Rachel E. Gate

memento: Generalized differential expression analysis of single-cell RNA-seq with method of moments estimation and efficient resampling

The paper introduces memento, a method for differential expression analysis of scRNA-seq data, and shows it identifies significant differences in mean, variability, and gene correlation across experimental conditions.

Mapping gene regulatory networks of primary CD4+ T cells using single-cell genomics and genome engineering

The paper uses CRISPR perturbations and single-cell transcriptomics to identify gene regulators and interactions in CD4+ T cells, revealing 134 regulators and 194 regulator pairs.

Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection

The paper identifies genetic variants influencing isoform usage in the anti-viral response, revealing ERAP2's role in balancing selection and influenza-specific regulation.

Genetic determinants of co-accessible chromatin regions in T cell activation across humans

The paper identifies genetic variants affecting chromatin accessibility in T cells and links them to gene expression and autoimmune disease.

Multiplexing droplet-based single cell RNA-sequencing using natural genetic barcodes

The paper introduces demuxlet, an algorithm that uses natural genetic variation to multiplex single-cell RNA-seq samples, enabling accurate sample identification and doublet detection in pooled experiments.

Discovery of an autoimmunity-associated IL2RA enhancer by unbiased targeting of transcriptional activation

The paper identifies an IL2RA enhancer associated with autoimmunity using CRISPRa and shows it affects gene activation timing without blocking expression.