Bioinformatics

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

The ISME Journal.

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

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

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

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

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 28). TOXICOLOGICAL SCIENCES.

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

PHYSICAL REVIEW C, 112(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. (2025, August 18).

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).

HAP-SAMPLE2: data-based resampling for association studies with admixture

BIOINFORMATICS, 41(6).

Interpretable Protein-DNA Interactions Captured by Structure-Sequence Optimization

Zhang, Y., Silvernail, I., Lin, Z., & Lin, X. (2025, June 9).

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).

Profiling the Tox21 Compound Library for Their Inhibitory Effects on Cytochrome P450 Enzymes

International Journal of Molecular Sciences.