{"id":"https://openalex.org/W3211299261","doi":"https://doi.org/10.1186/s12859-021-03964-5","title":"TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery","display_name":"TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery","publication_year":2021,"publication_date":"2021-10-01","ids":{"openalex":"https://openalex.org/W3211299261","doi":"https://doi.org/10.1186/s12859-021-03964-5","mag":"3211299261","pmid":"https://pubmed.ncbi.nlm.nih.gov/34689740"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-03964-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-03964-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-03964-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-03964-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045253111","display_name":"Yusong Liu","orcid":"https://orcid.org/0000-0003-4950-6304"},"institutions":[{"id":"https://openalex.org/I151727225","display_name":"Harbin Engineering University","ror":"https://ror.org/03x80pn82","country_code":"CN","type":"education","lineage":["https://openalex.org/I151727225"]},{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Yusong Liu","raw_affiliation_strings":["Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, 150001, Heilongjiang, China","Indiana University School of Medicine, Indianapolis, IN, 46202, USA","Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China","Indiana University School of Medicine, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, 150001, Heilongjiang, China","institution_ids":["https://openalex.org/I151727225"]},{"raw_affiliation_string":"Indiana University School of Medicine, Indianapolis, IN, 46202, USA","institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China","institution_ids":["https://openalex.org/I151727225"]},{"raw_affiliation_string":"Indiana University School of Medicine, Indianapolis, USA","institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083889663","display_name":"Xiufen Ye","orcid":"https://orcid.org/0000-0001-9812-2679"},"institutions":[{"id":"https://openalex.org/I151727225","display_name":"Harbin Engineering University","ror":"https://ror.org/03x80pn82","country_code":"CN","type":"education","lineage":["https://openalex.org/I151727225"]},{"id":"https://openalex.org/I4210105101","display_name":"Heilongjiang International University","ror":"https://ror.org/01cv0qm48","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210105101"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiufen Ye","raw_affiliation_strings":["Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, 150001, Heilongjiang, China. yexiufen@hrbeu.edu.cn","Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, 150001, Heilongjiang, China. yexiufen@hrbeu.edu.cn","institution_ids":["https://openalex.org/I151727225","https://openalex.org/I4210105101"]},{"raw_affiliation_string":"Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China","institution_ids":["https://openalex.org/I151727225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041863346","display_name":"Christina Y. Yu","orcid":"https://orcid.org/0000-0002-4165-6781"},"institutions":[{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christina Y. Yu","raw_affiliation_strings":["Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA","Indiana University School of Medicine, Indianapolis, IN, 46202, USA","Indiana University School of Medicine, Indianapolis, USA","Department of Biomedical Informatics, The Ohio State University, Columbus, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Indiana University School of Medicine, Indianapolis, IN, 46202, USA","institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana University School of Medicine, Indianapolis, USA","institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University, Columbus, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076674630","display_name":"Wei Shao","orcid":"https://orcid.org/0000-0003-1476-2068"},"institutions":[{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Shao","raw_affiliation_strings":["Indiana University School of Medicine, Indianapolis, IN, 46202, USA","Indiana University School of Medicine, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana University School of Medicine, Indianapolis, IN, 46202, USA","institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana University School of Medicine, Indianapolis, USA","institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003292372","display_name":"Jie Hou","orcid":"https://orcid.org/0000-0001-5979-8852"},"institutions":[{"id":"https://openalex.org/I151727225","display_name":"Harbin Engineering University","ror":"https://ror.org/03x80pn82","country_code":"CN","type":"education","lineage":["https://openalex.org/I151727225"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Hou","raw_affiliation_strings":["Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, 150001, Heilongjiang, China","Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, 150001, Heilongjiang, China","institution_ids":["https://openalex.org/I151727225"]},{"raw_affiliation_string":"Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China","institution_ids":["https://openalex.org/I151727225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102953680","display_name":"Weixing Feng","orcid":"https://orcid.org/0000-0002-6466-7918"},"institutions":[{"id":"https://openalex.org/I151727225","display_name":"Harbin Engineering University","ror":"https://ror.org/03x80pn82","country_code":"CN","type":"education","lineage":["https://openalex.org/I151727225"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weixing Feng","raw_affiliation_strings":["Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, 150001, Heilongjiang, China","Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, 150001, Heilongjiang, China","institution_ids":["https://openalex.org/I151727225"]},{"raw_affiliation_string":"Collage of Intelligent Systems Science and Engineering, Harbin Engineering