DNA Methylation and Chromatin Organization in Insects: Insights from the Ant Camponotus floridanus

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

A Role for H3K4 Monomethylation in Gene Repression and Partitioning of Chromatin Readers

(2014) Jemmie Cheng et al.   MOLECULAR CELL

Regulation of RNA polymerase II activation by histone acetylation in single living cells

(2014) Timothy J. Stasevich et al.   NATURE

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition

(2013) Alika K Maunakea et al.   CELL RESEARCH

Patterning and Regulatory Associations of DNA Methylation Are Mirrored by Histone Modifications in Insects

(2013) Brendan G. Hunt et al.   Genome Biology and Evolution

The Function of Intragenic DNA Methylation: Insights from Insect Epigenomes

(2013) B. G. Hunt et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Emerging roles for chromatin as a signal integration and storage platform

(2013) Aimee I. Badeaux et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Regulation of nucleosome dynamics by histone modifications

(2013) Gabriel E Zentner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Genome-wide association between DNA methylation and alternative splicing in an invertebrate

(2012) Kevin Flores et al.   BMC GENOMICS

Genome-wide and Caste-Specific DNA Methylomes of the Ants Camponotus floridanus and Harpegnathos saltator

(2012) Roberto Bonasio et al.   CURRENT BIOLOGY

A chromatin link to caste identity in the carpenter ant Camponotus floridanus

(2012) D. F. Simola et al.   GENOME RESEARCH

Set2 methylation of histone H3 lysine 36 suppresses histone exchange on transcribed genes

(2012) Swaminathan Venkatesh et al.   NATURE

Reversible switching between epigenetic states in honeybee behavioral subcastes

(2012) Brian R Herb et al.   NATURE NEUROSCIENCE

Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes

(2012) Devin Coleman-Derr et al.   PLoS Genetics

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao et al.   GENOME BIOLOGY

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates

(2011) L. Nanty et al.   GENOME RESEARCH

DNA methylation in insects: on the brink of the epigenomic era

(2011) K. M. Glastad et al.   INSECT MOLECULAR BIOLOGY

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

(2011) Sanjeev Shukla et al.   NATURE

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

Computational approaches for understanding the evolution of DNA methylation in animals

(2010) Soojin V. Yi et al.   Epigenetics

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Conserved role of intragenic DNA methylation in regulating alternative promoters

(2010) Alika K. Maunakea et al.   NATURE

Genomic Comparison of the Ants Camponotus floridanus and Harpegnathos saltator

(2010) R. Bonasio et al.   SCIENCE

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

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

(2010) Frank Lyko et al.   PLOS BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Modifications of RNA polymerase II are pivotal in regulating gene expression states

(2009) Emily Brookes et al.   EMBO REPORTS

An operational definition of epigenetics

(2009) S. L. Berger et al.   GENES & DEVELOPMENT

Differential chromatin marking of introns and expressed exons by H3K36me3

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

Linking DNA methylation and histone modification: patterns and paradigms

(2009) Howard Cedar et al.   NATURE REVIEWS GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks

(2008) Daniel Zilberman et al.   NATURE

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

Nutritional Control of Reproductive Status in Honeybees via DNA Methylation

(2008) R. Kucharski et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Nucleosome destabilization in the epigenetic regulation of gene expression

(2007) Steven Henikoff   NATURE REVIEWS GENETICS