Bioinformatics

To Accept or Not To Accept a Read-Across Adaptation: A Systematic Analysis of 15 Years of Testing Proposal Decisions by the European Chemicals Agency

Roe, H. M., Ball, N., Wright, F. A., Chiu, W. A., & Rusyn, I. (2024, September). TOXICOLOGY LETTERS, Vol. 399, pp. S63–S63.

Comparative toxicogenomics database's 20th anniversary: update 2025

Davis, A. P., Wiegers, T. C., Sciaky, D., Barkalow, F., Strong, M., Wyatt, B., … Mattingly, C. J. (2024, October 10). NUCLEIC ACIDS RESEARCH.

The GeoTox Package: Open-source software for connecting spatiotemporal exposure to individual and population-level risk

Messier, K. P., Reif, D. M., & Marvel, S. W. (2024, September 24).

Streamlining Phenotype Classification and Highlighting Feature Candidates: A Screening Method for Non-Targeted Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS) Data

Chappel, J. R., Kirkwood-Donelson, K. I., Dodds, J. N., Fleming, J., Reif, D. M., & Baker, E. S. (2024, September 18). ANALYTICAL CHEMISTRY, Vol. 9.

Risk-Based Prioritization of PFAS Using Phenotypic and Transcriptomic Data from Human Induced Pluripotent Stem Cell-Derived Hepatocytes and Cardiomyocytes

ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION, 41(3), 363–381.

Liver eQTL meta-analysis illuminates potential molecular mechanisms of cardiometabolic traits

AMERICAN JOURNAL OF HUMAN GENETICS, 111(9).

Taxanorm: a novel taxa-specific normalization approach for microbiome data

BMC BIOINFORMATICS, 25(1).

An in vitro and machine learning framework for quantifying serum albumin binding of per- and polyfluoroalkyl substances

Starnes, H. M., Green, A. J., Reif, D. M., & Belcher, S. M. (2024, October 3). TOXICOLOGICAL SCIENCES, Vol. 10.

Deep autoencoder-based behavioral pattern recognition outperforms standard statistical methods in high-dimensional zebrafish studies

PLOS COMPUTATIONAL BIOLOGY, 20(9).

Characterizing PFAS hazards and risks: a human population-based in vitro cardiotoxicity assessment strategy

HUMAN GENOMICS, 18(1).

Transforming environmental health datasets from the comparative toxicogenomics database into chord diagrams to visualize molecular mechanisms

FRONTIERS IN TOXICOLOGY, 6.

Informing Hazard Identification and Risk Characterization of Environmental Chemicals by Combining Transcriptomic and Functional Data from Human-Induced Pluripotent Stem-Cell-Derived Cardiomyocytes

Tsai, H.-H. D., Ford, L. C., Burnett, S. D., Dickey, A. N., Wright, F. A., Chiu, W. A., & Rusyn, I. (2024, July 24). CHEMICAL RESEARCH IN TOXICOLOGY.

Time for CHANGE: system-level interventions for bringing forward the date of effective use of NAMs in regulatory toxicology

Mathisen, G. H., Bearth, A., Jones, L. B., Hoffmann, S., Vist, G. E., Ames, H. M., … Whaley, P. (2024, June 14). ARCHIVES OF TOXICOLOGY.

Two-Stage Machine Learning-Based Approach to Predict Points of Departure for Human Noncancer and Developmental/Reproductive Effects

Kvasnicka, J., Aurisano, N., Borries, K., Lu, E.-H., Fantke, P., Jolliet, O., … Chiu, W. A. (2024, May 2). ENVIRONMENTAL SCIENCE & TECHNOLOGY.

Protein-adaptive differential scanning fluorimetry using conformationally responsive dyes

Wu, T., Yu, J. C., Suresh, A., Gale-Day, Z. J., Alteen, M. G., Woo, A. S., … Gestwicki, J. E. (2024, May 14). NATURE BIOTECHNOLOGY.

Hazard and risk characterization of 56 structurally diverse PFAS using a targeted battery of broad coverage assays using six human cell types

TOXICOLOGY, 503.

Control of false discoveries in grouped hypothesis testing for eQTL data

BMC BIOINFORMATICS, 25(1).

Genetic variation in severe cystic fibrosis liver disease is associated with novel mechanisms for disease pathogenesis

Stonebraker, J., Pace, R., Gallins, P., Dang, H., Aksit, M., Faino, A., … Knowles, M. (2024, March 27). HEPATOLOGY.

Investigating mouse hepatic lipidome dysregulation following exposure to emerging per- and polyfluoroalkyl substances (PFAS)

Chemosphere.

Guided optimization of ToxPi model weights using a Semi-Automated approach

COMPUTATIONAL TOXICOLOGY, 29.