{"id":"https://openalex.org/W4413374773","doi":"https://doi.org/10.1186/s12859-025-06249-3","title":"GeneSetCluster 2.0: a comprehensive toolset for summarizing and integrating gene-sets analysis","display_name":"GeneSetCluster 2.0: a comprehensive toolset for summarizing and integrating gene-sets analysis","publication_year":2025,"publication_date":"2025-08-21","ids":{"openalex":"https://openalex.org/W4413374773","doi":"https://doi.org/10.1186/s12859-025-06249-3","pmid":"https://pubmed.ncbi.nlm.nih.gov/40841877"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06249-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06249-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06249-3","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/s12859-025-06249-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5092386391","display_name":"Asier Ortega\u2010Legarreta","orcid":"https://orcid.org/0009-0000-3563-5362"},"institutions":[{"id":"https://openalex.org/I4210117069","display_name":"Navarrabiomed","ror":"https://ror.org/03atdda90","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I4210117069"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Asier Ortega-Legarreta","raw_affiliation_strings":["Translational Bioinformatics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad P\u00fablica de Navarra (UPNA), IdiSNA, 31008, Pamplona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Translational Bioinformatics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad P\u00fablica de Navarra (UPNA), IdiSNA, 31008, Pamplona, Spain","institution_ids":["https://openalex.org/I4210117069"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054754981","display_name":"Alberto Maillo","orcid":"https://orcid.org/0000-0002-3835-9794"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Alberto Maillo","raw_affiliation_strings":["Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072910935","display_name":"Daniel Mouzo","orcid":"https://orcid.org/0000-0002-0383-5703"},"institutions":[{"id":"https://openalex.org/I4210117069","display_name":"Navarrabiomed","ror":"https://ror.org/03atdda90","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I4210117069"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Daniel Mouzo","raw_affiliation_strings":["Translational Bioinformatics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad P\u00fablica de Navarra (UPNA), IdiSNA, 31008, Pamplona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Translational Bioinformatics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad P\u00fablica de Navarra (UPNA), IdiSNA, 31008, Pamplona, Spain","institution_ids":["https://openalex.org/I4210117069"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062654535","display_name":"Ana L\u00f3pez-P\u00e9rez","orcid":"https://orcid.org/0000-0002-5159-0122"},"institutions":[{"id":"https://openalex.org/I4210117069","display_name":"Navarrabiomed","ror":"https://ror.org/03atdda90","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I4210117069"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Ana Rosa L\u00f3pez-P\u00e9rez","raw_affiliation_strings":["Translational Bioinformatics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad P\u00fablica de Navarra (UPNA), IdiSNA, 31008, Pamplona, Spain"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Translational Bioinformatics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad P\u00fablica de Navarra (UPNA), IdiSNA, 31008, Pamplona, Spain","institution_ids":["https://openalex.org/I4210117069"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052348014","display_name":"Lara Kular","orcid":"https://orcid.org/0000-0002-2907-6071"},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Lara Kular","raw_affiliation_strings":["Department of Clinical Neuroscience, Karolinska Institutet, and Center for Molecular Medicine, Karolinska University Hospital, SE-171 76, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Neuroscience, Karolinska Institutet, and Center for Molecular Medicine, Karolinska University Hospital, SE-171 76, Stockholm, Sweden","institution_ids":["https://openalex.org/I1335113835"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051992202","display_name":"Majid Pahlevan Kakhki","orcid":"https://orcid.org/0000-0002-5407-3147"},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Majid Pahlevan Kakhki","raw_affiliation_strings":["Department of Clinical Neuroscience, Karolinska Institutet, and Center for Molecular Medicine, Karolinska University Hospital, SE-171 76, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Neuroscience, Karolinska Institutet, and Center for Molecular Medicine, Karolinska University Hospital, SE-171 76, Stockholm, Sweden","institution_ids":["https://openalex.org/I1335113835"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038894883","display_name":"Maja Jagodic","orcid":"https://orcid.org/0000-0003-0756-889X"},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Maja Jagodic","raw_affiliation_strings":["Department of Clinical Neuroscience, Karolinska Institutet, and Center for Molecular Medicine, Karolinska University Hospital, SE-171 76, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Neuroscience, Karolinska Institutet, and Center for Molecular Medicine, Karolinska University Hospital, SE-171 76, Stockholm, Sweden","institution_ids":["https://openalex.org/I1335113835"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035252549","display_name":"Jesper Tegn\u00e9r","orcid":"https://orcid.org/0000-0002-9568-5588"},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]},{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA","SE"],"is_corresponding":false,"raw_author_name":"Jesper Tegner","raw_affiliation_strings":["Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, L8:05, SE-171 76, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Unit of Computational Medicine, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, L8:05, SE-171 76, Stockholm, Sweden","institution_ids":["https://openalex.org/I1335113835","https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016518691","display_name":"Vincenzo Lagani","orcid":"https://orcid.org/0000-0002-6552-6076"},"institutions":[{"id":"https://openalex.org/I183003952","display_name":"Ilia State University","ror":"https://ror.org/051qn8h41","country_code":"GE","type":"education","lineage":["https://openalex.org/I183003952"]},{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["GE","SA"],"is_corresponding":false,"raw_author_name":"Vincenzo Lagani","raw_affiliation_strings":["Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","Institute of Chemical Biology, Ilia State University, 0162, Tbilisi, Georgia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Institute of Chemical Biology, Ilia State University, 0162, Tbilisi, Georgia","institution_ids":["https://openalex.org/I183003952"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082211608","display_name":"Ewoud Ewing","orcid":"https://orcid.org/0000-0001-8644-366X"},"institutions":[{"id":"https://openalex.org/I1335113835","display_name":"Karolinska University Hospital","ror":"https://ror.org/00m8d6786","country_code":"SE","type":"healthcare","lineage":["https://openalex.org/I1335113835"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Ewoud Ewing","raw_affiliation_strings":["Department of Clinical Neuroscience, Karolinska Institutet, and Center for Molecular Medicine, Karolinska University Hospital, SE-171 76, Stockholm, Sweden. ewoud.ewing@ki.se","Department of Clinical Neuroscience, Karolinska Institutet, and Center for Molecular Medicine, Karolinska University Hospital, SE-171 76, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Clinical Neuroscience, Karolinska Institutet, and Center for Molecular Medicine, Karolinska University Hospital, SE-171 76, Stockholm, Sweden. ewoud.ewing@ki.se","institution_ids":["https://openalex.org/I1335113835","https://openalex.org/I28166907"]},{"raw_affiliation_string":"Department of Clinical Neuroscience, Karolinska Institutet, and Center for Molecular Medicine, Karolinska University Hospital, SE-171 76, Stockholm, Sweden","institution_ids":["https://openalex.org/I1335113835"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078466508","display_name":"David G\u00f3mez-Cabrero","orcid":"https://orcid.org/0000-0003-4186-3788"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"David Gomez-Cabrero","raw_affiliation_strings":["Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia. david.gomezcabrero@kaust.edu.sa","Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia. david.gomezcabrero@kaust.edu.sa","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.4217,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.61647943,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"26","issue":"1","first_page":"219","last_page":"219"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9961000084877014,"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":0.9954000115394592,"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/dna-microarray","display_name":"DNA microarray","score":0.5746017694473267},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5559685230255127},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4606793522834778},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44452545046806335},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3327297270298004},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.31407827138900757},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2591540515422821},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18581300973892212},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.13743263483047485}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5746017694473267},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5559685230255127},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4606793522834778},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44452545046806335},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3327297270298004},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31407827138900757},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2591540515422821},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18581300973892212},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.13743263483047485}],"mesh":[{"descriptor_ui":"D000098430","descriptor_name":"Clustering 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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06249-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06249-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06249-3","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:40841877","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40841877","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:doaj.org/article:1bca2362ac8e4128b847ea3099270155","is_oa":true,"landing_page_url":"https://doaj.org/article/1bca2362ac8e4128b847ea3099270155","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 26, Iss 1, Pp 1-17 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11182185","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12372222","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/s12859-025-06249-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06249-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06249-3","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/G1727285392","display_name":null,"funder_award_id":"BAS/1/1093-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G7895849126","display_name":null,"funder_award_id":"BAS/1/1078-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320322168","display_name":"Hj\u00e4rnfonden","ror":"https://ror.org/014btj409"},{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"},{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"},{"id":"https://openalex.org/F4320334322","display_name":"HORIZON EUROPE Framework Programme","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413374773.pdf","grobid_xml":"https://content.openalex.org/works/W4413374773.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1979594866","https://openalex.org/W1984732406","https://openalex.org/W1987971958","https://openalex.org/W1989277387","https://openalex.org/W2011430131","https://openalex.org/W2025855398","https://openalex.org/W2035618305","https://openalex.org/W2040484093","https://openalex.org/W2045729458","https://openalex.org/W2079031049","https://openalex.org/W2084168100","https://openalex.org/W2100980426","https://openalex.org/W2103017472","https://openalex.org/W2120024428","https://openalex.org/W2120751691","https://openalex.org/W2126434293","https://openalex.org/W2130410032","https://openalex.org/W2132040456","https://openalex.org/W2133120537","https://openalex.org/W2136410628","https://openalex.org/W2138255346","https://openalex.org/W2144907278","https://openalex.org/W2166574880","https://openalex.org/W2169589032","https://openalex.org/W2171437346","https://openalex.org/W2214074259","https://openalex.org/W2611696724","https://openalex.org/W2624988670","https://openalex.org/W2889181799","https://openalex.org/W2910111050","https://openalex.org/W2912405236","https://openalex.org/W2928665623","https://openalex.org/W2942879774","https://openalex.org/W2977265011","https://openalex.org/W3015459088","https://openalex.org/W3092495933","https://openalex.org/W3133859624","https://openalex.org/W3164271582","https://openalex.org/W4225364107","https://openalex.org/W4229688926","https://openalex.org/W4233698560","https://openalex.org/W4248625327","https://openalex.org/W4281620292","https://openalex.org/W4308834893","https://openalex.org/W4391654308","https://openalex.org/W4399805503","https://openalex.org/W4399857147"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W2150084125","https://openalex.org/W2118505788","https://openalex.org/W1802639773","https://openalex.org/W1972196578","https://openalex.org/W1490878237","https://openalex.org/W1542823905","https://openalex.org/W2990314835"],"abstract_inverted_index":{"BACKGROUND:":[0],"Gene-Set":[1],"Analysis":[2],"(GSA)":[3],"is":[4,129],"commonly":[5],"used":[6],"to":[7,20,46,110,152,174,188],"analyze":[8],"high-throughput":[9],"experiments.":[10],"However,":[11],"GSA":[12,50],"cannot":[13],"readily":[14],"disentangle":[15],"clusters":[16,145],"or":[17],"pathways":[18],"due":[19],"redundancies":[21,70],"in":[22,61,68,204,228],"upstream":[23],"knowledge":[24],"bases,":[25],"which":[26],"hinders":[27],"comprehensive":[28,93],"exploration":[29],"and":[30,48,55,77,100,114,149,159,193,226,239,246,256],"interpretation":[31],"of":[32,80],"biological":[33,150,154],"findings.":[34],"To":[35,162],"address":[36,111],"this":[37],"challenge,":[38],"we":[39,54,165],"developed":[40,167],"GeneSetCluster,":[41],"an":[42],"R":[43,185,237],"package":[44,128,238],"designed":[45],"summarize":[47],"integrate":[49],"results.":[51],"Over":[52],"time,":[53],"users":[56,83,189],"as":[57,66],"well":[58],"identified":[59],"limitations":[60],"the":[62,127,184,194,202,222,257],"original":[63],"version,":[64],"such":[65],"difficulties":[67],"managing":[69],"across":[71],"multiple":[72],"gene-sets,":[73],"large":[74],"computational":[75],"times,":[76],"its":[78,217],"lack":[79],"accessibility":[81],"for":[82,131,157,197],"without":[84],"programming":[85,191],"expertise.":[86],"RESULTS:":[87],"We":[88,200],"present":[89],"GeneSetCluster":[90,104,138,211,231],"2.0,":[91],"a":[92,107,116,168,205],"upgrade":[94],"that":[95,120],"delivers":[96],"methodological,":[97],"computational,":[98],"interpretative,":[99],"user-experience":[101],"enhancements.":[102],"Methodologically,":[103],"2.0":[105,139,212,232],"introduces":[106],"novel":[108],"approach":[109],"duplicated":[112],"gene-sets":[113],"implements":[115],"seriation-based":[117],"clustering":[118],"algorithm":[119],"reorders":[121],"results,":[122],"aiding":[123],"pattern":[124],"identification.":[125],"Computationally,":[126],"optimized":[130],"parallel":[132],"processing,":[133],"significantly":[134],"reducing":[135],"execution":[136],"time.":[137],"enhances":[140],"cluster":[141],"annotations":[142],"by":[143,220],"associating":[144],"with":[146,190,243],"relevant":[147],"tissues":[148],"processes":[151],"improve":[153],"interpretation,":[155],"particularly":[156],"human":[158],"mouse":[160],"data.":[161],"broaden":[163],"accessibility,":[164],"have":[166],"user-friendly":[169],"web":[170,195,240,258],"application":[171,196,259],"enabling":[172],"non-programmers":[173],"use":[175],"it.":[176],"This":[177],"version":[178],"also":[179],"ensures":[180],"seamless":[181],"integration":[182],"between":[183,224],"package,":[186],"catering":[187],"expertise,":[192],"broader":[198],"audiences.":[199],"evaluated":[201],"updates":[203],"single-cell":[206],"RNA":[207],"public":[208],"dataset.":[209],"CONCLUSION:":[210],"offers":[213],"substantial":[214],"improvements":[215],"over":[216],"predecessor.":[218],"Furthermore,":[219],"bridging":[221],"gap":[223],"bioinformaticians":[225],"clinicians":[227],"multidisciplinary":[229],"teams,":[230],"facilitates":[233],"collaborative":[234],"research.":[235],"The":[236],"application,":[241],"along":[242],"detailed":[244],"installation":[245],"usage":[247],"guides,":[248],"are":[249],"available":[250],"on":[251],"GitHub":[252],"(":[253],"https://github.com/TranslationalBioinformaticsUnit/GeneSetCluster2.0":[254],"),":[255],"can":[260],"be":[261],"accessed":[262],"at":[263],"https://translationalbio.shinyapps.io/genesetcluster/":[264],".":[265]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}