Xiaomeng Zhang

MCLand is a Python program that visualizes Waddington's epigenetic landscape using Monte Carlo simulations to model gene regulatory networks and estimate cell state probabilities.

The paper reconstructs ancestral genomes using a new computational method and finds the monoploid chromosome number x = 9 for rosid and asterid orders.

FastIntegration integrates large-scale single-cell RNA-seq data efficiently and improves downstream analysis by providing batch-corrected gene expression values.

The paper introduces a Monte Carlo method to model and visualize the Waddington's epigenetic landscape of gene regulatory networks, showing how attractors and paths between them represent stability in biological systems.

cycleX infers multi-dimensional pseudotimes to reveal relationships between cell cycle and differentiation in dendritic cell progenitors.