Jonathan K Pritchard

Batch effects and the effective design of single-cell gene expression studies

This study identifies genotype as the major source of variation in scRNA-seq data and highlights technical replicate variation, suggesting a framework for effective study design.

Effects of variable mutation rates and epistasis on the distribution of allele frequencies in humans

This study examines how variable mutation rates and epistasis affect the phylogenetically-conditioned site frequency spectrum in humans using ExAC and primate genome data.

Detection of human adaptation during the past 2,000 years

This study detects recent human adaptation over the past 2,000 years using the Singleton Density Score, revealing selection signals for lactase, HLA, height, and other complex traits.

Whole genome sequencing identifies a novel factor required for secretory granule maturation in Tetrahymena thermophila

The paper identifies a novel gene MMA1 required for secretory granule maturation in Tetrahymena thermophila through whole genome sequencing of a mutant strain.

Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals.

The paper shows that tandem duplicate genes in mammals evolve slowly toward subfunctionalization due to co-regulation, supporting dosage-sharing as a key mechanism for their survival.

Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs

This study compares regulatory differences in iPSCs and finds that genetic variation, not cell type of origin, primarily drives these differences.

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

This study identifies 7,273 new human coding sequences using ribosome footprint profiling and validates their functionality through selective constraint and translation correlation analysis.

Reprogramming LCLs to iPSCs Results in Recovery of Donor-Specific Gene Expression Signature

This study shows that reprogramming LCLs to iPSCs recovers donor-specific gene expression signatures, suggesting iPSCs better reflect genetic influences on gene regulation than LCLs.

msCentipede: Modeling heterogeneity across genomic sites improves accuracy in the inference of transcription factor binding

The paper introduces msCentipede, a model that improves transcription factor binding site inference by better modeling DNase I cleavage pattern heterogeneity and spatial structure.

Variational Inference of Population Structure in Large SNP Datasets

The paper develops fast variational Bayesian algorithms for inferring population structure in large SNP datasets, achieving speed improvements over STRUCTURE and comparable accuracy to ADMIXTURE.