• University of Texas-Dallas (2012)

  • Computational and Systems Biology

  • S. Joshua Swamidass, M.D., Ph.D.

  • Modeling the Bioactivation and Subsequent Reactivity of Drugs

  • tyler@wustl.edu

Graduate Publications:

1) Koues, O. I., Kowalewski, R. A., Chang, L.-W., Pyfrom, S. C., Schmidt, J. A., Luo, H., Sandoval, L. E., Hughes, T. B., Bednarski, J. J., Cashen, A. F., Payton, J. E., and Oltz, E. M. (2015). Enhancer Sequence Variants and Transcription-Factor Deregulation Synergize to Construct Pathogenic Regulatory Circuits in B-Cell Lymphoma. Immunity 42(1), 186–198.

(2) Matlock, M. K., Hughes, T. B., and Swamidass, S. J. (2015). XenoSite server: a Web-Available Site of Metabolism Prediction Tool. Bioinformatics 31(7), 1136–1137.

(3) Zaretzki, J., Browning, M., Hughes, T., and Swamidass, S. J. (2015). Extending P450 Site-of-Metabolism Models with Region-Resolution Data. Bioinformatics 31(12), 1966-1973.

(4) Hughes, T. B., Miller, G. P., and Swamidass, S. J. (2015). Site of Reactivity Models Predict Molecular Reactivity of Diverse Chemicals with Glutathione. Chemical Research in Toxicology 28(4), 797–809.

(5) Hughes, T. B., Miller, G. P., and Swamidass, S. J. (2015). Modeling Epoxidation of Drug-like Molecules with a Deep Machine Learning Network. ACS Central Science 1(4), 168-180.

(6) Dang, N. L, Hughes, T. B., Krishnamurthy, V., and Swamidass, S. J. (2016). A Simple Model Predicts UGT-Mediated Metabolism. Bioinformatics 32(20), 3183-3189.

(7) Van Voorhis, W.C.,…, Hughes, T. B.,…, Willis, P. (2016). Open-source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond. PLOS Pathogens 12(7), e1005763.

(8) Hughes, T. B., Dang, N. L, Miller, G. P., and Swamidass, S. J. (2016). Modeling Reactivity to Biological Macromolecules with a Deep Multitask Network. ACS Central Science 2(8), 529–537.

(9) Hughes, T. B. and Swamidass, S. J. (2017). Deep Learning to Predict the Formation of Quinone Species in Drug Metabolism. Chemical Research in Toxicology 30(2), 642–656.

(10) Dang, N. L., Hughes, T. B., Miller, G. P., and Swamidass, S. J. (2017). A Computational Approach to Structural Alerts: Furans, Phenols, Nitroaromatics, and Thiophenes. Chemical Research in Toxicology 30(4), 1046–1059.

(11) Dang, N. L., Hughes, T. B., Miller, G. P., and Swamidass, S. J. (2018). Computationally Assessing the Bioactivation of Drugs by N-Dealkylation. Chemical Research in Toxicology, 31(2), 68–80.

(12) Wang, R., Lee, M., Kinghorn, K., Hughes, T. B., Chuckaree, I., Lohray, R., Chow, E., Pantano, P., and Draper, R. (2018). Quantitation of Cell-associated Carbon Nanotubes: Selective Binding and Accumulation of Carboxylated Carbon Nanotubes by Macrophages. Nanotoxicology, DOI: 10.1080/17435390.2018.1472309

(13) Matlock, M. K., Hughes, T. B., Dahlin, Jayme L. and Swamidass, S. J. (2018). Modeling Small-Molecule Reactivity Identifies Promiscuous Bioactive Compounds. Journal of Chemical Information and Modeling, DOI: 10.1021/acs.jcim.8b00104

Last Updated: 7/11/2018 6:15:32 PM

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