Two decades of describing the unseen majority of aquatic microbial diversity

Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis

(2011) Patrick D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

(2011) Xiaolin Hao et al.   BIOINFORMATICS

CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

(2011) Surendra Kumar et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

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

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

Biodiversity improves water quality through niche partitioning

(2011) Bradley J. Cardinale   NATURE

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

(2011) Pelin Yilmaz et al.   NATURE BIOTECHNOLOGY

Microbial seed banks: the ecological and evolutionary implications of dormancy

(2011) Jay T. Lennon et al.   NATURE REVIEWS MICROBIOLOGY

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

(2011) Lucie Zinger et al.   PLoS One

Repeated sampling reveals differential variability in measures of species richness and community composition in planktonic protists

(2011) John R. Dolan et al.   Environmental Microbiology Reports

Uncertain future for ocean algae

(2011) Michael Behrenfeld   Nature Climate Change

Spatial patterns of bacterial richness and evenness in the NW Mediterranean Sea explored by pyrosequencing of the 16S rRNA

(2010) T Pommier et al.   AQUATIC MICROBIAL ECOLOGY

Evaluation of DNA extraction methods from complex phototrophic biofilms

(2010) Isabel Ferrera et al.   BIOFOULING

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

SeqTrim: a high-throughput pipeline for preprocessing any type of sequence reads

(2010) Juan Falgueras et al.   BMC BIOINFORMATICS

Third Generation DNA Sequencing: Pacific Biosciences' Single Molecule Real Time Technology

(2010) Alice McCarthy   CHEMISTRY & BIOLOGY

Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist

(2010) Marti J. Anderson et al.   ECOLOGY LETTERS

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

Replicate or lie

(2010) James I. Prosser   ENVIRONMENTAL MICROBIOLOGY

Linking bacterial identities and ecosystem processes: can ‘omic’ analyses be more than the sum of their parts?

(2010) Sergio E. Morales et al.   FEMS MICROBIOLOGY ECOLOGY

Microbial community structure across the tree of life in the extreme Río Tinto

(2010) Linda A Amaral-Zettler et al.   ISME Journal

PANGEA: pipeline for analysis of next generation amplicons

(2010) Adriana Giongo 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

Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing

(2010) HÉLÈNE AGOGUÉ et al.   MOLECULAR ECOLOGY

Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets

(2010) Angélique Gobet et al.   NUCLEIC ACIDS RESEARCH

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

One Bacterial Cell, One Complete Genome

(2010) Tanja Woyke et al.   PLoS One

When metagenomics meets stable-isotope probing: progress and perspectives

(2010) Yin Chen et al.   TRENDS IN MICROBIOLOGY

Ecological consequences of bacterioplankton lifestyles: changes in concepts are needed

(2010) Hans-Peter Grossart   Environmental Microbiology Reports

The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies

(2010) Patrick D. Schloss   PLoS Computational Biology

Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology

(2009) D. A. Caron et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Global phylogenetic community structure and β-diversity patterns in surface bacterioplankton metacommunities

(2009) A Barberán et al.   AQUATIC MICROBIAL ECOLOGY

RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities

(2009) Thomas Pommier et al.   BIOINFORMATICS

Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure

(2009) Julie A. Huber et al.   ENVIRONMENTAL MICROBIOLOGY

The seasonal structure of microbial communities in the Western English Channel

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

Diversity of total and active free-living vs. particle-attached bacteria in the euphotic zone of the NW Mediterranean Sea

(2009) Jean-François Ghiglione et al.   FEMS MICROBIOLOGY LETTERS

Analyzing salt-marsh fungal diversity: comparing ARISA fingerprinting with clone sequencing and pyrosequencing

(2009) Patrick M. Gillevet et al.   Fungal Ecology

Nucleic acids as viability markers for bacteria detection using molecular tools

(2009) Claire Cenciarini-Borde et al.   Future Microbiology

Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing

(2009) Ben Temperton et al.   ISME Journal

Polymerase chain reaction primers miss half of rRNA microbial diversity

(2009) SunHee Hong et al.   ISME Journal

Microbial community structure in the North Pacific ocean

(2009) Mark V Brown et al.   ISME Journal

Global ecological patterns in uncultured Archaea

(2009) Jean-Christophe Auguet et al.   ISME Journal

Microbial community structure and its functional implications

(2009) Jed A. Fuhrman   NATURE

The 'rare biosphere': a reality check

(2009) Jens Reeder et al.   NATURE METHODS

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

Megx.net: integrated database resource for marine ecological genomics

(2009) R. Kottmann et al.   NUCLEIC ACIDS RESEARCH

ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences

(2009) Yijun Sun et al.   NUCLEIC ACIDS RESEARCH

New Insights into the Diversity of Marine Picoeukaryotes

(2009) Fabrice Not et al.   PLoS One

Groups without Cultured Representatives Dominate Eukaryotic Picophytoplankton in the Oligotrophic South East Pacific Ocean

(2009) Xiao Li Shi et al.   PLoS One

Ecology of the rare microbial biosphere of the Arctic Ocean

(2009) Pierre E. Galand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Infrequent marine–freshwater transitions in the microbial world

(2009) Ramiro Logares et al.   TRENDS IN MICROBIOLOGY

Molecular diversity of bacterioplankton: link to a predictive biogeochemistry of pelagic ecosystems

(2008) MG Höfle et al.   AQUATIC MICROBIAL ECOLOGY

Environmental rRNA inventories miss over half of protistan diversity

(2008) Sunok Jeon et al.   BMC MICROBIOLOGY

It's all relative: ranking the diversity of aquatic bacterial communities

(2008) Allison K. Shaw et al.   ENVIRONMENTAL MICROBIOLOGY

Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific

(2008) Akito Taniguchi et al.   ENVIRONMENTAL MICROBIOLOGY

Spatial comparison of total vs. active bacterial populations by coupling genetic fingerprinting and clone library analyses in the NW Mediterranean Sea

(2008) Arturo Rodríguez-Blanco et al.   FEMS MICROBIOLOGY ECOLOGY

Freshwater and marine virioplankton: a brief overview of commonalities and differences

(2008) STEVEN W. WILHELM et al.   FRESHWATER BIOLOGY

Microbial biodiversity in groundwater ecosystems

(2008) C. GRIEBLER et al.   FRESHWATER BIOLOGY

The rational exploration of microbial diversity

(2008) Christopher Quince et al.   ISME Journal

Method To Detect Only Live Bacteria during PCR Amplification

(2008) T. Soejima et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE

A Global Map of Human Impact on Marine Ecosystems

(2008) Benjamin S. Halpern et al.   SCIENCE

Microbial Biogeography: From Taxonomy to Traits

(2008) J. L. Green et al.   SCIENCE

DNA barcoding for ecologists

(2008) Alice Valentini et al.   TRENDS IN ECOLOGY & EVOLUTION