Rare-event sampling of epigenetic landscapes and phenotype transitions

BioNetGen 2.2: advances in rule-based modeling

(2016) Leonard A. Harris et al.   BIOINFORMATICS

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

(2016) Rory M. Donovan et al.   PLoS Computational Biology

Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements

(2016) Sahand Hormoz et al.   Cell Systems

DNA-Binding Kinetics Determines the Mechanism of Noise-Induced Switching in Gene Networks

(2015) Margaret J. Tse et al.   BIOPHYSICAL JOURNAL

Quantifying the Landscape for Development and Cancer from a Core Cancer Stem Cell Circuit

(2015) C. Li et al.   CANCER RESEARCH

Adaptive hybrid simulations for multiscale stochastic reaction networks

(2015) Benjamin Hepp et al.   JOURNAL OF CHEMICAL PHYSICS

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

(2015) Martin K. Scherer et al.   Journal of Chemical Theory and Computation

Network plasticity of pluripotency transcription factors in embryonic stem cells

(2015) Adam Filipczyk et al.   NATURE CELL BIOLOGY

Stochastic Phenotype Transition of a Single Cell in an Intermediate Region of Gene State Switching

(2015) Hao Ge et al.   PHYSICAL REVIEW LETTERS

Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency

(2014) Elsa Abranches et al.   DEVELOPMENT

Simultaneous Computation of Dynamical and Equilibrium Information Using a Weighted Ensemble of Trajectories

(2014) Ernesto Suárez et al.   Journal of Chemical Theory and Computation

WExplore: Hierarchical Exploration of High-Dimensional Spaces Using the Weighted Ensemble Algorithm

(2014) Alex Dickson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

(2014) Zakary S. Singer et al.   MOLECULAR CELL

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

Epigenetic state network approach for describing cell phenotypic transitions

(2014) P. Wang et al.   Interface Focus

Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories

(2013) Rory M. Donovan et al.   JOURNAL OF CHEMICAL PHYSICS

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

Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

(2013) Yusuke Ohnishi et al.   NATURE CELL BIOLOGY

Generation and Characterization of a Novel Mouse Embryonic Stem Cell Line with a Dynamic Reporter of Nanog Expression

(2013) Elsa Abranches et al.   PLoS One

Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification

(2013) Susanna Röblitz et al.   Advances in Data Analysis and Classification

Time Scales in Epigenetic Dynamics and Phenotypic Heterogeneity of Embryonic Stem Cells

(2013) Masaki Sasai et al.   PLoS Computational Biology

Small-Number Effects: A Third Stable State in a Genetic Bistable Toggle Switch

(2012) Rui Ma et al.   PHYSICAL REVIEW LETTERS

A new mechanism of stem cell differentiation through slow binding/unbinding of regulators to genes

(2012) Haidong Feng et al.   Scientific Reports

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

(2011) Sui Huang   BIOESSAYS

Rule-based multi-level modeling of cell biological systems

(2011) Carsten Maus et al.   BMC Systems Biology

A deterministic map of Waddington's epigenetic landscape for cell fate specification

(2011) Sudin Bhattacharya et al.   BMC Systems Biology

Stochastic State Transitions Give Rise to Phenotypic Equilibrium in Populations of Cancer Cells

(2011) Piyush B. Gupta et al.   CELL

Markov models of molecular kinetics: Generation and validation

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

Quantifying the Waddington landscape and biological paths for development and differentiation

(2011) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Search for Recipes to Generate Induced Pluripotent Stem Cells

(2011) Rui Chang et al.   PLoS Computational Biology

A Chromatin-Mediated Reversible Drug-Tolerant State in Cancer Cell Subpopulations

(2010) Sreenath V. Sharma et al.   CELL

The “weighted ensemble” path sampling method is statistically exact for a broad class of stochastic processes and binning procedures

(2010) Bin W. Zhang et al.   JOURNAL OF CHEMICAL PHYSICS

Reprogramming cell fates: reconciling rarity with robustness

(2009) Sui Huang   BIOESSAYS

Nanog Is the Gateway to the Pluripotent Ground State

(2009) Jose Silva et al.   CELL

Nonequilibrium umbrella sampling in spaces of many order parameters

(2009) Alex Dickson et al.   JOURNAL OF CHEMICAL PHYSICS

Separating forward and backward pathways in nonequilibrium umbrella sampling

(2009) Alex Dickson et al.   JOURNAL OF CHEMICAL PHYSICS

Forward flux sampling for rare event simulations

(2009) Rosalind J Allen et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Forcing cells to change lineages

(2009) Thomas Graf et al.   NATURE

Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations

(2009) Frank Noé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulated Fluctuations in Nanog Expression Mediate Cell Fate Decisions in Embryonic Stem Cells

(2009) Tibor Kalmar et al.   PLOS BIOLOGY

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

(2008) Hannah H. Chang et al.   NATURE

Stochastic switching as a survival strategy in fluctuating environments

(2008) Murat Acar et al.   NATURE GENETICS

Extinction and resurrection in gene networks

(2008) D. Schultz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA