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

Comparative Genomics of Apomictic Root-Knot Nematodes: Hybridization, Ploidy, and Dynamic Genome Change

(2017) Amir Szitenberg et al.   Genome Biology and Evolution

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

(2017) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Whole genome analysis of a schistosomiasis-transmitting freshwater snail

(2017) Coen M. Adema et al.   Nature Communications

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

(2017) Yuki Yoshida et al.   PLOS BIOLOGY

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes

(2017) Romain Blanc-Mathieu et al.   PLoS Genetics

The Genome of Intoshia linei Affirms Orthonectids as Highly Simplified Spiralians

(2016) Kirill V. Mikhailov et al.   CURRENT BIOLOGY

Genetic Exchange among Bdelloid Rotifers Is More Likely Due to Horizontal Gene Transfer Than to Meiotic Sex

(2016) Nicolas Debortoli et al.   CURRENT BIOLOGY

Evidence for meiotic sex in bdelloid rotifers

(2016) Ana Signorovitch et al.   CURRENT BIOLOGY

Response to Signorovitch et al.

(2016) Jean-François Flot et al.   CURRENT BIOLOGY

A functional difference between native and horizontally acquired genes in bdelloid rotifers

(2016) Elton G.G. Barbosa et al.   GENE

Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effect

(2016) S. L. Ament-Velásquez et al.   MOLECULAR ECOLOGY

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

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

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

Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats

(2015) Isobel Eyres et al.   BMC BIOLOGY

Spiralian Phylogeny Informs the Evolution of Microscopic Lineages

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

Multiple horizontally acquired genes from fungal and prokaryotic donors encode cellulolytic enzymes in the bdelloid rotifer Adineta ricciae

(2015) L. Szydlowski et al.   GENE

Allele Sharing and Evidence for Sexuality in a Mitochondrial Clade of Bdelloid Rotifers

(2015) Ana Signorovitch et al.   GENETICS

dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes

(2015) Yana Safonova et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

No Accumulation of Transposable Elements in Asexual Arthropods

(2015) Jens Bast et al.   MOLECULAR BIOLOGY AND EVOLUTION

The octopus genome and the evolution of cephalopod neural and morphological novelties

(2015) Caroline B. Albertin et al.   NATURE

Allele Sharing and Evidence for Sexuality in a Mitochondrial Clade of Bdelloid Rotifers

(2015) Ana Signorovitch et al.   GENETICS

Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes

(2015) Alastair Crisp et al.   GENOME BIOLOGY

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   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

Mechanisms and Regulation of Mitotic Recombination in Saccharomyces cerevisiae

(2014) L. S. Symington et al.   GENETICS

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

(2014) Rei Kajitani et al.   GENOME RESEARCH

Gateway to genetic exchange? DNA double-strand breaks in the bdelloid rotiferAdineta vagasubmitted to desiccation

(2014) B. Hespeels et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge

(2014) Oleg Gusev et al.   Nature Communications

The complex hybrid origins of the root knot nematodes revealed through comparative genomics

(2014) David H. Lunt et al.   PeerJ

L_RNA_scaffolder: scaffolding genomes with transcripts

(2013) Wei Xue et al.   BMC GENOMICS

Inventory and Phylogenetic Analysis of Meiotic Genes in Monogonont Rotifers

(2013) Sara J. Hanson et al.   JOURNAL OF HEREDITY

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

Population-genomic insights into the evolutionary origin and fate of obligately asexual Daphnia pulex

(2013) A. E. Tucker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Sujai Kumar et al.   Frontiers in Genetics

Long-Term Survival of Microscopic Animals Under Desiccation Is Not So Long

(2012) Diego Fontaneto et al.   ASTROBIOLOGY

Multiple functionally divergent and conserved copies of alpha tubulin in bdelloid rotifers

(2012) Isobel Eyres et al.   BMC EVOLUTIONARY BIOLOGY

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

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

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Insights into bilaterian evolution from three spiralian genomes

(2012) Oleg Simakov et al.   NATURE

Whole-genome sequence of Schistosoma haematobium

(2012) Neil D Young et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Revisiting an Old Riddle: What Determines Genetic Diversity Levels within Species?

(2012) Ellen M. Leffler et al.   PLOS BIOLOGY

Biochemical Diversification through Foreign Gene Expression in Bdelloid Rotifers

(2012) Chiara Boschetti et al.   PLoS Genetics

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Mapping copy number variation by population-scale genome sequencing

(2011) Ryan E. Mills et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Soil rotifer communities are extremely diverse globally but spatially autocorrelated locally

(2011) M. S. Robeson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient construction of an assembly string graph using the FM-index

(2010) J. T. Simpson et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Foreign genes and novel hydrophilic protein genes participate in the desiccation response of the bdelloid rotifer Adineta ricciae

(2010) C. Boschetti et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Genome Structure of Bdelloid Rotifers: Shaped by Asexuality or Desiccation?

(2010) E. A. Gladyshev et al.   JOURNAL OF HEREDITY

Dry and survive: Morphological changes during anhydrobiosis in a bdelloid rotifer

(2010) Roberto Marotta et al.   JOURNAL OF STRUCTURAL BIOLOGY

Anhydrobiosis-Associated Nuclear DNA Damage and Repair in the Sleeping Chironomid: Linkage with Radioresistance

(2010) Oleg Gusev et al.   PLoS One

Anciently Asexual Bdelloid Rotifers Escape Lethal Fungal Parasites by Drying Up and Blowing Away

(2010) C. G. Wilson et al.   SCIENCE

Evidence of Selection upon Genomic GC-Content in Bacteria

(2010) Falk Hildebrand et al.   PLoS Genetics

The Evolutionary Enigma of Sex

(2009) Sarah P. Otto   AMERICAN NATURALIST

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

DNA damage in storage cells of anhydrobiotic tardigrades

(2009) Simon Neumann et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Survival and DNA degradation in anhydrobiotic tardigrades

(2009) L. Rebecchi et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

A Fine-Structure Map of Spontaneous Mitotic Crossovers in the Yeast Saccharomyces cerevisiae

(2009) Phoebe S. Lee et al.   PLoS Genetics

Mitotic Recombination: Why? When? How? Where?

(2009) Matthew C. LaFave et al.   PLoS Genetics

Phenotypically Concordant and Discordant Monozygotic Twins Display Different DNA Copy-Number-Variation Profiles

(2008) Carl E.G. Bruder et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

The Effects of Recombination Rate on the Distribution and Abundance of Transposable Elements

(2008) E. S. Dolgin et al.   GENETICS

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Degenerate Tetraploidy Was Established Before Bdelloid Rotifer Families Diverged

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

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

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

Extreme resistance of bdelloid rotifers to ionizing radiation

(2008) Eugene Gladyshev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Massive Horizontal Gene Transfer in Bdelloid Rotifers

(2008) E. A. Gladyshev et al.   SCIENCE