Shafi Mahmud

T2G converts transcriptome-aligned BAM files to genome coordinates, improving specificity and splice junction accuracy across RNA sequencing technologies.

The paper integrates multi-omic data from yeast to identify translational programs during glucose starvation, revealing convergent cis-regulatory mechanisms in repressed genes.

SWARM improves detection of RNA modifications by reducing false positives and reveals new splicing-related pseudouridylation patterns.

The paper introduces DTI, a new RNA integrity metric based on nanopore sequencing, and the INDEGRA package to correct biases and enable accurate transcriptome comparisons.

CHEUI predicts m6A and m5C modifications at single-molecule resolution, revealing co-occurrence of these modifications in mRNAs across cell lines and tissues.

The paper analyzes ten-microsecond molecular dynamics simulations of SARS-CoV-2 dimeric main protease to study its conformational changes and flexibility.

This study designs a multi-epitope vaccine against Elizabethkingia anophelis using immunoinformatic methods and dynamic simulations, showing high immunogenicity and stability.