High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

(2018) Charissa Kim et al.   CELL

Capecitabine Efficacy Is Correlated with TYMP and RB1 Expression in PDX Established from Triple-Negative Breast Cancers

(2018) Elisabetta Marangoni et al.   CLINICAL CANCER RESEARCH

Single-cell multi-omics sequencing of human early embryos

(2018) Lin Li et al.   NATURE CELL BIOLOGY

The cis-regulatory dynamics of embryonic development at single-cell resolution

(2018) Darren A. Cusanovich et al.   NATURE

Next-Generation Sequencing Analysis and Algorithms for PDX and CDX Models

(2017) Garima Khandelwal et al.   MOLECULAR CANCER RESEARCH

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

(2017) Sydney M. Shaffer et al.   NATURE

Genome-wide base-resolution mapping of DNA methylation in single cells using single-cell bisulfite sequencing (scBS-seq)

(2017) Stephen J Clark et al.   Nature Protocols

Tumour heterogeneity and resistance to cancer therapies

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

Clonal genotype and population structure inference from single-cell tumor sequencing

(2016) Andrew Roth et al.   NATURE METHODS

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

Single-cell barcoding and sequencing using droplet microfluidics

(2016) Rapolas Zilionis et al.   Nature Protocols

Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data

(2016) Martin Barron et al.   Scientific Reports

Androgen receptor promotes tamoxifen agonist activity by activation of EGFR in ERα-positive breast cancer

(2015) Andrew Ciupek et al.   BREAST CANCER RESEARCH AND TREATMENT

DNA Methylation and Somatic Mutations Converge on the Cell Cycle and Define Similar Evolutionary Histories in Brain Tumors

(2015) Tali Mazor et al.   CANCER CELL

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Erosion of X Chromosome Inactivation in Human Pluripotent Cells Initiates with XACT Coating and Depends on a Specific Heterochromatin Landscape

(2015) Céline Vallot et al.   Cell Stem Cell

Epithelial-to-mesenchymal transition is dispensable for metastasis but induces chemoresistance in pancreatic cancer

(2015) Xiaofeng Zheng et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Epithelial-to-mesenchymal transition is not required for lung metastasis but contributes to chemoresistance

(2015) Kari R. Fischer et al.   NATURE

Transcriptional plasticity promotes primary and acquired resistance to BET inhibition

(2015) Philipp Rathert et al.   NATURE

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

Differential epigenetic reprogramming in response to specific endocrine therapies promotes cholesterol biosynthesis and cellular invasion

(2015) Van T. M. Nguyen et al.   Nature Communications

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures

(2014) D. H. Phanstiel et al.   BIOINFORMATICS

Acquired Resistance to Endocrine Treatments Is Associated with Tumor-Specific Molecular Changes in Patient-Derived Luminal Breast Cancer Xenografts

(2014) P. Cottu et al.   CLINICAL CANCER RESEARCH

CUSHAW3: Sensitive and Accurate Base-Space and Color-Space Short-Read Alignment with Hybrid Seeding

(2014) Yongchao Liu et al.   PLoS One

The role of the oncofetal IGF2 mRNA-binding protein 3 (IGF2BP3) in cancer

(2014) Marcell Lederer et al.   SEMINARS IN CANCER BIOLOGY

Optimization of tumor xenograft dissociation for the profiling of cell surface markers and nutrient transporters

(2013) Vincent Petit et al.   LABORATORY INVESTIGATION

Single-cell analysis and sorting using droplet-based microfluidics

(2013) Linas Mazutis et al.   Nature Protocols

Genome-wide reprogramming of the chromatin landscape underlies endocrine therapy resistance in breast cancer

(2013) L. Magnani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Methylation Alterations Exhibit Intraindividual Stability and Interindividual Heterogeneity in Prostate Cancer Metastases

(2013) M. J. Aryee et al.   Science Translational Medicine

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Modeling of response to endocrine therapy in a panel of human luminal breast cancer xenografts

(2011) P. Cottu et al.   BREAST CANCER RESEARCH AND TREATMENT

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

(2010) Matthew D. Wilkerson et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Beating Poisson encapsulation statistics using close-packed ordering

(2009) Adam R. Abate et al.   LAB ON A CHIP

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Tamoxifen Resistance in Breast Tumors Is Driven by Growth Factor Receptor Signaling with Repression of Classic Estrogen Receptor Genomic Function

(2008) S. Massarweh et al.   CANCER RESEARCH

Droplet-Based Microfluidic Platforms for the Encapsulation and Screening of Mammalian Cells and Multicellular Organisms

(2008) Jenifer Clausell-Tormos et al.   CHEMISTRY & BIOLOGY