Bioinformatics

Prevalence and Evolutionary Implications of Genome Rearrangements in Bacteria

Martinez-Gutierrez, C. A., Huang, Y., & Bobay, L.-M. (2026, January 13).

Genetic variation in a plant-parasitic nematode is associated with gene expression changes conserved across evolutionarily distant host plants

Nielsen, D. M. (2026, January 12).

Inferring toxicant susceptibility in global populations from gene-environment interactions involving the Aryl Hydrocarbon Receptor

Chimeh, U. S., Rogers, M. C., & Aylor, D. L. (2026, January 10).

Early-Life Environmental Exposures Reprogram Epigenomic Aging to Alter Gene Expression Trajectories

Grimm, S. L., Jangid, R., Bartolomei, M. S., Dolinoy, D. C., Aylor, D. L., Mutlu, G. M., … Walker, C. L. (2025, April 22). BioRxiv (Cold Spring Harbor Laboratory), Vol. 4.

Efficient RNA Folding Simulation via a Structure-Based Single-Site-Per-Nucleotide Model

Thornton, T., & Lin, X. (2025, December 14).

Assessing the effect of spaceflight stress on DNA sequence mutation using RNA-sequencing data

Knight, M. S., Doherty, C. J., & Nielsen, D. M. (2025, January 1). Gravitational and Space Research.

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny

Douglas, G. M., Tromas, N., Gaudin, M., Lypaczewski, P., Bobay, L.-M., Shapiro, B. J., & Chaffron, S. (2025, December 10). The ISME Journal.

MetaStrainer: Accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.

Sharaf, H., & Bobay, L.-M. (2025, December 9). Zenodo (CERN European Organization for Nuclear Research).

MetaStrainer: Accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.

Sharaf, H., & Bobay, L.-M. (2025, December 9). Zenodo (CERN European Organization for Nuclear Research).

Linking chemical data from the Comparative Toxicogenomics Database with adverse outcome pathways from the AOP-Wiki: a mechanistic data-oriented approach to help inform environmental health

Davis, A. P., Wiegers, T. C., Sciaky, D., Barkalow, F., Wyatt, B., Wiegers, J., … Mattingly, C. J. (2025, November 17). F1000Research.

mIDEA: An Interpretable Structure–Sequence Model for Methylation-Dependent Protein–DNA Binding Sensitivity

Zhang, Y., Li, R., Zhong, J., & Lin, X. (2025, November 16).

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

Nature Communications.

Active regulation of the epidermal growth factor receptor by the membrane bilayer

Srinivasan, S., Lin, X., Chen, X., Regmi, R., Zhang, B., & Schlau-Cohen, G. S. (2025, October 13).

Active regulation of the epidermal growth factor receptor by the membrane bilayer

Srinivasan, S., Lin, X., Chen, X., Regmi, R., Zhang, B., & Schlau-Cohen, G. S. (2025, October 13).

IRIS Integrates Sparse Sequence, Experimental, and AI-Predicted Structures for Protein-RNA Affinity Prediction and Motif Discovery

Rosa, E. C., Zhang, Y., & Lin, X. (2025, September 16).

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.

Two-body triton photodisintegration and Wigner-SU(4) symmetry

Lin, X., & Vanasse, J. (2025, June 30). Physical Review. C, Vol. 112.

Active regulation of the epidermal growth factor receptor by the membrane bilayer

Srinivasan, S., Lin, X., Chen, X., Regmi, R., Zhang, B., & Schlau-Cohen, G. S. (2025, August 18).

Genomic Evaluation of Canine Prostatic Carcinomas as a Model for the Human Disease: or ‘UC or not UC – that is the question’

Thomas, R., Luff, J. A., Dickey, A. N., Dillon, M. N., Livingston, I. G., Schrag, C. A., … Breen, M. (2025, July 23). Genomic Evaluation of Canine Prostatic Carcinomas as a Model for the Human Disease: or ‘UC or not UC – that is the question.’ Veterinary and Comparative Oncology, Vol. 7.

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.

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

Mills, K. J., Doyle, M., House, J. S., Witherspoon, J. G., Krakko, D., Stutts, W. L., … Smart, R. C. (2025, June 25). (S. H. A. Raza, Ed.). PLoS ONE, Vol. 20.

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

Zhou, Q., Alberto de la Paz, J., Stanowick, A. D., Lin, X., & Morcos, F. (2025, June 20). Nucleic Acids Research, Vol. 53.

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.