Ralph A Dean

Host induced gene silencing of Magnaporthe oryzae by targeting pathogenicity and development genes to control rice blast disease

FRONTIERS IN PLANT SCIENCE, 13.

Electronic nose system based on a functionalized capacitive micromachined ultrasonic transducer (CMUT) array for selective detection of plant volatiles

SENSORS AND ACTUATORS B-CHEMICAL, 341.

Soybean Cyst Nematodes Influence Aboveground Plant Volatile Signals Prior to Symptom Development

FRONTIERS IN PLANT SCIENCE, 12.

Comparative Genome Analyses of 18 Verticillium dahliae Tomato Isolates Reveals Phylogenetic and Race Specific Signatures

FRONTIERS IN MICROBIOLOGY, 11.

Comparative Proteomic Analysis of Wild Type and Mutant Lacking an SCF E3 Ligase F-Box Protein in Magnaporthe oryzae

JOURNAL OF PROTEOME RESEARCH, 19(9), 3761–3768.

Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds

FRONTIERS IN MICROBIOLOGY, 11.

Investigating host-pathogen meta-metabolic interactions of Magnaporthe oryzae infected barley using infrared matrix-assisted laser desorption electrospray ionization mass spectrometry

ANALYTICAL AND BIOANALYTICAL CHEMISTRY, 412(1), 139–147.

Movement of small RNAs in and between plants and fungi

[Review of ]. MOLECULAR PLANT PATHOLOGY, 21(4), 589–601.

Identification and Characterization of the Core Rice Seed Microbiome

PHYTOBIOMES JOURNAL, 3(2), 148–157.

Characterizing Small RNAs in Filamentous Fungi Using the Rice Blast Fungus, Magnaporthe oryzae, as an Example

PLANT PATHOGENIC FUNGI AND OOMYCETES: METHODS AND PROTOCOLS, Vol. 1848, pp. 53–66.

Host-Microbe Interactions: Fungi Vol 46

Dean, R. A., & Rouxel, T. (2018, December). CURRENT OPINION IN MICROBIOLOGY, Vol. 46, pp. III-V.

Sequential Phosphopeptide Enrichment for Phosphoproteome Analysis of Filamentous Fungi: A Test Case Using Magnaporthe oryzae

PLANT PATHOGENIC FUNGI AND OOMYCETES: METHODS AND PROTOCOLS, Vol. 1848, pp. 81–91.

To B or not to B: a tale of unorthodox chromosomes

[Review of ]. CURRENT OPINION IN MICROBIOLOGY, 46, 50–57.

Comparative proteomic analysis between nitrogen supplemented and starved conditions in Magnaporthe oryzae

Proteome Science, 15.

Identification and characterization of suppressors of plant cell death (SPD) effectors from Magnaporthe oryzae

MOLECULAR PLANT PATHOLOGY, 18(6), 850–863.

Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi

BMC GENOMICS, 17.

Examining ubiquitinated peptide enrichment efficiency through an epitope labeled protein

ANALYTICAL BIOCHEMISTRY, 512, 114–119.

Form and function of fungal and oomycete effectors

[Review of ]. FUNGAL BIOLOGY REVIEWS, 30(2), 62–73.

The influence of funding sources on the scientific method

Okagaki, L. H., & Dean, R. A. (2016, June). MOLECULAR PLANT PATHOLOGY, Vol. 17, pp. 651–653.

Genome sequences of three phytopathogenic species of the Magnaporthaceae family of fungi

G3-Genes Genomes Genetics, 5(12), 2539–2545.

Genome-wide profiling of DNA methylation provides insights into epigenetic regulation of fungal development in a plant pathogenic fungus, Magnaporthe oryzae

SCIENTIFIC REPORTS, 5.

Phosphoproteome Analysis Links Protein Phosphorylation to Cellular Remodeling and Metabolic Adaptation during Magnaporthe oryzae Appressorium Development

Journal of Proteome Research, 14(6), 2408–2424.

Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3

FEMS MICROBIOLOGY LETTERS, 352(2), 165–173.

Experimental Evolution Reveals Genome-Wide Spectrum and Dynamics of Mutations in the Rice Blast Fungus, Magnaporthe oryzae

PLOS ONE, 8(5).

Temporal Analysis of theMagnaporthe OryzaeProteome During Conidial Germination and Cyclic AMP (cAMP)-mediated Appressorium Formation

Molecular & Cellular Proteomics, 12(8), 2249–2265.

Comparative Analysis of the Genomes of Two Field Isolates of the Rice Blast Fungus Magnaporthe oryzae

PLOS GENETICS, 8(8).

Host-induced gene silencing: a tool for understanding fungal host interaction and for developing novel disease control strategies

[Review of ]. MOLECULAR PLANT PATHOLOGY, 13(5), 519–529.

In-Depth Analysis of the Magnaporthe oryzae Conidial Proteome

JOURNAL OF PROTEOME RESEARCH, 11(12), 5827–5835.

Phylogenetic Analysis and Classification of the Fungal bHLH Domain

MOLECULAR BIOLOGY AND EVOLUTION, 29(5), 1301–1318.

Polyubiquitin Is Required for Growth, Development and Pathogenicity in the Rice Blast Fungus Magnaporthe oryzae

PLoS ONE, 7(8), e42868.

The Top 10 fungal pathogens in molecular plant pathology

[Review of ]. MOLECULAR PLANT PATHOLOGY, 13(4), 414–430.

Characterization and application of small RNAs and RNA silencing mechanisms in fungi

Fungal Biology Reviews, 25(4), 172–180.

Comparison of stable-isotope labeling with amino acids in cell culture and spectral counting for relative quantification of protein expression

RAPID COMMUNICATIONS IN MASS SPECTROMETRY, 25(17), 2524–2532.

Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae

BMC Genomics, 12.

Evaluation of Normalization Methods on GeLC-MS/MS Label-Free Spectral Counting Data to Correct for Variation during Proteomic Workflows

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 22(12), 2199–2208.

Improving Proteome Coverage on a LTQ-Orbitrap Using Design of Experiments

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 22(4), 773–783.

Increasing proteome coverage with offline RP HPLC coupled to online RP nanoLC-MS

JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES, 879(9-10), 610–614.

MoSfl1 Is Important for Virulence and Heat Tolerance in Magnaporthe oryzae

PLOS ONE, 6(5).

Transcriptome profiling of the rice blast fungus during invasive plant infection and in vitro stresses

BMC GENOMICS, 12.

Combining ChIP-chip and Expression Profiling to Model the MoCRZ1 Mediated Circuit for Ca2+/Calcineurin Signaling in the Rice Blast Fungus

PLOS PATHOGENS, 6(5).

Direct Comparison of Stable Isotope Labeling by Amino Acids in Cell Culture and Spectral Counting for Quantitative Proteomics

ANALYTICAL CHEMISTRY, 82(20), 8696–8702.

Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology

[Review of ]. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, 74(4), 479–503.

Common processes in pathogenesis by fungal and oomycete plant pathogens, described with Gene Ontology terms

[Review of ]. BMC MICROBIOLOGY, 9.

Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae

[Review of ]. BMC MICROBIOLOGY, 9.

Infection strategies of filamentous microbes described with the Gene Ontology

[Review of ]. TRENDS IN MICROBIOLOGY, 17(7), 320–327.

Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens

BMC GENOMICS, 9.

Aspergillus flavus genomics as a tool for studying the mechanism of aflatoxin formation

FOOD ADDITIVES AND CONTAMINANTS PART A-CHEMISTRY ANALYSIS CONTROL EXPOSURE & RISK ASSESSMENT, Vol. 25, pp. 1152–1157.

Expression of a harpin-encoding gene in rice confers durable nonspecific resistance to Magnaporthe grisea

PLANT BIOTECHNOLOGY JOURNAL, 6(1), 73–81.

The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus

Current Genetics, 54(5), 241–269.

Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae

[Review of ]. GENOME BIOLOGY, 9(5).

A systematic analysis of T-DNA insertion events in Magnaporthe oryzae

FUNGAL GENETICS AND BIOLOGY, 44(10), 1050–1064.

Challenges in quantification of ligninolytic enzymes from Phanerochaete chrysosporium cultivation for pretreatment of cotton stalks

Transactions of the ASABE, 50(6), 2347–2354.

Development of a high throughput transformation system for insertional mutagenesis in Magnaporthe oryzae

FUNGAL GENETICS AND BIOLOGY, 44(10), 1035–1049.

Expressed sequence tags from Phytophthora sojae reveal genes specific to development and infection

MOLECULAR PLANT-MICROBE INTERACTIONS, 20(7), 781–793.

From genes to genomes: A new paradigm for studying fungal pathogenesis in magnaporthe oryzae

[Review of ]. Fungal genomics, 57, 175–218.

Fungal gene clusters

Dean, R. A. (2007, January). NATURE BIOTECHNOLOGY, Vol. 25, pp. 67–67.

Magnaporthe grisea infection triggers RNA variation and antisense transcript expression in rice

PLANT PHYSIOLOGY, 144(1), 524–533.

The Magnaporthe grisea snodprot1 homolog, MSPI, is required for virulence

FEMS MICROBIOLOGY LETTERS, 273(2), 157–165.

The evolutionary history of Cytochrome P450 genes in four filamentous Ascomycetes

BMC EVOLUTIONARY BIOLOGY, 7.

Trranscript profiling of a conifer pathosystem: response of Pinus sylvestris root tissues to pathogen (Heterobasidion annosum) invasion

TREE PHYSIOLOGY, 27(10), 1441–1458.

What can comparative genomics tell us about species concepts in the genus Aspergillus?

STUDIES IN MYCOLOGY, pp. 11–17.

Construction of a watermelon BAC library and identification of SSRs anchored to melon or Arabidopsis genomes

THEORETICAL AND APPLIED GENETICS, 112(8), 1553–1562.

Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods

BMC Genomics, 7.

Global gene expression during nitrogen starvation in the rice blast fungus, Magnaporthe grisea

FUNGAL GENETICS AND BIOLOGY, 43(9), 605–617.

MGOS: A resource for studying Magnaporthe grisea and Oryza sativa interactions

MOLECULAR PLANT-MICROBE INTERACTIONS, 19(10), 1055–1061.

Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae

[Review of ]. NUCLEIC ACIDS RESEARCH, 34(17), 4685–4701.

The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae

Genome Biology, 7(2).

Whole genome comparison of Aspergillus flavus and A-oryzae

Payne, G. A., Nierman, W. C., Wortman, J. R., Pritchard, B. L., Brown, D., Dean, R. A., … Yu, J. (2006, September). MEDICAL MYCOLOGY, Vol. 44, pp. S9–S11.

Alkahest NuclearBLAST: a user-friendly BLAST management and analysis system

BMC Bioinformatics, 6.

Genetic variation among Rhizoctonia solani isolates from warm-season turfgrasses

International Turfgrass Society Research Journal, 10, 230.

Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction

PLANT PHYSIOLOGY, 138(1), 105–115.

Novel G-protein-coupled receptor-like proteins in the plant pathogenic fungus Magnaporthe grisea

Genome Biology, 6(3).

PACLIMS: A component LIM system for high-throughput functional genomic analysis

BMC Bioinformatics, 6.

The genome sequence of the rice blast fungus Magnaporthe grisea

NATURE, 434(7036), 980–986.

Trust-Based Secure Workflow Path Construction

In B. Benatallah, F. Casati, & P. Traverso (Eds.), Service-Oriented Computing – ICSOC 2007 (pp. 382–395).

BAC end sequences and a physical map reveal transposable element content and clustering patterns in the genome of Magnaporthe grisea

FUNGAL GENETICS AND BIOLOGY, 41(7), 657–666.

Characterization of the protein processing and secretion pathways in a comprehensive set of expressed sequence tags from Trichoderma reesei

FEMS MICROBIOLOGY LETTERS, 230(2), 275–282.

Characterization of the protein processing and secretion pathways in a comprehensive set of expressed sequence tags from Trichoderma reesei (vol 230, pg 275, 2004)

FEMS Microbiology Letters, Vol. 235, p. 209.

Cloning, sequencing and functional analysis of Magnaporthe grisea MVP1 gene, a hex-1 homolog encoding a putative 'woronin body' protein

FEMS Microbiology Letters, 230(1), 85–90.

Cloning, sequencing and functional analysis of Magnaporthe grisea MVP1 gene, a hex-1 homolog encoding a putative ‘woronin body’ protein

FEMS Microbiology Letters, 230(1), 85–90.

Gene discovery and gene expression in the rice blast fungus, Magnaporthe grisea: Analysis of expressed sequence tags

MOLECULAR PLANT-MICROBE INTERACTIONS, 17(12), 1337–1347.

Identification of proteins that interact with two regulators of appressorium development, adenylate cyclase and cAMP-dependent protein kinase A, in the rice blast fungus Magnaporthe grisea

Molecular Genetics and Genomics, 270(6), 497–508.

Insight into Trichoderma reesei's genome content, organization and evolution revealed through BAC library characterization

FUNGAL GENETICS AND BIOLOGY, 41(12), 1077–1087.

Protocol for DNA extraction from watermelon leaves for SSR marker studies

Report (Cucurbit Genetics Cooperative), (27), 25.

Robust-LongSAGE (RL-SAGE): A substantially improved LongSAGE method for gene discovery and transcriptome analysis

PLANT PHYSIOLOGY, 134(3), 890–897.

The fusarium wilt resistance locus Fom-2 of melon contains a single resistance gene with complex features

PLANT JOURNAL, 39(3), 283–297.

AFLP analysis of a worldwide collection of Didymella bryoniae

MYCOLOGICAL RESEARCH, 107, 297–304.

An eight-cysteine-containing CFEM domain unique to a group of fungal membrane proteins

TRENDS IN BIOCHEMICAL SCIENCES, 28(3), 118–121.

In-depth view of structure, activity, and evolution of rice chromosome 10

Science, 300(5625), 1566–1569.

Isolation of a novel antimicrobial peptide gene (Sp-AMP) homologue from Pinus sylvestris (Scots pine) following infection with the root rot fungus Heterobasidion annosum

FEMS MICROBIOLOGY LETTERS, 228(1), 27–31.

Large scale parallel analysis of gene expression during infection-related morphogenesis of Magnaporthe grisea

MOLECULAR PLANT PATHOLOGY, 4(5), 337–346.

PI3K signaling is required for prostaglandin-induced mucosal recovery in ischemia-injured porcine ileum

American Journal of Physiology-Gastrointestinal and Liver Physiology, 284(1), G46–G56.

The rice blast pathosystem as a case study for the development of new tools and raw materials for genome analysis of fungal plant pathogens

[Review of ]. NEW PHYTOLOGIST, 159(1), 53–61.

Transcriptional regulation of biomass-degrading enzymes in the filamentous fungus Trichoderma reesei

JOURNAL OF BIOLOGICAL CHEMISTRY, 278(34), 31988–31997.

Cloning of disease-resistance homologues in end sequences of BAC clones linked to Fom-2, a gene conferring resistance to Fusarium wilt in melon (Cucumis melo L.)

GENOME, 45(3), 473–480.

Development of PCR-ELISA for detection and differentiation of Didymella bryoniae from related Phoma species

PLANT DISEASE, 86(7), 710–716.

Internal transcribed spacer regions 1 and 2 and random amplified polymorphic DNA analysis of Didymella bryoniae and related Phoma species isolated from cucurbits

PHYTOPATHOLOGY, 92(9), 997–1004.

MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea

NUCLEIC ACIDS RESEARCH, 30(1), 121–124.

Two novel fungal virulence genes specifically expressed in appressoria of the rice blast fungus

PLANT CELL, 14(9), 2107–2119.

A genetic linkage map for watermelon based on randomly amplified polymorphic DNA markers

JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE, 126(6), 730–737.

Global analysis of protein activities using proteome chips

SCIENCE, 293(5537), 2101–2105.

Melon bacterial artificial chromosome (BAC) library construction using improved methods and identification of clones linked to the locus conferring resistance to melon Fusarium wilt (Fom-2)

GENOME, 44(2), 154–162.

Genetic mapping of a fusarium wilt resistance gene (Fom-2) in melon (Cucumis melo L.)

MOLECULAR BREEDING, 6(4), 379–389.

Site-directed mutagenesis of the magB gene affects growth and development in Magnaporthe grisea

MOLECULAR PLANT-MICROBE INTERACTIONS, 13(11), 1214–1227.