NGSmethDB 2017: enhanced methylomes and differential methylation

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

(2016) Kun Qu et al.   NATURE METHODS

Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome

(2016) Junchen Gu et al.   G3-Genes Genomes Genetics

Roadmap for regulation

(2015) Casey E. Romanoski et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors

(2015) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Targeted deep DNA methylation analysis of circulating cell-free DNA in plasma using massively parallel semiconductor sequencing

(2015) Felipe Vaca-Paniagua et al.   Epigenomics

Extending reference assembly models

(2015) Deanna M Church et al.   GENOME BIOLOGY

Epigenome-wide association of DNA methylation markers in peripheral blood from Indian Asians and Europeans with incident type 2 diabetes: a nested case-control study

(2015) John C Chambers et al.   Lancet Diabetes & Endocrinology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

MOABS: model based analysis of bisulfite sequencing data

(2014) Deqiang Sun et al.   GENOME BIOLOGY

BSeQC: quality control of bisulfite sequencing experiments

(2013) Xueqiu Lin et al.   BIOINFORMATICS

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

(2013) B. J. Raney et al.   BIOINFORMATICS

DNA methylation contributes to natural human variation

(2013) H. Heyn et al.   GENOME RESEARCH

Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening

(2013) Silin Zhong et al.   NATURE BIOTECHNOLOGY

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer

(2013) Christoph Plass et al.   NATURE REVIEWS GENETICS

NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes

(2013) Stefanie Geisen et al.   NUCLEIC ACIDS RESEARCH

PEpiD: A Prostate Epigenetic Database in Mammals

(2013) Jiejun Shi et al.   PLoS One

CMS: A Web-Based System for Visualization and Analysis of Genome-Wide Methylation Data of Human Cancers

(2013) Fei Gu et al.   PLoS One

A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics

(2013) Qiang Song et al.   PLoS One

Base-Resolution Analyses of Sequence and Parent-of-Origin Dependent DNA Methylation in the Mouse Genome

(2012) Wei Xie et al.   CELL

Segmentation of time series with long-range fractal correlations

(2012) P. Bernaola-Galván et al.   EUROPEAN PHYSICAL JOURNAL B

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

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Altuna Akalin et al.   GENOME BIOLOGY

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

(2011) Felix Krueger et al.   BIOINFORMATICS

CpG islands and the regulation of transcription

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

The Dinucleotide CG as a Genomic Signalling Module

(2011) Adrian Bird   JOURNAL OF MOLECULAR BIOLOGY

Putting the DNA back into DNA methylation

(2011) Adrian Bird   NATURE GENETICS

MethylomeDB: a database of DNA methylation profiles of the brain

(2011) Yurong Xin et al.   NUCLEIC ACIDS RESEARCH

DiseaseMeth: a human disease methylation database

(2011) J. Lv et al.   NUCLEIC ACIDS RESEARCH

Genome-wide quantitative assessment of variation in DNA methylation patterns

(2011) Hehuang Xie et al.   NUCLEIC ACIDS RESEARCH

High-level organization of isochores into gigantic superstructures in the human genome

(2011) P. Carpena et al.   PHYSICAL REVIEW E

Prediction of CpG-island function: CpG clustering vs. sliding-window methods

(2010) Michael Hackenberg et al.   BMC GENOMICS

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data

(2010) M. Hackenberg et al.   NUCLEIC ACIDS RESEARCH

Epigenetic mechanisms and genome stability

(2010) Emily L. Putiri et al.   Clinical Epigenetics

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

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

Genome-wide high throughput analysis of DNA methylation in eukaryotes

(2008) Kyle R. Pomraning et al.   METHODS