897858720","https://openalex.org/W2900099657","https://openalex.org/W2915168078","https://openalex.org/W2946331502","https://openalex.org/W2947213478","https://openalex.org/W2983296354","https://openalex.org/W2989906520","https://openalex.org/W3005326935","https://openalex.org/W3098528364","https://openalex.org/W4239147634","https://openalex.org/W4247236552","https://openalex.org/W4306970977","https://openalex.org/W6828911396"],"related_works":["https://openalex.org/W2287125742","https://openalex.org/W2734532915","https://openalex.org/W2059596457","https://openalex.org/W2318071399","https://openalex.org/W2086464854","https://openalex.org/W1483993456","https://openalex.org/W2022883176","https://openalex.org/W2408582765","https://openalex.org/W3123729141","https://openalex.org/W2748195347"],"abstract_inverted_index":{"MOTIVATION:":[0],"Mammalian":[1],"cells":[2],"can":[3,30,57,97],"be":[4,31],"transcriptionally":[5],"reprogramed":[6],"to":[7,39,47,77,119,169],"other":[8,194],"cellular":[9,20,67],"phenotypes.":[10,68],"Controllability":[11],"of":[12,93,108,124,131,136,144,155,158,172],"such":[13],"complex":[14],"transitions":[15],"in":[16,53,82,138,176],"transcriptional":[17,42,55,84,160],"networks":[18],"underlying":[19,66],"phenotypes":[21],"is":[22,185],"an":[23],"inherent":[24],"biological":[25],"characteristic.":[26],"This":[27],"network":[28,63,86,101,116,140],"controllability":[29,157],"interpreted":[32],"by":[33],"operating":[34],"a":[35,88,113,198],"few":[36],"key":[37,51,59,80],"regulators":[38,52,81],"guide":[40],"the":[41,50,54,62,79,83,100,106,121,134,139,142,153,159,170,193],"program":[43,56],"from":[44,179],"one":[45],"state":[46,64,102],"another.":[48],"Finding":[49],"provide":[58],"insights":[60],"into":[61,152],"transition":[65],"RESULTS:":[69],"To":[70,162],"address":[71],"this":[72],"challenge,":[73],"here,":[74],"we":[75,111,166],"proposed":[76],"identify":[78],"co-expression":[85,127,146],"as":[87],"minimum":[89],"dominating":[90],"set":[91],"(MDS)":[92],"driver":[94,122,174],"nodes":[95,123,137],"that":[96],"fully":[98],"control":[99],"transition.":[103],"Based":[104],"on":[105],"theory":[107],"structural":[109],"controllability,":[110],"developed":[112],"weighted":[114],"MDS":[115],"model":[117],"(WMDS.net)":[118],"find":[120],"differential":[125],"gene":[126,145],"networks.":[128],"The":[129,180],"weight":[130],"WMDS.net":[132,168,184],"integrates":[133],"degree":[135],"and":[141,191,203],"significance":[143],"difference":[147],"between":[148,201],"two":[149],"physiological":[150],"states":[151],"measurement":[154],"node":[156],"network.":[161],"confirm":[163],"its":[164],"validity,":[165],"applied":[167],"discovery":[171],"cancer":[173,189],"genes":[175],"RNA-seq":[177],"datasets":[178,190],"Cancer":[181],"Genome":[182],"Atlas.":[183],"powerful":[186],"among":[187],"various":[188],"outperformed":[192],"top-tier":[195],"tools":[196],"with":[197],"better":[199],"balance":[200],"precision":[202],"recall.":[204],"AVAILABILITY":[205],"AND":[206],"IMPLEMENTATION:":[207],"https://github.com/chaofen123/WMDS.net.":[208],"SUPPLEMENTARY":[209],"INFORMATION:":[210],"Supplementary":[211],"data":[212],"are":[213],"available":[214],"at":[215],"Bioinformatics":[216],"online.":[217]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":8}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
