Hybridization and introgression drive genome evolution of Dutch elm disease pathogens

Worldwide emergence of resistance to antifungal drugs challenges human health and food security

(2018) Matthew C. Fisher et al.   SCIENCE

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

(2018) Floréal Cabanettes et al.   PeerJ

Balancing selection and introgression of newt immune-response genes

(2018) Anna Fijarczyk et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Major Facilitator Superfamily Transporter Regulated by the Stress-Responsive Transcription Factor Yap1 Is Required for Resistance to Fungicides, Xenobiotics, and Oxidants and Full Virulence in Alternaria alternata

(2018) Hsien-Che Lin et al.   Frontiers in Microbiology

Evidence that RNA Viruses Drove Adaptive Introgression between Neanderthals and Modern Humans

(2018) David Enard et al.   CELL

A genomic comparison of putative pathogenicity-related gene families in five members of the Ophiostomatales with different lifestyles

(2017) Ljerka Lah et al.   Fungal Biology

Exploring Evolutionary Relationships Across the Genome Using Topology Weighting

(2017) Simon H. Martin et al.   GENETICS

The Rapid Evolution of an Ohnolog Contributes to the Ecological Specialization of Incipient Yeast Species

(2017) Chris Eberlein et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic and genomic evidence of niche partitioning and adaptive radiation in mountain pine beetle fungal symbionts

(2017) Dario I. Ojeda Alayon et al.   MOLECULAR ECOLOGY

Evolution and genome architecture in fungal plant pathogens

(2017) Mareike Möller et al.   NATURE REVIEWS MICROBIOLOGY

Exploring Evolutionary Relationships Across the Genome Using Topology Weighting

(2017) Simon H. Martin et al.   GENETICS

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

Is There a Genetic Paradox of Biological Invasion?

(2016) Arnaud Estoup et al.   Annual Review of Ecology Evolution and Systematics

A novel major facilitator superfamily transporter in Penicillium digitatum (PdMFS2) is required for prochloraz resistance, conidiation and full virulence

(2016) Zhi Wu et al.   BIOTECHNOLOGY LETTERS

From yeast to hypha: defining transcriptomic signatures of the morphological switch in the dimorphic fungal pathogen Ophiostoma novo-ulmi

(2016) M. Nigg et al.   BMC GENOMICS

Interspecific hybridization impacts host range and pathogenicity of filamentous microbes

(2016) Jasper RL Depotter et al.   CURRENT OPINION IN MICROBIOLOGY

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2016) Fabrizio Menardo et al.   NATURE GENETICS

The Role of Hybridization in the Evolution and Emergence of New Fungal Plant Pathogens

(2016) Eva H. Stukenbrock   PHYTOPATHOLOGY

The population biology of fungal invasions

(2015) P. Gladieux et al.   MOLECULAR ECOLOGY

SpeedSeq: ultra-fast personal genome analysis and interpretation

(2015) Colby Chiang et al.   NATURE METHODS

Effector P: predicting fungal effector proteins from secretomes using machine learning

(2015) Jana Sperschneider et al.   NEW PHYTOLOGIST

Relationship between soil fungal diversity and temperature in the maritime Antarctic

(2015) Kevin K. Newsham et al.   Nature Climate Change

RNAseq Analysis Highlights Specific Transcriptome Signatures of Yeast and Mycelial Growth Phases in the Dutch Elm Disease Fungus Ophiostoma novo-ulmi

(2015) Martha Nigg et al.   G3-Genes Genomes Genetics

Dimorphism in Fungal Pathogens of Mammals, Plants, and Insects

(2015) Gregory M. Gauthier   PLoS Pathogens

ngsTools: methods for population genetics analyses from next-generation sequencing data

(2014) Matteo Fumagalli et al.   BIOINFORMATICS

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

Correction: Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

(2014) Zhongtao Zhao et al.   BMC GENOMICS

Vegetative Incompatibility Loci with Dedicated Roles in Allorecognition Restrict Mycovirus Transmission in Chestnut Blight Fungus

(2014) Dong-Xiu Zhang et al.   GENETICS

Functional Annotation of the Ophiostoma novo-ulmi Genome: Insights into the Phytopathogenicity of the Fungal Agent of Dutch Elm Disease

(2014) André M. Comeau et al.   Genome Biology and Evolution

Resistance to oxidative stress via regulating siderophore-mediated iron acquisition by the citrus fungal pathogen Alternaria alternata

(2014) L.-H. Chen et al.   MICROBIOLOGY-SGM

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

The effect of mating system on invasiveness: some genetic load may be advantageous when invading new environments

(2013) Éric Bazin et al.   BIOLOGICAL INVASIONS

A rapid virulence assay for the Dutch elm disease fungusOphiostoma novo-ulmiby inoculation of apple (Malus × domestica‘Golden Delicious’) fruits

(2013) K. V. Plourde et al.   PLANT PATHOLOGY

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

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

Emerging fungal threats to animal, plant and ecosystem health

(2012) Matthew C. Fisher et al.   NATURE

SnIPRE: Selection Inference Using a Poisson Random Effects Model

(2012) Kirsten E. Eilertson et al.   PLoS Computational Biology

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) Thibaut Jombart et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

Predicting invasion success of forest pathogenic fungi from species traits

(2011) Aurore Philibert et al.   JOURNAL OF APPLIED ECOLOGY

Testing for Ancient Admixture between Closely Related Populations

(2011) Eric Y. Durand et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Genome Portal of the Department of Energy Joint Genome Institute

(2011) I. V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen

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

EBImage--an R package for image processing with applications to cellular phenotypes

(2010) G. Pau et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude

(2010) X. Yi et al.   SCIENCE

A Draft Sequence of the Neandertal Genome

(2010) R. E. Green et al.   SCIENCE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Identification of a New Biocontrol Gene inTrichoderma atroviride: The Role of an ABC Transporter Membrane Pump in the Interaction with Different Plant-Pathogenic Fungi

(2009) Michelina Ruocco et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The ABC transporter BcatrB fromBotrytis cinereaexports camalexin and is a virulence factor onArabidopsis thaliana

(2009) Francesca L. Stefanato et al.   PLANT JOURNAL

Rapid emergence of hybrids between the two subspecies ofOphiostoma novo-ulmiwith a high level of pathogenic fitness

(2009) C. M. Brasier et al.   PLANT PATHOLOGY

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

(2008) Thibaut Jombart   BIOINFORMATICS

Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria

(2008) P M Bennett   BRITISH JOURNAL OF PHARMACOLOGY

Sequential Elimination of Major-Effect Contributors Identifies Additional Quantitative Trait Loci Conditioning High-Temperature Growth in Yeast

(2008) Himanshu Sinha et al.   GENETICS

High-throughput functional annotation and data mining with the Blast2GO suite

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

The role of hybridization in evolution

(2003) N. H. Barton   MOLECULAR ECOLOGY