Superfund Research Program

Research Support A: Computational Modeling of Mammalian Biomolecular Responses

Project Leader: Rory B. Conolly (U.S. Environmental Protection Agency (EPA))
Co-Investigator: Qiang Zhang (The Hamner Institutes for Health Sciences)
Grant Number: P42ES004911
Funding Period: 2006-2021

Project-Specific Links

Publications

2022

• Liu S, Pi J, Zhang Q. 2022. Signal amplification in the KEAP1-NRF2-ARE antioxidant response pathway. Redox Biol 54:102389. doi:10.1016/j.redox.2022.102389 PMID:35792437 PMCID:PMC9287733
• Shi Z, Xia M, Xiao S, Zhang Q. 2022. Identification of nonmonotonic concentration-responses in Tox21 high-throughput screening estrogen receptor assays. Toxicol Appl Pharmacol 452:116206. doi:10.1016/j.taap.2022.116206 PMID:35988584 PMCID:PMC9452481

2021

• Gingrich J, Filipovic D, Conolly RB, Veiga-Lopez A. 2021. Pregnancy-specific physiologically-based toxicokinetic models for bisphenol A and bisphenol S. Environ Int 147:106301. doi:10.1016/j.envint.2020.106301 PMID:33360411 PMCID:PMC7856209
• Liu S, Pi J, Zhang Q. 2021. Mathematical modeling reveals quantitative properties of KEAP1-NRF2 signaling. Redox Biol 47:doi:10.1016/j.redox.2021.102139 PMID:34600335 PMCID:PMC8531862
• Nault R, Fader KA, Zacharewski TR. 2021. Single-nuclei RNA sequencing assessment of the hepatic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin. Cell Mol Gastroenterol Hepatol 11:147-159. doi:10.1016/j.jcmgh.2020.07.012 PMID:32791302 PMCID:PMC7674514

2019

• Davis JD, Kumbale CM, Zhang Q, Voit EO. 2019. Dynamical systems approaches to personalized medicine. Curr Opin Biotechnol 58:168-174. doi:10.1016/j.copbio.2019.03.005 PMID:30978644 PMCID:PMC7050596
• Josyula N, Andersen ME, Kaminski NE, Dere E, Zacharewski TR, Bhattacharya S. 2019. Gene co-regulation and co-expression in the aryl hydrocarbon receptor-mediated transcriptional regulatory network in the mouse liver. Arch Toxicol 94:113-126. doi:10.1007/s00204-019-02620-5 PMID:31728591
• Zhang Q, Caudle W, Pi J, Bhattacharya S, Andersen ME, Kaminski NE, Conolly RB. 2019. Embracing systems toxicology at single-cell resolution. Curr Opin Toxicol 16:49-57. doi:10.1016/j.cotox.2019.04.003 PMID:31768481 PMCID:PMC6876623

2018

• Zhang Q, Li J, Middleton A, Bhattacharya S, Conolly RB. 2018. Bridging the data gap from in vitro toxicity testing to chemical safety assessment through computational modeling. Front Public Health 6:261. doi:10.3389/fpubh.2018.00261 PMID:30255008 PMCID:PMC6141783
• Zhou J, Zhang Q, Henriquez J, Crawford RB, Kaminski NE. 2018. Lymphocyte-specific protein tyrosine kinase (LCK) is involved in the aryl hydrocarbon receptor-mediated impairment of immunoglobulin secretion in human primary B cells. Toxicol Sci 165(2):322-334. doi:10.1093/toxsci/kfy133 PMID:29860352

2017

• Jagannathan L, Jose CC, Tanwar VS, Bhattacharya S, Cuddapah S. 2017. Identification of a unique gene expression signature in mercury and 2,3,7,8-tetrachlorodibenzo-p-dioxin co-exposed cells. Toxicol Res (Camb) 6(3):312-323. doi:10.1039/C6TX00432F PMID:29057067 PMCID:PMC5648359
• Mumtaz MM, Ruiz P, Zhang Q. 2017. Computational tools for chemical toxicity testing and risk assessment under the framework of adverse outcome pathways. Chapter 8 in: Computational Systems Pharmacology and Toxicology. Royal Society of Chemistry, pp.191-208.

2015

• Zhang Q, Bhattacharya S, Clewell RA, Carmichael PL, Andersen ME. 2015. Adaptive posttranslational control in cellular stress response pathways and its relationship to toxicity testing and safety assessment. Toxicol Sci 147(2):302-316. doi:10.1093/toxsci/kfv130 PMID:26408567 PMCID:PMC4707198

2014

• Zhang Q, Bhattacharya S, Conolly RB, Clewell H, Andersen ME. 2014. Molecular signaling network motifs provide a mechanistic basis for cellular threshold responses. Environ Health Perspect 122(12):1261-1270. doi:10.1289/ehp.1408244 PMID:25117432 PMCID:PMC4256703

2013

• Zhang Q, Bhattacharya S, Andersen ME. 2013. Ultrasensitive response motifs: Basic amplifiers in molecular signalling networks. Open Biol 3(4):130031. doi:10.1098/rsob.130031 PMID:23615029 PMCID:PMC3718334
• Zhang Q, Kline DE, Bhattacharya S, Crawford RB, Conolly RB, Thomas RS, Andersen ME, Kaminski NE. 2013. All-or-none suppression of B cell terminal differentiation by environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin. Toxicol Appl Pharmacol 268(1):17-26. doi:10.1016/j.taap.2013.01.015 PMID:23357550 PMCID:PMC3594464

2011

• Bhattacharya S, Zhang Q, Andersen ME. 2011. Double-negative feedback loops as a common design motif in the transcriptional networks regulating cell fate. International Journal of Design Engineering 4:41-57. doi:10.1504/IJDE.2011.041408

2010

• Andersen ME, Zhang Q, Bhattacharya S. 2010. Modeling Gene and Protein Expression - Nested Motifs in Cellular and Tissue Response Networks. Chapter 10 in: Quantitative Modeling in Toxicology. John Wiley & Sons, Hoboken, NJ.
• Bhattacharya S, Zhang Q, Andersen ME. 2010. Bistable Signaling Motifs and Cell Fate Decisions. Chapter 8 in: Quantitative Modeling in Toxicology. John Wiley & Sons, Hoboken, NJ.
• Zhang Q, Bhattacharya S, Andersen ME, Conolly RB. 2010. Computational systems biology and dose-response modeling in relation to new directions in toxicity testing. J Environ Sci Health B 13(2-4):253-76. doi:10.1080/10937404.2010.483943 PMID:20574901
• Zhang Q, Bhattacharya S, Kline DE, Crawford RB, Thomas RS, Kaminski NE, Andersen ME, Conolly RB. 2010. Stochastic modeling of B lymphocyte terminal differentiation and its suppression by dioxin. BMC Syst Biol 4:40. doi:10.1186/1752-0509-4-40 PMID:20359356 PMCID:PMC2859749
• Zhang Q, Bhattacharya S, Woods CG, Andersen ME. 2010. Ultrasensitive Response Motifs in Biochemical Networks. Chapter 9 in: Quantitative Modeling in Toxicology. John Wiley & Sons, Hoboken, NJ. pp.199-218.
• Zhang Q, Pi J, Woods CG, Andersen ME. 2010. A systems biology perspective on Nrf2-mediated antioxidant response. Toxicol Appl Pharmacol 244(1):84-97. doi:10.1016/j.taap.2009.08.018 PMID:19716833 PMCID:PMC2837757

2009

• Zhang Q, Pi J, Woods CG, Andersen ME. 2009. Phase I to II cross-induction of xenobiotic metabolizing enzymes: a feedforward control mechanism for potential hormetic responses. Toxicol Appl Pharmacol 237(3):345-356. doi:10.1016/j.taap.2009.04.005 PMID:19371757 PMCID:PMC2696203

2006

• Zhang Q, Thomas RS, Kaminski NE, Conolly RB, Andersen ME. 2006. Computational modeling of TCDD disruption of B-cell terminal differentiation. In: Superfund Basic Research Program Annual Meeting, December 11-12. La Jolla, CA.