Characterization of H3K9me3 and DNA methylation co-marked CpG-rich regions during mouse development

Allele-specific H3K9me3 and DNA methylation co-marked CpG-rich regions serve as potential imprinting control regions in pre-implantation embryo

(2022) Hui Yang et al.   NATURE CELL BIOLOGY

Dnmt1 has de novo activity targeted to transposable elements

(2021) Chuck Haggerty et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Interplay between chromatin marks in development and disease

(2021) Sanne M. Janssen et al.   NATURE REVIEWS GENETICS

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing

(2020) Kenjiro Shirane et al.   NATURE GENETICS

Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data

(2020) Wanqing Shao et al.   GENOME RESEARCH

Heterochromatin drives compartmentalization of inverted and conventional nuclei

(2019) Martin Falk et al.   NATURE

Roles and regulation of histone methylation in animal development

(2019) Ashwini Jambhekar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

The diverse roles of DNA methylation in mammalian development and disease

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

Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation

(2019) Soichiro Yamanaka et al.   DEVELOPMENTAL CELL

Distinct H3K9me3 and DNA methylation modifications during mouse spermatogenesis

(2019) Yingdong Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DNA sequence-dependent chromatin architecture and nuclear hubs formation

(2019) Kamel Jabbari et al.   Scientific Reports

Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development

(2018) Chenfei Wang et al.   NATURE CELL BIOLOGY

Individual retrotransposon integrants are differentially controlled by KZFP/KAP1-dependent histone methylation, DNA methylation and TET-mediated hydroxymethylation in naïve embryonic stem cells

(2018) Andrea Coluccio et al.   Epigenetics & Chromatin

Epigenetic reprogramming enables the transition from primordial germ cell to gonocyte

(2018) Peter W. S. Hill et al.   NATURE

Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis

(2018) Rongbin Zheng et al.   NUCLEIC ACIDS RESEARCH

The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis

(2017) Issam Aldiri et al.   NEURON

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

TACO produces robust multisample transcriptome assemblies from RNA-seq

(2016) Yashar S Niknafs et al.   NATURE METHODS

Erratum: Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse

(2016) Shenglin Mei et al.   NUCLEIC ACIDS RESEARCH

SCML2 Establishes the Male Germline Epigenome through Regulation of Histone H2A Ubiquitination

(2015) Kazuteru Hasegawa et al.   DEVELOPMENTAL CELL

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan et al.   NUCLEIC ACIDS RESEARCH

Performance of genetic programming optimised Bowtie2 on genome comparison and analytic testing (GCAT) benchmarks

(2015) W B Langdon   BioData Mining

Setdb1is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells

(2014) Sheng Liu et al.   GENES & DEVELOPMENT

Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1

(2014) D. Leung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MOABS: model based analysis of bisulfite sequencing data

(2014) Deqiang Sun et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence

(2012) Y. Liu et al.   GENES & DEVELOPMENT

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs

(2011) Mohammad M. Karimi et al.   Cell Stem Cell

In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions

(2011) Simon Quenneville et al.   MOLECULAR CELL

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

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

(2009) Da Wei Huang et al.   Nature Protocols

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY