Yadollah Shahryary

GenomicLinks: Deep learning predictions of 3Dchromatin loops in the maize genome

GenomicLinks predicts 3D chromatin loops in maize by identifying sequence features associated with transcription factor binding motifs, validated using single-cell co-accessibility data.

AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

AlphaBeta estimates epimutation rates and spectra from DNA methylation data in plants, showing conserved epimutation landscapes and providing a molecular clock for tree age-dating.

MethylStar: A fast and robust pre-processing pipeline for bulk or single-cell whole-genome bisulfite sequencing data

MethylStar is a pre-processing pipeline for WGBS data that improves speed and memory efficiency compared to existing tools.

The somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa

The paper quantifies age-related somatic mutations and epimutations in a wild Populus trichocarpa tree over 330 years, showing lower mutation rates than annuals and distinct epimutation origins.