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Development of a prioritization method for chemical-mediated effects on steroidogenesis using an integrated statistical analysis of high-throughput H295R data.

Haggard DE, Setzer RW, Judson RS, Paul Friedman K.

Regul Toxicol Pharmacol. 2019 Dec;109:104510. doi: 10.1016/j.yrtph.2019.104510. Epub 2019 Oct 29.


Ensemble QSAR Modeling to Predict Multispecies Fish Toxicity Lethal Concentrations and Points of Departure.

Sheffield TY, Judson RS.

Environ Sci Technol. 2019 Nov 5;53(21):12793-12802. doi: 10.1021/acs.est.9b03957. Epub 2019 Oct 10.


Characterizing cleft palate toxicants using ToxCast data, chemical structure, and the biomedical literature.

Baker NC, Sipes NS, Franzosa J, Belair DG, Abbott BD, Judson RS, Knudsen TB.

Birth Defects Res. 2019 Aug 30. doi: 10.1002/bdr2.1581. [Epub ahead of print]


Progress in data interoperability to support computational toxicology and chemical safety evaluation.

Watford S, Edwards S, Angrish M, Judson RS, Paul Friedman K.

Toxicol Appl Pharmacol. 2019 Oct 1;380:114707. doi: 10.1016/j.taap.2019.114707. Epub 2019 Aug 9.


Identification of potential endocrine disrupting chemicals using gene expression biomarkers.

Corton JC, Kleinstreuer NC, Judson RS.

Toxicol Appl Pharmacol. 2019 Oct 1;380:114683. doi: 10.1016/j.taap.2019.114683. Epub 2019 Jul 17. Review.


Predicting estrogen receptor activation by a group of substituted phenols: An integrated approach to testing and assessment case study.

Webster F, Gagné M, Patlewicz G, Pradeep P, Trefiak N, Judson RS, Barton-Maclaren TS.

Regul Toxicol Pharmacol. 2019 Aug;106:278-291. doi: 10.1016/j.yrtph.2019.05.017. Epub 2019 May 20.


Empirical models for anatomical and physiological changes in a human mother and fetus during pregnancy and gestation.

Kapraun DF, Wambaugh JF, Setzer RW, Judson RS.

PLoS One. 2019 May 2;14(5):e0215906. doi: 10.1371/journal.pone.0215906. eCollection 2019.


The Next Generation Blueprint of Computational Toxicology at the U.S. Environmental Protection Agency.

Thomas RS, Bahadori T, Buckley TJ, Cowden J, Deisenroth C, Dionisio KL, Frithsen JB, Grulke CM, Gwinn MR, Harrill JA, Higuchi M, Houck KA, Hughes MF, Hunter ES, Isaacs KK, Judson RS, Knudsen TB, Lambert JC, Linnenbrink M, Martin TM, Newton SR, Padilla S, Patlewicz G, Paul-Friedman K, Phillips KA, Richard AM, Sams R, Shafer TJ, Setzer RW, Shah I, Simmons JE, Simmons SO, Singh A, Sobus JR, Strynar M, Swank A, Tornero-Valez R, Ulrich EM, Villeneuve DL, Wambaugh JF, Wetmore BA, Williams AJ.

Toxicol Sci. 2019 Jun 1;169(2):317-332. doi: 10.1093/toxsci/kfz058.


Development, validation and integration of in silico models to identify androgen active chemicals.

Manganelli S, Roncaglioni A, Mansouri K, Judson RS, Benfenati E, Manganaro A, Ruiz P.

Chemosphere. 2019 Apr;220:204-215. doi: 10.1016/j.chemosphere.2018.12.131. Epub 2018 Dec 19.


Workflow for defining reference chemicals for assessing performance of in vitro assays.

Judson RS, Thomas RS, Baker N, Simha A, Howey XM, Marable C, Kleinstreuer NC, Houck KA.

ALTEX. 2019;36(2):261-276. doi: 10.14573/altex.1809281. Epub 2018 Dec 17.


Exploring non-linear distance metrics in the structure-activity space: QSAR models for human estrogen receptor.

Balabin IA, Judson RS.

J Cheminform. 2018 Sep 18;10(1):47. doi: 10.1186/s13321-018-0300-0.


