Ralph Dean

Summary

Affiliation: North Carolina State University
Country: USA

Publications

  1. pmc Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae
    Malali Gowda
    Fungal Genomics Laboratory, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27606, USA
    Nucleic Acids Res 38:7558-69. 2010
  2. pmc Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae
    Yeonyee Oh
    North Carolina State University, Center for Integrated Fungal Research, Raleigh, NC 27695 7251, USA
    Genome Biol 9:R85. 2008
  3. pmc The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae
    Michael R Thon
    Department of Plant Pathology and Microbiology, Texas A and M University, College Station, TX 77843, USA
    Genome Biol 7:R16. 2006
  4. pmc Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae
    Cristiano C Nunes
    Fungal Genomics Laboratory, Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
    BMC Genomics 12:288. 2011
  5. pmc The evolutionary history of cytochrome P450 genes in four filamentous Ascomycetes
    Jixin Deng
    Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
    BMC Evol Biol 7:30. 2007
  6. pmc Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system
    Stephen E Diener
    Fungal Genomics Laboratory, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
    BMC Bioinformatics 6:147. 2005
  7. pmc 'PACLIMS': a component LIM system for high-throughput functional genomic analysis
    Nicole Donofrio
    Department of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC, USA
    BMC Bioinformatics 6:94. 2005
  8. pmc Fungal biology reaps the benefit of genomics
    Ralph Dean
    Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
    Genome Biol 6:336. 2005
  9. ncbi request reprint The genome sequence of the rice blast fungus Magnaporthe grisea
    Ralph A Dean
    Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina 27695, USA
    Nature 434:980-6. 2005
  10. pmc MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea
    Stanton L Martin
    Fungal Genomics Laboratory, North Carolina State University, 840 Main Campus Drive, Suite 1200, Raleigh, NC 27606, USA
    Nucleic Acids Res 30:121-4. 2002

Collaborators

Detail Information

Publications38

  1. pmc Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae
    Malali Gowda
    Fungal Genomics Laboratory, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27606, USA
    Nucleic Acids Res 38:7558-69. 2010
    ..CPA-sRNAs were independently confirmed using a high affinity variant of eIF-4E to capture 5'-methylguanosine-capped RNA followed by 3'-RACE sequencing. These results expand the repertoire of small RNAs in filamentous fungi...
  2. pmc Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae
    Yeonyee Oh
    North Carolina State University, Center for Integrated Fungal Research, Raleigh, NC 27695 7251, USA
    Genome Biol 9:R85. 2008
    ..Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processes regulating appressorium formation are incompletely understood...
  3. pmc The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae
    Michael R Thon
    Department of Plant Pathology and Microbiology, Texas A and M University, College Station, TX 77843, USA
    Genome Biol 7:R16. 2006
    ....
  4. pmc Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae
    Cristiano C Nunes
    Fungal Genomics Laboratory, Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
    BMC Genomics 12:288. 2011
    ..Although significant progress has been made towards small RNA discovery and biogenesis in higher eukaryotes and other model organisms, knowledge in simple eukaryotes such as filamentous fungi remains limited...
  5. pmc The evolutionary history of cytochrome P450 genes in four filamentous Ascomycetes
    Jixin Deng
    Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
    BMC Evol Biol 7:30. 2007
    ....
  6. pmc Alkahest NuclearBLAST : a user-friendly BLAST management and analysis system
    Stephen E Diener
    Fungal Genomics Laboratory, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
    BMC Bioinformatics 6:147. 2005
    ..However, there are few options available which provide a free and user-friendly solution to the BLAST result storage and data mining needs of biologists...
  7. pmc 'PACLIMS': a component LIM system for high-throughput functional genomic analysis
    Nicole Donofrio
    Department of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC, USA
    BMC Bioinformatics 6:94. 2005
    ....
  8. pmc Fungal biology reaps the benefit of genomics
    Ralph Dean
    Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh, NC 27606, USA
    Genome Biol 6:336. 2005
    ..A report on the 23rd Fungal Genetics Conference, Pacific Grove, USA, 15-20 March 2005...
  9. ncbi request reprint The genome sequence of the rice blast fungus Magnaporthe grisea
    Ralph A Dean
    Center for Integrated Fungal Research, North Carolina State University, Raleigh, North Carolina 27695, USA
    Nature 434:980-6. 2005
    ..The M. grisea genome has been subject to invasion and proliferation of active transposable elements, reflecting the clonal nature of this fungus imposed by widespread rice cultivation...
  10. pmc MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea
    Stanton L Martin
    Fungal Genomics Laboratory, North Carolina State University, 840 Main Campus Drive, Suite 1200, Raleigh, NC 27606, USA
    Nucleic Acids Res 30:121-4. 2002
    ..grisea genome. This database, MagnaportheDB, can be accessed on the web at http://www.cals.ncsu.edu/fungal_genomics/mgdatabase/int.htm...
  11. ncbi request reprint BAC end sequences and a physical map reveal transposable element content and clustering patterns in the genome of Magnaporthe grisea
    Michael R Thon
    Center for Integrated Fungal Research, Department of Plant Pathology, North Carolina State University, Raleigh 27695 7251, USA
    Fungal Genet Biol 41:657-66. 2004
    ..This study illustrates the general utility of a physical map and BAC end sequences for the study of genome-wide repetitive DNA content and organization...
  12. pmc Combining ChIP-chip and expression profiling to model the MoCRZ1 mediated circuit for Ca/calcineurin signaling in the rice blast fungus
    Soonok Kim
    Department of Plant Pathology, The Ohio State University, Columbus, Ohio, USA
    PLoS Pathog 6:e1000909. 2010
    ..We present results from the ChIP-chip and expression analysis along with a refined model of calcium/calcineurin signaling in this important plant pathogen...
  13. pmc Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction
    Chatchawan Jantasuriyarat
    Department of Plant Pathology, The Ohio State University, Columbus, Ohio 43210, USA
    Plant Physiol 138:105-15. 2005
    ..The large cataloged collection of rice ESTs in this study provides a solid foundation for further characterization of the rice defense response and is a useful public genomic resource for rice functional genomics studies...
  14. pmc Magnaporthe grisea infection triggers RNA variation and antisense transcript expression in rice
    Malali Gowda
    Department of Plant Pathology, Ohio State University, Columbus, OH 43212, USA
    Plant Physiol 144:524-33. 2007
    ..These results demonstrate that there is a series of dynamic and complex transcript modifications and changes in the rice transcriptome at the M. grisea early infection stages...
  15. pmc Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae
    Shaowu Meng
    Center for Integrated Fungal Research, North Carolina State University, Raleigh NC 27695, USA
    BMC Microbiol 9:S8. 2009
    ..Gene Ontology (GO) annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly...
  16. ncbi request reprint Insight into Trichoderma reesei's genome content, organization and evolution revealed through BAC library characterization
    Stephen E Diener
    Fungal Genomics Laboratory, North Carolina State University, 840 Main Campus Drive, Suite 1200 Raleigh, NC 27606, USA
    Fungal Genet Biol 41:1077-87. 2004
    ..BAC clones were fingerprinted and analyzed using fingerprinted contigs (FPC) software resulting in 334 contigs covering 28 megabases of the genome. The assembly of these FPC contigs was verified by congruence with hybridization results...
  17. pmc Novel G-protein-coupled receptor-like proteins in the plant pathogenic fungus Magnaporthe grisea
    Resham D Kulkarni
    Fungal Genomics Laboratory, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
    Genome Biol 6:R24. 2005
    ..Do fungi contain only this handful or are there more receptors to be discovered? We asked this question using the recently sequenced genome of the fungal plant pathogen Magnaporthe grisea...
  18. ncbi request reprint A systematic analysis of T-DNA insertion events in Magnaporthe oryzae
    Yan Meng
    Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA
    Fungal Genet Biol 44:1050-64. 2007
    ..In addition, we found that the distribution of T-DNA inserts among the M. oryzae chromosomes was not random. The implications of these findings with regard to saturation mutagenesis of the M. oryzae genome are discussed...
  19. ncbi request reprint The Magnaporthe grisea snodprot1 homolog, MSP1, is required for virulence
    Jun Seop Jeong
    Department of Plant Pathology, Center for Integrated Fungal Research CIFR, North Carolina State University, Raleigh, NC 27695, USA
    FEMS Microbiol Lett 273:157-65. 2007
    ..When purified MSP1 protein was applied to wounded leaf tissue, no apparent phytotoxic effects were noted. This is the first report to the authors' knowledge that directly implicates a snodprot1 protein as a virulence factor...
  20. ncbi request reprint The Fusarium wilt resistance locus Fom-2 of melon contains a single resistance gene with complex features
    Tarek Joobeur
    Department of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC 27965, USA
    Plant J 39:283-97. 2004
    ..The Fom-2 physical region contained retroelement-like sequences and truncated genes, suggesting that this locus is complex...
  21. doi request reprint The Top 10 fungal pathogens in molecular plant pathology
    Ralph Dean
    Department of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC 27695, USA
    Mol Plant Pathol 13:414-30. 2012
    ..It will be interesting to see in future years how perceptions change and what fungi will comprise any future Top 10...
  22. pmc Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods
    Malali Gowda
    Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA
    BMC Genomics 7:310. 2006
    ....
  23. pmc Robust-LongSAGE (RL-SAGE): a substantially improved LongSAGE method for gene discovery and transcriptome analysis
    Malali Gowda
    Department of Plant Pathology, Ohio State University, Columbus, Ohio 43210, USA
    Plant Physiol 134:890-7. 2004
    ..5 million tags, within a month. We recently have constructed five libraries from rice (Oryza sativa), one from maize (Zea mays), and one from the rice blast fungus (Magnaporthe grisea)...
  24. ncbi request reprint An eight-cysteine-containing CFEM domain unique to a group of fungal membrane proteins
    Resham D Kulkarni
    Fungal Genomics Laboratory, Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
    Trends Biochem Sci 28:118-21. 2003
    ..Some CFEM-containing proteins (e.g. Pth11 from Magnaporthe grisea) are proposed to have important roles in fungal pathogenesis...
  25. pmc Common processes in pathogenesis by fungal and oomycete plant pathogens, described with Gene Ontology terms
    Shaowu Meng
    Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA
    BMC Microbiol 9:S7. 2009
    ..This set of standardized GO terms provides a solid base to further compare and contrast the molecular underpinnings of fungal and oomycete pathogenesis...
  26. pmc An integrated physical and genetic map of the rice genome
    Mingsheng Chen
    Clemson University Genomics Institute, 100 Jordan Hall, Clemson, South Carolina 29634 5727, USA
    Plant Cell 14:537-45. 2002
    ..Furthermore, the physical map will aid map-based cloning of agronomically important genes and will provide an important tool for the comparative analysis of grass genomes...
  27. pmc Two novel fungal virulence genes specifically expressed in appressoria of the rice blast fungus
    Chaoyang Xue
    Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
    Plant Cell 14:2107-19. 2002
    ..These two genes may belong to a class of proteins specific for filamentous fungi and function as novel virulence factors in fungal pathogens...
  28. pmc Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens
    Amy J Powell
    Department of Computational Systems Biology, Sandia National Laboratories, Albuquerque, NM, USA
    BMC Genomics 9:147. 2008
    ..To date, differential gene gain and loss have not been studied at genomic scales in fungal pathogens, despite this phenomenon's known importance in virulence in bacteria and viruses...
  29. ncbi request reprint Expression of a harpin-encoding gene in rice confers durable nonspecific resistance to Magnaporthe grisea
    Min Shao
    Key Laboratory of Monitoring and Management of Plant Diseases and Pests, Ministry of Agriculture of China, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
    Plant Biotechnol J 6:73-81. 2008
    ..These results suggest that harpins may offer new opportunities for generating broad-spectrum disease resistance in other crops...
  30. ncbi request reprint Transcript profiling of a conifer pathosystem: response of Pinus sylvestris root tissues to pathogen (Heterobasidion annosum) invasion
    Aleksandra Adomas
    Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, Sweden
    Tree Physiol 27:1441-58. 2007
    ....
  31. ncbi request reprint Expressed sequence tags from phytophthora sojae reveal genes specific to development and infection
    Trudy A Torto-Alalibo
    Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
    Mol Plant Microbe Interact 20:781-93. 2007
    ..Sequences identified with putative roles in pathogenesis included avirulence homologs possessing the RxLR motif, elicitins, and hydrolytic enzymes. This large collection of P. sojae ESTs will serve as a valuable public genomic resource...
  32. ncbi request reprint Cloning, sequencing and functional analysis of Magnaporthe grisea MVP1 gene, a hex-1 homolog encoding a putative 'woronin body' protein
    Frederick O Asiegbu
    Clemson University Genomics Institute, Clemson, SC, USA
    FEMS Microbiol Lett 230:85-90. 2004
    ..The pathological and other phenotypic consequences of gene disruption are discussed...
  33. ncbi request reprint From genes to genomes: a new paradigm for studying fungal pathogenesis in Magnaporthe oryzae
    Jin Rong Xu
    Department of Botany and Plant Pathology, Purdue University West Lafayette, Indiana 47907, USA
    Adv Genet 57:175-218. 2007
    ..The chapter concludes with new prospects in the area of systems biology, such as protein expression profiling, and highlighting remaining crucial information needed to fully appreciate host-pathogen interactions...
  34. ncbi request reprint Fungal gene clusters
    Ralph A Dean
    Nat Biotechnol 25:67. 2007
  35. ncbi request reprint AFLP analysis of a worldwide collection of Didymella bryoniae
    Ronald T Kothera
    Clemson University, Coastal Research and Education Center, 2865 Savannah Highway, Charleston, South Carolina 29414, USA
    Mycol Res 107:297-304. 2003
    ..However, isolates from the northern USA grouped separately from isolates originating from the southern USA...
  36. ncbi request reprint Development of a high throughput transformation system for insertional mutagenesis in Magnaporthe oryzae
    Melania F Betts
    Department of Plant Sciences, Division of Plant Pathology and Microbiology, University of Arizona, Tucson, AZ 85721 0036, USA
    Fungal Genet Biol 44:1035-49. 2007
    ..3% of conidia being transformed. The phenotypic data is accessible via a public database called MGOS and all strains are publicly available. This represents the most comprehensive insertional mutagenesis analysis of a fungal pathogen...
  37. ncbi request reprint Isolation of a novel antimicrobial peptide gene (Sp-AMP) homologue from Pinus sylvestris (Scots pine) following infection with the root rot fungus Heterobasidion annosum
    Frederick O Asiegbu
    Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, Box 7026, Uppsala, Sweden
    FEMS Microbiol Lett 228:27-31. 2003
    ..Southern analyses further confirmed that several copies of the gene are present in the Scots pine genome. The potential significance of Sp-AMP in the H. annosum-conifer pathosystem is discussed...
  38. ncbi request reprint 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.)
    Yi Hong Wang
    Clemson University Genomics Institute and Department of Plant Pathology and Physiology, Clemson University, SC 29634, USA
    Genome 45:473-80. 2002
    ..The sequence information may be useful for identifying NBS-LRR class of R genes in other cucurbits...