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

A defined Oct4 level governs cell state transitions of pluripotency entry and differentiation into all embryonic lineages

(2013) Aliaksandra Radzisheuskaya et al.   NATURE CELL BIOLOGY

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

Landscape and Global Stability of Nonadiabatic and Adiabatic Oscillations in a Gene Network

(2012) Haidong Feng et al.   BIOPHYSICAL JOURNAL

Bistability, Bifurcations, and Waddington's Epigenetic Landscape

(2012) James E. Ferrell   CURRENT BIOLOGY

Potential flux landscapes determine the global stability of a Lorenz chaotic attractor under intrinsic fluctuations

(2012) Chunhe Li et al.   JOURNAL OF CHEMICAL PHYSICS

Attractor Landscape Analysis Reveals Feedback Loops in the p53 Network That Control the Cellular Response to DNA Damage

(2012) M. Choi et al.   Science Signaling

Landscape and flux decomposition for exploring global natures of non-equilibrium dynamical systems under intrinsic statistical fluctuations

(2011) Chunhe Li et al.   CHEMICAL PHYSICS LETTERS

Progress in understanding reprogramming to the induced pluripotent state

(2011) Kathrin Plath et al.   NATURE REVIEWS GENETICS

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

Adiabatic and Non-Adiabatic Non-Equilibrium Stochastic Dynamics of Single Regulating Genes

(2010) Haidong Feng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Nuclear reprogramming to a pluripotent state by three approaches

(2010) Shinya Yamanaka et al.   NATURE

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

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

(2009) Krishanu Saha et al.   Cell Stem Cell

Cardiac Fibroblasts Regulate Myocardial Proliferation through β1 Integrin Signaling

(2009) Masaki Ieda et al.   DEVELOPMENTAL CELL

Simple, realistic models of complex biological processes: Positive feedback and bistability in a cell fate switch and a cell cycle oscillator

(2009) James E. Ferrell et al.   FEBS LETTERS

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

A New Look at Some Old Animals

(2009) Neil W Blackstone   PLOS BIOLOGY

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

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