Landscapes of cellular phenotypic diversity in breast cancer xenografts and their impact on drug response

The single-cell pathology landscape of breast cancer

(2020) Hartland W. Jackson et al.   NATURE

Cell-type-specific signaling networks in heterocellular organoids

(2020) Xiao Qin et al.   NATURE METHODS

Intratumor Heterogeneity: The Rosetta Stone of Therapy Resistance

(2020) Andriy Marusyk et al.   CANCER CELL

Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups

(2019) Oscar M. Rueda et al.   NATURE

A Single-Cell Atlas of the Tumor and Immune Ecosystem of Human Breast Cancer

(2019) Johanna Wagner et al.   CELL

Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens

(2019) Fiona M. Behan et al.   NATURE

Next-generation characterization of the Cancer Cell Line Encyclopedia

(2019) Mahmoud Ghandi et al.   NATURE

Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts

(2018) Maurizio Callari et al.   BMC GENOMICS

A Living Biobank of Breast Cancer Organoids Captures Disease Heterogeneity

(2018) Norman Sachs et al.   CELL

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

A PDX/Organoid Biobank of Advanced Prostate Cancers Captures Genomic and Phenotypic Heterogeneity for Disease Modeling and Therapeutic Screening

(2018) Michael L. Beshiri et al.   CLINICAL CANCER RESEARCH

Combined Inhibition of mTOR and CDK4/6 Is Required for Optimal Blockade of E2F Function and Long-term Growth Inhibition in Estrogen Receptor–positive Breast Cancer

(2018) Chrysiis Michaloglou et al.   MOLECULAR CANCER THERAPEUTICS

Enhancer mapping uncovers phenotypic heterogeneity and evolution in patients with luminal breast cancer

(2018) Darren K. Patten et al.   NATURE MEDICINE

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

(2018) Leeat Keren et al.   CELL

Capturing Colorectal Cancer Inter-Tumor Heterogeneity in Patient-Derived Xenograft (PDX) Models

(2018) Pramudita R. Prasetyanti et al.   INTERNATIONAL JOURNAL OF CANCER

A Universal Live Cell Barcoding-Platform for Multiplexed Human Single Cell Analysis

(2018) Felix J. Hartmann et al.   Scientific Reports

Phenotypic Plasticity: Driver of Cancer Initiation, Progression, and Therapy Resistance

(2018) Piyush B. Gupta et al.   Cell Stem Cell

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

(2017) Sydney M. Shaffer et al.   NATURE

An approach to suppress the evolution of resistance in BRAFV600E-mutant cancer

(2017) Yaohua Xue et al.   NATURE MEDICINE

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Mass Cytometric Analysis Reveals Viable Activated Caspase-3 + Luminal Progenitors in the Normal Adult Human Mammary Gland

(2017) David J.H.F. Knapp et al.   Cell Reports

A Biobank of Breast Cancer Explants with Preserved Intra-tumor Heterogeneity to Screen Anticancer Compounds

(2016) Alejandra Bruna et al.   CELL

Overcoming mTOR resistance mutations with a new-generation mTOR inhibitor

(2016) Vanessa S. Rodrik-Outmezguine et al.   NATURE

Spatial intratumoral heterogeneity and temporal clonal evolution in esophageal squamous cell carcinoma

(2016) Jia-Jie Hao et al.   NATURE GENETICS

Earth Mover’s Distance (EMD): A True Metric for Comparing Biomarker Expression Levels in Cell Populations

(2016) Darya Y. Orlova et al.   PLoS One

The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes

(2016) Bernard Pereira et al.   Nature Communications

Global Cancer Incidence and Mortality Rates and Trends--An Update

(2015) L. A. Torre et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

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

(2015) Jacob H. Levine et al.   CELL

Single-cell mass cytometry reveals intracellular survival/proliferative signaling in FLT3-ITD-mutated AML stem/progenitor cells

(2015) Lina Han et al.   CYTOMETRY PART A

AZD2014, an Inhibitor of mTORC1 and mTORC2, Is Highly Effective in ER+ Breast Cancer When Administered Using Intermittent or Continuous Schedules

(2015) S. M. Guichard et al.   MOLECULAR CANCER THERAPEUTICS

The evolutionary history of lethal metastatic prostate cancer

(2015) Gunes Gundem et al.   NATURE

Single-cell analysis reveals a stem-cell program in human metastatic breast cancer cells

(2015) Devon A. Lawson et al.   NATURE

High-throughput screening using patient-derived tumor xenografts to predict clinical trial drug response

(2015) Hui Gao et al.   NATURE MEDICINE

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

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

Subclonal diversification of primary breast cancer revealed by multiregion sequencing

(2015) Lucy R Yates et al.   NATURE MEDICINE

Potentiation of Growth Inhibitory Responses of the mTOR Inhibitor Everolimus by Dual mTORC1/2 Inhibitors in Cultured Breast Cancer Cell Lines

(2015) Euphemia Y. Leung et al.   PLoS One

RB1 dual role in proliferation and apoptosis: cell fate control and implications for cancer therapy

(2015) Paola Indovina et al.   Oncotarget

The Proteomic Landscape of Triple-Negative Breast Cancer

(2015) Robert T. Lawrence et al.   Cell Reports

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Assessing the clinical utility of cancer genomic and proteomic data across tumor types

(2014) Yuan Yuan et al.   NATURE BIOTECHNOLOGY

Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing

(2014) Marco Gerlinger et al.   NATURE GENETICS

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

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

Conditional density-based analysis of T cell signaling in single-cell data

(2014) S. Krishnaswamy et al.   SCIENCE

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

(2013) Y. Liao et al.   BIOINFORMATICS

Proteomic Characterization of Breast Cancer Xenografts Identifies Early and Late Bevacizumab-Induced Responses and Predicts Effective Drug Combinations

(2013) E. M. Lindholm et al.   CLINICAL CANCER RESEARCH

Single-cell mass cytometry for analysis of immune system functional states

(2013) Zach B Bjornson et al.   CURRENT OPINION IN IMMUNOLOGY

A new genome-driven integrated classification of breast cancer and its implications

(2013) Sarah-Jane Dawson et al.   EMBO JOURNAL

Mutational Analysis Reveals the Origin and Therapy-Driven Evolution of Recurrent Glioma

(2013) B. E. Johnson et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Proteomic Portrait of Human Breast Cancer Progression Identifies Novel Prognostic Markers

(2012) T. Geiger et al.   CANCER RESEARCH

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

(2012) Christina Curtis et al.   NATURE

Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators

(2012) Bernd Bodenmiller et al.   NATURE BIOTECHNOLOGY

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

MATH, a novel measure of intratumor genetic heterogeneity, is high in poor-outcome classes of head and neck squamous cell carcinoma

(2012) Edmund A. Mroz et al.   ORAL ONCOLOGY

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

(2011) Piyush B. Gupta et al.   CELL

Heterogeneity in breast cancer

(2011) Kornelia Polyak   JOURNAL OF CLINICAL INVESTIGATION

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Tumor grafts derived from women with breast cancer authentically reflect tumor pathology, growth, metastasis and disease outcomes

(2011) Yoko S DeRose et al.   NATURE MEDICINE

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

(2009) Dmitry R. Bandura et al.   ANALYTICAL CHEMISTRY

Inferring tumor progression from genomic heterogeneity

(2009) N. Navin et al.   GENOME RESEARCH

Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution

(2009) Sohrab P. Shah et al.   NATURE

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

Transcriptome Analysis of the Normal Human Mammary Cell Commitment and Differentiation Process

(2008) Afshin Raouf et al.   Cell Stem Cell