{"id":"https://openalex.org/W2579696773","doi":"https://doi.org/10.1093/bioinformatics/btw836","title":"Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies","display_name":"Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies","publication_year":2017,"publication_date":"2017-01-05","ids":{"openalex":"https://openalex.org/W2579696773","doi":"https://doi.org/10.1093/bioinformatics/btw836","mag":"2579696773","pmid":"https://pubmed.ncbi.nlm.nih.gov/28082455"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw836","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw836","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/9/1362/25151218/btw836.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/9/1362/25151218/btw836.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012431735","display_name":"Olga Nikolova","orcid":"https://orcid.org/0000-0001-8105-2440"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Olga Nikolova","raw_affiliation_strings":["Computational Biology Program, Oregon Health and Science University, Portland, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Program, Oregon Health and Science University, Portland, OR, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019966875","display_name":"Russell Moser","orcid":null},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Russell Moser","raw_affiliation_strings":["Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112265164","display_name":"Christopher J. Kemp","orcid":null},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher Kemp","raw_affiliation_strings":["Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019778058","display_name":"Mehmet G\u00f6nen","orcid":"https://orcid.org/0000-0002-2483-075X"},"institutions":[{"id":"https://openalex.org/I1351752","display_name":"Ko\u00e7 University","ror":"https://ror.org/00jzwgz36","country_code":"TR","type":"education","lineage":["https://openalex.org/I1351752"]},{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["TR","US"],"is_corresponding":false,"raw_author_name":"Mehmet G\u00f6nen","raw_affiliation_strings":["Computational Biology Program, Oregon Health and Science University, Portland, OR, USA","Department of Industrial Engineering, Ko\u00e7 University, \u0130stanbul, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Program, Oregon Health and Science University, Portland, OR, USA","institution_ids":["https://openalex.org/I165690674"]},{"raw_affiliation_string":"Department of Industrial Engineering, Ko\u00e7 University, \u0130stanbul, Turkey","institution_ids":["https://openalex.org/I1351752"]}]},{"author_position":"last","author":{"id":null,"display_name":"Adam A Margolin","orcid":null},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Adam A Margolin","raw_affiliation_strings":["Computational Biology Program, Oregon Health and Science University, Portland, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology Program, Oregon Health and Science University, Portland, OR, USA","institution_ids":["https://openalex.org/I165690674"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5012431735"],"corresponding_institution_ids":["https://openalex.org/I165690674"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6557,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.67122213,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"33","issue":"9","first_page":"1362","last_page":"1369"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.515500009059906,"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":0.515500009059906,"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":0.149399995803833,"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":0.056299999356269836,"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":0.6828588247299194},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.5033854842185974},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4973948299884796},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.4901960492134094},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4680445194244385},{"id":"https://openalex.org/keywords/personalized-medicine","display_name":"Personalized medicine","score":0.45399484038352966},{"id":"https://openalex.org/keywords/precision-medicine","display_name":"Precision medicine","score":0.4510679244995117},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4344298839569092},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.41130760312080383},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3691551685333252},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3288232088088989},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2900467813014984},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2002219557762146}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6828588247299194},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.5033854842185974},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4973948299884796},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.4901960492134094},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4680445194244385},{"id":"https://openalex.org/C32220436","wikidata":"https://www.wikidata.org/wiki/Q2072214","display_name":"Personalized medicine","level":2,"score":0.45399484038352966},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.4510679244995117},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4344298839569092},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.41130760312080383},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3691551685333252},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3288232088088989},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2900467813014984},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2002219557762146},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069558","descriptor_name":"Unsupervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069558","descriptor_name":"Unsupervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069558","descriptor_name":"Unsupervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000230","descriptor_name":"Adenocarcinoma","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002471","descriptor_name":"Cell Transformation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002471","descriptor_name":"Cell Transformation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002471","descriptor_name":"Cell Transformation, Neoplastic","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":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010190","descriptor_name":"Pancreatic Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D010190","descriptor_name":"Pancreatic Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D010190","descriptor_name":"Pancreatic Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D010190","descriptor_name":"Pancreatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010190","descriptor_name":"Pancreatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010190","descriptor_name":"Pancreatic Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010190","descriptor_name":"Pancreatic Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010190","descriptor_name":"Pancreatic Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010190","descriptor_name":"Pancreatic Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D052138","descriptor_name":"Genes, Neoplasm","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D052138","descriptor_name":"Genes, Neoplasm","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D052138","descriptor_name":"Genes, Neoplasm","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054316","descriptor_name":"Biomarkers, Pharmacological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054316","descriptor_name":"Biomarkers, Pharmacological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054316","descriptor_name":"Biomarkers, Pharmacological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw836","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw836","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/9/1362/25151218/btw836.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28082455","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28082455","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:4847533","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC5860077","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5860077","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860077","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw836","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw836","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/9/1362/25151218/btw836.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.5400000214576721,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G206364300","display_name":null,"funder_award_id":"U54 CA149237","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4793121878","display_name":null,"funder_award_id":"U24 CA143858","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4802061397","display_name":null,"funder_award_id":"U54 HG007990","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G6224538330","display_name":null,"funder_award_id":"U01 CA176303","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7813220096","display_name":null,"funder_award_id":"U54CA149237","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8739156282","display_name":null,"funder_award_id":"U01CA176303","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320322628","display_name":"T\u00fcrkiye Bilimler Akademisi","ror":"https://ror.org/00aqt9352"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W19078547","https://openalex.org/W1967220865","https://openalex.org/W1984983329","https://openalex.org/W1989277387","https://openalex.org/W1998612778","https://openalex.org/W2000391750","https://openalex.org/W2002583208","https://openalex.org/W2002830978","https://openalex.org/W2008929650","https://openalex.org/W2017166332","https://openalex.org/W2022093187","https://openalex.org/W2035055162","https://openalex.org/W2042386784","https://openalex.org/W2043398720","https://openalex.org/W2043696829","https://openalex.org/W2044433401","https://openalex.org/W2048205622","https://openalex.org/W2053719406","https://openalex.org/W2061912939","https://openalex.org/W2087075862","https://openalex.org/W2087962626","https://openalex.org/W2097360283","https://openalex.org/W2098290597","https://openalex.org/W2100714130","https://openalex.org/W2102701235","https://openalex.org/W2103017472","https://openalex.org/W2108933868","https://openalex.org/W2110071511","https://openalex.org/W2122825543","https://openalex.org/W2125789330","https://openalex.org/W2126707245","https://openalex.org/W2130186565","https://openalex.org/W2130448611","https://openalex.org/W2131848047","https://openalex.org/W2135046866","https://openalex.org/W2141978478","https://openalex.org/W2144903813","https://openalex.org/W2148043260","https://openalex.org/W2154790710","https://openalex.org/W2158330526","https://openalex.org/W2161884651","https://openalex.org/W2169273935","https://openalex.org/W2171304795","https://openalex.org/W2171973865","https://openalex.org/W2175970000","https://openalex.org/W2318605753","https://openalex.org/W2329648702","https://openalex.org/W4237335579","https://openalex.org/W4294541781","https://openalex.org/W6600744685","https://openalex.org/W6661315439","https://openalex.org/W6663949939","https://openalex.org/W6681437887"],"related_works":["https://openalex.org/W3082935376","https://openalex.org/W20047544","https://openalex.org/W3193951088","https://openalex.org/W4322484660","https://openalex.org/W4386960999","https://openalex.org/W2899657781","https://openalex.org/W2770866531","https://openalex.org/W4388011470","https://openalex.org/W4230423494","https://openalex.org/W4298001029"],"abstract_inverted_index":{"Motivation:":[0],"In":[1,119],"recent":[2],"years,":[3],"vast":[4],"advances":[5],"in":[6,23,52,128,217,229],"biomedical":[7],"technologies":[8],"and":[9,79,98,107,152,181,202,205,234,245],"comprehensive":[10],"sequencing":[11],"have":[12],"revealed":[13],"the":[14,30,40,53,158,176,182,192,212,230],"genomic":[15,43,100],"landscape":[16],"of":[17,20,29,36,77,113,131,133,160,167,214],"common":[18],"forms":[19],"human":[21],"cancer":[22],"unprecedented":[24],"detail.":[25],"The":[26,240,248],"broad":[27],"heterogeneity":[28],"disease":[31],"calls":[32],"for":[33,75,191,250],"rapid":[34],"development":[35],"personalized":[37],"therapies.":[38],"Translating":[39],"readily":[41],"available":[42,254,267],"data":[44,70,201,265],"into":[45],"useful":[46],"knowledge":[47],"that":[48,135,189],"can":[49],"be":[50,140],"applied":[51],"clinic":[54],"remains":[55],"a":[56,84,104,109,114],"challenge.":[57],"Computational":[58],"methods":[59],"are":[60,136,266],"needed":[61],"to":[62,139,142,148,227],"aid":[63],"these":[64],"efforts":[65],"by":[66,223],"robustly":[67],"analyzing":[68],"genome-scale":[69],"from":[71,198,239],"distinct":[72,99],"experimental":[73],"platforms":[74],"prioritization":[76],"targets":[78],"treatments.":[80],"Results:":[81],"We":[82,102,156,187,209],"propose":[83],"novel,":[85],"biologically":[86],"motivated,":[87],"Bayesian":[88,111],"multitask":[89,124],"approach,":[90],"which":[91,146],"explicitly":[92],"models":[93],"gene-centric":[94,193],"dependencies":[95,194],"across":[96],"multiple":[97],"platforms.":[101],"introduce":[103],"gene-wise":[105],"prior":[106],"present":[108],"fully":[110],"formulation":[112],"group":[115],"factor":[116],"analysis":[117],"model.":[118],"supervised":[120],"prediction":[121,204],"applications,":[122],"our":[123,161,215],"approach":[125],"leverages":[126],"similarities":[127],"response":[129],"profiles":[130],"groups":[132],"drugs":[134],"more":[137,149],"likely":[138],"related":[141],"true":[143],"biological":[144],"signal,":[145],"leads":[147],"robust":[150],"performance":[151,159],"improved":[153],"generalization":[154],"ability.":[155],"evaluate":[157],"method":[162,216],"on":[163],"molecularly":[164],"characterized":[165],"collections":[166],"cell":[168],"lines":[169],"profiled":[170],"against":[171],"two":[172],"compound":[173],"panels,":[174],"namely":[175],"Cancer":[177,183,241],"Cell":[178],"Line":[179],"Encyclopedia":[180],"Therapeutics":[184],"Response":[185],"Portal.":[186],"demonstrate":[188,211],"accounting":[190],"enables":[195],"leveraging":[196],"information":[197],"multi-omic":[199],"input":[200],"improves":[203],"feature":[206],"selection":[207],"performance.":[208],"further":[210],"applicability":[213],"an":[218],"unsupervised":[219],"dimensionality":[220],"reduction":[221],"application":[222],"inferring":[224],"genes":[225],"essential":[226],"tumorigenesis":[228],"pancreatic":[231],"ductal":[232],"adenocarcinoma":[233,236],"lung":[235],"patient":[237],"cohorts":[238],"Genome":[242],"Atlas.":[243],"Availability":[244],"Implementation:":[246],":":[247,258],"code":[249],"this":[251],"work":[252],"is":[253],"at":[255,268],"https://github.com/olganikolova/gbgfa.":[256],"Contact:":[257],"nikolova@ohsu.edu":[259],"or":[260],"margolin@ohsu.edu.":[261],"Supplementary":[262,264],"information:":[263],"Bioinformatics":[269],"online.":[270]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
