Feng Zhang

TIGRFinder annotated 6,685 TIGR arrays; cryo-EM structures show inactive RuvC domains, and E. coli reporter assays show CsTasR and MbTasA repress transcription in a guide-dependent manner.

This study determines the structural basis of phage terminase recognition by Avs2 and Upx, revealing distinct binding mechanisms despite structural differences.

This paper demonstrates the use of in vitro-assembled Drosophila Arc1 capsids to deliver gene editors to dystrophic muscle, achieving exon skipping and dystrophin restoration in mdx mice.

The paper shows chronic metabolic stress in liver cells drives developmental programs and functional loss, mirroring tumor states and predicting poor cancer survival.

This study uses spatial transcriptomics and TCR sequencing in mice to analyze thymus changes across lifespan, revealing structural and transcriptional alterations linked to immune decline.

This study compares CRISPR-Cas9 and TALEN gene editing in a mouse model of Machado-Joseph disease, showing CRISPR-Cas9 reduces ATXN3 aggregates and delays disease progression.

This paper develops a platform to model and manipulate human microglial states in vitro using single-cell RNA sequencing and genetic tools, identifying disease-associated transcriptional signatures.

The paper maps cellular changes in the aging human brain and identifies altered multicellular communities in Alzheimer's disease using single nucleus RNA-seq and bulk RNA-seq data.

This study removes a genomic duplication in a mouse model using DN-CRISPRs, improving synaptic transmission and behavior.

This study constructs a single-cell and spatial atlas of the choroid plexus in developing and adult mice, revealing cell types, regional gene expression, and cell-cell interactions.

The paper uses scRNA-seq to show increased transcriptional heterogeneity in neurodegenerative disease models, suggesting early regulatory imbalances.

This study uses in vivo Perturb-Seq to analyze the effects of 35 autism risk genes on neuronal and glial cells in the developing brain.

LAMP-Seq combines three-step isothermal RT-LAMP amplification with combinatorial barcoding to pool and sequence SARS-CoV-2 clinical samples en masse for scalable diagnostics.

The paper introduces an optical method to link genetic perturbations with phenotypic outcomes in a pooled setting, identifying novel regulators of immune responses.

The paper presents a protocol for designing, executing, and analyzing CRISPR genome editing experiments using CRISPOR and CRISPResso.

GUIDES designs CRISPR libraries for loss-of-function screens using RNA-seq and protein annotations to target exons and functional domains.

DroNc-Seq enables high-throughput single nucleus RNA-seq analysis of archived brain tissues, demonstrating efficient and unbiased cell type classification in mouse and human samples.

The paper introduces PASTAS, a method for in vivo CRISPR screening in mice, and demonstrates its use in identifying cancer driver variants in liver tumors.

This study uses an AAV-mediated CRISPR screen in mice to identify functional suppressors of glioblastoma, revealing novel and canonical tumor suppressors and their interactions.

This paper engineers Cpf1 variants with altered PAM specificities to expand their targeting range while maintaining specificity.

The paper tests 16 Cpf1 orthologs for genome editing activity in eukaryotic cells, identifying four active enzymes including Mb3Cpf1 with robust indel formation and PAM tolerance.

This paper describes a protocol for genome-scale CRISPR-Cas9 knockout and transcriptional activation screening, including library design, validation strategies, and timing estimates.

The paper demonstrates multiplex gene editing in mammalian cells and mouse brains using a single CRISPR array processed by Cpf1 without requiring additional factors.

BLISS quantifies DNA double-strand breaks in situ with high sensitivity and efficiency, showing Cpf1 has higher specificity than Cas9.

This paper uses a CRISPR screen to identify noncoding genomic elements that influence drug resistance in melanoma cells.

This study characterizes C2c2, a CRISPR-Cas effector that uses an RNA guide to target and cleave RNA, showing its potential as a programmable RNA-targeting tool.

Div-Seq tracks transcriptional dynamics of rare adult newborn neurons using single nucleus RNA-Seq and EdU labeling.

The paper introduces improved CRISPR screening vectors and libraries to enhance genome-wide loss-of-function studies in human and mouse cells.