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

Phenotype-based probabilistic analysis of heterogeneous responses to cancer drugs and their combination efficacy

(2020) Natacha Comandante-Lou et al.   PLoS Computational Biology

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

(2019) Geoffrey Schiebinger et al.   CELL

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

(2019) Yapeng Su et al.   PLoS Computational Biology

Visualizing structure and transitions in high-dimensional biological data

(2019) Kevin R. Moon et al.   NATURE BIOTECHNOLOGY

Surface Immobilization of Redox-Labile Fluorescent Probes Enables Single-Cell Co-Profiling of Aerobic Glycolysis and Oncogenic Protein Signaling Activities

(2018) Zhonghan Li et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

(2018) Jennifer Tsoi et al.   CANCER CELL

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Toward Minimal Residual Disease-Directed Therapy in Melanoma

(2018) Florian Rambow et al.   CELL

Integrated measurement of intracellular proteins and transcripts in single cells

(2018) Alexander M. Xu et al.   LAB ON A CHIP

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

Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells

(2017) Rhishikesh Bargaje et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Inhibiting Drivers of Non-mutational Drug Tolerance Is a Salvage Strategy for Targeted Melanoma Therapy

(2016) Michael P. Smith et al.   CANCER CELL

Single-Cell Phosphoproteomics Resolves Adaptive Signaling Dynamics and Informs Targeted Combination Therapy in Glioblastoma

(2016) Wei Wei et al.   CANCER CELL

Supramolecular Probes for Assessing Glutamine Uptake Enable Semi-Quantitative Metabolic Models in Single Cells

(2016) Min Xue et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A PGC1α-mediated transcriptional axis suppresses melanoma metastasis

(2016) Chi Luo et al.   NATURE

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Regional glutamine deficiency in tumours promotes dedifferentiation through inhibition of histone demethylation

(2016) Min Pan et al.   NATURE CELL BIOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Metabolic rewiring in melanoma

(2016) B I Ratnikov et al.   ONCOGENE

Intercellular signaling through secreted proteins induces free-energy gradient-directed cell movement

(2016) Nataly Kravchenko-Balasha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2016) Suresh Kumar Poovathingal et al.   Small

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

Non-genomic and Immune Evolution of Melanoma Acquiring MAPKi Resistance

(2015) Willy Hugo et al.   CELL

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

A Continuous Molecular Roadmap to iPSC Reprogramming through Progression Analysis of Single-Cell Mass Cytometry

(2015) Eli R. Zunder et al.   Cell Stem Cell

Sprouty2 Drives Drug Resistance and Proliferation in Glioblastoma

(2015) A. M. Walsh et al.   MOLECULAR CANCER RESEARCH

Systematic analysis of BRAFV600E melanomas reveals a role for JNK/c-Jun pathway in adaptive resistance to drug-induced apoptosis

(2015) M. Fallahi-Sichani et al.   Molecular Systems Biology

Combinatorial gene regulation by modulation of relative pulse timing

(2015) Yihan Lin et al.   NATURE

Single-cell analysis tools for drug discovery and development

(2015) James R. Heath et al.   NATURE REVIEWS DRUG DISCOVERY

Highly multiplexed profiling of single-cell effector functions reveals deep functional heterogeneity in response to pathogenic ligands

(2015) Yao Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Rachel Ramsdale et al.   Science Signaling

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

(2015) Rachel Ramsdale et al.   Science Signaling

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

Effects of AKT inhibitor therapy in response and resistance to BRAF inhibition in melanoma

(2014) Amanda Lassen et al.   Molecular Cancer

Glioblastoma cellular architectures are predicted through the characterization of two-cell interactions

(2014) N. Kravchenko-Balasha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Response of BRAF-Mutant Melanoma to BRAF Inhibition Is Mediated by a Network of Transcriptional Regulators of Glycolysis

(2014) T. J. Parmenter et al.   Cancer Discovery

A Melanoma Cell State Distinction Influences Sensitivity to MAPK Pathway Inhibitors

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

ERK1/2 Blockade Prevents Epithelial-Mesenchymal Transition in Lung Cancer Cells and Promotes Their Sensitivity to EGFR Inhibition

(2013) J. M. Buonato et al.   CANCER RESEARCH

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

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

Hypoxia Induces Phenotypic Plasticity and Therapy Resistance in Melanoma via the Tyrosine Kinase Receptors ROR1 and ROR2

(2013) M. P. O'Connell et al.   Cancer Discovery

A clinical microchip for evaluation of single immune cells reveals high functional heterogeneity in phenotypically similar T cells

(2011) Chao Ma et al.   NATURE MEDICINE

Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy

(2011) Jonathan W Young et al.   Nature Protocols

Improved Survival with Vemurafenib in Melanoma with BRAF V600E Mutation

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

Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells

(2011) Q. Shi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Impaired SHP2-Mediated Extracellular Signal-Regulated Kinase Activation Contributes to Gefitinib Sensitivity of Lung Cancer Cells with Epidermal Growth Factor Receptor–Activating Mutations

(2010) Matthew J. Lazzara et al.   CANCER RESEARCH

Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation

(2010) Ramin Nazarian et al.   NATURE

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

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

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