Assessing bioactivity-exposure profiles of fruit and vegetable extracts in the BioMAP profiling system.

Wetmore BA, Clewell RA, Cholewa B, Parks B, Pendse SN, Black MB, Mansouri K, Haider S, Berg EL, Judson RS, Houck KA, Martin M, Clewell HJ 3rd, Andersen ME, Thomas RS, McMullen PD.

Toxicol In Vitro. 2019 Feb;54:41-57. doi: 10.1016/j.tiv.2018.09.006. Epub 2018 Sep 12.


Uncertainty quantification in ToxCast high throughput screening.

Watt ED, Judson RS.

PLoS One. 2018 Jul 25;13(7):e0196963. doi: 10.1371/journal.pone.0196963. eCollection 2018.


Erratum to "High-Throughput H295R Steroidogenesis Assay: Utility as an Alternative and a Statistical Approach to Characterize Effects on Steroidogenesis".

Haggard DE, Karmaus AL, Martin MT, Judson RS, Setzer RW, Friedman KP.

Toxicol Sci. 2018 Aug 1;164(2):646. doi: 10.1093/toxsci/kfy148. No abstract available.


OPERA models for predicting physicochemical properties and environmental fate endpoints.

Mansouri K, Grulke CM, Judson RS, Williams AJ.

J Cheminform. 2018 Mar 8;10(1):10. doi: 10.1186/s13321-018-0263-1.


A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics.

Mav D, Shah RR, Howard BE, Auerbach SS, Bushel PR, Collins JB, Gerhold DL, Judson RS, Karmaus AL, Maull EA, Mendrick DL, Merrick BA, Sipes NS, Svoboda D, Paules RS.

PLoS One. 2018 Feb 20;13(2):e0191105. doi: 10.1371/journal.pone.0191105. eCollection 2018.


High-Throughput H295R Steroidogenesis Assay: Utility as an Alternative and a Statistical Approach to Characterize Effects on Steroidogenesis.

Haggard DE, Karmaus AL, Martin MT, Judson RS, Setzer RW, Paul Friedman K.

Toxicol Sci. 2018 Apr 1;162(2):509-534. doi: 10.1093/toxsci/kfx274. Erratum in: Toxicol Sci. 2018 Aug 1;164(2):646.


The CompTox Chemistry Dashboard: a community data resource for environmental chemistry.

Williams AJ, Grulke CM, Edwards J, McEachran AD, Mansouri K, Baker NC, Patlewicz G, Shah I, Wambaugh JF, Judson RS, Richard AM.

J Cheminform. 2017 Nov 28;9(1):61. doi: 10.1186/s13321-017-0247-6.


On selecting a minimal set of in vitro assays to reliably determine estrogen agonist activity.

Judson RS, Houck KA, Watt ED, Thomas RS.

Regul Toxicol Pharmacol. 2017 Dec;91:39-49. doi: 10.1016/j.yrtph.2017.09.022. Epub 2017 Oct 6.


Correction to Screening Chemicals for Estrogen Receptor Bioactivity Using a Computational Model.

Browne P, Judson RS, Casey W, Kleinstreuer N, Thomas RS.

Environ Sci Technol. 2017 Aug 15;51(16):9415. doi: 10.1021/acs.est.7b03317. Epub 2017 Aug 2. No abstract available.


An "EAR" on Environmental Surveillance and Monitoring: A Case Study on the Use of Exposure-Activity Ratios (EARs) to Prioritize Sites, Chemicals, and Bioactivities of Concern in Great Lakes Waters.

Blackwell BR, Ankley GT, Corsi SR, DeCicco LA, Houck KA, Judson RS, Li S, Martin MT, Murphy E, Schroeder AL, Smith ER, Swintek J, Villeneuve DL.

Environ Sci Technol. 2017 Aug 1;51(15):8713-8724. doi: 10.1021/acs.est.7b01613. Epub 2017 Jul 18.


Identifying environmental chemicals as agonists of the androgen receptor by using a quantitative high-throughput screening platform.

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.

Toxicology. 2017 Jun 15;385:48-58. doi: 10.1016/j.tox.2017.05.001. Epub 2017 May 4.


Retrospective mining of toxicology data to discover multispecies and chemical class effects: Anemia as a case study.

Judson RS, Martin MT, Patlewicz G, Wood CE.

Regul Toxicol Pharmacol. 2017 Jun;86:74-92. doi: 10.1016/j.yrtph.2017.02.015. Epub 2017 Feb 24.


Comment on "On the Utility of ToxCast™ and ToxPi as Methods for Identifying New Obesogens".

Houck KA, Judson RS, Knudsen TB, Martin MT, Richard AM, Crofton KM, Simeonov A, Paules RS, Bucher JR, Thomas RS.

Environ Health Perspect. 2017 Jan 1;125(1):A8-A11. doi: 10.1289/EHP881. No abstract available.


Editor's Highlight: Genetic Targets of Acute Toluene Inhalation in Drosophila melanogaster.

Bushnell PJ, Ward WO, Morozova TV, Oshiro WM, Lin MT, Judson RS, Hester SD, McKee JM, Higuchi M.

Toxicol Sci. 2017 Mar 1;156(1):230-239. doi: 10.1093/toxsci/kfw243.


In Silico Prediction of Physicochemical Properties of Environmental Chemicals Using Molecular Fingerprints and Machine Learning.

Zang Q, Mansouri K, Williams AJ, Judson RS, Allen DG, Casey WM, Kleinstreuer NC.

J Chem Inf Model. 2017 Jan 23;57(1):36-49. doi: 10.1021/acs.jcim.6b00625. Epub 2017 Jan 9.


An automated curation procedure for addressing chemical errors and inconsistencies in public datasets used in QSAR modelling.

Mansouri K, Grulke CM, Richard AM, Judson RS, Williams AJ.

SAR QSAR Environ Res. 2016 Nov;27(11):939-965.


The Next Generation of Risk Assessment Multi-Year Study-Highlights of Findings, Applications to Risk Assessment, and Future Directions.

Cote I, Andersen ME, Ankley GT, Barone S, Birnbaum LS, Boekelheide K, Bois FY, Burgoon LD, Chiu WA, Crawford-Brown D, Crofton KM, DeVito M, Devlin RB, Edwards SW, Guyton KZ, Hattis D, Judson RS, Knight D, Krewski D, Lambert J, Maull EA, Mendrick D, Paoli GM, Patel CJ, Perkins EJ, Poje G, Portier CJ, Rusyn I, Schulte PA, Simeonov A, Smith MT, Thayer KA, Thomas RS, Thomas R, Tice RR, Vandenberg JJ, Villeneuve DL, Wesselkamper S, Whelan M, Whittaker C, White R, Xia M, Yauk C, Zeise L, Zhao J, DeWoskin RS.

Environ Health Perspect. 2016 Nov;124(11):1671-1682. Epub 2016 Apr 19. Review.


tcpl: the ToxCast pipeline for high-throughput screening data.

Filer DL, Kothiya P, Setzer RW, Judson RS, Martin MT.

Bioinformatics. 2017 Feb 15;33(4):618-620. doi: 10.1093/bioinformatics/btw680.


ToxCast Chemical Landscape: Paving the Road to 21st Century Toxicology.

Richard AM, Judson RS, Houck KA, Grulke CM, Volarath P, Thillainadarajah I, Yang C, Rathman J, Martin MT, Wambaugh JF, Knudsen TB, Kancherla J, Mansouri K, Patlewicz G, Williams AJ, Little SB, Crofton KM, Thomas RS.

Chem Res Toxicol. 2016 Aug 15;29(8):1225-51. doi: 10.1021/acs.chemrestox.6b00135. Epub 2016 Jul 20.


In Silico Study of In Vitro GPCR Assays by QSAR Modeling.

Mansouri K, Judson RS.

Methods Mol Biol. 2016;1425:361-81. doi: 10.1007/978-1-4939-3609-0_16.


Systematically evaluating read-across prediction and performance using a local validity approach characterized by chemical structure and bioactivity information.

Shah I, Liu J, Judson RS, Thomas RS, Patlewicz G.

Regul Toxicol Pharmacol. 2016 Aug;79:12-24. doi: 10.1016/j.yrtph.2016.05.008. Epub 2016 May 9.


CERAPP: Collaborative Estrogen Receptor Activity Prediction Project.

Mansouri K, Abdelaziz A, Rybacka A, Roncaglioni A, Tropsha A, Varnek A, Zakharov A, Worth A, Richard AM, Grulke CM, Trisciuzzi D, Fourches D, Horvath D, Benfenati E, Muratov E, Wedebye EB, Grisoni F, Mangiatordi GF, Incisivo GM, Hong H, Ng HW, Tetko IV, Balabin I, Kancherla J, Shen J, Burton J, Nicklaus M, Cassotti M, Nikolov NG, Nicolotti O, Andersson PL, Zang Q, Politi R, Beger RD, Todeschini R, Huang R, Farag S, Rosenberg SA, Slavov S, Hu X, Judson RS.

Environ Health Perspect. 2016 Jul;124(7):1023-33. doi: 10.1289/ehp.1510267. Epub 2016 Feb 23.


Tiered High-Throughput Screening Approach to Identify Thyroperoxidase Inhibitors Within the ToxCast Phase I and II Chemical Libraries.

Paul Friedman K, Watt ED, Hornung MW, Hedge JM, Judson RS, Crofton KM, Houck KA, Simmons SO.

Toxicol Sci. 2016 May;151(1):160-80. doi: 10.1093/toxsci/kfw034. Epub 2016 Feb 15.


Systems Toxicology of Male Reproductive Development: Profiling 774 Chemicals for Molecular Targets and Adverse Outcomes.

Leung MC, Phuong J, Baker NC, Sipes NS, Klinefelter GR, Martin MT, McLaurin KW, Setzer RW, Darney SP, Judson RS, Knudsen TB.

Environ Health Perspect. 2016 Jul;124(7):1050-61. doi: 10.1289/ehp.1510385. Epub 2015 Dec 11.


Computational Exposure Science: An Emerging Discipline to Support 21st-Century Risk Assessment.

Egeghy PP, Sheldon LS, Isaacs KK, Özkaynak H, Goldsmith MR, Wambaugh JF, Judson RS, Buckley TJ.

Environ Health Perspect. 2016 Jun;124(6):697-702. doi: 10.1289/ehp.1509748. Epub 2015 Nov 6.


Using ToxCast™ Data to Reconstruct Dynamic Cell State Trajectories and Estimate Toxicological Points of Departure.

Shah I, Setzer RW, Jack J, Houck KA, Judson RS, Knudsen TB, Liu J, Martin MT, Reif DM, Richard AM, Thomas RS, Crofton KM, Dix DJ, Kavlock RJ.

Environ Health Perspect. 2016 Jul;124(7):910-9. doi: 10.1289/ehp.1409029. Epub 2015 Oct 16.


Integrated Model of Chemical Perturbations of a Biological Pathway Using 18 In Vitro High-Throughput Screening Assays for the Estrogen Receptor.

Judson RS, Magpantay FM, Chickarmane V, Haskell C, Tania N, Taylor J, Xia M, Huang R, Rotroff DM, Filer DL, Houck KA, Martin MT, Sipes N, Richard AM, Mansouri K, Setzer RW, Knudsen TB, Crofton KM, Thomas RS.

Toxicol Sci. 2015 Nov;148(1):137-54. doi: 10.1093/toxsci/kfv168. Epub 2015 Aug 13.


Incorporating High-Throughput Exposure Predictions With Dosimetry-Adjusted In Vitro Bioactivity to Inform Chemical Toxicity Testing.

Wetmore BA, Wambaugh JF, Allen B, Ferguson SS, Sochaski MA, Setzer RW, Houck KA, Strope CL, Cantwell K, Judson RS, LeCluyse E, Clewell HJ, Thomas RS, Andersen ME.

Toxicol Sci. 2015 Nov;148(1):121-36. doi: 10.1093/toxsci/kfv171. Epub 2015 Aug 6.


Screening Chemicals for Estrogen Receptor Bioactivity Using a Computational Model.

Browne P, Judson RS, Casey WM, Kleinstreuer NC, Thomas RS.

Environ Sci Technol. 2015 Jul 21;49(14):8804-14. doi: 10.1021/acs.est.5b02641. Epub 2015 Jun 26. Erratum in: Environ Sci Technol. 2017 Aug 15;51(16):9415.


Chemical Safety Assessment Using Read-Across: Assessing the Use of Novel Testing Methods to Strengthen the Evidence Base for Decision Making.

Berggren E, Amcoff P, Benigni R, Blackburn K, Carney E, Cronin M, Deluyker H, Gautier F, Judson RS, Kass GE, Keller D, Knight D, Lilienblum W, Mahony C, Rusyn I, Schultz T, Schwarz M, Schüürmann G, White A, Burton J, Lostia AM, Munn S, Worth A.

Environ Health Perspect. 2015 Dec;123(12):1232-40. doi: 10.1289/ehp.1409342. Epub 2015 May 8. Review.


Predicting hepatotoxicity using ToxCast in vitro bioactivity and chemical structure.

Liu J, Mansouri K, Judson RS, Martin MT, Hong H, Chen M, Xu X, Thomas RS, Shah I.

Chem Res Toxicol. 2015 Apr 20;28(4):738-51. doi: 10.1021/tx500501h. Epub 2015 Mar 9.


Exploring consumer exposure pathways and patterns of use for chemicals in the environment.

Dionisio KL, Frame AM, Goldsmith MR, Wambaugh JF, Liddell A, Cathey T, Smith D, Vail J, Ernstoff AS, Fantke P, Jolliet O, Judson RS.

Toxicol Rep. 2015 Jan 2;2:228-237. doi: 10.1016/j.toxrep.2014.12.009. eCollection 2015.


Profiling of the Tox21 10K compound library for agonists and antagonists of the estrogen receptor alpha signaling pathway.

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.

Sci Rep. 2014 Jul 11;4:5664. doi: 10.1038/srep05664.


Predictive endocrine testing in the 21st century using in vitro assays of estrogen receptor signaling responses.

Rotroff DM, Martin MT, Dix DJ, Filer DL, Houck KA, Knudsen TB, Sipes NS, Reif DM, Xia M, Huang R, Judson RS.

Environ Sci Technol. 2014;48(15):8706-16. doi: 10.1021/es502676e. Epub 2014 Jul 10.


Phenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanisms.

Kleinstreuer NC, Yang J, Berg EL, Knudsen TB, Richard AM, Martin MT, Reif DM, Judson RS, Polokoff M, Dix DJ, Kavlock RJ, Houck KA.

Nat Biotechnol. 2014 Jun;32(6):583-91. doi: 10.1038/nbt.2914. Epub 2014 May 18.


Development of a consumer product ingredient database for chemical exposure screening and prioritization.

Goldsmith MR, Grulke CM, Brooks RD, Transue TR, Tan YM, Frame A, Egeghy PP, Edwards R, Chang DT, Tornero-Velez R, Isaacs K, Wang A, Johnson J, Holm K, Reich M, Mitchell J, Vallero DA, Phillips L, Phillips M, Wambaugh JF, Judson RS, Buckley TJ, Dary CC.

Food Chem Toxicol. 2014 Mar;65:269-79. doi: 10.1016/j.fct.2013.12.029. Epub 2013 Dec 27.


Binary classification of a large collection of environmental chemicals from estrogen receptor assays by quantitative structure-activity relationship and machine learning methods.

Zang Q, Rotroff DM, Judson RS.

J Chem Inf Model. 2013 Dec 23;53(12):3244-61. doi: 10.1021/ci400527b. Epub 2013 Dec 11.


EADB: an estrogenic activity database for assessing potential endocrine activity.

Shen J, Xu L, Fang H, Richard AM, Bray JD, Judson RS, Zhou G, Colatsky TJ, Aungst JL, Teng C, Harris SC, Ge W, Dai SY, Su Z, Jacobs AC, Harrouk W, Perkins R, Tong W, Hong H.

Toxicol Sci. 2013 Oct;135(2):277-91. doi: 10.1093/toxsci/kft164. Epub 2013 Jul 28.


High-throughput models for exposure-based chemical prioritization in the ExpoCast project.

Wambaugh JF, Setzer RW, Reif DM, Gangwal S, Mitchell-Blackwood J, Arnot JA, Joliet O, Frame A, Rabinowitz J, Knudsen TB, Judson RS, Egeghy P, Vallero D, Cohen Hubal EA.

Environ Sci Technol. 2013 Aug 6;47(15):8479-88. doi: 10.1021/es400482g. Epub 2013 Jul 11.


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