Systems-level network modeling deciphers the master regulators of phenotypic plasticity and heterogeneity in melanoma

MITF reprograms the extracellular matrix and focal adhesion in melanoma

(2021) Ramile Dilshat et al.   eLife

CRISPR screens identify tumor‐promoting genes conferring melanoma cell plasticity and resistance

(2021) Arthur Gautron et al.   EMBO Molecular Medicine

Topological signatures in regulatory network enable phenotypic heterogeneity in small cell lung cancer

(2021) Lakshya Chauhan et al.   eLife

A Theoretical Approach to Coupling the Epithelial-Mesenchymal Transition (EMT) to Extracellular Matrix (ECM) Stiffness via LOXL2

(2021) Youyuan Deng et al.   Cancers

Detection and prognostic role of heterogeneous populations of melanoma circulating tumour cells

(2020) Carlos Alberto Aya-Bonilla et al.   BRITISH JOURNAL OF CANCER

Cooperative behaviour and phenotype plasticity evolve during melanoma progression

(2020) Emily J Rowling et al.   Pigment Cell & Melanoma Research

A mechanism for epithelial-mesenchymal heterogeneity in a population of cancer cells

(2020) Shubham Tripathi et al.   PLoS Computational Biology

Dissecting Mechanisms of Melanoma Resistance to BRAF and MEK Inhibitors Revealed Genetic and Non-Genetic Patient- and Drug-Specific Alterations and Remarkable Phenotypic Plasticity

(2020) Mariusz L. Hartman et al.   Cells

Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line

(2020) Yapeng Su et al.   Nature Communications

A plausible accelerating function of intermediate states in cancer metastasis

(2020) Hanah Goetz et al.   PLoS Computational Biology

The EMT Transcription Factor ZEB2 Promotes Proliferation of Primary and Metastatic Melanoma While Suppressing an Invasive, Mesenchymal-Like Phenotype

(2020) Niels Vandamme et al.   CANCER RESEARCH

Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors

(2020) Sydney M. Shaffer et al.   CELL

Genome‐wide cooperation of EMT transcription factor ZEB 1 with YAP and AP ‐1 in breast cancer

(2020) Nora Feldker et al.   EMBO JOURNAL

Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma

(2020) Jasper Wouters et al.   NATURE CELL BIOLOGY

How Do Cells Adapt? Stories Told in Landscapes

(2020) Luca Agozzino et al.   Annual Review of Chemical and Biomolecular Engineering

Epigenetic feedback and stochastic partitioning during cell division can drive resistance to EMT

(2020) Wen Jia et al.   Oncotarget

MicroRNA-222 Regulates Melanoma Plasticity

(2020) Maria Chiara Lionetti et al.   Journal of Clinical Medicine

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

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

Drug-Tolerant Idling Melanoma Cells Exhibit Theory-Predicted Metabolic Low-Low Phenotype

(2020) Dongya Jia et al.   Frontiers in Oncology

Drug tolerance to target therapy in melanoma revealed at single cell level: What next?

(2020) Domenico Liguoro et al.   BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER

Clinical Implications of Acquired BRAF Inhibitors Resistance in Melanoma

(2020) Paola Savoia et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Weighted gene co-expression network analysis to explain the relationship between plasma total carotenoids and lipid profile

(2019) Bénédicte L. Tremblay et al.   Genes and Nutrition

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

(2019) Yapeng Su et al.   PLoS Computational Biology

Melanoma plasticity and phenotypic diversity: therapeutic barriers and opportunities

(2019) Florian Rambow et al.   GENES & DEVELOPMENT

Dynamics of Phenotypic Heterogeneity during EMT and Stemness in Cancer Progression

(2019) Jolly et al.   Journal of Clinical Medicine

Lineage-Restricted Regulation of SCD and Fatty Acid Saturation by MITF Controls Melanoma Phenotypic Plasticity

(2019) Yurena Vivas-García et al.   MOLECULAR CELL

Systems-level network modeling of Small Cell Lung Cancer subtypes identifies master regulators and destabilizers

(2019) David J. Wooten et al.   PLoS Computational Biology

Mapping lung cancer epithelial-mesenchymal transition states and trajectories with single-cell resolution

(2019) Loukia G. Karacosta et al.   Nature Communications

A Nonquiescent “Idling” Population State in Drug-Treated, BRAF -Mutated Melanoma

(2018) B. Bishal Paudel et al.   BIOPHYSICAL JOURNAL

Multi-stage Differentiation Defines Melanoma Subtypes with Differential Vulnerability to Drug-Induced Iron-Dependent Oxidative Stress

(2018) Jennifer Tsoi et al.   CANCER CELL

Toward Minimal Residual Disease-Directed Therapy in Melanoma

(2018) Florian Rambow et al.   CELL

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Targeting Breast Cancer Stem Cell State Equilibrium through Modulation of Redox Signaling

(2018) Ming Luo et al.   Cell Metabolism

Cooperative targeting of melanoma heterogeneity with an AXL antibody-drug conjugate and BRAF/MEK inhibitors

(2018) Julia Boshuizen et al.   NATURE MEDICINE

RNA-seq analysis identifies different transcriptomic types and developmental trajectories of primary melanomas

(2018) Manfred Kunz et al.   ONCOGENE

BRN2, a POUerful driver of melanoma phenotype switching and metastasis

(2018) Mitchell E. Fane et al.   Pigment Cell & Melanoma Research

Massive mining of publicly available RNA-seq data from human and mouse

(2018) Alexander Lachmann et al.   Nature Communications

Microenvironment-Driven Dynamic Heterogeneity and Phenotypic Plasticity as a Mechanism of Melanoma Therapy Resistance

(2018) Farzana Ahmed et al.   Frontiers in Oncology

Identification of the tumour transition states occurring during EMT

(2018) Ievgenia Pastushenko et al.   NATURE

A PAX3/BRN2 rheostat controls the dynamics of BRAF mediated MITF regulation in MITFhigh /AXLlow melanoma

(2018) Michael P. Smith et al.   Pigment Cell & Melanoma Research

Targeting invasive properties of melanoma cells

(2017) Imanol Arozarena et al.   FEBS Journal

Translation reprogramming is an evolutionarily conserved driver of phenotypic plasticity and therapeutic resistance in melanoma

(2017) Paola Falletta et al.   GENES & DEVELOPMENT

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

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

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

Interrogating the topological robustness of gene regulatory circuits by randomization

(2017) Bin Huang et al.   PLoS Computational Biology

Phenotypic Plasticity and Cell Fate Decisions in Cancer: Insights from Dynamical Systems Theory

(2017) Dongya Jia et al.   Cancers

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

Mapping heterogeneity in patient-derived melanoma cultures by single-cell RNA-seq

(2016) Tobias Gerber et al.   Oncotarget

Metabolic reprogramming supports the invasive phenotype in malignant melanoma

(2015) Ingrid J. Bettum et al.   CANCER LETTERS

Non-genomic and Immune Evolution of Melanoma Acquiring MAPKi Resistance

(2015) Willy Hugo et al.   CELL

Matrix stiffness drives epithelial–mesenchymal transition and tumour metastasis through a TWIST1–G3BP2 mechanotransduction pathway

(2015) Spencer C. Wei et al.   NATURE CELL BIOLOGY

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

(2015) Aaron Goldman et al.   Nature Communications

Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state

(2015) Annelien Verfaillie et al.   Nature Communications

MITF and c-Jun antagonism interconnects melanoma dedifferentiation with pro-inflammatory cytokine responsiveness and myeloid cell recruitment

(2015) Stefanie Riesenberg et al.   Nature Communications

Identification of a ZEB2-MITF-ZEB1 transcriptional network that controls melanogenesis and melanoma progression

(2014) G Denecker et al.   CELL DEATH AND DIFFERENTIATION

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

(2014) Chong Sun et al.   NATURE

Low MITF/AXL ratio predicts early resistance to multiple targeted drugs in melanoma

(2014) Judith Müller et al.   Nature Communications

A Melanoma Cell State Distinction Influences Sensitivity to MAPK Pathway Inhibitors

(2014) D. J. Konieczkowski et al.   Cancer Discovery

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

A Switch in the Expression of Embryonic EMT-Inducers Drives the Development of Malignant Melanoma

(2013) Julie Caramel et al.   CANCER CELL

PGC1α Expression Defines a Subset of Human Melanoma Tumors with Increased Mitochondrial Capacity and Resistance to Oxidative Stress

(2013) Francisca Vazquez et al.   CANCER CELL

Circulating Breast Tumor Cells Exhibit Dynamic Changes in Epithelial and Mesenchymal Composition

(2013) M. Yu et al.   SCIENCE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

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

(2011) Piyush B. Gupta et al.   CELL

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

geWorkbench: an open source platform for integrative genomics

(2010) Aris Floratos et al.   BIOINFORMATICS

A Temporarily Distinct Subpopulation of Slow-Cycling Melanoma Cells Is Required for Continuous Tumor Growth

(2010) Alexander Roesch et al.   CELL

Gene Expression Signatures as a Guide to Treatment Strategies for In-Transit Metastatic Melanoma

(2010) Christina K. Augustine et al.   MOLECULAR CANCER THERAPEUTICS

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

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

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

In vivo Switching of Human Melanoma Cells between Proliferative and Invasive States

(2008) K. S. Hoek et al.   CANCER RESEARCH