Evolutionary Consequences of DNA Methylation in a Basal Metazoan

Germline DNA methylation in reef corals: patterns and potential roles in response to environmental change

(2016) James L. Dimond et al.   MOLECULAR ECOLOGY

A Comprehensive Analysis of Codon Usage Patterns in Blunt Snout Bream (Megalobrama amblycephala) Based on RNA-Seq Data

(2015) Xiaoke Duan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

(2015) Tuncay Baubec et al.   NATURE

Genome-wide patterns and properties of de novo mutations in humans

(2015) Laurent C Francioli et al.   NATURE GENETICS

CG gene body DNA methylation changes and evolution of duplicated genes in cassava

(2015) Haifeng Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic determinants of coral heat tolerance across latitudes

(2015) G. B. Dixon et al.   SCIENCE

On the presence and role of human gene-body DNA methylation

(2015) Daudi Jjingo et al.   Oncotarget

Cytosine DNA Methylation Is Found in Drosophila melanogaster but Absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Other Yeast Species

(2014) Floriana Capuano et al.   ANALYTICAL CHEMISTRY

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute

(2014) DA Willette et al.   BULLETIN OF MARINE SCIENCE

Gene expression profiles during short-term heat stress in the red sea coralStylophora pistillata

(2014) Keren Maor-Landaw et al.   GLOBAL CHANGE BIOLOGY

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

(2014) Peng Cui et al.   GENOME BIOLOGY

Synonymous codon usage bias is correlative to intron number and shows disequilibrium among exons in plants

(2013) Zhen Qin et al.   BMC GENOMICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides ) from different thermal environments

(2013) C. D. Kenkel et al.   MOLECULAR ECOLOGY

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

(2013) Henrik Nordberg et al.   NUCLEIC ACIDS RESEARCH

Gene body methylation is conserved between plant orthologs and is of evolutionary consequence

(2013) S. Takuno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identical sets of methylated and nonmethylated genes in Ciona intestinalis sperm and muscle cells

(2013) Miho M Suzuki et al.   Epigenetics & Chromatin

Function and Evolution of DNA Methylation in Nasonia vitripennis

(2013) Xu Wang et al.   PLoS Genetics

Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc

(2013) Mackenzie R. Gavery et al.   PeerJ

Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes

(2012) Susanta K. Behura et al.   BIOLOGICAL REVIEWS

Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression

(2012) Xin Li et al.   BMC GENOMICS

PcarnBase: Development of a Transcriptomic Database for the Brain Coral Platygyra carnosus

(2012) Jin Sun et al.   MARINE BIOTECHNOLOGY

The Evolution of Invertebrate Gene Body Methylation

(2012) S. Sarda et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole Transcriptome Analysis of the CoralAcropora milleporaReveals Complex Responses to CO2-driven Acidification during the Initiation of Calcification

(2012) A. MOYA et al.   MOLECULAR ECOLOGY

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

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

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

Production of a reference transcriptome and transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis

(2011) Nikki Traylor-Knowles et al.   BMC GENOMICS

Factors that Contribute to Variation in Evolutionary Rate among Arabidopsis Genes

(2011) L. Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative Analyses of DNA Methylation and Sequence Evolution Using Nasonia Genomes

(2011) J. Park et al.   MOLECULAR BIOLOGY AND EVOLUTION

Body-Methylated Genes in Arabidopsis thaliana Are Functionally Important and Evolve Slowly

(2011) S. Takuno et al.   MOLECULAR BIOLOGY AND EVOLUTION

Using the Acropora digitifera genome to understand coral responses to environmental change

(2011) Chuya Shinzato et al.   NATURE

Gene Discovery in the Threatened Elkhorn Coral: 454 Sequencing of the Acropora palmata Transcriptome

(2011) Nicholas R. Polato et al.   PLoS One

DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas)

(2010) Mackenzie R Gavery et al.   BMC GENOMICS

Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex

(2010) Assaf Zemach et al.   CURRENT BIOLOGY

Functional Conservation of DNA Methylation in the Pea Aphid and the Honeybee

(2010) Brendan G. Hunt et al.   Genome Biology and Evolution

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

(2010) R Alan Harris et al.   NATURE BIOTECHNOLOGY

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

A Comprehensive Phylogenetic Analysis of the Scleractinia (Cnidaria, Anthozoa) Based on Mitochondrial CO1 Sequence Data

(2010) Marcelo V. Kitahara et al.   PLoS One

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

Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont

(2009) Shinichi Sunagawa et al.   BMC GENOMICS

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

The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana

(2008) Felipe F Aceituno et al.   BMC GENOMICS

Coral Life History and Symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata

(2008) Jodi A Schwarz et al.   BMC GENOMICS

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL