Bioinformatics

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

Sharaf, H., & Bobay, L.-M. (2026, March 3).

BPS2026 – Integrating sparse sequence, experimental, and AI-predicted structures for protein-nucleic acid interaction predictions

Zhang, Y., Cisneros, E., Silvernail, I., Li, R., Thornton, T., & Lin, X. (2026, February 1). Biophysical Journal.

Circulating proteomic landscape of lung function

Lee, M., Austin, T. R., Lee, Y., Edris, A., Axelsson, G. T., Thareja, G., … London, S. J. (2026, February 19). European Respiratory Journal.

Cross-Species Exome Sequencing Reveals Recurrent Genomic Alterations in California Sea Lion (Zalophus californianus) Urogenital Carcinoma and Highlights a Recurrent PD-L1 Variant

Livingston, I. G., Wise, C. F., Dickey, A. N., Thomas, R., Deming, A. C., Halaska, B., … Breen, M. (2026, February 10). Genes, Vol. 2.

A biophysical framework for accurately identifying antigen single-amino acid escape variants and corresponding variant-specific compensatory TCR sequences

Ghoreyshi, Z. S., Levine, H., Lin, X., Onuchic, J. N., & George, J. T. (2026, February 5). (Vol. 2). Vol. 2.

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. (2026, January 20).

Prevalence and Evolutionary Implications of Genome Rearrangements in Bacteria

Martinez-Gutierrez, C. A., Huang, Y., & Bobay, L.-M. (2026, January 14). (R. Hershberg, Ed.). Genome Biology and Evolution.

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).

An approach to uncover significant direct and mediated relationships in multi-dimensional new approach methods (NAMs) data: A case study of hazard evaluation of petroleum UVCBs

Zhou, Y.-H., Gallins, P. J., Rusyn, I., & Wright, F. A. (2025, May 28). The Science of The Total Environment.

Strain and Sex Variability in Liver, Kidney and Lung Levels of DNA Adducts EB-GII and bis-N7G-BD Following Inhalation Exposure to 1,3-Butadiene in Collaborative Cross Mice

Moran, E., Goodman, S., Wright, F. A., Evans, R., Tretyakova, N. Y., & Rusyn, I. (2025, October 3). Toxics.

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., Zhang, Y., Li, R., & Zhong, J. (2025, November 16). BioRxiv (Cold Spring Harbor Laboratory).

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

Diop, A., Douglas, G. M., & Bobay, L.-M. (2025, November 13). 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. 6.