Smart-RRBS for single-cell methylome and transcriptome analysis

DNA methylation QTL analysis identifies new regulators of human longevity

(2020) Silke Szymczak et al.   HUMAN MOLECULAR GENETICS

Single-cell RNA counting at allele and isoform resolution using Smart-seq3

(2020) Michael Hagemann-Jensen et al.   NATURE BIOTECHNOLOGY

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

(2020) Jiarui Ding et al.   NATURE BIOTECHNOLOGY

Single-Cell Applications of Next-Generation Sequencing

(2019) Naishitha Anaparthy et al.   Cold Spring Harbor Perspectives in Medicine

A (fire)cloud-based DNA methylation data preprocessing and quality control platform

(2019) Divy Kangeyan et al.   BMC BIOINFORMATICS

Epigenetic evolution and lineage histories of chronic lymphocytic leukaemia

(2019) Federico Gaiti et al.   NATURE

Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL

(2019) Alessandro Pastore et al.   Nature Communications

Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression

(2019) Alexander M. Tsankov et al.   DEVELOPMENT

Cannabis use is associated with potentially heritable widespread changes in autism candidate gene DLGAP2 DNA methylation in sperm

(2019) Rose Schrott et al.   Epigenetics

Simultaneous profiling of 3D genome structure and DNA methylation in single human cells

(2019) Dong-Sung Lee et al.   NATURE METHODS

Joint profiling of DNA methylation and chromatin architecture in single cells

(2019) Guoqiang Li et al.   NATURE METHODS

Highly scalable generation of DNA methylation profiles in single cells

(2018) Ryan M Mulqueen et al.   NATURE BIOTECHNOLOGY

Global delay in nascent strand DNA methylation

(2018) Jocelyn Charlton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Global delay in nascent strand DNA methylation

(2018) Jocelyn Charlton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The DNA methylation landscape of glioblastoma disease progression shows extensive heterogeneity in time and space

(2018) Johanna Klughammer et al.   NATURE MEDICINE

Robust single-cell DNA methylome profiling with snmC-seq2

(2018) Chongyuan Luo et al.   Nature Communications

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer

(2017) Zachary D. Smith et al.   NATURE

Intragenic DNA methylation prevents spurious transcription initiation

(2017) Francesco Neri et al.   NATURE

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens 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

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Large-Scale Low-Cost NGS Library Preparation Using a Robust Tn5 Purification and Tagmentation Protocol

(2017) Bianca P. Hennig et al.   G3-Genes Genomes Genetics

A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications

(2017) Ashraful Haque et al.   Genome Medicine

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

(2016) Yu Hou et al.   CELL RESEARCH

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

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

(2016) Iain C Macaulay et al.   Nature Protocols

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Zeb2 Regulates Cell Fate at the Exit from Epiblast State in Mouse Embryonic Stem Cells

(2016) Agata Stryjewska et al.   STEM CELLS

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

(2015) Allon M. Klein et al.   CELL

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

(2015) Evan Z. Macosko et al.   CELL

The first five years of single-cell cancer genomics and beyond

(2015) Nicholas E. Navin   GENOME RESEARCH

Advances and Applications of Single-Cell Sequencing Technologies

(2015) Yong Wang et al.   MOLECULAR CELL

Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples

(2015) Wenfei Jin et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Function and information content of DNA methylation

(2015) Dirk Schübeler   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

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

(2015) Iain C Macaulay et al.   NATURE METHODS

Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing

(2015) Hongshan Guo et al.   Nature Protocols

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

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

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo 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

Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing

(2013) Junwen Wang et al.   BMC GENOMICS

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

(2013) H. Guo et al.   GENOME RESEARCH

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

(2013) Simone Picelli et al.   NATURE METHODS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

(2012) Patrick Boyle et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE