Stephen Zhang

A stem cell knockout village reveals lineage rewiring and a non-canonical islet cell fate in monogenic diabetes

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 hidden predictors of human haematopoietic clonal fate

The paper identifies clonal fate modules in human HSPCs using machine learning, revealing molecular predictors of lineage commitment and improving dendritic cell purity for immunotherapy.

A multi-track landscape of haematopoiesis informed by cellular barcoding and agent-based modelling

This study uses cellular barcoding and agent-based modeling to reveal clonal fate patterns in hematopoiesis, showing that stem and progenitor cells are often less multipotent than previously thought.

LoxCode in vivo clonal barcoding resolves mammalian epiblast contribution to fetal organs

The paper develops LoxCode barcoding to trace clonal fate of epiblast cells in vivo, finding lineage biases and tissue-specific contributions across fetal development.

Optimal transport analysis reveals trajectories in steady-state systems

This paper introduces StationaryOT, an optimal transport method to infer cell trajectories from single snapshots of equilibrium systems, validated on simulated and Arabidopsis root data.