10
R. Kusko and H. Hong
12. Ng HW, Doughty SW, Luo H, Ye H, Ge W, Tong W, Hong H (2015) Development and validation
of decision forest model for estrogen receptor binding prediction of chemicals using large data
sets. Chem Res Toxicol 28:2343–2351
13. Sakkiah S, Ng HW, Tong W, Hong H (2016) Structures of androgen receptor bound with ligands:
advancing understanding of biological functions and drug discovery. Expert Opin Ther Targets
20(10):1267–1282
14. Hong H, Shen J, Ng HW, Sakkiah S, Ye H, Ge W, Gong P, Xiao W (2016) A rat α-fetoprotein
binding activity prediction model to facilitate assessment of the endocrine disruption potential
of environmental chemicals. Int J Environ Res Public Health 13(4):372
15. Luo H, Ye H, Ng HW, Sakkiah S, Mendrick DL, Hong H (2016) sNebula, a network-based
algorithm to predict binding between human leukocyte antigens and peptides. Sci Rep 6:32115
16. Hong H, Thakkar T, Chen M, Tong W (2017) Development of decision forest models for
prediction of drug-induced liver injury in humans using a large set of FDA-approved drugs.
Sci Rep 7(1):17311
17. Selvaraj C, Sakkiah S, Tong W, Hong H (2018) Molecular dynamics simulations and applications in computational toxicology and nanotoxicology. Food Chem Toxicol 112:495–506
18. Ashby J, Tennant RW (1988) Chemical structure, Salmonella mutagenicity and extent of carcinogenicity as indicators of genotoxic carcinogenesis among 222 chemicals tested in rodents
by the U.S. NCI/NTP. Mutat Res 204:17–115
19. Hong H, Tong W, Fang H, Shi L, Xie Q, Wu J, Perkins R, Walker JD, Branham W, Sheehan
DM (2002) Prediction of estrogen receptor binding for 58,000 chemicals using an integrated
system of a tree-based model with structural alerts. Environ Health Perspect 110(1):29–36
20. Hong H, Zhang W, Shen J, Su Z, Ning B, Han T, Perkins R, Shi L, Tong W (2013) Critical
role of bioinformatics in translating huge amounts of next-generation sequencing data into
personalized medicine. Sci China Life Sci 56(2):110–118
21. Haghighat M, Abdel-Mottaleb M, Alhalabi W (2016) Discriminant correlation analysis: realtime feature level fusion for multimodal biometric recognition. IEEE Trans Inf Forensics Secur
11(9):1984–1996
22. Ye H, Luo H, Ng HW, Meehan J, Ge W, Tong W, Hong H (2016) Applying network analysis
and Nebula (neighbor-edges based and unbiased leverage algorithm) to ToxCast data. Environ
Int 89–90:81–92
23. Luo H, Ye H, Ng H, Shi L, Tong W, Mattes W, Mendrick D, Hong H (2015) Understanding
and predicting binding between human leukocyte antigens (HLAs) and peptides by network
analysis. BMC Bioinform 16(Suppl 13):S9
24. US EPA. Mechanisms and mode of dioxin action. Retrieved from https://web.archive.org/
web/20150226023800/, http://www.epa.gov/ncea/pdfs/dioxin/nas-review/pdfs/part3/dioxin_
pt3_ch03_oct2004.pdf. Accessed on 24 Nov 2018
25. Hong H, Xie Q, Ge W, Qian F, Fang H, Shi L, Su Z, Perkins R, Tong W (2008) Mold2, molecular
descriptors from 2D structures for chemoinformatics and toxicoinformatics. J Chem Inf Model
48(7):1337–1344
26. Wang C, Gong B, Bushel PR, Thierry-Mieg J et al (2014) The concordance between RNA-seq
and microarray data depends on chemical treatment and transcript abundance. Nat Biotechnol
32(9):926–932
27. Sakkiah S, Kusko R, Pan B, Guo W, Ge W, Tong W, Hong H (2018) Structural changes due to
antagonist binding in ligand binding pocket of androgen receptor elucidated through molecular
dynamics simulations. Front Pharmacol 9:492
28. Tetko IV, Sushko I, Pandey AK, Zhu H, Tropsha A, Papa E, Oberg T, Todeschini R, Fourches
D, Varnek A (2008) Critical assessment of QSAR models of environmental toxicity against
Tetrahymena pyriformis: focusing on applicability domain and overfitting by variable selection.
