Comparative transcriptomics reveal host-specific nucleotide variation in entomophthoralean fungi

Intracellular siderophore but not extracellular siderophore is required for full virulence in Metarhizium robertsii

(2015) Bruno Giuliano Garisto Donzelli et al.   FUNGAL GENETICS AND BIOLOGY

The acid trehalase, ATM1, contributes to the in vivo growth and virulence of the entomopathogenic fungus, Metarhizium acridum

(2015) Kai Jin et al.   FUNGAL GENETICS AND BIOLOGY

Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants

(2015) Ying Chang et al.   Genome Biology and Evolution

Transcriptome of an entomophthoralean fungus (Pandora formicae) shows molecular machinery adjusted for successful host exploitation and transmission

(2015) Joanna Małagocka et al.   JOURNAL OF INVERTEBRATE PATHOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Species-specific ant brain manipulation by a specialized fungal parasite

(2014) Charissa de Bekker et al.   BMC EVOLUTIONARY BIOLOGY

Tracking developmentally regulated post-synthetic processing of homogalacturonan and chitin using reciprocal oligosaccharide probes

(2014) J. Mravec et al.   DEVELOPMENT

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

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

Trajectory and genomic determinants of fungal-pathogen speciation and host adaptation

(2014) Xiao Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Running with the Red Queen: the role of biotic conflicts in evolution

(2014) M. A. Brockhurst et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolutionary Interaction Networks of Insect Pathogenic Fungi

(2013) Jacobus J. Boomsma et al.   Annual Review of Entomology

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics

(2013) Ya Yang et al.   BMC GENOMICS

Bidirectional Best Hits Miss Many Orthologs in Duplication-Rich Clades such as Plants and Animals

(2013) Daniel A. Dalquen et al.   Genome Biology and Evolution

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

Evolution, selection and isolation: a genomic view of speciation in fungal plant pathogens

(2013) Eva Holtgrewe Stukenbrock   NEW PHYTOLOGIST

Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution

(2013) D. M. de Vienne et al.   NEW PHYTOLOGIST

Phylogenetic lineages in Entomophthoromycota

(2013) A.P. Gryganskyi et al.   PERSOONIA

Sequential Utilization of Hosts from Different Fly Families by Genetically Distinct, Sympatric Populations within the Entomophthora muscae Species Complex

(2013) Andrii P. Gryganskyi et al.   PLoS One

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

THE ORIGIN OF SPECIFICITY BY MEANS OF NATURAL SELECTION: EVOLVED AND NONHOST RESISTANCE IN HOST-PATHOGEN INTERACTIONS

(2012) Janis Antonovics et al.   EVOLUTION

Molecular phylogeny of the Entomophthoromycota

(2012) Andrii P. Gryganskyi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Entomophthoromycota: a new phylum and reclassification for entomophthoroid fungi

(2012) Richard A. Humber   MYCOTAXON

Emerging fungal threats to animal, plant and ecosystem health

(2012) Matthew C. Fisher et al.   NATURE

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

The Gut Fungus Basidiobolus ranarum Has a Large Genome and Different Copy Numbers of Putatively Functionally Redundant Elongation Factor Genes

(2012) Daniel A. Henk et al.   PLoS One

Polyploidy in fungi: evolution after whole-genome duplication

(2012) W. Albertin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic perspectives on the evolution of fungal entomopathogenicity in Beauveria bassiana

(2012) Guohua Xiao et al.   Scientific Reports

A Population Genomics Perspective on the Emergence and Adaptation of New Plant Pathogens in Agro-Ecosystems

(2012) Eva H. Stukenbrock et al.   PLoS Pathogens

The Fungi: 1, 2, 3 … 5.1 million species?

(2011) Meredith Blackwell   AMERICAN JOURNAL OF BOTANY

The variant call format and VCFtools

(2011) P. Danecek 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

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

WebMGA: a customizable web server for fast metagenomic sequence analysis

(2011) Sitao Wu et al.   BMC GENOMICS

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Host specificity in phylogenetic and geographic space

(2011) Robert Poulin et al.   TRENDS IN PARASITOLOGY

Genome Sequencing and Comparative Transcriptomics of the Model Entomopathogenic Fungi Metarhizium anisopliae and M. acridum

(2011) Qiang Gao et al.   PLoS Genetics

Secretome of fungus-infected aphids documents high pathogen activity and weak host response

(2010) Morten N. Grell et al.   FUNGAL GENETICS AND BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

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

Trypsin-like proteins of the fungi as possible markers of pathogenicity

(2009) Aleksej G. Dubovenko et al.   Fungal Biology

Comparative EST analysis of a Zoophthora radicans isolate derived from Pieris brassicae and an isogenic strain adapted to Plutella xylostella

(2009) J. Xu et al.   MICROBIOLOGY-SGM

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Grain aphid population structure: no effect of fungal infections in a 2-year field study in Denmark

(2008) A. B. Jensen et al.   AGRICULTURAL AND FOREST ENTOMOLOGY

TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops

(2008) I. Milne et al.   BIOINFORMATICS

Speciation in fungi

(2008) Tatiana Giraud et al.   FUNGAL GENETICS AND BIOLOGY

Reconciliation with Non-Binary Species Trees

(2008) Benjamin Vernot et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Evolution of entomopathogenicity in fungi

(2008) Richard A. Humber   JOURNAL OF INVERTEBRATE PATHOLOGY

The McDonald-Kreitman Test and Slightly Deleterious Mutations

(2008) J. Charlesworth et al.   MOLECULAR BIOLOGY AND EVOLUTION

Infecting epidemiology with genetics: a new frontier in disease ecology

(2008) Elizabeth A. Archie et al.   TRENDS IN ECOLOGY & EVOLUTION

Host specificity under molecular and experimental scrutiny

(2007) Robert Poulin et al.   TRENDS IN PARASITOLOGY