Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

(2022) Joseph M. Replogle et al.   CELL

ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ

(2022) Ian Dardani et al.   NATURE METHODS

Genetic screening for single-cell variability modulators driving therapy resistance

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

Variability within rare cell states enables multiple paths toward drug resistance

(2021) Benjamin L. Emert et al.   NATURE BIOTECHNOLOGY

Clonal multi-omics reveals Bcor as a negative regulator of emergency dendritic cell development

(2021) Luyi Tian et al.   IMMUNITY

Evolutionary predictability of genetic versus nongenetic resistance to anticancer drugs in melanoma

(2021) Oskar Marin-Bejar et al.   CANCER CELL

Cycling cancer persister cells arise from lineages with distinct programs

(2021) Yaara Oren et al.   NATURE

Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro

(2021) Ian A. Mellis et al.   Cell Systems

Non-genetic determinants of malignant clonal fitness at single-cell resolution

(2021) Katie A. Fennell et al.   NATURE

Clonal populations of a human TNBC model display significant functional heterogeneity and divergent growth dynamics in distinct contexts

(2021) Hendrik J. Kuiken et al.   ONCOGENE

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

Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis

(2020) Alejo E. Rodriguez-Fraticelli et al.   NATURE

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

(2020) Christian Umkehrer et al.   NATURE BIOTECHNOLOGY

Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells

(2020) Zohar Meir et al.   NATURE GENETICS

Continuous versus intermittent BRAF and MEK inhibition in patients with BRAF-mutated melanoma: a randomized phase 2 trial

(2020) Alain P. Algazi et al.   NATURE MEDICINE

Cellpose: a generalist algorithm for cellular segmentation

(2020) Carsen Stringer et al.   NATURE METHODS

Transient commensal clonal interactions can drive tumor metastasis

(2020) Suha Naffar-Abu Amara et al.   Nature Communications

Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting

(2019) Orsolya Symmons et al.   PLoS Genetics

Acquisition of a hybrid E/M state is essential for tumorigenicity of basal breast cancer cells

(2019) Cornelia Kröger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

Toward Minimal Residual Disease-Directed Therapy in Melanoma

(2018) Florian Rambow et al.   CELL

Neoadjuvant plus adjuvant dabrafenib and trametinib versus standard of care in patients with high-risk, surgically resectable melanoma: a single-centre, open-label, randomised, phase 2 trial

(2018) Rodabe N Amaria et al.   LANCET ONCOLOGY

Genetic and transcriptional evolution alters cancer cell line drug response

(2018) Uri Ben-David et al.   NATURE

Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity

(2018) Joseph Rodriguez et al.   CELL

Single-cell mapping of lineage and identity in direct reprogramming

(2018) Brent A. Biddy et al.   NATURE

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS RESEARCH

Remodeling of the Collagen Matrix in Aging Skin Promotes Melanoma Metastasis and Affects Immune Cell Motility

(2018) Amanpreet Kaur et al.   Cancer Discovery

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

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

A Comprehensive Patient-Derived Xenograft Collection Representing the Heterogeneity of Melanoma

(2017) Clemens Krepler et al.   Cell Reports

Deterministic versus stochastic model of reprogramming: new evidence from cellular barcoding technique

(2017) Anastasia M. Yunusova et al.   Open Biology

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

(2016) Orsolya Symmons et al.   MOLECULAR CELL

sFRP2 in the aged microenvironment drives melanoma metastasis and therapy resistance

(2016) Amanpreet Kaur et al.   NATURE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

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

(2016) Michael Ramirez et al.   Nature Communications

dbEM: A database of epigenetic modifiers curated from cancerous and normal genomes

(2016) Jagpreet Singh Nanda et al.   Scientific Reports

Starcode: sequence clustering based on all-pairs search

(2015) Eduard Zorita et al.   BIOINFORMATICS

Epigenetic predisposition to reprogramming fates in somatic cells

(2015) M. Pour et al.   EMBO REPORTS

Studying clonal dynamics in response to cancer therapy using high-complexity barcoding

(2015) Hyo-eun C Bhang et al.   NATURE MEDICINE

Energy statistics: A class of statistics based on distances

(2013) Gábor J. Székely et al.   JOURNAL OF STATISTICAL PLANNING AND INFERENCE

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

(2013) Meghna Das Thakur et al.   NATURE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS