Ralph Dean

Cho, E., Lee, S. H., Dean, R. A., & Jeon, J. (2023). Distinct dynamics of the nucleolus in response to nutrient availability and during development in the rice blast fungus. MBIO, 9. https://doi.org/10.1128/mbio.01844-23

Dean, R. (2023). Issue Information. MOLECULAR PLANT PATHOLOGY, 24(9), 1015–1016. https://doi.org/10.1111/mpp.13384

Sennik, E., Kinoshita-Millard, S., Oh, Y., Kafer, C. W., Dean, R. A., & Oralkan, O. (2023). Plant Disease Detection Using an Electronic Nose. 2023 IEEE SENSORS. https://doi.org/10.1109/SENSORS56945.2023.10325015

Oh, Y., Ingram, T., Shekasteband, R., Adhikari, T., Louws, F. J., & Dean, R. A. (2023, May 15). Tissues and mechanisms associated with Verticillium wilt resistance in tomato using bi-grafted near-isogenic lines (M. Höfte, Ed.). JOURNAL OF EXPERIMENTAL BOTANY, Vol. 5. https://doi.org/10.1093/jxb/erad182

Wang, M., & Dean, R. A. (2022). Host induced gene silencing of Magnaporthe oryzae by targeting pathogenicity and development genes to control rice blast disease. FRONTIERS IN PLANT SCIENCE, 13. https://doi.org/10.3389/fpls.2022.959641

Sennik, E., Erden, F., Constantino, N., Oh, Y. Y., Dean, R. A., & Oralkan, O. (2021). 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. https://doi.org/10.1016/j.snb.2021.130001

Constantino, N., Oh, Y., Sennik, E., Andersen, B., Warden, M., Oralkan, O., & Dean, R. A. (2021). Soybean Cyst Nematodes Influence Aboveground Plant Volatile Signals Prior to Symptom Development. FRONTIERS IN PLANT SCIENCE, 12. https://doi.org/10.3389/fpls.2021.749014

Ingram, T. W., Oh, Y., Adhikari, T. B., Louws, F. J., & Dean, R. A. (2020). Comparative Genome Analyses of 18 Verticillium dahliae Tomato Isolates Reveals Phylogenetic and Race Specific Signatures. FRONTIERS IN MICROBIOLOGY, 11. https://doi.org/10.3389/fmicb.2020.573755

Kalmar, J. G., Oh, Y., Dean, R. A., & Muddiman, D. C. (2020). 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. https://doi.org/10.1021/acs.jproteome.0c00294

Wang, M., Eyre, A. W., Thon, M. R., Oh, Y., & Dean, R. A. (2020). Dynamic Changes in the Microbiome of Rice During Shoot and Root Growth Derived From Seeds. FRONTIERS IN MICROBIOLOGY, 11. https://doi.org/10.3389/fmicb.2020.559728

Kalmar, J. G., Oh, Y., Dean, R. A., & Muddiman, D. C. (2020). 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. https://doi.org/10.1007/s00216-019-02216-z

Wang, M., & Dean, R. A. (2020). [Review of Movement of small RNAs in and between plants and fungi]. MOLECULAR PLANT PATHOLOGY, 21(4), 589–601. https://doi.org/10.1111/mpp.12911

Eyre, A. W., Wang, M., Oh, Y., & Dean, R. A. (2019). Identification and Characterization of the Core Rice Seed Microbiome. PHYTOBIOMES JOURNAL, 3(2), 148–157. https://doi.org/10.1094/PBIOMES-01-19-0009-R

Raman, V., Meyers, B. C., Dean, R. A., & Donofrio, N. M. (2018). 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. https://doi.org/10.1007/978-1-4939-8724-5_5

Dean, R. A., & Rouxel, T. (2018, December). Host-Microbe Interactions: Fungi Vol 46. CURRENT OPINION IN MICROBIOLOGY, Vol. 46, pp. III-V. https://doi.org/10.1016/j.mib.2018.11.009

Oh, Y., Franck, W. L., & Dean, R. A. (2018). 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. https://doi.org/10.1007/978-1-4939-8724-5_7

Soyer, J. L., Balesdent, M.-H., Rouxel, T., & Dean, R. A. (2018). [Review of To B or not to B: a tale of unorthodox chromosomes]. CURRENT OPINION IN MICROBIOLOGY, 46, 50–57. https://doi.org/10.1016/j.mib.2018.01.012

Oh, Y., Robertson, S. L., Parker, J., Muddiman, D. C., & Dean, R. A. (2017). Comparative proteomic analysis between nitrogen supplemented and starved conditions in Magnaporthe oryzae. Proteome Science, 15.

Sharpee, W., Oh, Y., Yi, M., Franck, W., Eyre, A., Okagaki, L. H., … Dean, R. A. (2017). Identification and characterization of suppressors of plant cell death (SPD) effectors from Magnaporthe oryzae. MOLECULAR PLANT PATHOLOGY, 18(6), 850–863. https://doi.org/10.1111/mpp.12449

Okagaki, L. H., Sailsbery, J. K., Eyre, A. W., & Dean, R. A. (2016). Comparative genome analysis and genome evolution of members of the magnaporthaceae family of fungi. BMC GENOMICS, 17. https://doi.org/10.1186/s12864-016-2491-y

Parker, J., Oh, Y., Moazami, Y., Pierce, J. G., Loziuk, P. L., Dean, R. A., & Muddiman, D. C. (2016). Examining ubiquitinated peptide enrichment efficiency through an epitope labeled protein. ANALYTICAL BIOCHEMISTRY, 512, 114–119. https://doi.org/10.1016/j.ab.2016.08.017

Sharpee, W. C., & Dean, R. A. (2016). [Review of Form and function of fungal and oomycete effectors]. FUNGAL BIOLOGY REVIEWS, 30(2), 62–73. https://doi.org/10.1016/j.fbr.2016.04.001

Okagaki, L. H., & Dean, R. A. (2016, June). The influence of funding sources on the scientific method. MOLECULAR PLANT PATHOLOGY, Vol. 17, pp. 651–653. https://doi.org/10.1111/mpp.12380

Okagaki, L. H., Nunes, C. C., Sailsbery, J., Clay, B., Brown, D., John, T., … Kohn, L. M. (2015). Genome sequences of three phytopathogenic species of the Magnaporthaceae family of fungi. G3-Genes Genomes Genetics, 5(12), 2539–2545.

Jeon, J., Choi, J., Lee, G.-W., Park, S.-Y., Huh, A., Dean, R. A., & Lee, Y.-H. (2015). Genome-wide profiling of DNA methylation provides insights into epigenetic regulation of fungal development in a plant pathogenic fungus, Magnaporthe oryzae. SCIENTIFIC REPORTS, 5. https://doi.org/10.1038/srep08567

Franck, W. L., Gokce, E., Randall, S. M., Oh, Y., Eyre, A., Muddiman, D. C., & Dean, R. A. (2015). Phosphoproteome Analysis Links Protein Phosphorylation to Cellular Remodeling and Metabolic Adaptation during Magnaporthe oryzae Appressorium Development. Journal of Proteome Research, 14(6), 2408–2424. https://doi.org/10.1021/pr501064q

Losada, L., Pakala, S. B., Fedorova, N. D., Joardar, V., Shabalina, S. A., Hostetler, J., … Cubeta, M. A. (2014). Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3. FEMS MICROBIOLOGY LETTERS, 352(2), 165–173. https://doi.org/10.1111/1574-6968.12387

Jeon, J., Choi, J., Lee, G.-W., Dean, R. A., & Lee, Y.-H. (2013). Experimental Evolution Reveals Genome-Wide Spectrum and Dynamics of Mutations in the Rice Blast Fungus, Magnaporthe oryzae. PLOS ONE, 8(5). https://doi.org/10.1371/journal.pone.0065416

Franck, W. L., Gokce, E., Oh, Y., Muddiman, D. C., & Dean, R. A. (2013). Temporal Analysis of theMagnaporthe OryzaeProteome During Conidial Germination and Cyclic AMP (cAMP)-mediated Appressorium Formation. Molecular & Cellular Proteomics, 12(8), 2249–2265. https://doi.org/10.1074/mcp.m112.025874

Xue, M., Yang, J., Li, Z., Hu, S., Yao, N., Dean, R. A., … Peng, Y.-L. (2012). Comparative Analysis of the Genomes of Two Field Isolates of the Rice Blast Fungus Magnaporthe oryzae. PLOS GENETICS, 8(8). https://doi.org/10.1371/journal.pgen.1002869

Nunes, C. C., & Dean, R. A. (2012). [Review of Host-induced gene silencing: a tool for understanding fungal host interaction and for developing novel disease control strategies]. MOLECULAR PLANT PATHOLOGY, 13(5), 519–529. https://doi.org/10.1111/j.1364-3703.2011.00766.x

Gokce, E., Franck, W. L., Oh, Y., Dean, R. A., & Muddiman, D. C. (2012). In-Depth Analysis of the Magnaporthe oryzae Conidial Proteome. JOURNAL OF PROTEOME RESEARCH, 11(12), 5827–5835. https://doi.org/10.1021/pr300604s

Sailsbery, J. K., Atchley, W. R., & Dean, R. A. (2012). Phylogenetic Analysis and Classification of the Fungal bHLH Domain. MOLECULAR BIOLOGY AND EVOLUTION, 29(5), 1301–1318. https://doi.org/10.1093/molbev/msr288

Oh, Y., Franck, W. L., Han, S.-O., Shows, A., Gokce, E., Muddiman, D. C., & Dean, R. A. (2012). Polyubiquitin Is Required for Growth, Development and Pathogenicity in the Rice Blast Fungus Magnaporthe oryzae. PLoS ONE, 7(8), e42868. https://doi.org/10.1371/journal.pone.0042868

Dean, R., Van Kan, J. A. L., Pretorius, Z. A., Hammond-Kosack, K. E., Di Pietro, A., Spanu, P. D., … Foster, G. D. (2012). [Review of The Top 10 fungal pathogens in molecular plant pathology]. MOLECULAR PLANT PATHOLOGY, 13(4), 414–430. https://doi.org/10.1111/j.1364-3703.2011.00783.x

Nunes, C. C., Sailsbery, J. K., & Dean, R. A. (2011). Characterization and application of small RNAs and RNA silencing mechanisms in fungi. Fungal Biology Reviews, 25(4), 172–180. https://doi.org/10.1016/j.fbr.2011.10.001

Collier, T. S., Randall, S. M., Sarkar, P., Rao, B. M., Dean, R. A., & Muddiman, D. C. (2011). 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. https://doi.org/10.1002/rcm.5151

Nunes, C. C., Gowda, M., Sailsbery, J., Xue, M. F., Chen, F., Brown, D. E., … Dean, R. (2011). Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae. BMC Genomics, 12. https://doi.org/10.1186/1471-2164-12-288

Gokce, E., Shuford, C. M., Franck, W. L., Dean, R. A., & Muddiman, D. C. (2011). 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. https://doi.org/10.1007/s13361-011-0237-2

Andrews, G. L., Dean, R. A., Hawkridge, A. M., & Muddiman, D. C. (2011). Improving Proteome Coverage on a LTQ-Orbitrap Using Design of Experiments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 22(4), 773–783. https://doi.org/10.1007/s13361-011-0075-2

Gokce, E., Andrews, G. L., Dean, R. A., & Muddiman, D. C. (2011). 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. https://doi.org/10.1016/j.jchromb.2011.01.032

Li, G., Zhou, X., Kong, L., Wang, Y., Zhang, H., Zhu, H., … Xu, J.-R. (2011). MoSfl1 Is Important for Virulence and Heat Tolerance in Magnaporthe oryzae. PLOS ONE, 6(5). https://doi.org/10.1371/journal.pone.0019951

Mathioni, S. M., Belo, A., Rizzo, C. J., Dean, R. A., & Donofrio, N. M. (2011). Transcriptome profiling of the rice blast fungus during invasive plant infection and in vitro stresses. BMC GENOMICS, 12. https://doi.org/10.1186/1471-2164-12-49

Kim, S., Hu, J., Oh, Y., Park, J., Choi, J., Lee, Y.-H., … Mitchell, T. K. (2010). 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). https://doi.org/10.1371/journal.ppat.1000909

Collier, T. S., Sarkar, P., Franck, W. L., Rao, B. M., Dean, R. A., & Muddiman, D. C. (2010). Direct Comparison of Stable Isotope Labeling by Amino Acids in Cell Culture and Spectral Counting for Quantitative Proteomics. ANALYTICAL CHEMISTRY, 82(20), 8696–8702. https://doi.org/10.1021/ac101978b

Torto-Alalibo, T., Collmer, C. W., Gwinn-Giglio, M., Lindeberg, M., Meng, S., Chibucos, M. C., … Tyler, B. M. (2010). [Review of Unifying Themes in Microbial Associations with Animal and Plant Hosts Described Using the Gene Ontology]. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, 74(4), 479–503. https://doi.org/10.1128/mmbr.00017-10

Meng, S., Torto-Alalibo, T., Chibucos, M. C., Tyler, B. M., & Dean, R. A. (2009). [Review of Common processes in pathogenesis by fungal and oomycete plant pathogens, described with Gene Ontology terms]. BMC MICROBIOLOGY, 9. https://doi.org/10.1186/1471-2180-9-s1-s7

Meng, S., Brown, D. E., Ebbole, D. J., Torto-Alalibo, T., Oh, Y. Y., Deng, J., … Dean, R. A. (2009). [Review of Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae]. BMC MICROBIOLOGY, 9. https://doi.org/10.1186/1471-2180-9-s1-s8

Torto-Alalibo, T., Meng, S., & Dean, R. A. (2009). [Review of Infection strategies of filamentous microbes described with the Gene Ontology]. TRENDS IN MICROBIOLOGY, 17(7), 320–327. https://doi.org/10.1016/j.tim.2009.05.003

Powell, A. J., Conant, G. C., Brown, D. E., Carbone, I., & Dean, R. A. (2008). Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens. BMC GENOMICS, 9. https://doi.org/10.1186/1471-2164-9-147

Yu, J., Payne, G. A., Nierman, W. C., Machida, M., Bennett, J. W., Campbell, B. C., … Cleveland, T. E. (2008). 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. https://doi.org/10.1080/02652030802213375

Shao, M., Wang, J., Dean, R. A., Lin, Y., Gao, X., & Hu, S. (2008). Expression of a harpin-encoding gene in rice confers durable nonspecific resistance to Magnaporthe grisea. PLANT BIOTECHNOLOGY JOURNAL, 6(1), 73–81. https://doi.org/10.1111/j.1467-7652.2007.00304.x

Smith, C. A., Robertson, D., Yates, B., Nielsen, D. M., Brown, D., Dean, R. A., & Payne, G. A. (2008). The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus. Current Genetics, 54(5), 241–269. https://doi.org/10.1007/s00294-008-0215-9

Oh, Y., Donofrio, N., Pan, H., Coughlan, S., Brown, D. E., Meng, S., … Dean, R. A. (2008). [Review of Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae]. GENOME BIOLOGY, 9(5). https://doi.org/10.1186/gb-2008-9-5-r85

Meng, Y., Patel, G., Heist, M., Betts, M. F., Tucker, S. L., Galadima, N., … Farman, M. L. (2007). A systematic analysis of T-DNA insertion events in Magnaporthe oryzae. FUNGAL GENETICS AND BIOLOGY, 44(10), 1050–1064. https://doi.org/10.1016/j.fgb.2007.04.002

Shi, J., Sharma-Shivappa, R. R., Chinn, M., Dean, R., & Shivappa, R. B. (2007). Challenges in quantification of ligninolytic enzymes from Phanerochaete chrysosporium cultivation for pretreatment of cotton stalks. Transactions of the ASABE, 50(6), 2347–2354. https://doi.org/10.13031/2013.24071

Betts, M. F., Tucker, S. L., Galadima, N., Meng, Y., Patel, G., Li, L., … Orbach, M. J. (2007). Development of a high throughput transformation system for insertional mutagenesis in Magnaporthe oryzae. FUNGAL GENETICS AND BIOLOGY, 44(10), 1035–1049. https://doi.org/10.1016/j.fgb.2007.05.001

Torto-Alalibo, T. A., Tripathy, S., Smith, B. M., Arredondo, F. D., Zhou, L., Li, H., … Tyler, B. M. (2007). Expressed sequence tags from Phytophthora sojae reveal genes specific to development and infection. MOLECULAR PLANT-MICROBE INTERACTIONS, 20(7), 781–793. https://doi.org/10.1094/MPMI-20-7-0781

Xu, J. R., Zhao, X. H., & Dean, R. A. (2007). [Review of From genes to genomes: A new paradigm for studying fungal pathogenesis in magnaporthe oryzae]. Fungal genomics, 57, 175–218.

