Benjamin T. James

The paper constructs a 3D human brain model integrating multiple cell types to study Alzheimer's Disease mechanisms linked to APOE4.

This study examines how exercise training affects subcutaneous white adipose tissue transcriptomes in individuals with obesity and T2D, finding that exercise reverses detrimental gene expression patterns and correlates with improved metabolic markers.

ENCODE-rE2G, a classifier trained on K562 CRISPR perturbations, maps 13,455,443 enhancer-gene interactions across 352 biosamples, matching or exceeding prior models on CRISPR, eQTL, and GWAS benchmarks.

FASTCAR predicts pairwise DNA sequence identity scores using alignment-free methods and linear models, achieving faster performance than BLAST and USEARCH on large datasets.

This paper benchmarks alignment-free sequence comparison methods across five research applications and provides a web resource for evaluating and comparing these methods.

Look4TRs detects microsatellites using self-supervised HMMs, outperforming existing tools across eight genomes with higher accuracy and fewer false positives.

MeShClust2 clusters long bacterial genomes using identity scores without alignment, improving scalability over previous methods.

MeShClust uses mean shift and supervised learning to cluster DNA sequences accurately even with imprecise similarity parameters.