{"id":"https://openalex.org/W4410732777","doi":"https://doi.org/10.1186/s12859-025-06162-9","title":"DRaCOon: a novel algorithm for pathway-level differential co-expression analysis in transcriptomics","display_name":"DRaCOon: a novel algorithm for pathway-level differential co-expression analysis in transcriptomics","publication_year":2025,"publication_date":"2025-05-26","ids":{"openalex":"https://openalex.org/W4410732777","doi":"https://doi.org/10.1186/s12859-025-06162-9","pmid":"https://pubmed.ncbi.nlm.nih.gov/40419963"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06162-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06162-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06162-9","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/s12859-025-06162-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067900374","display_name":"Fernando M. Delgado-Chaves","orcid":"https://orcid.org/0000-0002-6171-1215"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]},{"id":"https://openalex.org/I4210136595","display_name":"Hamburg Institut (Germany)","ror":"https://ror.org/03t0n2419","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210136595"]},{"id":"https://openalex.org/I884043246","display_name":"Hamburg University of Technology","ror":"https://ror.org/04bs1pb34","country_code":"DE","type":"education","lineage":["https://openalex.org/I884043246"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Fernando M. Delgado-Chaves","raw_affiliation_strings":["Institute for Computational Systems Biology, University of Hamburg, Albert-Einstein-Ring 8-10, 22607, Hamburg, Hamburg, Germany. fernando.miguel.delgado-chaves@uni-hamburg.de"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Systems Biology, University of Hamburg, Albert-Einstein-Ring 8-10, 22607, Hamburg, Hamburg, Germany. fernando.miguel.delgado-chaves@uni-hamburg.de","institution_ids":["https://openalex.org/I4210136595","https://openalex.org/I159176309","https://openalex.org/I884043246"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093031091","display_name":"Ferdinand Spurny","orcid":null},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]},{"id":"https://openalex.org/I4210136595","display_name":"Hamburg Institut (Germany)","ror":"https://ror.org/03t0n2419","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210136595"]},{"id":"https://openalex.org/I884043246","display_name":"Hamburg University of Technology","ror":"https://ror.org/04bs1pb34","country_code":"DE","type":"education","lineage":["https://openalex.org/I884043246"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ferdinand Spurny","raw_affiliation_strings":["Institute for Computational Systems Biology, University of Hamburg, Albert-Einstein-Ring 8-10, 22607, Hamburg, Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Systems Biology, University of Hamburg, Albert-Einstein-Ring 8-10, 22607, Hamburg, Hamburg, Germany","institution_ids":["https://openalex.org/I4210136595","https://openalex.org/I159176309","https://openalex.org/I884043246"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071636302","display_name":"Tanja Laske","orcid":"https://orcid.org/0000-0002-7922-7595"},"institutions":[{"id":"https://openalex.org/I137251492","display_name":"Leibniz Institute of Virology (LIV)","ror":"https://ror.org/02r2q1d96","country_code":"DE","type":"facility","lineage":["https://openalex.org/I137251492","https://openalex.org/I315704651"]},{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]},{"id":"https://openalex.org/I4210136595","display_name":"Hamburg Institut (Germany)","ror":"https://ror.org/03t0n2419","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210136595"]},{"id":"https://openalex.org/I884043246","display_name":"Hamburg University of Technology","ror":"https://ror.org/04bs1pb34","country_code":"DE","type":"education","lineage":["https://openalex.org/I884043246"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tanja Laske","raw_affiliation_strings":["Institute for Computational Systems Biology, University of Hamburg, Albert-Einstein-Ring 8-10, 22607, Hamburg, Hamburg, Germany","Viral Systems Modeling, Leibniz Institute of Virology, Martinistra\u00dfe 52, 20251, Hamburg, Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Systems Biology, University of Hamburg, Albert-Einstein-Ring 8-10, 22607, Hamburg, Hamburg, Germany","institution_ids":["https://openalex.org/I4210136595","https://openalex.org/I159176309","https://openalex.org/I884043246"]},{"raw_affiliation_string":"Viral Systems Modeling, Leibniz Institute of Virology, Martinistra\u00dfe 52, 20251, Hamburg, Hamburg, Germany","institution_ids":["https://openalex.org/I137251492"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036694708","display_name":"Mhaned Oubounyt","orcid":"https://orcid.org/0000-0001-5011-6683"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]},{"id":"https://openalex.org/I4210136595","display_name":"Hamburg Institut (Germany)","ror":"https://ror.org/03t0n2419","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210136595"]},{"id":"https://openalex.org/I884043246","display_name":"Hamburg University of Technology","ror":"https://ror.org/04bs1pb34","country_code":"DE","type":"education","lineage":["https://openalex.org/I884043246"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Mhaned Oubounyt","raw_affiliation_strings":["Institute for Computational Systems Biology, University of Hamburg, Albert-Einstein-Ring 8-10, 22607, Hamburg, Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Systems Biology, University of Hamburg, Albert-Einstein-Ring 8-10, 22607, Hamburg, Hamburg, Germany","institution_ids":["https://openalex.org/I4210136595","https://openalex.org/I159176309","https://openalex.org/I884043246"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073222532","display_name":"Jan Baumbach","orcid":"https://orcid.org/0000-0002-0282-0462"},"institutions":[{"id":"https://openalex.org/I159176309","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956","country_code":"DE","type":"education","lineage":["https://openalex.org/I159176309"]},{"id":"https://openalex.org/I4210136595","display_name":"Hamburg Institut (Germany)","ror":"https://ror.org/03t0n2419","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210136595"]},{"id":"https://openalex.org/I884043246","display_name":"Hamburg University of Technology","ror":"https://ror.org/04bs1pb34","country_code":"DE","type":"education","lineage":["https://openalex.org/I884043246"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jan Baumbach","raw_affiliation_strings":["Institute for Computational Systems Biology, University of Hamburg, Albert-Einstein-Ring 8-10, 22607, Hamburg, Hamburg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Systems Biology, University of Hamburg, Albert-Einstein-Ring 8-10, 22607, Hamburg, Hamburg, Germany","institution_ids":["https://openalex.org/I4210136595","https://openalex.org/I159176309","https://openalex.org/I884043246"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5067900374"],"corresponding_institution_ids":["https://openalex.org/I159176309","https://openalex.org/I4210136595","https://openalex.org/I884043246"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.09552595,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"1","first_page":"137","last_page":"137"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.986299991607666,"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/T10604","display_name":"RNA Research and Splicing","score":0.9761000275611877,"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/benchmarking","display_name":"Benchmarking","score":0.8002372980117798},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5578347444534302},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5383703708648682},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4968555271625519},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4964752793312073},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44921424984931946},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4363898038864136},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3824772238731384},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3806281089782715},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.324393630027771},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3079019784927368},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.28849685192108154},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14089831709861755}],"concepts":[{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.8002372980117798},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5578347444534302},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5383703708648682},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4968555271625519},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4964752793312073},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44921424984931946},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4363898038864136},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3824772238731384},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3806281089782715},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.324393630027771},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3079019784927368},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.28849685192108154},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14089831709861755},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D020869","descriptor_name":"Gene Expression Profiling","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},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06162-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06162-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06162-9","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:40419963","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40419963","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:abce31f417434532a57228e5d5c83e99","is_oa":true,"landing_page_url":"https://doaj.org/article/abce31f417434532a57228e5d5c83e99","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 1-24 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12107744","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12107744","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/s12859-025-06162-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06162-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06162-9","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/3","score":0.6600000262260437,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G2890191835","display_name":null,"funder_award_id":"22.00115","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4500226907","display_name":null,"funder_award_id":"031L0309B","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G6492216678","display_name":null,"funder_award_id":"01ZX1910D","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320323381","display_name":"Universit\u00e4t Hamburg","ror":"https://ror.org/00g30e956"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410732777.pdf","grobid_xml":"https://content.openalex.org/works/W4410732777.grobid-xml"},"referenced_works_count":68,"referenced_works":["https://openalex.org/W139767586","https://openalex.org/W1555168845","https://openalex.org/W1891744697","https://openalex.org/W1965055200","https://openalex.org/W1966327575","https://openalex.org/W1996361385","https://openalex.org/W2019163875","https://openalex.org/W2025422403","https://openalex.org/W2049633694","https://openalex.org/W2076814413","https://openalex.org/W2080218141","https://openalex.org/W2095594404","https://openalex.org/W2095704110","https://openalex.org/W2095898243","https://openalex.org/W2103897566","https://openalex.org/W2104724027","https://openalex.org/W2106620396","https://openalex.org/W2107018762","https://openalex.org/W2110065044","https://openalex.org/W2114104545","https://openalex.org/W2116634113","https://openalex.org/W2119412782","https://openalex.org/W2119590375","https://openalex.org/W2124404375","https://openalex.org/W2137526110","https://openalex.org/W2143489962","https://openalex.org/W2143965359","https://openalex.org/W2146512944","https://openalex.org/W2147566730","https://openalex.org/W2171575266","https://openalex.org/W2181523240","https://openalex.org/W2203974440","https://openalex.org/W2297900194","https://openalex.org/W2341128841","https://openalex.org/W2380800094","https://openalex.org/W2494631976","https://openalex.org/W2532537254","https://openalex.org/W2544405043","https://openalex.org/W2577490495","https://openalex.org/W2749296525","https://openalex.org/W2767743008","https://openalex.org/W2782454362","https://openalex.org/W2891630602","https://openalex.org/W2910032875","https://openalex.org/W2931120067","https://openalex.org/W2965890438","https://openalex.org/W2967965779","https://openalex.org/W2979433844","https://openalex.org/W2983166786","https://openalex.org/W2983296354","https://openalex.org/W2999309192","https://openalex.org/W3014052409","https://openalex.org/W3083915579","https://openalex.org/W3110825127","https://openalex.org/W3112246030","https://openalex.org/W3123542318","https://openalex.org/W3175752499","https://openalex.org/W4200382460","https://openalex.org/W4200407943","https://openalex.org/W4200591407","https://openalex.org/W4221060455","https://openalex.org/W4225410780","https://openalex.org/W4319080861","https://openalex.org/W4319985723","https://openalex.org/W4319988093","https://openalex.org/W4389080245","https://openalex.org/W4406260625","https://openalex.org/W6893575384"],"related_works":["https://openalex.org/W2069695727","https://openalex.org/W1996185163","https://openalex.org/W2084813257","https://openalex.org/W2043690326","https://openalex.org/W2045929470","https://openalex.org/W4233500668","https://openalex.org/W2081127504","https://openalex.org/W1974145978","https://openalex.org/W1977867163","https://openalex.org/W3984577"],"abstract_inverted_index":{"Understanding":[0],"the":[1,37,130],"molecular":[2],"mechanisms":[3,173],"underlying":[4],"diseases":[5],"is":[6,36],"crucial":[7],"for":[8,20,45,70,90,100,170],"more":[9],"precise,":[10],"personalized":[11],"medicine.":[12],"Pathway-level":[13],"differential":[14,72,81,132],"co-expression":[15,73],"analysis,":[16],"a":[17,33,64,84,97,163,167],"powerful":[18,164],"approach":[19],"transcriptomics,":[21],"identifies":[22,153],"condition-specific":[23],"changes":[24],"in":[25,143],"gene-gene":[26,52],"interaction":[27],"networks,":[28],"offering":[29],"targeted":[30],"insights.":[31],"However,":[32],"key":[34],"challenge":[35],"lack":[38],"of":[39],"robust":[40,146],"methods":[41],"and":[42,61,67,80,109,117,129,152,166],"benchmarks":[43],"specifically":[44],"evaluating":[46],"algorithms'":[47],"ability":[48],"to":[49,147],"identify":[50],"disrupted":[51],"associations":[53],"across":[54],"conditions.":[55],"We":[56],"introduce":[57],"DRaCOoN":[58,75,94,159],"(Differential":[59],"Regulatory":[60],"Co-expression":[62],"Networks),":[63],"Python":[65],"package":[66],"web":[68],"tool":[69,165],"pathway-level":[71],"analysis.":[74],"uniquely":[76],"integrates":[77],"multiple":[78],"association":[79,127],"metrics,":[82],"with":[83,124],"novel,":[85],"computationally":[86],"efficient":[87],"permutation":[88],"test":[89],"significance":[91],"assessment.":[92],"Crucially,":[93],"also":[95],"provides":[96],"benchmarking":[98,105,168],"framework":[99,169],"comprehensive":[101],"method":[102],"evaluation.":[103],"Extensive":[104],"on":[106],"simulated":[107],"data":[108],"three":[110],"real-world":[111],"datasets":[112],"(bone":[113],"healing,":[114],"colorectal":[115],"cancer,":[116],"head/neck":[118],"carcinoma)":[119],"showed":[120],"that":[121],"DRaCOoN,":[122],"particularly":[123],"an":[125],"entropy-based":[126],"measure":[128],"s":[131],"metric,":[133],"consistently":[134],"outperforms":[135],"eight":[136],"other":[137],"methods.":[138],"It":[139],"remains":[140],"highly":[141],"accurate":[142],"balanced":[144],"datasets,":[145],"varying":[148],"gene":[149,183],"perturbation":[150],"levels,":[151],"biologically":[154],"relevant":[155],"regulatory":[156,184],"changes.":[157],"Furthermore,":[158],"serves":[160],"as":[161],"both":[162],"elucidating":[171],"disease":[172],"from":[174],"transcriptomics":[175],"data,":[176],"advancing":[177],"precision":[178],"medicine":[179],"by":[180],"uncovering":[181],"critical":[182],"alterations.":[185]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
