Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes

Local and long-range activation of innate immunity by infection and damage in C. elegans

(2016) Jonathan J. Ewbank et al.   CURRENT OPINION IN IMMUNOLOGY

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The genome of the truffle-parasite Tolypocladium ophioglossoides and the evolution of antifungal peptaibiotics

(2015) C. Alisha Quandt et al.   BMC GENOMICS

Analysis of the complete mitochondrial genome of Pochonia chlamydosporia suggests a close relationship to the invertebrate-pathogenic fungi in Hypocreales

(2015) Runmao Lin et al.   BMC MICROBIOLOGY

Microbial pathogenesis and host defense in the nematode C. elegans

(2015) Lianne B Cohen et al.   CURRENT OPINION IN MICROBIOLOGY

Development of a high-efficiency gene knockout system for Pochonia chlamydosporia

(2015) Baoming Shen et al.   MICROBIOLOGICAL RESEARCH

Development of a transformation system for Hirsutella spp. and visualization of the mode of nematode infection by GFP-labeled H. minnesotensis

(2015) Jingzu Sun et al.   Scientific Reports

Common protein sequence signatures associate with Sclerotinia borealis lifestyle and secretion in fungal pathogens of the Sclerotiniaceae

(2015) Thomas Badet et al.   Frontiers in Plant Science

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Independent Synchronized Control and Visualization of Interactions between Living Cells and Organisms

(2014) Vincent Rouger et al.   BIOPHYSICAL JOURNAL

Drechslerella stenobrocha genome illustrates the mechanism of constricting rings and the origin of nematode predation in fungi

(2014) Keke Liu et al.   BMC GENOMICS

Interspecific and host-related gene expression patterns in nematode-trapping fungi

(2014) Karl-Magnus Andersson et al.   BMC GENOMICS

Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia

(2014) Eduardo Larriba et al.   FUNGAL GENETICS AND BIOLOGY

Diversity and Variability of NOD-Like Receptors in Fungi

(2014) Witold Dyrka et al.   Genome Biology and Evolution

Comparative Genomics and Transcriptomics Analyses Reveal Divergent Lifestyle Features of Nematode Endoparasitic Fungus Hirsutella minnesotensis

(2014) Yiling Lai et al.   Genome Biology and Evolution

Activation of a G protein–coupled receptor by its endogenous ligand triggers the innate immune response of Caenorhabditis elegans

(2014) Olivier Zugasti et al.   NATURE IMMUNOLOGY

Independent Expansion of Zincin Metalloproteinases in Onygenales Fungi May Be Associated with Their Pathogenicity

(2014) Juan Li et al.   PLoS One

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

Human and Plant Fungal Pathogens: The Role of Secondary Metabolites

(2014) Daniel H. Scharf et al.   PLoS Pathogens

Systematic Analysis of Zn2Cys6 Transcription Factors Required for Development and Pathogenicity by High-Throughput Gene Knockout in the Rice Blast Fungus

(2014) Jianping Lu et al.   PLoS Pathogens

Phylogenetic-based nomenclatural proposals for Ophiocordycipitaceae (Hypocreales) with new combinations in Tolypocladium

(2014) C. Alisha Quandt et al.   IMA Fungus

Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes

(2013) Anthony Levasseur et al.   Biotechnology for Biofuels

Commensals, probiotics and pathogens in theCaenorhabditis elegansmodel

(2013) Laura C. Clark et al.   CELLULAR MICROBIOLOGY

Genome survey uncovers the secrets of sex and lifestyle in caterpillar fungus

(2013) Xiao Hu et al.   CHINESE SCIENCE BULLETIN

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Genomic Mechanisms Accounting for the Adaptation to Parasitism in Nematode-Trapping Fungi

(2013) Tejashwari Meerupati et al.   PLoS Genetics

The saposin-like protein SPP-12 is an antimicrobial polypeptide in the pharyngeal neurons ofCaenorhabditis elegansand participates in defence against a natural bacterial pathogen

(2012) Aylin Hoeckendorf et al.   BIOCHEMICAL JOURNAL

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Population dynamics and habitat sharing of natural populations of Caenorhabditis elegans and C. briggsae

(2012) Marie-Anne Félix et al.   BMC BIOLOGY

SPP-3, a saposin-like protein of Caenorhabditis elegans, displays antimicrobial and pore-forming activity and is located in the intestine and in one head neuron

(2012) Aylin Hoeckendorf et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

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

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

dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more

(2012) Hai Fang et al.   NUCLEIC ACIDS RESEARCH

The Pseudokinase NIPI-4 Is a Novel Regulator of Antimicrobial Peptide Gene Expression

(2012) Sid ahmed Labed et al.   PLoS One

Molecular Evolution of the Deuterolysin (M35) Family Genes in Coccidioides

(2012) Juan Li et al.   PLoS One

The Fungal Pathogen Moniliophthora perniciosa Has Genes Similar to Plant PR-1 That Are Highly Expressed during Its Interaction with Cacao

(2012) Paulo J.P.L. Teixeira et al.   PLoS One

Genomic perspectives on the evolution of fungal entomopathogenicity in Beauveria bassiana

(2012) Guohua Xiao et al.   Scientific Reports

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

(2012) Ruibang Luo et al.   GigaScience

Endo-β-1,3-Glucanase GLU1, from the Fruiting Body of Lentinula edodes, Belongs to a New Glycoside Hydrolase Family

(2011) Yuichi Sakamoto et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Transcriptome analysis shows differential gene expression in the saprotrophic to parasitic transition of Pochonia chlamydosporia

(2011) Laura C. Rosso et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Fungal enzyme sets for plant polysaccharide degradation

(2011) Joost van den Brink et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Viral subversion of immunogenic cell death

(2011) Oliver Kepp et al.   CELL CYCLE

Unusual Regulation of a STAT Protein by an SLC6 Family Transporter in C. elegans Epidermal Innate Immunity

(2011) Katja Dierking et al.   Cell Host & Microbe

C. elegans: model host and tool for antimicrobial drug discovery

(2011) J. J. Ewbank et al.   Disease Models & Mechanisms

Independent Subtilases Expansions in Fungi Associated with Animals

(2011) A. Muszewska et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

A Comprehensive Analysis of Gene Expression Changes Provoked by Bacterial and Fungal Infection in C. elegans

(2011) Ilka Engelmann et al.   PLoS One

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

(2011) Qiang Gao et al.   PLoS Genetics

Genomic and Proteomic Analyses of the Fungus Arthrobotrys oligospora Provide Insights into Nematode-Trap Formation

(2011) Jinkui Yang et al.   PLoS Pathogens

Overexpression of a cuticle-degrading protease Ver112 increases the nematicidal activity of Paecilomyces lilacinus

(2010) Jinkui Yang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Regulation of subtilisin-like protease prC expression by nematode cuticle in the nematophagous fungus Clonostachys rosea

(2010) Cheng-Gang Zou et al.   ENVIRONMENTAL MICROBIOLOGY

SMURF: Genomic mapping of fungal secondary metabolite clusters

(2010) Nora Khaldi et al.   FUNGAL GENETICS AND BIOLOGY

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Mrt, a Gene Unique to Fungi, Encodes an Oligosaccharide Transporter and Facilitates Rhizosphere Competency in Metarhizium robertsii

(2010) W. Fang et al.   PLANT PHYSIOLOGY

Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome

(2010) L. Baxter et al.   SCIENCE

Mobyle: a new full web bioinformatics framework

(2009) B. Neron et al.   BIOINFORMATICS

NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction

(2009) Alex N Nguyen Ba et al.   BMC BIOINFORMATICS

Caenopores are antimicrobial peptides in the nematode Caenorhabditis elegans instrumental in nutrition and immunity

(2009) Thomas Roeder et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Caenopore-5: The three-dimensional structure of an antimicrobial protein from Caenorhabditis elegans

(2009) Justyna Mysliwy et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Neuroimmune regulation of antimicrobial peptide expression by a noncanonical TGF-β signaling pathway in Caenorhabditis elegans epidermis

(2009) Olivier Zugasti et al.   NATURE IMMUNOLOGY

Network visualization and analysis of gene expression data using BioLayout Express3D

(2009) Athanasios Theocharidis et al.   Nature Protocols

The evolutionary conundrum of pathogen mimicry

(2009) Nels C. Elde et al.   NATURE REVIEWS MICROBIOLOGY

Insight into the molecular requirements for pathogenicity of Fusarium oxysporum f. sp. lycopersici through large-scale insertional mutagenesis

(2009) Caroline B Michielse et al.   GENOME BIOLOGY

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

Protein kinase A regulates production of virulence determinants by the entomopathogenic fungus, Metarhizium anisopliae

(2008) Weiguo Fang et al.   FUNGAL GENETICS AND BIOLOGY

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Co-evolution and exploitation of host cell signaling pathways by bacterial pathogens

(2008) Stephanie R. Shames et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

(2008) Diego Martinez et al.   NATURE BIOTECHNOLOGY

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Anti-Fungal Innate Immunity in C. elegans Is Enhanced by Evolutionary Diversification of Antimicrobial Peptides

(2008) Nathalie Pujol et al.   PLoS Pathogens

Paralysis of nematodes: shifts in the transcriptome of the nematode-trapping fungus Monacrosporium haptotylum during infection of Caenorhabditis elegans

(2007) Csaba Fekete et al.   ENVIRONMENTAL MICROBIOLOGY

Molecular phylogenetics of ascomycotal adhesins—A novel family of putative cell-surface adhesive proteins in fission yeasts

(2007) Tomas Linder et al.   FUNGAL GENETICS AND BIOLOGY