J Chem Inf Model 48(9):1733–1746
29. International Council for Harmonisation of Technical Requirements for Pharmaceuticals
for Human use (ICH). Assessment and control of DNA reactive (mutagenic) impurities
in pharmaceuticals to limit potential carcinogenic risk. Retrieved from https://www.ich.
org/fileadmin/Public_Web_Site/ICH_Products/Guidelines/Multidisciplinary/M7/M7_R1_
Addendum_Step_4_2017_0331.pdf. Accessed on Nov 26 2018
R. Kusko and H. Hong
12. Ng HW, Doughty SW, Luo H, Ye H, Ge W, Tong W, Hong H (2015) Development and validation
of decision forest model for estrogen receptor binding prediction of chemicals using large data
sets. Chem Res Toxicol 28:2343–2351
13. Sakkiah S, Ng HW, Tong W, Hong H (2016) Structures of androgen receptor bound with ligands:
advancing understanding of biological functions and drug discovery. Expert Opin Ther Targets
20(10):1267–1282
14. Hong H, Shen J, Ng HW, Sakkiah S, Ye H, Ge W, Gong P, Xiao W (2016) A rat α-fetoprotein
binding activity prediction model to facilitate assessment of the endocrine disruption potential
of environmental chemicals. Int J Environ Res Public Health 13(4):372
15. Luo H, Ye H, Ng HW, Sakkiah S, Mendrick DL, Hong H (2016) sNebula, a network-based
algorithm to predict binding between human leukocyte antigens and peptides. Sci Rep 6:32115
16. Hong H, Thakkar T, Chen M, Tong W (2017) Development of decision forest models for
prediction of drug-induced liver injury in humans using a large set of FDA-approved drugs.
Sci Rep 7(1):17311
17. Selvaraj C, Sakkiah S, Tong W, Hong H (2018) Molecular dynamics simulations and applications in computational toxicology and nanotoxicology. Food Chem Toxicol 112:495–506
18. Ashby J, Tennant RW (1988) Chemical structure, Salmonella mutagenicity and extent of carcinogenicity as indicators of genotoxic carcinogenesis among 222 chemicals tested in rodents
by the U.S. NCI/NTP. Mutat Res 204:17–115
19. Hong H, Tong W, Fang H, Shi L, Xie Q, Wu J, Perkins R, Walker JD, Branham W, Sheehan
DM (2002) Prediction of estrogen receptor binding for 58,000 chemicals using an integrated
system of a tree-based model with structural alerts. Environ Health Perspect 110(1):29–36
20. Hong H, Zhang W, Shen J, Su Z, Ning B, Han T, Perkins R, Shi L, Tong W (2013) Critical
role of bioinformatics in translating huge amounts of next-generation sequencing data into
personalized medicine. Sci China Life Sci 56(2):110–118
21. Haghighat M, Abdel-Mottaleb M, Alhalabi W (2016) Discriminant correlation analysis: realtime feature level fusion for multimodal biometric recognition. IEEE Trans Inf Forensics Secur
11(9):1984–1996
22. Ye H, Luo H, Ng HW, Meehan J, Ge W, Tong W, Hong H (2016) Applying network analysis
and Nebula (neighbor-edges based and unbiased leverage algorithm) to ToxCast data. Environ
Int 89–90:81–92
23. Luo H, Ye H, Ng H, Shi L, Tong W, Mattes W, Mendrick D, Hong H (2015) Understanding
and predicting binding between human leukocyte antigens (HLAs) and peptides by network
analysis. BMC Bioinform 16(Suppl 13):S9
24. US EPA. Mechanisms and mode of dioxin action. Retrieved from https://web.archive.org/
web/20150226023800/, http://www.epa.gov/ncea/pdfs/dioxin/nas-review/pdfs/part3/dioxin_
pt3_ch03_oct2004.pdf. Accessed on 24 Nov 2018
25. Hong H, Xie Q, Ge W, Qian F, Fang H, Shi L, Su Z, Perkins R, Tong W (2008) Mold2, molecular
descriptors from 2D structures for chemoinformatics and toxicoinformatics. J Chem Inf Model
48(7):1337–1344
26. Wang C, Gong B, Bushel PR, Thierry-Mieg J et al (2014) The concordance between RNA-seq
and microarray data depends on chemical treatment and transcript abundance. Nat Biotechnol
32(9):926–932
27. Sakkiah S, Kusko R, Pan B, Guo W, Ge W, Tong W, Hong H (2018) Structural changes due to
antagonist binding in ligand binding pocket of androgen receptor elucidated through molecular
dynamics simulations. Front Pharmacol 9:492
28. Tetko IV, Sushko I, Pandey AK, Zhu H, Tropsha A, Papa E, Oberg T, Todeschini R, Fourches
D, Varnek A (2008) Critical assessment of QSAR models of environmental toxicity against
Tetrahymena pyriformis: focusing on applicability domain and overfitting by variable selection.
J Chem Inf Model 48(9):1733–1746
29. International Council for Harmonisation of Technical Requirements for Pharmaceuticals
for Human use (ICH). Assessment and control of DNA reactive (mutagenic) impurities
in pharmaceuticals to limit potential carcinogenic risk. Retrieved from https://www.ich.
org/fileadmin/Public_Web_Site/ICH_Products/Guidelines/Multidisciplinary/M7/M7_R1_
Addendum_Step_4_2017_0331.pdf. Accessed on Nov 26 2018