Novel Primer Sets for Next Generation Sequencing-Based Analyses of Water Quality

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

(2015) A Apprill et al.   AQUATIC MICROBIAL ECOLOGY

Comparison of Sanger and next generation sequencing performance for genotyping Cryptosporidium isolates at the 18S rRNA and actin loci

(2015) Andrea Paparini et al.   EXPERIMENTAL PARASITOLOGY

Inhibition of the endosymbiont “Candidatus Midichloria mitochondrii” during 16S rRNA gene profiling reveals potential pathogens in Ixodes ticks from Australia

(2015) Alexander Gofton et al.   Parasites & Vectors

Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform

(2015) Lucas Sinclair et al.   PLoS One

Fiber supplementation influences phylogenetic structure and functional capacity of the human intestinal microbiome: follow-up of a randomized controlled trial

(2014) Hannah D Holscher et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Spatial biodiversity of bacteria along the largest Arctic river determined by next-generation sequencing

(2014) Olesya V. Kolmakova et al.   FEMS MICROBIOLOGY ECOLOGY

An Expanded Genomic Representation of the Phylum Cyanobacteria

(2014) Rochelle M. Soo et al.   Genome Biology and Evolution

Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers

(2014) Kenan Hadziavdic et al.   PLoS One

Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing

(2014) Shunsuke Takahashi et al.   PLoS One

Polyphasic identification of cyanobacterial isolates from Australia

(2014) Elvina Lee et al.   WATER RESEARCH

PCR primers for selective detection of intra-species variations in the bloom-forming cyanobacterium, Microcystis

(2013) Takafumi Kataoka et al.   HARMFUL ALGAE

Harmful Cyanobacterial Blooms: Causes, Consequences, and Controls

(2013) Hans W. Paerl et al.   MICROBIAL ECOLOGY

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

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

Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms

(2013) L. Kermarrec et al.   Molecular Ecology Resources

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Molecular genetic tools for environmental monitoring of New Zealand's aquatic habitats, past, present and the future

(2013) SA Wood et al.   NEW ZEALAND JOURNAL OF MARINE AND FRESHWATER RESEARCH

LPSN—list of prokaryotic names with standing in nomenclature

(2013) Aidan C. Parte   NUCLEIC ACIDS RESEARCH

Unveiling Distribution Patterns of Freshwater Phytoplankton by a Next Generation Sequencing Based Approach

(2013) Alexander Eiler et al.   PLoS One

Taxonomic Classification of Bacterial 16S rRNA Genes Using Short Sequencing Reads: Evaluation of Effective Study Designs

(2013) Orna Mizrahi-Man et al.   PLoS One

Preliminary Assessment of Microbiome Changes Following Blood-Feeding and Survivorship in the Amblyomma americanum Nymph-to-Adult Transition using Semiconductor Sequencing

(2013) Arturo C. Menchaca 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

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Microbial 16S rRNA Ion Tag and community metagenome sequencing using the Ion Torrent (PGM) Platform

(2012) Andrew S. Whiteley et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Phylogenetic and gene trees of Synechococcus: choice of the right marker to evaluate the population diversity in the Tucurui Hydroelectric Power Station Reservoir in Brazilian Amazonia

(2012) L. T. Dall'agnol et al.   JOURNAL OF PLANKTON RESEARCH

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

PCR Primers for Metazoan Nuclear 18S and 28S Ribosomal DNA Sequences

(2012) Ryuji J. Machida et al.   PLoS One

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & EVOLUTION

The golden age of DNA metasystematics

(2012) Mehrdad Hajibabaei   TRENDS IN GENETICS

Culture-independent methods for studying environmental microorganisms: methods, application, and perspective

(2011) Can Su et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA

(2011) Anders Lanzén et al.   FEMS MICROBIOLOGY ECOLOGY

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Toxicity of the cyanobacterium Limnothrix AC0243 to male Balb/c mice

(2011) Andrew Humpage et al.   WATER RESEARCH

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

An rpoB signature sequence provides unique resolution for the molecular typing of cyanobacteria

(2010) V. Gaget et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

(2010) S. CREER et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

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

A new quantitative PCR assay for the detection of hepatotoxigenic cyanobacteria

(2010) J. Al-Tebrineh et al.   TOXICON

Polymerase chain reaction primers miss half of rRNA microbial diversity

(2009) SunHee Hong et al.   ISME Journal

Molecular identification, typing and traceability of cyanobacteria from freshwater reservoirs

(2009) E. Valerio et al.   MICROBIOLOGY-SGM

Q Fever

(2008) Hervé Tissot-Dupont et al.   INFECTIOUS DISEASE CLINICS OF NORTH AMERICA

Development and field testing of a real-time PCR assay for cylindrospermopsin-producing cyanobacteria

(2008) J.P. Rasmussen et al.   JOURNAL OF APPLIED MICROBIOLOGY