Assessing the Diversity and Distribution of Apicomplexans in Host and Free-Living Environments Using High-Throughput Amplicon Data and a Phylogenetically Informed Reference Framework

A widespread coral-infecting apicomplexan with chlorophyll biosynthesis genes

(2019) Waldan K. Kwong et al.   NATURE

Global diversity and distribution of close relatives of apicomplexan parasites

(2018) Varsha Mathur et al.   ENVIRONMENTAL MICROBIOLOGY

High-throughput environmental sequencing reveals high diversity of litter and moss associated protist communities along a gradient of drainage and tree productivity

(2018) Thierry J. Heger et al.   ENVIRONMENTAL MICROBIOLOGY

Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

(2018) Sina M. Adl et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

EukRef: Phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution

(2018) Javier del Campo et al.   PLOS BIOLOGY

The apicoplast: now you see it, now you don’t

(2017) Geoffrey Ian McFadden et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Parasites dominate hyperdiverse soil protist communities in Neotropical rainforests

(2017) Frédéric Mahé et al.   Nature Ecology & Evolution

Protist metabarcoding and environmental biomonitoring: Time for change

(2016) J. Pawlowski et al.   EUROPEAN JOURNAL OF PROTISTOLOGY

Nematopsis temporariae(Gregarinasina, Apicomplexa, Alveolata) is an intracellular infectious agent of tadpole livers

(2016) Aurélie Chambouvet et al.   Environmental Microbiology Reports

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

(2015) Ramon Massana et al.   ENVIRONMENTAL MICROBIOLOGY

Marked seasonality and high spatial variability of protist communities in shallow freshwater systems

(2015) Marianne Simon et al.   ISME Journal

Metatranscriptomic census of active protists in soils

(2015) Stefan Geisen et al.   ISME Journal

Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives

(2015) Jan Janouškovec et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rethinking the marine carbon cycle: Factoring in the multifarious lifestyles of microbes

(2015) A. Z. Worden et al.   SCIENCE

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites

(2015) Yong H Woo et al.   eLife

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

VAMPS: a website for visualization and analysis of microbial population structures

(2014) Susan M Huse et al.   BMC BIOINFORMATICS

Gregarine site-heterogeneous 18S rDNA trees, revision of gregarine higher classification, and the evolutionary diversification of Sporozoa

(2014) Thomas Cavalier-Smith   EUROPEAN JOURNAL OF PROTISTOLOGY

The origins of malaria: there are more things in heaven and earth …

(2014) P. J. KEELING et al.   PARASITOLOGY

Environmental DNA for wildlife biology and biodiversity monitoring

(2014) Kristine Bohmann et al.   TRENDS IN ECOLOGY & EVOLUTION

Policy, phylogeny, and the parasite

(2014) Grant D. Stentiford et al.   TRENDS IN PARASITOLOGY

Environmental Survey Meta-analysis Reveals Hidden Diversity among Unicellular Opisthokonts

(2013) Javier del Campo et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Babesia: A world emerging

(2012) Leonhard Schnittger et al.   INFECTION GENETICS AND EVOLUTION

Environmental distribution of coral-associated relatives of apicomplexan parasites

(2012) Jan Janouškovec et al.   ISME Journal

Phylogenetic Position of the Adeleorinid Coccidia (Myzozoa, Apicomplexa, Coccidia, Eucoccidiorida, Adeleorina) Inferred Using 18S rDNA Sequences

(2012) John R. Barta et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Emerging fungal threats to animal, plant and ecosystem health

(2012) Matthew C. Fisher et al.   NATURE

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Sophisticated Adaptations of Gregarina cuneata (Apicomplexa) Feeding Stages for Epicellular Parasitism

(2012) Andrea Valigurová   PLoS One

Aligning short reads to reference alignments and trees

(2011) Simon A. Berger et al.   BIOINFORMATICS

Identification of a Divergent Environmental DNA Sequence Clade Using the Phylogeny of Gregarine Parasites (Apicomplexa) from Crustacean Hosts

(2011) Sonja Rueckert et al.   PLoS One

Emerging Diversity within Chrysophytes, Choanoflagellates and Bicosoecids Based on Molecular Surveys

(2011) Javier del Campo et al.   PROTIST

Morphology, Ultrastructure and Life Cycle of Vitrella brassicaformis n. sp., n. gen., a Novel Chromerid from the Great Barrier Reef

(2011) Miroslav Oborník et al.   PROTIST

Apicystis bombi (Apicomplexa: Neogregarinorida) parasitizing Apis mellifera and Bombus terrestris (Hymenoptera: Apidae) in Argentina

(2011) Santiago Plischuk et al.   Environmental Microbiology Reports

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

(2010) THORSTEN STOECK et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

When parasites become prey: ecological and epidemiological significance of eating parasites

(2010) Pieter T.J. Johnson et al.   TRENDS IN ECOLOGY & EVOLUTION

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

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

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

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

Marine gregarines: evolutionary prelude to the apicomplexan radiation?

(2008) Brian S. Leander   TRENDS IN PARASITOLOGY

Sequence heterogeneity in the 18S rRNA gene within Theileria equi and Babesia caballi from horses in South Africa

(2008) Raksha Bhoora et al.   VETERINARY PARASITOLOGY