Science Inventory

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Patlewicz, G., A. Williams, M. Adams, I. Shah, AND K. Friedman. A cheminformatics workflow to select representative TSCA chemicals for New Approach Methodology (NAM) screening. SOT, Salt Lake City, UT, March 10 - 14, 2024. https://doi.org/10.23645/epacomptox.25395526

Patlewicz, G., P. Karamertzanis, M. Sannicola, K. Friedman, AND I. Shah. A systematic comparison of read-across within REACH registration dossiers with Generalised Read-Across (GenRA). SOT, Salt Lake City, UT, March 10 - 14, 2024. https://doi.org/10.23645/epacomptox.25395493

Patlewicz, G., A. Ross, H. Bledsoe, J. Vidal, L. Groff, B. Hagan, AND I. Shah. Building a compendium of expert driven read-across cases to facilitate an analysis of the contribution that different similarity contexts play in read-across performance. SOT, Salt Lake City, UT, March 10 - 14, 2024. https://doi.org/10.23645/epacomptox.25395676

Harrill, J., L. Everett, D. Haggard, J. Bundy, C. Willis, I. Shah, K. Friedman, D. Basili, A. Middleton, AND R. Judson. Exploring the Effects of Experimental Parameters and Data Modeling Approaches on In Vitro Transcriptomic Point-of-Departure Estimates. TOXICOLOGY. Elsevier Science Ltd, New York, NY, 501:153694, (2024). https://doi.org/10.1016/j.tox.2023.153694

DeWoskin, R., T. Knudsen, AND I. Shah. Virtual Models (aka: in silico or computational models) (Encyclopedia of Toxicology 4th Edition). Philip Wexler (ed.), 4th edition of the Encyclopedia of Toxicology. Academic Press Incorporated, Orlando, FL, 9:779-793, (2024). https://doi.org/10.1016/B978-0-12-824315-2.00094-4

Reardon, A., R. Farmahin, A. Williams, M. Meier, G. Addicks, C. Yauk, E. Atlas, J. Harrill, L. Everett, I. Shah, R. Judson, S. Ramaiahgari, S. Ferguson, AND T. Barton-Maclaren. Advancing data interpretation approaches to support the use of transcriptomic points of departure for prioritization and assessment of chemical substances (WC12). 12th World Congress on Alternatives and Animal Use in the Life Sciences (WC12), Niagara Falls, Ontario, CANADA, August 27 - 31, 2023. https://doi.org/10.23645/epacomptox.25048352

Nyffeler, J., C. Willis, F. Harris, M. Foster, B. Chambers, M. Culbreth, R. Brockway, S. Davidson-Fritz, D. Dawson, I. Shah, K. Paul-Friedman, D. Chang, L. Everett, J. Wambaugh, G. Patlewicz, AND J. Harrill. Application of Cell Painting for chemical hazard evaluation in support of screening-level chemical assessments. TOXICOLOGY AND APPLIED PHARMACOLOGY. Academic Press Incorporated, Orlando, FL, 468:116513, (2023). https://doi.org/10.1016/j.taap.2023.116513

Hagan, B., G. Patlewicz, AND I. Shah. Characterizing Metabolic similarity within GenRA: MetGraph. SERMACS, Durham, NC, October 25 - 28, 2023. https://doi.org/10.23645/epacomptox.24498550

Taylor, L., L. Everett, J. Harrill, I. Shah, AND R. Judson. Comparing RNA-seq and TempO-seq mRNA data sets: a case study. Society of Toxicology 62nd Annual Meeting and ToxExpo 2023, Nashville, TN, March 19 - 23, 2023. https://doi.org/10.23645/epacomptox.22782854

Taylor, L., L. Everett, J. Harrill, I. Shah, AND R. Judson. Comparing TempO-seq and RNA-seq mRNA data sets: a case study (SOT 23). Society of Toxicology 62nd Annual Meeting and ToxExpo 2023, Nashville, TN, March 19 - 23, 2023. https://doi.org/10.23645/epacomptox.22654285

Patlewicz, G., P. Karamertzanis, M. Sannicola, K. Paul-Friedman, AND I. Shah. Comparison of read-across in REACH registration dossiers with GenRA. QSAR, Copenhagen, DENMARK, June 05 - 09, 2023. https://doi.org/10.23645/epacomptox.22939829

Adams, M., H. Hilde, D. Chang, A. Richard, A. Williams, I. Shah, AND G. Patlewicz. Development of a CSRML version of the Analog identification Methodology (AIM) fragments and their evaluation within the Generalised Read-Across (GenRA) approach. Computational Toxicology. Elsevier B.V., Amsterdam, Netherlands, 25:100256, (2023). https://doi.org/10.1016/j.comtox.2022.100256

Reardon, A., R. Farmahin, A. Williams, M. Meier, G. Addicks, C. Yauk, G. Matteo, E. Atlas, J. Harrill, L. Everett, I. Shah, R. Judson, S. Ramaiahgari, S. Ferguson, AND T. Barton-Maclaren. From vision toward best practices: Evaluating in vitro transcriptomic points of departure for application in risk assessment using a uniform workflow. Frontiers in Toxicology. Frontiers, Lausanne, Switzerland, 5:1194895, (2023). https://doi.org/10.3389/ftox.2023.1194895

Patlewicz, G., I. Shah, T. Brown, F. Valone, AND S. Hamilton. GenRA v.3.2. U.S. Environmental Protection Agency, Washington, DC, 2023.

Boyce, M., K. Favela, J. Bonzo, A. Chao, L. Lizarraga, L. Moody, E. Owens, G. Patlewicz, I. Shah, J. Sobus, R. Thomas, A. Williams, A. Yau, AND J. Wambaugh. Identifying xenobiotic metabolites with in silico prediction tools and LCMS suspect screening analysis. Frontiers in Toxicology. Frontiers, Lausanne, Switzerland, 5:1051483, (2023). https://doi.org/10.3389/ftox.2023.1051483

Everett, L., D. Haggard, J. Fredenburg, F. Harris, J. Rogers, J. Bundy, R. Judson, I. Shah, K. Paul-Friedman, AND J. Harrill. Leveraging in vitro Transcriptomic Points of Departure in Chemical Safety Evaluation (WC12). 12th World Congress on Alternatives and Animal Use in the Life Sciences (WC12), Niagara Falls, Ontario, CANADA, August 27 - 31, 2023. https://doi.org/10.23645/epacomptox.24036711.v1

Bundy, J., J. Rogers, K. Friedman, I. Shah, R. Judson, J. Harrill, AND L. Everett. MIEML: Predicting Molecular Initiating Events by Integrating Machine Learning with Concentration Response Analysis of High Throughput Transcriptomic Chemical Screening Data. Society of Toxicology 62nd Annual Meeting and ToxExpo 2023, Nashville, TN, March 19 - 23, 2023. https://doi.org/10.23645/epacomptox.22732112

Groff, L., I. Shah, AND G. Patlewicz. MetSim: Integrated Programmatic Access and Pathway Management for Xenobiotic Metabolism Tools. SOT, Nashville, TN, March 19 - 23, 2023. https://doi.org/10.23645/epacomptox.22637485

Chambers, B., D. Basili, L. Taylor, N. Baker, A. Middleton, R. Judson, AND I. Shah. Searching for LINCS to Stress: using text-mining to automate reference chemical curation. Society of Toxicology 62nd Annual Meeting and ToxExpo 2023, Nashville, TN, March 19 - 23, 2023. https://doi.org/10.23645/epacomptox.22731980

Patlewicz, G. AND I. Shah. Towards systematic read-across using Generalised Read-Across (QSAR 2023). QSAR, Copenhagen, DENMARK, June 05 - 09, 2023. https://doi.org/10.23645/epacomptox.22659157

Karamertzanis, P., G. Patlewicz, M. Sannicola, K. Paul-Friedman, AND I. Shah. Using machine learning to encode substance groups. QSAR, Copenhagen, DENMARK, June 05 - 09, 2023. https://doi.org/10.23645/epacomptox.23527902

Haggard, D., J. Bundy, J. Harrill, I. Shah, R. Judson, AND L. Everett. httrpl: A Targeted RNA-seq High-throughput Transcriptomics Analytical Pipeline for Environmental Chemical Screening. SOT, Nashville, TN, March 19 - 23, 2023. https://doi.org/10.23645/epacomptox.22263868

Bundy, J., R. Judson, A. Williams, C. Grulke, I. Shah, AND L. Everett. A Machine Learning Approach to Predicting Molecular Initiating Events by Integrating Chemical Target Annotations with Gene Expression. Cosmetics Europe Toxicogenomics Workgroup, Virtual, NC, March 04, 2022. https://doi.org/10.23645/epacomptox.24470509

Tetko, I., G. Klambauer, D. Clevert, I. Shah, AND E. Benfenati. Artificial Intelligence Meets Toxicology. CHEMICAL RESEARCH IN TOXICOLOGY. American Chemical Society, Washington, DC, 35(8):1289-1290, (2022). https://doi.org/10.1021/acs.chemrestox.2c00196

Taylor, L., L. Everett, J. Harrill, I. Shah, AND R. Judson. Comparing TempO-seq and RNA-seq mRNA data sets: a case study. Genetics and Environmental Mutagenesis Society (GEMS), Durham, NC, November 01, 2022. https://doi.org/10.23645/epacomptox.21766727