Bioinformatics

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

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

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.

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.

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, Vol. 10.

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).

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.