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Your Environment. Your Health.

Selected Publications

Toxicoinformatics Group

  1. Cui Y, Palii SS, Innes CL, Paules RS. Depletion of ATR selectively sensitizes ATM-deficient human mammary epithelial cells to ionizing radiation and DNA-damaging agents. Cell cycle (Georgetown, Tex.) 2014 13(22):3541-3550. [Abstract]
  2. Wang C, Gong B, Bushel PR, Thierry-Mieg J, Thierry-Mieg D, Xu J, Fang H, Hong H, Shen J, Su Z, Meehan J, Li X, Yang L, Li H, Łabaj PP, Kreil DP, Megherbi D, Gaj S, Caiment F, van Delft J, Kleinjans J, Scherer A, Devanarayan V, Wang J, Yang Y, Qian HR, Lancashire LJ, Bessarabova M, Nikolsky Y, Furlanello C, Chierici M, Albanese D, Jurman G, Riccadonna S, Filosi M, Visintainer R, Zhang KK, Li J, Hsieh JH, Svoboda DL, Fuscoe JC, Deng Y, Shi L, Paules RS, Auerbach SS, Tong W5. The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nature Biotechnology 2014 32(9):926-932. [Abstract]
  3. Omolo B, Carson C, Chu H, Zhou Y, Simpson DA, Hesse JE, Paules RS, Nyhan KC, Ibrahim JG, Kaufmann WK. A prognostic signature of G(2) checkpoint function in melanoma cell lines. Cell cycle (Georgetown, Tex.) 2013 12(7):1071-1082. [Abstract]
  4. Zhang L, Simpson DA, Innes CL, Chou J, Bushel PR, Paules RS, Kaufmann WK, Zhou T. Gene expression signatures but not cell cycle checkpoint functions distinguish AT carriers from normal individuals. Physiological genomics 2013 45(19):907-916.
  5. Hesse JE, Liu L, Innes CL, Cui Y, Palii SS, Paules RS. 2013. Genome-Wide Small RNA Sequencing and Gene Expression Analysis Reveals a microRNA Profile of Cancer Susceptibility in ATM-Deficient Human Mammary Epithelial Cells. PloS One,  8(5):e64779. [Abstract]
  6. Innes, C.L., J.E. Hesse, S.S. Palii, B.A. Helmink, A.J. Holub, B.P. Sleckman and R.S. Paules. 2013. DNA damage activates a complex transcriptional response in murine lymphocytes that includes both physiological and cancer-predisposition programs. BMC Genomics, 14(163):online-online. [Abstract]
  7. Palii SS, Cui Y, Innes CL, Paules RS. Dissecting Cellular Responses to Irraditaion Via Targeted Disruptions of the ATM - CHK1 – PP2A Circuit. Cell cycle (Georgetown, Tex.) 2013 12(7):1105-1118. [Abstract]
  8. Palii, S.S., Y. Cui, C.L. Innes, and R.S. Paules. 2013. Dissecting cellular responses to irradiation via targeted disruptions of the ATM – CHK1 – PP2A circuit. Cell Cycle. In press.
  9. Innes, C.L., J.E. Hesse, S.S. Palii, B.A. Helmink, A.J. Holub, B.P. Sleckman and R.S. Paules. 2013. DNA damage activates a complex transcriptional response in murine lymphocytes that includes both physiological and cancer-predisposition programs. BMC Genomics, 14(163):online-online. [Abstract]
  10. Vacchi-Suzzi C, Bauer Y, Berridge BR, Bongiovanni S, Gerrish K, Hamadeh HK, Letzkus M, Lyon J, Moggs J, Paules RS, Pognan F, Staedtler F, Vidgeon-Hart MP, Grenet O, Couttet P. 2012. Perturbation of microRNAs in rat heart during chronic doxorubicin treatment. PloS One, 7(7):e40395. [Abstract]
  11. Cui, Y., Huang, Q., Auman, J.T., Knight, B., Jin, X., Blanchard, K.T., Chou, J., Jayadev, S., and Paules, R.S. 2011. Genomic-derived markers for early detection of calcineurin inhibitor immunosuppressant-mediated nephrotoxicity. Toxicological sciences, 124(1):23-34. [Abstract]
  12. Paules, R.S., Aubrecht, J., Corvi, R., Garthoff, B., Kleinjans, J.C. 2011. Moving forward in human cancer risk assessment. Environmental health perspectives, 119(6):739-743. [Abstract]
  13. Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD Jr, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature biotechnology 2010 28(8):827-38.  [Abstract]
  14. 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. 2010. Genomic indicators in the blood predict drug-induced liver injury. The pharmacogenomics journal, 10(4):267-277. [Abstract]
  15. Bower, J., Zhou, Y., Zhou, T., Simpson, D.A., Arlander, S.J.H., Paules, R.S., Cordeiro-Stone, M., and Kaufmann, W.K. 2010. Revised genetic requirements for the decatenation G(2) checkpoint: the role of ATM. Cell cycle (Georgetown, Tex.), 9(8):1617-1628. [Abstract]
  16. Fu, D., Brophy, J., Chan, C.T., Atmore, K.A., Begley, U., Paules, R.S., Dedon, P.C., Begley, T.J., and Samson, L.D. 2010. Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival. Molecular and cellular biology, 30(10):2449-2459. [Abstract]
  17. Cui, Y., and R.S. Paules. 2010. Use of transcriptomics in understanding mechanisms of drug-induced toxicity. Pharmacogenomics, 11(4):573-585. [Abstract]
  18. Bredemeyer, A.L., B.A. Helmink, C.L. Innes, B. Calderon, L.M. McGinnis, G.K. Mahowald, E.J. Gapud, L.M. Walker, J.B. Collins, B.K. Weaver, L. Mandik-Nayak, R.D. Schreiber, P.M. Allen, M.J. May, R.S. Paules, C.H. Bassing, and B.P. Sleckman. 2008. DNA double-strand breaks activate a multi-functional genetic program in developing lymphocytes. Nature, 456 (7223):819-823. [Abstract]
  19. Lobenhofer, E.K., Auman, J.T., Blackshear, P.E., Boorman, G.A., Bushel, P.R., Cunningham, M.L., Fostel, J.M., Gerrish, K., Heinloth, A.N., Irwin, R.D., Malarkey, D.E., Merrick, B.A., Sieber, S.O., Tucker, C.J., Ward, S.M., Wilson, R.E., Hurban, P., Tennant, R.W., and R.S. Paules. 2008. Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype. Genome Biology, 9 (6):R100. [Abstract]
  20. Arlander, S.J.H., Greene, B.T., Innes, C.L., and R.S. Paules. 2008. DNA protein kinase-dependent G2 checkpoint revealed following knockdown of ataxia-telangiectasia mutated in human mammary epithelial cells. Cancer Research, 68 (1):89-97. [Abstract]
  21. Bushel, PR, Heinloth AN, Li J, Huang L, Chou JW, Boorman GA, Malarkey DE, Houle CD, Ward SM, Wilson RE, Fannin RD, Russo MW, Watkins PB, Tennant RW, and R.S. Paules. 2007. Blood gene expression signatures predict exposure levels. Proceedings of the National Academy of Sciences of the United States of America, 104(46):18211-18216. [Abstract]
  22. Chou, J.W., Zhou T, Kaufmann WK, Paules RS, and P.R. Bushel. 2007. Extracting gene expression patterns and identifying co-expressed genes from microarray data. BMC bioinformatics 8(1):427-427. [Abstract]
  23. Auman, J.T., G.A. Boorman, R.E. Wilson, G.S. Travlos, and R.S. Paules. 2007. Heat map visualization of high-density clinical chemistry data. Physiological Genomics, 2 352-356. [Abstract]
  24. Innes, C.L., A.N. Heinloth, K.G. Flores, S.O. Sieber, P.B. Deming, P.R. Bushel, W.K Kaufmann, and R.S. Paules. 2006. ATM requirement in gene expression responses to ionizing radiation in human lymphoblasts and fibroblasts. Mol. Cancer Res., 4, 197-207. [Abstract]
  25. Members of the Toxicogenomics Research Consortium. 2005. Standardizing global gene expression analysis between laboratories and across platforms. Nat. Methods, 2, 351-356. [Abstract]
  26. Fannin, R.D., J.T. Auman, M.E. Bruno, S.O. Sieber, S.M. Ward, C.J. Tucker, B.A. Merrick, and R.S. Paules. 2005. Differential gene expression profiling in whole blood during acute systemic inflammation in lipopolysaccharide-treated rats. Physiol. Genomics, 21, 92-104. [Abstract]
  27. Heinloth, A.N., R.D. Irwin, G.A. Boorman, P. Nettesheim, R.D. Fannin, S.O. Sieber, M.L. Snell, C. J. Tucker, L. Li, G.S. Travlos, G. Vansant, P.E. Blackshear, R.W. Tennant, M.L. Cunningham, and R.S. Paules. 2004. Gene expression profiling of rat livers reveals indicators of potential adverse effects. Toxicol. Sci., 80, 193-202. [Abstract]
  28. Heinloth, A.N., R.E. Shackelford, C.L. Innes, L. Bennett, L. Li, R.P. Amin, S.O. Sieber, K.G. Flores, P.R. Bushel, and R.S. Paules. 2003. Identification of distinct and common gene expression changes after oxidative stress and gamma and ultraviolet radiation. Mol. Carcinog., 37, 65-82. [Abstract]
  29. Heinloth, A.N., R.E. Shackelford, C.L. Innes, R.P. Amin, S.O. Sieber, K.G. Flores, L. Bennett, P.R. Bushel, and R.S. Paules. 2003. ATM-dependent and ATM-independent gene expression changes in response to oxidative stress, γ-radiation and UV-radiation. Rad. Res., 160, 273-290. [Abstract]
  30. Harding, H.P, Y. Zhang, H. Zeng, I. Novoa, P.D. Lu, B. Popko, R.S. Paules, T. Hettmann, J.M. Leiden, and D. Ron. 2003. An integrated stress response promotes resistance to oxidative stress through amino acid sufficiency. Mol. Cell, 11, 619-633. [Abstract]
  31. Heffernan, T.P., D.A. Simpson, A.R. Frank, A.N. Heinloth, R.S. Paules, M. Cordeiro-Stone, and W.K. Kaufmann. 2002. An ATR- and Chk1-dependent S checkpoint inhibits replicon initiation following UVC-induced DNA damage. Mol. Cell. Biol., 22, 8552-8561. [Abstract]
  32. Flores, K.G., P.B. Deming, C.S. Downes, R.S. Paules, and W.K. Kaufmann. 2002. ATR enforces the topoisomerase II-dependent G2 checkpoint through Plk1 kinase. J. Biol. Chem., 277, 36832-36838.
  33. Hamadeh, H.K., P.R. Bushel, S. Jayadev, K. Martin, O. DiSorba, S. Sieber, L. Bennett, R. Tennant, R. Stoll, J.C. Barrett, K. Blanchard, R.S. Paules, and C.A. Afshari. 2002. Gene expression analysis reveals chemical-specific profiles. Toxicol. Sci., 67, 219-231. [Abstract]
  34. Wolfinger, R.D., G. Gibson, E.D. Wolfinger, L. Bennett, H. Hamadeh, P. Bushel, C.A. Afshari, and R.S. Paules. 2001. Assessing gene significance from cDNA microarray expression data via mixed models. J. Comp. Biol., 8, 625-637. [Abstract]
  35. Shackelford, R.E, C.L. Innes, S.O. Sieber, A.N. Heinloth, S.A. Leadon, and R.S. Paules. 2001. The ataxia telangiectasia gene product is required for oxidative stress-induced G1 and G2 checkpoint function in human fibroblasts. J. Biol. Chem., 276, 21951-21959. [Abstract]
  36. Shackelford, R.E., W.K. Kaufmann, and R.S. Paules. 2000. Oxidative stress and cell cycle checkpoint function. Free Radic. Biol. Med., 28, 1387-1404. [Abstract]
  37. Kaufmann, W.K. and R.S. Paules. 1996. DNA damage and cell cycle checkpoints. The FASEB J., 10, 238-247. [Abstract]
  38. Paules, R.S., E.N. Levedakou, S.J. Wilson, C.L. Innes, N. Rhodes, T.D. Tlsty, D.A. Galloway, L.A. Donehower, M.A. Tainsky, and W.K. Kaufmann. 1995. Defective G2 checkpoint function in cells from individuals with familial cancer syndromes. Cancer Res., 55, 1763-1773. [Abstract]
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