Ali Saberi

A latent space thermodynamic model of cell differentiation

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

A Suite of Foundation Models Captures the Contextual Interplay Between Codons

The paper introduces cdsFM, a suite of codon-resolution large language models that predict the functional consequences of synonymous codon choices and identify pathogenic variants.

A long context RNA foundation model for predicting transcriptome architecture

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

Accurate isoform quantification in bulk and single-cell RNA-seq by integrating multi-platform sequencing data and sequence-to-expression models

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.

Perturbation-aware predictive modeling of RNA splicing using bidirectional transformers

The paper trains bidirectional transformer models to predict RNA splicing using perturbative RNA data, achieving state-of-the-art performance in splice junction prediction.

Revealing the Grammar of Small RNA Secretion Using Interpretable Machine Learning

This study introduces ExoGRU, a machine learning model that predicts small RNA secretion from sequence, identifies key RNA-binding proteins, and develops exoCLIP to map RNA interactomes in extracellular vesicles.