Xingjie Ren

De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes

The paper develops a computational method to predict structural variant impacts on genome folding and identifies ASD-associated variants disrupting neuronal regulatory interactions.

CRISPR tiling deletion screens reveal functional enhancers of neuropsychiatric risk genes and allelic compensation effects (ACE) on transcription

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

High throughput PRIME editing screens identify functional DNA variants in the human genome

This paper introduces PRIME, a high-throughput prime editing screen that identifies functional DNA variants in the human genome with base-pair resolution.

Functional characterization of gene regulatory elements and neuropsychiatric disease-associated risk loci in iPSCs and iPSC-derived neurons

The paper identifies functional CREs in iPSCs and neurons and links them to neuropsychiatric disease risk variants.

Multi-center integrated analysis of non-coding CRISPR screens

The paper reports 109 non-coding CRISPR screens analyzing 13.3Mb of the genome, identifies CRE-gene links, and provides guidelines and tools for screening non-coding regulatory elements.

Parallel Characterization of cis-Regulatory Elements for Multiple Genes Using CRISPRpath

CRISPRpath enables parallel characterization of cis-regulatory elements for multiple genes in a pathway, identifying functional enhancers and distinguishing their impact on gene expression.

The Mediator CDK8-Cyclin C complex modulates vein patterning in Drosophila by stimulating Mad-dependent transcription

This study identifies CDK8-CycC's role in Drosophila wing vein patterning by interacting with the Dpp/TGF{beta} pathway and regulating Mad-dependent transcription.

cis-Regulatory Chromatin Contacts in Neural Cells Reveal Contributions of Genetic Variants to Complex Neurological Disorders

The paper identifies cis-regulatory chromatin contacts in neural cells and links them to genetic variants associated with complex neurological disorders.

The lysine demethylase dKDM2 is non-essential for viability, but regulates circadian rhythms in Drosophila

This study shows that dKDM2 is not essential for Drosophila viability but regulates circadian rhythms, with loss-of-function mutants showing arrhythmic behavior and overexpression causing shorter periods.

Next generation CRISPR/Cas9 transcriptional activation in Drosophila using flySAM

This paper introduces flySAM, a CRISPRa tool for Drosophila that improves effectiveness, scalability, and ease-of-use compared to existing methods.