Combining morphological and metabarcoding approaches reveals the freshwater eukaryotic phytoplankton community

Applicability of DNA metabarcoding approach in the bioassessment of Portuguese rivers using diatoms

(2019) Andreia Mortágua et al.   ECOLOGICAL INDICATORS

Tracking a century of changes in microbial eukaryotic diversity in lakes driven by nutrient enrichment and climate warming

(2017) Eric Capo et al.   ENVIRONMENTAL MICROBIOLOGY

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

(2015) Philippe Esling et al.   NUCLEIC ACIDS RESEARCH

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

(2015) Leho Tedersoo et al.   MycoKeys

MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species

(2015) M. Miya et al.   Royal Society Open Science

A Higher Level Classification of All Living Organisms

(2015) Michael A. Ruggiero et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Metabarcoding vs. morphological identification to assess diatom diversity in environmental studies

(2014) Jonas Zimmermann et al.   Molecular Ecology Resources

Does the Cosmopolitan Diatom Gomphonema parvulum (Kützing) Kützing Have a Biogeography?

(2014) Nelida Abarca et al.   PLoS One

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Alexander Eiler et al.   PLoS One

First Evidence of the Existence of Semi-Cryptic Species and of a Phylogeographic Structure in the Gomphonema parvulum (Kützing) Kützing Complex (Bacillariophyta)

(2013) Lenaïg Kermarrec et al.   PROTIST

High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities

(2013) Aibin Zhan et al.   Methods in Ecology and Evolution

Effects of silver carp (Hypophthalmichthys molitrix) on spring phytoplankton community structure of Three-Gorges Reservoir (China): results from an enclosure experiment

(2012) Guangjie ZHOU et al.   JOURNAL OF LIMNOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Aligning short reads to reference alignments and trees

(2011) Simon A. Berger et al.   BIOINFORMATICS

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Molecular Detection of Invasive Species in Heterogeneous Mixtures Using a Microfluidic Carbon Nanotube Platform

(2011) Andrew R. Mahon et al.   PLoS One

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

Plastid evolution: gene transfer and the maintenance of 'stolen' organelles

(2010) Eunsoo Kim et al.   BMC BIOLOGY

The use of partialcox1,rbcL and LSU rDNA sequences for phylogenetics and species identification within theNitzschia paleaspecies complex (Bacillariophyceae)

(2010) Rosa Trobajo et al.   EUROPEAN JOURNAL OF PHYCOLOGY

Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean

(2010) Ludwig Jardillier et al.   ISME Journal

Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton

(2010) M. L. Cuvelier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

phyloXML: XML for evolutionary biology and comparative genomics

(2009) Mira V Han et al.   BMC BIOINFORMATICS

Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities

(2009) Thorsten Stoeck et al.   BMC BIOLOGY

High-Level Diversity of Dinoflagellates in the Natural Environment, Revealed by Assessment of Mitochondrial cox1 and cob Genes for Dinoflagellate DNA Barcoding

(2008) S. Lin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY