Recent Works
search all worksSorted by most recent date added to the index first, which may not be the same as publication date order.
2025 article
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.
2025 article
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).
2025 journal article
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.
2025 article
Connected Chromatin Amplifies Acetylation-Modulated Nucleosome Interactions
Li, R., & Lin, X. (2025, March 3). BIOCHEMISTRY, Vol. 3.
2025 journal article
Zebrafish Cyp1b1 knockout alters eye and brain metabolomic profiles, affecting ocular and neurobehavioral function
TOXICOLOGY AND APPLIED PHARMACOLOGY, 496.
2025 article
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.
2025 article
Interpretable Protein-DNA Interactions Captured by Structure-Sequence Optimization
Zhang, Y., Silvernail, I., Lin, Z., & Lin, X. (2025, February 7).

2025 article
Interpretable Protein-DNA Interactions Captured by Structure-Sequence Optimization
Zhang, Y., Silvernail, I., Lin, Z., & Lin, X. (2025, February 7).

2025 article
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).
2025 journal article
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).
2024 journal article
Bayesian gene set benchmark dose estimation for “omic” responses
Bioinformatics.
Ed(s): C. Kendziorski
2025 journal article
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.
2025 journal article
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).
2024 journal article
Is increased mutation driving genetic diversity in dogs within the Chornobyl exclusion zone?
PLOS ONE, 19(12).
2025 journal article
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.

2024 journal article
Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria
MOLECULAR BIOLOGY AND EVOLUTION, 41(12).
Ed(s): H. Hendrickson

2025 journal article
Homologous recombination shapes the architecture and evolution of bacterial genomes
Nucleic Acids Research.

2024 article
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).

2024 article
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.
2024 article
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.

2024 article
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.
2024 article
Connected Chromatin Amplifies Acetylation-modulated Nucleosome Interactions
Li, R., & Lin, X. (2024, October 13).
2024 article
Prevalence and Dynamics of Genome Rearrangements in Bacteria and Archaea
Martinez-Gutierrez, C. A., & Bobay, L.-M. (2024, October 5).
2024 article
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).
2024 article
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.