An enriched network motif family regulates multistep cell fate transitions with restricted reversibility

Nanog induced intermediate state in regulating stem cell differentiation and reprogramming

(2018) Peijia Yu et al.   BMC Systems Biology

Multiscale modeling of layer formation in epidermis

(2018) Huijing Du et al.   PLoS Computational Biology

Rare-event sampling of epigenetic landscapes and phenotype transitions

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

An intermediate cell state allows rerouting of cell fate

(2017) Xiukun Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

IL-4–Induced Gene 1: A Negative Immune Checkpoint Controlling B Cell Differentiation and Activation

(2017) Lloyd Bod et al.   JOURNAL OF IMMUNOLOGY

The T-ALL related gene BCL11B regulates the initial stages of human T-cell differentiation

(2017) V L Ha et al.   LEUKEMIA

A spectrum of modularity in multi‐functional gene circuits

(2017) Alba Jiménez et al.   Molecular Systems Biology

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

(2017) Chunhe Li   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network

(2017) William J. R. Longabaugh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst

(2017) William R. Holmes et al.   PLoS Computational Biology

Interrogating the topological robustness of gene regulatory circuits by randomization

(2017) Bin Huang et al.   PLoS Computational Biology

Modeling continuum of epithelial mesenchymal transition plasticity

(2016) Mousumi Mandal et al.   Integrative Biology

Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment

(2016) Hao Yuan Kueh et al.   NATURE IMMUNOLOGY

Irreversibility of T-Cell Specification: Insights from Computational Modelling of a Minimal Network Architecture

(2016) Erica Manesso et al.   PLoS One

Stability of the hybrid epithelial/mesenchymal phenotype

(2016) Mohit Kumar Jolly et al.   Oncotarget

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process

(2016) Angélique Richard et al.   PLOS BIOLOGY

Cell Fate Decision as High-Dimensional Critical State Transition

(2016) Mitra Mojtahedi et al.   PLOS BIOLOGY

Realization of tristability in a multiplicatively coupled dual-loop genetic network

(2016) Bo Huang et al.   Scientific Reports

A Mathematical Framework for Understanding Four-Dimensional Heterogeneous Differentiation of $$\hbox {CD4}^{+}$$ CD4 + T Cells

(2015) Tian Hong et al.   BULLETIN OF MATHEMATICAL BIOLOGY

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

(2015) C. Li et al.   CANCER RESEARCH

Stemness of the hybrid Epithelial/Mesenchymal State in Breast Cancer and Its Association with Poor Survival

(2015) Anne Grosse-Wilde et al.   PLoS One

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

Reciprocal Encoding of Signal Intensity and Duration in a Glucose-Sensing Circuit

(2014) Yan Fu et al.   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

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

Controlling low rates of cell differentiation through noise and ultrahigh feedback

(2014) R. Ahrends et al.   SCIENCE

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

(2014) J. Zhang et al.   Science Signaling

Non-equilibrium transition state rate theory

(2014) Haidong Feng et al.   Chemical Science

Epigenetic state network approach for describing cell phenotypic transitions

(2014) P. Wang et al.   Interface Focus

GATA-3 promotes T-cell specification by repressing B-cell potential in pro-T cells in mice

(2013) M. E. Garcia-Ojeda et al.   BLOOD

In Vivo Mapping of Notch Pathway Activity in Normal and Stress Hematopoiesis

(2013) Philmo Oh et al.   Cell Stem Cell

Msn2 Coordinates a Stoichiometric Gene Expression Program

(2013) Jacob Stewart-Ornstein et al.   CURRENT BIOLOGY

Architecture of a lymphomyeloid developmental switch controlled by PU.1, Notch and Gata3

(2013) M. M. Del Real et al.   DEVELOPMENT

Tristability in Cancer-Associated MicroRNA-TF Chimera Toggle Switch

(2013) Mingyang Lu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Minimal Transcriptional Controlling Network of Regulatory T Cell Development

(2013) Chen Liao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

The Utility of Paradoxical Components in Biological Circuits

(2013) Yuval Hart et al.   MOLECULAR CELL

The transcriptional landscape of αβ T cell differentiation

(2013) Michael Mingueneau et al.   NATURE IMMUNOLOGY

The Duration of T Cell Stimulation Is a Critical Determinant of Cell Fate and Plasticity

(2013) N. Miskov-Zivanov et al.   Science Signaling

An EMT spectrum defines an anoikis-resistant and spheroidogenic intermediate mesenchymal state that is sensitive to e-cadherin restoration by a src-kinase inhibitor, saracatinib (AZD0530)

(2013) R Y-J Huang et al.   Cell Death & Disease

Hybrid T-Helper Cells: Stabilizing the Moderate Center in a Polarized System

(2013) Sui Huang   PLOS 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

Checkpoints of B cell differentiation: visualizing Ig-centric processes

(2012) Magdalena A. Berkowska et al.   Annals of the New York Academy of Sciences

A Differentiation Checkpoint Limits Hematopoietic Stem Cell Self-Renewal in Response to DNA Damage

(2012) Jianwei Wang et al.   CELL

Gene Regulatory Logic for Reading the Sonic Hedgehog Signaling Gradient in the Vertebrate Neural Tube

(2012) Nikolaos Balaskas et al.   CELL

Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity

(2012) Jingli A. Zhang et al.   CELL

Duration of Shh signaling contributes to mDA neuron diversity

(2012) Lindsay Hayes et al.   DEVELOPMENTAL BIOLOGY

Computational modelling of T-cell formation kinetics: output regulated by initial proliferation-linked deferral of developmental competence

(2012) E. Manesso et al.   Journal of the Royal Society Interface

The earliest thymic T cell progenitors sustain B cell and myeloid lineage potential

(2012) Sidinh Luc et al.   NATURE IMMUNOLOGY

Ikaros represses and activates PU.1 cell-type-specifically through the multifunctional Sfpi1 URE and a myeloid specific enhancer

(2012) M A Zarnegar et al.   ONCOGENE

Network Topologies and Dynamics Leading to Endotoxin Tolerance and Priming in Innate Immune Cells

(2012) Yan Fu et al.   PLoS Computational Biology

Morphogen Gradients: From Generation to Interpretation

(2011) Katherine W. Rogers et al.   Annual Review of Cell and Developmental Biology

Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells

(2011) M. Leddin et al.   BLOOD

Functional and Epigenetic Studies Reveal Multistep Differentiation and Plasticity of In Vitro-Generated and In Vivo-Derived Follicular T Helper Cells

(2011) Kristina T. Lu et al.   IMMUNITY

T Cell Lineage Commitment: Identity and Renunciation

(2011) E. V. Rothenberg   JOURNAL OF IMMUNOLOGY

A critical role for TCF-1 in T-lineage specification and differentiation

(2011) Brittany Nicole Weber et al.   NATURE

T-cell factor 1 is a gatekeeper for T-cell specification in response to Notch signaling

(2011) K. Germar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Fine-Scale Staging of T Cell Lineage Commitment in Adult Mouse Thymus

(2010) M. A. Yui et al.   JOURNAL OF IMMUNOLOGY

Noncooperative Interactions between Transcription Factors and Clustered DNA Binding Sites Enable Graded Transcriptional Responses to Environmental Inputs

(2010) Luca Giorgetti et al.   MOLECULAR CELL

Reprogramming of T Cells to Natural Killer-Like Cells upon Bcl11b Deletion

(2010) P. Li et al.   SCIENCE

An Early T Cell Lineage Commitment Checkpoint Dependent on the Transcription Factor Bcl11b

(2010) L. Li et al.   SCIENCE

An Essential Developmental Checkpoint for Production of the T Cell Lineage

(2010) T. Ikawa et al.   SCIENCE

Defining Network Topologies that Can Achieve Biochemical Adaptation

(2009) Wenzhe Ma et al.   CELL

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis

(2009) Sabrina L. Spencer et al.   NATURE

Forcing cells to change lineages

(2009) Thomas Graf et al.   NATURE

Epidermal homeostasis: a balancing act of stem cells in the skin

(2009) Cédric Blanpain et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cell fate decision mediated by p53 pulses

(2009) X.-P. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An early decrease in Notch activation is required for human TCR-   lineage differentiation at the expense of TCR-   T cells

(2008) I. Van de Walle et al.   BLOOD

Adaptive minimum action method for the study of rare events

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

A bistable Rb–E2F switch underlies the restriction point

(2008) Guang Yao et al.   NATURE CELL BIOLOGY

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

Modeling a Snap-Action, Variable-Delay Switch Controlling Extrinsic Cell Death

(2008) John G Albeck et al.   PLOS BIOLOGY

Multistable Decision Switches for Flexible Control of Epigenetic Differentiation

(2008) Raúl Guantes et al.   PLoS Computational Biology