{"id":"https://openalex.org/W4393142382","doi":"https://doi.org/10.1371/journal.pcbi.1011814","title":"PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration","display_name":"PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration","publication_year":2024,"publication_date":"2024-03-25","ids":{"openalex":"https://openalex.org/W4393142382","doi":"https://doi.org/10.1371/journal.pcbi.1011814","pmid":"https://pubmed.ncbi.nlm.nih.gov/38527092"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011814","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011814","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011814&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011814&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029500459","display_name":"Cecilia Wieder","orcid":"https://orcid.org/0000-0003-1548-4346"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Cecilia Wieder","raw_affiliation_strings":["Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049665024","display_name":"Juliette Cooke","orcid":"https://orcid.org/0000-0003-2085-0339"},"institutions":[{"id":"https://openalex.org/I134560555","display_name":"Universit\u00e9 Toulouse III - Paul Sabatier","ror":"https://ror.org/02v6kpv12","country_code":"FR","type":"education","lineage":["https://openalex.org/I134560555"]},{"id":"https://openalex.org/I176063091","display_name":"\u00c9cole Nationale V\u00e9t\u00e9rinaire de Toulouse","ror":"https://ror.org/03m3gzv89","country_code":"FR","type":"education","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210117091","https://openalex.org/I4405258862"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210100066","display_name":"Toxicologie Alimentaire","ror":"https://ror.org/0111a5077","country_code":"FR","type":"facility","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210088668","https://openalex.org/I4210089154","https://openalex.org/I4210100066","https://openalex.org/I4210117091","https://openalex.org/I4405258862","https://openalex.org/I4405258862"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Juliette Cooke","raw_affiliation_strings":["Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France"],"affiliations":[{"raw_affiliation_string":"Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France","institution_ids":["https://openalex.org/I4210100066","https://openalex.org/I17866349","https://openalex.org/I134560555","https://openalex.org/I176063091","https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081946997","display_name":"Cl\u00e9ment Frainay","orcid":"https://orcid.org/0000-0003-4313-2786"},"institutions":[{"id":"https://openalex.org/I134560555","display_name":"Universit\u00e9 Toulouse III - Paul Sabatier","ror":"https://ror.org/02v6kpv12","country_code":"FR","type":"education","lineage":["https://openalex.org/I134560555"]},{"id":"https://openalex.org/I176063091","display_name":"\u00c9cole Nationale V\u00e9t\u00e9rinaire de Toulouse","ror":"https://ror.org/03m3gzv89","country_code":"FR","type":"education","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210117091","https://openalex.org/I4405258862"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210100066","display_name":"Toxicologie Alimentaire","ror":"https://ror.org/0111a5077","country_code":"FR","type":"facility","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210088668","https://openalex.org/I4210089154","https://openalex.org/I4210100066","https://openalex.org/I4210117091","https://openalex.org/I4405258862","https://openalex.org/I4405258862"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Clement Frainay","raw_affiliation_strings":["Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France"],"affiliations":[{"raw_affiliation_string":"Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France","institution_ids":["https://openalex.org/I4210100066","https://openalex.org/I17866349","https://openalex.org/I134560555","https://openalex.org/I176063091","https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051880093","display_name":"Nathalie Poupin","orcid":"https://orcid.org/0000-0002-3393-1405"},"institutions":[{"id":"https://openalex.org/I134560555","display_name":"Universit\u00e9 Toulouse III - Paul Sabatier","ror":"https://ror.org/02v6kpv12","country_code":"FR","type":"education","lineage":["https://openalex.org/I134560555"]},{"id":"https://openalex.org/I176063091","display_name":"\u00c9cole Nationale V\u00e9t\u00e9rinaire de Toulouse","ror":"https://ror.org/03m3gzv89","country_code":"FR","type":"education","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210117091","https://openalex.org/I4405258862"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]},{"id":"https://openalex.org/I4210100066","display_name":"Toxicologie Alimentaire","ror":"https://ror.org/0111a5077","country_code":"FR","type":"facility","lineage":["https://openalex.org/I176063091","https://openalex.org/I4210088668","https://openalex.org/I4210089154","https://openalex.org/I4210100066","https://openalex.org/I4210117091","https://openalex.org/I4405258862","https://openalex.org/I4405258862"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Nathalie Poupin","raw_affiliation_strings":["Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France"],"affiliations":[{"raw_affiliation_string":"Toxalim (Research Centre in Food Toxicology), Universit\u00e9 de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France","institution_ids":["https://openalex.org/I4210100066","https://openalex.org/I17866349","https://openalex.org/I134560555","https://openalex.org/I176063091","https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017665414","display_name":"Russell P. Bowler","orcid":"https://orcid.org/0000-0003-4651-363X"},"institutions":[{"id":"https://openalex.org/I3019586173","display_name":"National Jewish Health","ror":"https://ror.org/016z2bp30","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019586173"]},{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Russell Bowler","raw_affiliation_strings":["National Jewish Health, Denver, Colorado, United States of America"],"affiliations":[{"raw_affiliation_string":"National Jewish Health, Denver, Colorado, United States of America","institution_ids":["https://openalex.org/I3019586173","https://openalex.org/I921990950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008100854","display_name":"Fabien Jourdan","orcid":"https://orcid.org/0000-0001-9401-2894"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Fabien Jourdan","raw_affiliation_strings":["MetaboHUB-Metatoul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France"],"affiliations":[{"raw_affiliation_string":"MetaboHUB-Metatoul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022404035","display_name":"Katerina Kechris","orcid":"https://orcid.org/0000-0002-3725-5459"},"institutions":[{"id":"https://openalex.org/I151808059","display_name":"Colorado School of Public Health","ror":"https://ror.org/005x9g035","country_code":"US","type":"education","lineage":["https://openalex.org/I151808059"]},{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Katerina J. Kechris","raw_affiliation_strings":["Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America","institution_ids":["https://openalex.org/I151808059","https://openalex.org/I51713134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003933808","display_name":"Rachel Lai","orcid":"https://orcid.org/0000-0003-3418-850X"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Rachel PJ Lai","raw_affiliation_strings":["Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056339769","display_name":"Timothy M. D. Ebbels","orcid":"https://orcid.org/0000-0002-3372-8423"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Timothy Ebbels","raw_affiliation_strings":["Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Section of Bioinformatics, Division of Systems Medicine, Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5003933808","https://openalex.org/A5008100854","https://openalex.org/A5017665414","https://openalex.org/A5022404035","https://openalex.org/A5029500459","https://openalex.org/A5049665024","https://openalex.org/A5051880093","https://openalex.org/A5056339769","https://openalex.org/A5081946997"],"corresponding_institution_ids":["https://openalex.org/I134560555","https://openalex.org/I151808059","https://openalex.org/I176063091","https://openalex.org/I17866349","https://openalex.org/I3019586173","https://openalex.org/I4210088668","https://openalex.org/I4210100066","https://openalex.org/I47508984","https://openalex.org/I51713134","https://openalex.org/I921990950"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":5.8482,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.96998554,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"20","issue":"3","first_page":"e1011814","last_page":"e1011814"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":1.0,"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":1.0,"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":0.9973999857902527,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9943000078201294,"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/computer-science","display_name":"Computer science","score":0.6652992963790894},{"id":"https://openalex.org/keywords/omics","display_name":"Omics","score":0.597735583782196},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5348291397094727},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.5292004346847534},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.47238731384277344},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.45377877354621887},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.41959476470947266},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3929588496685028},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.34700143337249756},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3358782231807709},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1740410327911377}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6652992963790894},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.597735583782196},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5348291397094727},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.5292004346847534},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.47238731384277344},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45377877354621887},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.41959476470947266},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3929588496685028},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.34700143337249756},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3358782231807709},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1740410327911377},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1011814","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011814","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011814&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:38527092","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38527092","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:HAL:hal-04597222v1","is_oa":true,"landing_page_url":"https://hal.science/hal-04597222","pdf_url":"https://hal.science/hal-04597222/document","source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, 2024, 20 (3), pp.e1011814. ⟨10.1371/journal.pcbi.1011814⟩","raw_type":"Journal articles"},{"id":"pmh:oai:pubmedcentral.nih.gov:10994553","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10994553","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10994553/pdf/pcbi.1011814.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1011814","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011814","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:d2cc81da3c5e4dfc905dda29ad6a12c4","is_oa":true,"landing_page_url":"https://doaj.org/article/d2cc81da3c5e4dfc905dda29ad6a12c4","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 20, Iss 3, p e1011814 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011814","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011814","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011814&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1050179613","display_name":"STEROID PROTECTION FROM TUBERCULOSIS-ASSOCIATED IMMUNE RECONSTITUTION INFLAMMATORY SYNDROME","funder_award_id":"MR/R008922/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G1502031688","display_name":null,"funder_award_id":"MR/S019669/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G1701253693","display_name":null,"funder_award_id":"222837/Z/21/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"},{"id":"https://openalex.org/G1990576317","display_name":null,"funder_award_id":"BBSRC","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G2014166693","display_name":"Standardised metabolite annotation workflows for enhanced biological interpretation in metabolomic data repositories","funder_award_id":"BB/T007974/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G2241581363","display_name":null,"funder_award_id":"BB/W002345/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G2347075150","display_name":null,"funder_award_id":"EDCTP2","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2360844975","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320307765","funder_display_name":"Pfizer"},{"id":"https://openalex.org/G2459364264","display_name":null,"funder_award_id":"BB/T007974/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G2644038179","display_name":null,"funder_award_id":"U01 HL089897","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G2945562962","display_name":null,"funder_award_id":"75N92023D00011","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3214677586","display_name":null,"funder_award_id":"MR/R008922/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G3298056745","display_name":null,"funder_award_id":"R01HL","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G3530239307","display_name":null,"funder_award_id":"NHLBI","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3898619757","display_name":"2020BBSRC-NSF/BIO: Linking Mass Spectrometry Computational Ecosystems to Enhance Biological Insights of Publicly-Available Data","funder_award_id":"BB/W002345/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G4154720402","display_name":null,"funder_award_id":"R01HL152735","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G477588041","display_name":null,"funder_award_id":"U01 HL08989","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G5258357286","display_name":null,"funder_award_id":"HL089897","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G5400420060","display_name":null,"funder_award_id":"HL089897","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5732303109","display_name":null,"funder_award_id":"R01 AI145436","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G5861375725","display_name":null,"funder_award_id":"U01 HL089856","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G5903061775","display_name":null,"funder_award_id":"NIAID","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6257285610","display_name":null,"funder_award_id":"U01 HL089856","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6345853531","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6470844488","display_name":null,"funder_award_id":"U01 HL089897","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6503215303","display_name":null,"funder_award_id":"R01HL152735","funder_id":"https://openalex.org/F4320306080","funder_display_name":"Foundation for the National Institutes of Health"},{"id":"https://openalex.org/G6851345361","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G6955973506","display_name":null,"funder_award_id":"GlaxoSmithKline","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G7063735130","display_name":null,"funder_award_id":"EDCTP2","funder_id":"https://openalex.org/F4320338462","funder_display_name":"European and Developing Countries Clinical Trials Partnership"},{"id":"https://openalex.org/G7116188982","display_name":null,"funder_award_id":"grants","funder_id":"https://openalex.org/F4320307765","funder_display_name":"Pfizer"},{"id":"https://openalex.org/G7122601629","display_name":null,"funder_award_id":"grant","funder_id":"https://openalex.org/F4320307765","funder_display_name":"Pfizer"},{"id":"https://openalex.org/G7153552438","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320307773","funder_display_name":"GlaxoSmithKline"},{"id":"https://openalex.org/G7445402995","display_name":null,"funder_award_id":"NHLBI,","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G7670003343","display_name":null,"funder_award_id":"EDCTP2 programme","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7948161897","display_name":null,"funder_award_id":"HL089856","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7986271162","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320307770","funder_display_name":"AstraZeneca"},{"id":"https://openalex.org/G8003643215","display_name":null,"funder_award_id":"ANR-INBS-0010","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G8051717526","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8354759825","display_name":null,"funder_award_id":"HL089856","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G8584623199","display_name":null,"funder_award_id":"grants","funder_id":"https://openalex.org/F4320307770","funder_display_name":"AstraZeneca"},{"id":"https://openalex.org/G8643874822","display_name":null,"funder_award_id":"NCT00608764","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G8819318481","display_name":null,"funder_award_id":"NCT00608764","funder_id":"https://openalex.org/F4320310320","funder_display_name":"COPD Foundation"}],"funders":[{"id":"https://openalex.org/F4320306080","display_name":"Foundation for the National Institutes of Health","ror":"https://ror.org/00k86s890"},{"id":"https://openalex.org/F4320307765","display_name":"Pfizer","ror":"https://ror.org/01xdqrp08"},{"id":"https://openalex.org/F4320307770","display_name":"AstraZeneca","ror":"https://ror.org/04r9x1a08"},{"id":"https://openalex.org/F4320307773","display_name":"GlaxoSmithKline","ror":"https://ror.org/01xsqw823"},{"id":"https://openalex.org/F4320310320","display_name":"COPD Foundation","ror":"https://ror.org/02qfkky73"},{"id":"https://openalex.org/F4320311407","display_name":"Sunovion","ror":"https://ror.org/030zc7t66"},{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320313933","display_name":"Minist\u00e8re de l'Enseignement sup\u00e9rieur, de la Recherche et de l'Innovation","ror":null},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332193","display_name":"Genentech","ror":"https://ror.org/04gndp242"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320338462","display_name":"European and Developing Countries Clinical Trials Partnership","ror":"https://ror.org/031jv9v19"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4393142382.pdf"},"referenced_works_count":82,"referenced_works":["https://openalex.org/W1541175366","https://openalex.org/W1992045522","https://openalex.org/W2003868744","https://openalex.org/W2017184667","https://openalex.org/W2027286764","https://openalex.org/W2031218556","https://openalex.org/W2071813447","https://openalex.org/W2073503722","https://openalex.org/W2082907106","https://openalex.org/W2100980426","https://openalex.org/W2101234009","https://openalex.org/W2110073322","https://openalex.org/W2114661156","https://openalex.org/W2116687544","https://openalex.org/W2130410032","https://openalex.org/W2135000328","https://openalex.org/W2140652752","https://openalex.org/W2155158051","https://openalex.org/W2158384363","https://openalex.org/W2159707944","https://openalex.org/W2170376772","https://openalex.org/W2264481086","https://openalex.org/W2269467896","https://openalex.org/W2567080747","https://openalex.org/W2624701078","https://openalex.org/W2771318548","https://openalex.org/W2781751290","https://openalex.org/W2790942900","https://openalex.org/W2808845633","https://openalex.org/W2892587974","https://openalex.org/W2900821465","https://openalex.org/W2909472027","https://openalex.org/W2912557854","https://openalex.org/W2949819623","https://openalex.org/W2950985821","https://openalex.org/W2954876467","https://openalex.org/W2963491244","https://openalex.org/W2984424339","https://openalex.org/W2989619704","https://openalex.org/W3003047249","https://openalex.org/W3003192283","https://openalex.org/W3004773979","https://openalex.org/W3004968944","https://openalex.org/W3005087874","https://openalex.org/W3014057592","https://openalex.org/W3015986104","https://openalex.org/W3025133004","https://openalex.org/W3094386380","https://openalex.org/W3095016916","https://openalex.org/W3107804378","https://openalex.org/W3112212292","https://openalex.org/W3112351970","https://openalex.org/W3122914802","https://openalex.org/W3124323918","https://openalex.org/W3127124050","https://openalex.org/W3136308181","https://openalex.org/W3139601120","https://openalex.org/W3159995035","https://openalex.org/W3163279211","https://openalex.org/W3170986249","https://openalex.org/W3173905692","https://openalex.org/W3195358767","https://openalex.org/W3196948502","https://openalex.org/W3217346306","https://openalex.org/W4200293873","https://openalex.org/W4214825051","https://openalex.org/W4221051468","https://openalex.org/W4221098111","https://openalex.org/W4221157354","https://openalex.org/W4226152036","https://openalex.org/W4226230425","https://openalex.org/W4226298065","https://openalex.org/W4229043361","https://openalex.org/W4245241719","https://openalex.org/W4282939468","https://openalex.org/W4294074103","https://openalex.org/W4306640162","https://openalex.org/W4308948103","https://openalex.org/W4319759388","https://openalex.org/W6671162180","https://openalex.org/W6675354045","https://openalex.org/W6779733042"],"related_works":["https://openalex.org/W2924366642","https://openalex.org/W4392558563","https://openalex.org/W2307569040","https://openalex.org/W2131941936","https://openalex.org/W2366067673","https://openalex.org/W3173875945","https://openalex.org/W3159101980","https://openalex.org/W2966125521","https://openalex.org/W2060096282","https://openalex.org/W3003192283"],"abstract_inverted_index":{"As":[0],"terabytes":[1],"of":[2,20,33,70,123,130,143,160,186],"multi-omics":[3,24,61,88,111,189],"data":[4,138,176],"are":[5],"being":[6],"generated,":[7],"there":[8],"is":[9,49,192],"an":[10,37,195],"ever-increasing":[11],"need":[12],"for":[13,59,78],"methods":[14,26],"facilitating":[15],"the":[16,45,91,94,106,118,121,128,141,158],"integration":[17,25,183],"and":[18,73,96,127,174,184],"interpretation":[19,185],"such":[21,79],"data.":[22,107],"Current":[23],"typically":[27],"output":[28],"lists,":[29],"clusters,":[30],"or":[31,101],"subnetworks":[32],"molecules":[34,145],"related":[35],"to":[36,67,86,93,104,117,148,162],"outcome.":[38],"Even":[39],"with":[40],"expert":[41],"domain":[42],"knowledge,":[43],"discerning":[44],"biological":[46,71],"processes":[47],"involved":[48],"a":[50,57,98,134],"time-consuming":[51],"activity.":[52],"Here":[53],"we":[54,139,177],"propose":[55],"PathIntegrate,":[56],"method":[58],"integrating":[60],"datasets":[62,89],"based":[63],"on":[64],"pathways,":[65],"designed":[66],"exploit":[68],"knowledge":[69],"systems":[72],"thus":[74],"provide":[75],"interpretable":[76],"models":[77],"studies.":[80],"PathIntegrate":[81,161,180,191],"employs":[82],"single-sample":[83],"pathway":[84],"analysis":[85],"transform":[87],"from":[90],"molecular":[92],"pathway-level,":[95],"applies":[97],"predictive":[99],"single-view":[100],"multi-view":[102],"model":[103],"integrate":[105],"Model":[108],"outputs":[109],"include":[110],"pathways":[112,147,166],"ranked":[113],"by":[114],"their":[115],"contribution":[116,122],"outcome":[119],"prediction,":[120],"each":[124,131],"omics":[125],"layer,":[126],"importance":[129],"molecule":[132],"in":[133,151],"pathway.":[135],"Using":[136],"semi-synthetic":[137],"demonstrate":[140],"benefit":[142],"grouping":[144],"into":[146],"detect":[149],"signals":[150],"low":[152,168],"signal-to-noise":[153],"scenarios,":[154],"as":[155,157,194],"well":[156],"ability":[159],"precisely":[163],"identify":[164],"important":[165],"at":[167],"effect":[169],"sizes.":[170],"Finally,":[171],"using":[172],"COPD":[173],"COVID-19":[175],"showcase":[178],"how":[179],"enables":[181],"convenient":[182],"complex":[187],"high-dimensional":[188],"datasets.":[190],"available":[193],"open-source":[196],"Python":[197],"package.":[198]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":6}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}