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

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

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

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

Optimizing sparse sequencing of single cells for highly multiplex copy number profiling

(2015) Timour Baslan et al.   GENOME RESEARCH

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Advances and Applications of Single-Cell Sequencing Technologies

(2015) Yong Wang et al.   MOLECULAR CELL

Single-cell transcriptogenomics reveals transcriptional exclusion of ENU-mutated alleles

(2015) Wenge Li et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Integrated genome and transcriptome sequencing of the same cell

(2015) Siddharth S Dey et al.   NATURE BIOTECHNOLOGY

Interactive analysis and assessment of single-cell copy-number variations

(2015) Tyler Garvin et al.   NATURE METHODS

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

(2015) Iain C Macaulay et al.   NATURE METHODS

Cell Lineage Analysis in Human Brain Using Endogenous Retroelements

(2015) Gilad D. Evrony et al.   NEURON

Comparison of variations detection between whole-genome amplification methods used in single-cell resequencing

(2015) Yong Hou et al.   GigaScience

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Clonal evolution in breast cancer revealed by single nucleus genome sequencing

(2014) Yong Wang et al.   NATURE

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

A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods

(2014) Charles F. A. de Bourcy et al.   PLoS One

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

(2014) D. A. Jaitin et al.   SCIENCE

Co-detection and sequencing of genes and transcripts from the same single cells facilitated by a microfluidics platform

(2014) Lin Han et al.   Scientific Reports

Single-Cell, Genome-wide Sequencing Identifies Clonal Somatic Copy-Number Variation in the Human Brain

(2014) Xuyu Cai et al.   Cell Reports

Single Cell Genomics: Advances and Future Perspectives

(2014) Iain C. Macaulay et al.   PLoS Genetics

Copynumber: Efficient algorithms for single- and multi-track copy number segmentation

(2013) Gro Nilsen et al.   BMC GENOMICS

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

(2013) Simone Picelli et al.   NATURE METHODS

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

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Single-cell paired-end genome sequencing reveals structural variation per cell cycle

(2013) Thierry Voet et al.   NUCLEIC ACIDS RESEARCH

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain

(2012) Gilad D. Evrony et al.   CELL

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

Genome-wide copy number analysis of single cells

(2012) Timour Baslan et al.   Nature Protocols

Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing

(2012) Saiful Islam et al.   Nature Protocols

Two methods for full-length RNA sequencing for low quantities of cells and single cells

(2012) X. Pan 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

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

(2012) Tamar Hashimshony et al.   Cell Reports

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

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

(2011) Michael Gundry et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Chromosome instability is common in human cleavage-stage embryos

(2009) Evelyne Vanneste et al.   NATURE MEDICINE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS