Integration of DNA methylation and gene transcription across nineteen cell types reveals cell type-specific and genomic region-dependent regulatory patterns

DNA methylation dynamics: identification and functional annotation

(2016) Hongbo Liu et al.   Briefings in Functional Genomics

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

Bayesian analysis of multi-type recurrent events and dependent termination with nonparametric covariate functions

(2015) Li-An Lin et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

Intermediate DNA methylation is a conserved signature of genome regulation

(2015) GiNell Elliott et al.   Nature Communications

CGMD: An integrated database of cancer genes and markers

(2015) Jangampalli Adi Pradeepkiran et al.   Scientific Reports

MCMCpack: Markov Chain Monte Carlo inR

(2015) Andrew D. Martin et al.   Journal of Statistical Software

DNMT3A Arg882 mutation drives chronic myelomonocytic leukemia through disturbing gene expression/DNA methylation in hematopoietic cells

(2014) J. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer

(2014) Christopher J. Kemp et al.   Cell Reports

Pan-cancer patterns of DNA methylation

(2014) Tania Witte et al.   Genome Medicine

Detection of significantly differentially methylated regions in targeted bisulfite sequencing data

(2013) Katja Hebestreit et al.   BIOINFORMATICS

DNA Methylation of Transcriptional Enhancers and Cancer Predisposition

(2013) Dvir Aran et al.   CELL

Dynamic DNA methylation across diverse human cell lines and tissues

(2013) K. E. Varley et al.   GENOME RESEARCH

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Individual and combined effects of DNA methylation and copy number alterations on miRNA expression in breast tumors

(2013) Miriam Aure et al.   GENOME BIOLOGY

Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia

(2013) Jessica Nordlund et al.   GENOME BIOLOGY

DNA methylation arrays as surrogate measures of cell mixture distribution

(2012) Eugene Houseman et al.   BMC BIOINFORMATICS

DNA methylation profiling in breast cancer discordant identical twins identifies DOK7 as novel epigenetic biomarker

(2012) H. Heyn et al.   CARCINOGENESIS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The ENCODE project

(2012) Natalie de Souza   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

TSGene: a web resource for tumor suppressor genes

(2012) Min Zhao et al.   NUCLEIC ACIDS RESEARCH

ENCODE Project Writes Eulogy for Junk DNA

(2012) E. Pennisi   SCIENCE

Hierarchical Modularity in ERα Transcriptional Network Is Associated with Distinct Functions and Implicates Clinical Outcomes

(2012) Binhua Tang et al.   Scientific Reports

DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation

(2012) Yongheng Chen et al.   Cell Reports

DNA methylation signatures for breast cancer classification and prognosis

(2012) Moshe Szyf   Genome Medicine

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

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips

(2012) Jovana Maksimovic 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

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

High density DNA methylation array with single CpG site resolution

(2011) Marina Bibikova et al.   GENOMICS

CTCF-mediated functional chromatin interactome in pluripotent cells

(2011) Lusy Handoko et al.   NATURE GENETICS

QDMR: a quantitative method for identification of differentially methylated regions by entropy

(2011) Yan Zhang et al.   NUCLEIC ACIDS RESEARCH

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

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

(2010) R Alan Harris et al.   NATURE BIOTECHNOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

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