Semiconductor-based sequencing of genome-wide DNA methylation states

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

Comprehensive analysis of DNA methylation data with RnBeads

(2014) Yassen Assenov et al.   NATURE METHODS

Performance Comparison between Rapid Sequencing Platforms for Ultra-Low Coverage Sequencing Strategy

(2014) Shengpei Chen et al.   PLoS One

RNA-Seq Based Transcriptome Analysis of Hepatitis E Virus (HEV) and Hepatitis B Virus (HBV) Replicon Transfected Huh-7 Cells

(2014) Neetu Jagya et al.   PLoS One

Increased binding of MeCP2 to the GAD1 and RELN promoters may be mediated by an enrichment of 5-hmC in autism spectrum disorder (ASD) cerebellum

(2014) A Zhubi et al.   Translational Psychiatry

MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments

(2013) Matthias Lienhard et al.   BIOINFORMATICS

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition

(2013) Alika K Maunakea et al.   CELL RESEARCH

DNA modifications repaired by base excision repair are epigenetic

(2013) Stephen P.G. Moore et al.   DNA REPAIR

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

(2013) M. Stevens et al.   GENOME RESEARCH

Assessing the Fecal Microbiota: An Optimized Ion Torrent 16S rRNA Gene-Based Analysis Protocol

(2013) Christian Milani et al.   PLoS One

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Methylation of Histone H3 on Lysine 79 Associates with a Group of Replication Origins and Helps Limit DNA Replication Once per Cell Cycle

(2013) Haiqing Fu et al.   PLoS Genetics

Genome-wide incorporation dynamics reveal distinct categories of turnover for the histone variant H3.3

(2013) Daniel C Kraushaar et al.   GENOME BIOLOGY

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Progress in Ion Torrent semiconductor chip based sequencing

(2012) Barry Merriman et al.   ELECTROPHORESIS

Ion Torrent Personal Genome Machine Sequencing for Genomic Typing of Neisseria meningitidis for Rapid Determination of Multiple Layers of Typing Information

(2012) Ulrich Vogel et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Methylome analysis using MeDIP-seq with low DNA concentrations

(2012) Oluwatosin Taiwo et al.   Nature Protocols

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

The Dynamics of DNA Methylation in Schizophrenia and Related Psychiatric Disorders

(2012) Dennis R Grayson et al.   NEUROPSYCHOPHARMACOLOGY

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

Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias

(2011) Shalima S. Nair et al.   Epigenetics

Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome

(2011) Juan Sandoval et al.   Epigenetics

CpG islands and the regulation of transcription

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

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

(2011) Gabriella Ficz et al.   NATURE

An integrated semiconductor device enabling non-optical genome sequencing

(2011) Jonathan M. Rothberg et al.   NATURE

5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging

(2011) Keith E Szulwach et al.   NATURE NEUROSCIENCE

Genomic mapping of 5-hydroxymethylcytosine in the human brain

(2011) Seung-Gi Jin et al.   NUCLEIC ACIDS RESEARCH

Evaluation of the Infinium Methylation 450K technology

(2011) Sarah Dedeurwaerder et al.   Epigenomics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Epigenome Mapping in Normal and Disease States

(2010) Alika K. Maunakea et al.   CIRCULATION RESEARCH

Epigenetic Modifications in Double-Strand Break DNA Damage Signaling and Repair

(2010) D. Rossetto et al.   CLINICAL CANCER RESEARCH

Conserved role of intragenic DNA methylation in regulating alternative promoters

(2010) Alika K. Maunakea et al.   NATURE

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Contrasting chromatin organization of CpG islands and exons in the human genome

(2010) Jung Kyoon Choi   GENOME BIOLOGY

Finding the fifth base: Genome-wide sequencing of cytosine methylation

(2009) R. Lister et al.   GENOME RESEARCH

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

(2009) Rafael A Irizarry et al.   NATURE GENETICS

MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome

(2009) David Serre et al.   NUCLEIC ACIDS RESEARCH

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY