Śaunak Sen

The paper improves metabolite effect estimation by incorporating external biological knowledge through a Bayesian hierarchical framework, showing consistent gains in both simulated and real datasets.

This study identifies genetic loci affecting lifespan dynamics, sex differences, and body weight trade-offs in mice using an actuarial approach.

GNQA, a retrieval-augmented GPT question-answering system over 3000 GeneNetwork, aging and diabetes papers, cites source paragraphs; RAGAS rated answer relevance above human thumbs-up ratings (89% vs 76%).

The paper develops a matrix linear model to connect metabolite composition with individual characteristics, showing it can separate overlapping metabolite features.

BulkLMM accelerates genome-wide scans for multiple quantitative traits using LMMs by employing vectorized operations and regularization, achieving fast results on large datasets.

The paper identifies a regulatory hotspot, meQTL.5a, that influences DNA methylation, gene expression, and aging traits in mice through genetic and age-related factors.

The paper examines how diet and genetics interact to affect longevity and weight gain in mice, finding that genetic differences significantly influence the impact of high-fat diets on lifespan.

The paper develops GPU-accelerated algorithms for fast eQTL scans in BXD mice, reducing runtime to seconds for large transcriptome datasets.

The paper identifies Fibronectin 1 as a genetic modifier in a Col4a1 mutant mouse model of Gould syndrome, showing it suppresses ocular and muscular phenotypes through increased expression and integrin signaling.

This paper introduces FlxQTL, a flexible multivariate linear mixed model for genetic mapping of multiple correlated traits, adjusting for relatedness and modeling multiple environments or timepoints.

BXD mouse family doubled to 150 inbred strains segregating over 6 million variants, with roughly 10,000 located recombinations and a public phenome exceeding 7000 traits.

This paper introduces matrix linear models for analyzing chemical genetic screens, showing improved performance over traditional methods in handling categorical and continuous data.

The paper describes a process for cleaning SNP genotype data from Diversity Outbred mice, focusing on identifying and handling low-quality samples and markers.

R/qtl2 is a software tool for QTL mapping in multi-parent populations and high-dimensional data, offering features like linear mixed models and SNP imputation.

This study identifies pharmacogenetic variants associated with albuterol bronchodilator response in minority children with asthma using whole genome sequencing.