Liver Toxicity Knowledge Base Publications

 

Year	Title	Authors	Full Citation
2024	Computational Models for Predicting Liver Toxicity in the Deep Learning Era.	Mostafa F. and Chen M.	Computational Models for Predicting Liver Toxicity in the Deep Learning Era.  Mostafa F. and Chen M.  Front Toxicol. 2024, 5:1340860. doi: 10.3389/ftox.2023.1340860.
2023	In Silico Modeling-based New Alternative Methods to Predict Drug and Herb-induced Liver Injury: A Review.	Shin H.K., Huang R., and Chen M.	In Silico Modeling-based New Alternative Methods to Predict Drug and Herb-induced Liver Injury: A Review. Shin H.K., Huang R., and Chen M.  Food Chem Toxicol. 2023, 179:113948. doi: 10.1016/j.fct.2023.113948.
2023	Single-cell RNA-sequencing and Subcellular Spatial Transcriptomics Facilitate the Translation of Liver Microphysiological Systems for Regulatory Application.	Li D., Fang Z., Shi Q., Zhang N., Gong B., Tong W., Coskun A.F., and Xu J.	Single-cell RNA-sequencing and Subcellular Spatial Transcriptomics Facilitate the Translation of Liver Microphysiological Systems for Regulatory Application.  Li D., Fang Z., Shi Q., Zhang N., Gong B., Tong W., Coskun A.F., and Xu J.  J Pharm Anal. 2023, 13(7):691-693. doi: 10.1016/j.jpha.2023.06.013.
2022	Whole Exome Sequencing Reveals Genetic Variants in HLA Class II Genes Associated With Transplant-free Survival of Indeterminate Acute Liver Failure.	Liao T.J., Pan B., Hong H., Hayashi P., Rule J.A., Ganger D., Lee W.M., Rakela J., and Chen M.	Whole Exome Sequencing Reveals Genetic Variants in HLA Class II Genes Associated With Transplant-free Survival of Indeterminate Acute Liver Failure.  Liao T.J., Pan B., Hong H., Hayashi P., Rule J.A., Ganger D., Lee W.M., Rakela J., and Chen M. Clin Transl Gastroenterol. 2022, 13(7):e00502.
2022	Integrative Approaches for Studying the Role of Noncoding RNAs in Influencing Drug Efficacy and Toxicity.	Li D., Chen M., Hong H., Tong W., and Ning B.	Integrative Approaches for Studying the Role of Noncoding RNAs in Influencing Drug Efficacy and Toxicity. Li D., Chen M., Hong H., Tong W. and Ning B. Expert Opin Drug Metab Toxicol. 2022, 18(2):151-163. doi: 10.1080/17425255.2022.2054802.
2021	BERT-Based Natural Language Processing of Drug Labeling Documents: A Case Study for Classifying Drug-Induced Liver Injury Risk.	Wu Y., Liu Z., Wu L., Chen M., and Tong W.	BERT-Based Natural Language Processing of Drug Labeling Documents: A Case Study for Classifying Drug-Induced Liver Injury Risk. Wu Y., Liu Z., Wu L., Chen M., and Tong W. Front Artif Intell. 2021, 4:729834.
2021	Elevated Bilirubin, Alkaline Phosphatase at Onset, and Drug Metabolism Are Associated With Prolonged Recovery From DILI.	Ashby K., Zhuang W., González-Jimenez A., Alvarez-Alvarez I., Lucena M.I., Andrade R.J., Aithal G.P., Suzuki A., and Chen M.	Elevated Bilirubin, Alkaline Phosphatase at Onset, and Drug Metabolism Are Associated With Prolonged Recovery From DILI. Ashby K., Zhuang W., González-Jimenez A., Alvarez-Alvarez I., Lucena M.I., Andrade R.J., Aithal G.P., Suzuki A., and Chen M. J Hepatol. 2021, 75(2):333-341.
2021	Machine Learning to Identify Interaction of Single-Nucleotide Polymorphisms as a Risk Factor for Chronic Drug-Induced Liver Injury.	Moore R., Ashby K., Liao T.J., and Chen M.	Machine Learning to Identify Interaction of Single-Nucleotide Polymorphisms as a Risk Factor for Chronic Drug-Induced Liver Injury. Moore R., Ashby K., Liao T.J., and Chen M. Int J Environ Res Public Health. 2021, 18(20):10603.
2021	A Systematic Comparison of Hepatobiliary Adverse Drug Reactions in FDA and EMA Drug Labeling Reveals Discrepancies.	Wu Y., Xiao W., Tong W., Borlak J., and Chen M.	A Systematic Comparison of Hepatobiliary Adverse Drug Reactions in FDA and EMA Drug Labeling Reveals Discrepancies. Wu Y., Xiao W., Tong W., Borlak J., and Chen M. Drug Discov Today. 2021, S1359-6446(21)00403-7.
2021	Drug Properties and Host Factors Contribute to Biochemical Presentation of Drug-Induced Liver Injury: A Prediction Model From a Machine Learning Approach.	Gonzalez-Jimenez A., Suzuki A., Chen M., Ashby K., Alvarez-Alvarez I., Andrade R.J., and Lucena M.I.	Drug Properties and Host Factors Contribute to Biochemical Presentation of Drug-Induced Liver Injury: A Prediction Model From a Machine Learning Approach. Gonzalez-Jimenez A., Suzuki A., Chen M., Ashby K., Alvarez-Alvarez I., Andrade R.J., Lucena M.I. Arch Toxicol. 2021, 95(5):1793-1803.
2021	Performance of Preclinical Models in Predicting Drug-Induced Liver Injury in Humans: A Systematic Review.	Dirven H., Vist G.E., Bandhakavi S., Mehta J., Fitch S.E., Pound P., Ram R., Kincaid B., Leenaars C.H.C., Chen M., Wright R.A., and Tsaioun K.	Performance of Preclinical Models in Predicting Drug-Induced Liver Injury in Humans: A Systematic Review. Dirven H., Vist G.E., Bandhakavi S., Mehta J., Fitch S.E., Pound P., Ram R., Kincaid B., Leenaars C.H.C., Chen M., Wright R.A., and Tsaioun K. Sci Rep. 2021, 11(1):6403.
2021	Machine Learning for Predicting Risk of Drug-Induced Autoimmune Diseases by Structural Alerts and Daily Dose.	Wu Y., Zhu J., Fu P., Tong W., Hong H., and Chen M.	Machine Learning for Predicting Risk of Drug-Induced Autoimmune Diseases by Structural Alerts and Daily Dose. Wu Y., Zhu J., Fu P., Tong W., Hong H., and Chen M. Int J Environ Res Public Health. 2021, 18(13):7139.
2020	Cancer Genomics Predicts Disease Relapse and Therapeutic Response to Neoadjuvant Chemotherapy of Hormone Sensitive Breast Cancers.	Zhu J., Muskhelishvili L., Tong W., Borlak J., and Chen M.	Cancer Genomics Predicts Disease Relapse and Therapeutic Response to Neoadjuvant Chemotherapy of Hormone Sensitive Breast Cancers. Zhu J., Muskhelishvili L., Tong W., Borlak J., and Chen M. Scientific Report. 2020, 10, 1-12.
2020	Integrating Adverse Outcome Pathways (AOPs) and High Throughput In Vitro Assays for Better Risk Evaluations, a Study with Drug-Induced Liver Injury (DILI).	Khadka K., Chen M., Liu Z., Tong W., and Wang D.	Integrating Adverse Outcome Pathways (AOPs) and High Throughput In Vitro Assays for Better Risk Evaluations, a Study with Drug-Induced Liver Injury (DILI). Khadka K., Chen M., Liu Z., Tong W., and Wang D. ALTEX. 2020, 37 (2), 187-196.
2020	Deep Learning for Toxicity and Disease Prediction.	Gong P., Zhang C., and Chen M.	Deep Learning for Toxicity and Disease Prediction. Gong P., Zhang C., and Chen M. Frontiers in Genetics. 2020, 11, 175-176.
2020	The Landscape of Hepatobiliary Adverse Reactions Across 53 Herbal and Dietary Supplements Reveals Immune-Mediated Injury as a Common Cause of Hepatitis.	Zhu J., Chen M., Borlak J., and Tong W.	The Landscape of Hepatobiliary Adverse Reactions Across 53 Herbal and Dietary Supplements Reveals Immune-Mediated Injury as a Common Cause of Hepatitis. Zhu J., Chen M., Borlak J., and Tong W. Archives of Toxicology. 2020, 94 (1), 273-293.
2020	DeepDILI: Deep Learning-Powered Drug-Induced Liver Injury Prediction Using Model-Level Representation.	Li T., Tong W., Roberts R., Liu Z., and Thakkar S.	DeepDILI: Deep Learning-Powered Drug-Induced Liver Injury Prediction Using Model-Level Representation. Li T., Tong W., Roberts R., Liu Z., and Thakkar S. Chemical Research in Toxicology. 2020, 34 (2), 550-565.
2020	Development of a Battery of In Silico Prediction Tools for Drug-Induced Liver Injury from the Vantage Point of Translational Safety Assessment.	Rathman J., Yang C., Ribeiro J.V., Mostrag A., Thakkar S., Tong W., Hobocienski B., Sacher O., Magdziarz T., and Bienfait B.	Development of a Battery of In Silico Prediction Tools for Drug-Induced Liver Injury from the Vantage Point of Translational Safety Assessment. Rathman J., Yang C., Ribeiro J.V., Mostrag A., Thakkar S., Tong W., Hobocienski B., Sacher O., Magdziarz T., and Bienfait B.  Chemical Research in Toxicology. 2020, 34 (2), 601-615.
2020	Deep Learning on High-Throughput Transcriptomics to Predict Drug-Induced Liver Injury.	Li T., Tong W., Roberts R., Liu Z., and Thakkar S.	Deep Learning on High-Throughput Transcriptomics to Predict Drug-Induced Liver Injury. Li T., Tong W., Roberts R., Liu Z., and Thakkar S. Front Bioeng Biotechnol. 2020, 27;8:562677.
2020	Drug-Induced Liver Injury Severity and Toxicity (DILIst): Binary Classification of 1279 Drugs by Human Hepatotoxicity.	Thakkar S., Li T., Liu Z., Wu L., Roberts R., and Tong W.	Drug-Induced Liver Injury Severity and Toxicity (DILIst): Binary Classification of 1279 Drugs by Human Hepatotoxicity. Thakkar S., Li T., Liu Z., Wu L., Roberts R., and Tong W. Drug Discov Today. 2020, 25(1):201-208.
2019	The Influence of Drug Properties and Host Factors on Delayed Onset of Symptoms in Drug‐Induced Liver Injury.	Gonzalez-Jimenez A., McEuen K., Chen M., Suzuki A., Robles-Diaz M., Medina‐Caliz I., Bessone F., Hernandez N., Arrese M., Parana P., Lucena M., Stephens C., and Andrade R.	The Influence of Drug Properties and Host Factors on Delayed Onset of Symptoms in Drug‐Induced Liver Injury. Gonzalez-Jimenez A., McEuen K., Chen M., Suzuki A., Robles-Diaz M., Medina‐Caliz I., Bessone F., Hernandez N., Arrese M., Parana P., Lucena M., Stephens C., and Andrade R. Liver International. 2019, 39(2), 401-410.
2018	Drug-Induced Liver Toxicity.	Chen M. and Will Y. (Ed)	Drug-Induced Liver Toxicity. Chen M. and Will Y. (Ed) Humana Press. 2018.
2018	A Review on Machine Learning Methods for In Silico Toxicity Prediction.	Idakwo G., Luttrell J., Chen M., Hong H., Zhou Z., Gong P., and Zhang C.	A Review on Machine Learning Methods for In Silico Toxicity Prediction. Idakwo G., Luttrell J., Chen M., Hong H., Zhou Z., Gong P., and Zhang C. Journal of Environmental Science and Health, Part C. 2018, 36(4),169-191.
2018	Target-Specific Toxicity Knowledgebase (TsTKb): A Novel Toolkit for In Silico Predictive Toxicology.	Li Y., Idakwo G., Thangapandian S., Chen M., Hong H., Zhang C., and Gong P.	Target-Specific Toxicity Knowledgebase (TsTKb): A Novel Toolkit for In Silico Predictive Toxicology. Li Y., Idakwo G., Thangapandian S., Chen M., Hong H., Zhang C., and Gong P. Journal of Environmental Science and Health, Part C. 2018, 36(4):219-236.
2018	Pediatric Intestinal Failure–Associated Liver Disease: Challenges in Identifying Clinically Relevant Biomarkers.	Gura K., Mulberg A., Mitchell P., Yap J., Kim C., Chen M., Potemkin A., and Puder M.	Pediatric Intestinal Failure–Associated Liver Disease: Challenges in Identifying Clinically Relevant Biomarkers. Gura K., Mulberg A., Mitchell P., Yap J., Kim C., Chen M., Potemkin A., and Puder M. Journal of Parenteral and Enteral Nutrition, 2018. 42(2),455-462.
2018	The Development of a Database for Herbal and Dietary Supplement Induced Liver Toxicity.	Zhu J., Seo J., Wang S., Ashby K., Ballard R., Yu D., Ning B., Agarwal R., Borlak J., Tong W., and Chen M.	The Development of a Database for Herbal and Dietary Supplement Induced Liver Toxicity. Zhu J., Seo J., Wang S., Ashby K., Ballard R., Yu D., Ning B., Agarwal R., Borlak J., Tong W., and Chen M. International Journal of Molecular Sciences. 2018, 19 (10), 2955.
2018	Review Article: Therapeutic Bile Acids and the Risks for Hepatotoxicity.	McEuen A., Navarro Almario E., Borlak J., Tong W., Mehta R., and Chen M.	Review Article: Therapeutic Bile Acids and the Risks for Hepatotoxicity. McEuen A., Navarro Almario E., Borlak J., Tong W., Mehta R., and Chen M. Alimentary Pharmacology & Therapeutics. 2018, 47(12) 1623-1638.
2018	The Liver Toxicity Knowledge Base (LTKB) and Drug-Induced Liver Injury (DILI) Classification for Assessment of Human Liver Injury.	Thakkar S., Chen M., Fang H., Liu Z., Roberts R., and Tong W.	The Liver Toxicity Knowledge Base (LTKB) and Drug-Induced Liver Injury (DILI) Classification for Assessment of Human Liver Injury. Thakkar S., Chen M., Fang H., Liu Z., Roberts R., and Tong W.  Expert Review of Gastroenterology & Gepatology. 2018, 12 (1), 31-38.
2017	Development of Decision Forest Models for Prediction of Drug-Induced Liver Injury in Humans Using a Large Set of FDA-approved Drugs.	Hong H., Thakkar S., Chen M., and Tong W.	Development of Decision Forest Models for Prediction of Drug-Induced Liver Injury in Humans Using a Large Set of FDA-approved Drugs. Hong H., Thakkar S., Chen M., and Tong W.  Scientific Report. 2017, 7(1), 17311.
2017	Integrating Drug’s Mode of Action into Quantitative Structure–Activity Relationships for Improved Prediction of Drug-Induced Liver Injury.	Wu L., Liu Z., Auerbach S., Huang R., Chen M., McEuen K., Xu J., Fang H., and Tong W.	Integrating Drug’s Mode of Action into Quantitative Structure–Activity Relationships for Improved Prediction of Drug-Induced Liver Injury.  Wu L., Liu Z., Auerbach S., Huang R., Chen M., McEuen K., Xu J., Fang H., and Tong W.  Journal of Chemical Information and Modeling. 2017, 57 (4), 1000-1006.
2017	Drug-Induced Liver Injury	Almario E., Borlak J., Suzuki A., and Chen M.	Drug-Induced Liver Injury. Almario E., Borlak J., Suzuki A., and Chen M. BioMed Research International. 2017: 2461694.
2017	Associations of Drug Lipophilicity and Extent of Metabolism with Drug-Induced Liver Injury.	McEuen K., Borlak J., Tong W., Chen M.	Associations of Drug Lipophilicity and Extent of Metabolism with Drug-Induced Liver Injury. McEuen K., Borlak J., Tong W., Chen M.  International Journal of Molecular Sciences. 2017, 18 (7), 1335.
2017	Direct-Acting Antivirals for Chronic Hepatitis C: Can Drug Properties Signal Potential for Liver Injury?	Mishra P. and Chen M.	Direct-Acting Antivirals for Chronic Hepatitis C: Can Drug Properties Signal Potential for Liver Injury? Mishra P. and Chen M. Gastroenterology. 152(6), 1270–1274.
2017	In Vitro to In Vivo Extrapolation for Drug-Induced Liver Injury Using a Pair Ranking Method.	Liu Z., Fang H., Borlak J., Roberts R., and Tong W.	In Vitro to In Vivo Extrapolation for Drug-Induced Liver Injury Using a Pair Ranking Method. Liu Z., Fang H., Borlak J., Roberts R., and Tong W.  ALTEX. 2017, 34(3):399-407.
2016	A Model to Predict Severity of Drug-Induced Liver Injury in Humans.	Chen M., Borlak J., and Tong W.	A Model to Predict Severity of Drug-Induced Liver Injury in Humans. Chen M., Borlak J., and Tong W.   Hepatology. 2016, 64 (3), 931-940.
2016	Key Challenges and Opportunities Associated with the Use of In Vitro Models to Detect Human DILI: Integrated Risk Assessment and Mitigation Plans.	Atienzar F., Blomme E.A., Chen M., Hewitt M., Kenna G., Labbe G., et al.	Key Challenges and Opportunities Associated with the Use of In Vitro Models to Detect Human DILI: Integrated Risk Assessment and Mitigation Plans. Atienzar F., Blomme E.A., Chen M., Hewitt M., Kenna G., Labbe G., et al. BioMed Research International. 2016, 2016:9737920.
2016	DILIrank — The Largest Reference Drug List Ranked by the Risk for Developing Drug-Induced Liver Injury in Humans.	Chen M., Suzuki A., Shraddha T., Yu K., Hu C., and Tong W.	DILIrank — The Largest Reference Drug List Ranked by the Risk for Developing Drug-Induced Liver Injury in Humans. Chen M., Suzuki A., Shraddha T., Yu K., Hu C., and Tong W.  Drug Discov Today. 2016, 21(4):648-653.
2016	Mechanistically Linked Serum miRNAs Distinguish Between Drug Induced and Fatty Liver Disease of Different Grades.	Liu Z., Wang Y., Borlak J., and Tong W.	Mechanistically Linked Serum miRNAs Distinguish Between Drug Induced and Fatty Liver Disease of Different Grades. Liu Z., Wang Y., Borlak J., and Tong W.  Sci Rep. 2016, 6:23709.
2015	NETBAGs: A Network-Based Clustering Approach with Gene Signatures for Cancer Subtyping Analysis.	Wu L., Liu Z., Xu J., Chen M., Fang H., Tong W., and Xiao W.	NETBAGs: A Network-Based Clustering Approach with Gene Signatures for Cancer Subtyping Analysis. Wu L., Liu Z., Xu J., Chen M., Fang H., Tong W., and Xiao W. Biomarkers in Medicine. 2015, 9 (11), 1053-1065.
2015	Drug-Induced Liver Injury: Interaction Between Drug Properties and Host Factors.	Chen M., Suzuki A., Borlak J., Andrade R.J., and Lucena M.I.	Drug-Induced Liver Injury: Interaction Between Drug Properties and Host Factors. Chen M., Suzuki A., Borlak J., Andrade R.J., and Lucena M.I. Journal of Hepatology. 2015, 63(2): 503-514.
2015	Predicting Hepatotoxicity Using ToxCast In Vitro Bioactivity and Chemical Structure.	Liu J., Mansouri K., Judson R.S., Martin M.T., Hong H., Chen M., Xu X., Thomas R.S., and Shah I.	Predicting Hepatotoxicity Using ToxCast In Vitro Bioactivity and Chemical Structure. Liu J., Mansouri K., Judson R.S., Martin M.T., Hong H., Chen M., Xu X., Thomas R.S., and Shah I. Chemical Research in Toxicology. 2015, 28(4), 738-751.
2014	HighDaily Dose and Being a Substrate of Cytochrome P450 Enzymes are Two Important Predictors of Drug-induced Liver Injury.	Yu K., Geng X., Chen M., Zhang J., Wang B., and Tong W.	HighDaily Dose and Being a Substrate of Cytochrome P450 Enzymes are Two Important Predictors of Drug-induced Liver Injury. Yu K., Geng X., Chen M., Zhang J., Wang B., and Tong W. Drug Metabolism and Disposition. 2014, 42(4):744-750.
2014	Predicting Idiosyncratic Drug-Induced Liver Injury: Some Recent Advances.	Chen, M., J. Borlak, and Tong, W.	Predicting Idiosyncratic Drug-Induced Liver Injury: Some Recent Advances. Chen, M., J. Borlak, and Tong, W. Expert review of gastroenterology & hepatology, 2014. 8(7):721-723.
2014	A Testing Strategy to Predict Risk for Drug-Induced Liver Injury in Humans Using High-Content Screening Assays and the 'Rule-of-two' Model.	Chen M., Tung C., Shi Q., Guo L., Shi L., Fang H., Borlak J., and Tong W.	A Testing Strategy to Predict Risk for Drug-Induced Liver Injury in Humans Using High-Content Screening Assays and the 'Rule-of-two' Model. Chen M., Tung C., Shi Q., Guo L., Shi L., Fang H., Borlak J., and Tong W. Arch Toxicol. 2014, 88(7):1439-1449.
2014	Toward Predictive Models for Drug-Induced Liver Injury in Humans: Are We There Yet?	Chen M., Bisgin H., Tong L., Hong H., Fang H., Borlak J., and Tong W.	Toward Predictive Models for Drug-Induced Liver Injury in Humans: Are We There Yet? Chen M., Bisgin H., Tong L., Hong H., Fang H., Borlak J., and Tong W. Biomark Med. 2014, 8(2):201-213.
2014	MiRNAs and Their Application in Drug-Induced Liver Injury.	Wang Y., Chen T., and Tong W.	MiRNAs and Their Application in Drug-Induced Liver Injury. Wang Y., Chen T., and Tong W. Biomark Med. 2014, 8(2):161-172.
2013	A Systems Approach for Analysis of High Content Screening Assay Data with Topic Modeling.	Bisgin H., Chen M., Wang Y., Kelly R., Fang H., Xu X., and Tong, W.	A Systems Approach for Analysis of High Content Screening Assay Data with Topic Modeling. Bisgin H., Chen M., Wang Y., Kelly R., Fang H., Xu X., and Tong, W. BMC Bioinformatics. 2013, 14 Suppl 14:S11.
2013	High Lipophilicity and High Daily Dose of Oral Medications are Associated with Significant Risk for Drug-Induced Liver Injury.	Chen M., Borlak J., and Tong W.	High Lipophilicity and High Daily Dose of Oral Medications are Associated with Significant Risk for Drug-Induced Liver Injury. Chen M., Borlak J., and Tong W. Hepatology. 2013, 58(1):388-396.
2013	Quantitative Structure-Activity Relationship Models for Predicting Drug-Induced Liver Injury Based on FDA-Approved Drug Labeling Annotation and Using a Large Collection of Drugs.	Chen M., Hong H., Fang H., Zhou G., Kelly R., Borlak J., and Tong, W.	Quantitative Structure-Activity Relationship Models for Predicting Drug-Induced Liver Injury Based on FDA-Approved Drug Labeling Annotation and Using a Large Collection of Drugs. Chen M., Hong H., Fang H., Zhou G., Kelly R., Borlak J., and Tong, W. Toxicological Sciences. 2013, 136(1):242-249.
2013	Phenotypic Anchoring of Liver Injury in Rats by Gene Expression Profiling.	Chen M., Kelly R., Tong L., Borlak J., and Tong W.	Phenotypic Anchoring of Liver Injury in Rats by Gene Expression Profiling. Chen M., Kelly R., Tong L., Borlak J., and Tong W. Microarrays: Principles, Applications and Technologies, Nova Science Publishers, in press.
2013	Liver Toxicity Knowledge Base (LTKB) – A Systems Approach to a Complex Endpoint.	Chen M., Zhang J., Wang Y., Liu Z., Kelly R., Zhou G., Fang H., Borlak J., and Tong W.	Liver Toxicity Knowledge Base (LTKB) – A Systems Approach to a Complex Endpoint. Chen M., Zhang J., Wang Y., Liu Z., Kelly R., Zhou G., Fang H., Borlak J., and Tong W. Clinical Pharmacology & Therapeutics. 2013, 93(5):409-412. (pmid: 23486446)
2013	Toxicogenomic and Pharmacogenomic Biomarkers for Drug Discovery and Personalized Medicine.	Uehara T., Wang Y., and Tong W.	Toxicogenomic and Pharmacogenomic Biomarkers for Drug Discovery and Personalized Medicine. Uehara T., Wang Y., and Tong W. Biomarkers in Disease: Methods, Discoveries and Applications. Springer, in press.
2013	Toxicogenomics—A Drug Development Perspective.	Wang Y., Borlak J., and Tong W.	Toxicogenomics—A Drug Development Perspective. Wang Y., Borlak J., and Tong W. Genomic Biomarkers for Pharmaceutical Development. Elsevier 2013.
2013	A Unifying Ontology to Integrate Histological and Clinical Observations for Drug-Induced Liver Injury.	Wang Y., Lin Z., Liu Z., Harris S., Kelly R., Zhang J., Ge W., Chen M., Borlak J., and Tong W.	A Unifying Ontology to Integrate Histological and Clinical Observations for Drug-Induced Liver Injury. Wang Y., Lin Z., Liu Z., Harris S., Kelly R., Zhang J., Ge W., Chen M., Borlak J., and Tong W. American Journal of Pathology, 2013, 182(4):1180-1187.
2012	A Decade of Toxicogenomic Research and Its Contribution to Toxicological Science.	Chen M., Zhang M., Borlak J., and Tong, W.	A Decade of Toxicogenomic Research and Its Contribution to Toxicological Science. Chen M., Zhang M., Borlak J., and Tong, W. Toxicological Sciences. 2012, 130(2):217-228.
2012	atBioNet – An Integrated Network Analysis Tool for Genomics and Biomarker Discovery.	Ding Y., Chen M., Liu Z., Ding D., Ye Y., Zhang M., Kelly R., Guo L., Su Z., Harris S.C., Qian F., Ge W., Fang H., Xu X., and Tong W.	atBioNet – An Integrated Network Analysis Tool for Genomics and Biomarker Discovery. Ding Y., Chen M., Liu Z., Ding D., Ye Y., Zhang M., Kelly R., Guo L., Su Z., Harris S.C., Qian F., Ge W., Fang H., Xu X., and Tong W. BMC Genomics. 2012, 13:325.
2012	Is Toxicogenomics a More Reliable and Sensitive Biomarker than Conventional Indicators From Rats to Predict Drug-Induced Liver Injury in Humans?	Zhang M., Chen M., and Tong W.	Is Toxicogenomics a More Reliable and Sensitive Biomarker than Conventional Indicators From Rats to Predict Drug-Induced Liver Injury in Humans? Zhang M., Chen M., and Tong W. Chem Res Toxicol. 2012, 25(1):122-129.
2011	FDA-Approved Drug Labeling for the Study of Drug-Induced Liver Injury.	Liu Z., Shi Q., Ding D., Kelly R., Fang H., and Tong W.	FDA-Approved Drug Labeling for the Study of Drug-Induced Liver Injury. Chen M.J., Vijay V., Shi Q., Liu Z.C., Fang H., and Tong W.D. Drug Discovery Today. 2011, 16(15-16):697-703.
2011	Translating Clinical Findings into Knowledge in Drug Safety Evaluation – Drug Induced Liver Injury Prediction System (DILIps).	Liu Z., Shi Q., Ding D., Kelly R., Fang H., and Tong W.	Translating Clinical Findings into Knowledge in Drug Safety Evaluation – Drug Induced Liver Injury Prediction System (DILIps). Liu Z., Shi Q., Ding D., Kelly R., Fang H., and Tong W. PLoS Comput Biol. 2011, 7(12):e1002310.
2011	Unravelling Sex Differences in Drug-Induced Liver Injury.	Tong W.D., Shi Q., Salminen W., Chen M., Fang H., Suzuki A., and Mendrick D.L.	Unravelling Sex Differences in Drug-Induced Liver Injury. Tong W.D., Shi Q., Salminen W., Chen M., Fang H., Suzuki A., and Mendrick D.L. General, Applied and Systems Toxicology. 2011.
2010	Genomic Indicators in the Blood Predict Drug-Induced Liver Injury.	Huang J., Shi W., Zhang J., Chou J.W., Paules R.S., Gerrish K., Li J., Luo J., Wolfinger R.D., Bao W., Chu T.M., Nikolsky Y., Nikolskaya T., Dosymbekov D., Tsyganova M.O., Shi L., Fan X., Corton J.C., Chen M., Cheng Y., Tong W., Fang H., and Bushel P.R.	Genomic Indicators in the Blood Predict Drug-Induced Liver Injury. Huang J., Shi W., Zhang J., Chou J.W., Paules R.S., Gerrish K., Li J., Luo J., Wolfinger R.D., Bao W., Chu T.M., Nikolsky Y., Nikolskaya T., Dosymbekov D., Tsyganova M.O., Shi L., Fan X., Corton J.C., Chen M., Cheng Y., Tong W., Fang H., and Bushel P.R. Pharmacogenomics J. 2010, 10(4): 267-277.
2010	Biomarkers for Drug-Induced Liver Injury.	Shi Q., Hong H., Senior J., and Tong W.	Biomarkers for Drug-Induced Liver Injury. Shi Q., Hong H., Senior J., and Tong W. Expert Rev Gastroenterol Hepatol. 2010, 4(2):225-34.
2009	The Liver Toxicity Biomarker Study: Phase I Design and Preliminary Results.	McBurney R.N., Hines W.M., Von Tungeln L.S., Schnackenberg L.K., Beger R.D., Moland C. L., Han T., Fuscoe J.C., Chang C.W., Chen J.J., Su Z., Fan X.H., Tong W., Booth S.A., Balasubramanian R., Courchesne P.L., Campbell J.M., Graber A., Guo Y., Juhasz P.J., Li T.Y., Lynch M.D., Morel N.M., Plasterer T.N., Takach E.J., Zeng C., and Beland F. A.	The Liver Toxicity Biomarker Study: Phase I Design and Preliminary Results. McBurney R.N., Hines W.M., Von Tungeln L.S., Schnackenberg L.K., Beger R.D., Moland C. L., Han T., Fuscoe J.C., Chang C.W., Chen J.J., Su Z., Fan X.H., Tong W., Booth S.A., Balasubramanian R., Courchesne P.L., Campbell J.M., Graber A., Guo Y., Juhasz P.J., Li T.Y., Lynch M.D., Morel N.M., Plasterer T.N., Takach E.J., Zeng C., and Beland F. A. Toxicol Pathol. 2009, 37(1):52-64. Epub 2009 Jan26.