Intronic Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees

RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee

(2013) H. Li-Byarlay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

(2012) Miao Yu et al.   CELL

DNA methylome analysis using short bisulfite sequencing data

(2012) Felix Krueger et al.   NATURE METHODS

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

(2012) M. Lohse et al.   NUCLEIC ACIDS RESEARCH

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

(2012) M. J. Booth et al.   SCIENCE

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids

(2011) Lakshminarayan M. Iyer et al.   CELL CYCLE

Cell Fate Potential of Human Pluripotent Stem Cells Is Encoded by Histone Modifications

(2011) Seok-Ho Hong et al.   Cell Stem Cell

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells

(2011) H. Wu et al.   GENES & DEVELOPMENT

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams et al.   NATURE

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

(2011) William A. Pastor et al.   NATURE

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

(2011) Gabriella Ficz et al.   NATURE

Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons

(2011) Violaine Saint-André et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Comparative characterization of the PvuRts1I family of restriction enzymes and their application in mapping genomic 5-hydroxymethylcytosine

(2011) Hua Wang et al.   NUCLEIC ACIDS RESEARCH

Characterization of PvuRts1I endonuclease as a tool to investigate genomic 5–hydroxymethylcytosine

(2011) Aleksandra Szwagierczak et al.   NUCLEIC ACIDS RESEARCH

Insects as innovative models for functional studies of DNA methylation

(2011) Frank Lyko et al.   TRENDS IN GENETICS

A comparative analysis of DNA methylation across human embryonic stem cell lines

(2011) Pao-Yang Chen et al.   GENOME BIOLOGY

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

(2010) Heng Li et al.   BIOINFORMATICS

dumpyinteracts with a large number of genes in the developing wing ofDrosophila melanogaster

(2010) Amber Carmon et al.   FLY

Developmental origins of disruptive behaviour problems: the ‘original sin’ hypothesis, epigenetics and their consequences for prevention

(2010) Richard E. Tremblay   JOURNAL OF CHILD PSYCHOLOGY AND PSYCHIATRY

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers

(2010) Frank Lyko et al.   PLOS BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Epigenetic regulation of the honey bee transcriptome: unravelling the nature of methylated genes

(2009) Sylvain Foret et al.   BMC GENOMICS

In Silico Prediction of Two Classes of Honeybee Genes with CpG Deficiency or CpG Enrichment and Sorting According to Gene Ontology Classes

(2009) Yong Wang et al.   JOURNAL OF MOLECULAR EVOLUTION

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

Control of alternative splicing through siRNA-mediated transcriptional gene silencing

(2009) Mariano Alló et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Honey bee aggression supports a link between gene regulation and behavioral evolution

(2009) C. Alaux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA methylation is widespread and associated with differential gene expression in castes of the honeybee, Apis mellifera

(2009) N. Elango et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing

(2009) I. E. Schor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Genome-wide high throughput analysis of DNA methylation in eukaryotes

(2008) Kyle R. Pomraning et al.   METHODS

Nutritional Control of Reproductive Status in Honeybees via DNA Methylation

(2008) R. Kucharski et al.   SCIENCE

Oxytocin, Vasopressin, and the Neurogenetics of Sociality

(2008) Z. R. Donaldson et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY