Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals

Sugar enrichment provides evidence for a role of nitrogen fixation in coral bleaching

(2017) Claudia Pogoreutz et al.   GLOBAL CHANGE BIOLOGY

Biogeography and molecular diversity of coral symbionts in the genus Symbiodinium around the Arabian Peninsula

(2017) Maren Ziegler et al.   JOURNAL OF BIOGEOGRAPHY

Global warming and recurrent mass bleaching of corals

(2017) Terry P. Hughes et al.   NATURE

Bacterial community dynamics are linked to patterns of coral heat tolerance

(2017) Maren Ziegler et al.   Nature Communications

Empty Niches after Extinctions Increase Population Sizes of Modern Corals

(2016) Carlos Prada et al.   CURRENT BIOLOGY

Coral microbial community dynamics in response to anthropogenic impacts near a major city in the central Red Sea

(2016) Maren Ziegler et al.   MARINE POLLUTION BULLETIN

The transcriptomic response of the coralAcropora digitiferato a competentSymbiodiniumstrain: the symbiosome as an arrested early phagosome

(2016) A. R. Mohamed et al.   MOLECULAR ECOLOGY

Ancestral genetic diversity associated with the rapid spread of stress-tolerant coral symbionts in response to Holocene climate change

(2016) Benjamin C. C. Hume et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reefgenomics.Org - a repository for marine genomics data

(2016) Yi Jin Liew et al.   Database-The Journal of Biological Databases and Curation

Comparative genomics explains the evolutionary success of reef-forming corals

(2016) Debashish Bhattacharya et al.   eLife

Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes

(2016) Kevin R. Theis et al.   mSystems

Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle

(2016) M. Aranda et al.   Scientific Reports

Rapid Acclimation Ability Mediated by Transcriptome Changes in Reef-Building Corals

(2015) Rachael A. Bay et al.   Genome Biology and Evolution

The role of transcriptome resilience in resistance of corals to bleaching

(2015) Francois O. Seneca et al.   MOLECULAR ECOLOGY

The genome ofAiptasia, a sea anemone model for coral symbiosis

(2015) Sebastian Baumgarten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nitrogen cycling in corals: the key to understanding holobiont functioning?

(2015) Nils Rädecker et al.   TRENDS IN MICROBIOLOGY

Projections of climate conditions that increase coral disease susceptibility and pathogen abundance and virulence

(2015) Jeffrey Maynard et al.   Nature Climate Change

Bicarbonate transporters in corals point towards a key step in the evolution of cnidarian calcification

(2015) Didier Zoccola et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

TIR-domain-containing protein repertoire of nine anthozoan species reveals coral–specific expansions and uncharacterized proteins

(2014) Angela Z. Poole et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Structural Molecular Components of Septate Junctions in Cnidarians Point to the Origin of Epithelial Junctions in Eukaryotes

(2014) Philippe Ganot et al.   MOLECULAR BIOLOGY AND EVOLUTION

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

(2014) Erik L.L. Sonnhammer et al.   NUCLEIC ACIDS RESEARCH

Identification of MicroRNAs in the Coral Stylophora pistillata

(2014) Yi Jin Liew et al.   PLoS One

The “Naked Coral” Hypothesis Revisited – Evidence for and Against Scleractinian Monophyly

(2014) Marcelo V. Kitahara et al.   PLoS One

L_RNA_scaffolder: scaffolding genomes with transcripts

(2013) Wei Xue et al.   BMC GENOMICS

Draft Assembly of the Symbiodinium minutum Nuclear Genome Reveals Dinoflagellate Gene Structure

(2013) Eiichi Shoguchi et al.   CURRENT BIOLOGY

Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides ) from different thermal environments

(2013) C. D. Kenkel et al.   MOLECULAR ECOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

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

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA barcoding reveals the coral “laboratory-rat”, Stylophora pistillata encompasses multiple identities

(2013) Shashank Keshavmurthy et al.   Scientific Reports

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Cell Biology of Cnidarian-Dinoflagellate Symbiosis

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

The Complex NOD-Like Receptor Repertoire of the Coral Acropora digitifera Includes Novel Domain Combinations

(2012) Mayuko Hamada et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

EVOLUTIONARY DIVERSIFICATION OF REEF CORALS: A COMPARISON OF THE MOLECULAR AND FOSSIL RECORDS

(2011) Carl Simpson et al.   EVOLUTION

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

Using the Acropora digitifera genome to understand coral responses to environmental change

(2011) Chuya Shinzato et al.   NATURE

The UniProt-GO Annotation database in 2011

(2011) E. C. Dimmer et al.   NUCLEIC ACIDS RESEARCH

Rapid Evolution of Coral Proteins Responsible for Interaction with the Environment

(2011) Christian R. Voolstra et al.   PLoS One

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Coral immunology and resistance to disease

(2010) KC Reed et al.   DISEASES OF AQUATIC ORGANISMS

The dynamic genome of Hydra

(2010) Jarrod A. Chapman et al.   NATURE

A Comprehensive Phylogenetic Analysis of the Scleractinia (Cnidaria, Anthozoa) Based on Mitochondrial CO1 Sequence Data

(2010) Marcelo V. Kitahara et al.   PLoS One

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

More than just orphans: are taxonomically-restricted genes important in evolution?

(2009) Konstantin Khalturin et al.   TRENDS IN GENETICS

Cloning and Use of a Coral 36B4 Gene to Study the Differential Expression of Coral Genes Between Light and Dark Conditions

(2008) Aurélie Moya et al.   MARINE BIOTECHNOLOGY

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

Mitochondrial and Nuclear Genes Suggest that Stony Corals Are Monophyletic but Most Families of Stony Corals Are Not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria)

(2008) Hironobu Fukami et al.   PLoS One

One-Third of Reef-Building Corals Face Elevated Extinction Risk from Climate Change and Local Impacts

(2008) K. E. Carpenter et al.   SCIENCE