Arsham Mikaeili Namini

The paper identifies intra-genic mutational robustness through alternative splicing in cancer, showing it can complement inter-genic robustness and is associated with worse disease outcomes.

This paper introduces scLSD, a thermodynamics-inspired model for cell differentiation that reconstructs differentiation trajectories and predicts fate commitment, outperforming existing methods.

The paper introduces Mach-1, an RNA foundation model that predicts transcriptome architecture from DNA sequence, validated through experimental perturbations and CRISPR editing.

This paper introduces MPAQT, a framework that improves isoform quantification in bulk and single-cell RNA-seq by integrating short- and long-read data and using sequence-to-expression models.

The paper analyzes SARS-CoV-2 mutations from 10.5 million sequences to identify stable mutations and their geographic distribution, providing insights for vaccine and diagnostic development.