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

Cooperativity in Cellular Biochemical Processes: Noise-Enhanced Sensitivity, Fluctuating Enzyme, Bistability with Nonlinear Feedback, and Other Mechanisms for Sigmoidal Responses

(2012) Hong Qian   Annual Review of Biophysics

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

(2012) Haidong Feng et al.   Scientific Reports

Landscape Topography Determines Global Stability and Robustness of a Metabolic Network

(2012) Chunhe Li et al.   ACS Synthetic Biology

Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit

(2012) Dmitry Nevozhay et al.   PLoS Computational Biology

Potential Landscape and Probabilistic Flux of a Predator Prey Network

(2011) Chunhe Li et al.   PLoS One

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

The Potential Landscape of Genetic Circuits Imposes the Arrow of Time in Stem Cell Differentiation

(2010) Jin Wang et al.   BIOPHYSICAL JOURNAL

Nanog Overcomes Reprogramming Barriers and Induces Pluripotency in Minimal Conditions

(2010) Thorold W. Theunissen et al.   CURRENT BIOLOGY

A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity

(2010) Na-Yu Chia et al.   NATURE

Nuclear reprogramming to a pluripotent state by three approaches

(2010) Shinya Yamanaka et al.   NATURE

Nanog Variability and Pluripotency Regulation of Embryonic Stem Cells - Insights from a Mathematical Model Analysis

(2010) Ingmar Glauche et al.   PLoS One

Potential and flux landscapes quantify the stability and robustness of budding yeast cell cycle network

(2010) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach

(2009) Lukas Chavez et al.   BMC GENOMICS

Technical Challenges in Using Human Induced Pluripotent Stem Cells to Model Disease

(2009) Krishanu Saha et al.   Cell Stem Cell

Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse

(2009) J. Rossant et al.   DEVELOPMENT

Global view of bionetwork dynamics: adaptive landscape

(2009) Ping Ao   Journal of Genetics and Genomics

Elite and stochastic models for induced pluripotent stem cell generation

(2009) Shinya Yamanaka   NATURE

Forcing cells to change lineages

(2009) Thomas Graf et al.   NATURE

Extreme Makeover: Converting One Cell into Another

(2008) Qiao Zhou et al.   Cell Stem Cell

A core Klf circuitry regulates self-renewal of embryonic stem cells

(2008) Jianming Jiang et al.   NATURE CELL BIOLOGY

Stochasticity and the Molecular Mechanisms of Induced Pluripotency

(2008) Ben D. MacArthur et al.   PLoS One

A Computational Model for Understanding Stem Cell, Trophectoderm and Endoderm Lineage Determination

(2008) Vijay Chickarmane et al.   PLoS One

Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations

(2008) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA