Publications
Andersen, M.E., Clewell, H.J., Bermudez, E., Dodd, D.E., Willson, G.A., Campbell, J.L. and Thomas, R.S. Formaldehyde: Integrating Dosimetry, Cytotoxicity and Genomics to Understand Dose-Dependent Transitions for an Endogenous Compound. Toxicol Sci. (In Press).
De Abrew, K.N., Kaminski, N.E., and Thomas, R.S. An integrated genomic analysis of aryl hydrocarbon receptor-mediated inhibition of B-cell differentiation. Toxicol Sci. (In Press). (link)
Boellmann, F., Zhang, L., Clewell, H.J., Schroth, G.P., Kenyon, E.M., Andersen, M.E., and Thomas R.S. (2010). Genome wide analysis of DNA methylation and gene expression changes in the mouse lung following subchronic arsenate exposure. Toxicol Sci. (In Press). (link)
Rotroff, D.M., Wetmore, B.A., Dix, D.J., Ferguson, S.S., Clewell, H.J., Houck, K.A., Lecluyse, E.L., Andersen, M.E., Judson, R.S., Smith, C.M., Sochaski, M.A., Kavlock, R.J., Boellmann, F., Martin, M.T., Reif, D.M., Wambaugh, J.F., and Thomas, R.S. (2010). Incorporating human dosimetry and exposure into high-throughput in vitro toxicity screening. Toxicol Sci. (In Press). (link)
Boellmann, F. and Thomas, R.S. (2010). The identification of protein kinase C iota as a regulator of the Mammalian heat shock response using functional genomic screens. PLoS One 5(7):e11850. (link)
Shi, L., Campbell, G., Jones, W.D., Campagne, F., Wen, Z., Walker, S.J., Su, Z., Chu, T.M., Goodsaid, F.M., Pusztai, L., Shaughnessy, J.D. Jr, Oberthuer, A., Thomas, R.S., et al. (2010). The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol. 28(8):827-38. (link)
Shi, W., Bessarabova, M., Dosymbekov, D., Dezso, Z., Nikolskaya, T., Dudoladova, M., Serebryiskaya, T., Bugrim, A., Guryanov, A., Brennan, R.J., Shah, R., Dopazo, J., Chen, M., Deng, Y., Shi, T., Jurman, G., Furlanello, C., Thomas, R.S., Corton, J.C., Tong, W., Shi, L., and Nikolsky, Y. (2010). Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes. Pharmacogenomics J. 10(4):310-23. (link)
Luo, J., Schumacher, M., Scherer, A., Sanoudou, D., Megherbi, D., Davison, T., Shi, T., Tong, W., Shi, L., Hong, H., Zhao, C., Elloumi, F., Shi, W., Thomas, R., Lin, S., Tillinghast, G., Liu, G., Zhou, Y., Herman, D., Li, Y., Deng, Y., Fang, H., Bushel, P., Woods, M., Zhang, J. (2010). A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data. Pharmacogenomics J. 10(4):278-91. (link)
Zhang, Q., Bhattacharya, S., Kline, D.E., Crawford, R.B., Conolly, R.B., Thomas, R.S., Kaminski, N.E. and Andersen, M.E. (2010). Stochastic modeling of B lymphocyte terminal differentiation and its suppression by dioxin. BMC Systems Biology 4(1):40. (link)
Wetmore, B.A., Brees, D.J., Singh, R., Watkins, P.B., Andersen, M.E., Loy, J. and Thomas, R.S. (2010). Quantiative analyses and transcriptomic profiling of circulating messenger RNAs as biomarkers of rat liver injury. Hepatology 51(6):2127-2139. (link)
Bhattacharya, S., Conolly, R.B., Kaminski, N.E., Thomas, R.S., Andersen, M.E., and Zhang, Q. (2010). A Bistable Switch Underlying B Cell Differentiation and Its Disruption by the Environmental Contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin. Toxicol. Sci. 115(1):51-65. (link)
Hall, J.M., Barhoover, M.A., Kazmin, D., McDonnell, D.P., Greenlee, W.F., and Thomas, R.S. (2010). Activation of the aryl-hydrocarbon receptor inhibits invasive and metastatic features of human breast cancer cells and promotes breast cancer cell differentiation. Mol. Endocrinol. 24(2):359-69. (link)
Barhoover, M.A., Hall, J.M., Greenlee, W.F., and Thomas R.S. (2010). The AHR regulates cell cycle progression in human breast cancer cells via a functional interaction with CDK4. Mol. Pharmacol. 77(2):195-201. (link)
Thomas, R.S., Bao, W., Chu, T.M., Bessarabova, M., Nikolskaya, T., Nikolsky, Y., Andersen, M.E., and Wolfinger, R.D. (2009). Use of Short-term Transcriptional Profiles to Assess the Long-term Cancer-Related Safety of Environmental and Industrial Chemicals. Toxicol. Sci. 112(2):311-321. (link)
DuSell, C.D., Nelson, E.R., Wittmann, B.M., Fretz, J.A., Kazmin, D., Thomas, R.S., Pike, J.W., and McDonnell, D.P. (2009). Regulation of aryl hydrocarbon receptor function by Selective Estrogen Receptor Modulators. Mol. Endocrinol. 24(1):33-46. (link)
Chu, T.M., Bao, W., Thomas, R.S., and Wolfinger, R.D. (2009). Batch Profile Estimation, Correction, and Scoring. In Batch Effects and Noise in Microarray Experiments: Sources and Solutions (A. Scherer, Ed.). John Wiley & Sons, Ltd., Hoboken, NJ.
Clewell, R.A., Pluta, L., Thomas, R.S., and Andersen, M.E. (2009). In utero exposure to chloroquine alters sexual development in the male fetal rat. Toxicol. Appl. Pharmacol. 237(3):366-74. (link)
Woods, C.G., Fu, J, Xue, P., Hou, Y., Pluta, L.J., Yang, L., Zhang, Q., Thomas, R.S., Andersen, M.E., and Pi, J. (2009). Dose-dependent transitions in Nrf2-mediated adaptive response and related stress responses to hypochlorous acid in mouse macrophages. Toxicol. Appl. Pharmacol. 238(1):27-36. (link)
Andersen, M.E., Clewell, H.J. 3rd, Bermudez, E., Willson, G.A., and Thomas R.S. (2008). Genomic signatures and dose dependent transitions in nasal epithelial responses to inhaled formaldehyde in the rat. Toxicol. Sci. 105(2):368-383. (link)
Roberts, E., Struve, M., Thomas, R.S., and Dorman, D. (2008). Gene Expression Changes Following Acute Hydrogen Sulfide (H2S)-Induced Nasal Respiratory Epithelial Injury. Tox. Pathol. 36(4):560-567. (link)
Yang, L., Walker, J.R., Hogenesch, J.B., and Thomas, R.S. (2007). NetAtlas: A Cytoscape plugin to examine signaling networks based on tissue gene expression. In Silico Biol. 8:0005. (link)
Yang, L., Allen, B.C., and Thomas, R.S. (2007). BMDExpress: A software tool for the benchmark dose analyses of genomic data. BMC Genomics 8:387. (link)
Roberts, E., Struve, M., Thomas, R.S., and Dorman, D. (2007). Basal gene expression in male and female Sprague-Dawley rat nasal respiratory and olfactory epithelium. Inhal. Toxicol. 19(11): 941-949. (link)
Clewell, H.J., Thomas, R.S., Gentry, P.R., Crump, K.S., Kenyon, E.M., El-Masri, H.A., and Yager, J.W. (2007). Research toward the development of a biologically based dose response assessment for inorganic arsenic carcinogenicity: A progress report. Toxicol. Appl. Pharmacol. 222(3): 388-398. (link)
Thomas, R.S., Allen, B.C., Nong, A., Yang, L., Bermudez, E., Clewell, H.J., and Andersen, M.E. (2007). A method to integrate benchmark dose estimates with genomic data to assess the functional effects of chemical exposure. Toxicol. Sci. 98(1): 240-248. (link)
Halsey, T.A., Yang, L., Walker, J.R., Hogenesch, J.B., and Thomas, R.S. (2007). A functional map of NFκB signaling identifies novel modulators and multiple system controls. Genome Biol. 8(6):R104. (link)
Ingram, J.L., Antao-Menezes, A., Turpin, E.A., Wallace, D.G., Mangum, J.B., Pluta, L.J., Thomas, R.S., and Bonner, J.C. (2007). Genomic analysis of human lung fibroblasts exposed to vanadium pentoxide to identify candidate genes for occupational bronchitis. Respir. Res. 8:34. (link)
Conolly, R.B., and Thomas, R.S. (2007). Biologically motivated approaches to extrapolation from high to low doses and the advent of systems biology: The road to toxicological safety assessment. Human Ecol. Risk Assessment, 13: 52–56.
Thomas, R.S., Pluta, L., Yang, L., and Halsey, T.A. (2007) Application of genomic biomarkers to predict increased lung tumor incidence in two-year rodent cancer bioassays. Toxicol. Sci. 97(1): 55-64. (link)
Thomas, R.S., O’Connell, T.M., Pluta, L., Wolfinger, R.D., Yang, L. and Page, T.J. (2007). A comparison of transcriptomic and metabonomic technologies for identifying biomarkers predictive of two-year rodent cancer bioassays. Toxicol. Sci. 96(1): 40-46. (link)