Scott S. Auerbach, Ph.D.
Leader, Toxicoinformatics

Tel 984-287-3108
Fax 919-541-3647
auerbachs@niehs.nih.gov

Curriculum Vitae Scott Auerbach (344KB)

P.O. Box 12233

Mail Drop K2-17

Durham, N.C. 27709

Delivery Instructions

Research Summary

The Toxicoinformatics Group leads the development of data analytic approaches related to Tox21 data and provides informatics support for a variety of projects within the Biomolecular Screening Branch  and across the National Toxicology Program.

Specific projects include:

• Development of toxicogenomic models that predict apical toxicological outcomes
• Evaluation of methods for scaling toxicogenomic technologies
• In vitro / In vivo extrapolation
• Analytics pipeline development for Tox21 high throughput screening data
• Development of network-based inference  approaches for biological read-across using Tox21 data
• Development of software for genomic benchmark dose analysis

Selected Publications

1. Chen S, Hsieh JH, Huang R, Sakamuru S , Hsin LY, Xia M, Shockley KR, Auerbach S, Kanaya N, Lu H, Svoboda D, Witt KL, Merrick BA, Teng CT, Tice RR. Cell-Based High-Throughput Screening for Aromatase Inhibitors in the Tox21 10K Library. Toxicological sciences: an official journal of the Society of Toxicology 2015 147(2):446-457. [Abstract Chen S, Hsieh JH, Huang R, Sakamuru S , Hsin LY, Xia M, Shockley KR, Auerbach S, Kanaya N, Lu H, Svoboda D, Witt KL, Merrick BA, Teng CT, Tice RR. Cell-Based High-Throughput Screening for Aromatase Inhibitors in the Tox21 10K Library. Toxicological sciences: an official journal of the Society of Toxicology 2015 147(2):446-457.]
2. SEQC/MAQC-III Consortium. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nature Biotechnology 2014 32(9):903-914. [Abstract SEQC/MAQC-III Consortium. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nature Biotechnology 2014 32(9):903-914.]
3. 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 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.]
4. Kleensang, A., Maertens, A., Rosenberg, M., Fitzpatrick, S., Lamb, J., Auerbach, S., Brennan, R., Crofton, K.M., Gordon, B., Fornace Jr, A.J., et al. (2013). t4 Workshop Report: Pathways of Toxicity. Altex. 31(1):53-61 [Abstract Kleensang, A., Maertens, A., Rosenberg, M., Fitzpatrick, S., Lamb, J., Auerbach, S., Brennan, R., Crofton, K.M., Gordon, B., Fornace Jr, A.J., et al. (2013). t4 Workshop Report: Pathways of Toxicity. Altex. 31(1):53-61]
5. Thomas RS, Philbert MA, Auerbach SS, Wetmore BA, Devito MJ, Cote I, Rowlands JC, Whelan MP, Hays SM, Andersen ME, Meek ME, Reiter LW, Lambert JC, Clewell HJ 3rd, Stephens ML, Zhao QJ, Wesselkamper SC, Flowers L, Carney EW, Pastoor TP, Petersen DD, Yauk CL, Nong A. Incorporating New Technologies Into Toxicity Testing and Risk Assessment: Moving From 21st Century Vision to a Data-Driven Framework. Toxicol Sci 2013. Sep 19. [Epub ahead of print]. [Abstract Thomas RS, Philbert MA, Auerbach SS, Wetmore BA, Devito MJ, Cote I, Rowlands JC, Whelan MP, Hays SM, Andersen ME, Meek ME, Reiter LW, Lambert JC, Clewell HJ 3rd, Stephens ML, Zhao QJ, Wesselkamper SC, Flowers L, Carney EW, Pastoor TP, Petersen DD, Yauk CL, Nong A. Incorporating New Technologies Into Toxicity Testing and Risk Assessment: Moving From 21st Century Vision to a Data-Driven Framework. Toxicol Sci 2013. Sep 19. [Epub ahead of print].]
6. Thomas R, Thomas RS, Auerbach SS, Portier CJ. Biological networks for predicting chemical hepatocarcinogenicity using gene expression data from treated mice and relevance across human and rat species. PLoS One 2013. 30;8(5):e63308. [Abstract Thomas R, Thomas RS, Auerbach SS, Portier CJ. Biological networks for predicting chemical hepatocarcinogenicity using gene expression data from treated mice and relevance across human and rat species. PLoS One 2013. 30;8(5):e63308.]
7. Merrick BA, Phadke DP, Auerbach SS, Mav D, Stiegelmeyer SM, Shah RR, Tice RR. RNA-Seq profiling reveals novel hepatic gene expression pattern in aflatoxin B1 treated rats. PLOS ONE 2013 8(4):e61768-. [Abstract Merrick BA, Phadke DP, Auerbach SS, Mav D, Stiegelmeyer SM, Shah RR, Tice RR. RNA-Seq profiling reveals novel hepatic gene expression pattern in aflatoxin B1 treated rats. PLOS ONE 2013 8(4):e61768-.]
8. Merrick BA, Auerbach SS, Stockton PS, Foley JF, Malarkey DE, Sills RC, Irwin RD, Tice RR. (2012) Testing an aflatoxin B1 gene signature in rat archival tissues. Chemical research in toxicology.  25(5):1132-44. [Abstract Merrick BA, Auerbach SS, Stockton PS, Foley JF, Malarkey DE, Sills RC, Irwin RD, Tice RR. (2012) Testing an aflatoxin B1 gene signature in rat archival tissues. Chemical research in toxicology.  25(5):1132-44.]
9. Fielden, M. R., Adai, A., Dunn, R. T., 2nd, Olaharski, A., Searfoss, G., Sina, J., Aubrecht, J., Boitier, E., Nioi, P., Auerbach, S., Jacobson-Kram, D., Raghavan, N., Yang, Y., Kincaid, A., Sherlock, J., Chen, S. J. and Car, B. (2011). Development and Evaluation of a Genomic Signature for the Prediction and Mechanistic Assessment of Nongenotoxic Hepatocarcinogens in the Rat. Toxicol Sci. [Abstract Fielden, M. R., Adai, A., Dunn, R. T., 2nd, Olaharski, A., Searfoss, G., Sina, J., Aubrecht, J., Boitier, E., Nioi, P., Auerbach, S., Jacobson-Kram, D., Raghavan, N., Yang, Y., Kincaid, A., Sherlock, J., Chen, S. J. and Car, B. (2011). Development and Evaluation of a Genomic Signature for the Prediction and Mechanistic Assessment of Nongenotoxic Hepatocarcinogens in the Rat. Toxicol Sci.]  
10. Hoenerhoff, M. J., Pandiri, A. R., Lahousse, S. A., Hong, H. H., Ton, T. V., Masinde, T., Auerbach, S. S., Gerrish, K., Bushel, P. R., Shockley, K. R., Peddada, S. D. and Sills, R. C. (2011). Global gene profiling of spontaneous hepatocellular carcinoma in B6C3F1 mice: similarities in the molecular landscape with human liver cancer. Toxicologic pathology 39, 678-699. [Abstract Hoenerhoff, M. J., Pandiri, A. R., Lahousse, S. A., Hong, H. H., Ton, T. V., Masinde, T., Auerbach, S. S., Gerrish, K., Bushel, P. R., Shockley, K. R., Peddada, S. D. and Sills, R. C. (2011). Global gene profiling of spontaneous hepatocellular carcinoma in B6C3F1 mice: similarities in the molecular landscape with human liver cancer. Toxicologic pathology 39, 678-699.]  
11. Seibold, M. A., Wise, A. L., Speer, M. C., Steele, M. P., Brown, K. K., Loyd, J. E., Fingerlin, T. E., Zhang, W., Gudmundsson, G., Groshong, S. D., Evans, C. M., Garantziotis, S., Adler, K. B., Dickey, B. F., du Bois, R. M., Yang, I. V., Herron, A., Kervitsky, D., Talbert, J. L., Markin, C., Park, J., Crews, A. L., Slifer, S. H., Auerbach, S., Roy, M. G., Lin, J., Hennessy, C. E., Schwarz, M. I. and Schwartz, D. A. (2011). A common MUC5B promoter polymorphism and pulmonary fibrosis. N Engl J Med 364, 1503-12. [Abstract Seibold, M. A., Wise, A. L., Speer, M. C., Steele, M. P., Brown, K. K., Loyd, J. E., Fingerlin, T. E., Zhang, W., Gudmundsson, G., Groshong, S. D., Evans, C. M., Garantziotis, S., Adler, K. B., Dickey, B. F., du Bois, R. M., Yang, I. V., Herron, A., Kervitsky, D., Talbert, J. L., Markin, C., Park, J., Crews, A. L., Slifer, S. H., Auerbach, S., Roy, M. G., Lin, J., Hennessy, C. E., Schwarz, M. I. and Schwartz, D. A. (2011). A common MUC5B promoter polymorphism and pulmonary fibrosis. N Engl J Med 364, 1503-12.]  
12. Auerbach, S. S., Thomas, R., Shah, R., Xu, H., Vallant, M. K., Nyska, A. and Dunnick, J. K. (2010). Comparative phenotypic assessment of cardiac pathology, physiology, and gene expression in C3H/HeJ, C57BL/6J, and B6C3F1/J mice. Toxicol Pathol 38, 923-42. [Abstract Auerbach, S. S., Thomas, R., Shah, R., Xu, H., Vallant, M. K., Nyska, A. and Dunnick, J. K. (2010). Comparative phenotypic assessment of cardiac pathology, physiology, and gene expression in C3H/HeJ, C57BL/6J, and B6C3F1/J mice. Toxicol Pathol 38, 923-42.]  
13. Auerbach, S. S., Shah, R. R., Mav, D., Smith, C. S., Walker, N. J., Vallant, M. K., Boorman, G. A. and Irwin, R. D. (2010). Predicting the hepatocarcinogenic potential of alkenylbenzene flavoring agents using toxicogenomics and machine learning. Toxicol Appl Pharmacol 243, 300-14. [Abstract Auerbach, S. S., Shah, R. R., Mav, D., Smith, C. S., Walker, N. J., Vallant, M. K., Boorman, G. A. and Irwin, R. D. (2010). Predicting the hepatocarcinogenic potential of alkenylbenzene flavoring agents using toxicogenomics and machine learning. Toxicol Appl Pharmacol 243, 300-14.]  
14. Auerbach, S. S., Bristol, D. W., Peckham, J. C., Travlos, G. S., Hebert, C. D. and Chhabra, R. S. (2010). Toxicity and carcinogenicity studies of methylene blue trihydrate in F344N rats and B6C3F1 mice. Food Chem Toxicol 48, 169-77. [Abstract Auerbach, S. S., Bristol, D. W., Peckham, J. C., Travlos, G. S., Hebert, C. D. and Chhabra, R. S. (2010). Toxicity and carcinogenicity studies of methylene blue trihydrate in F344N rats and B6C3F1 mice. Food Chem Toxicol 48, 169-77.]  
15. DeKeyser, J. G., Stagliano, M. C., Auerbach, S. S., Prabhu, K. S., Jones, A. D. and Omiecinski, C. J. (2009). Di(2-ethylhexyl) phthalate is a highly potent agonist for the human constitutive androstane receptor splice variant CAR2. Mol Pharmacol 75, 1005-13. [Abstract DeKeyser, J. G., Stagliano, M. C., Auerbach, S. S., Prabhu, K. S., Jones, A. D. and Omiecinski, C. J. (2009). Di(2-ethylhexyl) phthalate is a highly potent agonist for the human constitutive androstane receptor splice variant CAR2. Mol Pharmacol 75, 1005-13.]  
16. Auerbach, S. S., Mahler, J., Travlos, G. S. and Irwin, R. D. (2008). A comparative 90-day toxicity study of allyl acetate, allyl alcohol and acrolein. Toxicology 253, 79-88. [Abstract Auerbach, S. S., Mahler, J., Travlos, G. S. and Irwin, R. D. (2008). A comparative 90-day toxicity study of allyl acetate, allyl alcohol and acrolein. Toxicology 253, 79-88.]  
17. Auerbach, S. S., Dekeyser, J. G., Stoner, M. A. and Omiecinski, C. J. (2007). CAR2 displays unique ligand binding and RXRalpha heterodimerization characteristics. Drug Metab Dispos 35, 428-39. [Abstract Auerbach, S. S., Dekeyser, J. G., Stoner, M. A. and Omiecinski, C. J. (2007). CAR2 displays unique ligand binding and RXRalpha heterodimerization characteristics. Drug Metab Dispos 35, 428-39.]  
18. Stoner, M. A., Auerbach, S. S., Zamule, S. M., Strom, S. C. and Omiecinski, C. J. (2007). Transactivation of a DR-1 PPRE by a human constitutive androstane receptor variant expressed from internal protein translation start sites. Nucleic Acids Res 35, 2177-90 Auerbach, S. S., Stoner, M. A., Su, S. and Omiecinski, C. J. (2005). Retinoid X receptor-alpha-dependent transactivation by a naturally occurring structural variant of human constitutive androstane receptor (NR1I3). Mol Pharmacol 68, 1239-53. [Abstract Stoner, M. A., Auerbach, S. S., Zamule, S. M., Strom, S. C. and Omiecinski, C. J. (2007). Transactivation of a DR-1 PPRE by a human constitutive androstane receptor variant expressed from internal protein translation start sites. Nucleic Acids Res 35, 2177-90 Auerbach, S. S., Stoner, M. A., Su, S. and Omiecinski, C. J. (2005). Retinoid X receptor-alpha-dependent transactivation by a naturally occurring structural variant of human constitutive androstane receptor (NR1I3). Mol Pharmacol 68, 1239-53.]  
19. Auerbach, S. S., Ramsden, R., Stoner, M. A., Verlinde, C., Hassett, C. and Omiecinski, C. J. (2003). Alternatively spliced isoforms of the human constitutive androstane receptor. Nucleic Acids Res 31, 3194-207. [Abstract Auerbach, S. S., Ramsden, R., Stoner, M. A., Verlinde, C., Hassett, C. and Omiecinski, C. J. (2003). Alternatively spliced isoforms of the human constitutive androstane receptor. Nucleic Acids Res 31, 3194-207.]

Software

• Tox21 Toolbox
  The Tox21 toolbox contains useful tools for accessing and visualizing the Tox21 quantitative high throughput screening (qHTS) 10K library data, as well as integrating with other publicly available data.