Ralph Dean

William Neal Reynolds Distinguished Professor
ralph_dean@ncsu.edu

Research

For more information about my program, please visit:
http://www.cifr.ncsu.edu/faculty/deanbio.html

Selected Publications (total 186, h-index 57, i10-index 128)

Parker J, Oh Y, Moazami Y, Pierce JG, Loziuk PL, Dean RA, Muddiman DC. Examining ubiquitinated peptide enrichment efficiency through an epitope labeled protein. Anal Biochem. 2016 Nov 1;512:114-9. doi: 10.1016/j.ab.2016.08.017. Epub 2016 Aug 22. PubMed PMID: 27562526.

Sharpee W, Oh Y, Yi M, Franck W, Eyre A, Okagaki LH, Valent B, Dean RA. Identification and characterization of suppressors of plant cell death (SPD) effectors from Magnaporthe oryzae. Mol Plant Pathol. 2016 Jun 15. doi: 10.1111/mpp.12449. [Epub ahead of print] PubMed PMID: 27301772.

Okagaki LH, Sailsbery JK, Eyre AW, Dean RA. Comparative genome analysis and genome evolution of members of the Magnaporthaceae family of fungi. BMC Genomics. 2016 Feb 25;17:135. doi: 10.1186/s12864-016-2491-y. PubMed PMID: 26911875; PubMed Central PMCID: PMC4766678.

Okagaki LH, Dean RA. The influence of funding sources on the scientific method. Mol Plant Pathol. 2016 Jun;17(5):651-3. doi: 10.1111/mpp.12380. PubMed PMID: 26840926.

Okagaki LH, Nunes CC, Sailsbery J, Clay B, Brown D, John T, Oh Y, Young N, Fitzgerald M, Haas BJ, Zeng Q, Young S, Adiconis X, Fan L, Levin JZ, Mitchell TK, Okubara PA, Farman ML, Kohn LM, Birren B, Ma LJ, Dean RA. Genome Sequences of Three Phytopathogenic Species of the Magnaporthaceae Family of Fungi. G3 (Bethesda). 2015 Sep 28;5(12):2539-45. doi: 10.1534/g3.115.020057. PubMed PMID: 26416668; PubMed Central PMCID: PMC4683626.

Franck, W, E. Gokce, S. Randall, Y. Oh, A. Eyre, D. Muddiman, RA. Dean. Phosphoproteome analysis links protein phosphorylation to cellular remodeling and metabolic adaptation during appressorium development. Journal of Proteome Research 2015 Apr 30. [Epub ahead of print]

Jeon, J, J Choi, GW Lee, SY Park, A Huh, RA Dean, and YH Lee. Genome-wide profiling of DNA methylation provides insights into epigenetic regulation of fungal development in a plant pathogenic fungus, Magnaporthe oryzae. Scientific Reports  2015 Feb 24;5:8567. doi: 10.1038/srep08567.

Nierman WC, J. Yu, ND. Fedorova-Abrams, L. Losada, TE. Cleveland, D. Bhatnagar, JW. Bennett, RA. Dean, GA. Payne. Genome Sequence of Aspergillus flavus NRRL 3357, a Strain That Causes Aflatoxin Contamination of Food and Feed. Genome Announcements 2015 Apr 16;3(2). pii: e00168-15. doi: 10.1128/genomeA.00168-15

Cubeta, MA, E Thomas, RA Dean, S Jabaji, SM Neate, S Tavantzis, et al, Draft genome sequence of the plant-pathogenic soil fungus Rhizoctonia solani anastomonas group 3 strain Rhs1AP. Genome Announcements 2014, 2 (5), e01072-14

Losada, L, SB Pakala, ND Fedorova, V Joardar, SA Shabalina, J Hostetler, Dean RA et al. Mobile elements and mitochondrila genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG3 FEMS microbiology letters 2014 352 (2), 165-173

Jeon J, Choi J, Lee GW, Dean RA, Lee YH., 2013. Experimental evolution reveals genome-wide spectrum and dynamics of mutations in the rice blast fungus, Magnaporthe oryzae. PLoS One. 2013 May 31;8(5):e65416. doi: 10.1371/journal.pone.0065416. Print 2013.

Franck WL, Gokce E, Oh Y, Muddiman DC, Dean RA., 2013. Temporal analysis of the Magnaporthe oryzae proteome during conidial germination and cyclic AMP (cAMP)-mediated appressorium formation. Mol Cell Proteomics. 2013 Aug;12(8):2249-65. doi: 10.1074/mcp.M112.025874. Epub 2013 May 12.

Sailsbery, J.K.; Dean, R.A. 2012. Accurate discrimination of bHLH domains in plants, animals, and fungi using biologically meaningful sites, BMC Evolutionary Biology,12,1,154.

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.

Grokce, 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.

Xue, M.; Yang, J.; Li, Z.; Hu, S.; Yao, N.; Dean, R.A.; Zhao, W.; Shen, M.; Zhang, H.; Li, C. 2012. Comparative Analysis of the Genomes of Two Field Isolates of the Rice Blast Fungus Magnaporthe oryzae, PLoS Genetics,8,8,e1002869.

Dean, R.; Van Kan, J.A.L.; Pretorius, Z.A.; Hammond-Kosack, K.E.; Di Pietro, A.; Spanu, P.D.; Rudd, J.J.; Dickman, M.; Kahmann, R.; Ellis, J. 2012. The Top 10 fungal pathogens in molecular plant pathology, Molecular Plant Pathology,13,4,414-430.

Sailsbery JK, Atchley W, Dean RA. 2011. Phylogenetic Analysis and Classification of the Fungal bHLH Domain. Mol Biol Evol. 2011 Nov 22. [Epub ahead of print]

Nunes CC, Dean RA. 2011, Host-induced gene silencing: a tool for understanding fungal host interaction and for developing novel disease control strategies. Mol Plant Pathol. 2011 Nov 24. doi: 10.1111/j.1364-3703.2011.00766.x. [Epub ahead of print]

Nunes CC, Sailsbery JK, Dean RA. 2011, Characterization and application of small RNAs and RNA silencing mechanisms in fungi. Fun. Biol. Rev. 25:172-180.

Gokce E, Shuford CM, Franck WL, Dean RA, Muddiman DC. 2011. Evaluation of normalization methods on GeLC-MS/MS label-free spectral counting data to correct for variation during proteomic workflows. J Am Soc Mass Spectrom. 2011 Dec;22(12):2199-208. Epub 2011 Sep 24.

Collier TS, Randall SM, Sarkar P, Rao BM, Dean RA, Muddiman DC. 2011. Comparison of stable-isotope labeling with amino acids in cell culture and spectral counting for relative quantification of protein expression. Rapid Commun Mass Spectrom. 2011 Sep 15;25(17):2524-32. doi: 10.1002/rcm.5151.

Nunes, C. C., Gowda, M., Sailsbery, J., Xue, M., Chen, F., Brown, D. E., Oh, Y. Y., Mitchell, T. K., Dean, R. A. 2011. Diverse and tissue-enriched small RNAs in the plant pathogenic fungus, Magnaporthe oryzae. BMC Genomics, 12:288 doi:10.1186/1471-2164-12-288

Li G, Zhou X, Kong L, Wang Y, Zhang H, Zhu H, Mitchell TK, Dean RA, Xu JR. 2011. MoSfl1 is important for virulence and heat tolerance in Magnaporthe oryzae. PLoS One. 2011;6(5):e19951. Epub 2011 May 19.

Andrews, G.L., Dean, R.A., Hawkridge, A.M., and Muddiman, D.C. 2011. Improving Proteome Coverage on a LTQ-Orbitrap Using Design of Experiments. J Am Soc Mass Spectrom 22(4):773-83. Epub 2011 Feb 15.

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. 19;12(1):49. [Epub ahead of print]

Gokce, E., Andrews, G.L., Dean, R.A., and Muddiman, D.C. 2011. Increasing Proteome Coverage with Offline RP HPLC Coupled to Online RP NanoLC-MS. Journal of Chromatography B, 879(9-10):610-4. (Epub ahead of print)

Torto-Alalibo, T., Collmer, C.W., Gwinn-Giglio, M., Lindeberg, M., Meng, S., Chibucos, M.C., Tseng, T.T., Lomax, J., Biehl, B., Ireland, A., Bird, D., Dean, R.A., Glasner, J.D., Perna, N., Setubal, J.C. Collmer, A., Tyler, B.M.. 2010. Unifying Themes in Microbial Associations With Animal and Plant Hosts Described Using The Gene Ontology. Microbiology and Molecular Biology Reviews 74(4):479-503.

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.

Gowda, M., Nunes, C.C., Sailsbery, J., Xue, M., Chen, F., Nelson, C.A., Brown, D.E., Oh, Y., Meng, S., Mitchell, T., Hagedorn, C.H., Dean, R.A. 2010. Genome-wide characterization of methylguanosine-capped and polyadenylated small RNAs in the rice blast fungus Magnaporthe oryzae. Nucleic Acids Research 38(21):7558-69.

Kim, S., Hu, J., Oh, Y.Y., Park, J., Choi, J., Lee, Y.-H., Dean, R.A., Mitchell, T.K. 2010. Modeling the MoCRZ1 mediation regulatory circuitry for calcium/calcineurin signaling in the rice blast fungus, Magnaporthe oryzae. PLOS-Pathogens 6(5):e100090