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Much of the work carried out by DTT is in support of the National Toxicology Program (NTP), an interagency partnership of the Food and Drug Administration, National Institute for Occupational Safety and Health, and NIEHS.

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Toxicoinformatics Group

Scott S. Auerbach, Ph.D.
Scott S. Auerbach, Ph.D.
Leader, Toxicoinformatics
Tel 984-287-3108
Fax 919-541-3647
[email protected]
Curriculum Vitae (344KB)
P.O. Box 12233
Mail Drop K2-17
Durham, NC 27709
Liver Point7 Network

Scott S. Auerbach, Ph.D., DABT is a Molecular Toxicologist that leads the Toxicoinformatics Group within the Predictive Toxicology Branch of the Division of Translational Toxicology at NIEHS. In additional to his role as Toxicoinformatics Group Leader, he leads efforts related to the analysis and interpretation of multivariate data sets (i.e., microarray, RNA-seq, High-throughput screening) for purposes of informing toxicological assessment.

His specific responsibilities include:

  • Oversight of the NTP DrugMatrix resource and genomic dose-response analysis tools, BMDExpress 2 and BMDExpress 3
  • Multivariate data analysis and modeling with the purpose of prioritizing chemicals for targeted toxicological assessment
  • Use of machine learning approaches to develop multivariate data models that diagnosis and predict toxicological pathology and disease
  • Application of short-term in vivo transcriptomic studies to allow for the identification of genomic benchmark dose values and mechanistic characterization
  • Pathway and network level characterization of toxicity related omics results with the goal of understanding mechanisms of target organ toxicity
  • Use of literature mining and data driven bioinformatics approaches to understand the relationship between chemogenomic perturbations and disease
  • High dimensional data analysis and visualization via network topology
  • Auerbach also helped lead the NTP team's toxicology efforts related to the West Virginia chemical spill that occurred in 2014
  • Leadership of a research group that has developed numerous tools and resources for analyzing and accessing predictive toxicology data

Auerbach received a B.S. in biochemistry and molecular biology from the Pennsylvania State University, State College, Pennsylvania and a Ph.D. in pharmacology from the University of Washington, Seattle, Washington.

Complete list of publications

Selected Publications

  1. Alves VM, Bobrowski T, Melo-Filho CC, Korn D, Auerbach S, Schmitt C, Muratov EN, Tropsha A. 2021. QSAR Modeling of SARS-CoV M pro Inhibitors Identifies Sufugolix, Cenicriviroc, Proglumetacin, and other Drugs as Candidates for Repurposing against SARS-CoV-2. Mol Inform 40(1):e2000113. [Abstract Alves VM, Bobrowski T, Melo-Filho CC, Korn D, Auerbach S, Schmitt C, Muratov EN, Tropsha A. 2021. QSAR Modeling of SARS-CoV M pro Inhibitors Identifies Sufugolix, Cenicriviroc, Proglumetacin, and other Drugs as Candidates for Repurposing against SARS-CoV-2. Mol Inform 40(1):e2000113.]
  2. Bobrowski T, Melo-Filho C, Korn D, Alves VM, Popov KI, Auerbach S, Schmitt C, Moorman N, Muratov E, Tropsha A. 2020. Learning from history: do not flatten the curve of antiviral research! Drug Discov Today; doi: 10.1016/j.drudis.2020.07.008 [Online 15 July 2020]. [Abstract Bobrowski T, Melo-Filho C, Korn D, Alves VM, Popov KI, Auerbach S, Schmitt C, Moorman N, Muratov E, Tropsha A. 2020. Learning from history: do not flatten the curve of antiviral research! Drug Discov Today; doi: 10.1016/j.drudis.2020.07.008 [Online 15 July 2020].]
  3. Gwinn WM, Auerbach SS, Parham F, Stout MD, Waidyanatha S, Mutlu E, Collins B, Paules RS, Merrick BA, Ferguson S, Ramaiahgari S, Bucher JR, Sparrow B, Toy H, Gorospe J, Machesky N, Shah RR, Balik-Meisner MR, Mav D, Phadke DP, Roberts G, DeVito MJ. 2020. Evaluation of 5-Day In Vivo Rat Liver and Kidney With High-Throughput Transcriptomics for Estimating Benchmark Doses of Apical Outcomes. Toxicol Sci; doi: 10.1093/toxsci/kfaa081 [Online 3 June 2020]. [Abstract Gwinn WM, Auerbach SS, Parham F, Stout MD, Waidyanatha S, Mutlu E, Collins B, Paules RS, Merrick BA, Ferguson S, Ramaiahgari S, Bucher JR, Sparrow B, Toy H, Gorospe J, Machesky N, Shah RR, Balik-Meisner MR, Mav D, Phadke DP, Roberts G, DeVito MJ. 2020. Evaluation of 5-Day In Vivo Rat Liver and Kidney With High-Throughput Transcriptomics for Estimating Benchmark Doses of Apical Outcomes. Toxicol Sci; doi: 10.1093/toxsci/kfaa081 [Online 3 June 2020].]
  4. Bushel PR, Paules RS, Auerbach SS. A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples. Frontiers in Genetics 2018 9():485-. [Abstract Bushel PR, Paules RS, Auerbach SS. A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples. Frontiers in Genetics 2018 9():485-.]
  5. Gwinn WM, Bousquet RW, Perry CE, Auerbach SS. NTP Research Report on the Preliminary Evaluation of 4-Methylcyclohexylmethanol in an In Vitro Human Airway Model: Research Report 7. NTP Research Report 2018 ():-. [Abstract Gwinn WM, Bousquet RW, Perry CE, Auerbach SS. NTP Research Report on the Preliminary Evaluation of 4-Methylcyclohexylmethanol in an In Vitro Human Airway Model: Research Report 7. NTP Research Report 2018 ():-.]
  6. Roberts GK, Gardner D, Foster PM, Howard PC, Lui E, Walker L, van Breemen RB, Auerbach SS. Finding the bad actor: Challenges in identifying toxic constituents in botanical dietary supplements. Food and Chemical Toxicology: an international journal published for the British Industrial Biological Research Association 2018 ():-. [Abstract Roberts GK, Gardner D, Foster PM, Howard PC, Lui E, Walker L, van Breemen RB, Auerbach SS. Finding the bad actor: Challenges in identifying toxic constituents in botanical dietary supplements. Food and Chemical Toxicology: an international journal published for the British Industrial Biological Research Association 2018 ():-.]
  7. Pelch KE, Wignall J, Goldstone AE, Ross PK, Blain RB, Shapiro AJ, Holmgren SD, Hsieh JH, Svoboda D, Auerbach SS, Parham FM, Masten SA, Thayer KA. Biological Activity of Bisphenol A (BPA) Structural Analogues and Functional Alternatives. NTP Research Report 2017 RR-04():1-80. [Abstract Pelch KE, Wignall J, Goldstone AE, Ross PK, Blain RB, Shapiro AJ, Holmgren SD, Hsieh JH, Svoboda D, Auerbach SS, Parham FM, Masten SA, Thayer KA. Biological Activity of Bisphenol A (BPA) Structural Analogues and Functional Alternatives. NTP Research Report 2017 RR-04():1-80.]
  8. Dennis KK, Auerbach SS, Balshaw DM, Cui Y, Fallin MD, Smith MT, Spira A, Sumner SJ, Miller GW. The Importance of the Biological Impact of Exposure to the Concept of the Exposome. Environmental health perspectives 2016 124(10):1504-1510. [Abstract Dennis KK, Auerbach SS, Balshaw DM, Cui Y, Fallin MD, Smith MT, Spira A, Sumner SJ, Miller GW. The Importance of the Biological Impact of Exposure to the Concept of the Exposome. Environmental health perspectives 2016 124(10):1504-1510.]
  9. 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.]
  10. 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.]
  11. 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.]
  12. 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]
  13. 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].]
  14. 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.]
  15. 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-.]
  16. 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.]
  17. 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.]
  18. 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.]
  19. 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.]
  20. 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.]
  21. 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.]
  22. 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.]
  23. 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.]
  24. 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.]
  25. 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.]
  26. 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.]
  27. 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.]