8 An Overview of National Toxicology Program’s Toxicogenomic …
157
28. Mulas F, Li A, Sherr DH, Monti S (2017) Network-based analysis of transcriptional profiles
from chemical perturbations experiments. BMC Bioinform 18(Suppl 5):130
29. Taguchi YH (2017) Identification of candidate drugs using tensor-decomposition-based unsupervised feature extraction in integrated analysis of gene expression between diseases and
DrugMatrix datasets. Sci Rep 7(1):13733
30. Sutherland JJ, Webster YW, Willy JA, Searfoss GH, Goldstein KM, Irizarry AR, Hall DG,
Stevens JL (2017) Toxicogenomic module associations with pathogenesis: a network-based
approach to understanding drug toxicity. Pharmacogenomics J
31. Gong B, Wang C, Su Z, Hong H, Thierry-Mieg J, Thierry-Mieg D, Shi L, Auerbach SS, Tong
W, Xu J (2014) Transcriptomic profiling of rat liver samples in a comprehensive study design
by RNA-Seq. Sci Data 1:140021
32. Romer M, Backert L, Eichner J, Zell A (2014) ToxDBScan: large-scale similarity screening of
toxicological databases for drug candidates. Int J Mol Sci 15(10):19037–19055
33. Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins
SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma’ayan A
(2016) Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic
Acids Res 44(W1):W90–W97
34. Liu L, Tsompana M, Wang Y, Wu D, Zhu L, Zhu R (2016) Connection map for compounds
(CMC): a server for combinatorial drug toxicity and efficacy analysis. J Chem Inf Model
56(9):1615–1621
35. Xing L, Wu L, Liu Y, Ai N, Lu X, Fan X (2014) LTMap: a web server for assessing the potential
liver toxicity by genome-wide transcriptional expression data. J Appl Toxicol 34(7):805–809
36. Hur J, Danes L, Hsieh JH, McGregor B, Krout D, Auerbach S (2018) Tox21 enricher: webbased chemical/biological functional annotation analysis tool based on Tox21 toxicity screening
platform. Mol Inform 37(5):e1700129
37. Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson
F, Bellis LJ, Cibrian-Uhalte E, Davies M, Dedman N, Karlsson A, Magarinos MP, Overington
JP, Papadatos G, Smit I, Leach AR (2017) The ChEMBL database in 2017. Nucleic Acids Res
45(D1):D945–D954
38. Kupershmidt I, Su QJ, Grewal A, Sundaresh S, Halperin I, Flynn J, Shekar M, Wang H, Park
J, Cui W, Wall GD, Wisotzkey R, Alag S, Akhtari S, Ronaghi M (2010) Ontology-based
meta-analysis of global collections of high-throughput public data. PLoS One 5(9)
39. Kohonen P, Benfenati E, Bower D, Ceder R, Crump M, Cross K, Grafstrom RC, Healy L,
Helma C, Jeliazkova N, Jeliazkov V, Maggioni S, Miller S, Myatt G, Rautenberg M, Stacey
G, Willighagen E, Wiseman J, Hardy B (2013) The toxbank data warehouse: supporting the
replacement of in vivo repeated dose systemic toxicity testing. Mol Inform 32(1):47–63
40. Lea IA, Gong H, Paleja A, Rashid A, Fostel J (2017) CEBS: a comprehensive annotated
database of toxicological data. Nucleic Acids Res 45(D1):D964–D971
Daniel L. Svoboda is a Data Scientist at Sciome LLC. He primarily collaborates with the Division of the National Toxicology Program, National Institute of Environmental Health Sciences.
His work is focused on the application of molecular and high-dimensional data to toxicological
assessment, and the development and maintenance of pertinent software applications.
Trey Saddler is a contract Data Scientist in the Office of Data Science at the National Toxicology Program. Trey mainly writes web applications and data analysis pipelines in R and Python to
analyze genomic data.
Scott S. Auerbach is a Group Leader in Toxicoinformatics at the National Toxicology Program. His research focuses on application of molecular and high-dimensional data to toxicological
assessment.
157
28. Mulas F, Li A, Sherr DH, Monti S (2017) Network-based analysis of transcriptional profiles
from chemical perturbations experiments. BMC Bioinform 18(Suppl 5):130
29. Taguchi YH (2017) Identification of candidate drugs using tensor-decomposition-based unsupervised feature extraction in integrated analysis of gene expression between diseases and
DrugMatrix datasets. Sci Rep 7(1):13733
30. Sutherland JJ, Webster YW, Willy JA, Searfoss GH, Goldstein KM, Irizarry AR, Hall DG,
Stevens JL (2017) Toxicogenomic module associations with pathogenesis: a network-based
approach to understanding drug toxicity. Pharmacogenomics J
31. Gong B, Wang C, Su Z, Hong H, Thierry-Mieg J, Thierry-Mieg D, Shi L, Auerbach SS, Tong
W, Xu J (2014) Transcriptomic profiling of rat liver samples in a comprehensive study design
by RNA-Seq. Sci Data 1:140021
32. Romer M, Backert L, Eichner J, Zell A (2014) ToxDBScan: large-scale similarity screening of
toxicological databases for drug candidates. Int J Mol Sci 15(10):19037–19055
33. Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins
SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma’ayan A
(2016) Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic
Acids Res 44(W1):W90–W97
34. Liu L, Tsompana M, Wang Y, Wu D, Zhu L, Zhu R (2016) Connection map for compounds
(CMC): a server for combinatorial drug toxicity and efficacy analysis. J Chem Inf Model
56(9):1615–1621
35. Xing L, Wu L, Liu Y, Ai N, Lu X, Fan X (2014) LTMap: a web server for assessing the potential
liver toxicity by genome-wide transcriptional expression data. J Appl Toxicol 34(7):805–809
36. Hur J, Danes L, Hsieh JH, McGregor B, Krout D, Auerbach S (2018) Tox21 enricher: webbased chemical/biological functional annotation analysis tool based on Tox21 toxicity screening
platform. Mol Inform 37(5):e1700129
37. Gaulton A, Hersey A, Nowotka M, Bento AP, Chambers J, Mendez D, Mutowo P, Atkinson
F, Bellis LJ, Cibrian-Uhalte E, Davies M, Dedman N, Karlsson A, Magarinos MP, Overington
JP, Papadatos G, Smit I, Leach AR (2017) The ChEMBL database in 2017. Nucleic Acids Res
45(D1):D945–D954
38. Kupershmidt I, Su QJ, Grewal A, Sundaresh S, Halperin I, Flynn J, Shekar M, Wang H, Park
J, Cui W, Wall GD, Wisotzkey R, Alag S, Akhtari S, Ronaghi M (2010) Ontology-based
meta-analysis of global collections of high-throughput public data. PLoS One 5(9)
39. Kohonen P, Benfenati E, Bower D, Ceder R, Crump M, Cross K, Grafstrom RC, Healy L,
Helma C, Jeliazkova N, Jeliazkov V, Maggioni S, Miller S, Myatt G, Rautenberg M, Stacey
G, Willighagen E, Wiseman J, Hardy B (2013) The toxbank data warehouse: supporting the
replacement of in vivo repeated dose systemic toxicity testing. Mol Inform 32(1):47–63
40. Lea IA, Gong H, Paleja A, Rashid A, Fostel J (2017) CEBS: a comprehensive annotated
database of toxicological data. Nucleic Acids Res 45(D1):D964–D971
Daniel L. Svoboda is a Data Scientist at Sciome LLC. He primarily collaborates with the Division of the National Toxicology Program, National Institute of Environmental Health Sciences.
His work is focused on the application of molecular and high-dimensional data to toxicological
assessment, and the development and maintenance of pertinent software applications.
Trey Saddler is a contract Data Scientist in the Office of Data Science at the National Toxicology Program. Trey mainly writes web applications and data analysis pipelines in R and Python to
analyze genomic data.
Scott S. Auerbach is a Group Leader in Toxicoinformatics at the National Toxicology Program. His research focuses on application of molecular and high-dimensional data to toxicological
assessment.