{"id":"https://openalex.org/W4386084329","doi":"https://doi.org/10.1093/bioinformatics/btad522","title":"Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression","display_name":"Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression","publication_year":2023,"publication_date":"2023-08-01","ids":{"openalex":"https://openalex.org/W4386084329","doi":"https://doi.org/10.1093/bioinformatics/btad522","pmid":"https://pubmed.ncbi.nlm.nih.gov/37610338"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad522","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad522","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad522/51234005/btad522.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad522/51234005/btad522.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076345149","display_name":"Kim Philipp Jablonski","orcid":"https://orcid.org/0000-0002-4166-4343"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Kim Philipp Jablonski","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich , Basel 4058, Switzerland","SIB Swiss Institute of Bioinformatics , Basel 4058, Switzerland","SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland","Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-4166-4343","affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich , Basel 4058, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics , Basel 4058, Switzerland","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035497488","display_name":"Niko Beerenwinkel","orcid":"https://orcid.org/0000-0002-0573-6119"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Niko Beerenwinkel","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich , Basel 4058, Switzerland","SIB Swiss Institute of Bioinformatics , Basel 4058, Switzerland","SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland","Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-0573-6119","affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich , Basel 4058, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics , Basel 4058, Switzerland","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, Basel, 4058, Switzerland","institution_ids":["https://openalex.org/I12708293"]},{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, 4058, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5076345149"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I35440088"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.1454,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.58578688,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"39","issue":"8","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9866999983787537,"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":0.9866999983787537,"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":0.00800000037997961,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0006000000284984708,"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/bioconductor","display_name":"Bioconductor","score":0.8534244298934937},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.8279276490211487},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.731078028678894},{"id":"https://openalex.org/keywords/kegg","display_name":"KEGG","score":0.727830171585083},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.591235876083374},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5296516418457031},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.4870905876159668},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41841423511505127},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.31874436140060425},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.3089013695716858},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22275593876838684},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17297285795211792},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12032154202461243},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.11815905570983887},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11463162302970886},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08917728066444397}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.8534244298934937},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8279276490211487},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.731078028678894},{"id":"https://openalex.org/C152724338","wikidata":"https://www.wikidata.org/wiki/Q909442","display_name":"KEGG","level":5,"score":0.727830171585083},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.591235876083374},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5296516418457031},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.4870905876159668},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41841423511505127},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31874436140060425},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.3089013695716858},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22275593876838684},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17297285795211792},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12032154202461243},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.11815905570983887},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11463162302970886},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08917728066444397}],"mesh":[{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad522","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad522","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad522/51234005/btad522.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37610338","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37610338","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10471899","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10471899","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10471899/pdf/btad522.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad522","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad522","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad522/51234005/btad522.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6200000047683716,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386084329.pdf"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W1513895168","https://openalex.org/W1527927437","https://openalex.org/W1659833910","https://openalex.org/W1854123316","https://openalex.org/W1966716734","https://openalex.org/W1969353942","https://openalex.org/W1998643818","https://openalex.org/W2025729801","https://openalex.org/W2034269086","https://openalex.org/W2038963685","https://openalex.org/W2056782561","https://openalex.org/W2060987350","https://openalex.org/W2089467986","https://openalex.org/W2091589316","https://openalex.org/W2097948046","https://openalex.org/W2100761975","https://openalex.org/W2104488717","https://openalex.org/W2106410227","https://openalex.org/W2111940674","https://openalex.org/W2112840798","https://openalex.org/W2117380790","https://openalex.org/W2117692326","https://openalex.org/W2120024428","https://openalex.org/W2121343862","https://openalex.org/W2127536416","https://openalex.org/W2128049108","https://openalex.org/W2130410032","https://openalex.org/W2130879249","https://openalex.org/W2131532450","https://openalex.org/W2133465414","https://openalex.org/W2135046866","https://openalex.org/W2138019504","https://openalex.org/W2139070508","https://openalex.org/W2140954822","https://openalex.org/W2146512944","https://openalex.org/W2147714160","https://openalex.org/W2148342654","https://openalex.org/W2152370879","https://openalex.org/W2153236083","https://openalex.org/W2159482845","https://openalex.org/W2165816035","https://openalex.org/W2169589032","https://openalex.org/W2290195878","https://openalex.org/W2329659234","https://openalex.org/W2479117119","https://openalex.org/W2520521911","https://openalex.org/W2546815213","https://openalex.org/W2562162676","https://openalex.org/W2591941343","https://openalex.org/W2593201514","https://openalex.org/W2606595919","https://openalex.org/W2611696724","https://openalex.org/W2614146260","https://openalex.org/W2766913095","https://openalex.org/W2768302346","https://openalex.org/W2895487334","https://openalex.org/W2909273376","https://openalex.org/W2921808337","https://openalex.org/W2949093503","https://openalex.org/W2968778759","https://openalex.org/W2996005515","https://openalex.org/W3004747635","https://openalex.org/W3037513375","https://openalex.org/W3039150496","https://openalex.org/W3122109253","https://openalex.org/W3167226232","https://openalex.org/W3175752499","https://openalex.org/W3216122825","https://openalex.org/W4200374506","https://openalex.org/W4210522554","https://openalex.org/W4210644165","https://openalex.org/W4225724261","https://openalex.org/W6762654376","https://openalex.org/W6797786779"],"related_works":["https://openalex.org/W2100625056","https://openalex.org/W2567219477","https://openalex.org/W2554253784","https://openalex.org/W2551839783","https://openalex.org/W4386401670","https://openalex.org/W2956207900","https://openalex.org/W2790781282","https://openalex.org/W4313887725","https://openalex.org/W2334025507","https://openalex.org/W4375856186"],"abstract_inverted_index":{"MOTIVATION:":[0],"Gene":[1,45,60],"set":[2,46,92],"enrichment":[3,47,80,93,126],"methods":[4],"are":[5,26,33,64],"a":[6,89,101],"common":[7],"tool":[8],"to":[9,114,121,135,148,155,198],"improve":[10],"the":[11,59,70,78,125,143,194],"interpretability":[12],"of":[13,72,145],"gene":[14,22,91,111],"lists":[15],"as":[16,55,152,154,177,184,186],"obtained,":[17],"for":[18,118],"example,":[19,119],"from":[20,168],"differential":[21],"expression":[23],"analyses.":[24],"They":[25],"based":[27,99],"on":[28,50,100,181,187],"computing":[29],"whether":[30],"dysregulated":[31],"genes":[32],"located":[34],"in":[35,66,69,124,160],"certain":[36,115],"biological":[37,116],"pathways":[38,151],"more":[39,133],"often":[40],"than":[41,137],"expected":[42],"by":[43],"chance.":[44],"tools":[48],"rely":[49],"pre-existing":[51],"pathway":[52],"databases":[53,63],"such":[54],"KEGG,":[56],"Reactome,":[57],"or":[58],"Ontology.":[61],"These":[62],"increasing":[65],"size":[67],"and":[68,87,106],"number":[71],"redundancies":[73],"between":[74,110],"pathways,":[75],"which":[76,97],"complicates":[77],"statistical":[79],"computation.":[81,127],"RESULTS:":[82],"We":[83,128],"address":[84],"this":[85],"problem":[86],"develop":[88],"novel":[90,157],"method,":[94],"called":[95],"pareg,":[96],"is":[98,132,174],"regularized":[102],"generalized":[103],"linear":[104],"model":[105],"directly":[107],"incorporates":[108],"dependencies":[109],"sets":[112],"related":[113],"functions,":[117],"due":[120],"shared":[122],"genes,":[123],"show":[129],"that":[130],"pareg":[131,173],"robust":[134],"noise":[136],"competing":[138],"methods.":[139],"Additionally,":[140],"we":[141],"demonstrate":[142],"ability":[144],"our":[146],"method":[147],"recover":[149],"known":[150],"well":[153,185],"suggest":[156],"treatment":[158],"targets":[159],"an":[161,178],"exploratory":[162],"analysis":[163],"using":[164],"breast":[165],"cancer":[166],"samples":[167],"TCGA.":[169],"AVAILABILITY":[170],"AND":[171],"IMPLEMENTATION:":[172],"freely":[175],"available":[176],"R":[179],"package":[180],"Bioconductor":[182],"(https://bioconductor.org/packages/release/bioc/html/pareg.html)":[183],"https://github.com/cbg-ethz/pareg.":[188],"The":[189],"GitHub":[190],"repository":[191],"also":[192],"contains":[193],"Snakemake":[195],"workflows":[196],"needed":[197],"reproduce":[199],"all":[200],"results":[201],"presented":[202],"here.":[203]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
