Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells

Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects

(2016) Xiaoyan Zhang et al.   CANCER RESEARCH

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

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

Q-RRBS: a quantitative reduced representation bisulfite sequencing method for single-cell methylome analyses

(2015) Kangli Wang et al.   Epigenetics

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

Multiplexed locus-specific analysis of DNA methylation in single cells

(2015) Lih Feng Cheow et al.   Nature Protocols

Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification

(2015) Yusi Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intermediate DNA methylation is a conserved signature of genome regulation

(2015) GiNell Elliott et al.   Nature Communications

Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics

(2015) Matthias Farlik et al.   Cell Reports

Transcriptome Signature and Regulation in Human Somatic Cell Reprogramming

(2015) Yoshiaki Tanaka et al.   Stem Cell Reports

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

(2015) Yong Hou et al.   GigaScience

Every Cell Is Special: Genome-wide Studies Add a New Dimension to Single-Cell Biology

(2014) Jan Philipp Junker et al.   CELL

The evidence for functional non-CpG methylation in mammalian cells

(2014) Vibha Patil et al.   Epigenetics

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

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

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

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods

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

Single Cell Genomics: Advances and Future Perspectives

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

Replacement of Oct4 by Tet1 during iPSC Induction Reveals an Important Role of DNA Methylation and Hydroxymethylation in Reprogramming

(2013) Yawei Gao et al.   Cell Stem Cell

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

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

(2013) G. K. Marinov et al.   GENOME RESEARCH

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods

(2013) M. Stevens et al.   GENOME RESEARCH

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain

(2013) Junjie U Guo et al.   NATURE NEUROSCIENCE

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

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

A Single Cell Level Based Method for Copy Number Variation Analysis by Low Coverage Massively Parallel Sequencing

(2013) Chunlei Zhang et al.   PLoS One

Single-Cell DNA-Methylation Analysis Reveals Epigenetic Chimerism in Preimplantation Embryos

(2013) C. Lorthongpanich et al.   SCIENCE

DNA methylation age of human tissues and cell types

(2013) Steve Horvath   GENOME BIOLOGY

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

(2012) A. Kundaje et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Evaluation of single CpG sites as proxies of CpG island methylation states at the genome scale

(2012) Víctor Barrera et al.   NUCLEIC ACIDS RESEARCH

A Comparison of the Whole Genome Approach of MeDIP-Seq to the Targeted Approach of the Infinium HumanMethylation450 BeadChip® for Methylome Profiling

(2012) Christine Clark et al.   PLoS One

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

Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population

(2012) Jordana T. Bell et al.   PLoS Genetics

Cell type-specific DNA methylation at intragenic CpG islands in the immune system

(2011) A. M. Deaton et al.   GENOME RESEARCH

Genome-scale analysis of aberrant DNA methylation in colorectal cancer

(2011) T. Hinoue et al.   GENOME RESEARCH

High density DNA methylation array with single CpG site resolution

(2011) Marina Bibikova et al.   GENOMICS

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

A high-throughput DNA methylation analysis of a single cell

(2011) Martin Kantlehner et al.   NUCLEIC ACIDS RESEARCH

DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time

(2011) Koichiro Nishino et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

(2010) R Alan Harris et al.   NATURE BIOTECHNOLOGY

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils

(2010) Yukio Yasukochi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

(2010) Robert S. Illingworth et al.   PLoS Genetics

Genome-wide screen of promoter methylation identifies novel markers in melanoma

(2009) Y. Koga et al.   GENOME RESEARCH

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

(2009) Akiko Doi et al.   NATURE GENETICS