Dynamics of marine bacterial community diversity of the coastal waters of the reefs, inlets, and wastewater outfalls of southeast Florida

Metataxonomic profiling and prediction of functional behaviour of wheat straw degrading microbial consortia

(2014) Diego Jiménez et al.   Biotechnology for Biofuels

Mo1905 Microbiome-Metabonome Linked Analysis of Ascending Colon Cancer by 1HNMR MAS Spectrometry and 16S rRNA Gene Analysis (Metataxonomics)

(2014) James Kinross et al.   GASTROENTEROLOGY

Defining and Dividing the Greater Caribbean: Insights from the Biogeography of Shorefishes

(2014) D. Ross Robertson et al.   PLoS One

Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors

(2014) L. W. Kelly et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Linking activity and function to ecosystem dynamics in a coastal bacterioplankton community

(2014) Scott M. Gifford et al.   Frontiers in Microbiology

Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities

(2014) Regina Lamendella 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

Climate Change Influences on Marine Infectious Diseases: Implications for Management and Society

(2013) Colleen A. Burge et al.   Annual Review of Marine Science

Coastal Bacterioplankton Community Dynamics in Response to a Natural Disturbance

(2013) Sara K. Yeo et al.   PLoS One

Temperature-driven shifts in the epibiotic bacterial community composition of the brown macroalgaFucus vesiculosus

(2013) Stephanie B Stratil et al.   MicrobiologyOpen

EMPeror: a tool for visualizing high-throughput microbial community data

(2013) Yoshiki Vázquez-Baeza et al.   GigaScience

Denaturing Gradient Gel Electrophoresis and Barcoded Pyrosequencing Reveal Unprecedented Archaeal Diversity in Mangrove Sediment and Rhizosphere Samples

(2012) Ana C. C. Pires et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization of a Newly Discovered Symbiont of the Whitefly Bemisia tabaci (Hemiptera: Aleyrodidae)

(2012) Xiao-Li Bing et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Performance of Two Quantitative PCR Methods for Microbial Source Tracking of Human Sewage and Implications for Microbial Risk Assessment in Recreational Waters

(2012) Christopher Staley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomics: microbial diversity through a scratched lens

(2012) Ben Temperton et al.   CURRENT OPINION IN MICROBIOLOGY

Genome Sequences of the Primary Endosymbiont “Candidatus Portiera aleyrodidarum” in the Whitefly Bemisia tabaci B and Q Biotypes

(2012) Zi-Feng Jiang et al.   JOURNAL OF BACTERIOLOGY

Environmental microbiology through the lens of high-throughput DNA sequencing: Synopsis of current platforms and bioinformatics approaches

(2012) Ramiro Logares et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Spatial Analyses of Benthic Habitats to Define Coral Reef Ecosystem Regions and Potential Biogeographic Boundaries along a Latitudinal Gradient

(2012) Brian K. Walker   PLoS One

Pyrosequencing of Bacterial Symbionts within Axinella corrugata Sponges: Diversity and Seasonal Variability

(2012) James R. White et al.   PLoS One

Near-future ocean acidification causes differences in microbial associations within diverse coral reef taxa

(2012) N. S. Webster et al.   Environmental Microbiology Reports

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

(2012) Daniel McDonald et al.   GigaScience

The Rare Bacterial Biosphere

(2011) Carlos Pedrós-Alió   Annual Review of Marine Science

Temporal Variability of Coastal Planctomycetes Clades at Kabeltonne Station, North Sea

(2011) Ilaria Pizzetti et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

(2011) Samuel V Angiuoli et al.   BMC BIOINFORMATICS

Bacterial species may exist, metagenomics reveal

(2011) Alejandro Caro-Quintero et al.   ENVIRONMENTAL MICROBIOLOGY

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Marine bacterial, archaeal and protistan association networks reveal ecological linkages

(2011) Joshua A Steele et al.   ISME Journal

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Evaluation of sewage source and fate on southeast Florida coastal reefs

(2011) J. Carrie Futch et al.   MARINE POLLUTION BULLETIN

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems

(2011) Lucie Zinger et al.   PLoS One

The Earth Microbiome Project: Meeting report of the “1st EMP meeting on sample selection and acquisition” at Argonne National Laboratory October 6th 2010.

(2011) Jack A. Gilbert et al.   Standards in Genomic Sciences

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Detection of WWE2-related Lentisphaerae by 16S rRNA gene sequencing and fluorescence in situ hybridization in landfill leachate

(2010) Rim Driss Limam et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Human sewage identified as likely source of white pox disease of the threatened Caribbean elkhorn coral, Acropora palmata

(2010) Kathryn Patterson Sutherland et al.   ENVIRONMENTAL MICROBIOLOGY

The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genes

(2010) David L. Kirchman et al.   ENVIRONMENTAL MICROBIOLOGY

The pathology of sponge orange band disease affecting the Caribbean barrel sponge Xestospongia muta

(2010) Hilde Angermeier et al.   FEMS MICROBIOLOGY ECOLOGY

Dating the cyanobacterial ancestor of the chloroplast

(2010) Luisa I Falcón et al.   ISME Journal

Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean

(2010) Paola R Gómez-Pereira et al.   ISME Journal

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

The Taxonomic and Functional Diversity of Microbes at a Temperate Coastal Site: A ‘Multi-Omic’ Study of Seasonal and Diel Temporal Variation

(2010) Jack A. Gilbert et al.   PLoS One

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Florida reef sponges harbor coral disease-associated microbes

(2010) Karita Negandhi et al.   SYMBIOSIS

Traditional and molecular analyses for fecal indicator bacteria in non-point source subtropical recreational marine waters

(2010) Christopher D. Sinigalliano et al.   WATER RESEARCH

Presence of Pathogens and Indicator Microbes at a Non-Point Source Subtropical Recreational Marine Beach

(2009) A. M. Abdelzaher et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokaryotic Genomes and Diversity in Surface Ocean Waters: Interrogating the Global Ocean Sampling Metagenome

(2009) E. J. Biers et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Culture-Independent Characterization of Bacterial Communities Associated with the Cold-Water Coral Lophelia pertusa in the Northeastern Gulf of Mexico

(2009) C. A. Kellogg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

The seasonal structure of microbial communities in the Western English Channel

(2009) Jack A. Gilbert et al.   ENVIRONMENTAL MICROBIOLOGY

Ecology and nutrition of invasive Caulerpa brachypus f. parvifolia blooms on coral reefs off southeast Florida, U.S.A.

(2009) Brian E. Lapointe et al.   HARMFUL ALGAE

Wandonia haliotis gen. nov., sp. nov., a marine bacterium of the family Cryomorphaceae, phylum Bacteroidetes

(2009) D.-H. Lee et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data

(2009) Micah Hamady et al.   ISME Journal

Microbial load from animal feces at a recreational beach

(2009) Mary E. Wright et al.   MARINE POLLUTION BULLETIN

The microbial ocean from genomes to biomes

(2009) Edward F. DeLong   NATURE

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

Validation and field testing of library-independent microbial source tracking methods in the Gulf of Mexico

(2009) Valerie J. Harwood et al.   WATER RESEARCH

Phenotype-Specific Bacterial Communities in the Cold-Water Coral Lophelia pertusa (Scleractinia) and Their Implications for the Coral's Nutrition, Health, and Distribution

(2008) S. C. Neulinger et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Unveiling new microbial eukaryotes in the surface ocean

(2008) Ramon Massana et al.   CURRENT OPINION IN MICROBIOLOGY

Mapping Coral Reef Habitats in Southeast Florida Using a Combined Technique Approach

(2008) Brian K. Walker et al.   JOURNAL OF COASTAL RESEARCH