Genomics and transcriptomics of epizoic Seisonidea (Rotifera, syn. Syndermata) reveal strain formation and gradual gene loss with growing ties to the host

Evolutionary dynamics of transposable elements in bdelloid rotifers

(2021) Reuben W Nowell et al.   eLife

Complete mitochondrial genome of the marine monogonont rotifer Proales similis (Rotifera, Proalidae)

(2020) Beom-Soon Choi et al.   Mitochondrial DNA Part B-Resources

The genome of the marine rotifer Brachionus koreanus sheds light on the antioxidative defense system in response to 2-ethyl-phenanthrene and piperonyl butoxide

(2020) Jun Chul Park et al.   AQUATIC TOXICOLOGY

Characterization of the complete mitogenome of Centrorhynchus clitorideus (Meyer, 1931) (Palaeacanthocephala: Centrorhynchidae), the largest mitochondrial genome in Acanthocephala, and its phylogenetic implications

(2020) Nehaz Muhammad et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

The genome, transcriptome, and proteome of the fish parasite Pomphorhynchus laevis (Acanthocephala)

(2020) Katharina Mauer et al.   PLoS One

Mitigating Anticipated Effects of Systematic Errors Supports Sister-Group Relationship between Xenacoelomorpha and Ambulacraria

(2019) Hervé Philippe et al.   CURRENT BIOLOGY

An integrative taxonomic approach to reveal the status of the genus Pomphorhynchus Monticelli, 1905 (Acanthocephala: Pomphorhynchidae) in Austria

(2019) Susanne Reier et al.   International Journal for Parasitology-Parasites and Wildlife

Temperature-dependent demographic differences in sessile rotifers of the genus Limnias (Rotifera: Gnesiotrocha)

(2019) M.A. Jiménez-Santos et al.   JOURNAL OF ENVIRONMENTAL BIOLOGY

Revisiting metazoan phylogeny with genomic sampling of all phyla

(2019) Christopher E. Laumer et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The genome of the marine monogonont rotifer Brachionus plicatilis: Genome-wide expression profiles of 28 cytochrome P450 genes in response to chlorpyrifos and 2-ethyl-phenanthrene

(2019) Jeonghoon Han et al.   AQUATIC TOXICOLOGY

Small, but surprisingly repetitive genomes: transposon expansion and not polyploidy has driven a doubling in genome size in a metazoan species complex

(2019) J. Blommaert et al.   BMC GENOMICS

Description of Acanthocephalus anguillae balkanicus subsp. n. (Acanthocephala: Echinorhynchidae) from Proteus anguinus Laurenti (Amphibia: Proteidae) and the cave ecomorph of Asellus aquaticus (Crustacea: Asellidae) in Slovenia

(2019) Omar M. Amin et al.   FOLIA PARASITOLOGICA

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of the freshwater monogonont rotifer Brachionus calyciflorus

(2018) Hui-Su Kim et al.   Molecular Ecology Resources

A hyper-diverse genus of acanthocephalans revealed by tree-based and non-tree-based species delimitation methods: Ten cryptic species of Neoechinorhynchus in Middle American freshwater fishes

(2018) Carlos Daniel Pinacho-Pinacho et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

An integrative approach to discovering cryptic species within the Bemisia tabaci whitefly species complex

(2018) Soňa Vyskočilová et al.   Scientific Reports

Expression of NK cluster genes in the onychophoran Euperipatoides rowelli: implications for the evolution of NK family genes in nephrozoans

(2018) Sandra Treffkorn et al.   EvoDevo

Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species

(2018) Reuben W. Nowell et al.   PLOS BIOLOGY

Genomic signatures of local adaptation to the degree of environmental predictability in rotifers

(2018) Lluis Franch-Gras et al.   Scientific Reports

An Annotated Draft Genome for Radix auricularia (Gastropoda, Mollusca)

(2017) Tilman Schell et al.   Genome Biology and Evolution

The impact of Neoechinorhynchus buttnerae (Golvan, 1956) (Eoacanthocephala: Neochinorhynchidae) outbreaks on productive and economic performance of the tambaqui Colossoma macropomum (Cuvier, 1818), reared in ponds

(2017) Ana L. Silva Gomes et al.   Latin American Journal of Aquatic Research

SMS: Smart Model Selection in PhyML

(2017) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rotiferan Hox genes give new insights into the evolution of metazoan bodyplans

(2017) Andreas C. Fröbius et al.   Nature Communications

Conditional Loss of Hoxa5 Function Early after Birth Impacts on Expression of Genes with Synaptic Function

(2017) Benoit Lizen et al.   Frontiers in Molecular Neuroscience

Phylogeny of Syndermata (syn. Rotifera): Mitochondrial gene order verifies epizoic Seisonidea as sister to endoparasitic Acanthocephala within monophyletic Hemirotifera

(2016) Malte Sielaff et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Mitogenomic phylogeny of Acanthocephala reveals novel Class relationships

(2016) Mohiuddin Gazi et al.   ZOOLOGICA SCRIPTA

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Spiralian Phylogeny Informs the Evolution of Microscopic Lineages

(2015) Christopher E. Laumer et al.   CURRENT BIOLOGY

De Novo Assembly and Annotation of the Asian Tiger Mosquito (Aedes albopictus) Repeatome with dnaPipeTE from Raw Genomic Reads and Comparative Analysis with the Yellow Fever Mosquito (Aedes aegypti)

(2015) Clément Goubert et al.   Genome Biology and Evolution

A new species and ten new records of bdelloid rotifers from Korea

(2015) MIN OK SONG et al.   ZOOTAXA

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Platyzoan Paraphyly Based on Phylogenomic Data Supports a Noncoelomate Ancestry of Spiralia

(2014) Torsten H. Struck et al.   MOLECULAR BIOLOGY AND EVOLUTION

RepARK—de novo creation of repeat libraries from whole-genome NGS reads

(2014) Philipp Koch et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Data Reveal Syndermatan Relationships and Suggest the Evolution of Endoparasitism in Acanthocephala via an Epizoic Stage

(2014) Alexandra R. Wey-Fabrizius et al.   PLoS One

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

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

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

(2013) Jean-François Flot et al.   NATURE

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Platyzoan mitochondrial genomes

(2012) Alexandra R. Wey-Fabrizius et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

FastML: a web server for probabilistic reconstruction of ancestral sequences

(2012) H. Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

A new species of Paraseison (Rotifera: Seisonacea) from the coast of California, USA

(2011) Francesca Leasi et al.   JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Conserved and novel roles for the Gsh2 transcription factor in primary neurogenesis

(2010) E. F. Winterbottom et al.   DEVELOPMENT

Cryptic diversity in the genus Adineta Hudson & Gosse, 1886 (Rotifera: Bdelloidea: Adinetidae): a DNA taxonomy approach

(2010) Diego Fontaneto et al.   HYDROBIOLOGIA

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

TEclass--a tool for automated classification of unknown eukaryotic transposable elements

(2009) G. Abrusan et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Eurotatorian paraphyly: Revisiting phylogenetic relationships based on the complete mitochondrial genome sequence of Rotaria rotatoria (Bdelloidea: Rotifera: Syndermata)

(2009) Gi-Sik Min et al.   BMC GENOMICS

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Support for the monophyletic origin of Gnathifera from phylogenomics

(2009) Alexander Witek et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

EST based phylogenomics of Syndermata questions monophyly of Eurotatoria

(2008) Alexander Witek et al.   BMC EVOLUTIONARY BIOLOGY

Degenerate Tetraploidy Was Established Before Bdelloid Rotifer Families Diverged

(2008) J. H. Hur et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic Organization and Expression Demonstrate Spatial and Temporal Hox Gene Colinearity in the Lophotrochozoan Capitella sp. I

(2008) Andreas C. Fröbius et al.   PLoS One

Evidence for degenerate tetraploidy in bdelloid rotifers

(2008) David B. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA