QSER1 protects DNA methylation valleys from de novo methylation

Genome-scale screens identify JNK–JUN signaling as a barrier for pluripotency exit and endoderm differentiation

(2019) Qing V. Li et al.   NATURE GENETICS

A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice

(2019) Gintarė Sendžikaitė et al.   Nature Communications

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

DNA Methylation: Shared and Divergent Features across Eukaryotes

(2019) Robert J. Schmitz et al.   TRENDS IN GENETICS

EGR1 recruits TET1 to shape the brain methylome during development and upon neuronal activity

(2019) Zhixiong Sun et al.   Nature Communications

Impact of epigenetics in aging and age related neurodegenerative diseases

(2018) Omkaram Gangisetty   Frontiers in Bioscience-Landmark

De novo apparent loss-of-function mutations in PRR12 in three patients with intellectual disability and iris abnormalities

(2018) Magalie S. Leduc et al.   HUMAN GENETICS

Bcor insufficiency promotes initiation and progression of myelodysplastic syndrome

(2018) Shiro Tara et al.   BLOOD

Identification of Novel Candidate Markers of Type 2 Diabetes and Obesity in Russia by Exome Sequencing with a Limited Sample Size

(2018) Yury Barbitoff et al.   Genes

Gain-of-function DNMT3A mutations cause microcephalic dwarfism and hypermethylation of Polycomb-regulated regions

(2018) Patricia Heyn et al.   NATURE GENETICS

Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps

(2018) Anubha Mahajan et al.   NATURE GENETICS

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells

(2017) Nipun Verma et al.   NATURE GENETICS

Dynamic epigenomic landscapes during early lineage specification in mouse embryos

(2017) Yu Zhang et al.   NATURE GENETICS

TET-mediated active DNA demethylation: mechanism, function and beyond

(2017) Xiaoji Wu et al.   NATURE REVIEWS GENETICS

Genome Editing of Lineage Determinants in Human Pluripotent Stem Cells Reveals Mechanisms of Pancreatic Development and Diabetes

(2016) Zengrong Zhu et al.   Cell Stem Cell

Role of TET enzymes in DNA methylation, development, and cancer

(2016) Kasper Dindler Rasmussen et al.   GENES & DEVELOPMENT

A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations

(2016) Dali Han et al.   MOLECULAR CELL

TET-mediated DNA demethylation controls gastrulation by regulating Lefty–Nodal signalling

(2016) Hai-Qiang Dai et al.   NATURE

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Epigenetics and Human Disease

(2016) Huda Y. Zoghbi et al.   Cold Spring Harbor Perspectives in Biology

Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer

(2016) Stephan H. Bernhart et al.   Scientific Reports

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Tracing Dynamic Changes of DNA Methylation at Single-Cell Resolution

(2015) Yonatan Stelzer et al.   CELL

Tet1 and Tet2 Protect DNA Methylation Canyons against Hypermethylation

(2015) Laura Wiehle et al.   MOLECULAR AND CELLULAR BIOLOGY

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells

(2015) Jing Liao et al.   NATURE GENETICS

FBXL10 protects Polycomb-bound genes from hypermethylation

(2015) Mathieu Boulard et al.   NATURE GENETICS

A de novo t(10;19)(q22.3;q13.33) leads to ZMIZ1/PRR12 reciprocal fusion transcripts in a girl with intellectual disability and neuropsychiatric alterations

(2015) Carlos Córdova-Fletes et al.   NEUROGENETICS

Epigenomic evolution in diffuse large B-cell lymphomas

(2015) Heng Pan et al.   Nature Communications

PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells

(2015) Partha Pratim Das et al.   Cell Reports

An iCRISPR Platform for Rapid, Multiplexable, and Inducible Genome Editing in Human Pluripotent Stem Cells

(2014) Federico González et al.   Cell Stem Cell

Loss of Tet Enzymes Compromises Proper Differentiation of Embryonic Stem Cells

(2014) Meelad M. Dawlaty et al.   DEVELOPMENTAL CELL

Role of Tet proteins in enhancer activity and telomere elongation

(2014) Falong Lu et al.   GENES & DEVELOPMENT

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

A double take on bivalent promoters

(2013) P. Voigt et al.   GENES & DEVELOPMENT

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

NANOG-dependent function of TET1 and TET2 in establishment of pluripotency

(2013) Yael Costa et al.   NATURE

Large conserved domains of low DNA methylation maintained by Dnmt3a

(2013) Mira Jeong et al.   NATURE GENETICS

DNA methylation: roles in mammalian development

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

Coordinate Regulation of DNA Methylation and H3K27me3 in Mouse Embryonic Stem Cells

(2013) James A. Hagarman et al.   PLoS One

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

(2013) Hannah K Long et al.   eLife

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains

(2010) V. K. Rakyan et al.   GENOME RESEARCH

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine

(2010) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

Genomewide association study for onset age in Parkinson disease

(2009) Jeanne C Latourelle et al.   BMC Medical Genetics

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY