Dingyu Liu

This paper introduces Perturbscape, a framework that uses perturbation-induced gene programs to identify disease-relevant genes and pathways, showing higher heritability informativeness than steady-state approaches.

The paper identifies pre-established chromatin regions in human ESCs that enable rapid activation of lineage-specific genes during differentiation.

The paper introduces pertTF, a transformer-based model for predicting genetic perturbation responses, showing improved performance in expression prediction and cell identity shifts across cellular contexts.

This paper develops a human organoid model of early PDAC that identifies genetic and epigenetic barriers to lineage plasticity, showing CDKN2A loss is essential with KRAS/TP53 mutations and TET1 suppression links ERK signaling to transcription factor silencing.

CausalGRN infers causal gene regulatory networks from single-cell CRISPR screens and predicts responses to unseen perturbations with improved accuracy.

This study uses a knockout village framework to analyze how mutations in diabetes genes alter pancreatic beta cell development, revealing non-canonical cell fate shifts and identifying ISL1 as a key regulator.

The paper identifies two NANOG enhancers in human embryonic stem cells and shows their critical role in maintaining self-renewal and preventing differentiation.

The paper uses CRISPR-Cas9 screens to identify genes affecting stem cell fitness versus pluripotency identity, finding distinct and overlapping roles for chromatin and metabolic regulators.

The paper introduces a method to quantify diverse perturbation responses and discover novel biological insights in single-cell perturbation datasets.