Jérémy Guez

PESTO classifies gene-phenotype associations as Novel, Hypothesized, Existing, or Established using a large language model and structured genetic evidence, identifying 7% as Novel and 21% as Hypothesized in 940 associations.

The paper identifies abundant alternate translation products in human proteins, showing their association with protein stability and disease.

The paper estimates mutation rates and variant effects using 700k exomes to identify genes with mutational hotspots and improve variant prioritization for genetic diagnostics.

The paper develops a framework to map rare variants onto protein structures and identifies disease-associated 3D neighborhoods in 872 genes for Mendelian disease and others for autism, epilepsy, and schizophrenia.

The paper establishes a global consortium to discover rare genetic associations by integrating data from multiple biobanks, identifying 514 gene-trait associations, many detectable only through cross-ancestry meta-analysis.

The paper performs large-scale GWAS and RVAS on 392,030 whole genomes from All of Us, identifying 49,863 associations and 193 novel pLoF gene-phenotype links through meta-analysis with UK Biobank.

gnomAD v4 (730,947 exomes) brings LOFTEE-2 loss-of-function annotation (0.90 precision, strict mode), missense-aware constraint, and LLM-mined literature evidence combined with constraint to rank disease genes.

The paper identifies naturally variable exons in human transcripts, showing their prevalence and impact on gene expression and genetic interpretation.

The paper introduces VCF Zarr, a format for efficiently storing and processing large-scale genetic variation data, demonstrating improved performance and scalability over traditional VCF formats.

This study evaluates variant scoring methods across different selection regimes, showing their performance depends on variant-to-gene and gene-to-disease factors.

This paper shows that cultural transmission of reproductive success affects genomic diversity, coalescent tree topologies, and demographic inferences by altering effective population size and distorting tree structures.