Bioinformatics

Genomic Evaluation of Canine Prostatic Carcinomas as a Model for the Human Disease

Thomas, R., Luff, J. A., Dickey, A. N., Dillon, M. N., Livingston, I. G., Schrag, C. A., … Breen, M. (2025, July 23). VETERINARY AND COMPARATIVE ONCOLOGY, Vol. 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.

Interpretable protein-DNA interactions captured by structure-sequence optimization

ELife.

Conditional knockout of C/EBPβ in epidermis results in dysregulated lipid biosynthesis and a defect in skin barrier function

PLOS ONE, 20(6).

Characterizing DNA recognition preferences of transcription factors using global couplings and high-throughput sequencing

NUCLEIC ACIDS RESEARCH, 53(12).

Asian diversity in human immune cells

CELL, 188(8).

The integration of quantitative trait locus mapping and transcriptome studies reveals candidate genes for water stress response in St. Augustinegrass

BMC Plant Biology, 25(1).

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.

Co-occurrence drives horizontal gene transfer among marine prokaryotes

Douglas, G. M., Tromas, N., Gaudin, M., Lypaczewksi, P., Bobay, L.-M., Shapiro, B. J., & Chaffron, S. (2025, March 28).

Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION, 2025.

Connected Chromatin Amplifies Acetylation-Modulated Nucleosome Interactions

Li, R., & Lin, X. (2025, March 3). BIOCHEMISTRY, Vol. 3.

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.

Interpretable Protein-DNA Interactions Captured by Structure-Sequence Optimization

Zhang, Y., Silvernail, I., Lin, Z., & Lin, X. (2025, February 7).

Interpretable protein-DNA interactions captured by structure-sequence optimization

ELIFE, 14.

Updated Guidance for Communicating PFAS Identification Confidence with Ion Mobility Spectrometry

Boatman, A. K., Chappel, J. R., Kirkwood-Donelson, K. I., Fleming, J. F., Reif, D. M., Schymanski, E. L., … Baker, E. S. (2025, January 28).

Bayesian analysis of the rate of spontaneous malignant mesothelioma among <i>BAP1</i> mutant mice in the absence of asbestos exposure

SCIENTIFIC REPORTS, 15(1).

Bayesian gene set benchmark dose estimation for “omic” responses

Bioinformatics.

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.

Comparative analysis of the physiological and transport functions of various sources of renal proximal tubule cells under static and fl uidic conditions in PhysioMimix T12 platform

DRUG METABOLISM AND DISPOSITION, 53(1).

Is increased mutation driving genetic diversity in dogs within the Chornobyl exclusion zone?

PLOS ONE, 19(12).

Phenotype variability in diet-induced obesity and response to (−)-epigallocatechin gallate supplementation in a Diversity Outbred mouse cohort: A model for exploring gene x diet interactions for dietary bioactives

Nutrition Research, 133, 78–93.

Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria

MOLECULAR BIOLOGY AND EVOLUTION, 41(12).

Homologous recombination shapes the architecture and evolution of bacterial genomes

Nucleic Acids Research.