Tony Zeng

Mapping the regulatory wiring of endothelial cell differentiation reveals a critical role for Hippo mechanosignaling

The paper maps gene regulators of endothelial cell differentiation using CRISPR and single-cell RNA-seq, identifying Hippo mechanosignaling as critical for endothelial identity.

Systematic mapping of enhancers, silencers, and topological elements with prime editing deletion screens

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.

Causal modeling of gene effects from regulators to programs to traits: integration of genetic associations and Perturb-seq

The paper integrates genetic associations with Perturb-seq data to build causal graphs linking genes to traits through regulatory programs.

Small-cohort GWAS discovery with AI over massive functional genomics knowledge graph

KGWAS improves GWAS power in small cohorts by integrating a functional knowledge graph, discovering more associations for rare diseases.

Interpreting variants associated with congenital heart disease with a regulatory map of the human fetal heart

This study creates a gene regulation map of the human fetal heart to interpret genetic variants associated with congenital heart disease and cardiac traits, identifying valvular interstitial cells as key regulators.

Bayesian estimation of gene constraint from an evolutionary model with gene features

This paper introduces a Bayesian framework combining population genetics and machine learning to estimate gene constraint, improving accuracy for short genes and providing a flexible tool for gene-level property estimation.

Mapping the convergence of genes for coronary artery disease onto endothelial cell programs

The paper maps coronary artery disease risk loci to endothelial cell gene programs, identifying convergence on the CCM pathway and a new CAD gene, TLNRD1.

Predicting RNA splicing from DNA sequence using Pangolin

Pangolin is a deep learning model that predicts RNA splicing from DNA sequence, outperforming existing methods and accurately identifying pathogenic variants.

Alternative polyadenylation mediates genetic regulation of gene expression

The paper identifies genetic variants affecting alternative polyadenylation (APA) and shows their impact on gene expression, protein levels, and disease risk.