University, Harbin, China","institution_ids":["https://openalex.org/I151727225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100436623","display_name":"Jie Zhang","orcid":"https://orcid.org/0000-0001-6939-7905"},"institutions":[{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jie Zhang","raw_affiliation_strings":["Indiana University School of Medicine, Indianapolis, IN, 46202, USA","Indiana University School of Medicine, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana University School of Medicine, Indianapolis, IN, 46202, USA","institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Indiana University School of Medicine, Indianapolis, USA","institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057366605","display_name":"Kun Huang","orcid":"https://orcid.org/0000-0002-8530-370X"},"institutions":[{"id":"https://openalex.org/I1324682000","display_name":"Regenstrief Institute","ror":"https://ror.org/05f2ywb48","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1324682000"]},{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kun Huang","raw_affiliation_strings":["Indiana University School of Medicine, Indianapolis, IN, 46202, USA. kunhuang@iu.edu","Regenstrief Institute, Indianapolis, IN, 46202, USA. kunhuang@iu.edu","Indiana University School of Medicine, Indianapolis, USA","Regenstrief Institute, Indianapolis, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Indiana University School of Medicine, Indianapolis, IN, 46202, USA. kunhuang@iu.edu","institution_ids":["https://openalex.org/I55769427"]},{"raw_affiliation_string":"Regenstrief Institute, Indianapolis, IN, 46202, USA. kunhuang@iu.edu","institution_ids":["https://openalex.org/I1324682000"]},{"raw_affiliation_string":"Indiana University School of Medicine, Indianapolis, USA","institution_ids":["https://openalex.org/I4394709130","https://openalex.org/I55769427"]},{"raw_affiliation_string":"Regenstrief Institute, Indianapolis, USA","institution_ids":["https://openalex.org/I1324682000"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5057366605","https://openalex.org/A5083889663"],"corresponding_institution_ids":["https://openalex.org/I1324682000","https://openalex.org/I151727225","https://openalex.org/I4210105101","https://openalex.org/I4394709130","https://openalex.org/I55769427"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.6661,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.66672102,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"22","issue":"S4","first_page":"111","last_page":"111"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5985000133514404,"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":0.5985000133514404,"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":0.2921999990940094,"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":0.04529999941587448,"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/cluster-analysis","display_name":"Cluster analysis","score":0.6484198570251465},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5848526954650879},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5478531718254089},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5434120297431946},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5077377557754517},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.48657381534576416},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.47939372062683105},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.44910335540771484},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.447219580411911},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.43006134033203125},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4243384003639221},{"id":"https://openalex.org/keywords/spectral-clustering","display_name":"Spectral clustering","score":0.4130179286003113},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.38249456882476807},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3612210750579834},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.32047998905181885},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2722265124320984},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2513121962547302},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.1698603332042694},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.11960136890411377}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6484198570251465},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5848526954650879},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5478531718254089},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5434120297431946},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5077377557754517},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.48657381534576416},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.47939372062683105},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.44910335540771484},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.447219580411911},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.43006134033203125},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4243384003639221},{"id":"https://openalex.org/C105611402","wikidata":"https://www.wikidata.org/wiki/Q2976589","display_name":"Spectral clustering","level":3,"score":0.4130179286003113},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.38249456882476807},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3612210750579834},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.32047998905181885},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2722265124320984},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2513121962547302},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.1698603332042694},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.11960136890411377}],"mesh":[{"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1186/s12859-021-03964-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-03964-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-03964-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34689740","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34689740","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:scholarworks.iupui.edu:1805/32042","is_oa":true,"landing_page_url":"https://hdl.handle.net/1805/32042","pdf_url":"https://scholarworks.indianapolis.iu.edu/bitstreams/72ab396c-7b18-414b-a59c-1dd4ac1ae1f1/download","source":{"id":"https://openalex.org/S4306400987","display_name":"IUScholarWorks (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"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":"PMC","raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:3a92de7478ba4401933a0b36bf455721","is_oa":true,"landing_page_url":"https://doaj.org/article/3a92de7478ba4401933a0b36bf455721","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss S4, Pp 1-19 (2021)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:7433019","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8543836","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8543836","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8543836","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-03964-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-03964-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-03964-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1366516505","display_name":null,"funder_award_id":"2017YFC0306001","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G3992587728","display_name":null,"funder_award_id":"2018YFC0310102","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6135089572","display_name":null,"funder_award_id":"201806680029","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"}],"funders":[{"id":"https://openalex.org/F4320309291","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3211299261.pdf","grobid_xml":"https://content.openalex.org/works/W3211299261.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1490161904","https://openalex.org/W1609519580","https://openalex.org/W1712015452","https://openalex.org/W1964305071","https://openalex.org/W1966327575","https://openalex.org/W1975191997","https://openalex.org/W1989277387","https://openalex.org/W2023265004","https://openalex.org/W2060705109","https://openalex.org/W2073799618","https://openalex.org/W2109890125","https://openalex.org/W2117692326","https://openalex.org/W2122185352","https://openalex.org/W2124649657","https://openalex.org/W2132914434","https://openalex.org/W2133254377","https://openalex.org/W2133465414","https://openalex.org/W2142019735","https://openalex.org/W2146653758","https://openalex.org/W2158414019","https://openalex.org/W2159482845","https://openalex.org/W2163480486","https://openalex.org/W2171115585","https://openalex.org/W2327182611","https://openalex.org/W2364622788","https://openalex.org/W2488022192","https://openalex.org/W2516042726","https://openalex.org/W2537679995","https://openalex.org/W2577490495","https://openalex.org/W2579970155","https://openalex.org/W2588500934","https://openalex.org/W2752197020","https://openalex.org/W2783382315","https://openalex.org/W2808376344","https://openalex.org/W2900504844","https://openalex.org/W2901824420","https://openalex.org/W2970128476","https://openalex.org/W2981206386","https://openalex.org/W4233698560","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W1482912984","https://openalex.org/W2069695727","https://openalex.org/W1996185163","https://openalex.org/W2084813257","https://openalex.org/W2045929470","https://openalex.org/W2081127504","https://openalex.org/W2122223946","https://openalex.org/W4233500668","https://openalex.org/W1974145978","https://openalex.org/W1977867163"],"abstract_inverted_index":{"BACKGROUND:":[0],"Gene":[1],"co-expression":[2,58,87,200],"networks":[3,149,201],"are":[4],"widely":[5],"studied":[6],"in":[7,56,85,114],"the":[8,124,155],"biomedical":[9],"field,":[10],"with":[11,117,150,182],"algorithms":[12,27],"such":[13,30],"as":[14,31,143,145],"WGCNA":[15],"and":[16,34,77,108,154,161,188],"lmQCM":[17],"having":[18],"been":[19],"developed":[20,138],"to":[21,52,81,141,157,207],"detect":[22,82,158],"co-expressed":[23,83],"modules.":[24,163],"However,":[25],"these":[26],"have":[28],"limitations":[29],"insufficient":[32],"granularity":[33,110],"unbalanced":[35],"module":[36,59,70,106],"size,":[37],"which":[38],"prevent":[39],"full":[40],"acquisition":[41],"of":[42,102,185],"knowledge":[43,55],"from":[44,148,171],"data":[45,170],"mining.":[46],"In":[47,63,122,135,164],"addition,":[48,123,165],"it":[49],"is":[50,194],"difficult":[51],"incorporate":[53],"prior":[54,132],"current":[57,112,180],"detection":[60,71],"algorithms.":[61],"RESULTS:":[62],"this":[64,192],"paper,":[65],"we":[66,137],"propose":[67],"a":[68,139],"novel":[69,95],"algorithm":[72,80,126],"based":[73],"on":[74,91],"topology":[75],"potential":[76],"spectral":[78],"clustering":[79],"modules":[84,116,129],"gene":[86,199],"networks.":[88],"By":[89],"testing":[90],"TCGA":[92],"data,":[93],"our":[94,166],"method":[96,140,167,176,193],"can":[97,127,168,203],"provide":[98],"more":[99,104,159],"complete":[100,183],"coverage":[101,153,184],"genes,":[103],"balanced":[105],"size":[107],"finer":[109,189],"than":[111,179],"methods":[113,181],"detecting":[115],"significant":[118],"overall":[119],"survival":[120],"difference.":[121],"proposed":[125,175],"identify":[128],"by":[130],"incorporating":[131],"knowledge.":[133],"CONCLUSION:":[134],"summary,":[136],"obtain":[142],"much":[144],"possible":[146],"information":[147],"increased":[151],"input":[152,186],"ability":[156],"size-balanced":[160],"granular":[162],"integrate":[169],"different":[172],"sources.":[173],"Our":[174],"performs":[177],"better":[178],"genes":[187],"granularity.":[190],"Moreover,":[191],"designed":[195],"not":[196],"only":[197],"for":[198],"but":[202],"also":[204],"be":[205],"applied":[206],"any":[208],"general":[209],"fully":[210],"connected":[211],"weighted":[212],"network.":[213]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}