{"id":"https://openalex.org/W4413944006","doi":"https://doi.org/10.1016/j.compbiolchem.2025.108669","title":"Identifying meaningful drug response biomarkers from public pharmacogenomic datasets with biologically informed interpretable neural networks","display_name":"Identifying meaningful drug response biomarkers from public pharmacogenomic datasets with biologically informed interpretable neural networks","publication_year":2025,"publication_date":"2025-09-02","ids":{"openalex":"https://openalex.org/W4413944006","doi":"https://doi.org/10.1016/j.compbiolchem.2025.108669","pmid":"https://pubmed.ncbi.nlm.nih.gov/40914994"},"language":"en","primary_location":{"id":"doi:10.1016/j.compbiolchem.2025.108669","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.compbiolchem.2025.108669","pdf_url":null,"source":{"id":"https://openalex.org/S104924063","display_name":"Computational Biology and Chemistry","issn_l":"1476-9271","issn":["1476-9271","1476-928X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Biology and Chemistry","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112987235","display_name":"Maoxin Ran","orcid":null},"institutions":[{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Maoxin Ran","raw_affiliation_strings":["Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macao Special Administrative Region of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macao Special Administrative Region of China","institution_ids":["https://openalex.org/I204512498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103210132","display_name":"Shaolin Zhang","orcid":"https://orcid.org/0000-0002-1544-2552"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shao-Lin Zhang","raw_affiliation_strings":["School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Sciences, Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Chongqing University, Chongqing 401331, PR China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061680277","display_name":"Kin Yip Tam","orcid":"https://orcid.org/0000-0001-5507-8524"},"institutions":[{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Kin Yip Tam","raw_affiliation_strings":["Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macao Special Administrative Region of China. Electronic address: kintam@um.edu.mo"],"raw_orcid":"https://orcid.org/0000-0001-5507-8524","affiliations":[{"raw_affiliation_string":"Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macao Special Administrative Region of China. Electronic address: kintam@um.edu.mo","institution_ids":["https://openalex.org/I204512498"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3320,"currency":"USD","value_usd":3320},"apc_paid":null,"fwci":0.6844,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.76189294,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"120","issue":"Pt 1","first_page":"108669","last_page":"108669"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9958999752998352,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9958999752998352,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9944000244140625,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9941999912261963,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pharmacogenomics","display_name":"Pharmacogenomics","score":0.7760496139526367},{"id":"https://openalex.org/keywords/drug-response","display_name":"Drug response","score":0.6216965913772583},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45996007323265076},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4244660437107086},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4166285991668701},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4112457036972046},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3562023639678955},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.2816930413246155},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23852750658988953},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.1915925145149231},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.19141000509262085},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19009894132614136}],"concepts":[{"id":"https://openalex.org/C170734499","wikidata":"https://www.wikidata.org/wiki/Q1152227","display_name":"Pharmacogenomics","level":2,"score":0.7760496139526367},{"id":"https://openalex.org/C2994119904","wikidata":"https://www.wikidata.org/wiki/Q1251001","display_name":"Drug response","level":3,"score":0.6216965913772583},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45996007323265076},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4244660437107086},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4166285991668701},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4112457036972046},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3562023639678955},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.2816930413246155},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23852750658988953},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.1915925145149231},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.19141000509262085},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19009894132614136}],"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":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"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":"D010597","descriptor_name":"Pharmacogenetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010597","descriptor_name":"Pharmacogenetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010597","descriptor_name":"Pharmacogenetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019008","descriptor_name":"Drug Resistance, Neoplasm","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D019008","descriptor_name":"Drug Resistance, Neoplasm","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D019008","descriptor_name":"Drug Resistance, Neoplasm","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D045744","descriptor_name":"Cell Line, Tumor","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1016/j.compbiolchem.2025.108669","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.compbiolchem.2025.108669","pdf_url":null,"source":{"id":"https://openalex.org/S104924063","display_name":"Computational Biology and Chemistry","issn_l":"1476-9271","issn":["1476-9271","1476-928X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computational Biology and Chemistry","raw_type":"journal-article"},{"id":"pmid:40914994","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40914994","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":"Computational biology and chemistry","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1891430685","display_name":null,"funder_award_id":"0138/2022/A","funder_id":"https://openalex.org/F4320323893","funder_display_name":"Fundo para o Desenvolvimento das Ci\u00eancias e da Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320322841","display_name":"Universidade de Macau","ror":"https://ror.org/01r4q9n85"},{"id":"https://openalex.org/F4320323893","display_name":"Fundo para o Desenvolvimento das Ci\u00eancias e da Tecnologia","ror":"https://ror.org/05vna4324"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W1904060183","https://openalex.org/W2139132031","https://openalex.org/W2216946510","https://openalex.org/W2461427403","https://openalex.org/W2530508394","https://openalex.org/W2741508285","https://openalex.org/W2747965175","https://openalex.org/W2750972785","https://openalex.org/W2770828094","https://openalex.org/W2781759361","https://openalex.org/W2903961100","https://openalex.org/W2944727022","https://openalex.org/W2952216056","https://openalex.org/W2952285211","https://openalex.org/W2971879199","https://openalex.org/W2978256445","https://openalex.org/W2979930936","https://openalex.org/W2990714382","https://openalex.org/W3001475835","https://openalex.org/W3035604179","https://openalex.org/W3154648057","https://openalex.org/W3159354324","https://openalex.org/W3159857369","https://openalex.org/W3167603310","https://openalex.org/W3169321271","https://openalex.org/W3190604864","https://openalex.org/W3193677732","https://openalex.org/W3199772305","https://openalex.org/W3203034670","https://openalex.org/W4206221654","https://openalex.org/W4223622421","https://openalex.org/W4224240402","https://openalex.org/W4224990478","https://openalex.org/W4229376968","https://openalex.org/W4233060585","https://openalex.org/W4240976793","https://openalex.org/W4281569605","https://openalex.org/W4285288952","https://openalex.org/W4288726916","https://openalex.org/W4294168198","https://openalex.org/W4294541781","https://openalex.org/W4297964719","https://openalex.org/W4300862723","https://openalex.org/W4306403480","https://openalex.org/W4321783350","https://openalex.org/W4360851817","https://openalex.org/W4376983366","https://openalex.org/W4377819784","https://openalex.org/W4382317778","https://openalex.org/W4385224149","https://openalex.org/W4385707422","https://openalex.org/W4386387831","https://openalex.org/W4387728976","https://openalex.org/W4389856652","https://openalex.org/W4390621251","https://openalex.org/W4392298389","https://openalex.org/W4392348944","https://openalex.org/W4396523603","https://openalex.org/W4399387478","https://openalex.org/W4400663683","https://openalex.org/W4403479110","https://openalex.org/W4408149479","https://openalex.org/W4410717529"],"related_works":["https://openalex.org/W2494489566","https://openalex.org/W4231349869","https://openalex.org/W2896304141","https://openalex.org/W4239789534","https://openalex.org/W4387225326","https://openalex.org/W2019271482","https://openalex.org/W1537547840","https://openalex.org/W4392425672","https://openalex.org/W4411111155","https://openalex.org/W2563611238"],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}