Oligotrophic lagoons of the South Pacific Ocean are home to a surprising number of novel eukaryotic microorganisms

Marine protist diversity in European coastal waters and sediments as revealed by high-throughput sequencing

(2015) Ramon Massana et al.   ENVIRONMENTAL MICROBIOLOGY

Rarity in aquatic microbes: placing protists on the map

(2015) Ramiro Logares et al.   RESEARCH IN MICROBIOLOGY

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Patterns of Rare and Abundant Marine Microbial Eukaryotes

(2014) Ramiro Logares et al.   CURRENT BIOLOGY

Taxon-Rich Phylogenomic Analyses Resolve the Eukaryotic Tree of Life and Reveal the Power of Subsampling by Sites

(2014) Laura A. Katz et al.   SYSTEMATIC BIOLOGY

Palpitomonas bilix represents a basal cryptist lineage: insight into the character evolution in Cryptista

(2014) Akinori Yabuki et al.   Scientific Reports

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Colponemids Represent Multiple Ancient Alveolate Lineages

(2013) Jan Janouškovec et al.   CURRENT BIOLOGY

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities

(2013) Ramiro Logares et al.   ENVIRONMENTAL MICROBIOLOGY

Phylogeny and evolution of Planomonadida (Sulcozoa): Eight new species and new genera Fabomonas and Nutomonas

(2013) Edvard Glücksman et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles

(2013) Ramon Massana et al.   ISME Journal

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Picomonas judraskeda Gen. Et Sp. Nov.: The First Identified Member of the Picozoa Phylum Nov., a Widespread Group of Picoeukaryotes, Formerly Known as ‘Picobiliphytes’

(2013) Ramkumar Seenivasan et al.   PLoS One

Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads

(2013) M. W. Brown et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The World Ocean Silica Cycle

(2012) Paul J. Tréguer et al.   Annual Review of Marine Science

Adding unaligned sequences into an existing alignment using MAFFT and LAST

(2012) Kazutaka Katoh et al.   BIOINFORMATICS

Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing

(2012) Ramiro Logares et al.   ISME Journal

Comparing the Hyper-Variable V4 and V9 Regions of the Small Subunit rDNA for Assessment of Ciliate Environmental Diversity

(2012) Micah Dunthorn et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

The Revised Classification of Eukaryotes

(2012) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Collodictyon--An Ancient Lineage in the Tree of Eukaryotes

(2012) S. Zhao et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Oxnerella micra sp. n. (Oxnerellidae fam. n.), a Tiny Naked Centrohelid, and the Diversity and Evolution of Heliozoa

(2012) Thomas Cavalier-Smith et al.   PROTIST

Rigifila ramosa n. gen., n. sp., a Filose Apusozoan with a Distinctive Pellicle, is Related to Micronuclearia

(2012) Akinori Yabuki et al.   PROTIST

Ultrastructure and Molecular Phylogeny of the Cryptomonad Goniomonas avonlea sp. nov.

(2012) Eunsoo Kim et al.   PROTIST

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing

(2011) Jan Pawlowski et al.   PLoS One

Newly identified and diverse plastid-bearing branch on the eukaryotic tree of life

(2011) E. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microheliella maris (Microhelida ord. n.), an Ultrastructurally Highly Distinctive New Axopodial Protist Species and Genus, and the Unity of Phylum Heliozoa

(2011) Akinori Yabuki et al.   PROTIST

Single-Cell Genomics Reveals Organismal Interactions in Uncultivated Marine Protists

(2011) H. S. Yoon et al.   SCIENCE

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Telonemia-specific environmental 18S rDNA PCR reveals unknown diversity and multiple marine-freshwater colonizations

(2010) Jon Bråte et al.   BMC MICROBIOLOGY

Palpitomonas bilix gen. et sp. nov.: A Novel Deep-branching Heterotroph Possibly Related to Archaeplastida or Hacrobia

(2010) Akinori Yabuki et al.   PROTIST

Phylogeny and Evolution of Apusomonadida (Protozoa: Apusozoa): New Genera and Species

(2010) Thomas Cavalier-Smith et al.   PROTIST

The Novel Marine Gliding Zooflagellate Genus Mantamonas (Mantamonadida ord. n.: Apusozoa)

(2010) Edvard Glücksman et al.   PROTIST

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

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

Molecular Evidence that Phylogenetically Diverged Ciliates Are Active in Microbial Mats of Deep-Sea Cold-Seep Sediment

(2009) KIYOTAKA TAKISHITA et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

The life of diatoms in the world's oceans

(2009) E. Virginia Armbrust   NATURE

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2009) Linda A. Amaral-Zettler et al.   PLoS One

New Insights into the Diversity of Marine Picoeukaryotes

(2009) Fabrice Not et al.   PLoS One

Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups"

(2009) V. Hampl et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial eukaryotes in the hypersaline anoxic L'Atalante deep-sea basin

(2008) Eva Alexander et al.   ENVIRONMENTAL MICROBIOLOGY

A three-genome phylogeny of malaria parasites (Plasmodium and closely related genera): Evolution of life-history traits and host switches

(2007) Ellen S. Martinsen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION