James K. Nuñez

The paper maps transcription factor effector domains in plants and compares their function across eukaryotes, revealing conserved and lineage-specific regulatory principles.

The paper shows RNA m6A modifications coordinate with de novo DNA methylation to establish heritable epigenetic silencing in human cells.

This paper develops a virus-like particle-based system for CRISPR gene editing and screening in primary human myeloid cells, identifying TNFAIP3 as a key regulator of inflammatory polarization.

The paper identifies regulators of microglial activation states using CRISPR screens and single-cell transcriptomics, revealing functional roles of ZNF532, PRDM1, and DNMT1 in disease-associated microglial states.

CRISPRtune is a programmable tool that tunes transcriptional repression by fusing MeCP2 to dCas9, enabling intermediate gene expression control in human cells.

The paper introduces MOSAIC, a multimodal adaptive optical microscope that enables non-invasive imaging across biological scales in live specimens.

LEMONmethyl-seq profiles DNA methylation dynamics in mammalian cells, revealing CRISPR-induced changes and endogenous patterns, including non-canonical CpH methylation.

The paper develops a toolkit of chromatin regulators with cross-kingdom functionality for programmable transcriptional repression and activation in eukaryotic cells.

This paper introduces RENDER, a method for transient delivery of CRISPR-based epigenome editors as ribonucleoproteins to modulate gene expression in human cells, achieving durable epigenetic silencing.

This paper describes a protocol for CRISPRoff epigenetic editing to silence genes in human cells without DNA breaks, showing heritable transcriptional repression.

This study uses Perturb-seq to functionally interrogate SARS-CoV-2 host factors in human lung epithelial cells, identifying key factors that influence infection and host response.

This paper demonstrates CRISPR-Cpf1-based transcription factors for inducible and tunable regulation of human gene expression, enabling combinatorial gene activation.