scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

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

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

(2017) Sebastian Pott   eLife

Higher order methylation features for clustering and prediction in epigenomic studies

(2016) Chantriolnt-Andreas Kapourani et al.   BIOINFORMATICS

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

(2016) Yu Hou et al.   CELL RESEARCH

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

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 chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

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

(2015) Iain C Macaulay et al.   NATURE METHODS

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

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

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency

(2013) Gabriella Ficz et al.   Cell Stem Cell

Dynamic DNA methylation across diverse human cell lines and tissues

(2013) K. E. Varley et al.   GENOME RESEARCH

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

(2013) Simone Picelli et al.   NATURE METHODS

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

(2012) T. K. Kelly et al.   GENOME RESEARCH

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Protogenin Defines a Transition Stage during Embryonic Neurogenesis and Prevents Precocious Neuronal Differentiation

(2010) Y.-H. Wong et al.   JOURNAL OF NEUROSCIENCE

Independent filtering increases detection power for high-throughput experiments

(2010) R. Bourgon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling

(2009) Vladimir R. Ramirez-Carrozzi et al.   CELL

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE