Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

Liposomes with diverse compositions are protected during desiccation by LEA proteins from Artemia franciscana and trehalose

(2016) Daniel S. Moore et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

The Compact Body Plan of Tardigrades Evolved by the Loss of a Large Body Region

(2016) Frank W. Smith et al.   CURRENT BIOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Ensembl 2017

(2016) Bronwen L. Aken et al.   NUCLEIC ACIDS RESEARCH

Reply to Bemm et al. and Arakawa: Identifying foreign genes in independentHypsibius dujardinigenome assemblies

(2016) Thomas C. Boothby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome of a tardigrade: Horizontal gene transfer or bacterial contamination?

(2016) Felix Bemm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

No evidence for extensive horizontal gene transfer from the draft genome of a tardigrade

(2016) Kazuharu Arakawa   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

No evidence for extensive horizontal gene transfer in the genome of the tardigradeHypsibius dujardini

(2016) Georgios Koutsovoulos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein

(2016) Takuma Hashimoto et al.   Nature Communications

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies

(2016) Tom O. Delmont et al.   PeerJ

Genome sequencing of a single tardigrade Hypsibius dujardini individual

(2016) Kazuharu Arakawa et al.   Scientific Data

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

WormBase 2016: expanding to enable helminth genomic research

(2015) Kevin L. Howe et al.   NUCLEIC ACIDS RESEARCH

The Dfam database of repetitive DNA families

(2015) Robert Hubley et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Evidence for extensive horizontal gene transfer from the draft genome of a tardigrade

(2015) Thomas C. Boothby et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Neural development in the tardigrade Hypsibius dujardini based on anti-acetylated α-tubulin immunolabeling

(2015) Vladimir Gross et al.   EvoDevo

Novel Mitochondria-Targeted Heat-Soluble Proteins Identified in the Anhydrobiotic Tardigrade Improve Osmotic Tolerance of Human Cells

(2015) Sae Tanaka et al.   PLoS One

Suggested Involvement of PP1/PP2A Activity and De Novo Gene Expression in Anhydrobiotic Survival in a Tardigrade, Hypsibius dujardini, by Chemical Genetic Approach

(2015) Koyuki Kondo et al.   PLoS One

The Ensembl REST API: Ensembl Data for Any Language

(2014) Andrew Yates et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads

(2014) Hongshan Jiang et al.   BMC BIOINFORMATICS

Onychophoran Hox genes and the evolution of arthropod Hox gene expression

(2014) Ralf Janssen et al.   Frontiers in Zoology

FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies

(2014) Patrick Kück et al.   Frontiers in Zoology

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

(2014) Rei Kajitani et al.   GENOME RESEARCH

A transcriptome approach to ecdysozoan phylogeny

(2014) Janus Borner et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

The triradiate sucking pharynx in animal phylogeny

(2013) Claus Nielsen   INVERTEBRATE BIOLOGY

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

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

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Analysis of DNA Repair and Protection in the Tardigrade Ramazzottius varieornatus and Hypsibius dujardini after Exposure to UVC Radiation

(2013) Daiki D. Horikawa et al.   PLoS One

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

(2013) Sujai Kumar et al.   Frontiers in Genetics

RNA interference can be used to disrupt gene function in tardigrades

(2012) Jennifer R. Tenlen et al.   DEVELOPMENT GENES AND EVOLUTION

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Two Novel Heat-Soluble Protein Families Abundantly Expressed in an Anhydrobiotic Tardigrade

(2012) Ayami Yamaguchi et al.   PLoS One

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Biochemical Diversification through Foreign Gene Expression in Bdelloid Rotifers

(2012) Chiara Boschetti et al.   PLoS Genetics

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

The induction of anhydrobiosis in the sleeping chironomid: Current status of our knowledge

(2011) Richard Cornette et al.   IUBMB LIFE

Ultraviolet radiation tolerance in hydrated and desiccated eutardigrades

(2011) Tiziana Altiero et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Extreme stress tolerance in tardigrades: surviving space conditions in low earth orbit

(2011) Dennis Persson et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades

(2011) Marc R. Friedländer et al.   NUCLEIC ACIDS RESEARCH

MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda

(2011) L. I. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer

(2010) Brahim Mali et al.   BMC GENOMICS

Antioxidant defences in hydrated and desiccated states of the tardigrade Paramacrobiotus richtersi

(2010) Angela M. Rizzo et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

A new bioinformatics analysis tools framework at EMBL-EBI

(2010) M. Goujon et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Murasaki: A Fast, Parallelizable Algorithm to Find Anchors from Multiple Genomes

(2010) Kris Popendorf et al.   PLoS One

Condition-adapted stress and longevity gene regulation byCaenorhabditis elegansSKN-1/Nrf

(2009) Riva P. Oliveira et al.   AGING CELL

Arthropod phylogeny: An overview from the perspectives of morphology, molecular data and the fossil record

(2009) Gregory D. Edgecombe   ARTHROPOD STRUCTURE & DEVELOPMENT

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Stress response in tardigrades: differential gene expression of molecular chaperones

(2009) Andy Reuner et al.   CELL STRESS & CHAPERONES

Freeze tolerance, supercooling points and ice formation: comparative studies on the subzero temperature survival of limno-terrestrial tardigrades

(2009) S. Hengherr et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Establishment of a Rearing System of the Extremotolerant Tardigrade Ramazzottius varieornatus: A New Model Animal for Astrobiology

(2008) Daiki D. Horikawa et al.   ASTROBIOLOGY

The role of trehalose and its transporter in protection against reactive oxygen species

(2008) Débora da Costa Morato Nery et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

KEGG Atlas mapping for global analysis of metabolic pathways

(2008) S. Okuda et al.   NUCLEIC ACIDS RESEARCH