Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum

Grapevine xylem response to fungi involved in trunk diseases

(2016) P. Gómez et al.   ANNALS OF APPLIED BIOLOGY

Fatty acid esters produced by Lasiodiplodia theobromae function as growth regulators in tobacco seedlings

(2016) Carla C. Uranga et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Assemblytics: a web analytics tool for the detection of variants from an assembly

(2016) Maria Nattestad et al.   BIOINFORMATICS

Host-preferential Fusarium graminearum gene expression during infection of wheat, barley, and maize

(2016) Linda J. Harris et al.   Fungal Biology

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens

(2015) Abraham Morales-Cruz et al.   BMC GENOMICS

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

Phytotoxic metabolites from Neofusicoccum parvum, a pathogen of Botryosphaeria dieback of grapevine

(2015) Eliane Abou-Mansour et al.   PHYTOCHEMISTRY

Genes Expressed in Grapevine Leaves Reveal Latent Wood Infection by the Fungal Pathogen Neofusicoccum parvum

(2015) Stefan Czemmel et al.   PLoS One

Exploring genome characteristics and sequence quality without a reference

(2014) Jared T. Simpson   BIOINFORMATICS

Adaptive genomic structural variation in the grape powdery mildew pathogen, Erysiphe necator

(2014) Laura Jones et al.   BMC GENOMICS

Fungal Cytochrome P450 Monooxygenases: Their Distribution, Structure, Functions, Family Expansion, and Evolutionary Origin

(2014) Wanping Chen et al.   Genome Biology and Evolution

Integration of mapped RNA-Seq reads into automatic training of eukaryotic gene finding algorithm

(2014) Alexandre Lomsadze et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Anthony Levasseur et al.   Biotechnology for Biofuels

Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum

(2013) Katherine Lawler et al.   BMC Systems Biology

Regulation of Cellulase and Hemicellulase Gene Expression in Fungi

(2013) Antonella Amore et al.   CURRENT GENOMICS

Degradation of the plant defence hormone salicylic acid by the biotrophic fungusUstilago maydis

(2013) Franziska Rabe et al.   MOLECULAR MICROBIOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Susceptibility of Cultivated and Wild Vitis spp. to Wood Infection by Fungal Trunk Pathogens

(2013) Renaud Travadon et al.   PLANT DISEASE

Systems Analysis of Lactose Metabolism in Trichoderma reesei Identifies a Lactose Permease That Is Essential for Cellulase Induction

(2013) Christa Ivanova et al.   PLoS One

Incorporating Motif Analysis into Gene Co-expression Networks Reveals Novel Modular Expression Pattern and New Signaling Pathways

(2013) Shisong Ma et al.   PLoS Genetics

Fungal aryl-alcohol oxidase: a peroxide-producing flavoenzyme involved in lignin degradation

(2012) Aitor Hernández-Ortega et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Development and application of a 6.5 million feature Affymetrix Genechip® for massively parallel discovery of single position polymorphisms in lettuce (Lactuca spp.)

(2012) Kevin Stoffel et al.   BMC GENOMICS

Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes

(2012) Venkatesh Moktali et al.   BMC GENOMICS

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Regulation of fungal secondary metabolism

(2012) Axel A. Brakhage   NATURE REVIEWS MICROBIOLOGY

Grapevine trunk diseases: complex and still poorly understood

(2012) C. Bertsch et al.   PLANT PATHOLOGY

Transcriptomic Responses of the Softwood-Degrading White-Rot Fungus Phanerochaete carnosa during Growth on Coniferous and Deciduous Wood

(2011) Jacqueline MacDonald et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fungal enzyme sets for plant polysaccharide degradation

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

Arsenal of plant cell wall degrading enzymes reflects host preference among plant pathogenic fungi

(2011) Brian C King et al.   Biotechnology for Biofuels

Heterochromatin influences the secondary metabolite profile in the plant pathogen Fusarium graminearum

(2011) Yazmid Reyes-Dominguez et al.   FUNGAL GENETICS AND BIOLOGY

Transcriptional regulatory elements in fungal secondary metabolism

(2011) Wenbing Yin et al.   JOURNAL OF MICROBIOLOGY

Analysis of theAspergillus fumigatusProteome Reveals Metabolic Changes and the Activation of the Pseurotin A Biosynthesis Gene Cluster in Response to Hypoxia

(2011) Martin Vödisch et al.   JOURNAL OF PROTEOME RESEARCH

The Transcriptome of the Reference Potato Genome Solanum tuberosum Group Phureja Clone DM1-3 516R44

(2011) Alicia N. Massa et al.   PLoS One

Phytotoxins Produced by Fungi Associated with Grapevine Trunk Diseases

(2011) Anna Andolfi et al.   Toxins

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

(2010) A. McKenna et al.   GENOME RESEARCH

Susceptibility of grapevine pruning wounds to infection by Lasiodiplodia theobromae and Neofusicoccum parvum

(2010) J. R. Úrbez-Torres et al.   PLANT PATHOLOGY

A Short-chain Dehydrogenase/reductase Gene is Required for Infection-related Development and Pathogenicity in Magnaporthe oryzae

(2010) Min-Jung Kwon et al.   Plant Pathology Journal

Functional genomic profiling of Aspergillus fumigatus biofilm reveals enhanced production of the mycotoxin gliotoxin

(2010) Sandra Bruns et al.   PROTEOMICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Metabolic engineering strategies for the improvement of cellulase production by Hypocrea jecorina

(2009) Christian P Kubicek et al.   Biotechnology for Biofuels

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Pathogenicity of Botryosphaeriaceae Species Isolated from Grapevine Cankers in California

(2009) J. R. Úrbez-Torres et al.   PLANT DISEASE

Efflux in Fungi: La Pièce de Résistance

(2009) Jeffrey J. Coleman et al.   PLoS Pathogens

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Functional Characterization of the Biosynthesis of Radicicol, an Hsp90 Inhibitor Resorcylic Acid Lactone from Chaetomium chiversii

(2008) Shuhao Wang et al.   CHEMISTRY & BIOLOGY

Production of phytotoxic metabolites by five species of Botryosphaeriaceae causing decline on grapevines, with special interest in the species Neofusicoccum luteum and N. parvum

(2008) Soledad Martos et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

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

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

Pathogenesis ofEutypa latain Grapevine: Identification of Virulence Factors and Biochemical Characterization of Cordon Dieback

(2008) P. E. Rolshausen et al.   PHYTOPATHOLOGY

Strangers in the matrix: plant cell walls and pathogen susceptibility

(2008) Dario Cantu et al.   TRENDS IN PLANT SCIENCE