James Hane

Publications

• The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species.
• Accessories Make the Outfit: Accessory Chromosomes and Other Dispensable DNA Regions in Plant-Pathogenic Fungi.
• Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations
• Dothideomycete-plant interactions illuminated by genome sequencing and EST analysis of the wheat pathogen Stagonospora nodorum
• Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis
• Evolution of Linked Avirulence Effectors in Leptosphaeria maculans Is Affected by Genomic Environment and Exposure to Resistance Genes in Host Plants
• A whole genome scan of SNP data suggests a lack of abundant hard selective sweeps in the genome of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum
• Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence
• Construction of a comparative genetic map in faba bean (Vicia faba L.); conservation of genome structure with Lens culinaris
• Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum
• Development of genomic resources for the narrow-leafed lupin (Lupinus angustifolius): construction of a bacterial artificial chromosome (BAC) library and BAC-end sequencing
• In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes
• A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi
• Ubiquity of ToxA and absence of ToxB in Australian populations of Pyrenophora tritici-repentis
• A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres
• Transcriptome analysis of Stagonospora nodorum: gene models, effectors, metabolism and pantothenate dispensability
• Pan-Parastagonospora Comparative Genome Analysis - effector prediction and genome evolution.
• Selective sweeps in populations of the broad host range plant pathogenic fungus Sclerotinia sclerotiorum
• The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin.
• A comparative hidden Markov model analysis pipeline identifies proteins characteristic of cereal-infecting fungi.
• Resequencing and comparative genomics of Stagonospora nodorum: sectional gene absence and effector discovery.
• Adapting legume crops to climate change using genomic approaches.
• Comparative genomics of the wheat fungal pathogen Pyrenophora tritici-repentis reveals chromosomal variations and genome plasticity.
• Bioinformatic prediction of plant-pathogenicity effector proteins of fungi.
• Exploring the genetic and adaptive diversity of a pan-Mediterranean crop wild relative: narrow-leafed lupin.
• Comparative secretome analysis of Rhizoctonia solani isolates with different host ranges reveals unique secretomes and cell death inducing effectors.
• A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant-microbe interactions and legume evolution.
• OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes.
• Mass-spectrometry data for Rhizoctonia solani proteins produced during infection of wheat and vegetative growth.
• Utilizing Gene Tree Variation to Identify Candidate Effector Genes in Zymoseptoria tritici.
• Reactive Oxygen Species Play a Role in the Infection of the Necrotrophic Fungi, Rhizoctonia solani in Wheat.
• Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors.
• Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics.
• Proteomic Analysis of Rhizoctonia solani Identifies Infection-specific, Redox Associated Proteins and Insight into Adaptation to Different Plant Hosts.
• The Arabidopsis KH-Domain RNA-Binding Protein ESR1 Functions in Components of Jasmonate Signalling, Unlinking Growth Restraint and Resistance to Stress.
• Evaluation of Secretion Prediction Highlights Differing Approaches Needed for Oomycete and Fungal Effectors.
• Next-generation re-sequencing as a tool for rapid bioinformatic screening of presence and absence of genes and accessory chromosomes across isolates of Zymoseptoria tritici.
• Overview of genomic and bioinformatic resources for Zymoseptoria tritici.
• Analysis of conglutin seed storage proteins across lupin species using transcriptomic, protein and comparative genomic approaches.
• CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts.
• Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers.
• Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8.
• Draft genome sequence of Bacillus thuringiensis strain DAR 81934, which exhibits molluscicidal activity.
• Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement.
• Reference Genome Assembly for Australian Ascochyta rabiei Isolate ArME14
• Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement
• RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences
• Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi
• Chromosome-level genome assembly and manually-curated proteome of model necrotroph Parastagonospora nodorum Sn15 reveals a genome-wide trove of candidate effector homologs, and redundancy of virulence-related functions within an accessory chromosome
• Pathogenicity effector candidates and accessory genome revealed by pan-genomic analysis of Parastagonospora nodorum
• Extensive macrosynteny between Medicago truncatula and Lens culinaris ssp culinaris
• The first gene-based map of Lupinus angustifolius L.-location of domestication genes and conserved synteny with Medicago truncatula