5 papers
Large Language Models for Variant-Centric Functional Evidence Mining
Ali Saadat, Jacques Fellay
Functional evidence is essential for clinical interpretation of genomic variants, but identifying relevant studies and translating experimental results into structured evidence rem…
Proteome-wide prediction of mode of inheritance and molecular mechanism underlying genetic diseases using structural interactomics
Ali Saadat, Jacques Fellay
Genetic diseases can be classified according to their modes of inheritance and their underlying molecular mechanisms. Autosomal dominant disorders often result from DNA variants th…
Fine-tuning the ESM2 protein language model to understand the functional impact of missense variants
Ali Saadat, Jacques Fellay
Elucidating the functional effect of missense variants is of crucial importance, yet challenging. To understand the impact of such variants, we fine-tuned the ESM2 protein language…
From Mutation to Degradation: Predicting Nonsense-Mediated Decay with NMDEP
Ali Saadat, Jacques Fellay
Nonsense-mediated mRNA decay (NMD) is a critical post-transcriptional surveillance mechanism that degrades transcripts with premature termination codons, safeguarding transcriptome…
DNA Language Model and Interpretable Graph Neural Network Identify Genes and Pathways Involved in Rare Diseases
Ali Saadat, Jacques Fellay
Identification of causal genes and pathways is a critical step for understanding the genetic underpinnings of rare diseases. We propose novel approaches to gene prioritization and…