The coral symbiont Candidatus Aquarickettsia is variably abundant in threatened Caribbean acroporids and transmitted horizontally

Genomic variation of an endosymbiotic dinoflagellate ( Symbiodinium ‘fitti’ ) among closely related coral hosts

(2021) Hannah G. Reich et al.   MOLECULAR ECOLOGY

Host-associated microbe PCR (hamPCR) enables convenient measurement of both microbial load and community composition

(2021) Derek S Lundberg et al.   eLife

STAGdb: a 30K SNP genotyping array and Science Gateway for Acropora corals and their dinoflagellate symbionts

(2020) S. A. Kitchen et al.   Scientific Reports

Parasitic ‘ Candidatus Aquarickettsia rohweri’ is a marker of disease susceptibility in Acropora cervicornis but is lost during thermal stress

(2020) Grace Klinges et al.   ENVIRONMENTAL MICROBIOLOGY

Coral Microbiomes Demonstrate Flexibility and Resilience Through a Reduction in Community Diversity Following a Thermal Stress Event

(2020) Rebecca L. Maher et al.   Frontiers in Ecology and Evolution

Effects of thermal stress on amount, composition, and antibacterial properties of coral mucus

(2019) Rachel M. Wright et al.   PeerJ

Optimizing de novo genome assembly from PCR-amplified metagenomes

(2019) Simon Roux et al.   PeerJ

Considerations for maximizing the adaptive potential of restored coral populations in the western Atlantic

(2019) Iliana B. Baums et al.   ECOLOGICAL APPLICATIONS

Nitrogen enrichment, altered stoichiometry, and coral reef decline at Looe Key, Florida Keys, USA: a 3-decade study

(2019) Brian E. Lapointe et al.   MARINE BIOLOGY

Structure and stability of the coral microbiome in space and time

(2019) Courtney M. Dunphy et al.   Scientific Reports

Impact of Host DNA and Sequencing Depth on the Taxonomic Resolution of Whole Metagenome Sequencing for Microbiome Analysis

(2019) Joana Pereira-Marques et al.   Frontiers in Microbiology

Strong Purifying Selection is Associated with Genome Streamlining in Epipelagic Marinimicrobia

(2019) Carolina Alejandra Martinez-Gutierrez et al.   Genome Biology and Evolution

Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov

(2019) J. Grace Klinges et al.   ISME Journal

Horizontally transmitted symbiont populations in deep-sea mussels are genetically isolated

(2019) Devani Romero Picazo et al.   ISME Journal

Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment

(2019) Lydia J Baker et al.   eLife

Ecology, histopathology, and microbial ecology of a white-band disease outbreak in the threatened staghorn coral Acropora cervicornis

(2019) SA Gignoux-Wolfsohn et al.   DISEASES OF AQUATIC ORGANISMS

Optimising conditions for in vitro fertilization success of Acropora tenuis, A. millepora and Favites colemani corals in northwestern Philippines

(2019) Dexter W. dela Cruz et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Sexual production of corals for reef restoration in the Anthropocene

(2019) CJ Randall et al.   MARINE ECOLOGY PROGRESS SERIES

Microbiome differences in disease-resistant vs. susceptible Acropora corals subjected to disease challenge assays

(2019) Stephanie M. Rosales et al.   Scientific Reports

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

HMMER web server: 2018 update

(2018) Simon C Potter et al.   NUCLEIC ACIDS RESEARCH

Intrahost Genetic Diversity of Bacterial Symbionts Exhibits Evidence of Mixed Infections and Recombinant Haplotypes

(2017) Shelbi L. Russell et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of host-symbiont dependence

(2017) Roberta M. Fisher et al.   Nature Communications

Extended genomes: symbiosis and evolution

(2017) Gregory D. D. Hurst   Interface Focus

Zooplankton as a potential vector for white band disease transmission in the endangered coral, Acropora cervicornis

(2017) Rebecca H. Certner et al.   PeerJ

Trans-generational specificity within a cnidarian–algal symbiosis

(2016) D. M. Poland et al.   CORAL REEFS

Genome Evolution in the Obligate but Environmentally Active Luminous Symbionts of Flashlight Fish

(2016) Tory A. Hendry et al.   Genome Biology and Evolution

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

(2016) Robert Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

How old are you? Genet age estimates in a clonal animal

(2016) M. K. Devlin-Durante et al.   MOLECULAR ECOLOGY

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

The BIG Data Center: from deposition to integration to translation

(2016)   NUCLEIC ACIDS RESEARCH

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

Influence of sperm dilution and gamete contact time on the fertilization rate of scleractinian corals

(2015) Yoko Nozawa et al.   CORAL REEFS

The natural occurrence of secondary bacterial symbionts in aphids

(2015) SHARON E. ZYTYNSKA et al.   ECOLOGICAL ENTOMOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Massively parallel sequencing (MPS) assays for sequencing mitochondrial genomes: the phylogenomic implications for Acropora staghorn corals (Scleractinia; Acroporidae)

(2015) Shang-Yin Vanson Liu et al.   MARINE BIOLOGY

Identification of Population Bottlenecks and Colonization Factors during Assembly of Bacterial Communities within the Zebrafish Intestine

(2015) W. Zac Stephens et al.   mBio

Rapid Recent Warming of Coral Reefs in the Florida Keys

(2015) Derek P. Manzello   Scientific Reports

The Tiniest Tiny Genomes

(2014) Nancy A. Moran et al.   Annual Review of Microbiology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

New insights into the dynamics between reef corals and their associated dinoflagellate endosymbionts from population genetic studies

(2014) Iliana B. Baums et al.   MOLECULAR ECOLOGY

Multi-gene analysis ofSymbiodiniumdinoflagellates: a perspective on rarity, symbiosis, and evolution

(2014) Xavier Pochon et al.   PeerJ

Genotypic variation influences reproductive success and thermal stress tolerance in the reef building coral, Acropora palmata

(2013) I. B. Baums et al.   CORAL REEFS

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

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

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

(2013) Henrik Nordberg et al.   NUCLEIC ACIDS RESEARCH

Evidence for Horizontal Transmission of Secondary Endosymbionts in the Bemisia tabaci Cryptic Species Complex

(2013) Muhammad Z. Ahmed et al.   PLoS One

PACo: A Novel Procrustes Application to Cophylogenetic Analysis

(2013) Juan Antonio Balbuena et al.   PLoS One

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

White Band Disease transmission in the threatened coral, Acropora cervicornis

(2012) S. A. Gignoux-Wolfsohn et al.   Scientific Reports

Caribbean acroporid coral hybrids are viable across life history stages

(2011) ND Fogarty   MARINE ECOLOGY PROGRESS SERIES

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

(2011) Chuya Shinzato et al.   NATURE

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

Human Pathogen Shown to Cause Disease in the Threatened Eklhorn Coral Acropora palmata

(2011) Kathryn Patterson Sutherland et al.   PLoS One

Evolutionary transitions in bacterial symbiosis

(2011) J. L. Sachs et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal transmission of the insect symbiont Rickettsia is plant-mediated

(2011) A. Caspi-Fluger et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome

(2010) A. R. Quinlan et al.   GENOME RESEARCH

A complex journey: transmission of microbial symbionts

(2010) Monika Bright et al.   NATURE REVIEWS MICROBIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Systematic and Biogeographical Patterns in the Reproductive Biology of Scleractinian Corals

(2009) Andrew H. Baird et al.   Annual Review of Ecology Evolution and Systematics

Genomics and Evolution of Heritable Bacterial Symbionts

(2008) Nancy A. Moran et al.   Annual Review of Genetics

Evolution, Population Structure, and Phylogeography of Genetically Monomorphic Bacterial Pathogens

(2008) Mark Achtman   Annual Review of Microbiology

Population Structure of Vibrio fischeri within the Light Organs of Euprymna scolopes Squid from Two Oahu (Hawaii) Populations

(2008) M. S. Wollenberg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics