The red coral (Corallium rubrum ) transcriptome: a new resource for population genetics and local adaptation studies

Gonad transcriptome analysis of pearl oyster Pinctada margaritifera: identification of potential sex differentiation and sex determining genes

(2014) Vaihiti Teaniniuraitemoana et al.   BMC GENOMICS

Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian

(2014) Derek J Stefanik et al.   BMC GENOMICS

Observing mixed layer depth, nitrate and chlorophyll concentrations in the northwestern Mediterranean: A combined satellite and NO3 profiling floats experiment

(2014) Fabrizio D'Ortenzio et al.   GEOPHYSICAL RESEARCH LETTERS

Comparative population genomics in animals uncovers the determinants of genetic diversity

(2014) J. Romiguier et al.   NATURE

Transcriptome Analysis of the Scleractinian Coral Stylophora pistillata

(2014) Sarit Karako-Lampert et al.   PLoS One

Mechanisms of reef coral resistance to future climate change

(2014) S. R. Palumbi et al.   SCIENCE

Translational environmental biology: cell biology informing conservation

(2014) Nikki Traylor-Knowles et al.   TRENDS IN CELL BIOLOGY

Cnidarian phylogenetic relationships as revealed by mitogenomics

(2013) Ehsan Kayal et al.   BMC EVOLUTIONARY BIOLOGY

Genotype – environment correlations in corals from the Great Barrier Reef

(2013) Petra Lundgren et al.   BMC GENETICS

Adaptive abilities of the Mediterranean red coral Corallium rubrum in a heterogeneous and changing environment: from population to functional genetics

(2013) A. Haguenauer et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Diagnostic gene expression biomarkers of coral thermal stress

(2013) C. D. Kenkel et al.   Molecular Ecology Resources

Genes Related to Ion-Transport and Energy Production Are Upregulated in Response to CO2-Driven pH Decrease in Corals: New Insights from Transcriptome Analysis

(2013) Jeremie Vidal-Dupiol et al.   PLoS One

Gene Expression Signatures of Energetic Acclimatisation in the Reef Building Coral Acropora millepora

(2013) Line K. Bay et al.   PLoS One

Genomic basis for coral resilience to climate change

(2013) Daniel J. Barshis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Immune response of the Caribbean sea fan, Gorgonia ventalina, exposed to an Aplanochytrium parasite as revealed by transcriptome sequencing

(2013) Colleen A. Burge et al.   Frontiers in Physiology

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

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

DIFFERENCES IN THE REGULATION OF GROWTH AND BIOMINERALIZATION GENES REVEALED THROUGH LONG-TERM COMMON-GARDEN ACCLIMATION AND EXPERIMENTAL GENOMICS IN THE PURPLE SEA URCHIN

(2012) Melissa H. Pespeni et al.   EVOLUTION

Cell Biology of Cnidarian-Dinoflagellate Symbiosis

(2012) S. K. Davy et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

Transcriptome-wide polymorphisms of red abalone (Haliotis rufescens) reveal patterns of gene flow and local adaptation

(2012) Pierre De Wit et al.   MOLECULAR ECOLOGY

Low connectivity and declining genetic variability along a depth gradient in Corallium rubrum populations

(2011) F. Costantini et al.   CORAL REEFS

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record

(2011) Eunji Park et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

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

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

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Fine-scale genetic structure and inferences on population biology in the threatened Mediterranean red coral, Corallium rubrum

(2010) J.-B. LEDOUX et al.   MOLECULAR ECOLOGY

Genetic survey of shallow populations of the Mediterranean red coral [Corallium rubrum(Linnaeus, 1758)]: new insights into evolutionary processes shaping nuclear diversity and implications for conservation

(2010) J.-B. LEDOUX et al.   MOLECULAR ECOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

ABINs: A20 binding inhibitors of NF-κB and apoptosis signaling

(2009) Lynn Verstrepen et al.   BIOCHEMICAL PHARMACOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Sequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx

(2009) Eli Meyer et al.   BMC GENOMICS

Transcriptomic responses to heat stress and bleaching in the elkhorn coral Acropora palmata

(2009) MK DeSalvo et al.   MARINE ECOLOGY PROGRESS SERIES

An ancient and variable mannose-binding lectin from the coral Acropora millepora binds both pathogens and symbionts

(2008) E. Charlotte E. Kvennefors et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Upper thermal thresholds of shallow vs. deep populations of the precious Mediterranean red coral Corallium rubrum (L.): Assessing the potential effects of warming in the NW Mediterranean

(2008) O. Torrents et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS