Ziwei Chen

This paper introduces Swap-seq, a method to systematically delete and quantify the effects of enhancers, silencers, and topological elements on gene expression in human cells.

The paper characterizes regulatory variants in human neurons using lentiMPRA and shows that variant effects are influenced by regulatory element activity and sequence context, not population frequency.

The paper studies how dietary metabolites interact with genetic variants to influence colon cancer risk through transcriptional regulation.

The paper introduces Variant-FlowFISH to measure the effects of DNA sequence variants on gene expression, identifies regulatory mechanisms, and benchmarks predictive models.

The paper develops criteria for identifying, sharing, and reporting novel candidate genes in clinical genomic testing to improve diagnostic yield for Mendelian conditions.

The paper identifies novel transcripts, eQTLs, and caQTLs in African populations and fine-maps GWAS signals for complex diseases.

The paper introduces a graph-based pangenome representation for the Collaborative Cross mouse genetic reference population, enabling analysis of multiple genomes in a unified framework.