Variability within rare cell states enables multiple paths toward drug resistance

Genetic screening for single-cell variability modulators driving therapy resistance

(2021) Eduardo A. Torre et al.   NATURE GENETICS

Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts

(2021) Jeffrey J. Quinn et al.   SCIENCE

Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors

(2020) Killian Hurley et al.   Cell Stem Cell

Lineage tracing on transcriptional landscapes links state to fate during differentiation

(2020) Caleb Weinreb et al.   SCIENCE

Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer

(2020) Lea Schuh et al.   Cell Systems

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

(2020) Sydney M. Shaffer et al.   CELL

Isolating live cell clones from barcoded populations using CRISPRa-inducible reporters

(2020) Christian Umkehrer et al.   NATURE BIOTECHNOLOGY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Third-generationin situhybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

(2018) Harry M. T. Choi et al.   DEVELOPMENT

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

DEPTOR at the Nexus of Cancer, Metabolism, and Immunity

(2018) Alexandre Caron et al.   PHYSIOLOGICAL REVIEWS

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

Control of Lineage-Specific Gene Expression by Functionalized gRNA Barcodes

(2018) Aziz M. Al’Khafaji et al.   ACS Synthetic Biology

Single-cell mapping of lineage and identity in direct reprogramming

(2018) Brent A. Biddy et al.   NATURE

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

(2017) Sydney M. Shaffer et al.   NATURE

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

What’s Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism

(2016) Orsolya Symmons et al.   MOLECULAR CELL

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

Starcode: sequence clustering based on all-pairs search

(2015) Eduard Zorita et al.   BIOINFORMATICS

MITF Modulates Therapeutic Resistance through EGFR Signaling

(2015) Zhenyu Ji et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Relief of Profound Feedback Inhibition of Mitogenic Signaling by RAF Inhibitors Attenuates Their Activity in BRAFV600E Melanomas

(2012) Piro Lito et al.   CANCER CELL

EGFR-Mediated Reactivation of MAPK Signaling Contributes to Insensitivity of BRAF -Mutant Colorectal Cancers to RAF Inhibition with Vemurafenib

(2012) Ryan B. Corcoran et al.   Cancer Discovery

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

(2011) Piyush B. Gupta et al.   CELL

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

(2010) Sreenath V. Sharma et al.   CELL

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

(2010) Alexander Roesch et al.   CELL

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis

(2009) Sabrina L. Spencer et al.   NATURE

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

(2008) Arjun Raj et al.   CELL

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

Dynamic Proteomics of Individual Cancer Cells in Response to a Drug

(2008) A. A. Cohen et al.   SCIENCE