Quantitative landscapes reveal trajectories of cell-state transitions associated with drug resistance in melanoma

Computational Model of Heterogeneity in Melanoma: Designing Therapies and Predicting Outcomes

(2022) Arran Hodgkinson et al.   Frontiers in Oncology

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 Dimension Reduction Approach for Energy Landscape: Identifying Intermediate States in Metabolism‐EMT Network

(2021) Xin Kang et al.   Advanced Science

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

(2021) Jintong Lang et al.   BIOPHYSICAL JOURNAL

CDK7 and MITF repress a transcription program involved in survival and drug tolerance in melanoma

(2021) Pietro Berico et al.   EMBO REPORTS

Statistically derived geometrical landscapes capture principles of decision-making dynamics during cell fate transitions

(2021) Meritxell Sáez et al.   Cell Systems

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

(2021) Maalavika Pillai et al.   iScience

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

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

(2020) Jasper Wouters et al.   NATURE CELL BIOLOGY

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

(2019) Yapeng Su et al.   PLoS Computational Biology

MEK inhibition remodels the active chromatin landscape and induces SOX10 genomic recruitment in BRAF(V600E) mutant melanoma cells

(2019) Temesgen D. Fufa et al.   Epigenetics & Chromatin

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

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

RACIPE: a computational tool for modeling gene regulatory circuits using randomization

(2018) Bin Huang et al.   BMC Systems Biology

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

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

(2018) Livnat Jerby-Arnon et al.   CELL

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

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

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

MAPK Pathway Inhibitors Sensitize BRAF-Mutant Melanoma to an Antibody-Drug Conjugate Targeting GPNMB

(2016) A. A. N. Rose et al.   CLINICAL CANCER RESEARCH

Construction of the landscape for multi-stable systems: Potential landscape, quasi-potential, A-type integral and beyond

(2016) Peijie Zhou et al.   JOURNAL OF CHEMICAL PHYSICS

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

(2015) C. Li et al.   CANCER RESEARCH

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

(2015) Annelien Verfaillie et al.   Nature Communications

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

(2014) Chong Sun et al.   NATURE

Single-cell gene expression signatures reveal melanoma cell heterogeneity

(2014) M Ennen et al.   ONCOGENE

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

A Melanoma Cell State Distinction Influences Sensitivity to MAPK Pathway Inhibitors

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

Cellular network entropy as the energy potential in Waddington's differentiation landscape

(2013) Christopher R. S. Banerji et al.   Scientific Reports

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

Attractor Landscape Analysis Reveals Feedback Loops in the p53 Network That Control the Cellular Response to DNA Damage

(2012) M. Choi et al.   Science Signaling

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

Cancer stem cells versus phenotype-switching in melanoma

(2010) Keith S. Hoek et al.   Pigment Cell & Melanoma Research

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

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

Adaptive minimum action method for the study of rare events

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

Oncogenic BRAF Regulates Melanoma Proliferation through the Lineage Specific Factor MITF

(2008) Claudia Wellbrock et al.   PLoS One