Using long-read sequencing to detect imprinted DNA methylation

Enhanced JBrowse plugins for epigenomics data visualization

(2018) Brigitte T. Hofmeister et al.   BMC BIOINFORMATICS

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Dynamics of the epigenetic landscape during the maternal-to-zygotic transition

(2018) Melanie A. Eckersley-Maslin et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

DNA Methylation Divergence and Tissue Specialization in the Developing Mouse Placenta

(2017) Benjamin E. Decato et al.   MOLECULAR BIOLOGY AND EVOLUTION

Maternal H3K27me3 controls DNA methylation-independent imprinting

(2017) Azusa Inoue et al.   NATURE

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Mapping DNA methylation with high-throughput nanopore sequencing

(2017) Arthur C Rand et al.   NATURE METHODS

Mapping the mouse Allelome reveals tissue-specific regulation of allelic expression

(2017) Daniel Andergassen et al.   eLife

New Perspectives on Genomic Imprinting, an Essential and Multifaceted Mode of Epigenetic Control in the Developing and Adult Brain

(2016) Julio D. Perez et al.   Annual Review of Neuroscience

Differential methylation analysis for BS-seq data under general experimental design

(2016) Yongseok Park et al.   BIOINFORMATICS

Gtsf1l and Gtsf2 Are Specifically Expressed in Gonocytes and Spermatids but Are Not Essential for Spermatogenesis

(2016) Noriaki Takemoto et al.   PLoS One

Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing

(2016) Andrew Keniry et al.   Epigenetics & Chromatin

Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS)

(2015) Yao Yang et al.   BMC GENOMICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

DNA methylation profiling: comparison of genome-wide sequencing methods and the Infinium Human Methylation 450 Bead Chip

(2015) Denise L Walker et al.   Epigenomics

A Survey of Imprinted Gene Expression in Mouse Trophoblast Stem Cells

(2015) J. Mauro Calabrese et al.   G3-Genes Genomes Genetics

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Maternal bias and escape from X chromosome imprinting in the midgestation mouse placenta

(2014) Elizabeth H. Finn et al.   DEVELOPMENTAL BIOLOGY

The Gpr1/Zdbf2 locus provides new paradigms for transient and dynamic genomic imprinting in mammals

(2014) R. Duffie et al.   GENES & DEVELOPMENT

Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment

(2014) F. Court et al.   GENOME RESEARCH

Genomic Imprinting in Mammals

(2014) D. P. Barlow et al.   Cold Spring Harbor Perspectives in Biology

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

(2013) Y. Liao et al.   BIOINFORMATICS

Coadaptation and conflict, misconception and muddle, in the evolution of genomic imprinting

(2013) D Haig   HEREDITY

RNA sequencing-based identification of aberrant imprinting in cloned mice

(2013) Hiroaki Okae et al.   HUMAN MOLECULAR GENETICS

Smchd1 regulates a subset of autosomal genes subject to monoallelic expression in addition to being critical for X inactivation

(2013) Arne W Mould et al.   Epigenetics & Chromatin

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

A unique regulatory phase of DNA methylation in the early mammalian embryo

(2012) Zachary D. Smith et al.   NATURE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Contribution of Intragenic DNA Methylation in Mouse Gametic DNA Methylomes to Establish Oocyte-Specific Heritable Marks

(2012) Hisato Kobayashi et al.   PLoS Genetics

ggbio: an R package for extending the grammar of graphics for genomic data

(2012) Tengfei Yin et al.   GENOME BIOLOGY

Dominantly Inherited Constitutional Epigenetic Silencing of MLH1 in a Cancer-Affected Family Is Linked to a Single Nucleotide Variant within the 5′UTR

(2011) Megan P. Hitchins et al.   CANCER CELL

A Survey for Novel Imprinted Genes in the Mouse Placenta by mRNA-seq

(2011) Xu Wang et al.   GENETICS

Re-investigation and RNA sequencing-based identification of genes with placenta-specific imprinted expression

(2011) Hiroaki Okae et al.   HUMAN MOLECULAR GENETICS

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

Dynamic CpG island methylation landscape in oocytes and preimplantation embryos

(2011) Sébastien A Smallwood et al.   NATURE GENETICS

Genomic imprinting: the emergence of an epigenetic paradigm

(2011) Anne C. Ferguson-Smith   NATURE REVIEWS GENETICS

WAMIDEX: A web atlas of murine genomic imprinting and differential expression

(2010) Reiner Schulz et al.   Epigenetics

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

The Importance of Imprinting in the Human Placenta

(2010) Jennifer M. Frost et al.   PLoS Genetics

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Allele-specific DNA methylation in mouse strains is mainly determined by cis-acting sequences

(2009) E. Schilling et al.   GENOME RESEARCH

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

Genomic imprinting at the mammalian Dlk1-Dio3 domain

(2008) Simao Teixeira da Rocha et al.   TRENDS IN GENETICS