{"id":"https://openalex.org/W4414850698","doi":"https://doi.org/10.1093/bioinformatics/btaf490","title":"MPAC: a computational framework for inferring pathway activities from multi-omic data","display_name":"MPAC: a computational framework for inferring pathway activities from multi-omic data","publication_year":2025,"publication_date":"2025-09-10","ids":{"openalex":"https://openalex.org/W4414850698","doi":"https://doi.org/10.1093/bioinformatics/btaf490","pmid":"https://pubmed.ncbi.nlm.nih.gov/41046136"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf490","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf490","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btaf490","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100346808","display_name":"Peng Liu","orcid":"https://orcid.org/0000-0002-3095-0352"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I4210103341","display_name":"University of Wisconsin Carbone Cancer Center","ror":"https://ror.org/01e4byj08","country_code":"US","type":"funder","lineage":["https://openalex.org/I2799905417","https://openalex.org/I4210103341","https://openalex.org/I4210132596"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peng Liu","raw_affiliation_strings":["Carbone Cancer Center, University of Wisconsin\u2013Madison , Madison, WI 53792,","Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison , Madison, WI 53726,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Carbone Cancer Center, University of Wisconsin\u2013Madison , Madison, WI 53792,","institution_ids":["https://openalex.org/I4210103341"]},{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison , Madison, WI 53726,","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036424514","display_name":"David Page","orcid":"https://orcid.org/0000-0003-3353-4300"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I4210103341","display_name":"University of Wisconsin Carbone Cancer Center","ror":"https://ror.org/01e4byj08","country_code":"US","type":"funder","lineage":["https://openalex.org/I2799905417","https://openalex.org/I4210103341","https://openalex.org/I4210132596"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David Page","raw_affiliation_strings":["Carbone Cancer Center, University of Wisconsin\u2013Madison , Madison, WI 53792,","Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison , Madison, WI 53726,","Department of Computer Sciences, University of Wisconsin\u2013Madison , Madison, WI 53706,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Carbone Cancer Center, University of Wisconsin\u2013Madison , Madison, WI 53792,","institution_ids":["https://openalex.org/I4210103341"]},{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison , Madison, WI 53726,","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Computer Sciences, University of Wisconsin\u2013Madison , Madison, WI 53706,","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026899432","display_name":"Paul Ahlquist","orcid":"https://orcid.org/0000-0003-4584-9318"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]},{"id":"https://openalex.org/I4210103341","display_name":"University of Wisconsin Carbone Cancer Center","ror":"https://ror.org/01e4byj08","country_code":"US","type":"funder","lineage":["https://openalex.org/I2799905417","https://openalex.org/I4210103341","https://openalex.org/I4210132596"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Ahlquist","raw_affiliation_strings":["Institute for Molecular Virology, University of Wisconsin\u2013Madison , Madison, WI 53706,","John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research , Madison, WI 53715,","McArdle Laboratory for Cancer Research, University of Wisconsin\u2013Madison , Madison, WI 53705,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Molecular Virology, University of Wisconsin\u2013Madison , Madison, WI 53706,","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research , Madison, WI 53715,","institution_ids":["https://openalex.org/I29680605"]},{"raw_affiliation_string":"McArdle Laboratory for Cancer Research, University of Wisconsin\u2013Madison , Madison, WI 53705,","institution_ids":["https://openalex.org/I135310074","https://openalex.org/I4210103341"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019665472","display_name":"Irene M. Ong","orcid":"https://orcid.org/0000-0002-9353-6941"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I4210103341","display_name":"University of Wisconsin Carbone Cancer Center","ror":"https://ror.org/01e4byj08","country_code":"US","type":"funder","lineage":["https://openalex.org/I2799905417","https://openalex.org/I4210103341","https://openalex.org/I4210132596"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Irene M Ong","raw_affiliation_strings":["Carbone Cancer Center, University of Wisconsin\u2013Madison , Madison, WI 53792,","Center for Human Genomics and Precision Medicine, University of Wisconsin\u2013Madison , Madison, WI 53705,","Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison , Madison, WI 53726,","Department of Obstetrics and Gynecology, University of Wisconsin\u2013Madison , Madison, WI 53705,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Carbone Cancer Center, University of Wisconsin\u2013Madison , Madison, WI 53792,","institution_ids":["https://openalex.org/I4210103341"]},{"raw_affiliation_string":"Center for Human Genomics and Precision Medicine, University of Wisconsin\u2013Madison , Madison, WI 53705,","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison , Madison, WI 53726,","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Obstetrics and Gynecology, University of Wisconsin\u2013Madison , Madison, WI 53705,","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083286341","display_name":"Anthony Gitter","orcid":"https://orcid.org/0000-0002-5324-9833"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I29680605","display_name":"Morgridge Institute for Research","ror":"https://ror.org/05cb4rb43","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I135310074","https://openalex.org/I29680605"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anthony Gitter","raw_affiliation_strings":["Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison , Madison, WI 53726,","Department of Computer Sciences, University of Wisconsin\u2013Madison , Madison, WI 53706,","John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research , Madison, WI 53715,"],"raw_orcid":"https://orcid.org/0000-0002-5324-9833","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison , Madison, WI 53726,","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Computer Sciences, University of Wisconsin\u2013Madison , Madison, WI 53706,","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research , Madison, WI 53715,","institution_ids":["https://openalex.org/I29680605"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.17050505,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"10","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":0.8532999753952026,"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":0.8532999753952026,"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/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.0544000007212162,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.009999999776482582,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.8198999762535095},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.6086000204086304},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4377000033855438},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.34950000047683716}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.8198999762535095},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7508999705314636},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.6086000204086304},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46320000290870667},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4377000033855438},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35989999771118164},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.34950000047683716},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.3433000147342682},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.25999999046325684},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2572999894618988}],"mesh":[{"descriptor_ui":"D000077195","descriptor_name":"Squamous Cell Carcinoma of Head and Neck","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000077195","descriptor_name":"Squamous Cell Carcinoma of Head and Neck","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000077195","descriptor_name":"Squamous Cell Carcinoma of Head and Neck","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000077195","descriptor_name":"Squamous Cell Carcinoma of Head and Neck","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000077195","descriptor_name":"Squamous Cell Carcinoma of Head and Neck","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000077195","descriptor_name":"Squamous Cell Carcinoma of Head and Neck","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000077195","descriptor_name":"Squamous Cell Carcinoma of Head and Neck","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000077195","descriptor_name":"Squamous Cell Carcinoma of Head and Neck","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000077195","descriptor_name":"Squamous Cell Carcinoma of Head and Neck","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000077195","descriptor_name":"Squamous Cell Carcinoma of Head and Neck","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006258","descriptor_name":"Head and Neck Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006258","descriptor_name":"Head and Neck Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006258","descriptor_name":"Head and Neck Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006258","descriptor_name":"Head and Neck Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006258","descriptor_name":"Head and Neck Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006258","descriptor_name":"Head and Neck Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006258","descriptor_name":"Head and Neck Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006258","descriptor_name":"Head and Neck Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006258","descriptor_name":"Head and Neck Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006258","descriptor_name":"Head and Neck Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf490","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf490","pdf_url":null,"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:41046136","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41046136","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:europepmc.org:11305777","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12496133","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12496133","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12496133/","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf490","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf490","pdf_url":null,"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":[],"awards":[{"id":"https://openalex.org/G2661639429","display_name":null,"funder_award_id":"UL1 TR002373","funder_id":"https://openalex.org/F4320310176","funder_display_name":"University of Wisconsin Carbone Cancer Center"},{"id":"https://openalex.org/G349625549","display_name":null,"funder_award_id":"UL1 TR002373","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G4039876303","display_name":null,"funder_award_id":"P30 CA014520","funder_id":"https://openalex.org/F4320310176","funder_display_name":"University of Wisconsin Carbone Cancer Center"},{"id":"https://openalex.org/G4319453063","display_name":null,"funder_award_id":"P50 CA278595","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G8820405586","display_name":null,"funder_award_id":"P01 CA022443","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320310176","display_name":"University of Wisconsin Carbone Cancer Center","ror":"https://ror.org/02mqqhj42"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W1967220865","https://openalex.org/W1985987855","https://openalex.org/W1986241711","https://openalex.org/W1987219048","https://openalex.org/W2096766502","https://openalex.org/W2100714130","https://openalex.org/W2121270008","https://openalex.org/W2127611185","https://openalex.org/W2132623845","https://openalex.org/W2148317584","https://openalex.org/W2338223499","https://openalex.org/W2540833380","https://openalex.org/W2603204749","https://openalex.org/W2771542157","https://openalex.org/W2795441251","https://openalex.org/W2795989238","https://openalex.org/W2796153844","https://openalex.org/W2913710075","https://openalex.org/W2950245999","https://openalex.org/W2950322442","https://openalex.org/W3004773979","https://openalex.org/W3015259728","https://openalex.org/W3027051073","https://openalex.org/W3085677572","https://openalex.org/W3094540299","https://openalex.org/W3119681293","https://openalex.org/W3120816783","https://openalex.org/W3124569282","https://openalex.org/W3134323447","https://openalex.org/W3173875945","https://openalex.org/W3181637650","https://openalex.org/W3187466590","https://openalex.org/W3207811959","https://openalex.org/W3211402536","https://openalex.org/W4200247705","https://openalex.org/W4206662285","https://openalex.org/W4210670182","https://openalex.org/W4212964416","https://openalex.org/W4225288431","https://openalex.org/W4225690840","https://openalex.org/W4291286390","https://openalex.org/W4300960603","https://openalex.org/W4306640162","https://openalex.org/W4307425304","https://openalex.org/W4308801774","https://openalex.org/W4311065941","https://openalex.org/W4312003682","https://openalex.org/W4323036511","https://openalex.org/W4367051143","https://openalex.org/W4376643505","https://openalex.org/W4382632237","https://openalex.org/W4386438154","https://openalex.org/W4386723368","https://openalex.org/W4388409275","https://openalex.org/W4390988930","https://openalex.org/W4401556795","https://openalex.org/W6907225408"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Fully":[1],"capturing":[2],"cellular":[3],"state":[4],"requires":[5],"examining":[6],"genomic,":[7],"epigenomic,":[8],"transcriptomic,":[9],"proteomic,":[10],"and":[11,18,27,53,57,99,114,124,141,146],"other":[12],"assays":[13],"for":[14,97],"a":[15,68,89,165],"biological":[16,79,116],"sample":[17],"comprehensive":[19],"computational":[20,69],"modeling":[21],"to":[22,92,109,121,169,193],"reason":[23],"with":[24,127,133,176],"the":[25],"complex":[26],"sometimes":[28],"conflicting":[29],"measurements.":[30],"Modeling":[31],"these":[32],"so-called":[33],"multi-omic":[34,73,104,208],"data":[35,46,74,143,180],"is":[36,219],"especially":[37],"beneficial":[38],"in":[39,86],"disease":[40],"analysis,":[41],"where":[42],"observations":[43],"across":[44],"omic":[45,179],"types":[47],"may":[48],"reveal":[49],"unexpected":[50],"patient":[51,134,166],"groupings":[52],"inform":[54],"clinical":[55,129,194],"outcomes":[56],"treatments.":[58],"RESULTS:":[59],"We":[60],"present":[61],"Multi-omic":[62],"Pathway":[63],"Analysis":[64],"of":[65],"Cells":[66],"(MPAC),":[67],"framework":[70],"that":[71,162],"interprets":[72],"through":[75,88],"prior":[76],"knowledge":[77],"from":[78,103,144,152],"pathways.":[80],"MPAC":[81,163,203,217],"leverages":[82],"network":[83],"relationships":[84],"encoded":[85],"pathways":[87],"factor":[90],"graph":[91],"infer":[93],"consensus":[94],"activity":[95,112],"levels":[96],"proteins":[98,126,184],"associated":[100,132],"pathway":[101,119,190],"entities":[102],"data,":[105],"runs":[106],"permutation":[107],"testing":[108],"eliminate":[110],"spurious":[111],"predictions,":[113],"groups":[115],"samples":[117],"by":[118,174],"activities":[120,191],"allow":[122],"identifying":[123],"prioritizing":[125],"potential":[128],"relevance,":[130],"e.g.":[131],"prognosis.":[135],"Using":[136],"DNA":[137],"copy":[138],"number":[139],"alteration":[140],"RNA-seq":[142],"head":[145],"neck":[147],"squamous":[148],"cell":[149,200],"carcinoma":[150],"patients":[151],"The":[153,216],"Cancer":[154],"Genome":[155],"Atlas":[156],"as":[157,196,198],"an":[158],"example,":[159],"we":[160],"demonstrate":[161],"predicts":[164],"subgroup":[167,188],"related":[168,192],"immune":[170,199],"responses":[171],"not":[172],"identified":[173,185],"analysis":[175],"either":[177],"input":[178],"type":[181],"alone.":[182],"Key":[183],"via":[186],"this":[187],"have":[189],"outcome":[195],"well":[197],"composition.":[201],"Our":[202],"R":[204],"package":[205,218],"enables":[206],"similar":[207],"analyses":[209],"on":[210],"new":[211],"datasets.":[212],"AVAILABILITY":[213],"AND":[214],"IMPLEMENTATION:":[215],"available":[220],"at":[221],"Bioconductor":[222],"https://bioconductor.org/packages/MPAC.":[223]},"counts_by_year":[],"updated_date":"2026-07-16T13:24:37.021932","created_date":"2025-10-10T00:00:00"}
