University of Kentucky College of Agriculture

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Mark L. Farman

Mark L. Farman, Ph.D.
Director, UK Advanced Genetic Technologies Center

Department of Plant Pathology
University of Kentucky
225 Plant Science Building
Lexington, KY 40546-0312

telephone: (859) 218-0728
fax: (859) 323-1961

Farman Lab


Education Ph.D. in Molecular Biology, 1990, University of East Anglia, United Kingdom
B.S. in Biology, 1983, University of East Anglia, United Kingdom
Focus Research
The Farman lab uses genomic approaches to study mechanisms of pathogenesis in the fungal phytopathogen, Magnaporthe oryzae. Areas of special interest include
  • Fungal genome evolution and dynamics
  • The roles of telomeres in pathogenic variation
  • Methods for high throughput fungal protein localization during host infection.
Employment Highlights
  • Director of the University of Kentucky Advanced Genetic Technologies Center, 2012-present
  • Professor, University of Kentucky, 2009-present
  • Associate Professor, University of Kentucky, 2003-2009
  • Assistant Professor, University of Kentucky, 1997-2003
  • Postdoctoral Scholar, University of Wisconsin-Madison, 1990-1997
Awards, Recognition, Service
  • Basil O' Connor Starter Scholar, 1999
Recent Research Publications
  • Gong, X., Hurtado, O., Wang, B., Yi, M., Giraldo, M., Wu, C., Valent, B., Goodin, M., and Farman, M. 2014. pFPL vectors for high-throughput protein localization in fungi: detecting cytoplasmic accumulation of putative effector proteins. Molec Plant-Microbe Interact 28: 107-121.
  • Farman, M., Novikova, O.S., Starnes, J.H., and Thornbury, D.W. 2014. Subtelomere organization, evolution, and dynamics in the rice blast fungus Magnaporthe oryzae. Pages 71-99 in: Subtelomeres, E.J. Louis and M.M. Becker, eds. Springer-Verlag, Berlin, Heidelberg.
  • Nelson P, Estus S, Abner E, Parikh I, Malik M, Neltner J, Ighodaro E, Wang W-X, Wilfred B, Wang L-S, Kukull W, Nandakumar K, Farman, M, Poon W, Corrada M, Kawas C, Cribbs D, Bennett D, Schneider J, Larson E, Crane P, Valladares O, Schmidtt F, Kryscio R, Jicha G, Smith C, Scheff S, Sonnen J, Haines L, Pericak-Vance M, Mayeux R, Farrer L, Van Eldik L, Horbinski C, Green R, Gearing M, Poon L, Kramer P, Woltjer R, Montine T, Partch A, Rajic A, Richmire K, Mosell S, Alzheimer’s Disease Genetic Consortium, Schellenberg G, and Fardo D (2014) ABCC9 gene polymorphism is associated with hippocampal sclerosis of aging pathology. Acta Neuropathol. 127: 825-843.
  • Schardl, C.L., Young, C.A., Pan, J., Florea, S., Takach, J.E., Panaccione, D.G., Farman, M.L., Webb, J.S., Jaromczyk, J., Charlton, N.D., Nagabhyru, P., Chen, L., Shi, C., and Leuchtmann, A. 2013a. Currencies of mutualisms: sources of alkaloid genes in vertically transmitted epichloae. Toxins 5:1064-1088.
  • Ramalho, T.O., Figueira, A.R., Sotero, A.J., Wang, R., Geraldino Duarte, P.S., Farman, M., and Goodin, M.M. 2014. Characterization of Coffee ringspot virus-Lavras: A model for an emerging threat to coffee production and quality. Virology 464-465:385-396.
  • Bec S, Ward, T., Farman, M., O'Donnell, K., Hershman, D., Van Sanford, D., and Vaillancourt, L. 2014. Characterization of Fusarium strains recovered from wheat with symptoms of head blight in Kentucky. Plant Disease.
  • Schardl CL, Young CA, Hesse U, Amyotte SG, Andreeva K, Calie PJ, Fleetwood DJ, Haws DC, Moore N, Oeser B, Panaccione DG, Schweri KK, Voisey CR, Farman ML et al (2013) Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the Clavicipitaceae reveals dynamics of alkaloid loci. PLoS Genetics 9: e1003323. doi. 10.1371/journal.pgen.1003323.
  • O’Connell R, Thon M, Hacquard S, Amyotte S, Kleemann J, Torres M, Damm U, Buiate E, Epstein L, Alkan N, Altmuller J, Alvarado-Balderrama L, Bauser C, Becker C, Birren B, Chen Z, Choi J, Crouch JA, Duvick J, Farman M et al (2012) Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses. Nature Genetics 44:1060-1065. Faculty of 1000 recommended reading.
  • Starnes J, Thornbury D, Novikova O, Rehmeyer C and Farman M (2012). Telomere-targeted retrotransposons in the rice blast fungus Magnaporthe oryzae: agents of genome instability. Genetics 191:389-406. Faculty of 1000 recommended reading.
  • Stajich J, Wilke S, Ahren D, Au C-H, Birren B, Bordovsky M, Burns C, Canback B, Casselton L, Cheng C, Deng J, Dietrich F, Fargo D, Farman M et al. (2010) Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinopsis cinereus). Proceedings of the National Academy of Sciences, USA 107:11889-11894.
  • de Sa P, Li H, Havens W, Farman M. Ghabrial S (2010) Overexpression of the victoriocin genes in Helminthosporium (Cochliobolus) victoriae enhances the antifungal activity of culture filtrates. Phytopathology 100:890-896.
  • Schwartz S and Farman M (2010) Systematic overrepresentation of DNA ends and underrepresentation of DNA termini among sequencing templates prepared from hydrodynamically sheared DNA molecules. BMC Genomics 11: 87.
  • Coleman J, Rounsley S, Rodriguez-Carres M, Kuo A, Wasmann C, Grimwood J, Schmutz J, Taga M, White G, Zhou S, Schwartz D, Freitag M, Ma L-J, Danchin E, Henrissat B, Coutinho P, Nelson D, Straney D, Napoli C, Barker B, Gribskov M, Rep M, Kroken S, Molnár I, Rensing C, Kennell J, Zamora J, Farman M, Selker E, Salamov A, Shapiro H, Pangilinan J, Lindquist E, Lamers C, Grigoriev I, Geiser D, Covert S, Temporini E, Vanetten H (2009) The genome of Nectria haematococca: contributions of supernumary chromosomes to gene expansion. PLoS Genet 5: e1000618.
  • Rehmeyer C, Li W, Kusaba M, Farman, M (2009) The telomere-linked helicase (TLH) gene family in Magnaporthe oryzae: Revised gene structure reveals a novel TLH-specific protein motif. Current Genetics 55: 253-262.
  • Wu C, Kim, Y-S, Smith K, Li W, Hood H, Staben C, Selker E, Sachs M, Farman M (2009) Characterization of chromosome ends in the filamentous fungus Neurospora crassa. Genetics 181: 1129-1145.


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