Chirag J. Patel

This paper introduces SLMC to select minimal gene programs for disease-aligned representations in single-cell RNA-seq data, finding greedy methods outperform LASSO with small gene budgets.

The paper investigates how different high-fat diets affect host and microbiome multi-omic states over time and shows that some changes persist even after returning to a control diet.

The paper develops a comprehensive oral microbiome atlas linking host features like age, disease, and exposures to 1,349 taxa in a 10,000-person US population, identifying 45,757 significant associations.

This paper improves genetic discovery and polygenic risk prediction for respiratory diseases by analyzing multiple traits and ancestries, identifying novel loci and developing a new polygenic risk score method.

XTree aligns sequencing reads to large genome databases efficiently and accurately, outperforming existing tools in precision and recall.

The paper introduces MAGUS, a toolkit for analyzing metagenomic data from eukaryote-dominated symbiotic communities, and demonstrates its ability to resolve multiple genomes and gene catalogs from coral and hydrozoan samples.

The paper introduces PCRR, a method using protein ratio features to improve disease prediction in proteomics, showing significant gains in Alzheimer's classification and generalizability across datasets.

The paper introduces a decomposition approach to detect genetic modifiers of the relationship between dietary omega-3 fatty acids, plasma biomarkers, and hsCRP in the UK Biobank, improving statistical power.

PYPE automates phenome-wide association studies and Mendelian Randomization analyses on biobank data, enabling causal inference and visualization of genotype-phenotype associations.

This study compares microbiome and genome-wide association study predictive power for 13 diseases, finding microbiome indicators outperform genetic variants in disease discrimination.

The paper develops a poly-exposure score (PXS) to assess combined genetic and non-genetic risk factors for four diseases, showing PXS outperforms polygenic risk scores in some cases.

This study identifies 30 transcripts associated with physical activity through a transcriptome-wide association study, finding some linked to obesity, aging, and mental health.

The paper analyzes gene expression differences in monozygotic twins discordant for seven phenotypes to identify common and distinct environmental influences on gene expression.

Aether uses linear programming to optimally deploy cloud resources for genomics tasks, achieving cost savings and efficiency in metagenomic assembly.

This study identifies potential drug repositioning hypotheses by analyzing clinical phenotypes and prescription drug usage in a healthy population.

The paper uses DNA methylation data and a repositioning method to identify potential drugs for acute myeloid leukemia.