Analysis of DNA Methylation and Hydroxymethylation in the Genome of Crustacean Daphnia pulex

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TGF-β induces global changes in DNA methylation during the epithelial-to-mesenchymal transition in ovarian cancer cells

(2014) Horacio Cardenas et al.   Epigenetics

Lineage-specific expansions of TET/JBP genes and a new class of DNA transposons shape fungal genomic and epigenetic landscapes

(2014) Lakshminarayan M. Iyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain

(2014) Lu Wen et al.   GENOME BIOLOGY

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Epigenetic memory of environmental organisms: A reflection of lifetime stressor exposures

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The developmental control of size in insects

(2013) H. Frederik Nijhout et al.   Wiley Interdisciplinary Reviews-Developmental Biology

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

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TAp73 depletion accelerates aging through metabolic dysregulation

(2012) A. Rufini et al.   GENES & DEVELOPMENT

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

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

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

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

TGF-β Regulates DNA Methyltransferase Expression in Prostate Cancer, Correlates with Aggressive Capabilities, and Predicts Disease Recurrence

(2011) Qiang Zhang et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

The Ecoresponsive Genome of Daphnia pulex

(2011) J. K. Colbourne et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Predator-induced defences in Daphnia pulex: Selection and evaluation of internal reference genes for gene expression studies with real-time PCR

(2010) Katina I Spanier et al.   BMC MOLECULAR BIOLOGY

Aphid wing dimorphisms: linking environmental and genetic control of trait variation

(2010) Jennifer A. Brisson   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A gene catalogue for post-diapause development of an anhydrobiotic arthropod Artemia franciscana

(2009) Wie-Hua Chen et al.   BMC GENOMICS

Comparative metagenomics of Daphnia symbionts

(2009) Weihong Qi et al.   BMC GENOMICS

Quantitative DNA-methylation in Daphnia magna and effects of multigeneration Zn exposure

(2009) M.B. Vandegehuchte et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY

Occurrence of DNA methylation in Daphnia magna and influence of multigeneration Cd exposure

(2009) Michiel B. Vandegehuchte et al.   ENVIRONMENT INTERNATIONAL

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

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Model-based Analysis of ChIP-Seq (MACS)

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