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

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

Genome evolution in the allotetraploid frog Xenopus laevis

(2016) Adam M. Session et al.   NATURE

Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species

(2016) Fabrizio Menardo et al.   NATURE GENETICS

No evidence that sex and transposable elements drive genome size variation in evening primroses

(2015) J. Arvid Ågren et al.   EVOLUTION

Polyploidy can drive rapid adaptation in yeast

(2015) Anna M. Selmecki et al.   NATURE

Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

(2015) Jun Inoue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unreduced gametes: meiotic mishap or evolutionary mechanism?

(2015) Annaliese S. Mason et al.   TRENDS IN GENETICS

The polyploidy revolution then...and now: Stebbins revisited

(2014) D. E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Parasitic success without sex - the nematode experience

(2014) P. Castagnone-Sereno et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Recurrent Loss of Sex Is Associated with Accumulation of Deleterious Mutations in Oenothera

(2014) Jesse D. Hollister et al.   MOLECULAR BIOLOGY AND EVOLUTION

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

A Synergism between Adaptive Effects and Evolvability Drives Whole Genome Duplication to Fixation

(2014) Thomas D. Cuypers et al.   PLoS Computational Biology

The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode

(2014) James A Cotton et al.   GENOME BIOLOGY

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

(2014) David H. Lunt et al.   PeerJ

Diversity and Evolution of Root-Knot Nematodes, GenusMeloidogyne: New Insights from the Genomic Era

(2013) Philippe Castagnone-Sereno et al.   Annual Review of Phytopathology

Sizing up arthropod genomes: an evaluation of the impact of environmental variation on genome size estimates by flow cytometry and the use of qPCR as a method of estimation

(2013) T. Ryan Gregory et al.   GENOME

Shared Subgenome Dominance Following Polyploidization Explains Grass Genome Evolutionary Plasticity from a Seven Protochromosome Ancestor with 16K Protogenes

(2013) Florent Murat et al.   Genome Biology and Evolution

Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

(2013) R. de Jonge et al.   GENOME RESEARCH

Top 10 plant-parasitic nematodes in molecular plant pathology

(2013) John T. Jones et al.   MOLECULAR PLANT PATHOLOGY

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

(2013) Jean-François Flot et al.   NATURE

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Identification of Novel Target Genes for Safer and More Specific Control of Root-Knot Nematodes from a Pan-Genome Mining

(2013) Etienne G. J. Danchin et al.   PLoS Pathogens

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Transgressive Hybrids as Hopeful Monsters

(2012) Dylan R. Dittrich-Reed et al.   Evolutionary Biology

Polyploidy and its effect on evolutionary success: old questions revisited with new tools

(2012) A Madlung   HEREDITY

Transposon proliferation in an asexual parasitoid

(2012) KEN KRAAIJEVELD et al.   MOLECULAR ECOLOGY

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

EvolView, an online tool for visualizing, annotating and managing phylogenetic trees

(2012) Huangkai Zhang et al.   NUCLEIC ACIDS RESEARCH

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

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

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Deleterious Mutation Accumulation in Asexual Timema Stick Insects

(2011) Lee Henry et al.   MOLECULAR BIOLOGY AND EVOLUTION

Boechera, a model system for ecological genomics

(2011) CATHERINE A. RUSHWORTH et al.   MOLECULAR ECOLOGY

The draft genome of the parasitic nematode Trichinella spiralis

(2011) Makedonka Mitreva et al.   NATURE GENETICS

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Tm1: A Mutator/Foldback Transposable Element Family in Root-Knot Nematodes

(2011) Stephen M. Gross et al.   PLoS One

Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus

(2011) Taisei Kikuchi et al.   PLoS Pathogens

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A little bit is better than nothing: the incomplete parthenogenesis of salamanders, frogs and fish

(2010) Kathrin P Lampert et al.   BMC BIOLOGY

Sister chromosome pairing maintains heterozygosity in parthenogenetic lizards

(2010) Aracely A. Lutes et al.   NATURE

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

DNA transposons and the role of recombination in mutation accumulation in Daphnia pulex

(2010) Sarah Schaack et al.   GENOME BIOLOGY

What Can Asexual Lineage Age Tell Us about the Maintenance of Sex?

(2009) Maurine Neiman et al.   Annals of the New York Academy of Sciences

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Crosses prior to parthenogenesis explain the current genetic diversity of tropical plant-parasitic Meloidogyne species (Nematoda: Tylenchida)

(2009) Mireille Fargette et al.   INFECTION GENETICS AND EVOLUTION

Accelerated Mutation Accumulation in Asexual Lineages of a Freshwater Snail

(2009) M. Neiman et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Invasive hybrid tiger salamander genotypes impact native amphibians

(2009) M. E. Ryan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genome-wide view of Caenorhabditis elegans base-substitution mutation processes

(2009) D. R. Denver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Genetic tests of ancient asexuality in Root Knot Nematodes reveal recent hybrid origins

(2008) David H Lunt   BMC EVOLUTIONARY BIOLOGY

High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies

(2008) Jean-Marc Aury et al.   BMC GENOMICS

Genome Annotation in Plants and Fungi: EuGene as a Model Platform

(2008) Sylvain Foissac et al.   Current Bioinformatics

Homoploid hybrid speciation in animals

(2008) JESÚS MAVÁREZ et al.   MOLECULAR ECOLOGY

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

(2008) Pierre Abad et al.   NATURE BIOTECHNOLOGY

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

The genome of Brugia malayi — All worms are not created equal

(2008) Alan L. Scott et al.   PARASITOLOGY INTERNATIONAL

Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism

(2008) C. H. Opperman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA