{"id":"https://openalex.org/W3205709567","doi":"https://doi.org/10.1371/journal.pcbi.1008986","title":"PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes","display_name":"PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes","publication_year":2021,"publication_date":"2021-10-22","ids":{"openalex":"https://openalex.org/W3205709567","doi":"https://doi.org/10.1371/journal.pcbi.1008986","mag":"3205709567","pmid":"https://pubmed.ncbi.nlm.nih.gov/34679079"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008986","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008986","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1008986","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061426767","display_name":"Charlie M. Carpenter","orcid":"https://orcid.org/0000-0002-4698-1516"},"institutions":[{"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"]},{"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":"Charlie M. Carpenter","raw_affiliation_strings":["Department of Biostatistics and Informatics, University of Colorado Denver, Anschutz Medical campus, Denver, Colorado, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Informatics, University of Colorado Denver, Anschutz Medical campus, Denver, Colorado, United States of America","institution_ids":["https://openalex.org/I51713134","https://openalex.org/I921990950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101756435","display_name":"Weiming Zhang","orcid":"https://orcid.org/0000-0002-1953-4016"},"institutions":[{"id":"https://openalex.org/I4210105783","display_name":"Syneos Health (United States)","ror":"https://ror.org/01r74wp43","country_code":"US","type":"company","lineage":["https://openalex.org/I4210105783"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weiming Zhang","raw_affiliation_strings":["Syneos Health, Morrisville, North Carolina, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Syneos Health, Morrisville, North Carolina, United States of America","institution_ids":["https://openalex.org/I4210105783"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054972170","display_name":"Lucas A. Gillenwater","orcid":"https://orcid.org/0000-0002-6995-0130"},"institutions":[{"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"]},{"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":false,"raw_author_name":"Lucas Gillenwater","raw_affiliation_strings":["Computational Bioscience Program, University of Colorado Denver, Anschutz medical campus, Denver, Colorado, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-6995-0130","affiliations":[{"raw_affiliation_string":"Computational Bioscience Program, University of Colorado Denver, Anschutz medical campus, Denver, Colorado, United States of America","institution_ids":["https://openalex.org/I51713134","https://openalex.org/I921990950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022187876","display_name":"Cameron Severn","orcid":"https://orcid.org/0000-0001-9562-581X"},"institutions":[{"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"]},{"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":false,"raw_author_name":"Cameron Severn","raw_affiliation_strings":["Department of Biostatistics and Informatics, University of Colorado Denver, Anschutz Medical campus, Denver, Colorado, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-9562-581X","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Informatics, University of Colorado Denver, Anschutz Medical campus, Denver, Colorado, United States of America","institution_ids":["https://openalex.org/I51713134","https://openalex.org/I921990950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000295265","display_name":"Tusharkanti Ghosh","orcid":"https://orcid.org/0000-0002-7537-6374"},"institutions":[{"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"]},{"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":false,"raw_author_name":"Tusharkanti Ghosh","raw_affiliation_strings":["Department of Biostatistics and Informatics, University of Colorado Denver, Anschutz Medical campus, Denver, Colorado, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-7537-6374","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Informatics, University of Colorado Denver, Anschutz Medical campus, Denver, Colorado, United States of America","institution_ids":["https://openalex.org/I51713134","https://openalex.org/I921990950"]}]},{"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/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]},{"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":false,"raw_author_name":"Russell Bowler","raw_affiliation_strings":["Department of Medicine, National Jewish Health, Denver; University of Colorado Denver, Anschutz Medical Campus, Denver, Colorado, United States of America","University of Colorado Denver, Anschutz Medical Campus, Denver, Colorado, United States of America","Department of Medicine, National Jewish Health, Denver"],"raw_orcid":"https://orcid.org/0000-0003-4651-363X","affiliations":[{"raw_affiliation_string":"Department of Medicine, National Jewish Health, Denver; University of Colorado Denver, Anschutz Medical Campus, Denver, Colorado, United States of America","institution_ids":["https://openalex.org/I3019586173","https://openalex.org/I921990950"]},{"raw_affiliation_string":"University of Colorado Denver, Anschutz Medical Campus, Denver, Colorado, United States of America","institution_ids":["https://openalex.org/I51713134","https://openalex.org/I921990950"]},{"raw_affiliation_string":"Department of Medicine, National Jewish Health, Denver","institution_ids":["https://openalex.org/I3019586173","https://openalex.org/I921990950"]}]},{"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/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]},{"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":false,"raw_author_name":"Katerina Kechris","raw_affiliation_strings":["Department of Biostatistics and Informatics, University of Colorado Denver, Anschutz Medical campus, Denver, Colorado, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-3725-5459","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Informatics, University of Colorado Denver, Anschutz Medical campus, Denver, Colorado, United States of America","institution_ids":["https://openalex.org/I51713134","https://openalex.org/I921990950"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100625252","display_name":"Debashis Ghosh","orcid":"https://orcid.org/0000-0001-6618-1316"},"institutions":[{"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"]},{"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":false,"raw_author_name":"Debashis Ghosh","raw_affiliation_strings":["Department of Biostatistics and Informatics, University of Colorado Denver, Anschutz Medical campus, Denver, Colorado, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-6618-1316","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Informatics, University of Colorado Denver, Anschutz Medical campus, Denver, Colorado, United States of America","institution_ids":["https://openalex.org/I51713134","https://openalex.org/I921990950"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5061426767"],"corresponding_institution_ids":["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":0.6665,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.66535237,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"17","issue":"10","first_page":"e1008986","last_page":"e1008986"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9986000061035156,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9912999868392944,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.625336229801178},{"id":"https://openalex.org/keywords/graph-kernel","display_name":"Graph kernel","score":0.5153738856315613},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.508255660533905},{"id":"https://openalex.org/keywords/kernel-method","display_name":"Kernel method","score":0.49268633127212524},{"id":"https://openalex.org/keywords/metabolomics","display_name":"Metabolomics","score":0.4757268726825714},{"id":"https://openalex.org/keywords/disjoint-sets","display_name":"Disjoint sets","score":0.4666730463504791},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.45488905906677246},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.41134870052337646},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.403473436832428},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.38089072704315186},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3634079098701477},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3465951085090637},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23754724860191345},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15747401118278503},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.14655554294586182},{"id":"https://openalex.org/keywords/polynomial-kernel","display_name":"Polynomial kernel","score":0.14154034852981567},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10127106308937073},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.0966726541519165}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.625336229801178},{"id":"https://openalex.org/C100595998","wikidata":"https://www.wikidata.org/wiki/Q11731931","display_name":"Graph kernel","level":5,"score":0.5153738856315613},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.508255660533905},{"id":"https://openalex.org/C122280245","wikidata":"https://www.wikidata.org/wiki/Q620622","display_name":"Kernel method","level":3,"score":0.49268633127212524},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.4757268726825714},{"id":"https://openalex.org/C45340560","wikidata":"https://www.wikidata.org/wiki/Q215382","display_name":"Disjoint sets","level":2,"score":0.4666730463504791},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.45488905906677246},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.41134870052337646},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.403473436832428},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38089072704315186},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3634079098701477},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3465951085090637},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23754724860191345},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15747401118278503},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.14655554294586182},{"id":"https://openalex.org/C160446489","wikidata":"https://www.wikidata.org/wiki/Q7226642","display_name":"Polynomial kernel","level":4,"score":0.14154034852981567},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10127106308937073},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.0966726541519165},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012044","descriptor_name":"Regression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000097","qualifier_name":"blood","is_major_topic":false},{"descriptor_ui":"D029424","descriptor_name":"Pulmonary Disease, Chronic Obstructive","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029424","descriptor_name":"Pulmonary Disease, Chronic Obstructive","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029424","descriptor_name":"Pulmonary Disease, Chronic Obstructive","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029424","descriptor_name":"Pulmonary Disease, Chronic Obstructive","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029424","descriptor_name":"Pulmonary Disease, Chronic Obstructive","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029424","descriptor_name":"Pulmonary Disease, Chronic Obstructive","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D029424","descriptor_name":"Pulmonary Disease, Chronic Obstructive","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D029424","descriptor_name":"Pulmonary Disease, Chronic Obstructive","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D029424","descriptor_name":"Pulmonary Disease, Chronic Obstructive","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D029424","descriptor_name":"Pulmonary Disease, Chronic Obstructive","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1008986","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008986","pdf_url":null,"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:34679079","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34679079","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:RePEc:plo:pcbi00:1008986","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008986","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:5676f381da3d41819c493b41c1b39486","is_oa":true,"landing_page_url":"https://doaj.org/article/5676f381da3d41819c493b41c1b39486","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":"PLoS Computational Biology, Vol 17, Iss 10, p e1008986 (2021)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:7454850","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8565741","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8565741","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8565741","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1008986","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008986","pdf_url":null,"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/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/G3124021205","display_name":null,"funder_award_id":"U01 CA235488","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5180013511","display_name":null,"funder_award_id":"R01 HL137995","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G521018959","display_name":null,"funder_award_id":"R01 HL095432","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/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/G7714755286","display_name":null,"funder_award_id":"U01 CA235488","funder_id":"https://openalex.org/F4320338333","funder_display_name":"Division of Cancer Epidemiology and Genetics, National Cancer Institute"},{"id":"https://openalex.org/G820522361","display_name":null,"funder_award_id":"U01 HL089897 and U01 HL089856","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"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"}],"funders":[{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320338333","display_name":"Division of Cancer Epidemiology and Genetics, National Cancer Institute","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":68,"referenced_works":["https://openalex.org/W229097380","https://openalex.org/W1511160855","https://openalex.org/W1516274582","https://openalex.org/W1538574688","https://openalex.org/W1774304772","https://openalex.org/W1843428036","https://openalex.org/W1906461790","https://openalex.org/W1966327575","https://openalex.org/W1973207991","https://openalex.org/W1993418188","https://openalex.org/W1998349455","https://openalex.org/W2008620264","https://openalex.org/W2024193591","https://openalex.org/W2028133290","https://openalex.org/W2028159081","https://openalex.org/W2059618800","https://openalex.org/W2062551369","https://openalex.org/W2067100182","https://openalex.org/W2071011202","https://openalex.org/W2078739747","https://openalex.org/W2082907106","https://openalex.org/W2083157509","https://openalex.org/W2088944177","https://openalex.org/W2093824159","https://openalex.org/W2097502538","https://openalex.org/W2099107563","https://openalex.org/W2108299701","https://openalex.org/W2112814716","https://openalex.org/W2120345775","https://openalex.org/W2132132957","https://openalex.org/W2134736660","https://openalex.org/W2136582936","https://openalex.org/W2138630147","https://openalex.org/W2154164391","https://openalex.org/W2159482845","https://openalex.org/W2165009258","https://openalex.org/W2165681080","https://openalex.org/W2192043071","https://openalex.org/W2203621986","https://openalex.org/W2274495055","https://openalex.org/W2292058622","https://openalex.org/W2486096428","https://openalex.org/W2557833574","https://openalex.org/W2582743722","https://openalex.org/W2586052295","https://openalex.org/W2593178466","https://openalex.org/W2767914218","https://openalex.org/W2795123374","https://openalex.org/W2807206274","https://openalex.org/W2888303476","https://openalex.org/W2898924061","https://openalex.org/W2901402567","https://openalex.org/W2907577147","https://openalex.org/W2914349589","https://openalex.org/W2938032333","https://openalex.org/W2949918167","https://openalex.org/W2962681781","https://openalex.org/W2992021992","https://openalex.org/W3046506911","https://openalex.org/W3101919829","https://openalex.org/W3102351945","https://openalex.org/W3103436731","https://openalex.org/W3104974184","https://openalex.org/W3119573237","https://openalex.org/W3133707592","https://openalex.org/W4211085285","https://openalex.org/W4294216483","https://openalex.org/W6786370094"],"related_works":["https://openalex.org/W1592261055","https://openalex.org/W2078320823","https://openalex.org/W2043334680","https://openalex.org/W4285213554","https://openalex.org/W4287862919","https://openalex.org/W3008854474","https://openalex.org/W2098940859","https://openalex.org/W3099811568","https://openalex.org/W3044028388","https://openalex.org/W1515878412"],"abstract_inverted_index":{"High-throughput":[0],"data":[1,12,168,191,218],"such":[2],"as":[3,34],"metabolomics,":[4],"genomics,":[5],"transcriptomics,":[6],"and":[7,30,138,142,162,184,188],"proteomics":[8],"have":[9,39],"become":[10],"familiar":[11],"types":[13],"within":[14,55],"the":[15,56,68,88,170,177,189,211],"\"-omics\"":[16],"family.":[17],"For":[18],"this":[19,64,156,180],"work,":[20],"we":[21,66],"focus":[22],"on":[23],"subsets":[24],"that":[25],"interact":[26],"with":[27,220],"one":[28],"another":[29],"represent":[31],"these":[32],"\"pathways\"":[33],"graphs.":[35],"Observed":[36],"pathways":[37,137,149],"often":[38],"disjoint":[40],"components,":[41],"i.e.,":[42],"nodes":[43,47],"or":[44,120],"sets":[45],"of":[46,106,140,179,196],"(metabolites,":[48],"etc.)":[49],"not":[50],"connected":[51],"to":[52,165,182,206,216],"any":[53],"other":[54,217],"pathway,":[57],"which":[58],"notably":[59],"lessens":[60],"testing":[61,197],"power.":[62],"In":[63],"paper":[65,101],"propose":[67],"Pathway":[69],"Integrated":[70],"Regression-based":[71],"Kernel":[72],"Association":[73],"Test":[74],"(PaIRKAT),":[75],"a":[76,107,118,124,221],"new":[77],"kernel":[78,90,97,109],"machine":[79,98],"regression":[80,91],"method":[81,111,157,181],"for":[82,112,133,150,204],"incorporating":[83,117],"known":[84],"pathway":[85,186,208],"information":[86],"into":[87,123],"semi-parametric":[89],"framework.":[92],"This":[93,100],"work":[94],"extends":[95],"previous":[96],"approaches.":[99],"also":[102],"contributes":[103],"an":[104,163],"application":[105,164,205],"graph":[108,122],"regularization":[110],"overcoming":[113],"disconnected":[114],"pathways.":[115,200],"By":[116],"regularized":[119],"\"smoothed\"":[121],"score":[125],"test,":[126],"PaIRKAT":[127,201],"can":[128],"provide":[129],"more":[130],"powerful":[131],"tests":[132],"associations":[134],"between":[135],"biological":[136],"phenotypes":[139],"interest":[141],"will":[143],"be":[144],"helpful":[145],"in":[146,199],"identifying":[147],"novel":[148],"targeted":[151],"clinical":[152],"research.":[153],"We":[154],"evaluate":[155],"through":[158],"several":[159],"simulation":[160,174],"studies":[161,175],"real":[166,190],"metabolomics":[167],"from":[169],"COPDGene":[171],"study.":[172],"Our":[173],"illustrate":[176],"robustness":[178],"incorrect":[183],"incomplete":[185],"knowledge,":[187],"analysis":[192],"shows":[193],"meaningful":[194],"improvements":[195],"power":[198],"was":[202],"developed":[203],"metabolomic":[207],"data,":[209],"but":[210],"techniques":[212],"are":[213],"easily":[214],"generalizable":[215],"sources":[219],"graph-like":[222],"structure.":[223]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":6},{"year":2021,"cited_by_count":2}],"updated_date":"2026-07-27T08:26:11.824852","created_date":"2025-10-10T00:00:00"}