Dean, R. A. (2007, January). Fungal gene clusters. NATURE BIOTECHNOLOGY, Vol. 25, pp. 67–67. https://doi.org/10.1038/nbt0107-67

Gowda, M., Venu, R.-C., Li, H., Jantasuriyarat, C., Chen, S., Bellizzi, M., … Wang, G.-L. (2007). Magnaporthe grisea infection triggers RNA variation and antisense transcript expression in rice. PLANT PHYSIOLOGY, 144(1), 524–533. https://doi.org/10.1104/pp.107.095653

Jeong, J. S., Mitchell, T. K., & Dean, R. A. (2007). The Magnaporthe grisea snodprot1 homolog, MSPI, is required for virulence. FEMS MICROBIOLOGY LETTERS, 273(2), 157–165. https://doi.org/10.1111/j.1574-6968.2007.00796.x

Deng, J., Carbone, I., & Dean, R. A. (2007). The evolutionary history of Cytochrome P450 genes in four filamentous Ascomycetes. BMC EVOLUTIONARY BIOLOGY, 7. https://doi.org/10.1186/1471-2148-7-30

Adomas, A., Heller, G., Li, G., Olson, A., Chu, T.-M., Osborne, J., … Asiegbu, F. O. (2007). Trranscript profiling of a conifer pathosystem: response of Pinus sylvestris root tissues to pathogen (Heterobasidion annosum) invasion. TREE PHYSIOLOGY, 27(10), 1441–1458. https://doi.org/10.1093/treephys/27.10.1441

Rokas, A., Payne, G., Fedorova, N. D., Baker, S. E., Machida, M., Yu, J., … Nierman, W. C. (2007). What can comparative genomics tell us about species concepts in the genus Aspergillus? STUDIES IN MYCOLOGY, pp. 11–17. https://doi.org/10.3114/sim.2007.59.02

Joobeur, T., Gusmini, G., Zhang, X., Levi, A., Xu, Y., Wehner, T. C., … Dean, R. A. (2006). Construction of a watermelon BAC library and identification of SSRs anchored to melon or Arabidopsis genomes. THEORETICAL AND APPLIED GENETICS, 112(8), 1553–1562. https://doi.org/10.1007/s00122-006-0258-6

Gowda, M., Venu, R. C., Raghupathy, M. B., Nobuta, K., Li, H. M., Wing, R., … Wang, G. L. (2006). Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods. BMC Genomics, 7.

Donofrio, N. M., Oh, Y., Lundy, R., Pan, H., Brown, D. E., Jeong, J. S., … Dean, R. A. (2006). Global gene expression during nitrogen starvation in the rice blast fungus, Magnaporthe grisea. FUNGAL GENETICS AND BIOLOGY, 43(9), 605–617. https://doi.org/10.1016/j.fgb.2006.03.005

Soderlund, C., Haller, K., Pampanwar, V., Ebbole, D., Farman, M., Orbach, M. J., … Dean, R. (2006). MGOS: A resource for studying Magnaporthe grisea and Oryza sativa interactions. MOLECULAR PLANT-MICROBE INTERACTIONS, 19(10), 1055–1061. https://doi.org/10.1094/MPMI-19-1055

Rehmeyer, C., Li, W., Kusaba, M., Kim, Y.-S., Brown, D., Staben, C., … Farman, M. (2006). [Review of Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae]. NUCLEIC ACIDS RESEARCH, 34(17), 4685–4701. https://doi.org/10.1093/nar/gkl588

Thon, M. R., Pan, H. Q., Diener, S., Papalas, J., Taro, A., Mitchell, T. K., & Dean, R. A. (2006). The  role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae. Genome Biology, 7(2).

Payne, G. A., Nierman, W. C., Wortman, J. R., Pritchard, B. L., Brown, D., Dean, R. A., … Yu, J. (2006, September). Whole genome comparison of Aspergillus flavus and A-oryzae. MEDICAL MYCOLOGY, Vol. 44, pp. S9–S11. https://doi.org/10.1080/13693780600835716

Diener, S. E., Houfek, T. D., Kalat, S. E., Windham, D. E., Burke, M., Opperman, C., & Dean, R. A. (2005). Alkahest NuclearBLAST: a user-friendly BLAST management and analysis system. BMC Bioinformatics, 6.

Li, J. F., Martin, S. B., Jeffers, S. N., Dean, R. A., & Camberato, J. J. (2005). Genetic variation among Rhizoctonia solani isolates from warm-season turfgrasses. International Turfgrass Society Research Journal, 10, 230.

Jantasuriyarat, C., Gowda, M., Haller, K., Hatfield, J., Lu, G. D., Stahlberg, E., … Wang, G. L. (2005). Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction. PLANT PHYSIOLOGY, 138(1), 105–115. https://doi.org/10.1104/pp.104.055624

Kulkarni, R. D., Thon, M. R., Pan, H. Q., & Dean, R. A. (2005). Novel G-protein-coupled receptor-like proteins in the plant pathogenic fungus Magnaporthe grisea. Genome Biology, 6(3).

Donofrio, N., Rajagopalon, R., Brown, D., Diener, S., Windham, D., Nolin, S., … Dean, R. A. (2005). PACLIMS: A component LIM system for high-throughput functional genomic analysis. BMC Bioinformatics, 6.

Dean, R. A., Talbot, N. J., Ebbole, D. J., Farman, M. L., Mitchell, T. K., Orbach, M. J., … Birren, B. W. (2005). The genome sequence of the rice blast fungus Magnaporthe grisea. NATURE, 434(7036), 980–986. https://doi.org/10.1038/nature03449

Altunay, M., Brown, D., Byrd, G., & Dean, R. (2005). Trust-Based Secure Workflow Path Construction. In B. Benatallah, F. Casati, & P. Traverso (Eds.), Service-Oriented Computing – ICSOC 2007 (pp. 382–395). https://doi.org/10.1007/11596141_29

Thon, M. R., Martin, S. L., Goff, S., Wing, R. A., & Dean, R. A. (2004). 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. https://doi.org/10.1016/j.fgb.2004.02.003

Diener, S. E., Dunn-Coleman, N., Foreman, P., Houfek, T. D., Teunissen, P. J. M., Solingen, P., … Dean, R. A. (2004). 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. https://doi.org/10.1016/S0378-1097(03)00916-9

Diener, S. E., Dunn-Coleman, N., Foreman, P., Houfek, T. D., Teunissen, P. J. M., Solingen, P. V., … Dean, R. (2004). 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. https://doi.org/10.1111/j.1574-6968.2004.tb09588.x

Asiegbu, F. O., Choi, W., Jeong, J. S., & Dean, R. (2004). 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. https://doi.org/10.1016/S0378-1097(03)0858-9

Asiegbu, F. O., Choi, W., Jeong, J. S., & Dean, R. A. (2004). 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. https://doi.org/10.1016/S0378-1097(03)00858-9

Ebbole, D. J., Jin, Y., Thon, M., Pan, H. Q., Bhattarai, E., Thomas, T., & Dean, R. (2004). 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. https://doi.org/10.1094/MPMI.2004.17.12.1337

Kulkarni, R. D., & Dean, R. (2004). 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. https://doi.org/10.1007/s00438-003-0935-y

Diener, S. E., Chellappan, M. K., Mitchell, T. K., Dunn-Coleman, N., Ward, M., & Dean, R. A. (2004). Insight into Trichoderma reesei's genome content, organization and evolution revealed through BAC library characterization. FUNGAL GENETICS AND BIOLOGY, 41(12), 1077–1087. https://doi.org/10.1016/j.fgb.2004.08.007

Gusmini, G., Wehner, T. C., Joobeur, T., Dean, R. A., & Levi, A. (2004). Protocol for DNA extraction from watermelon leaves for SSR marker studies. Report (Cucurbit Genetics Cooperative), (27), 25.

Gowda, M., Jantasuriyarat, C., Dean, R. A., & Wang, G. L. (2004). Robust-LongSAGE (RL-SAGE): A substantially improved LongSAGE method for gene discovery and transcriptome analysis. PLANT PHYSIOLOGY, 134(3), 890–897. https://doi.org/10.1104/pp.103.034496

Joobeur, T., King, J. J., Nolin, S. J., Thomas, C. E., & Dean, R. A. (2004). The fusarium wilt resistance locus Fom-2 of melon contains a single resistance gene with complex features. PLANT JOURNAL, 39(3), 283–297. https://doi.org/10.1111/j.1365-313X.2004.02134.x

Kothera, R. T., Keinath, A. P., Dean, R. A., & Farnham, M. W. (2003). AFLP analysis of a worldwide collection of Didymella bryoniae. MYCOLOGICAL RESEARCH, 107, 297–304. https://doi.org/10.1017/S0953756203007470

Kulkarni, R. D., Kelkar, H. S., & Dean, R. A. (2003). An eight-cysteine-containing CFEM domain unique to a group of fungal membrane proteins. TRENDS IN BIOCHEMICAL SCIENCES, 28(3), 118–121. https://doi.org/10.1016/S0968-0004(03)00025-2

In-depth view of structure, activity, and evolution of rice chromosome 10. (2003). Science, 300(5625), 1566–1569.

Asiegbu, F. O., Choi, W. B., Li, G. S., Nahalkova, J., & Dean, R. A. (2003). 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. https://doi.org/10.1016/S0378-1097(03)00697-9

Takano, Y., Choi, W. B., Mitchell, T. K., Okuno, T., & Dean, R. A. (2003). Large scale parallel analysis of gene expression during infection-related morphogenesis of Magnaporthe grisea. MOLECULAR PLANT PATHOLOGY, 4(5), 337–346. https://doi.org/10.1046/J.1364-3703.2003.00182.X

Little, D., Dean, R. A., Young, K. M., McKane, S. A., Martin, L. D., Jones, S. L., & Blikslager, A. T. (2003). 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. https://doi.org/10.1152/ajpgi.00121.2002

Mitchell, T. K., Thon, M. R., Jeong, J. S., Brown, D., Deng, J. X., & Dean, R. A. (2003). [Review of The rice blast pathosystem as a case study for the development of new tools and raw materials for genome analysis of fungal plant pathogens]. NEW PHYTOLOGIST, 159(1), 53–61. https://doi.org/10.1046/j.1469-8137.2003.00787.x

Foreman, P. K., Brown, D., Dankmeyer, L., Dean, R., Diener, S., Dunn-Coleman, N. S., … Ward, M. (2003). Transcriptional regulation of biomass-degrading enzymes in the filamentous fungus Trichoderma reesei. JOURNAL OF BIOLOGICAL CHEMISTRY, 278(34), 31988–31997. https://doi.org/10.1074/jbc.M304750200

Wang, Y. H., Choi, W. B., Thomas, C. E., & Dean, R. A. (2002). 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. https://doi.org/10.1139/G02-005

Somai, B. M., Keinath, A. P., & Dean, R. A. (2002). Development of PCR-ELISA for detection and differentiation of Didymella bryoniae from related Phoma species. PLANT DISEASE, 86(7), 710–716. https://doi.org/10.1094/PDIS.2002.86.7.710

Somai, B. M., Dean, R. A., Farnham, M. W., Zitter, T. A., & Keinath, A. P. (2002). 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. https://doi.org/10.1094/PHYTO.2002.92.9.997

Martin, S. L., Blackmon, B. P., Rajagopalan, R., Houfek, T. D., Sceeles, R. G., Denn, S. O., … Dean, R. A. (2002). 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. https://doi.org/10.1093/nar/30.1.121

Xue, C. Y., Park, G., Choi, W. B., Zheng, L., Dean, R. A., & Xu, JR. (2002). Two novel fungal virulence genes specifically expressed in appressoria of the rice blast fungus. PLANT CELL, 14(9), 2107–2119. https://doi.org/10.1105/tpc.003426

Levi, A., Thomas, C. E., Zhang, X. P., Joobeur, T., Dean, R. A., Wehner, T. C., & Carle, B. R. (2001). 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. https://doi.org/10.21273/jashs.126.6.730

Zhu, H., Bilgin, M., Bangham, R., Hall, D., Casamayor, A., Bertone, P., … Snyder, M. (2001). Global analysis of protein activities using proteome chips. SCIENCE, 293(5537), 2101–2105. https://doi.org/10.1126/science.1062191

Luo, M. Z., Wang, Y. H., Frisch, D., Joobeur, T., Wing, R. A., & Dean, R. A. (2001). 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. https://doi.org/10.1139/gen-44-2-154

Wang, Y. H., Thomas, C. E., & Dean, R. A. (2000). Genetic mapping of a fusarium wilt resistance gene (Fom-2) in melon (Cucumis melo L.). MOLECULAR BREEDING, 6(4), 379–389. https://doi.org/10.1023/A:1009671925793

Fang, E. G. C., & Dean, R. A. (2000). Site-directed mutagenesis of the magB gene affects growth and development in Magnaporthe grisea. MOLECULAR PLANT-MICROBE INTERACTIONS, 13(11), 1214–1227. https://doi.org/10.1094/MPMI.2000.13.11.1214