A comprehensive epigenomic analysis of phenotypically distinguishable, genetically identical female and male Daphnia pulex

Complementary roles of photoperiod and temperature in environmental sex determination in Daphnia spp

(2019) Allison A. Camp et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Use of 5-azacytidine in a proof-of-concept study to evaluate the impact of pre-natal and post-natal exposures, as well as within generation persistent DNA methylation changes in Daphnia

(2018) Camila Gonçalves Athanasio et al.   ECOTOXICOLOGY

Identification of General Patterns of Sex-Biased Expression in Daphnia , a Genus with Environmental Sex Determination

(2018) Cécile Molinier et al.   G3-Genes Genomes Genetics

Histone Modifications: Insights into Their Influence on Gene Expression

(2018) Bruce Stillman   CELL

Pattern of DNA Methylation in Daphnia: Evolutionary Perspective

(2018) Jouni Kvist et al.   Genome Biology and Evolution

When males outlive females: Sex-specific effects of temperature on lifespan in a cyclic parthenogen

(2018) Barbara Pietrzak et al.   Ecology and Evolution

Can epigenetics translate environmental cues into phenotypes?

(2018) Parisa Norouzitallab et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Epigenetic Potential as a Mechanism of Phenotypic Plasticity in Vertebrate Range Expansions

(2017) Holly J. Kilvitis et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

A New Reference Genome Assembly for the Microcrustacean Daphnia pulex

(2017) Zhiqiang Ye et al.   G3-Genes Genomes Genetics

Mapping the expression of the sex determining factor Doublesex1 in Daphnia magna using a knock-in reporter

(2017) Quang Dang Nong et al.   Scientific Reports

Bisulfite Sequencing with Daphnia Highlights a Role for Epigenetics in Regulating Stress Response to Microcystis through Preferential Differential Methylation of Serine and Threonine Amino Acids

(2016) Jana Asselman et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex

(2016) R. T. Raborn et al.   GENETICS

Population Genomics ofDaphnia pulex

(2016) Michael Lynch et al.   GENETICS

Gene Body Methylation Patterns inDaphniaAre Associated with Gene Family Size

(2016) Jana Asselman et al.   Genome Biology and Evolution

De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical ParthenogeneticDaphnia galeata

(2016) Ann Kathrin Huylmans et al.   Genome Biology and Evolution

ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

(2016) Guangchuang Yu et al.   Molecular BioSystems

Population Genomics ofDaphnia pulex

(2016) Michael Lynch et al.   GENETICS

Optimisation of DNA extraction from the crustaceanDaphnia

(2016) Camila Gonçalves Athanasio et al.   PeerJ

Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors

(2016) Luisa Orsini et al.   Scientific Data

Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer

(2016) Stephan H. Bernhart et al.   Scientific Reports

Male meiosis in Crustacea: synapsis, recombination, epigenetics and fertility in Daphnia magna

(2015) Rocío Gómez et al.   CHROMOSOMA

The Reactome pathway Knowledgebase

(2015) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

The ubiquity and ancestry of insect doublesex

(2015) Dana C. Price et al.   Scientific Reports

Functional genomics of acclimation and adaptation in response to thermal stress in Daphnia

(2014) Lev Y Yampolsky et al.   BMC GENOMICS

Poised chromatin in the mammalian germ line

(2014) B. J. Lesch et al.   DEVELOPMENT

Relationship between heat shock protein 70 expression and life span in Daphnia

(2014) Charles Schumpert et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Molecular Chaperone Functions in Protein Folding and Proteostasis

(2013) Yujin E. Kim et al.   Annual Review of Biochemistry

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

A double take on bivalent promoters

(2013) P. Voigt et al.   GENES & DEVELOPMENT

Polycomb-Dependent H3K27me1 and H3K27me2 Regulate Active Transcription and Enhancer Fidelity

(2013) Karin J. Ferrari et al.   MOLECULAR CELL

The evolutionary time machine: using dormant propagules to forecast how populations can adapt to changing environments

(2013) Luisa Orsini et al.   TRENDS IN ECOLOGY & EVOLUTION

The correlation between histone modifications and gene expression

(2013) Xianjun Dong et al.   Epigenomics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

c-Myc Is a Universal Amplifier of Expressed Genes in Lymphocytes and Embryonic Stem Cells

(2012) Zuqin Nie et al.   CELL

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Coordinated histone modifications are associated with gene expression variation within and between species

(2011) M. Ha et al.   GENOME RESEARCH

Differential Levels of Stress Proteins (HSPs) in Male and Female Daphnia magna in Response to Thermal Stress: A Consequence of Sex-Related Behavioral Differences?

(2011) Andrzej Mikulski et al.   JOURNAL OF CHEMICAL ECOLOGY

Diet-switching experiments show rapid accumulation and preferential retention of highly unsaturated fatty acids in Daphnia

(2011) Sami J. Taipale et al.   OIKOS

The Ecoresponsive Genome of Daphnia pulex

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

Environmental Sex Determination in the Branchiopod Crustacean Daphnia magna: Deep Conservation of a Doublesex Gene in the Sex-Determining Pathway

(2011) Yasuhiko Kato et al.   PLoS Genetics

SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures

(2010) Hong-Qiang Wang et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos

(2009) Robert C. Akkers et al.   DEVELOPMENTAL CELL

The Shock of Aging: Molecular Chaperones and the Heat Shock Response in Longevity and Aging – A Mini-Review

(2009) Stuart K. Calderwood et al.   GERONTOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY