Bioinformatics

Nucleosome condensate and linker DNA alter chromatin folding pathways and rates

Qiu, Y., Liu, S., Lin, X., Unarta, I. C., Huang, X., & Zhang, B. (2024, November 16).

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.

Profiling the cancer-prone microenvironment in a zebrafish model for MPNST

Cero, C., House, J. S., Verdi, V., Ferguson, J. L., Jima, D. D., Selmek, A. A., … Shive, H. R. (2024, November 7). ONCOGENE, Vol. 11.

Connected Chromatin Amplifies Acetylation-modulated Nucleosome Interactions

Li, R., & Lin, X. (2024, October 13).

Prevalence and Dynamics of Genome Rearrangements in Bacteria and Archaea

Martinez-Gutierrez, C. A., & Bobay, L.-M. (2024, October 5).

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).

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

HUMAN GENOMICS, 18(1).

Evolution of homologous recombination rates across bacteria

Proceedings of the National Academy of Sciences, 121(18), e2316302121.

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.

Biomass yields, reproductive fertility, compositional analysis, and genetic diversity of newly developed triploid giant miscanthus hybrids

GLOBAL CHANGE BIOLOGY BIOENERGY, 16(7).

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.

Adaptive selection at G6PD and disparities in diabetes complications

Nature Medicine.

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.

Homologous Recombination Shapes the Architecture and Evolution of Bacterial Genomes

Torrance, E. L., Diop, A., & Bobay, L.-M. (2024, June 3).

Interpretable Protein-DNA Interactions Captured by Structure-based Optimization

Zhang, Y., Silvernail, I., Lin, Z., & Lin, X. (2024, May 27).

RACER-m leverages structural features for sparse T cell specificity prediction

SCIENCE ADVANCES, 10(20).

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy

Diop, A., & Bobay, L.-M. (2024, May 9).

Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies

BIOPHYSICAL JOURNAL, 123(6), 681–692.

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

TOXICOLOGY, 503.