Evaluation of whole-genome DNA methylation sequencing library preparation protocols

Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing

(2019) Li Zhou et al.   Scientific Reports

DNA methylation loss in late-replicating domains is linked to mitotic cell division

(2018) Wanding Zhou et al.   NATURE GENETICS

Guidelines for whole genome bisulphite sequencing of intact and FFPET DNA on the Illumina HiSeq X Ten

(2018) Shalima S. Nair et al.   Epigenetics & Chromatin

Sensitive tumour detection and classification using plasma cell-free DNA methylomes

(2018) Shu Yi Shen et al.   NATURE

The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia

(2017) Maria Tiana et al.   NUCLEIC ACIDS RESEARCH

High grade serous ovarian carcinomas originate in the fallopian tube

(2017) S. Intidhar Labidi-Galy et al.   Nature Communications

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Quantitative comparison of DNA methylation assays for biomarker development and clinical applications

(2016) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Non-CG Methylation in the Human Genome

(2015) Yupeng He et al.   Annual Review of Genomics and Human Genetics

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

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

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Predicting the molecular complexity of sequencing libraries

(2013) Timothy Daley et al.   NATURE METHODS

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

(2012) Gilad Landan et al.   NATURE GENETICS

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging

(2012) Fumihito Miura et al.   NUCLEIC ACIDS RESEARCH

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE