Mark L. Farman Associate Professor
	Publications: 2009 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, in press. 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. 2008 Vincelli P, Farman, M. (2008) Gray Leaf Spot of annual ryegrass: susceptibility of selected cultivars of forage grasses and relatedness of the pathogen to strains from other grasses. Forage and Grazinglands. doi:10.1094/FG-2008-0226-01-RS. 2007 Vincelli, P and Farman, M (2007) Update on fungicide resistance in gray leaf spot. Golf Course Management, 75: 124-127. Farman M. (2007) Telomeres in the rice blast fungus Magnaporthe oryzae: the world of the end as we know it. FEMS Lett. 273: 125-132. Betts M, Tucker S, Galadima N, Meng Y, Patel G, Li L, Donofrio N, Floyd A, Nolin S, Brown D, Mandel A, Mitchell T, Xu J-R, Dean R, Farman M, Orbach M (2007) Development of a high throughput transformation system for insertional mutagenesis in Magnaporthe oryzae. Fungal Genet. Biol. 44: 1035-1049. Meng Y, Patel G, Heist M, Betts M, Tucker, Galadima N, Donofrio N, Brown D, Mitchell T, Li L, Xu J R, Orbach M, Thon M, Dean R, Farman M (2007) A systematic analysis of T-DNA insertion events in Magnaporthe oryzae. Fungal Genet. Biol. 44: 1050-1064. Chakrabarty R., Banerjee R., Chung, S-M., Farman M. L., Citovsky V., Hogenhout, S. A. Tzfira T., Goodin M. M. (2007) pSITE vectors for stable integration or transient expression of autofluorescent protein fusions in plants: probing Nicotiana benthamiana-virus interactions. Molec. Plant Microbe Interact. 20: 740-750. 2006 Soderlund, C, Haller K, Panpanwar V, Ebbole D, Farman M, Orbach M, Wang G L, Wing R, Xu J R, Brown D, Mitchell T and Dean R (2006) MGOS: A resource for studying Magnaporthe grisea and Oryza sativa interactions. Molec. Plant Microbe Interact. 10: 1055-1061. Rehmeyer C, Li W, Kusaba M, Kim Y-S, Brown D, Staben C, Dean R and Farman M (2006) Organization of chromosome ends in the plant pathogenic fungus Magnaporthe oryzae. Nucleic Acids Res., 34: 4685-4701. Kämper J, Kahmann R, Bölker M, Ma L-J, Brefort T, Saville B, Banuett F, Kronstad J, Gold S, Müller O, Perlin M, Wösten H, deVries R, Ruiz-Herrera J, Reynaga-Peña C, Snetselaar K, McCann M, Pérez-Martín J, Feldbrügge M, Basse1 C, Steinberg G, Ibeas J, Holloman W, Guzman P, Farman M, Stajich J, Sentandreu R, González-Prietro J, Kennell J, Molina L, Schirawski J, Mendoza-Mendoza A, Greilinger D, Münch K, Rössel N, Scherer M, Vranes M, Ladendorf O, Vincon V, Fuchs U, Sandrock B, Meng S, Ho E, Cahill M, Boyce K, Klose J, Klosterman S, Deelstra H, Ortiz-Castellanos L, Li W, Sanchez-Alonso P, Schreier P, Häuser-Hahn I, Vaupel M, Koopmann E, Friedrich G, Voss H, Schlüter T, Platt D, Swimmer C, Gnirke A, Chen F, Vysotskaia V, Mannhaupt G, Güldener U, Münsterkötter M, Haase D, Oesterheld M, Mewes H-W, Mauceli E, DeCaprio D, Wade C, Butler J, Young S, Jaffe D, Calvo S, Nusbaum C, Galagan J, and Birren B (2006) Insights from the genome of the biotrophic fungal pathogen Ustilago maydis. Nature, 444: 97-101. 2005 Donofrio N, Rajagopalan R, Brown D, Diener S, Windham D, Nolin S, Floyd A, Mitchell T, Galadima N, Tucker S, Orbach M, Patel G, Farman M, Pampanwar V, Soderlund C, Lee Y H and R Dean (2005) PACLIMS: A component LIM system for high throughput functional genomic analysis. BMC Bioinformatics 6: 94. Nierman W, Pain A, Anderson M, Wortman J, Kim H, Arroya J, Berriman M, Abe K, Archer D, Bermejo C, Bennett J, Bowyer P, Chen D, Collins M, Coulsen R, Davies R, Dyer P, Farman M, Fedorova N, Fedorova N, Feldblyum T, Fischer R, Fosker N, Fraser A, Garcia J, Garcia M, Goble A, Goldman G, Gomi, K, Griffith-Jones S, Gwilliam R, Haas H, Harris D, Horiuchi H, Huang J, Humphrey S, Jimenez J. J, Keller N, Khouri H, Kitamoto K, Kobayashi T, Kulkarni R, Kumagai T, Lafton A, Latge J-P, Lord A, Lu C, Majoros W, May G, Miller B, Mohamoud Y, Molina M, Monod M, Mouyna I, Mulligan S, Murphy L, O'Neil S, Paulsen I, Penalva M, Pertea M, Price C, Pritchard B, Quail M, Rabbinowitsch E, Rawlins N, Rajandream M-A, Reichard U, Renauld H, Robson G, de Cordoba S, Rodrigues-Pena J, Ronning C, Rutter S, Salzberg S, Sanchez M, Sanchez-Ferrero J, Saunders D, Seeger K, Squares R, Squares S, Takeuchi M, Tekaia F, Turner G, Vasquez de Aldana C, Weidman J, White O, Woodward J, Yu J-H, Fraser C, Galagan J, Asai K, Machida M, Hall N, Barrell B, Denning D (2005) Genomic sequence of the pathogenic and allergenic Aspergillus fumigatus. Nature, 438:1151-1156. Galagan, J, Calvo, S, Cuomo C, Ma L-J, Wortman J, Batzoglou S, Lee S, Bas¸türkmen M, Spevak C, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus G, Draht O, Busch S, D’Enfert C, Bouchier C, Goldman G, Bell-Pedersen D, Griffiths-Jones S, Doonan J, Yu J, Vienken K, Pain A, Freitag M, Selker E, Archer D, Peñalva M, Oakley B, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman W, Denning D, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs M, Osmani S, and Birren B (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature, 438:1105-1115. Dean R, Talbot N, Ebbole D, Farman M, Mitchell T, Orbach M, Thon M, Kulkarni R, Xu J-R, Pan H, Read N, Lee Y-H, Carbone I, Brown D, Oh Y, Donofrio N, Jeong J, Soanes D, Djonovic S, Kolomiets E, Rehmeyer C, Li W, Harding M, Kim S, Lebrun M-H, Bohnert H, Coughlan S, Butler J, Calvo S, Ma L-J, Nicol, R, Purcell S, Nusbaum C, Galagan J, Birren B (2005). Analysis of the genome sequence of the plant pathogenic fungus Magnaporthe grisea, the causal agent of rice blast disease. Nature 434: 980-986. Li, W., Rehmeyer, C., Staben, C., Farman, M. L. (2004) TERMINUS – Telomeric End Read Mining IN Unassembled Sequences. Bioinformatics (Advance Access), bti181 Li, W., Rehmeyer, C., Staben, C., Farman, M. L. (2005) TruMatch – a BLAST post-processor for identifying and reporting bona fide sequence matches. Bioinformatics (Advance Access), bti257. Kim, Y.-S. and M. L. Farman (2005) Telomere hypervariability in Magnaporthe oryzae. Molecular Plant Pathology (accepted for publication). 2003 Kim, Y.-S., Dixon, E. W., Vincelli, P. and M. L. Farman (2003) Field resistance to strobilurin (QoI) fungicides in Pyricularia grisea caused by mutations in the mitochondrial cytochrome b gene. Phytopathology 93: 891-900. 2002 Sukno, S., Taylor, A. and M. L. Farman (2002) Development of contamination-free restriction fragment length polymorphism probes for the obligate biotroph Peronospora tabacina, an oomycete causing blue mold disease of tobacco. Phytopathology 92: 1227-1235. Sukno, S., Taylor, A. and M. L. Farman (2002) Genetic uniformity among isolates of Peronospora tabacina, the blue mold pathogen. Phytopathology 92: 1236-1244. Chauhan, R., Farman, M. L., Ronald, P., Zhang, H-B., and S. A. Leong. Genetic and physical mapping of a rice blast resistance locus, Pi-CO39(t), corresponding to AVR1-CO39 of Magnaporthe grisea. Mol. Gen. Genomics 267: 603-612. http://link.springer.de/link/service/journals/00438/contents/02/00691/) Farman, M. L. (2002) Pyricularia grisea isolates causing gray leaf spot of perennial ryegrass (Lolium perenne) in the United States: Relationship to P. grisea isolates from other host plants. Phytopathology 92: 245-254. Farman, M. L. (2002) Meiotic deletion at the Magnaporthe grisea BUF1 locus is controlled by interaction with the homologous chromosome. Genetics 160: 137-148. Farman, M. L., Eto, Y., Nakao, T., Tosa, Y., Nakayashiki, H., Mayama, S., and S. A. Leong (2002) Analysis of the structure of the AVR1-CO39 avirulence locus in virulent rice-infecting isolates of Magnaporthe grisea. Molec. Plant-Microbe Interact. 15: 6-16. 2000 Thornbury D. W. and M. L. Farman (2000) Re-use of nylon membranes for radioactive hybridizations. Biotechniques 29: 1250-1254. 1998 Farman M. L., and S. A. Leong (1998) Chromosome walking to the AVR1-CO39 gene of Magnaporthe grisea. Discrepancy between the genetic and physical maps. Genetics 150: 1049-1058. 1997 Nitta N., M. L. Farman, S. A. Leong (1997) Genome organization of Magnaporthe grisea: Integration of genetic maps, clustering of transposable elements and occurrence of genome duplications and rearrangements. Theor. Appl. Genet. 95: 20-32. 1996 Farman M. L., Y. Tosa, N. Nitta and S. A. Leong (1996) MAGGY, a retrotransposon in the genome of the rice blast fungus, Magnaporthe grisea. Mol. Gen. Genet. 251: 665-674. Farman M. L., S. Taura and S. A. Leong (1996) The Magnaporthe grisea DNA fingerprinting probe, MGR586, contains the 3' end of an inverted repeat transposon. Mol. Gen. Genet. 251: 675-680. An Z., Farman M. L., Budde A. D., Taura S., and S. A. Leong (1996) New cosmid vectors for library construction, chromosome walking and restriction mapping in filamentous fungi. Gene 176: 93-96. 1995 Farman M. L., and S. A. Leong (1995) Genetic and physical mapping of telomeres in the rice blast fungus, Magnaporthe grisea. Genetics 140: 479-492. Skinner D. Z., A. D. Budde, M. L. Farman, J. R. Smith, H. Leung and S. A. Leong (1993). Genome organization of the rice blast fungus: Genetic map, electrophoretic karyotype and occurrence of repeated DNAs. Theor. Appl. Genet. 87:545-557.