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

Gene Body Methylation Patterns inDaphniaAre Associated with Gene Family Size

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

TransRate: reference-free quality assessment of de novo transcriptome assemblies

(2016) Richard Smith-Unna et al.   GENOME RESEARCH

Evolving Perspectives on Monopolization and Priority Effects

(2016) Luc De Meester et al.   TRENDS IN ECOLOGY & EVOLUTION

Fast turnover of genome transcription across evolutionary time exposes entire non-coding DNA to de novo gene emergence

(2016) Rafik Neme et al.   eLife

Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome

(2016) Loren A. Honaas et al.   PLoS One

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

NMDA receptor activation upstream of methyl farnesoate signaling for short day-induced male offspring production in the water flea, Daphnia pulex

(2015) Kenji Toyota et al.   BMC GENOMICS

Males on demand: the environmental-neuro-endocrine control of male sex determination in daphnids

(2015) Gerald A. LeBlanc et al.   FEBS Journal

Variation in the X:Autosome Distribution of Male-Biased Genes amongDrosophila melanogasterTissues and Its Relationship with Dosage Compensation

(2015) Ann Kathrin Huylmans et al.   Genome Biology and Evolution

Methyl farnesoate synthesis is necessary for the environmental sex determination in the water flea Daphnia pulex

(2015) Kenji Toyota et al.   JOURNAL OF INSECT PHYSIOLOGY

Correction: Transcriptome Analysis of Resistant and Susceptible Alfalfa Cultivars Infected With Root-Knot Nematode Meloidogyne incognita

(2015)   PLoS One

Cloning and expression analysis of a transformer gene in Daphnia pulex during different reproduction stages

(2014) Ping Chen et al.   ANIMAL REPRODUCTION SCIENCE

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Sex-lethal gene of the Chinese mitten crab Eriocheir sinensis: cDNA cloning, induction by eyestalk ablation, and expression of two splice variants in males and females

(2014) Huaishun Shen et al.   DEVELOPMENT GENES AND EVOLUTION

Combining Transcriptome Assemblies from Multiple De Novo Assemblers in the Allo-Tetraploid Plant Nicotiana benthamiana

(2014) Kenlee Nakasugi et al.   PLoS One

Comparison of JH signaling in insects and crustaceans

(2014) Hitoshi Miyakawa et al.   Current Opinion in Insect Science

NextGenMap: fast and accurate read mapping in highly polymorphic genomes

(2013) Fritz J. Sedlazeck et al.   BIOINFORMATICS

Function, diversity, and application of insect juvenile hormone epoxidases (CYP15)

(2013) Takaaki Daimon et al.   BIOTECHNOLOGY AND APPLIED BIOCHEMISTRY

Molecular cloning of doublesex genes of four cladocera (water flea) species

(2013) Kenji Toyota et al.   BMC GENOMICS

The time- and age-dependent effects of the juvenile hormone analog pesticide, pyriproxyfen on Daphnia magna reproduction

(2013) Gautam K. Ginjupalli et al.   CHEMOSPHERE

The evolutionary causes and consequences of sex-biased gene expression

(2013) John Parsch et al.   NATURE REVIEWS GENETICS

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

FlyBase 102—advanced approaches to interrogating FlyBase

(2013) Susan E. St. Pierre et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

A Transgenerational Endocrine Signaling Pathway in Crustacea

(2013) Gerald A. LeBlanc et al.   PLoS One

Masculinization of the X Chromosome in the Pea Aphid

(2013) Julie Jaquiéry et al.   PLoS Genetics

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Simplification and Desexualization of Gene Expression in Self-Fertile Nematodes

(2012) Cristel G. Thomas et al.   CURRENT BIOLOGY

Disentangling the relationship between sex-biased gene expression and X-linkage

(2012) R. P. Meisel et al.   GENOME RESEARCH

OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

(2012) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) T. Magoc et al.   BIOINFORMATICS

Growing large and bulky in the presence of the enemy: Daphnia magna gradually switches the mode of inducible morphological defences

(2011) Max Rabus et al.   FUNCTIONAL ECOLOGY

The Resolution of Sexual Antagonism by Gene Duplication

(2011) T. Connallon et al.   GENETICS

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

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

Sequence divergence and expression of a transformer gene in the branchiopod crustacean, Daphnia magna

(2010) Yasuhiko Kato et al.   GENOMICS

Clonal diversity, clonal persistence and rapid taxon replacement in natural populations of species and hybrids of the Daphnia longispina complex

(2010) MINGBO YIN et al.   MOLECULAR ECOLOGY

Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species

(2010) J. H. Werren et al.   SCIENCE

KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies

(2010) Dapeng Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Evolution of Sex-Dependent Gene Expression in Three Recently Diverged Species of Drosophila

(2009) Z.-F. Jiang et al.   GENETICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Relative importance of different dispersal vectors for small aquatic invertebrates in a rock pool metacommunity

(2008) Bram Vanschoenwinkel et al.   ECOGRAPHY

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Evolution of protein-coding genes in Drosophila

(2008) Amanda M. Larracuente et al.   TRENDS IN GENETICS