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Biomarkers & Molecular Toxicity Pathways

Modules, or gene groups associated with specific adverse outcomes, offer a source of potential diagnostic biomarkers. We explore unbiased systems approaches to identify toxicity modules for specific histopathologies of liver and kidney injuries. Projects include, identifying molecular toxicity pathways associated with such injuries (e.g., fibrosis and steatosis); developing and validating biomarkers in animal models; examining in vitro–in vivo correlations; and studying specific chemical exposures in detail.


Pannala, V. R., K. C. Vinnakota, K. D. Rawls, S. K. Estes, T. P. O'Brien, R. L. Printz, J. A. Papin, J. Reifman, M. Shiota, J. D. Young, and A. Wallqvist. Mechanistic identification of biofluid metabolite changes as markers of acetaminophen-induced liver toxicity in rats. Toxicology and Applied Pharmacology. 2019 June 1; 372:19-32. [PDF, PubMed]

Vinnakota, K. C., V. R. Pannala, M. L. Wall, M. Rahim, S. K. Estes, I. Trenary, T. P. O'Brien, R. L. Printz, J. Reifman, M. Shiota, J. D. Young, and A. Wallqvist. Network modeling of liver metabolism to predict plasma metabolite changes during short-term fasting in the laboratory rat. Frontiers in Physiology. 2019 March 1; 10:161. [PDF, PubMed]

Schyman, P., R. L. Printz, S. K. Estes, K. L. Boyd, M. Shiota, and A. Wallqvist. Identification of the toxicity pathways associated with thioacetamide-induced injuries in rat liver and kidney. Frontiers in Pharmacology. 2018 November 6; 9(1272). [PDF, PubMed]

Pannala, V. R., M. L. Wall, S. K. Estes, I. Trenary, T. P. O’Brien, R. L. Printz, K. C. Vinnakota, J. Reifman, M. Shiota, J. D. Young, and A. Wallqvist. Metabolic network-based predictions of toxicant-induced metabolite changes in the laboratory rat. Scientific Reports. 2018 August 3; 8:11678. [PDF, PubMed]

Liu, R., R. L. Printz, E. C. Jenkins, T. P. O'Brien, J. A. Te, M. Shiota, and A. Wallqvist. Genome-wide gene expression changes associated with exposure of rat liver, heart, and kidney cells to endosulfan. Toxicology in Vitro. 2018 April; 48:244-254. [PDF, PubMed]

McDyre, B. C., M. D. M. AbdulHameed, M. G. Permenter, W. E. Dennis, C. E. Baer, J. M. Koontz, M. H. Boyle, A. Wallqvist, J. A. Lewis, and D. L. Ippolito. Comparative proteomic analysis of liver steatosis and fibrosis after oral hepatotoxicant administration in Sprague-Dawley rats. Toxicologic Pathology. 2018 February; 46(2):202-223. [PDF, PubMed]

Liu, R., M. D. M. AbdulHameed, and A. Wallqvist. Molecular structure-based large-scale prediction of chemical-induced gene expression changes. Journal of Chemical Information and Modeling. 2017 September 25; 57(9):2194-2202. [PDF, PubMed]

Liu, R., X. Yu, and A. Wallqvist. Using chemical-induced gene expression in cultured human cells to predict chemical toxicity. Chemical Research in Toxicology. 2016 November 21; 29(11):1883-1893. [PDF, PubMed]

AbdulHameed, M. D., D. L. Ippolito, and A. Wallqvist. Predicting rat and human pregnane X receptor activators using Bayesian classification models. Chemical Research in Toxicology. 2016 October 17; 29(10):1729-1740. [PDF, PubMed]

AbdulHameed, M. D., D. L. Ippolito, J. D. Stallings, and A. Wallqvist. Mining kidney toxicogenomics using gene co-expression modules. BMC Genomics. 2016 October 10; 17:790. [PDF, PubMed]

Te, J. A., M. D. AbdulHameed, and A. Wallqvist. Systems toxicology of chemically induced liver and kidney injuries: histopathology-associated gene co-expression modules. Journal of Applied Toxicology. 2016 September; 36(9):1137-1149. [PDF, PubMed]

Ippolito, D. L., M. D. AbdulHameed, G. J. Tawa, C. E. Baer, M. G. Permenter, B. C. McDyre, W. E. Dennis, M. H. Boyle, C. A. Hobbs, M. A. Streicker, B. S. Snowden, J. A. Lewis, A. Wallqvist, and J. D. Stallings. Gene expression patterns associated with histopathology in toxic liver fibrosis. Toxicological Sciences. 2016 January; 149(1):67-88. [PDF, PubMed]

Stallings, J. D., D. L. Ippolito, A. Wallqvist, B. C. McDyre, and J. Reifman. Host response to environmental hazards: using literature, bioinformatics, and computation to derive candidate biomarkers of toxic industrial chemical exposure. Proceedings of the HFM-254 Symposium on Health Surveillance and Informatics in Missions: Multidisciplinary Approaches and Perspectives. Paris, France. 2015 October 12-14; 7:1-14. [PDF, DTIC]

Te, J. A., K. D. Spradling-Reeves, J. F. Dillman III, and A. Wallqvist. Neuroprotective mechanisms activated in non-seizing rats exposed to sarin. Brain Research. 2015 June 4; 1618:136-148. [PDF, PubMed]

AbdulHameed, M. D., G. J. Tawa, K. Kumar, D. L. Ippolito, J. A. Lewis, J. D. Stallings, and A. Wallqvist. Systems level analysis and identification of pathways and networks associated with liver fibrosis. PLOS ONE. 2014 November 8; 9(11):e112193. [PDF, PubMed]

Tawa, G. J., M. D. AbdulHameed, X. Yu, K. Kumar, D. L. Ippolito, J. A. Lewis, J. D. Stallings, and A. Wallqvist. Characterization of chemically induced liver injuries using gene co-expression modules. PLOS ONE. 2014 September; 9(9):e107230. [PDF, PubMed]