Lei Zhang

TRINUS decouples cell lineage identity from niche pressure to uncover interaction syntax in spatial transcriptomics data, showing improved clustering and domain detection across biological systems.

This paper introduces the Hyper Solution Landscape (HSL) method to analyze cell fate decisions by exploring gene regulatory network configurations and their dynamic changes.

The paper analyzes single-cell dynamics during state transitions, finding that cell states are sensitive to few 'stiff' parameters and robust to many 'sloppy' parameters, suggesting a principle of least action.

This paper introduces a high-density, flexible ECoG device (NeuroCam) with 4096 channels and 44 sites/mm2 density, validated in a rabbit epilepsy model for high-resolution spatial mapping of neural activity.

This study investigates FUS-ERG fusion oncoprotein-DNA co-condensates, revealing nested asymmetric phase separation and their potential for DNA-based information manipulation.

The paper introduces SCIM, a method using information geometry to quantify cell phenotype transition manifolds by analyzing curvature and velocity in single-cell gene expression data.

This study constructs a logic-incorporated gene regulatory network model to analyze how regulatory logic and noise influence cell fate decisions in differentiation and reprogramming.

The paper identifies network design principles for robust oscillatory behaviors in transcriptional regulatory networks under biological noise.

This study profiles colorectal cancer specific enhancers and reveals their regulation network using HiChIP, Hi-C, and RNA-seq data, showing their role in cancer progression.

The paper develops a mathematical model to explain the formation and function of bivalent chromatin by analyzing the dynamics of H3K4me3 and H3K27me3 modifications.

The paper develops a data-driven phase field model to simulate early C. elegans embryo morphogenesis using imaging data, revealing the roles of cell division and cell-cell attraction.

The paper develops a mathematical model to uncover the nonequilibrium mechanism behind drug synergy between Activators and Noise Enhancers in HIV latency reactivation.

This study examines the effects of sugars and lipids on C. elegans growth, finding that excessive intake reduces lifespan, reproductive capacity, and body length while altering gene expression.