Macrophage phenotype transitions in a stochastic gene-regulatory network model

Landscape and flux quantify the stochastic transition dynamics for p53 cell fate decision

(2021) Leijun Ye et al.   JOURNAL OF CHEMICAL PHYSICS

Transcriptional circuitry atlas of genetic diverse unstimulated murine and human macrophages define disparity in population-wide innate immunity

(2021) Bharat Mishra et al.   Scientific Reports

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

(2021) Jintong Lang et al.   BIOPHYSICAL JOURNAL

Uncovering the cell fate decision in lysis–lysogeny transition and stem cell development via Markov state modeling

(2021) Xiaoguang Li et al.   JOURNAL OF CHEMICAL PHYSICS

Cancer cell heterogeneity and plasticity: A paradigm shift in glioblastoma

(2021) Yahaya A Yabo et al.   NEURO-ONCOLOGY

Noise distorts the epigenetic landscape and shapes cell-fate decisions

(2021) Megan A. Coomer et al.   Cell Systems

Reprogramming of macrophages employing gene regulatory and metabolic network models

(2020) Franziska Hörhold et al.   PLoS Computational Biology

Matrix-Targeting Immunotherapy Controls Tumor Growth and Spread by Switching Macrophage Phenotype

(2020) Claire Deligne et al.   Cancer Immunology Research

A plausible accelerating function of intermediate states in cancer metastasis

(2020) Hanah Goetz et al.   PLoS Computational Biology

The role of tumor-associated macrophages (TAMs) in tumor progression and relevant advance in targeted therapy

(2020) Qiyao Yang et al.   Acta Pharmaceutica Sinica B

Extending Transition Path Theory: Periodically Driven and Finite-Time Dynamics

(2020) Luzie Helfmann et al.   JOURNAL OF NONLINEAR SCIENCE

Bifurcation and sensitivity analysis reveal key drivers of multistability in a model of macrophage polarization

(2020) Anna S Frank et al.   JOURNAL OF THEORETICAL BIOLOGY

Human tumor-associated monocytes/macrophages and their regulation of T cell responses in early-stage lung cancer

(2019) Sunil Singhal et al.   Science Translational Medicine

NF-κB Signaling in Macrophages: Dynamics, Crosstalk, and Signal Integration

(2019) Michael G. Dorrington et al.   Frontiers in Immunology

Agent-based modeling and bifurcation analysis reveal mechanisms of macrophage polarization and phenotype pattern distribution

(2019) Niloofar Nickaeen et al.   Scientific Reports

A mechanistic integrative computational model of macrophage polarization: Implications in human pathophysiology

(2019) Chen Zhao et al.   PLoS Computational Biology

Melanoma exosomes promote mixed M1 and M2 macrophage polarization

(2018) Gina T. Bardi et al.   CYTOKINE

The Transcription Factor STAT6 Mediates Direct Repression of Inflammatory Enhancers and Limits Activation of Alternatively Polarized Macrophages

(2018) Zsolt Czimmerer et al.   IMMUNITY

Macrophage plasticity, polarization, and function in health and disease

(2018) Abbas Shapouri-Moghaddam et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Rare-event sampling of epigenetic landscapes and phenotype transitions

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

Self-renewing resident cardiac macrophages limit adverse remodeling following myocardial infarction

(2018) Sarah A. Dick et al.   NATURE IMMUNOLOGY

Gene Regulatory Network Modeling of Macrophage Differentiation Corroborates the Continuum Hypothesis of Polarization States

(2018) Alessandro Palma et al.   Frontiers in Physiology

Tissue-resident versus monocyte-derived macrophages in the tumor microenvironment

(2016) Qods Lahmar et al.   BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER

Statistical ensemble of gene regulatory networks of macrophage differentiation

(2016) Filippo Castiglione et al.   BMC BIOINFORMATICS

Regulation of macrophage polarization and plasticity by complex activation signals

(2016) Tim D. Smith et al.   Integrative Biology

Plasticity of Macrophage Function during Tumor Progression: Regulation by Distinct Molecular Mechanisms

(2014) S. K. Biswas et al.   JOURNAL OF IMMUNOLOGY

Molecular Mechanisms That Influence the Macrophage M1–M2 Polarization Balance

(2014) Nan Wang et al.   Frontiers in Immunology

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

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

JAK and STAT Signaling Molecules in Immunoregulation and Immune-Mediated Disease

(2012) John J. O'Shea et al.   IMMUNITY

Macrophage plasticity and polarization: in vivo veritas

(2012) Antonio Sica et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2011) Piyush B. Gupta et al.   CELL

Nkx6 Transcription Factors and Ptf1a Function as Antagonistic Lineage Determinants in Multipotent Pancreatic Progenitors

(2010) Ashleigh E. Schaffer et al.   DEVELOPMENTAL CELL

Macrophage plasticity and interaction with lymphocyte subsets: cancer as a paradigm

(2010) Subhra K Biswas et al.   NATURE IMMUNOLOGY

Understanding gene circuits at cell-fate branch points for rational cell reprogramming

(2010) Joseph X. Zhou et al.   TRENDS IN GENETICS

Transition Path Theory for Markov Jump Processes

(2009) Philipp Metzner et al.   MULTISCALE MODELING & SIMULATION

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

Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events

(2008) Weinan E et al.   Annual Review of Physical Chemistry

Stochastic dynamics and non-equilibrium thermodynamics of a bistable chemical system: the Schlogl model revisited

(2008) M. Vellela et al.   Journal of the Royal Society Interface

Tyrosine phosphorylation regulates the partitioning of STAT1 between different dimer conformations

(2008) N. Wenta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA