Genomic innovations linked to infection strategies across emerging pathogenic chytrid fungi

Transposons to toxins: the provenance, architecture and diversification of a widespread class of eukaryotic effectors

(2016) Dapeng Zhang et al.   NUCLEIC ACIDS RESEARCH

Transcriptome Analysis of the Entomopathogenic Oomycete Lagenidium giganteum Reveals Putative Virulence Factors

(2014) Paula F. Quiroz Velasquez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2014) Rei Kajitani et al.   GENOME RESEARCH

Amphibians acquire resistance to live and dead fungus overcoming fungal immunosuppression

(2014) Taegan A. McMahon et al.   NATURE

Recent introduction of a chytrid fungus endangers Western Palearctic salamanders

(2014) A. Martel et al.   SCIENCE

Pfam: the protein families database

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

Batrachochytrium salamandrivorans sp. nov. causes lethal chytridiomycosis in amphibians

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

Using False Discovery Rates to Benchmark SNP-callers in next-generation sequencing projects

(2013) Rhys A. Farrer et al.   Scientific Reports

Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen Saprolegnia parasitica

(2013) Rays H. Y. Jiang et al.   PLoS Genetics

Chromosomal Copy Number Variation, Selection and Uneven Rates of Recombination Reveal Cryptic Genome Diversity Linked to Pathogenicity

(2013) Rhys A. Farrer et al.   PLoS Genetics

Emerging fungal threats to animal, plant and ecosystem health

(2012) Matthew C. Fisher et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Germ Tube Mediated Invasion of Batrachochytrium dendrobatidis in Amphibian Skin Is Host Dependent

(2012) Pascale Van Rooij et al.   PLoS One

Species-Specific Chitin-Binding Module 18 Expansion in the Amphibian Pathogen Batrachochytrium dendrobatidis

(2012) J. Abramyan et al.   mBio

A Glycosylphosphatidylinositol Anchor Is Required for Membrane Localization but Dispensable for Cell Wall Association of Chitin Deacetylase 2 in Cryptococcus neoformans

(2012) N. M. Gilbert et al.   mBio

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Evidence for acquisition of virulence effectors in pathogenic chytrids

(2011) Guiling Sun et al.   BMC EVOLUTIONARY BIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage

(2011) R. A. Farrer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Genomic Transition to Pathogenicity in Chytrid Fungi

(2011) Suzanne Joneson et al.   PLoS Pathogens

Ancient class of translocated oomycete effectors targets the host nucleus

(2010) S. Schornack et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage

(2010) S. Raffaele et al.   SCIENCE

Global Emergence ofBatrachochytrium dendrobatidisand Amphibian Chytridiomycosis in Space, Time, and Host

(2009) Matthew C. Fisher et al.   Annual Review of Microbiology

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

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

(2009) Brian J. Haas et al.   NATURE

Pathogenesis of Chytridiomycosis, a Cause of Catastrophic Amphibian Declines

(2009) J. Voyles et al.   SCIENCE

ALLPATHS: De novo assembly of whole-genome shotgun microreads

(2008) J. Butler et al.   GENOME RESEARCH

Are we in the midst of the sixth mass extinction? A view from the world of amphibians

(2008) D. B. Wake et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

(2008) Martin C. Frith et al.   PLoS Computational Biology

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY