Genome-wide polymorphism and signatures of selection in the symbiotic sea anemone Aiptasia

Elucidating the evolutionary relationships of the Aiptasiidae, a widespread cnidarian–dinoflagellate model system (Cnidaria: Anthozoa: Actiniaria: Metridioidea)

(2016) Alejandro Grajales et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Study of Cnidarian-Algal Symbiosis in the “Omics” Age

(2016) Eli Meyer et al.   BIOLOGICAL BULLETIN

Patterns of Symbiodinium spp. associations within the family Aiptasiidae, a monophyletic lineage of symbiotic of sea anemones (Cnidaria, Actiniaria)

(2015) Alejandro Grajales et al.   CORAL REEFS

Symbiodiniumtranscriptome and global responses of cells to immediate changes in light intensity when grown under autotrophic or mixotrophic conditions

(2015) Tingting Xiang et al.   PLANT JOURNAL

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

Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress

(2014) Nedeljka Rosic et al.   BMC GENOMICS

Change in algal symbiont communities after bleaching, not prior heat exposure, increases heat tolerance of reef corals

(2014) Rachel N. Silverstein et al.   GLOBAL CHANGE BIOLOGY

Expanding the population genetic perspective of cnidarian-Symbiodiniumsymbioses

(2014) Scott R. Santos   MOLECULAR ECOLOGY

ExploringSymbiodiniumdiversity and host specificity inAcroporacorals from geographical extremes of Western Australia with 454 amplicon pyrosequencing

(2014) L. Thomas et al.   MOLECULAR ECOLOGY

Sea anemones possess dynamic mitogenome structures

(2014) Åse Emblem et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Snapshot of a Coral “Holobiont”: A Transcriptome Assembly of the Scleractinian Coral, Porites, Captures a Wide Variety of Genes from Both the Host and Symbiotic Zooxanthellae

(2014) Chuya Shinzato et al.   PLoS One

Mechanisms of reef coral resistance to future climate change

(2014) S. R. Palumbi et al.   SCIENCE

Morphological revision of the genus Aiptasia and the family Aiptasiidae (Cnidaria, Actiniaria, Metridioidea)

(2014) ALEJANDRO GRAJALES et al.   ZOOTAXA

Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data

(2013) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Exceptionally high cumulative percentage of NUMTs originating from linear mitochondrial DNA molecules in the Hydra magnipapillata genome

(2013) Shen Song et al.   BMC GENOMICS

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

(2013) Eiichi Shoguchi et al.   CURRENT BIOLOGY

Incorporating adaptive responses into future projections of coral bleaching

(2013) Cheryl A. Logan et al.   GLOBAL CHANGE BIOLOGY

Population genetic data of a model symbiotic cnidarian system reveal remarkable symbiotic specificity and vectored introductions across ocean basins

(2013) Daniel J. Thornhill et al.   MOLECULAR ECOLOGY

Going where traditional markers have not gone before: utility of and promise for RAD sequencing in marine invertebrate phylogeography and population genomics

(2013) A. M. Reitzel et al.   MOLECULAR ECOLOGY

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

Extensive Differences in Gene Expression Between Symbiotic and Aposymbiotic Cnidarians

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

Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis: the transcriptome of aposymbiotic A. pallida

(2012) Erik M Lehnert et al.   BMC GENOMICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

A genetics-based description ofSymbiodinium minutumsp. nov. andS. psygmophilumsp. nov. (Dinophyceae), two dinoflagellates symbiotic with cnidaria

(2012) Todd C. Lajeunesse et al.   JOURNAL OF PHYCOLOGY

Cell Biology of Cnidarian-Dinoflagellate Symbiosis

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

Symbiont communities and host genetic structure of the brain coralPlatygyra verweyi, at the outlet of a nuclear power plant and adjacent areas

(2012) SHASHANK KESHAVMURTHY et al.   MOLECULAR ECOLOGY

Specificity is rarely absolute in coral-algal symbiosis: implications for coral response to climate change

(2012) R. N. Silverstein et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The adaptation of coral reefs to climate change: Is the Red Queen being outpaced?

(2012) Ove Hoegh-Guldberg   SCIENTIA MARINA

Signaling in Innate Immunity and Inflammation

(2012) K. Newton et al.   Cold Spring Harbor Perspectives in Biology

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

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

(2011) Chuya Shinzato et al.   NATURE

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Projecting Coral Reef Futures Under Global Warming and Ocean Acidification

(2011) J. M. Pandolfi et al.   SCIENCE

Adaptations to Endosymbiosis in a Cnidarian-Dinoflagellate Association: Differential Gene Expression and Specific Gene Duplications

(2011) Philippe Ganot et al.   PLoS Genetics

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

(2010) A. McKenna et al.   GENOME RESEARCH

A new Symbiodinium clade (Dinophyceae) from soritid foraminifera in Hawai’i

(2010) Xavier Pochon et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The dynamic genome of Hydra

(2010) Jarrod A. Chapman et al.   NATURE

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

Environmental Symbiont Acquisition May Not Be the Solution to Warming Seas for Reef-Building Corals

(2010) Mary Alice Coffroth et al.   PLoS One

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

Generation and analysis of transcriptomic resources for a model system on the rise: the sea anemone Aiptasia pallida and its dinoflagellate endosymbiont

(2009) Shinichi Sunagawa et al.   BMC GENOMICS

The Impact of Sampling Schemes on the Site Frequency Spectrum in Nonequilibrium Subdivided Populations

(2009) T. Stadler et al.   GENETICS

The Genomics of Speciation in Drosophila: Diversity, Divergence, and Introgression Estimated Using Low-Coverage Genome Sequencing

(2009) Rob J. Kulathinal et al.   PLoS Genetics

Cellular mechanisms of Cnidarian bleaching: stress causes the collapse of symbiosis

(2008) V. M. Weis   JOURNAL OF EXPERIMENTAL BIOLOGY

GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis

(2008) Qi Zheng et al.   NUCLEIC ACIDS RESEARCH

A community change in the algal endosymbionts of a scleractinian coral following a natural bleaching event: field evidence of acclimatization

(2008) A.M Jones et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Cell biology in model systems as the key to understanding corals

(2008) Virginia M. Weis et al.   TRENDS IN ECOLOGY & EVOLUTION