Tumour heterogeneity and metastasis at single-cell resolution

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

(2018) Charissa Kim et al.   CELL

Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing

(2018) Anna K. Casasent et al.   CELL

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

(2018) Tetsutaro Hayashi et al.   Nature Communications

Macrophages orchestrate breast cancer early dissemination and metastasis

(2018) Nina Linde et al.   Nature Communications

Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer

(2017) Marco L. Leung et al.   GENOME RESEARCH

Analytical Validation of the Next-Generation Sequencing Assay for a Nationwide Signal-Finding Clinical Trial

(2017) Chih-Jian Lih et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

Cancer stem cells revisited

(2017) Eduard Batlle et al.   NATURE MEDICINE

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson et al.   NATURE METHODS

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

(2017) Susanne C van den Brink et al.   NATURE METHODS

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

(2017) Todd M Gierahn et al.   NATURE METHODS

The immune contexture in cancer prognosis and treatment

(2017) Wolf H. Fridman et al.   Nature Reviews Clinical Oncology

The evolution of tumour phylogenetics: principles and practice

(2017) Russell Schwartz et al.   NATURE REVIEWS GENETICS

seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus

(2017) Sheel Shah et al.   NEURON

Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy

(2017) John M. Bell et al.   NUCLEIC ACIDS RESEARCH

Comparison of whole genome amplification techniques for human single cell exome sequencing

(2017) Erik Borgström et al.   PLoS One

Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq

(2017) Lihe Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)

(2017) Chongyi Chen et al.   SCIENCE

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq

(2017) Andrew S. Venteicher et al.   SCIENCE

Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma

(2017) Spyros Darmanis et al.   Cell Reports

A Targetable EGFR-Dependent Tumor-Initiating Program in Breast Cancer

(2017) Paul Savage et al.   Cell Reports

Tumor Heterogeneity--A 'Contemporary Concept Founded on Historical Insights and Predictions

(2016) D. R. Welch   CANCER RESEARCH

Metastatic Latency and Immune Evasion through Autocrine Inhibition of WNT

(2016) Srinivas Malladi et al.   CELL

Single-cell triple omics sequencing reveals genetic, epigenetic and transcriptomic heterogeneity in hepatocellular carcinomas

(2016) Yu Hou et al.   CELL RESEARCH

Early dissemination seeds metastasis in breast cancer

(2016) Hedayatollah Hosseini et al.   NATURE

Metastatic colonization by circulating tumour cells

(2016) Joan Massagué et al.   NATURE

Mechanism of early dissemination and metastasis in Her2+ mammary cancer

(2016) Kathryn L. Harper et al.   NATURE

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

(2016) Itay Tirosh et al.   NATURE

Single-cell sequencing of the small-RNA transcriptome

(2016) Omid R Faridani et al.   NATURE BIOTECHNOLOGY

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction

(2016) Dylan Mooijman et al.   NATURE BIOTECHNOLOGY

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

The heterogeneity of human CD127+ innate lymphoid cells revealed by single-cell RNA sequencing

(2016) Åsa K Björklund et al.   NATURE IMMUNOLOGY

Molecular analysis of circulating tumor cells identifies distinct copy-number profiles in patients with chemosensitive and chemorefractory small-cell lung cancer

(2016) Louise Carter et al.   NATURE MEDICINE

Genotyping tumor clones from single-cell data

(2016) Nicholas E Navin et al.   NATURE METHODS

Dense transcript profiling in single cells by image correlation decoding

(2016) Ahmet F Coskun et al.   NATURE METHODS

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

Highly multiplexed targeted DNA sequencing from single nuclei

(2016) Marco L Leung et al.   Nature Protocols

Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq

(2016) Iain C Macaulay et al.   Nature Protocols

Computational genomics tools for dissecting tumour–immune cell interactions

(2016) Hubert Hackl et al.   NATURE REVIEWS GENETICS

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

High-Dimensional Analysis of Acute Myeloid Leukemia Reveals Phenotypic Changes in Persistent Cells during Induction Therapy

(2016) Paul Brent Ferrell et al.   PLoS One

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

(2016) N. McGranahan et al.   SCIENCE

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

(2016) I. Tirosh et al.   SCIENCE

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

(2016) Naomi Habib et al.   SCIENCE

Single-cell TCRseq: paired recovery of entire T-cell alpha and beta chain transcripts in T-cell receptors from single-cell RNAseq

(2016) David Redmond et al.   Genome Medicine

Single-Cell Transcriptomics Bioinformatics and Computational Challenges

(2016) Olivier B. Poirion et al.   Frontiers in Genetics

Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications

(2015) Lei Huang et al.   Annual Review of Genomics and Human Genetics

Biological and Therapeutic Impact of Intratumor Heterogeneity in Cancer Evolution

(2015) Nicholas McGranahan et al.   CANCER CELL

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

(2015) Allon M. Klein et al.   CELL

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

(2015) Jacob H. Levine et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Hypoxia drives transient site-specific copy gain and drug-resistant gene expression

(2015) Joshua C. Black et al.   GENES & DEVELOPMENT

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Single-cell analysis of targeted transcriptome predicts drug sensitivity of single cells within human myeloma tumors

(2015) A K Mitra et al.   LEUKEMIA

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

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

(2015) Devon A. Lawson et al.   NATURE

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

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

Integrated genome and transcriptome sequencing of the same cell

(2015) Siddharth S Dey et al.   NATURE BIOTECHNOLOGY

Subclonal diversification of primary breast cancer revealed by multiregion sequencing

(2015) Lucy R Yates et al.   NATURE MEDICINE

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

(2015) Je Hyuk Lee et al.   Nature Protocols

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

RNA-Seq of single prostate CTCs implicates noncanonical Wnt signaling in antiandrogen resistance

(2015) D. T. Miyamoto et al.   SCIENCE

Somatic mutation in single human neurons tracks developmental and transcriptional history

(2015) M. A. Lodato et al.   SCIENCE

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Mass Cytometric Functional Profiling of Acute Myeloid Leukemia Defines Cell-Cycle and Immunophenotypic Properties That Correlate with Known Responses to Therapy

(2015) G. K. Behbehani et al.   Cancer Discovery

SNES: single nucleus exome sequencing

(2015) Marco L Leung et al.   GENOME BIOLOGY

Circulating Tumor Cell Clusters Are Oligoclonal Precursors of Breast Cancer Metastasis

(2014) Nicola Aceto et al.   CELL

Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing

(2014) Chang Yu et al.   CELL RESEARCH

Evolution of the Cancer Stem Cell Model

(2014) Antonija Kreso et al.   Cell Stem Cell

Single cell analysis of cancer genomes

(2014) Peter Van Loo et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Molecular profiling of single circulating tumor cells with diagnostic intention

(2014) B. Polzer et al.   EMBO Molecular Medicine

C. eleganswhole-genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency

(2014) Bettina Meier et al.   GENOME RESEARCH

Heterogeneity of PIK3CA mutational status at the single cell level in circulating tumor cells from metastatic breast cancer patients

(2014) Marta Pestrin et al.   Molecular Oncology

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer

(2014) Jens G Lohr et al.   NATURE BIOTECHNOLOGY

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen 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

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics

(2014) Charles Gawad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

High intratumor genetic heterogeneity is related to worse outcome in patients with head and neck squamous cell carcinoma

(2013) Edmund A. Mroz et al.   CANCER

Complex Tumor Genomes Inferred from Single Circulating Tumor Cells by Array-CGH and Next-Generation Sequencing

(2013) E. Heitzer et al.   CANCER RESEARCH

Collective Invasion in Breast Cancer Requires a Conserved Basal Epithelial Program

(2013) Kevin J. Cheung et al.   CELL

Hypoxia Contributes to Melanoma Heterogeneity by Triggering HIF1α-Dependent Phenotype Switching

(2013) Daniel S. Widmer et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Evidence for APOBEC3B mutagenesis in multiple human cancers

(2013) Michael B Burns et al.   NATURE GENETICS

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

Microenvironmental regulation of tumor progression and metastasis

(2013) Daniela F Quail et al.   NATURE MEDICINE

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

RNA-sequencing from single nuclei

(2013) R. V. Grindberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients

(2013) X. Ni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) B. E. Johnson et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Quantitative Transcriptomics using Designed Primer-based Amplification

(2013) Vipul Bhargava et al.   Scientific Reports

Patterns of genomic loss of heterozygosity predict homologous recombination repair defects in epithelial ovarian cancer

(2012) V Abkevich et al.   BRITISH JOURNAL OF CANCER

Ploidy and Large-Scale Genomic Instability Consistently Identify Basal-like Breast Carcinomas with BRCA1/2 Inactivation

(2012) T. Popova et al.   CANCER RESEARCH

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

(2012) Marco Gerlinger et al.   NEW ENGLAND JOURNAL OF MEDICINE

Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole-Genome Sequencing

(2012) S. Lu et al.   SCIENCE

Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development

(2011) Philip J. Stephens et al.   CELL

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Interactions between cancer stem cells and their niche govern metastatic colonization

(2011) Ilaria Malanchi et al.   NATURE

Single-cell dissection of transcriptional heterogeneity in human colon tumors

(2011) Piero Dalerba et al.   NATURE BIOTECHNOLOGY

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

(2010) Roel G.W. Verhaak et al.   CANCER CELL

PIK3CA Mutations in In situ and Invasive Breast Carcinomas

(2010) A. Miron et al.   CANCER RESEARCH

Highly multiparametric analysis by mass cytometry

(2010) Olga Ornatsky et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Genome remodelling in a basal-like breast cancer metastasis and xenograft

(2010) Li Ding et al.   NATURE

Distant metastasis occurs late during the genetic evolution of pancreatic cancer

(2010) Shinichi Yachida et al.   NATURE

Interaction of Hypoxia-Inducible Factor-1α and Notch Signaling Regulates Medulloblastoma Precursor Proliferation and Fate

(2010) Francesca Pistollato et al.   STEM CELLS

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

Quantitative analysis of gene expression in a single cell by qPCR

(2009) Kiyomi Taniguchi et al.   NATURE METHODS

Flow cytometric immunophenotyping for hematologic neoplasms

(2008) F. E. Craig et al.   BLOOD

Systemic Spread Is an Early Step in Breast Cancer

(2008) Yves Hüsemann et al.   CANCER CELL

Efficient tumour formation by single human melanoma cells

(2008) Elsa Quintana et al.   NATURE