Related references
Note: Only part of the references are listed.Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis
Patrick D. Schloss et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)
Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering
Xiaolin Hao et al.
BIOINFORMATICS (2011)
CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation
Surendra Kumar et al.
BMC BIOINFORMATICS (2011)
Removing Noise From Pyrosequenced Amplicons
Christopher Quince et al.
BMC BIOINFORMATICS (2011)
Navigating the multiple meanings of beta diversity: a roadmap for the practicing ecologist
Marti J. Anderson et al.
ECOLOGY LETTERS (2011)
Linking bacterial identities and ecosystem processes: can 'omic' analyses be more than the sum of their parts?
Sergio E. Morales et al.
FEMS MICROBIOLOGY ECOLOGY (2011)
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
Brian J. Haas et al.
GENOME RESEARCH (2011)
Microbial community structure across the tree of life in the extreme Rio Tinto
Linda A. Amaral-Zettler et al.
ISME JOURNAL (2011)
Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing
Helene Agogue et al.
MOLECULAR ECOLOGY (2011)
Biodiversity improves water quality through niche partitioning
Bradley J. Cardinale
NATURE (2011)
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
Pelin Yilmaz et al.
NATURE BIOTECHNOLOGY (2011)
Microbial seed banks: the ecological and evolutionary implications of dormancy
Jay T. Lennon et al.
NATURE REVIEWS MICROBIOLOGY (2011)
Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems
Lucie Zinger et al.
PLOS ONE (2011)
Repeated sampling reveals differential variability in measures of species richness and community composition in planktonic protists
John R. Dolan et al.
ENVIRONMENTAL MICROBIOLOGY REPORTS (2011)
BIOLOGY Uncertain future for ocean algae
Michael Behrenfeld
NATURE CLIMATE CHANGE (2011)
Anthropogenic perturbations in marine microbial communities
Balbina Nogales et al.
FEMS MICROBIOLOGY REVIEWS (2011)
Spatial patterns of bacterial richness and evenness in the NW Mediterranean Sea explored by pyrosequencing of the 16S rRNA
Thomas Pommier et al.
AQUATIC MICROBIAL ECOLOGY (2010)
Global phylogenetic community structure and beta-diversity patterns in surface bacterioplankton metacommunities
Albert Barberan et al.
AQUATIC MICROBIAL ECOLOGY (2010)
Evaluation of DNA extraction methods from complex phototrophic biofilms
Isabel Ferrera et al.
BIOFOULING (2010)
Search and clustering orders of magnitude faster than BLAST
Robert C. Edgar
BIOINFORMATICS (2010)
SeqTrim: a high-throughput pipeline for pre-processing any type of sequence read
Juan Falgueras et al.
BMC BIOINFORMATICS (2010)
Third Generation DNA Sequencing: Pacific Biosciences' Single Molecule Real Time Technology
Alice McCarthy
CHEMISTRY & BIOLOGY (2010)
Ironing out the wrinkles in the rare biosphere through improved OTU clustering
Susan M. Huse et al.
ENVIRONMENTAL MICROBIOLOGY (2010)
Global ecological patterns in uncultured Archaea
Jean-Christophe Auguet et al.
ISME JOURNAL (2010)
PANGEA: pipeline for analysis of next generation amplicons
Adriana Giongo et al.
ISME JOURNAL (2010)
Distinct flavobacterial communities in contrasting water masses of the North Atlantic Ocean
Paola R. Gomez-Pereira et al.
ISME JOURNAL (2010)
Multiple marker parallel tag environmental DNA sequencing reveals a highly complex eukaryotic community in marine anoxic water
T. Stoeck et al.
MOLECULAR ECOLOGY (2010)
Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions
Jens Reeder et al.
NATURE METHODS (2010)
QIIME allows analysis of high-throughput community sequencing data
J. Gregory Caporaso et al.
NATURE METHODS (2010)
Megx.net: integrated database resource for marine ecological genomics
Renzo Kottmann et al.
NUCLEIC ACIDS RESEARCH (2010)
Multivariate Cutoff Level Analysis (MultiCoLA) of large community data sets
Angelique Gobet et al.
NUCLEIC ACIDS RESEARCH (2010)
Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions
Marcus J. Claesson et al.
NUCLEIC ACIDS RESEARCH (2010)
One Bacterial Cell, One Complete Genome
Tanja Woyke et al.
PLOS ONE (2010)
When metagenomics meets stable-isotope probing: progress and perspectives
Yin Chen et al.
TRENDS IN MICROBIOLOGY (2010)
Ecological consequences of bacterioplankton lifestyles: changes in concepts are needed
Hans-Peter Grossart
ENVIRONMENTAL MICROBIOLOGY REPORTS (2010)
The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies
Patrick D. Schloss
PLOS COMPUTATIONAL BIOLOGY (2010)
Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology
David A. Caron et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2009)
RAMI: a tool for identification and characterization of phylogenetic clusters in microbial communities
Thomas Pommier et al.
BIOINFORMATICS (2009)
Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure
Julie A. Huber et al.
ENVIRONMENTAL MICROBIOLOGY (2009)
The seasonal structure of microbial communities in the Western English Channel
Jack A. Gilbert et al.
ENVIRONMENTAL MICROBIOLOGY (2009)
Spatial comparison of total vs. active bacterial populations by coupling genetic fingerprinting and clone library analyses in the NW Mediterranean Sea
Arturo Rodriguez-Blanco et al.
FEMS MICROBIOLOGY ECOLOGY (2009)
Diversity of total and active free-living vs. particle-attached bacteria in the euphotic zone of the NW Mediterranean Sea
Jean-Francois Ghiglione et al.
FEMS MICROBIOLOGY LETTERS (2009)
Microbial biodiversity in groundwater ecosystems
C. Griebler et al.
FRESHWATER BIOLOGY (2009)
Analyzing salt-marsh fungal diversity: comparing ARISA fingerprinting with clone sequencing and pyrosequencing
Patrick M. Gillevet et al.
FUNGAL ECOLOGY (2009)
Nucleic acids as viability markers for bacteria detection using molecular tools
Claire Cenciarini-Borde et al.
FUTURE MICROBIOLOGY (2009)
Bias in assessments of marine microbial biodiversity in fosmid libraries as evaluated by pyrosequencing
Ben Temperton et al.
ISME JOURNAL (2009)
Polymerase chain reaction primers miss half of rRNA microbial diversity
SunHee Hong et al.
ISME JOURNAL (2009)
Microbial community structure in the North Pacific ocean
Mark V. Brown et al.
ISME JOURNAL (2009)
Microbial community structure and its functional implications
Jed A. Fuhrman
NATURE (2009)
The 'rare biosphere': a reality check
Jens Reeder et al.
NATURE METHODS (2009)
Accurate determination of microbial diversity from 454 pyrosequencing data
Christopher Quince et al.
NATURE METHODS (2009)
ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences
Yijun Sun et al.
NUCLEIC ACIDS RESEARCH (2009)
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
J. R. Cole et al.
NUCLEIC ACIDS RESEARCH (2009)
New Insights into the Diversity of Marine Picoeukaryotes
Fabrice Not et al.
PLOS ONE (2009)
Groups without Cultured Representatives Dominate Eukaryotic Picophytoplankton in the Oligotrophic South East Pacific Ocean
Xiao Li Shi et al.
PLOS ONE (2009)
Ecology of the rare microbial biosphere of the Arctic Ocean
Pierre E. Galand et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
DNA barcoding for ecologists
Alice Valentini et al.
TRENDS IN ECOLOGY & EVOLUTION (2009)
Infrequent marine-freshwater transitions in the microbial world
Ramiro Logares et al.
TRENDS IN MICROBIOLOGY (2009)
Molecular diversity of bacterioplankton: link to a predictive biogeochemistry of pelagic ecosystems
Manfred G. Hoefle et al.
AQUATIC MICROBIAL ECOLOGY (2008)
Environmental rRNA inventories miss over half of protistan diversity
Sunok Jeon et al.
BMC MICROBIOLOGY (2008)
It's all relative: ranking the diversity of aquatic bacterial communities
Allison K. Shaw et al.
ENVIRONMENTAL MICROBIOLOGY (2008)
Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific
Akito Taniguchi et al.
ENVIRONMENTAL MICROBIOLOGY (2008)
Freshwater and marine virioplankton: a brief overview of commonalities and differences
Steven W. Wilhelm et al.
FRESHWATER BIOLOGY (2008)
The rational exploration of microbial diversity
Christopher Quince et al.
ISME JOURNAL (2008)
Method to detect only live bacteria during PCR amplification
Takashi Soejima et al.
JOURNAL OF CLINICAL MICROBIOLOGY (2008)
Next-generation DNA sequencing
Jay Shendure et al.
NATURE BIOTECHNOLOGY (2008)
Microbial community gene expression in ocean surface waters
Jorge. Frias-Lopez et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Alignment uncertainty and genomic analysis
Karen M. Wong et al.
SCIENCE (2008)
The microbial engines that drive Earth's biogeochemical cycles
Paul G. Falkowski et al.
SCIENCE (2008)
A global map of human impact on marine ecosystems
Benjamin S. Halpern et al.
SCIENCE (2008)
Microbial biogeography: From taxonomy to traits
Jessica L. Green et al.
SCIENCE (2008)
Measuring rDNA diversity in eukaryotic microbial systems: how intragenomic variation, pseudogenes, and PCR artifacts confound biodiversity estimates
Daniel J. Thornhill et al.
MOLECULAR ECOLOGY (2007)
SILVA:: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB
Elmar Pruesse et al.
NUCLEIC ACIDS RESEARCH (2007)
Microbial oceanography: paradigms, processes and promise
David M. Karl
NATURE REVIEWS MICROBIOLOGY (2007)
Short pyrosequencing reads suffice for accurate microbial community analysis
Zongzhi Liu et al.
NUCLEIC ACIDS RESEARCH (2007)
Use of propidium monoazide for live/dead distinction in microbial ecology
Andreas Nocker et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)
Extracellular nucleic acids
Valentin V. Vlassov et al.
BIOESSAYS (2007)
Essay - The role of ecological theory in microbial ecology
James I. Prosser et al.
NATURE REVIEWS MICROBIOLOGY (2007)
A molecular approach to identify active microbes in environmental eukaryote clone libraries
Thorsten Stoeck et al.
MICROBIAL ECOLOGY (2007)
Global patterns of diversity and community structure in marine bacterioplankton
T. Pommier et al.
MOLECULAR ECOLOGY (2007)
Accuracy and quality of massively parallel DNA pyrosequencing
Susan M. Huse et al.
GENOME BIOLOGY (2007)
The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through Eastern Tropical Pacific
Douglas B. Rusch et al.
PLOS BIOLOGY (2007)
Measuring species richness based on microbial community fingerprints: The emperor has no clothes
Stephen J. Bent et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)
Impacts of biodiversity loss on ocean ecosystem services
Boris Worm et al.
SCIENCE (2006)
Spatial variability in the abundance and composition of the free-living bacterioplankton community in the pelagic zone of Lake Bourget (France)
Ursula Dorigo et al.
FEMS MICROBIOLOGY ECOLOGY (2006)
Microbial diversity in the deep sea and the underexplored rare biosphere
Mitchell L. Sogin et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Weizhong Li et al.
BIOINFORMATICS (2006)
Freshwater biodiversity:: importance, threats, status and conservation challenges
David Dudgeon et al.
BIOLOGICAL REVIEWS (2006)
FastGroupII: A web-based bioinformatics platform for analyses of large 16S rDNA libraries
YN Yu et al.
BMC BIOINFORMATICS (2006)
Why biodiversity is important to oceanography: potential roles of genetic, species, and trophic diversity in pelagic ecosystem processes
J. Emmett Duffy et al.
MARINE ECOLOGY PROGRESS SERIES (2006)
Zooplankton and the oceanography of the eastern tropical Pacific: A review
Maria Ana Fernandez-Alamo et al.
PROGRESS IN OCEANOGRAPHY (2006)
PCR-induced sequence artifacts and bias: Insights from comparison of two 16S rRNA clone libraries constructed from the same sample
SG Acinas et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2005)
Spatial and temporal scales of variation in bacterioplankton community structure in the NW Mediterranean Sea
JF Ghiglione et al.
AQUATIC MICROBIAL ECOLOGY (2005)
The extent of protist diversity:: insights from molecular ecology of freshwater eukaryotes
J Slapeta et al.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2005)
Molecular diversity and ecology of microbial plankton
SJ Giovannoni et al.
NATURE (2005)
Genomic perspectives in microbial oceanography
EF DeLong et al.
NATURE (2005)
Predation on prokaryotes in the water column and its ecological implications
J Pernthaler
NATURE REVIEWS MICROBIOLOGY (2005)
Multiple displacement amplification as a pre-polymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy number sequences from natural environments
JM Gonzalez et al.
ENVIRONMENTAL MICROBIOLOGY (2005)
Molecular approaches to the assessment of biodiversity in aquatic microbial communities
U Dorigo et al.
WATER RESEARCH (2005)
Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene
F Zhu et al.
FEMS MICROBIOLOGY ECOLOGY (2005)
Development of procedures for direct extraction of Cryptosporidium DNA from water concentrates and for relief of PCR inhibitors
JL Jiang et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2005)
A comparison of DNA- and RNA-based clone libraries from the same marine bacterioplankton community
MM Moeseneder et al.
FEMS MICROBIOLOGY ECOLOGY (2005)
The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
JR Cole et al.
NUCLEIC ACIDS RESEARCH (2005)
Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons
SG Acinas et al.
JOURNAL OF BACTERIOLOGY (2004)
Protist taxonomy: an ecological perspective
BJ Finlay
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2004)
Environmental genome shotgun sequencing of the Sargasso Sea
JC Venter et al.
SCIENCE (2004)
MUSCLE: multiple sequence alignment with high accuracy and high throughput
RC Edgar
NUCLEIC ACIDS RESEARCH (2004)
Bellerophon: a program to detect chimeric sequences in multiple sequence alignments
T Huber et al.
BIOINFORMATICS (2004)
Fine-scale phylogenetic architecture of a complex bacterial community
SG Acinas et al.
NATURE (2004)
Dynamics of microbial communities on marine snow aggregates: Colonization, growth, detachment, and grazing mortality of attached bacteria
T Kiorboe et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2003)
Single-molecule PCR using water-in-oil emulsion
M Nakano et al.
JOURNAL OF BIOTECHNOLOGY (2003)
Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases
P Hugenholtz et al.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2003)
Estimating prokaryotic diversity and its limits
TP Curtis et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
K Katoh et al.
NUCLEIC ACIDS RESEARCH (2002)
Large fraction of dead and inactive bacteria in coastal marine sediments: Comparison of protocols for determination and ecological significance
GM Luna et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2002)
Small players, large role: Microbial influence on biogeochemical processes in pelagic aquatic ecosystems
JB Cotner et al.
ECOSYSTEMS (2002)
Ecology - Biodiversity and ecosystem functioning: Current knowledge and future challenges
M Loreau et al.
SCIENCE (2001)
Lateral gene transfer and the nature of bacterial innovation
H Ochman et al.
NATURE (2000)