High-dimensional Integration of Biological Systems

Computational Framework for Therapeutic Target Discovery via Perturbation Simulation: Application to Cystic Fibrosis Airway Disease

Sun, G., & Zhou, Y.-H. (2026, March 3).

Hierarchical Multi-Omics Trajectory Prediction for Fecal Microbiota Transplantation: A Novel Machine Learning Framework for Small-Sample Longitudinal Multi-Omics Integration

Zhou, Y.-H., & Sun, G. (2026, February 23).

An approach to uncover significant direct and mediated relationships in multi-dimensional new approach methods (NAMs) data: A case study of hazard evaluation of petroleum UVCBs

Zhou, Y.-H., Gallins, P. J., Rusyn, I., & Wright, F. A. (2025, May 28). The Science of The Total Environment.

Strain and Sex Variability in Liver, Kidney and Lung Levels of DNA Adducts EB-GII and bis-N7G-BD Following Inhalation Exposure to 1,3-Butadiene in Collaborative Cross Mice

Moran, E., Goodman, S., Wright, F. A., Evans, R., Tretyakova, N. Y., & Rusyn, I. (2025, October 3). Toxics.

Detecting Algorithmic Bias in ICU Clinical Decision: A Doubly-Robust Framework for Auditing Treatment Recommendation Disparities

Zhou, Y.-H., & Sun, G. (2025, November 17). BioRxiv (Cold Spring Harbor Laboratory).

Computation of Ancestry Scores with Mixed Families and Unrelated Individuals

Marron, J. S., & Wright, F. A. (2025, October 25). UNC Libraries.

Genetic Modifiers of Cystic Fibrosis Lung Disease Severity: Whole-Genome Analysis of 7,840 Patients.

Zhou, Y.-H., Gallins, P. J., Pace, R. G., Dang, H., Aksit, M. A., Blue, E. E., … Knowles, M. R. (2025, October 22). UNC Libraries.

Organophosphate Flame Retardants Disrupt Autism-Relevant Gene Networks Across Development: A Cross-Species Multi-Omics Study

Zhou, Y.-H., & Sun, G. (2025, September 3). Environmental Research.

Mediation analysis of the molecular phenotypes in a severe MASH-like liver injury mouse model

Song, Z., Tryndyak, V. P., Willett, R. A., Pogribny, I. P., Rusyn, I., & Wright, F. A. (2025, August 8). Toxicological Sciences.

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

Cai, Y., Leitz-Najarian, G. M., Rosen, R., Hutson, K. A., Moatti, A., Li, C., … Greenbaum, A. (2025, June 18). IScience.

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

Currin, K. W., Perrin, H. J., Pandey, G. K., Alkhawaja, A. A., Vadlamudi, S., Musser, A. E., … Mohlke, K. L. (2025, May 20). Genome Research.

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

Tryndyak, V. P., Willett, R. A., Song, Z., Dreval, K., Hanks, J. M. H., Avigan, M. I., … Pogribny, I. P. (2025, June 15). Toxicology and Applied Pharmacology.

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

Sun, G., Ting, B. W., Wright, F. A., & Zhou, Y.-H. (2025, June 1). (J. Kelso, Ed.). Bioinformatics.

Asian diversity in human immune cells

Kock, K. H., Tan, L. M., Han, K. Y., Ando, Y., Jevapatarakul, D., Chatterjee, A., … Prabhakar, S. (2025, March 19). Cell.

MagicalRsq: Machine-learning-based genotype imputation quality calibration

Yang, Y., Jiang, M.-Z., Chen, J., Liu, W., Wen, J., Raffield, L. M., … Li, Y. (2025, May 1). UNC Libraries.

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, March 20). Toxicological Sciences.

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

Perone, D. M., Annalora, A. J., Goldstone, J. V., Dickey, A. N., Salanga, M. C., Francolini, R. D., … Garcia-Jaramillo, M. (2025, January 29). Toxicology and Applied Pharmacology.

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, January 30). Toxicological Sciences.

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

Sun, G., & Zhou, Y.-H. (2025, February 8). Computers in Biology and Medicine.

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

Polkoff, K. M., Lampe, R., Gupta, N. K., Murphy, Y., Chung, J., Carter, A., … Piedrahita, J. A. (2024, November 5). American Journal of Respiratory Cell and Molecular Biology, Vol. 72, pp. 496–509.

Systematic analysis of read-across adaptations in testing proposal evaluations by the European Chemicals Agency

Roe, H., Tsai, H.-H., Ball, N., Wright, F., Chiu, W., & Rusyn, I. (2024, January 1). ALTEX.

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

Li, C., Rai, M. R., Cai, Y., Ghashghaei, H. T., & Greenbaum, A. (2024, January 1). Intelligent Computing.

OS03-02 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 1). Toxicology Letters.

Control of false discoveries in grouped hypothesis testing for eQTL data

Rudra, P., Zhou, Y.-H., Nobel, A., & Wright, F. A. (2024, April 11). Springer Nature.

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

Broadaway, K. A., Brotman, S. M., Rosen, J. D., Currin, K. W., Alkhawaja, A. A., Etheridge, A. S., … Mohlke, K. L. (2024, August 22). The American Journal of Human Genetics, Vol. 111.