Rachit Kumar

ARCHER-LD: Rapid Long-Range Linkage Disequilibrium Calculations at Biobank Scale using GPU Acceleration

The paper introduces ARCHER-LD, a GPU-accelerated method to compute long-range linkage disequilibrium at biobank scale, achieving significant speedups over existing tools.

PMBB Geno-Pheno Toolkit: A suite of scalable, reproducible pipelines for cross-biobank association analyses

The PMBB Geno-Pheno Toolkit provides modular pipelines for cross-biobank association analyses, supporting GWAS, ExWAS, and PheWAS with containerized workflows.

AE-PocketMiner Uses Attention to Simultaneously Predict Cryptic Pockets and Their Allosteric Coupling

AE-PocketMiner predicts cryptic protein pockets and their allosteric coupling using a graph neural network, outperforming existing methods and validating predictions experimentally.

Platform-dependent effects of genetic variants on plasma APOL1

The paper identifies platform-dependent effects of APOL1 variants on plasma levels measured by different proteomic technologies.

CASTER-DTA: Equivariant Graph Neural Networks for Predicting Drug-Target Affinity

CASTER-DTA predicts drug-target affinity using equivariant graph neural networks, achieving state-of-the-art performance and generating a resource of binding affinities for all FDA-approved drugs against the human proteome.

Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates

The paper reports on a competition to predict maize yield using genetic and environmental data, showing that diverse modeling approaches can achieve good results.

Accelerating Genome- and Phenome-Wide Association Studies using GPUs - A case study using data from the Million Veteran Program

This paper optimizes the SAIGE algorithm using GPUs to accelerate GWAS on large datasets, achieving 20x speedup on the Million Veteran Program data.