Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex

Proteomic analysis of Daphnia magna hints at molecular pathways involved in defensive plastic responses

(2014) Kathrin A Otte et al.   BMC GENOMICS

Genome-Wide Transcription Profiles Reveal Genotype-Dependent Responses of Biological Pathways and Gene-Families in Daphnia Exposed to Single and Mixed Stressors

(2014) Dieter I. M. De Coninck et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

Transcriptomics in the RNA-seq era

(2013) Paul A McGettigan   CURRENT OPINION IN CHEMICAL BIOLOGY

Gene expression profiling of three different stressors in the water flea Daphnia magna

(2013) Mieke Jansen et al.   ECOTOXICOLOGY

Identification of the Precise Kairomone-sensitive Period and Histological Characterization of Necktooth Formation in Predator-induced Polyphenism inDaphnia pulex

(2013) Yuka Naraki et al.   ZOOLOGICAL SCIENCE

The evolution of salinity tolerance inDaphnia: a functional genomics approach

(2012) Leigh C. Latta et al.   ECOLOGY LETTERS

Identification of Pathways, Gene Networks, and Paralogous Gene Families in Daphnia pulex Responding to Exposure to the Toxic Cyanobacterium Microcystis aeruginosa

(2012) Jana Asselman et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Costs of predator-induced morphological defences in Daphnia

(2012) HOWARD P. RIESSEN   FRESHWATER BIOLOGY

Daphnia as a model organism in limnology and aquatic biology: introductory remarks

(2012) Jaromir SEDA et al.   JOURNAL OF LIMNOLOGY

Neckteeth formation in two species of the Daphnia curvirostris complex (Crustacea: Cladocera)

(2012) Petr Jan JURAČKA et al.   JOURNAL OF LIMNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

(2012) Intawat Nookaew et al.   NUCLEIC ACIDS RESEARCH

Chaoborus and Gasterosteus Anti-Predator Responses in Daphnia pulex Are Mediated by Independent Cholinergic and Gabaergic Neuronal Signals

(2012) Linda C. Weiss et al.   PLoS One

Linking genes to communities and ecosystems: Daphnia as an ecogenomic model

(2012) B. E. Miner et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

Determination of mRNA expression of DMRT93B, vitellogenin, and cuticle 12 in Daphnia magna and their biomarker potential for endocrine disruption

(2011) Jungkon Kim et al.   ECOTOXICOLOGY

PREDATOR-INDUCED DEFENSE MAKES DAPHNIA MORE VULNERABLE TO PARASITES

(2011) Mingbo Yin et al.   EVOLUTION

An Integrated Multi-Disciplinary Approach for Studying Multiple Stressors in Freshwater Ecosystems: Daphnia as a Model Organism

(2011) Ianina Altshuler et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Reticulate evolution of the Daphnia pulex complex as revealed by nuclear markers

(2011) ROLAND VERGILINO et al.   MOLECULAR ECOLOGY

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

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Ecological genomics: steps towards unraveling the genetic basis of inducible defenses in Daphnia

(2010) Ralph Tollrian et al.   BMC BIOLOGY

Gene up-regulation in response to predator kairomones in the water flea, Daphnia pulex

(2010) Hitoshi Miyakawa et al.   BMC DEVELOPMENTAL BIOLOGY

Unusual duplication of the insulin-like receptor in the crustacean Daphnia pulex

(2010) Philippe Boucher et al.   BMC EVOLUTIONARY BIOLOGY

Both Noncoding and Protein-Coding RNAs Contribute to Gene Expression Evolution in the Primate Brain

(2010) Courtney C. Babbitt et al.   Genome Biology and Evolution

The Primary Role of Fibrinogen-Related Proteins in Invertebrates Is Defense, Not Coagulation

(2010) Patrick C. Hanington et al.   Journal of Innate Immunity

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME 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

The chemoreceptor genes of the waterflea Daphnia pulex: many Grs but no Ors

(2009) D Carolina Peñalva-Arana et al.   BMC EVOLUTIONARY BIOLOGY

Annotation, phylogenetics, and expression of the nuclear receptors in Daphnia pulex

(2009) Susanne A Thomson et al.   BMC GENOMICS

The components of the Daphnia pulex immune system as revealed by complete genome sequencing

(2009) Seanna J McTaggart et al.   BMC GENOMICS

A "crown of thorns" is an inducible defense that protects Daphnia against an ancient predator

(2009) A. Petrusek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Domain-Based and Family-Specific Sequence Identity Thresholds Increase the Levels of Reliable Protein Function Transfer

(2008) Sarah Addou et al.   JOURNAL OF MOLECULAR BIOLOGY

Daphniacomes of age: an ecological model in the genomic era

(2008) SARAH SCHAACK   MOLECULAR ECOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS