High-dimensional Integration of Biological Systems

Spiner, deep learning-based automated detection of spiral ganglion neurons in intact cochleae

ISCIENCE, 28(7).

Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits

GENOME RESEARCH, 35(7), 1485–1502.

Signature gene expression model for quantitative evaluation of MASH-like liver injury in mice☆

TOXICOLOGY AND APPLIED PHARMACOLOGY, 502.

HAP-SAMPLE2: data-based resampling for association studies with admixture

BIOINFORMATICS, 41(6).

Asian diversity in human immune cells

CELL, 188(8).

A workflow for human health hazard evaluation using transcriptomic data and Key Characteristics-based gene sets

Tsai, H.-H. D., Oware, K. D., Wright, F. A., Chiu, W. A., & Rusyn, I. (2025, April 3). TOXICOLOGICAL SCIENCES.

Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles, affecting ocular and neurobehavioral function

TOXICOLOGY AND APPLIED PHARMACOLOGY, 496.

Examining risk assessment implications of genetic and dose-dependent dynamics of lead exposure in breastfeeding using the collaborative cross mouse population

Cuomo, D., Song, Z., Nitcher, M., Lynch, R., Barba, E., Feinberg, A. P., … Threadgill, D. W. (2025, February 11). TOXICOLOGICAL SCIENCES.

Identifying novel therapeutic targets in cystic fibrosis through advanced single-cell transcriptomics analysis

Computers in Biology and Medicine.

Novel Porcine Model Reveals Two Distinct LGR5 Cell Types during and Homeostasis

AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY, 72(5), 496–509.

A Systematic Analysis of Read-Across Adaptations in Testing Proposal Evaluations by the European Chemicals Agency

ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION, 42(1), 22–38.

Intelligent Beam Optimization for Light-Sheet Fluorescence Microscopy through Deep Learning

INTELLIGENT COMPUTING, 3.

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.

Control of false discoveries in grouped hypothesis testing for eQTL data

Springer Nature.

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

AMERICAN JOURNAL OF HUMAN GENETICS, 111(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.

Roadmap on computational methods in optical imaging and holography [invited]

[Review of APPLIED PHYSICS B-LASERS AND OPTICS, 130(9).

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

HUMAN GENOMICS, 18(1).

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.

A gene edited pig model for studying LGR5<SUP>+</SUP> stem cells: implications for future applications in tissue regeneration and biomedical research

[Review of ]. FRONTIERS IN GENOME EDITING, 6.

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.

Predicting Microbiome Growth Dynamics under Environmental Perturbations

Applied Microbiology.

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).