Sutanay Choudhury

Illuminating dark genes and dark metabolites: calibrated functional association across kingdoms with autoencoders and correlation

VaLPAS pairs a bi-directional autoencoder with correlation for omics guilt-by-association with calibrated confidence; in L. starkeyi its autoencoder linked 176 unidentified metabolites to known-function proteins at ≥50% confidence.

Genomic and transcriptomic insights into antipsychotic-induced changes in total cholesterol and body mass index in a multi-ancestry cohort of the US veterans

The paper conducts a GWAS on antipsychotic-induced changes in total cholesterol and BMI in a multi-ancestry cohort, identifying genetic loci and pathways associated with these metabolic effects.

PathwaySeeker: Evidence-Grounded AI Reasoning over Organism-Specific Metabolic Networks

PathwaySeeker uses AI to reason about organism-specific metabolic networks using proteomic and metabolomic data, distinguishing confirmed reactions from hypotheses.