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

Inference of Intercellular Communications and Multilayer Gene-Regulations of Epithelial–Mesenchymal Transition From Single-Cell Transcriptomic Data

(2021) Yutong Sha et al.   Frontiers in Genetics

A Computational Systems Biology Approach Identifies SLUG as a Mediator of Partial Epithelial-Mesenchymal Transition (EMT)

(2021) Ayalur R. Subbalakshmi et al.   CELLS TISSUES ORGANS

The Physics of Cellular Decision Making During Epithelial–Mesenchymal Transition

(2020) Shubham Tripathi et al.   Annual Review of Biophysics

SMAD7 and SERPINE1 as novel dynamic network biomarkers detect and regulate the tipping point of TGF-beta induced EMT

(2020) Zhonglin Jiang et al.   Science Bulletin

A plausible accelerating function of intermediate states in cancer metastasis

(2020) Hanah Goetz et al.   PLoS Computational Biology

Identifying inhibitors of epithelial–mesenchymal plasticity using a network topology-based approach

(2020) Kishore Hari et al.   npj Systems Biology and Applications

Anticipating critical transitions in epithelial–hybrid-mesenchymal cell-fate determination

(2019) Sukanta Sarkar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Landscape reveals critical network structures for sharpening gene expression boundaries

(2018) Chunhe Li et al.   BMC Systems Biology

Topography of epithelial–mesenchymal plasticity

(2018) Francesc Font-Clos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of the tumour transition states occurring during EMT

(2018) Ievgenia Pastushenko et al.   NATURE

DensityPath: an algorithm to visualize and reconstruct cell state-transition path on density landscape for single-cell RNA sequencing data

(2018) Ziwei Chen et al.   BIOINFORMATICS

Quantifying resilience of humans and other animals

(2018) Marten Scheffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hysteresis control of epithelial-mesenchymal transition dynamics conveys a distinct program with enhanced metastatic ability

(2018) Toni Celià-Terrassa et al.   Nature Communications

Identifying the optimal anticancer targets from the landscape of a cancer–immunity interaction network

(2017) Chunhe Li   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Decoding early myelopoiesis from dynamics of core endogenous network

(2017) Hang Su et al.   Science China-Life Sciences

Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures

(2017) Faiz M. Khan et al.   Nature Communications

Interrogating the topological robustness of gene regulatory circuits by randomization

(2017) Bin Huang et al.   PLoS Computational Biology

LOXL2 drives epithelial-mesenchymal transition via activation of IRE1-XBP1 signalling pathway

(2017) Eva P. Cuevas et al.   Scientific Reports

Novel Hybrid Phenotype Revealed in Small Cell Lung Cancer by a Transcription Factor Network Model That Can Explain Tumor Heterogeneity

(2016) Akshata R. Udyavar et al.   CANCER RESEARCH

Quantifying the landscape and kinetic paths for epithelial–mesenchymal transition from a core circuit

(2016) Chunhe Li et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2015) C. Li et al.   CANCER RESEARCH

Critical transitions in chronic disease: transferring concepts from ecology to systems medicine

(2015) Christophe Trefois et al.   CURRENT OPINION IN BIOTECHNOLOGY

Coupling the modules of EMT and stemness: A tunable ‘stemness window’ model

(2015) Mohit Kumar Jolly et al.   Oncotarget

Energy Landscape Reveals That the Budding Yeast Cell Cycle Is a Robust and Adaptive Multi-stage Process

(2015) Cheng Lv et al.   PLoS Computational Biology

Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration

(2015) David P. A. Cohen et al.   PLoS Computational Biology

An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States

(2015) Tian Hong et al.   PLoS Computational Biology

Implications of the Hybrid Epithelial/Mesenchymal Phenotype in Metastasis

(2015) Mohit Kumar Jolly   Frontiers in Oncology

TGF-β stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level

(2014) Khalid Abnaof et al.   BMC Systems Biology

Network Modeling of TGF  Signaling in Hepatocellular Carcinoma Epithelial-to-Mesenchymal Transition Reveals Joint Sonic Hedgehog and Wnt Pathway Activation

(2014) S. N. Steinway et al.   CANCER RESEARCH

Interaction network based early-warning indicators of vegetation transitions

(2014) G. Tirabassi et al.   Ecological Complexity

miR-141 regulates TGF-β1-induced epithelial-mesenchymal transition through repression of HIPK2 expression in renal tubular epithelial cells

(2014) YUANHANG HUANG et al.   INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE

Construction of an Effective Landscape for Multistate Genetic Switches

(2014) Mingyang Lu et al.   PHYSICAL REVIEW LETTERS

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

Landscape and flux reveal a new global view and physical quantification of mammalian cell cycle

(2014) Chunhe Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TGF- -induced epithelial-to-mesenchymal transition proceeds through stepwise activation of multiple feedback loops

(2014) J. Zhang et al.   Science Signaling

Coupled Reversible and Irreversible Bistable Switches Underlying TGFβ-induced Epithelial to Mesenchymal Transition

(2013) Xiao-Jun Tian et al.   BIOPHYSICAL JOURNAL

MicroRNA-based regulation of epithelial-hybrid-mesenchymal fate determination

(2013) M. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Landscapes of non-gradient dynamics without detailed balance: Stable limit cycles and multiple attractors

(2012) Hao Ge et al.   CHAOS

Quantifying limits to detection of early warning for critical transitions

(2012) C. Boettiger et al.   Journal of the Royal Society Interface

Methods for Detecting Early Warnings of Critical Transitions in Time Series Illustrated Using Simulated Ecological Data

(2012) Vasilis Dakos et al.   PLoS One

Generic Indicators for Loss of Resilience Before a Tipping Point Leading to Population Collapse

(2012) L. Dai et al.   SCIENCE

Anticipating Critical Transitions

(2012) M. Scheffer et al.   SCIENCE

Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers

(2012) Luonan Chen et al.   Scientific Reports

Conditional Heteroscedasticity as a Leading Indicator of Ecological Regime Shifts

(2011) David A. Seekell et al.   AMERICAN NATURALIST

Recovery rates reflect distance to a tipping point in a living system

(2011) Annelies J. Veraart et al.   NATURE

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

Early Warnings of Regime Shifts: A Whole-Ecosystem Experiment

(2011) S. R. Carpenter et al.   SCIENCE

Early warning of climate tipping points

(2011) Timothy M. Lenton   Nature Climate Change

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

The basics of epithelial-mesenchymal transition

(2009) Raghu Kalluri et al.   JOURNAL OF CLINICAL INVESTIGATION

Changing skewness: an early warning signal of regime shifts in ecosystems

(2008) Vishwesha Guttal et al.   ECOLOGY LETTERS

Adaptive minimum action method for the study of rare events

(2008) Xiang Zhou et al.   JOURNAL OF CHEMICAL PHYSICS

Ecology for bankers

(2008) Robert M. May et al.   NATURE

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