{"id":"https://openalex.org/W2905498282","doi":"https://doi.org/10.1186/1471-2105-13-s10-s7","title":"A systematic comparison of genome-scale clustering algorithms","display_name":"A systematic comparison of genome-scale clustering algorithms","publication_year":2012,"publication_date":"2012-06-01","ids":{"openalex":"https://openalex.org/W2905498282","doi":"https://doi.org/10.1186/1471-2105-13-s10-s7","mag":"2905498282","pmid":"https://pubmed.ncbi.nlm.nih.gov/22759431"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-s10-s7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s10-s7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S10-S7","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/counter/pdf/10.1186/1471-2105-13-S10-S7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014072628","display_name":"Jeremy J. Jay","orcid":"https://orcid.org/0000-0002-5761-7533"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy J Jay","raw_affiliation_strings":["The Jackson Laboratory, Bar Harbor, ME 04609, USA","The Jackson Laboratory, Bar Harbor, ME, 04609, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory, Bar Harbor, ME 04609, USA","institution_ids":["https://openalex.org/I4210115256"]},{"raw_affiliation_string":"The Jackson Laboratory, Bar Harbor, ME, 04609, USA","institution_ids":["https://openalex.org/I4210115256"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070196212","display_name":"John D. Eblen","orcid":"https://orcid.org/0000-0002-5755-3381"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John D Eblen","raw_affiliation_strings":["Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100734210","display_name":"Yun Zhang","orcid":"https://orcid.org/0000-0001-5075-727X"},"institutions":[{"id":"https://openalex.org/I209244073","display_name":"Pioneer Hi-Bred","ror":"https://ror.org/02nn4s922","country_code":"US","type":"company","lineage":["https://openalex.org/I209244073"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yun Zhang","raw_affiliation_strings":["Pioneer Hi-Bred International Incorporated, Johnston, IA, 50131, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pioneer Hi-Bred International Incorporated, Johnston, IA, 50131, USA","institution_ids":["https://openalex.org/I209244073"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049770857","display_name":"Mikael Benson","orcid":"https://orcid.org/0000-0002-7753-9181"},"institutions":[{"id":"https://openalex.org/I102134673","display_name":"Link\u00f6ping University","ror":"https://ror.org/05ynxx418","country_code":"SE","type":"education","lineage":["https://openalex.org/I102134673"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Mikael Benson","raw_affiliation_strings":["Link\u00f6ping University, SE-581 85, Link\u00f6ping, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Link\u00f6ping University, SE-581 85, Link\u00f6ping, Sweden","institution_ids":["https://openalex.org/I102134673"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005914571","display_name":"Andy Perkins","orcid":"https://orcid.org/0000-0002-3583-1010"},"institutions":[{"id":"https://openalex.org/I99041443","display_name":"Mississippi State University","ror":"https://ror.org/0432jq872","country_code":"US","type":"education","lineage":["https://openalex.org/I4210141039","https://openalex.org/I99041443"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andy D Perkins","raw_affiliation_strings":["Mississippi State University, Mississippi State, MS 39762, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mississippi State University, Mississippi State, MS 39762, USA","institution_ids":["https://openalex.org/I99041443"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041646784","display_name":"Arnold M. Saxton","orcid":"https://orcid.org/0000-0003-3345-5127"},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arnold M Saxton","raw_affiliation_strings":["University of Tennessee, Knoxville, TN, 37996, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Tennessee, Knoxville, TN, 37996, USA","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007918640","display_name":"Brynn H. Voy","orcid":"https://orcid.org/0000-0003-1923-9110"},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brynn H Voy","raw_affiliation_strings":["University of Tennessee, Knoxville, TN, 37996, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Tennessee, Knoxville, TN, 37996, USA","institution_ids":["https://openalex.org/I75027704"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022843316","display_name":"Elissa J. Chesler","orcid":"https://orcid.org/0000-0002-5642-5062"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elissa J Chesler","raw_affiliation_strings":["The Jackson Laboratory, Bar Harbor, ME, 04609, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory, Bar Harbor, ME, 04609, USA","institution_ids":["https://openalex.org/I4210115256"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011863644","display_name":"Michael A. Langston","orcid":"https://orcid.org/0000-0001-5945-5796"},"institutions":[{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael A Langston","raw_affiliation_strings":["University of Tennessee, Knoxville, TN, 37996, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Tennessee, Knoxville, TN, 37996, USA","institution_ids":["https://openalex.org/I75027704"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5011863644"],"corresponding_institution_ids":["https://openalex.org/I75027704"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.5774,"has_fulltext":true,"cited_by_count":60,"citation_normalized_percentile":{"value":0.90520915,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"13","issue":"S10","first_page":"S7","last_page":"S7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.6344000101089478,"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/T10885","display_name":"Gene expression and cancer classification","score":0.6344000101089478,"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":0.3255999982357025,"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/T10637","display_name":"Advanced Clustering Algorithms Research","score":0.004399999976158142,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/jaccard-index","display_name":"Jaccard index","score":0.8863466382026672},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.7294518351554871},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5848721861839294},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.5748589038848877},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.5734708309173584},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5578920841217041},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4668724238872528},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.34881776571273804},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.30189844965934753},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22597292065620422},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1279415488243103},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12651371955871582},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.11325708031654358},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09595140814781189}],"concepts":[{"id":"https://openalex.org/C203519979","wikidata":"https://www.wikidata.org/wiki/Q865360","display_name":"Jaccard index","level":3,"score":0.8863466382026672},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7294518351554871},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5848721861839294},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.5748589038848877},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.5734708309173584},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5578920841217041},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4668724238872528},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34881776571273804},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30189844965934753},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22597292065620422},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1279415488243103},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12651371955871582},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.11325708031654358},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09595140814781189}],"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":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-13-s10-s7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s10-s7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S10-S7","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:22759431","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22759431","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:osti.gov:1626292","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1626292","pdf_url":"https://www.osti.gov/servlets/purl/1626292","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:DiVA.org:liu-79697","is_oa":true,"landing_page_url":"http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-79697","pdf_url":null,"source":{"id":"https://openalex.org/S4306401559","display_name":"KTH Publication Database DiVA (KTH Royal Institute of Technology)","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:europepmc.org:2388109","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3382433","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-s10-s7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s10-s7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-13-S10-S7","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":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.41999998688697815}],"awards":[{"id":"https://openalex.org/G1286236842","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1337544421","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G1581387393","display_name":null,"funder_award_id":"No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G1677143136","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320317220","funder_display_name":"National Energy Research Scientific Computing Center"},{"id":"https://openalex.org/G1787554530","display_name":null,"funder_award_id":"R01-AA-018776","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"},{"id":"https://openalex.org/G2503023272","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G2512333561","display_name":null,"funder_award_id":"0903787","funder_id":"https://openalex.org/F4320338283","funder_display_name":"Office of Experimental Program to Stimulate Competitive Research"},{"id":"https://openalex.org/G2667172306","display_name":null,"funder_award_id":"R01-AA-018776","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2973790809","display_name":null,"funder_award_id":"FP7/2007-2013","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3083819904","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3407362588","display_name":null,"funder_award_id":"U01-AA-016662","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"},{"id":"https://openalex.org/G3432487278","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G3944918260","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4104599821","display_name":null,"funder_award_id":"FP7/2007-2013","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4478365492","display_name":null,"funder_award_id":"EPS-0903787","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4501827968","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4565140552","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G498139845","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5076365615","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320317220","funder_display_name":"National Energy Research Scientific Computing Center"},{"id":"https://openalex.org/G5137536791","display_name":null,"funder_award_id":"R01 AA018776","funder_id":"https://openalex.org/F4320337330","funder_display_name":"National Institute on Alcohol Abuse and Alcoholism"},{"id":"https://openalex.org/G5296923526","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320317220","funder_display_name":"National Energy Research Scientific Computing Center"},{"id":"https://openalex.org/G5411396108","display_name":null,"funder_award_id":"EPS-0903787","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6088333139","display_name":null,"funder_award_id":"R01-MH-074460","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G6348972864","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6558272803","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6652958823","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G6805318589","display_name":"Modeling and Simulation of Complex Systems","funder_award_id":"0903787","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7233692708","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7314163092","display_name":null,"funder_award_id":"EPS-0903787","funder_id":"https://openalex.org/F4320338283","funder_display_name":"Office of Experimental Program to Stimulate Competitive Research"},{"id":"https://openalex.org/G7538560101","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7629237052","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G7672463193","display_name":null,"funder_award_id":"No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G7787287669","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G805243471","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G969889393","display_name":null,"funder_award_id":"DE-AC02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320317220","display_name":"National Energy Research Scientific Computing Center","ror":"https://ror.org/05v3mvq14"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320337330","display_name":"National Institute on Alcohol Abuse and Alcoholism","ror":"https://ror.org/02jzrsm59"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337509","display_name":"Biological and Environmental Research","ror":"https://ror.org/0114b2m14"},{"id":"https://openalex.org/F4320338283","display_name":"Office of Experimental Program to Stimulate Competitive Research","ror":"https://ror.org/04k9mqs78"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2905498282.pdf","grobid_xml":"https://content.openalex.org/works/W2905498282.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W45534775","https://openalex.org/W1513910506","https://openalex.org/W1530803355","https://openalex.org/W1556472699","https://openalex.org/W1580304490","https://openalex.org/W1766157213","https://openalex.org/W1975152892","https://openalex.org/W1976208596","https://openalex.org/W1977556410","https://openalex.org/W1992452843","https://openalex.org/W2001781153","https://openalex.org/W2016381774","https://openalex.org/W2016493165","https://openalex.org/W2019997982","https://openalex.org/W2020448260","https://openalex.org/W2020681752","https://openalex.org/W2039777025","https://openalex.org/W2060705109","https://openalex.org/W2087886864","https://openalex.org/W2091480648","https://openalex.org/W2099182237","https://openalex.org/W2100990314","https://openalex.org/W2102992354","https://openalex.org/W2103017472","https://openalex.org/W2109174028","https://openalex.org/W2116007667","https://openalex.org/W2122683221","https://openalex.org/W2123060905","https://openalex.org/W2130479394","https://openalex.org/W2131456395","https://openalex.org/W2133098435","https://openalex.org/W2135187880","https://openalex.org/W2135230352","https://openalex.org/W2140736261","https://openalex.org/W2141012957","https://openalex.org/W2141885858","https://openalex.org/W2152360905","https://openalex.org/W2153283265","https://openalex.org/W2157305458","https://openalex.org/W2162735386","https://openalex.org/W2164928285","https://openalex.org/W2165533101","https://openalex.org/W2170584976","https://openalex.org/W2330846461","https://openalex.org/W2582743722","https://openalex.org/W2611831635","https://openalex.org/W4210323379","https://openalex.org/W4235169531","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W4254879869","https://openalex.org/W3022576529","https://openalex.org/W2628526247","https://openalex.org/W2596401011","https://openalex.org/W2913569734","https://openalex.org/W3127229356","https://openalex.org/W2000801317","https://openalex.org/W2294604808","https://openalex.org/W2093888054","https://openalex.org/W4226263291"],"abstract_inverted_index":{"BACKGROUND:":[0],"A":[1],"wealth":[2],"of":[3,19,45,89,109,138,181,228,232,260,283],"clustering":[4,66,114,132,233,256,275],"algorithms":[5,14,115],"has":[6,68],"been":[7,97],"applied":[8],"to":[9,30,48,55,79,146,165,219,241,247],"gene":[10,38,264],"co-expression":[11,39,91],"experiments.":[12],"These":[13],"cover":[15],"a":[16,107,123,136,224],"broad":[17],"range":[18],"approaches,":[20,276],"from":[21,126],"conventional":[22,274],"techniques":[23,272],"such":[24,33],"as":[25,34,194],"k-means":[26],"and":[27,42,59,87,111,154,158,174,177,192,281],"hierarchical":[28],"clustering,":[29],"graphical":[31],"approaches":[32],"k-clique":[35],"communities,":[36],"weighted":[37],"networks":[40],"(WGCNA)":[41],"paraclique.":[43],"Comparison":[44],"these":[46],"methods":[47,75],"evaluate":[49],"their":[50],"relative":[51,230],"effectiveness":[52,231],"provides":[53],"guidance":[54],"algorithm":[56],"selection,":[57],"development":[58,280],"implementation.":[60],"Most":[61],"prior":[62],"work":[63],"on":[64,70,234],"comparative":[65],"evaluation":[67],"focused":[69],"parametric":[71,110],"methods.":[72,257],"Graph":[73],"theoretical":[74,113],"are":[76,116],"recent":[77],"additions":[78],"the":[80,84,104,159,166,178,182,195,203,216,229,235],"tool":[81],"set":[82],"for":[83,202,268],"global":[85],"analysis":[86],"decomposition":[88],"microarray":[90],"matrices":[92],"that":[93,267,278],"have":[94],"not":[95],"generally":[96],"included":[98],"in":[99,187],"earlier":[100],"methodological":[101],"comparisons.":[102],"In":[103],"present":[105],"study,":[106,135],"variety":[108,137],"graph":[112],"compared":[117],"using":[118],"well-characterized":[119],"transcriptomic":[120],"data":[121],"at":[122],"genome":[124],"scale":[125],"Saccharomyces":[127],"cerevisiae.":[128],"METHODS:":[129],"For":[130],"each":[131,148,188,210],"method":[133,211],"under":[134],"parameters":[139],"were":[140,169,190,212,238,245],"tested.":[141],"Jaccard":[142,161,179],"similarity":[143],"was":[144,163],"used":[145],"measure":[147],"cluster's":[149],"agreement":[150],"with":[151,251],"every":[152],"GO":[153],"KEGG":[155],"annotation":[156],"set,":[157],"highest":[160],"score":[162,180,201],"assigned":[164],"cluster.":[167],"Clusters":[168,207],"grouped":[170],"into":[171],"small,":[172],"medium,":[173],"large":[175],"bins,":[176],"top":[183,198],"five":[184],"scoring":[185],"clusters":[186,249,261],"bin":[189],"averaged":[191],"reported":[193],"best":[196],"average":[197],"5":[199],"(BAT5)":[200],"particular":[204],"method.":[205],"RESULTS:":[206],"produced":[208],"by":[209,254],"evaluated":[213],"based":[214],"upon":[215],"positive":[217],"match":[218],"known":[220,263],"pathways.":[221],"This":[222],"produces":[223],"readily":[225],"interpretable":[226],"ranking":[227],"genes.":[236],"Methods":[237],"also":[239],"tested":[240],"determine":[242],"whether":[243],"they":[244],"able":[246],"identify":[248],"consistent":[250],"those":[252],"identified":[253],"other":[255],"CONCLUSIONS:":[258],"Validation":[259],"against":[262],"classifications":[265],"demonstrate":[266],"this":[269],"data,":[270],"graph-based":[271],"outperform":[273],"suggesting":[277],"further":[279],"application":[282],"combinatorial":[284],"strategies":[285],"is":[286],"warranted.":[287]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":1}],"updated_date":"2026-07-18T07:39:51.176621","created_date":"2025-10-10T00:00:00"}
