{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T23:28:50Z","timestamp":1761780530235,"version":"build-2065373602"},"reference-count":68,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T00:00:00Z","timestamp":1760140800000},"content-version":"vor","delay-in-days":10,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100019920","name":"Naif Arab University for Security Sciences","doi-asserted-by":"publisher","award":["NAUSS-23-R18","NAUSS-23-R19"],"award-info":[{"award-number":["NAUSS-23-R18","NAUSS-23-R19"]}],"id":[{"id":"10.13039\/100019920","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Understanding the genetic basis of drug-induced toxicity is crucial for drug development. In-silico analysis of toxicogenomics datasets facilitates early detection of toxicity biomarkers. However, existing tools struggle with the complex interdependencies among hierarchically structured variables, leading to inaccurate biomarker identification. To address this limitation, we developed a Hierarchical Linear Model (HLM) and implemented it in the R package ToxAssay, offering extensive functionality for comprehensive toxicity assessment.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>ToxAssay outperforms existing methods by improving biomarker detection and computational efficiency. Applied to glutathione depletion-induced toxicity, it prioritized 71\u2009key genes and identified 26 core genes with high discriminative accuracy (AUC\u2009=\u20090.97) and strong cross-correlation (Pearson\u2019s r\u2009=\u20090.88) with external datasets. Additionally, our advance outcome pathway (AOP) analysis algorithm uncovered disease outcomes linked to glutathione depletion. These findings provide precise insights into the molecular mechanisms driving drug-induced toxicity.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>ToxAssay is available as an open-source R package at https:\/\/github.com\/Fun-Gene\/toxassay.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf561","type":"journal-article","created":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T12:17:47Z","timestamp":1760012267000},"source":"Crossref","is-referenced-by-count":0,"title":["ToxAssay: a hierarchical model-driven tool for advanced toxicogenomics biomarker discovery"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5468-6613","authenticated-orcid":false,"given":"Md Masud","family":"Rana","sequence":"first","affiliation":[{"name":"National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing, 100101,","place":["China"]},{"name":"University of Chinese Academy of Sciences , Beijing, 100049,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3883-3396","authenticated-orcid":false,"given":"Md Nurul Haque","family":"Mollah","sequence":"additional","affiliation":[{"name":"Bioinformatics Laboratory, Department of Statistics, University of Rajshahi , Rajshahi, 6205,","place":["Bangladesh"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohammed H","family":"Albujja","sequence":"additional","affiliation":[{"name":"Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences , Riyadh, Kingdom","place":["Saudi Arabia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sibte Syed","family":"Hadi","sequence":"additional","affiliation":[{"name":"Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences , Riyadh, Kingdom","place":["Saudi Arabia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9241-8161","authenticated-orcid":false,"given":"Fan","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Forensic Sciences, College of Criminal Justice, Naif Arab University for Security Sciences , Riyadh, Kingdom","place":["Saudi Arabia"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,10,11]]},"reference":[{"key":"2025102919272002300_btaf561-B1","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/nn.3648","article-title":"A solution to dependency: using multilevel analysis to accommodate nested data","volume":"17","author":"Aarts","year":"2014","journal-title":"Nat Neurosci."},{"key":"2025102919272002300_btaf561-B2","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1002\/hep.24493","article-title":"Aldo-keto reductase-7A protects liver cells and tissues from acetaminophen-induced oxidative stress and hepatotoxicity","volume":"54","author":"Ahmed","year":"2011","journal-title":"Hepatology"},{"key":"2025102919272002300_btaf561-B3","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1039\/C8MO00042E","article-title":"Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data","volume":"14","author":"Alexander-Dann","year":"2018","journal-title":"Mol Omics"},{"key":"2025102919272002300_btaf561-B4","doi-asserted-by":"crossref","first-page":"9290","DOI":"10.1007\/s11356-020-11250-9","article-title":"Flavonoid-rich fraction attenuates permethrin-induced toxicity by modulating ROS-mediated hepatic oxidative stress and mitochondrial dysfunction ex vivo and in vivo in rat","volume":"28","author":"Aoiadni","year":"2021","journal-title":"Environ Sci Pollut Res Int."},{"key":"2025102919272002300_btaf561-B5","doi-asserted-by":"crossref","first-page":"42054","DOI":"10.1038\/srep42054","article-title":"The NRF2 transcriptional target, OSGIN1, contributes to monomethyl fumarate-mediated cytoprotection in human astrocytes","volume":"7","author":"Brennan","year":"2017","journal-title":"Sci Rep."},{"key":"2025102919272002300_btaf561-B6","doi-asserted-by":"crossref","first-page":"104983","DOI":"10.1016\/j.isci.2022.104983","article-title":"Heme oxygenase-1 mitigates liver injury and fibrosis via modulation of LNX1\/Notch1 pathway in myeloid cells","volume":"25","author":"Canesin","year":"2022","journal-title":"iScience"},{"key":"2025102919272002300_btaf561-B7","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1016\/j.drudis.2016.02.015","article-title":"DILIrank: the largest reference drug list ranked by the risk for developing drug-induced liver injury in humans","volume":"21","author":"Chen","year":"2016","journal-title":"Drug Discov Today."},{"key":"2025102919272002300_btaf561-B8","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1186\/s12864-015-1970-x","article-title":"Dynamic association rules for gene expression data analysis","volume":"16","author":"Chen","year":"2015","journal-title":"BMC Genomics"},{"key":"2025102919272002300_btaf561-B9","doi-asserted-by":"crossref","first-page":"066111","DOI":"10.1103\/PhysRevE.70.066111","article-title":"Finding community structure in very large networks","volume":"70","author":"Clauset","year":"2004","journal-title":"Phys Rev E Stat Nonlin Soft Matter Phys."},{"key":"2025102919272002300_btaf561-B10","doi-asserted-by":"crossref","first-page":"D691","DOI":"10.1093\/nar\/gkq1018","article-title":"Reactome: a database of reactions, pathways and biological processes","volume":"39","author":"Croft","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2025102919272002300_btaf561-B11","doi-asserted-by":"crossref","first-page":"D1257","DOI":"10.1093\/nar\/gkac833","article-title":"Comparative toxicogenomics database (CTD): update 2023","volume":"51","author":"Davis","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2025102919272002300_btaf561-B12","doi-asserted-by":"crossref","DOI":"10.3390\/toxics9110292","article-title":"Pharmacogenetics and forensic toxicology: a new step towards a multidisciplinary approach","volume":"9","author":"Di Nunno","year":"2021","journal-title":"Toxics"},{"key":"2025102919272002300_btaf561-B13","doi-asserted-by":"crossref","first-page":"1019","DOI":"10.1016\/S0006-2952(02)01172-3","article-title":"Cellular glutathione and thiols metabolism","volume":"64","author":"Dickinson","year":"2002","journal-title":"Biochem Pharmacol."},{"key":"2025102919272002300_btaf561-B14","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/d41573-019-00074-z","article-title":"Trends in clinical success rates and therapeutic focus","volume":"18","author":"Dowden","year":"2019","journal-title":"Nat Rev Drug Discov."},{"key":"2025102919272002300_btaf561-B15","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.mrfmmm.2007.06.010","article-title":"Prediction of a carcinogenic potential of rat hepatocarcinogens using toxicogenomics analysis of short-term in vivo studies","volume":"637","author":"Ellinger-Ziegelbauer","year":"2008","journal-title":"Mutat Res."},{"key":"2025102919272002300_btaf561-B16","doi-asserted-by":"crossref","first-page":"1429","DOI":"10.1002\/etc.3770","article-title":"Practical approaches to adverse outcome pathway development and weight-of-evidence evaluation as illustrated by ecotoxicological case studies","volume":"36","author":"Fay","year":"2017","journal-title":"Environ Toxicol Chem."},{"key":"2025102919272002300_btaf561-B17","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.mam.2008.08.006","article-title":"Glutathione: overview of its protective roles, measurement, and biosynthesis","volume":"30","author":"Forman","year":"2009","journal-title":"Mol Aspects Med."},{"key":"2025102919272002300_btaf561-B18","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.2217\/14622416.7.7.1025","article-title":"Toxicogenomics in drug discovery and development: mechanistic analysis of compound\/class-dependent effects using the DrugMatrix database","volume":"7","author":"Ganter","year":"2006","journal-title":"Pharmacogenomics"},{"key":"2025102919272002300_btaf561-B19","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.taap.2010.06.015","article-title":"Mechanism-based biomarker gene sets for glutathione depletion-related hepatotoxicity in rats","volume":"247","author":"Gao","year":"2010","journal-title":"Toxicol Appl Pharmacol."},{"key":"2025102919272002300_btaf561-B20","doi-asserted-by":"crossref","first-page":"7821","DOI":"10.1073\/pnas.122653799","article-title":"Community structure in social and biological networks","volume":"99","author":"Girvan","year":"2002","journal-title":"Proc Natl Acad Sci USA."},{"key":"2025102919272002300_btaf561-B21","doi-asserted-by":"crossref","first-page":"794547","DOI":"10.3389\/fbinf.2021.794547","article-title":"Extending association rule mining to microbiome pattern analysis: tools and guidelines to support real applications","volume":"1","author":"Giulia","year":"2021","journal-title":"Front Bioinform."},{"key":"2025102919272002300_btaf561-B22","doi-asserted-by":"crossref","first-page":"i451","DOI":"10.1093\/bioinformatics\/bts389","article-title":"EnrichNet: network-based gene set enrichment analysis","volume":"28","author":"Glaab","year":"2012","journal-title":"Bioinformatics"},{"key":"2025102919272002300_btaf561-B23","doi-asserted-by":"crossref","first-page":"8685","DOI":"10.1073\/pnas.0701361104","article-title":"The human disease network","volume":"104","author":"Goh","year":"2007","journal-title":"Proc Natl Acad Sci USA."},{"key":"2025102919272002300_btaf561-B24","doi-asserted-by":"crossref","first-page":"D258","DOI":"10.1093\/nar\/gkh036","article-title":"The gene ontology (GO) database and informatics resource","volume":"32","author":"Harris","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2025102919272002300_btaf561-B25","doi-asserted-by":"crossref","first-page":"516","DOI":"10.3389\/fgene.2018.00516","article-title":"Robust co-clustering to discover toxicogenomic biomarkers and their regulatory doses of chemical compounds using logistic probabilistic hidden variable model","volume":"9","author":"Hasan","year":"2018","journal-title":"Front Genet."},{"key":"2025102919272002300_btaf561-B26","doi-asserted-by":"crossref","first-page":"41176","DOI":"10.1038\/srep41176","article-title":"Identification of consensus biomarkers for predicting non-genotoxic hepatocarcinogens","volume":"7","author":"Huang","year":"2017","journal-title":"Sci Rep."},{"key":"2025102919272002300_btaf561-B27","doi-asserted-by":"crossref","first-page":"D921","DOI":"10.1093\/nar\/gku955","article-title":"Open TG-GATEs: a large-scale toxicogenomics database","volume":"43","author":"Igarashi","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2025102919272002300_btaf561-B28","doi-asserted-by":"crossref","first-page":"D353","DOI":"10.1093\/nar\/gkw1092","article-title":"KEGG: new perspectives on genomes, pathways, diseases and drugs","volume":"45","author":"Kanehisa","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2025102919272002300_btaf561-B29","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1016\/j.drudis.2013.11.001","article-title":"Current status and future prospects of toxicogenomics in drug discovery","volume":"19","author":"Khan","year":"2014","journal-title":"Drug Discov Today"},{"key":"2025102919272002300_btaf561-B30","doi-asserted-by":"crossref","first-page":"1465","DOI":"10.1016\/j.bcp.2004.05.053","article-title":"Evaluation of glutathione deficiency in rat livers by microarray analysis","volume":"68","author":"Kiyosawa","year":"2004","journal-title":"Biochem Pharmacol."},{"key":"2025102919272002300_btaf561-B31","doi-asserted-by":"crossref","first-page":"469","DOI":"10.2131\/jts.32.469","article-title":"Identification of glutathione depletion-responsive genes using phorone-treated rat liver","volume":"32","author":"Kiyosawa","year":"2007","journal-title":"J Toxicol Sci."},{"key":"2025102919272002300_btaf561-B32","doi-asserted-by":"crossref","first-page":"16116","DOI":"10.1074\/jbc.M110.116210","article-title":"Rapid activation of glutamate cysteine ligase following oxidative stress","volume":"285","author":"Krejsa","year":"2010","journal-title":"J Biol Chem."},{"key":"2025102919272002300_btaf561-B33","doi-asserted-by":"crossref","first-page":"e1010061","DOI":"10.1371\/journal.pcbi.1010061","article-title":"Analyzing nested experimental designs-A user-friendly resampling method to determine experimental significance","volume":"18","author":"Kulkarni","year":"2022","journal-title":"PLoS Comput Biol."},{"key":"2025102919272002300_btaf561-B34","doi-asserted-by":"crossref","first-page":"D964","DOI":"10.1093\/nar\/gkw1077","article-title":"CEBS: a comprehensive annotated database of toxicological data","volume":"45","author":"Lea","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2025102919272002300_btaf561-B35","doi-asserted-by":"crossref","first-page":"1768","DOI":"10.1002\/hep.30467","article-title":"Induction of oxidative stress through inhibition of thioredoxin reductase 1 is an effective therapeutic approach for hepatocellular carcinoma","volume":"69","author":"Lee","year":"2019","journal-title":"Hepatology"},{"key":"2025102919272002300_btaf561-B36","doi-asserted-by":"crossref","DOI":"10.3390\/genes8100246","article-title":"Pathway enrichment analysis with networks","volume":"8","author":"Liu","year":"2017","journal-title":"Genes (Basel)"},{"key":"2025102919272002300_btaf561-B37","doi-asserted-by":"crossref","first-page":"3143","DOI":"10.1016\/j.bbagen.2012.09.008","article-title":"Glutathione synthesis","volume":"1830","author":"Lu","year":"2013","journal-title":"Biochim Biophys Acta"},{"key":"2025102919272002300_btaf561-B38","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1016\/j.livres.2020.05.003","article-title":"Dysregulation of glutathione synthesis in liver disease","volume":"4","author":"Lu","year":"2020","journal-title":"Liver Res."},{"key":"2025102919272002300_btaf561-B39","doi-asserted-by":"crossref","first-page":"274","DOI":"10.1007\/s00357-014-9161-z","article-title":"Ward\u2019s hierarchical agglomerative clustering method: which algorithms implement ward\u2019s criterion?","volume":"31","author":"Murtagh","year":"2014","journal-title":"J Classif."},{"key":"2025102919272002300_btaf561-B40","doi-asserted-by":"crossref","first-page":"W455","DOI":"10.1093\/nar\/gkaa390","article-title":"ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets","volume":"48","author":"Nair","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2025102919272002300_btaf561-B41","doi-asserted-by":"crossref","first-page":"3080","DOI":"10.1093\/bioinformatics\/btt531","article-title":"Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform","volume":"29","author":"Nystr\u00f6m-Persson","year":"2013","journal-title":"Bioinformatics"},{"key":"2025102919272002300_btaf561-B42","doi-asserted-by":"crossref","first-page":"1390","DOI":"10.1038\/s41598-017-01500-1","article-title":"Interactive toxicogenomics: gene set discovery, clustering and analysis in toxygates","volume":"7","author":"Nystr\u00f6m-Persson","year":"2017","journal-title":"Sci Rep."},{"key":"2025102919272002300_btaf561-B43","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1016\/j.tox.2016.04.004","article-title":"An integrative data mining approach to identifying adverse outcome pathway signatures","volume":"350-352","author":"Oki","year":"2016","journal-title":"Toxicology"},{"key":"2025102919272002300_btaf561-B44","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1038\/s41573-022-00633-x","article-title":"The evolving role of investigative toxicology in the pharmaceutical industry","volume":"22","author":"Pognan","year":"2023","journal-title":"Nat Rev Drug Discov."},{"key":"2025102919272002300_btaf561-B45","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1007\/11569596_31","volume-title":"Computer and Information Sciences-ISCIS 2005: 20th International Symposium","author":"Pons","year":"2005"},{"key":"2025102919272002300_btaf561-B46","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1080\/10715769800300601","article-title":"Oxidative DNA damage in vivo: relationship to age, plasma antioxidants, drug metabolism, glutathione-S-transferase activity and urinary creatinine excretion","volume":"29","author":"Poulsen","year":"1998","journal-title":"Free Radic Res."},{"key":"2025102919272002300_btaf561-B47","article-title":"Association rule mining for genome-wide association studies through gibbs sampling","author":"Qian","year":"2023","journal-title":"Int J Data Sci Anal."},{"key":"2025102919272002300_btaf561-B48","doi-asserted-by":"crossref","first-page":"57","DOI":"10.3329\/jbs.v25i0.37499","article-title":"A novel computational approach for toxicogenomics biomarker discovery in drug development pipeline","volume":"25","author":"Rana","year":"2018","journal-title":"J Bio-Sci"},{"key":"2025102919272002300_btaf561-B49","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1053\/jhep.2003.50331","article-title":"Cotransport of reduced glutathione with bile salts by MRP4 (ABCC4) localized to the basolateral hepatocyte membrane","volume":"38","author":"Rius","year":"2003","journal-title":"Hepatology"},{"key":"2025102919272002300_btaf561-B50","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/s41597-023-02321-w","article-title":"A curated gene and biological system annotation of adverse outcome pathways related to human health","volume":"10","author":"Saarim\u00e4ki","year":"2023","journal-title":"Sci Data"},{"key":"2025102919272002300_btaf561-B51","doi-asserted-by":"crossref","first-page":"101448","DOI":"10.1016\/j.jbc.2021.101448","article-title":"USP10 inhibits the dopamine-induced reactive oxygen species-dependent apoptosis of neuronal cells by stimulating the antioxidant Nrf2 activity","volume":"298","author":"Sango","year":"2022","journal-title":"J Biol Chem."},{"key":"2025102919272002300_btaf561-B52","doi-asserted-by":"crossref","first-page":"225","DOI":"10.2131\/jts.44.225","article-title":"Safety biomarker applications in drug development","volume":"44","author":"Schomaker","year":"2019","journal-title":"J Toxicol Sci."},{"key":"2025102919272002300_btaf561-B53","doi-asserted-by":"crossref","first-page":"D661","DOI":"10.1093\/nar\/gkx1064","article-title":"WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research","volume":"46","author":"Slenter","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2025102919272002300_btaf561-B54","doi-asserted-by":"crossref","first-page":"2759","DOI":"10.1007\/s00204-019-02551-1","article-title":"Development and analysis of an adverse outcome pathway network for human neurotoxicity","volume":"93","author":"Spinu","year":"2019","journal-title":"Arch Toxicol."},{"key":"2025102919272002300_btaf561-B55","doi-asserted-by":"crossref","first-page":"1437","DOI":"10.1016\/j.cell.2017.10.049","article-title":"A next generation connectivity map: l 1000 platform and the first 1,000,000 profiles","volume":"171","author":"Subramanian","year":"2017","journal-title":"Cell"},{"key":"2025102919272002300_btaf561-B56","doi-asserted-by":"crossref","first-page":"3049","DOI":"10.1016\/j.apsb.2022.02.002","article-title":"Why 90% of clinical drug development fails and how to improve it?","volume":"12","author":"Sun","year":"2022","journal-title":"Acta Pharm Sin B."},{"key":"2025102919272002300_btaf561-B57","doi-asserted-by":"crossref","first-page":"D605","DOI":"10.1093\/nar\/gkaa1074","article-title":"The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene\/measurement sets","volume":"49","author":"Szklarczyk","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2025102919272002300_btaf561-B58","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1089\/crispr.2020.0116","article-title":"RNA binding proteins as regulators of oxidative stress identified by a targeted CRISPR-Cas9 single guide RNA library","volume":"4","author":"Turner","year":"2021","journal-title":"Crispr J."},{"key":"2025102919272002300_btaf561-B59","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.tox.2008.05.013","article-title":"A toxicogenomics approach for early assessment of potential non-genotoxic hepatocarcinogenicity of chemicals in rats","volume":"250","author":"Uehara","year":"2008","journal-title":"Toxicology"},{"key":"2025102919272002300_btaf561-B60","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1002\/mnfr.200900169","article-title":"The japanese toxicogenomics project: application of toxicogenomics","volume":"54","author":"Uehara","year":"2010","journal-title":"Mol Nutr Food Res."},{"key":"2025102919272002300_btaf561-B61","article-title":"Changes in glutathione content in liver diseases: an update","volume":"10","author":"Vairetti","year":"2021","journal-title":"Antioxidants (Basel)"},{"key":"2025102919272002300_btaf561-B62","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1093\/bioinformatics\/btm087","article-title":"A new method to measure the semantic similarity of GO terms","volume":"23","author":"Wang","year":"2007","journal-title":"Bioinformatics"},{"key":"2025102919272002300_btaf561-B63","doi-asserted-by":"crossref","first-page":"e1361","DOI":"10.1002\/wfs2.1361","article-title":"Pharmacogenetics and the postmortem molecular autopsy","volume":"2","author":"Wendt","year":"2020","journal-title":"WIRES Forensic Sci."},{"key":"2025102919272002300_btaf561-B64","doi-asserted-by":"crossref","first-page":"1183824","DOI":"10.3389\/ftox.2023.1183824","article-title":"Development of a data-driven approach to adverse outcome pathway network generation: a case study on the EATS-modalities","volume":"5","author":"Wiklund","year":"2023","journal-title":"Front Toxicol."},{"key":"2025102919272002300_btaf561-B65","doi-asserted-by":"crossref","first-page":"D1432","DOI":"10.1093\/nar\/gkac1074","article-title":"TOXRIC: a comprehensive database of toxicological data and benchmarks","volume":"51","author":"Wu","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2025102919272002300_btaf561-B66","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1007\/s00204-010-0632-7","article-title":"Hepatic transcriptome and proteome responses against diethyl maleate-induced glutathione depletion in the rat","volume":"85","author":"Yamauchi","year":"2011","journal-title":"Arch Toxicol."},{"key":"2025102919272002300_btaf561-B67","doi-asserted-by":"crossref","first-page":"3673","DOI":"10.1038\/s41467-023-39401-9","article-title":"SLC7A11 expression level dictates differential responses to oxidative stress in cancer cells","volume":"14","author":"Yan","year":"2023","journal-title":"Nat Commun."},{"key":"2025102919272002300_btaf561-B68","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.mam.2008.08.003","article-title":"Glutathione in liver diseases and hepatotoxicity","volume":"30","author":"Yuan","year":"2009","journal-title":"Mol Aspects Med."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaf561\/64639096\/btaf561.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/10\/btaf561\/64639096\/btaf561.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/41\/10\/btaf561\/64639096\/btaf561.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T23:27:35Z","timestamp":1761780455000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btaf561\/8283540"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2025,10]]},"references-count":68,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2025,10,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaf561","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2025,10]]},"published":{"date-parts":[[2025,10]]},"article-number":"btaf561"}}