Comparative Metagenomics of the Polymicrobial Black Band Disease of Corals

Microbial transcriptome profiling of black band disease in a Faviid coral during a seasonal disease peak

(2016) L Arotsker et al.   DISEASES OF AQUATIC ORGANISMS

Integrated approach to understanding the onset and pathogenesis of black band disease in corals

(2016) Yui Sato et al.   ENVIRONMENTAL MICROBIOLOGY

Unraveling the Physiological Roles of the Cyanobacterium Geitlerinema sp. BBD and Other Black Band Disease Community Members through Genomic Analysis of a Mixed Culture

(2016) Paul A. Den Uyl et al.   PLoS One

Photosynthetic Versatility in the Genome of Geitlerinema sp. PCC 9228 (Formerly Oscillatoria limnetica ‘Solar Lake’), a Model Anoxygenic Photosynthetic Cyanobacterium

(2016) Sharon L. Grim et al.   Frontiers in Microbiology

CRISPR-Cas Defense System and Potential Prophages in Cyanobacteria Associated with the Coral Black Band Disease

(2016) Patrick Buerger et al.   Frontiers in Microbiology

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

(2016) Tom O. Delmont et al.   PeerJ

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Microbiome shifts and the inhibition of quorum sensing by Black Band Disease cyanobacteria

(2015) Julie L Meyer et al.   ISME Journal

Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics

(2015) Rendy Ruvindy et al.   ISME Journal

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Organic Matter Degradation Drives Benthic Cyanobacterial Mat Abundance on Caribbean Coral Reefs

(2015) Hannah J. Brocke et al.   PLoS One

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Description of new filamentous toxicCyanobacteria(Oscillatoriales) colonizing the sulfidic periphyton mat in marine mangroves

(2014) Chantal Guidi-Rontani et al.   FEMS MICROBIOLOGY LETTERS

Influence of local and global environmental parameters on the composition of cyanobacterial mats in a tropical lagoon

(2014) Isidora Echenique-Subiabre et al.   MICROBIAL ECOLOGY

Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions

(2014) Jessica K. Cole et al.   Frontiers in Microbiology

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

(2014) Jai Ram Rideout et al.   PeerJ

Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets

(2013) Luis M. Rodriguez-R et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Ecology of marine Bacteroidetes: a comparative genomics approach

(2013) Beatriz Fernández-Gómez et al.   ISME Journal

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology

(2013) A. Murat Eren et al.   PLoS One

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

(2013) P. M. Shih et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sulfur-oxidizing bacterial populations within cyanobacterial dominated coral disease lesions

(2013) David G. Bourne et al.   Environmental Microbiology Reports

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Cyanobacterial life at low O2: community genomics and function reveal metabolic versatility and extremely low diversity in a Great Lakes sinkhole mat

(2012) A. A. VOORHIES et al.   Geobiology

Biogeochemical conditions determine virulence of black band disease in corals

(2012) Martin S Glas et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Characterization of Roseofilum reptotaenium (Oscillatoriales, Cyanobacteria) gen. et sp. nov. isolated from Caribbean black band disease

(2012) Dale Casamatta et al.   PHYCOLOGIA

Effects of temperature and light on the progression of black band disease on the reef coral, Montipora hispida

(2011) Y. Sato et al.   CORAL REEFS

Biologically active secondary metabolites from marine cyanobacteria

(2010) Joshawna K Nunnery et al.   CURRENT OPINION IN BIOTECHNOLOGY

A meta-analysis of 16S rRNA gene clone libraries from the polymicrobial black band disease of corals

(2010) Aaron W. Miller et al.   FEMS MICROBIOLOGY ECOLOGY

Changes in sulfate-reducing bacterial populations during the onset of black band disease

(2010) David G Bourne et al.   ISME Journal

The roles of temperature and light in black band disease (BBD) progression on corals of the genus Diploria in Bermuda

(2010) Kristin Kuehl et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Malyngolide from the cyanobacterium Lyngbya majuscula interferes with quorum sensing circuitry

(2010) Sergey Dobretsov et al.   Environmental Microbiology Reports

Organization, Evolution, and Expression Analysis of the Biosynthetic Gene Cluster for Scytonemin, a Cyanobacterial UV-Absorbing Pigment

(2009) C. M. Sorrels et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Coral-Associated Bacteria and Their Role in the Biogeochemical Cycling of Sulfur

(2009) J.-B. Raina et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Sulfide, microcystin, and the etiology of black band disease

(2009) LL Richardson et al.   DISEASES OF AQUATIC ORGANISMS

Vibriosp. as a potentially important member of  the Black Band Disease (BBD) consortium inFaviasp. corals

(2009) Luba Arotsker et al.   FEMS MICROBIOLOGY ECOLOGY

A new structure-based classification of sulfide:quinone oxidoreductases

(2009) Marco Marcia et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH