Rick Farouni

This study shows that the niche environment significantly influences skeletal muscle stem cell transcriptional activity, with some age-related changes being reversible through exposure to a young niche.

The paper introduces a probabilistic model to estimate and correct sample index hopping in single-cell RNA-seq data, reducing phantom molecules by up to 85%.

The paper identifies a batch effect in 1000 Genomes Project data causing spurious mutation calls and affecting GWAS results, suggesting legacy data may need to be retired or upgraded.

CRISPResso2 is a software tool for analyzing genome editing data, providing allele-specific quantification and scalable alignment to assess editing efficiency and safety.

CRISPR-SURF deconvolves CRISPR tiling screen data to identify functional regulatory elements across CRISPR-Cas, CRISPRi, and CRISPRa experiments.

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.

The paper introduces AmpUMI, a tool for designing and analyzing UMI-based amplicon sequencing experiments, providing a model to determine optimal UMI length and quality control features.

Haystack identifies epigenetic variability hotspots and cell-type specific regulatory elements across multiple cell types using a computational pipeline.

ALTRE is an R package and web app for analyzing chromatin accessibility data to identify altered regulatory elements across cell types.