Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts

(2015) Alison C Testa et al.   BMC GENOMICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Effectors as Tools in Disease Resistance Breeding Against Biotrophic, Hemibiotrophic, and Necrotrophic Plant Pathogens

(2014) Vivianne G. A. A. Vleeshouwers et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Sensitivity to three Parastagonospora nodorum necrotrophic effectors in current Australian wheat cultivars and the presence of further fungal effectors

(2014) Kar-Chun Tan et al.   Crop & Pasture Science

Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8

(2014) James K. Hane et al.   PLoS Genetics

Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis

(2013) Jonathan G. Lees et al.   NUCLEIC ACIDS RESEARCH

Sizing up Septoria

(2013) W. Quaedvlieg et al.   STUDIES IN MYCOLOGY

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis , Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

(2013) Viola A. Manning et al.   G3-Genes Genomes Genetics

Resequencing and Comparative Genomics of Stagonospora nodorum : Sectional Gene Absence and Effector Discovery

(2013) Robert Andrew Syme et al.   G3-Genes Genomes Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Web Apollo: a web-based genomic annotation editing platform

(2013) Eduardo Lee et al.   GENOME BIOLOGY

A comparative analysis of the heterotrimeric G-protein Gα, Gβ and Gγ subunits in the wheat pathogen Stagonospora nodorum

(2012) Joel P A Gummer et al.   BMC MICROBIOLOGY

The Human Respiratory Syncytial Virus Nonstructural Protein 1 Regulates Type I and Type II Interferon Pathways

(2012) Marcus L. Hastie et al.   MOLECULAR & CELLULAR PROTEOMICS

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Novel Necrotrophic Effectors from Stagonospora nodorum and Corresponding Host Sensitivities in Winter Wheat Germplasm in the Southeastern United States

(2012) A. D. Crook et al.   PHYTOPATHOLOGY

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

(2012) Robin A. Ohm et al.   PLoS Pathogens

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

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

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

The impact of next-generation sequencing on genomics

(2011) Jun Zhang et al.   Journal of Genetics and Genomics

Faster SEQUEST Searching for Peptide Identification from Tandem Mass Spectra

(2011) Benjamin J. Diament et al.   JOURNAL OF PROTEOME RESEARCH

Transcriptome analysis of Stagonospora nodorum: gene models, effectors, metabolism and pantothenate dispensability

(2011) SIMON V. S. IPCHO et al.   MOLECULAR PLANT PATHOLOGY

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

(2011) Thierry Rouxel et al.   Nature Communications

A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi

(2011) James K Hane et al.   GENOME BIOLOGY

In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes

(2010) James K Hane et al.   BMC GENOMICS

The Transcription Factor StuA Regulates Central Carbon Metabolism, Mycotoxin Production, and Effector Gene Expression in the Wheat Pathogen Stagonospora nodorum

(2010) Simon V. S. IpCho et al.   EUKARYOTIC CELL

Proteinaceous necrotrophic effectors in fungal virulence

(2010) Kar-Chun Tan et al.   FUNCTIONAL PLANT BIOLOGY

Fungal Effector Proteins

(2009) Ioannis Stergiopoulos et al.   Annual Review of Phytopathology

Estimating disease losses to the Australian wheat industry

(2009) Gordon M. Murray et al.   AUSTRALASIAN PLANT PATHOLOGY

Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum

(2009) Scott Bringans et al.   BMC BIOINFORMATICS

Trehalose biosynthesis is involved in sporulation of Stagonospora nodorum

(2009) Rohan G.T. Lowe et al.   FUNGAL GENETICS AND BIOLOGY

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

Quantitative proteomic analysis of G-protein signalling inStagonospora nodorumusing isobaric tags for relative and absolute quantification

(2009) Tammy Casey et al.   PROTEOMICS

Genome Project Standards in a New Era of Sequencing

(2009) P. S. G. Chain et al.   SCIENCE

SnTox3 Acts in Effector Triggered Susceptibility to Induce Disease on Wheat Carrying the Snn3 Gene

(2009) Zhaohui Liu et al.   PLoS Pathogens

Host-specific toxins: effectors of necrotrophic pathogenicity

(2008) Timothy L. Friesen et al.   CELLULAR MICROBIOLOGY

A Signaling-Regulated, Short-Chain Dehydrogenase ofStagonospora nodorumRegulates Asexual Development

(2008) Kar-Chun Tan et al.   EUKARYOTIC CELL

Rapid and Accurate Peptide Identification from Tandem Mass Spectra

(2008) Christopher Y. Park et al.   JOURNAL OF PROTEOME RESEARCH

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY