Single-cell sequencing-based technologies will revolutionize whole-organism science

Use of somatic mutations to quantify random contributions to mouse development

(2013) Wenyu Zhou et al.   BMC GENOMICS

High-throughput sequencing of the paired human immunoglobulin heavy and light chain repertoire

(2013) Brandon J DeKosky et al.   NATURE BIOTECHNOLOGY

Comprehensive Mutation Analysis for Congenital Muscular Dystrophy: A Clinical PCR-Based Enrichment and Next-Generation Sequencing Panel

(2013) C. Alexander Valencia et al.   PLoS One

A Melanoma Brain Metastasis with a Donor-Patient Hybrid Genome following Bone Marrow Transplantation: First Evidence for Fusion in Human Cancer

(2013) Rossitza Lazova et al.   PLoS One

Real-time single-molecule co-immunoprecipitation analyses reveal cancer-specific Ras signalling dynamics

(2013) Hong-Won Lee et al.   Nature Communications

Characterizing and measuring bias in sequence data

(2013) Michael G Ross et al.   GENOME BIOLOGY

Molecular live cell bioimaging in stem cell research

(2012) Max Endele et al.   Annals of the New York Academy of Sciences

Cell lineage analysis of acute leukemia relapse uncovers the role of replication-rate heterogeneity and microsatellite instability

(2012) L. I. Shlush et al.   BLOOD

Targeted genomic sequencing of pediatric Burkitt lymphoma identifies recurrent alterations in antiapoptotic and chromatin-remodeling genes

(2012) L. Giulino-Roth et al.   BLOOD

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

(2012) Xun Xu et al.   CELL

Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm

(2012) Yong Hou et al.   CELL

Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm

(2012) Jianbin Wang et al.   CELL

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Microfluidic Amplification as a Tool for Massive Parallel Sequencing of the Familial Hypercholesterolemia Genes

(2012) S. Hollants et al.   CLINICAL CHEMISTRY

Microfluidic single cell analysis: from promise to practice

(2012) Véronique Lecault et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Maintenance of  -Cell Maturity and Plasticity in the Adult Pancreas: Developmental Biology Concepts in Adult Physiology

(2012) M. Szabat et al.   DIABETES

Multidimensional regulation of gene expression in the C. elegans embryo

(2012) J. I. Murray et al.   GENOME RESEARCH

Fate Mapping Reveals Origins and Dynamics of Monocytes and Tissue Macrophages under Homeostasis

(2012) Simon Yona et al.   IMMUNITY

Monitoring the dynamics of primary T cell activation and differentiation using long term live cell imaging in microwell arrays

(2012) Irina Zaretsky et al.   LAB ON A CHIP

Droplet microfluidics for high-throughput biological assays

(2012) Mira T. Guo et al.   LAB ON A CHIP

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

(2012) Timothy M Walker et al.   LANCET INFECTIOUS DISEASES

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells

(2012) Brock A. Peters et al.   NATURE

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

(2012) Li Ding et al.   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues

(2012) Gilad Landan et al.   NATURE GENETICS

Library-free methylation sequencing with bisulfite padlock probes

(2012) Dinh Diep et al.   NATURE METHODS

Robust 4C-seq data analysis to screen for regulatory DNA interactions

(2012) Harmen J G van de Werken et al.   NATURE METHODS

Genome-wide copy number analysis of single cells

(2012) Timour Baslan et al.   Nature Protocols

Evolution of the cancer genome

(2012) Lucy R. Yates et al.   NATURE REVIEWS GENETICS

Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing

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

Whole-Exome Sequencing Efficiently Detects Rare Mutations in Autosomal Recessive Nonsyndromic Hearing Loss

(2012) Oscar Diaz-Horta et al.   PLoS One

Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes

(2012) K. Shiroguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell

(2012) C. Zong et al.   SCIENCE

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

(2012) S. Lu et al.   SCIENCE

Lineage Tracing Reveals Lgr5+ Stem Cell Activity in Mouse Intestinal Adenomas

(2012) A. G. Schepers et al.   SCIENCE

Clonal Evolution of Preleukemic Hematopoietic Stem Cells Precedes Human Acute Myeloid Leukemia

(2012) M. Jan et al.   Science Translational Medicine

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Mitochondrial Variability as a Source of Extrinsic Cellular Noise

(2012) Iain G. Johnston et al.   PLoS Computational Biology

In Vivo Control of CpG and Non-CpG DNA Methylation by DNA Methyltransferases

(2012) Julia Arand et al.   PLoS Genetics

Cell Lineage Analysis of the Mammalian Female Germline

(2012) Yitzhak Reizel et al.   PLoS Genetics

V(D)J Recombination: Mechanisms of Initiation

(2011) David G. Schatz et al.   Annual Review of Genetics

Genomic Analysis at the Single-Cell Level

(2011) Tomer Kalisky et al.   Annual Review of Genetics

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Repeatedly identified differentially expressed proteins (RIDEPs) from antibody microarray proteomic analysis

(2011) Victoria C. Hodgkinson et al.   Journal of Proteomics

A first step towards practical single cell proteomics: a microfluidic antibody capture chip with TIRF detection

(2011) Ali Salehi-Reyhani et al.   LAB ON A CHIP

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Central dogma at the single-molecule level in living cells

(2011) Gene-Wei Li et al.   NATURE

Probing cellular protein complexes using single-molecule pull-down

(2011) Ankur Jain et al.   NATURE

Single-cell dissection of transcriptional heterogeneity in human colon tumors

(2011) Piero Dalerba et al.   NATURE BIOTECHNOLOGY

Decoding cell lineage from acquired mutations using arbitrary deep sequencing

(2011) Cheryl A Carlson et al.   NATURE METHODS

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

Adult Neurogenesis in the Mammalian Brain: Significant Answers and Significant Questions

(2011) Guo-li Ming et al.   NEURON

Direct, genome-wide assessment of DNA mutations in single cells

(2011) Michael Gundry et al.   NUCLEIC ACIDS RESEARCH

A high-throughput DNA methylation analysis of a single cell

(2011) Martin Kantlehner et al.   NUCLEIC ACIDS RESEARCH

Tracking epigenetic histone modifications in single cells using Fab-based live endogenous modification labeling

(2011) Yoko Hayashi-Takanaka et al.   NUCLEIC ACIDS RESEARCH

A method for counting PCR template molecules with application to next-generation sequencing

(2011) J. A. Casbon et al.   NUCLEIC ACIDS RESEARCH

ProteinSeq: High-Performance Proteomic Analyses by Proximity Ligation and Next Generation Sequencing

(2011) Spyros Darmanis et al.   PLoS One

Muscle-Bound Primordial Stem Cells Give Rise to Myofiber-Associated Myogenic and Non-Myogenic Progenitors

(2011) Elad Segev et al.   PLoS One

Counting individual DNA molecules by the stochastic attachment of diverse labels

(2011) G. K. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput microfluidic single-cell RT-qPCR

(2011) A. K. White et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells

(2011) Q. Shi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) S. C. Bendall et al.   SCIENCE

Colon Stem Cell and Crypt Dynamics Exposed by Cell Lineage Reconstruction

(2011) Yitzhak Reizel et al.   PLoS Genetics

Toward Clinical Proteomics on a Next-Generation Sequencing Platform

(2010) Daniel J. Turner et al.   ANALYTICAL CHEMISTRY

Development and optimization of a process for automated recovery of single cells identified by microengraving

(2010) Jae Hyeok Choi et al.   BIOTECHNOLOGY PROGRESS

Phylogenetic analysis of developmental and postnatal mouse cell lineages

(2010) Stephen J. Salipante et al.   EVOLUTION & DEVELOPMENT

Exome sequencing: the sweet spot before whole genomes

(2010) J. K. Teer et al.   HUMAN MOLECULAR GENETICS

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

The therapeutic promise of the cancer stem cell concept

(2010) Natasha Y. Frank et al.   JOURNAL OF CLINICAL INVESTIGATION

Genetic variegation of clonal architecture and propagating cells in leukaemia

(2010) Kristina Anderson et al.   NATURE

Distant metastasis occurs late during the genetic evolution of pancreatic cancer

(2010) Shinichi Yachida et al.   NATURE

Whole-genome molecular haplotyping of single cells

(2010) H Christina Fan et al.   NATURE BIOTECHNOLOGY

Visualization of omics data for systems biology

(2010) Nils Gehlenborg et al.   NATURE METHODS

Targeted resequencing of candidate genes using selector probes

(2010) H. Johansson et al.   NUCLEIC ACIDS RESEARCH

Somatic Mutation Profiles of MSI and MSS Colorectal Cancer Identified by Whole Exome Next Generation Sequencing and Bioinformatics Analysis

(2010) Bernd Timmermann et al.   PLoS One

Tumor Self-Seeding by Circulating Cancer Cells

(2009) Mi-Young Kim et al.   CELL

Multiplex padlock targeted sequencing reveals human hypermutable CpG variations

(2009) J. B. Li et al.   GENOME RESEARCH

Quantification of Cardiovascular Biomarkers in Patient Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution

(2009) Hasmik Keshishian et al.   MOLECULAR & CELLULAR PROTEOMICS

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

Targeted capture and massively parallel sequencing of 12 human exomes

(2009) Sarah B. Ng et al.   NATURE

Microdroplet-based PCR enrichment for large-scale targeted sequencing

(2009) Ryan Tewhey et al.   NATURE BIOTECHNOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Identity crisis for adult periventricular neural stem cells: subventricular zone astrocytes, ependymal cells or both?

(2009) Andrew K. Chojnacki et al.   NATURE REVIEWS NEUROSCIENCE

Inferring clonal expansion and cancer stem cell dynamics from DNA methylation patterns in colorectal cancers

(2009) K. D. Siegmund et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Perspectives and Challenges of Emerging Single-Molecule DNA Sequencing Technologies

(2009) Mingsheng Xu et al.   Small

Amplification of multiple genomic loci from single cells isolated by laser micro-dissection of tissues

(2008) Dan Frumkin et al.   BMC BIOTECHNOLOGY

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

(2008) Arjun Raj et al.   CELL

Optical tweezers for single cells

(2008) H. Zhang et al.   Journal of the Royal Society Interface

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Here, there, everywhere?

(2008) Connie J. Eaves   NATURE

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Automated analysis of embryonic gene expression with cellular resolution in C. elegans

(2008) John Isaac Murray et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

The evolution of cell types in animals: emerging principles from molecular studies

(2008) Detlev Arendt   NATURE REVIEWS GENETICS

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

(2008) R. Jothi et al.   NUCLEIC ACIDS RESEARCH

Reconstruction of Cell Lineage Trees in Mice

(2008) Adam Wasserstrom et al.   PLoS One

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

Single-Molecule DNA Sequencing of a Viral Genome

(2008) T. D. Harris et al.   SCIENCE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE