14 Predictive Modeling of Tox21 Data
295
9. Hsu CW, Zhao J, Huang R, Hsieh JH, Hamm J, Chang X, Houck K, Xia M (2014) Quantitative
high-throughput profiling of environmental chemicals and drugs that modulate farnesoid X
receptor. Sci Rep 4:6437. https://doi.org/10.1038/srep06437
10. Huang R, Sakamuru S, Martin MT, Reif DM, Judson RS, Houck KA, Casey W, Hsieh JH,
Shockley KR, Ceger P, Fostel J, Witt KL, Tong W, Rotroff DM, Zhao T, Shinn P, Simeonov A,
Dix DJ, Austin CP, Kavlock RJ, Tice RR, Xia M (2014) Profiling of the Tox21 10K compound
library for agonists and antagonists of the estrogen receptor alpha signaling pathway. Sci Rep
4:5664. https://doi.org/10.1038/srep05664
11. Huang R, Xia M, Cho MH, Sakamuru S, Shinn P, Houck KA, Dix DJ, Judson RS, Witt
KL, Kavlock RJ, Tice RR, Austin CP (2011) Chemical genomics profiling of environmental
chemical modulation of human nuclear receptors. Environ Health Perspect 119(8):1142–1148
12. Lynch C, Zhao J, Huang R, Kanaya N, Bernal L, Hsieh JH, Auerbach SS, Witt KL, Merrick
BA, Chen S, Teng CT, Xia M (2018) Identification of estrogen-related receptor alpha agonists
in the Tox21 compound library. Endocrinology 159(2):744–753
13. Lynch C, Sakamuru S, Huang R, Stavreva DA, Varticovski L, Hager GL, Judson RS, Houck
KA, Kleinstreuer NC, Casey W, Paules RS, Simeonov A, Xia M (2017) Identifying environmental chemicals as agonists of the androgen receptor by using a quantitative high-throughput
screening platform. Toxicology 385:48–58
14. Attene-Ramos MS, Huang R, Michael S, Witt KL, Richard A, Tice RR, Simeonov A, Austin
CP, Xia M (2015) Profiling of the Tox21 chemical collection for mitochondrial function to
identify compounds that acutely decrease mitochondrial membrane potential. Environ Health
Perspect 123(1):49–56
15. Nishihara K, Huang R, Zhao J, Shahane SA, Witt KL, Smith-Roe SL, Tice RR, Takeda S, Xia
M (2015) Identification of genotoxic compounds using isogenic DNA repair deficient DT40
cell lines on a quantitative high throughput screening platform. Mutagenesis 31(1):69–81
16. Witt KL, Hsieh JH, Smith-Roe SL, Xia M, Huang R, Zhao J, Auerbach SS, Hur J, Tice
RR (2017) Assessment of the DNA damaging potential of environmental chemicals using
a quantitative high-throughput screening approach to measure p53 activation. Environ Mol
Mutagen 58(7):494–507
17. Huang R, Xia M, Sakamuru S, Zhao J, Shahane SA, Attene-Ramos M, Zhao T, Austin CP,
Simeonov A (2016) Modelling the Tox21 10K chemical profiles for in vivo toxicity prediction
and mechanism characterization. Nat Commun 7:10425
18. PubChem (2016) Tox21 phase II data 2016 [cited 16 Nov 2013]. Available from http://www.
ncbi.nlm.nih.gov/pcassay?term=tox21
19. Huang R, Xia M, Sakamuru S, Zhao J, Lynch C, Zhao T, Zhu H, Austin CP, Simeonov A
(2018) Expanding biological space coverage enhances the prediction of drug adverse effects
in human using in vitro activity profiles. Sci Rep 8(1):3783
20. Huang R, Southall N, Wang Y, Yasgar A, Shinn P, Jadhav A, Nguyen DT, Austin CP (2011)
The NCGC pharmaceutical collection: a comprehensive resource of clinically approved drugs
enabling repurposing and chemical genomics. Sci Transl Med 3(80):80ps16
21. Huang R (2016) A quantitative high-throughput screening data analysis pipeline for activity
profiling. In: Zhu H, Xia M (eds) High-throughput screening assays in toxicology. Methods in
molecular biology, vol 1473. Humana Press
22. Wang Y, Huang R (2016) Correction of microplate data from high throughput screening. In:
Zhu H, Xia M (eds) High-throughput screening assays in toxicology. Methods in molecular
biology, vol 1473. Humana Press
23. Kohonen T (2006) Self-organizing neural projections. Neural Networks Official J Int Neural
Network Soc 19(6–7):723–733
295
9. Hsu CW, Zhao J, Huang R, Hsieh JH, Hamm J, Chang X, Houck K, Xia M (2014) Quantitative
high-throughput profiling of environmental chemicals and drugs that modulate farnesoid X
receptor. Sci Rep 4:6437. https://doi.org/10.1038/srep06437
10. Huang R, Sakamuru S, Martin MT, Reif DM, Judson RS, Houck KA, Casey W, Hsieh JH,
Shockley KR, Ceger P, Fostel J, Witt KL, Tong W, Rotroff DM, Zhao T, Shinn P, Simeonov A,
Dix DJ, Austin CP, Kavlock RJ, Tice RR, Xia M (2014) Profiling of the Tox21 10K compound
library for agonists and antagonists of the estrogen receptor alpha signaling pathway. Sci Rep
4:5664. https://doi.org/10.1038/srep05664
11. Huang R, Xia M, Cho MH, Sakamuru S, Shinn P, Houck KA, Dix DJ, Judson RS, Witt
KL, Kavlock RJ, Tice RR, Austin CP (2011) Chemical genomics profiling of environmental
chemical modulation of human nuclear receptors. Environ Health Perspect 119(8):1142–1148
12. Lynch C, Zhao J, Huang R, Kanaya N, Bernal L, Hsieh JH, Auerbach SS, Witt KL, Merrick
BA, Chen S, Teng CT, Xia M (2018) Identification of estrogen-related receptor alpha agonists
in the Tox21 compound library. Endocrinology 159(2):744–753
13. Lynch C, Sakamuru S, Huang R, Stavreva DA, Varticovski L, Hager GL, Judson RS, Houck
KA, Kleinstreuer NC, Casey W, Paules RS, Simeonov A, Xia M (2017) Identifying environmental chemicals as agonists of the androgen receptor by using a quantitative high-throughput
screening platform. Toxicology 385:48–58
14. Attene-Ramos MS, Huang R, Michael S, Witt KL, Richard A, Tice RR, Simeonov A, Austin
CP, Xia M (2015) Profiling of the Tox21 chemical collection for mitochondrial function to
identify compounds that acutely decrease mitochondrial membrane potential. Environ Health
Perspect 123(1):49–56
15. Nishihara K, Huang R, Zhao J, Shahane SA, Witt KL, Smith-Roe SL, Tice RR, Takeda S, Xia
M (2015) Identification of genotoxic compounds using isogenic DNA repair deficient DT40
cell lines on a quantitative high throughput screening platform. Mutagenesis 31(1):69–81
16. Witt KL, Hsieh JH, Smith-Roe SL, Xia M, Huang R, Zhao J, Auerbach SS, Hur J, Tice
RR (2017) Assessment of the DNA damaging potential of environmental chemicals using
a quantitative high-throughput screening approach to measure p53 activation. Environ Mol
Mutagen 58(7):494–507
17. Huang R, Xia M, Sakamuru S, Zhao J, Shahane SA, Attene-Ramos M, Zhao T, Austin CP,
Simeonov A (2016) Modelling the Tox21 10K chemical profiles for in vivo toxicity prediction
and mechanism characterization. Nat Commun 7:10425
18. PubChem (2016) Tox21 phase II data 2016 [cited 16 Nov 2013]. Available from http://www.
ncbi.nlm.nih.gov/pcassay?term=tox21
19. Huang R, Xia M, Sakamuru S, Zhao J, Lynch C, Zhao T, Zhu H, Austin CP, Simeonov A
(2018) Expanding biological space coverage enhances the prediction of drug adverse effects
in human using in vitro activity profiles. Sci Rep 8(1):3783
20. Huang R, Southall N, Wang Y, Yasgar A, Shinn P, Jadhav A, Nguyen DT, Austin CP (2011)
The NCGC pharmaceutical collection: a comprehensive resource of clinically approved drugs
enabling repurposing and chemical genomics. Sci Transl Med 3(80):80ps16
21. Huang R (2016) A quantitative high-throughput screening data analysis pipeline for activity
profiling. In: Zhu H, Xia M (eds) High-throughput screening assays in toxicology. Methods in
molecular biology, vol 1473. Humana Press
22. Wang Y, Huang R (2016) Correction of microplate data from high throughput screening. In:
Zhu H, Xia M (eds) High-throughput screening assays in toxicology. Methods in molecular
biology, vol 1473. Humana Press
23. Kohonen T (2006) Self-organizing neural projections. Neural Networks Official J Int Neural
Network Soc 19(6–7):723–733