Bisulfite oligonucleotide-capture sequencing for targeted base- and strand-specific absolute 5-methylcytosine quantitation

Genome-Wide DNA Methylation Profiling Reveals Epigenetic Changes in the Rat Nucleus Accumbens Associated With Cross-Generational Effects of Adolescent THC Exposure

(2015) Corey T Watson et al.   NEUROPSYCHOPHARMACOLOGY

Post-conversion targeted capture of modified cytosines in mammalian and plant genomes

(2015) Qing Li et al.   NUCLEIC ACIDS RESEARCH

Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2

(2015) Benyam Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tet3 mediates stable glucocorticoid-induced alterations in DNA methylation and Dnmt3a/Dkk1 expression in neural progenitors

(2015) R Bose et al.   Cell Death & Disease

2015 Guidelines for Establishing Genetically Modified Rat Models for Cardiovascular Research

(2015) Michael J. Flister et al.   Journal of Cardiovascular Translational Research

Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants

(2015) Fiona Allum et al.   Nature Communications

Targeted DNA Methylation Analysis by Next-generation Sequencing

(2015) Dustin R. Masser et al.   Jove-Journal of Visualized Experiments

Performance comparison of four exome capture systems for deep sequencing

(2014) Chandra Sekhar Chilamakuri et al.   BMC GENOMICS

Accurate mitochondrial DNA sequencing using off-target reads provides a single test to identify pathogenic point mutations

(2014) Helen R. Griffin et al.   GENETICS IN MEDICINE

Methylation levels of the SCD1 gene promoter and LINE-1 repeat region are associated with weight change: An intervention study

(2014) Gracia María Martín-Núñez et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

(2014) Michael J Ziller et al.   NATURE METHODS

The UCSC Genome Browser database: 2015 update

(2014) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Methylation and Gene Expression Changes in Newborn Rats following Maternal Protein Restriction and Reversal by Folic Acid

(2014) Gioia Altobelli et al.   PLoS One

NGSUtils: a software suite for analyzing and manipulating next-generation sequencing datasets

(2013) Marcus R. Breese et al.   BIOINFORMATICS

The Control Region of Mitochondrial DNA Shows an Unusual CpG and Non-CpG Methylation Pattern

(2013) D. Bellizzi et al.   DNA RESEARCH

Regionally Specific and Genome-Wide Analyses Conclusively Demonstrate the Absence of CpG Methylation in Human Mitochondrial DNA

(2013) E. E. Hong et al.   MOLECULAR AND CELLULAR BIOLOGY

In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes

(2013) Maxim Ivanov et al.   NUCLEIC ACIDS RESEARCH

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Finding the lost treasures in exome sequencing data

(2013) David C. Samuels et al.   TRENDS IN GENETICS

Focused, high accuracy 5-methylcytosine quantitation with base resolution by benchtop next-generation sequencing

(2013) Dustin R Masser et al.   Epigenetics & Chromatin

Diametrically opposite methylome-transcriptome relationships in high- and low-CpG promoter genes in postmitotic neural rat tissue

(2012) Theresa Hartung et al.   Epigenetics

DNA methylome analysis using short bisulfite sequencing data

(2012) Felix Krueger et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

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

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Promoter methylation and age-related downregulation of Klotho in rhesus monkey

(2011) Gwendalyn D. King et al.   AGE

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

(2011) Felix Krueger et al.   BIOINFORMATICS

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

(2011) Juan Sandoval et al.   Epigenetics

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Rats!

(2009) P. M. Iannaccone et al.   Disease Models & Mechanisms

The completion of the Mammalian Gene Collection (MGC)

(2009) et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

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