Symbiont type and environmental factors affect transcriptome-wide gene expression in the coral Montipora capitata

Coral color and depth drive symbiosis ecology of Montipora capitata in Kāne‘ohe Bay, O‘ahu, Hawai‘i

(2018) T. Innis et al.   CORAL REEFS

Contrasting effects of Symbiodinium identity on coral host transcriptional profiles across latitudes

(2018) Sarah J. Barfield et al.   MOLECULAR ECOLOGY

Systematic Revision of Symbiodiniaceae Highlights the Antiquity and Diversity of Coral Endosymbionts

(2018) Todd C. LaJeunesse et al.   CURRENT BIOLOGY

Rare symbionts may contribute to the resilience of coral–algal assemblages

(2017) Maren Ziegler et al.   ISME Journal

Optimal nutrient exchange and immune responses operate in partner specificity in the cnidarian-dinoflagellate symbiosis

(2017) Jennifer L. Matthews et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heritability of the Symbiodinium community in vertically- and horizontally-transmitting broadcast spawning corals

(2017) Kate M. Quigley et al.   Scientific Reports

Identifying nitrogen sources to thermal tide pools in Kapoho, Hawai'i, U.S.A, using a multi-stable isotope approach

(2016) Tracy N. Wiegner et al.   MARINE POLLUTION BULLETIN

Most Low-Abundance “Background” Symbiodinium spp. Are Transitory and Have Minimal Functional Significance for Symbiotic Corals

(2016) Moo Joon Lee et al.   MICROBIAL ECOLOGY

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

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

Noncoding RNAs, Emerging Regulators in Root Endosymbioses

(2016) Christine Lelandais-Brière et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Symbiodinium thermophilum sp. nov., a thermotolerant symbiotic alga prevalent in corals of the world's hottest sea, the Persian/Arabian Gulf

(2015) B. C. C. Hume et al.   Scientific Reports

Intraspecific diversity among partners drives functional variation in coral symbioses

(2015) John Everett Parkinson et al.   Scientific Reports

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

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

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

(2013) Eiichi Shoguchi et al.   CURRENT BIOLOGY

Surface Water Metabolism Potential in Groundwater-Fed Coastal Waters of Hawaii Island, USA

(2013) Erik E. Johnson et al.   Estuaries and Coasts

Mechanisms and Dynamics of Orphan Gene Emergence in Insect Genomes

(2013) Lothar Wissler et al.   Genome Biology and Evolution

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Does Coral Disease Affect Symbiodinium? Investigating the Impacts of Growth Anomaly on Symbiont Photophysiology

(2013) John Henrik Robert Burns et al.   PLoS One

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

Fungal Small RNAs Suppress Plant Immunity by Hijacking Host RNA Interference Pathways

(2013) Arne Weiberg et al.   SCIENCE

Extensive Differences in Gene Expression Between Symbiotic and Aposymbiotic Cnidarians

(2013) Erik M. Lehnert et al.   G3-Genes Genomes Genetics

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Endosymbiotic flexibility associates with environmental sensitivity in scleractinian corals

(2012) H. M. Putnam et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phenotypic Plasticity of the Drosophila Transcriptome

(2012) Shanshan Zhou et al.   PLoS Genetics

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Conjugating effects of symbionts and environmental factors on gene expression in deep-sea hydrothermal vent mussels

(2011) Isabelle Boutet et al.   BMC GENOMICS

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

(2011) Chuya Shinzato et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

Variation in Symbiodinium ITS2 Sequence Assemblages among Coral Colonies

(2011) Michael Stat et al.   PLoS One

Rapid Evolution of Coral Proteins Responsible for Interaction with the Environment

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

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

The Ecoresponsive Genome of Daphnia pulex

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

Coupling Metabolite Flux to Transcriptomics: Insights Into the Molecular Mechanisms Underlying Primary Productivity by the Hydrothermal Vent Tubeworm Ridgeia piscesae

(2010) Spencer V. Nyholm et al.   BIOLOGICAL BULLETIN

Coral larvae exhibit few measurable transcriptional changes during the onset of coral-dinoflagellate endosymbiosis

(2010) Christine E. Schnitzler et al.   Marine Genomics

Isolation by distance across the Hawaiian Archipelago in the reef-building coral Porites lobata

(2010) NICHOLAS R. POLATO et al.   MOLECULAR ECOLOGY

Coral host transcriptomic states are correlated withSymbiodiniumgenotypes

(2010) M. K. DeSALVO et al.   MOLECULAR ECOLOGY

Potential Costs of Acclimatization to a Warmer Climate: Growth of a Reef Coral with Heat Tolerant vs. Sensitive Symbiont Types

(2010) Alison Jones et al.   PLoS One

Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis

(2010) A. M. Wier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The host transcriptome remains unaltered during the establishment of coral-algal symbioses

(2009) CHRISTIAN R. VOOLSTRA et al.   MOLECULAR ECOLOGY

The Roles and Interactions of Symbiont, Host and Environment in Defining Coral Fitness

(2009) Jos C. Mieog et al.   PLoS One

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Effects of colonization, luminescence, and autoinducer on host transcription during development of the squid-vibrio association

(2008) C. K. Chun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA