A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen

Machine-learning predicts genomic determinants of meiosis-driven structural variation in a eukaryotic pathogen

(2021) Thomas Badet et al.   Nature Communications

A 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici

(2020) Thomas Badet et al.   BMC BIOLOGY

The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster

(2020) Shiqi Luo et al.   BMC EVOLUTIONARY BIOLOGY

Telomere-to-telomere assembly of a complete human X chromosome

(2020) Karen H. Miga et al.   NATURE

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria

(2020) Alice Feurtey et al.   BMC GENOMICS

Genome size evolution: towards new model systems for old questions

(2020) Julie Blommaert   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Stress-driven transposable element de-repression dynamics and virulence evolution in a fungal pathogen

(2019) Simone Fouché et al.   MOLECULAR BIOLOGY AND EVOLUTION

Expansion of a single transposable element family is associated with genome-size increase and radiation in the genus Hydra

(2019) Wai Yee Wong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Versatile genome assembly evaluation with QUAST-LG

(2018) Alla Mikheenko et al.   BIOINFORMATICS

Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat

(2018) Parvathy Krishnan et al.   BMC BIOLOGY

Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen

(2018) Lamprinos Frantzeskakis et al.   BMC GENOMICS

Genome-wide evidence for divergent selection between populations of a major agricultural pathogen

(2018) Fanny E. Hartmann et al.   MOLECULAR ECOLOGY

A fungal avirulence factor encoded in a highly plastic genomic region triggers partial resistance to septoria tritici blotch

(2018) Lukas Meile et al.   NEW PHYTOLOGIST

Pathogenic adaptations of Colletotrichum fungi revealed by genome wide gene family evolutionary analyses

(2018) Xiaofei Liang et al.   PLoS One

Recent Activity in Expanding Populations and Purifying Selection Have Shaped Transposable Element Landscapes across Natural Accessions of the Mediterranean Grass Brachypodium distachyon

(2017) Christoph Stritt et al.   Genome Biology and Evolution

A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements

(2017) Fanny E Hartmann et al.   ISME Journal

Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen

(2017) Fanny E. Hartmann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tracking the genome-wide outcomes of a transposable element burst over decades of amplification

(2017) Lu Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

McClintock: An Integrated Pipeline for Detecting Transposable Element Insertions in Whole-Genome Shotgun Sequencing Data

(2017) Michael G. Nelson et al.   G3-Genes Genomes Genetics

Plasticity of the MFS1 Promoter Leads to Multidrug Resistance in the Wheat Pathogen Zymoseptoria tritici

(2017) Selim Omrane et al.   mSphere

The genome of newly classified Ochroconis mirabilis: Insights into fungal adaptation to different living conditions

(2016) Su Mei Yew et al.   BMC GENOMICS

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

The Evolution of Orphan Regions in Genomes of a Fungal Pathogen of Wheat

(2016) Clémence Plissonneau et al.   mBio

Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum

(2016) Martina Peter et al.   Nature Communications

The Arabidopsis thaliana mobilome and its impact at the species level

(2016) Leandro Quadrana et al.   eLife

Population scale mapping of transposable element diversity reveals links to gene regulation and epigenomic variation

(2016) Tim Stuart et al.   eLife

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Fungicide efflux and the MgMFS1 transporter contribute to the multidrug resistance phenotype inZymoseptoria triticifield isolates

(2015) Selim Omrane et al.   ENVIRONMENTAL MICROBIOLOGY

Zymoseptoria tritici: A major threat to wheat production, integrated approaches to control

(2015) Stefano F.F. Torriani et al.   FUNGAL GENETICS AND BIOLOGY

The Impact of Recombination Hotspots on Genome Evolution of a Fungal Plant Pathogen

(2015) D. Croll et al.   GENETICS

Emergence and early evolution of fungicide resistance in North American populations ofZymoseptoria tritici

(2015) L. K. Estep et al.   PLANT PATHOLOGY

RNA-seq-Based Gene Annotation and Comparative Genomics of Four Fungal Grass Pathogens in the Genus Zymoseptoria Identify Novel Orphan Genes and Species-Specific Invasions of Transposable Elements

(2015) Jonathan Grandaubert et al.   G3-Genes Genomes Genetics

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

TE-Tracker: systematic identification of transposition events through whole-genome resequencing

(2014) Arthur Gilly et al.   BMC BIOINFORMATICS

Comparative primate genomics: emerging patterns of genome content and dynamics

(2014) Jeffrey Rogers et al.   NATURE REVIEWS GENETICS

Identification of Fusarium oxysporum Genes Associated with Lignocellulose Bioconversion Competency

(2013) Shahin S. Ali et al.   BioEnergy Research

Mobilization of a plant transposon by expression of the transposon-encoded anti-silencing factor

(2013) Yu Fu et al.   EMBO JOURNAL

Transposable Elements: Powerful Contributors to Angiosperm Evolution and Diversity

(2013) Keith R. Oliver et al.   Genome Biology and Evolution

Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources

(2013) Julie M. Cridland 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

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

(2013) Quan Long et al.   NATURE GENETICS

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Breakage-fusion-bridge Cycles and Large Insertions Contribute to the Rapid Evolution of Accessory Chromosomes in a Fungal Pathogen

(2013) Daniel Croll et al.   PLoS Genetics

rehh: an R package to detect footprints of selection in genome-wide SNP data from haplotype structure

(2012) Mathieu Gautier et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

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

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

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genome evolution in filamentous plant pathogens: why bigger can be better

(2012) Sylvain Raffaele et al.   NATURE REVIEWS MICROBIOLOGY

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Whole Genome Resequencing Reveals Natural Target Site Preferences of Transposable Elements in Drosophila melanogaster

(2012) Raquel S. Linheiro et al.   PLoS One

BamTools: a C++ API and toolkit for analyzing and managing BAM files

(2011) D. W. Barnett et al.   BIOINFORMATICS

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species

(2011) E. H. Stukenbrock et al.   GENOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

(2011) Thierry Rouxel et al.   Nature Communications

Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis

(2011) Stephen B. Goodwin et al.   PLoS Genetics

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

(2010) Ben C Stöver et al.   BMC BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Epigenetic silencing of transposable elements: A trade-off between reduced transposition and deleterious effects on neighboring gene expression

(2009) J. D. Hollister et al.   GENOME RESEARCH

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome

(2008) R. S. Baucom et al.   GENOME RESEARCH

Transposable elements and the evolution of regulatory networks

(2008) Cédric Feschotte   NATURE REVIEWS GENETICS