An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

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

(2020) Sydney M. Shaffer et al.   CELL

Why geneticists stole cancer research even though cancer is primarily a signaling disease

(2019) Michael B. Yaffe   Science Signaling

Quantifying Drug Combination Synergy along Potency and Efficacy Axes

(2019) Christian T. Meyer et al.   Cell Systems

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Functional interpretation of single cell similarity maps

(2019) David DeTomaso et al.   Nature Communications

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

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

Drug-Driven Phenotypic Convergence Supports Rational Treatment Strategies of Chronic Infections

(2018) Lejla Imamovic et al.   CELL

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Targeting cancer stem cells in the clinic: Current status and perspectives

(2018) Stephanie Annett et al.   PHARMACOLOGY & THERAPEUTICS

Landscaping the epigenetic landscape of cancer

(2018) Armando Aranda-Anzaldo et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Genetic and transcriptional evolution alters cancer cell line drug response

(2018) Uri Ben-David et al.   NATURE

Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer

(2018) Tyler Risom et al.   Nature Communications

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Sources, propagation and consequences of stochasticity in cellular growth

(2018) Philipp Thomas et al.   Nature Communications

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

(2017) Sydney M. Shaffer et al.   NATURE

Drug-tolerant persister cancer cells are vulnerable to GPX4 inhibition

(2017) Matthew J. Hangauer et al.   NATURE

Functional precision cancer medicine—moving beyond pure genomics

(2017) Anthony Letai   NATURE MEDICINE

Tumour heterogeneity and resistance to cancer therapies

(2017) Ibiayi Dagogo-Jack et al.   Nature Reviews Clinical Oncology

Recurrent Tumor Cell–Intrinsic and –Extrinsic Alterations during MAPKi-Induced Melanoma Regression and Early Adaptation

(2017) Chunying Song et al.   Cancer Discovery

Mechanisms of resistance to irreversible epidermal growth factor receptor tyrosine kinase inhibitors and therapeutic strategies in non-small cell lung cancer

(2017) Jing Xu et al.   Oncotarget

Engineering of a synthetic quadrastable gene network to approach Waddington landscape and cell fate determination

(2017) Fuqing Wu et al.   eLife

Dependence On Glycolysis Sensitizes BRAF-mutated Melanomas For Increased Response To Targeted BRAF Inhibition

(2017) Keisha N. Hardeman et al.   Scientific Reports

BioNetGen 2.2: advances in rule-based modeling

(2016) Leonard A. Harris et al.   BIOINFORMATICS

Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution

(2016) Boyang Zhao et al.   CELL

vcfr: a package to manipulate and visualize variant call format data in R

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition

(2016) Aaron N Hata et al.   NATURE MEDICINE

An unbiased metric of antiproliferative drug effect in vitro

(2016) Leonard A Harris et al.   NATURE METHODS

Diverse drug-resistance mechanisms can emerge from drug-tolerant cancer persister cells

(2016) Michael Ramirez et al.   Nature Communications

DNA-Binding Kinetics Determines the Mechanism of Noise-Induced Switching in Gene Networks

(2015) Margaret J. Tse et al.   BIOPHYSICAL JOURNAL

Non-genetic cancer cell plasticity and therapy-induced stemness in tumour relapse: ‘What does not kill me strengthens me’

(2015) A O Pisco et al.   BRITISH JOURNAL OF CANCER

Non-genomic and Immune Evolution of Melanoma Acquiring MAPKi Resistance

(2015) Willy Hugo et al.   CELL

Quantifying heterogeneity and dynamics of clonal fitness in response to perturbation

(2015) Peter L. Frick et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Comprehensive genomic characterization of head and neck squamous cell carcinomas

(2015)   NATURE

Pan-cancer analysis of the extent and consequences of intratumor heterogeneity

(2015) Noemi Andor et al.   NATURE MEDICINE

The cancer stem cell gamble

(2015) J. Kaiser   SCIENCE

A decade of EGFR inhibition in EGFR-mutated non small cell lung cancer (NSCLC): Old successes and future perspectives

(2015) Alessandro Russo et al.   Oncotarget

Quantifying Intrinsic and Extrinsic Variability in Stochastic Gene Expression Models

(2014) Abhyudai Singh et al.   PLoS One

Intratumor heterogeneity alters most effective drugs in designed combinations

(2014) B. Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial and temporal diversity in genomic instability processes defines lung cancer evolution

(2014) E. C. de Bruin et al.   SCIENCE

Regulation of Noise in Gene Expression

(2013) Alvaro Sanchez et al.   Annual Review of Biophysics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Genetic and non-genetic instability in tumor progression: link between the fitness landscape and the epigenetic landscape of cancer cells

(2013) Sui Huang   CANCER AND METASTASIS REVIEWS

Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance

(2013) P. Jia et al.   GENOME RESEARCH

Perspective: Stochastic algorithms for chemical kinetics

(2013) Daniel T. Gillespie et al.   JOURNAL OF CHEMICAL PHYSICS

Programming biological models in Python using PySB

(2013) C. F. Lopez et al.   Molecular Systems Biology

The causes and consequences of genetic heterogeneity in cancer evolution

(2013) Rebecca A. Burrell et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Modelling vemurafenib resistance in melanoma reveals a strategy to forestall drug resistance

(2013) Meghna Das Thakur et al.   NATURE

Use of Collateral Sensitivity Networks to Design Drug Cycling Protocols That Avoid Resistance Development

(2013) L. Imamovic et al.   Science Translational Medicine

How to escape the cancer attractor: Rationale and limitations of multi-target drugs

(2013) Sui Huang et al.   SEMINARS IN CANCER BIOLOGY

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems

(2013) Lily A. Chylek et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers

(2012) Ramaswamy Govindan et al.   CELL

Sequential Application of Anticancer Drugs Enhances Cell Death by Rewiring Apoptotic Signaling Networks

(2012) Michael J. Lee et al.   CELL

Quasi-potential landscape in complex multi-stable systems

(2012) J. X. Zhou et al.   Journal of the Royal Society Interface

Exploiting Evolution To Treat Drug Resistance: Combination Therapy and the Double Bind

(2012) David Basanta et al.   MOLECULAR PHARMACEUTICS

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

Fractional proliferation: a method to deconvolve cell population dynamics from single-cell data

(2012) Darren R Tyson et al.   NATURE METHODS

The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post-Darwinian biology?

(2011) Sui Huang   BIOESSAYS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) Piyush B. Gupta et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Separating intrinsic from extrinsic fluctuations in dynamic biological systems

(2011) A. Hilfinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

(2010) G. Yu et al.   BIOINFORMATICS

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

(2010) Sreenath V. Sharma et al.   CELL

The patterns and dynamics of genomic instability in metastatic pancreatic cancer

(2010) Peter J. Campbell et al.   NATURE

Non-genetic heterogeneity from stochastic partitioning at cell division

(2010) Dann Huh et al.   NATURE GENETICS

Tumor heterogeneity: Causes and consequences

(2009) Andriy Marusyk et al.   BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER

Non-genetic cell-to-cell variability and the consequences for pharmacology

(2009) Mario Niepel et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Non-genetic heterogeneity of cells in development: more than just noise

(2009) S. Huang   DEVELOPMENT

Non-genetic heterogeneity — a mutation-independent driving force for the somatic evolution of tumours

(2009) Amy Brock et al.   NATURE REVIEWS GENETICS

Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective

(2009) Sui Huang et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Reduced Erlotinib Sensitivity of Epidermal Growth Factor Receptor-Mutant Non-Small Cell Lung Cancer following Cisplatin Exposure: A Cell Culture Model of Second-line Erlotinib Treatment

(2008) T. M. Chin et al.   CLINICAL CANCER RESEARCH