Nam Nguyen

LEUTX mediates amplification of DUX4 signaling and aberrant myotube differentiation in facioscapulohumeral muscular dystrophy

This study identifies LEUTX as a key amplifier of DUX4 signaling in FSHD, showing its role in disrupting myotube differentiation and promoting aberrant gene expression.

Interpretable variant effect prediction from genomic foundation model embeddings

A low-rank covariance probe on Evo 2 embeddings predicts ClinVar pathogenicity across SNVs and indels, while annotation probes plus an LLM produce mechanistic hypotheses; scores released for 4.2 million variants.

Genome modeling and design across all domains of life with Evo 2

A 40B-parameter DNA model trained on 9.3 trillion tokens scores coding and noncoding variants zero-shot, exposes interpretable sequence features, and writes chromosome-scale sequences.

Creating a universal SNP and small indel variant caller with deep neural networks

A convolutional network on read-pileup images outperforms hand-built statistical variant callers, won an FDA challenge award for SNPs, learns new sequencing technologies and generalizes to other mammals.