Jacob W. Freimer

Cis-Regulatory Element and Transcription Factor Circuitry Required for Cell-Type Specific Expression of FOXP3

The paper identifies cis-regulatory elements and transcription factors controlling FOXP3 expression in human Tregs and Tconvs, revealing mechanisms that restrict FOXP3 to Tregs in mice.

Gene regulatory network inference from CRISPR perturbations in primary CD4+ T cells elucidates the genomic basis of immune disease

This study uses CRISPR perturbations in CD4+ T cells to infer a gene regulatory network, revealing trans-regulatory mechanisms linking immune GWAS genes to signaling pathways.

A model for accurate quantification of CRISPR effects in pooled FACS screens

The paper develops a Bayesian model and software for analyzing CRISPR screens and validates its effectiveness in maintaining statistical power under low coverage conditions.

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks

The paper identifies upstream regulators of immune genes in human T cells and maps their regulatory network, revealing its enrichment for immune disease variants.

Decoupling the impact of microRNAs on translational repression versus RNA degradation in embryonic stem cells

The paper investigates the role of DDX6 in linking microRNA functions to mRNA stability and translation in ESCs, finding that DDX6 loss separates microRNA's translational repression from transcript destabilization.