Phenotypic heterogeneity and evolution of melanoma cells associated with targeted therapy resistance

Adaptive resistance of melanoma cells to RAF inhibition via reversible induction of a slowly dividing de‐differentiated state

(2017) Mohammad Fallahi‐Sichani et al.   Molecular Systems Biology

Single-cell analysis resolves the cell state transition and signaling dynamics associated with melanoma drug-induced resistance

(2017) Yapeng Su et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic plasticity and the hallmarks of cancer

(2017) William A. Flavahan et al.   SCIENCE

Critical Points in Tumorigenesis: A Carcinogen-Initiated Phase Transition Analyzed via Single-Cell Proteomics

(2016) Suresh Kumar Poovathingal et al.   Small

Stability of the hybrid epithelial/mesenchymal phenotype

(2016) Mohit Kumar Jolly et al.   Oncotarget

Cell Fate Decision as High-Dimensional Critical State Transition

(2016) Mitra Mojtahedi et al.   PLOS BIOLOGY

JUN dependency in distinct early and late BRAF inhibition adaptation states of melanoma

(2016) Bjoern Titz et al.   Cell Discovery

Entropy, Ergodicity, and Stem Cell Multipotency

(2015) Sonya J. Ridden et al.   PHYSICAL REVIEW LETTERS

Cooperative induction of apoptosis in NRAS mutant melanoma by inhibition of MEK and ROCK

(2015) Celia J. Vogel et al.   Pigment Cell & Melanoma Research

The transcription cofactor c-JUN mediates phenotype switching and BRAF inhibitor resistance in melanoma

(2015) Rachel Ramsdale et al.   Science Signaling

Temporally sequenced anticancer drugs overcome adaptive resistance by targeting a vulnerable chemotherapy-induced phenotypic transition

(2015) Aaron Goldman et al.   Nature Communications

The transcription cofactor c-JUN mediates phenotype switching and BRAF inhibitor resistance in melanoma

(2015) Rachel Ramsdale et al.   Science Signaling

Effects of MAPK and PI3K Pathways on PD-L1 Expression in Melanoma

(2014) M. Atefi et al.   CLINICAL CANCER RESEARCH

Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma

(2014) Chong Sun et al.   NATURE

Nonequilibrium Population Dynamics of Phenotype Conversion of Cancer Cells

(2014) Joseph Xu Zhou et al.   PLoS One

Surprisal analysis characterizes the free energy time course of cancer cells undergoing epithelial-to-mesenchymal transition

(2014) S. Zadran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BRAF Inhibition Is Associated with Enhanced Melanoma Antigen Expression and a More Favorable Tumor Microenvironment in Patients with Metastatic Melanoma

(2013) D. T. Frederick et al.   CLINICAL CANCER RESEARCH

Hypoxia induces a phase transition within a kinase signaling network in cancer cells

(2013) W. Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Targeted Therapy Resistance Mediated by Dynamic Regulation of Extrachromosomal Mutant EGFR DNA

(2013) David A. Nathanson et al.   SCIENCE

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Melanomas resist T-cell therapy through inflammation-induced reversible dedifferentiation

(2012) Jennifer Landsberg et al.   NATURE

On a fundamental structure of gene networks in living cells

(2012) N. Kravchenko-Balasha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting rates of cell state change caused by stochastic fluctuations using a data-driven landscape model

(2012) D. R. Sisan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variable Clonal Repopulation Dynamics Influence Chemotherapy Response in Colorectal Cancer

(2012) A. Kreso et al.   SCIENCE

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

(2011) Piyush B. Gupta et al.   CELL

Whose Entropy: A Maximal Entropy Analysis of Phosphorylation Signaling

(2011) F. Remacle et al.   JOURNAL OF STATISTICAL PHYSICS

Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation

(2011) Paul B. Chapman et al.   NEW ENGLAND JOURNAL OF MEDICINE

Selective BRAFV600E Inhibition Enhances T-Cell Recognition of Melanoma without Affecting Lymphocyte Function

(2010) A. Boni et al.   CANCER RESEARCH

A Chromatin-Mediated Reversible Drug-Tolerant State in Cancer Cell Subpopulations

(2010) Sreenath V. Sharma et al.   CELL

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Minimization of a free-energy-like potential for non-equilibrium flow systems at steady state

(2010) R. K. Niven   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Microdynamics and Criticality of Adaptive Regulatory Networks

(2010) Ben D. MacArthur et al.   PHYSICAL REVIEW LETTERS

Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation

(2010) Daniele Merico et al.   PLoS One

Information-theoretic analysis of phenotype changes in early stages of carcinogenesis

(2010) F. Remacle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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