Uncovering the cell fate decision in lysis–lysogeny transition and stem cell development via Markov state modeling

Landscape and kinetic path quantify critical transitions in epithelial-mesenchymal transition

(2021) Jintong Lang et al.   BIOPHYSICAL JOURNAL

Generalized Markov State Modeling Method for Nonequilibrium Biomolecular Dynamics: Exemplified on Amyloid β Conformational Dynamics Driven by an Oscillating Electric Field

(2018) Bernhard Reuter et al.   Journal of Chemical Theory and Computation

Direct pericyte-to-neuron reprogramming via unfolding of a neural stem cell-like program

(2018) Marisa Karow et al.   NATURE NEUROSCIENCE

A stochastic and dynamical view of pluripotency in mouse embryonic stem cells

(2018) Yen Ting Lin et al.   PLoS Computational Biology

Rare-event sampling of epigenetic landscapes and phenotype transitions

(2018) Margaret J. Tse et al.   PLoS Computational Biology

Mouse embryonic stem cells can differentiate via multiple paths to the same state

(2017) James Alexander Briggs et al.   eLife

Construction of the landscape for multi-stable systems: Potential landscape, quasi-potential, A-type integral and beyond

(2016) Peijie Zhou et al.   JOURNAL OF CHEMICAL PHYSICS

Landscape and flux theory of non-equilibrium dynamical systems with application to biology

(2015) Jin Wang   ADVANCES IN PHYSICS

Constructing the Energy Landscape for Genetic Switching System Driven by Intrinsic Noise

(2014) Cheng Lv et al.   PLoS One

Stem cell differentiation as a many-body problem

(2014) B. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Markov State Models for Rare Events in Molecular Dynamics

(2013) Marco Sarich et al.   Entropy

Quantifying Waddington landscapes and paths of non-adiabatic cell fate decisions for differentiation, reprogramming and transdifferentiation

(2013) C. Li et al.   Journal of the Royal Society Interface

Quantifying Cell Fate Decisions for Differentiation and Reprogramming of a Human Stem Cell Network: Landscape and Biological Paths

(2013) Chunhe Li et al.   PLoS Computational Biology

Bistability, Bifurcations, and Waddington's Epigenetic Landscape

(2012) James E. Ferrell   CURRENT BIOLOGY

The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post-Darwinian biology?

(2011) Sui Huang   BIOESSAYS

Markov models of molecular kinetics: Generation and validation

(2011) Jan-Hendrik Prinz et al.   JOURNAL OF CHEMICAL PHYSICS

Kinetic paths, time scale, and underlying landscapes: A path integral framework to study global natures of nonequilibrium systems and networks

(2010) Jin Wang et al.   JOURNAL OF CHEMICAL PHYSICS

Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda

(2010) Y. Cao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nanog Is the Gateway to the Pluripotent Ground State

(2009) Jose Silva et al.   CELL

Transition Path Theory for Markov Jump Processes

(2009) Philipp Metzner et al.   MULTISCALE MODELING & SIMULATION

Forcing cells to change lineages

(2009) Thomas Graf et al.   NATURE

Collective Decision Making in Bacterial Viruses

(2008) Joshua S. Weitz et al.   BIOPHYSICAL JOURNAL

Optimal partition and effective dynamics of complex networks

(2008) W. E et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA