Patrick Flaherty

The paper uses transposon sequencing to identify stress-specific vulnerabilities in protein homeostasis by analyzing gene fitness under proteotoxic stresses in bacteria.

The paper uses transposon mutagenesis and computational analysis to identify genetic modulators of protein homeostasis in Caulobacter crescentus, finding limited overlap in essential genes across environmental and genetic perturbations.

The paper introduces a method to identify significant gene expression changes in multiple perturbation experiments using knockoffs and applies it to data from the LINCS program.

The paper introduces a model-based method to identify conditionally-essential genes using transposon-insertion sequencing data, finding a set of genes essential under specific stress conditions in Caulobacter crescentus.

This paper introduces a Bayesian nonparametric model to infer subclonal populations from structured DNA sequencing data, showing improved performance over existing methods.

SCSIM simulates correlated single-cell and bulk DNA sequencing data for testing variant callers and analysis tools.