Research Publications

2019

Wamucho A, Unrine JM, Kieran TJ, Glenn TC, Schultz CL, Farman M, Svendsen C, Spurgeon DJ, Tsyusko OV (2019) Genomic mutations are multigenerational exposure of Caenorhabditis elegans to pristine and sulfidized silver nanoparticles. Environmental Pollution 254: 113078. https://doi.org/10.1016/j.envpol.2019.113078

Rahnama M, Novikova O, Starnes J, Chen L, Zhang S, Farman M. (2019) Transposon-mediated telomere destabilization: a driver of genome evolution in the blast fungus. bioRxiv 845669; doi: https://doi.org/10.1101/845669

Peng Z, Oliveira-Garcia E, Lin G, Hu Y, Dalby M, Migeon P, Tang H, Farman M, Cook D, White FF, Valent B, Liu S (2019) Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus. PLoS Genetics 15(9). e1008272. 

Yasuhara-Bell J, Pieck ML, Ruck A, Farman ML, Peterson GL, Stack JP, Valent B, Pedley KF. A Response to Gupta et al. (2019) Regarding the MoT3 Wheat Blast Diagnostic Assay. Phytopathology 109:509-511. doi: 10.1094/PHYTO-10-18-0397-LE. Epub 2019 Mar 20. PubMed PMID: 30565503.

Valent B, Farman M, Tosa Y, Begerow D, Fournier E, Gladieux P, Islam MT, Kamoun S, Kemler M, Kohn LM, Lebrun MH, Stajich JE, Talbot NJ, Terauchi R, Tharreau D, Zhang N. (2019) Pyricularia graminis-tritici is not the correct species name for the wheat blast fungus: response to Ceresini et al. (MPP 20:2). Mol Plant Pathol. 20:173-179. doi: 10.1111/mpp.12778. PubMed PMID: 30697917; PubMed Central PMCID: PMC6637902.

2018

Yasuhara-Bell J, Pedley KF, Farman M, Valent B, Stack JP. (2018) Specific Detection of the Wheat Blast Pathogen (Magnaporthe oryzae Triticum) by Loop-Mediated Isothermal Amplification. Plant Dis. 102:2550-2559. doi: 10.1094/PDIS-03-18-0512-RE. Epub 2018 Oct 15. PubMed PMID: 30320534. 

Gladieux P, Condon B, Ravel S, Soanes D, Maciel JLN, Nhani A Jr, Chen L, Terauchi R, Lebrun MH, Tharreau D, Mitchell T, Pedley KF, Valent B, Talbot NJ, Farman M, Fournier E. (2018) Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae. mBio. 9(1). doi: 10.1128/mBio.01219-17. PubMed PMID: 29487238; PubMed Central PMCID: PMC5829825.

2017

Inoue Y, Vy TTP, Yashida K, Asano H, Mitsuoka C, Asuke S, Anh VL, Cumagun CJR, Chuma I, Terauchi R, Kato K, Mitchell T, Valent B, Farman M, Tosa Y. (2017) Evolution of the wheat blast fungus through functional losses in a host specificity determinant, Science 357:80-83.

Jang C; Wang R; Wells J; Leon F; Farman M; Hammond J; Goodin M (accepted for publication) Genome sequence variation in the constricta strain dramatically alters the protein interaction and localization map of Potato Yellow Dwarf virus. J. Gen. Virol.

Elshahawi SI, Cao H, Shaaban KA, Ponomareva LV, Subramanian T, Farman ML, Spielmann HP, Phillips GN Jr, Thorson JS, Singh S. (2017) Structure and specificity of a permissive bacterial C-prenyltransferase. Nature Chem. Biol. oi: 10.1038/nchembio.2285.

Buiate E, Xavier X, Moore N, Farman M, Schardl, C, Vaillancourt L. (2017) A comparative genomic analysis of putative pathogenicity genes in the host-specific sibling species Colletotrichum graminicola and Colletotrichum sublineola. BMC Genomics 18: 67.

Farman M, Peterson G, Chen L, Valent B, Bachi P, Murdock L, Hershman D, Pedley K, Fernandes M, Bavaresco J. (2017) The Lolium pathotype of Magnaporthe oryzae recovered from a single blasted wheat plant in the United States. Plant Dis. http://dx.doi.org/10.1094/PDIS-05-16-0700-RE

Pieck M, Farman M, Peterson G, Stack J, Valent B, Pedley K. (2017) Genomics-based marker discovery and diagnostic assay development for wheat blast. Plant Dis. 101: 103-109.

2016

Florea S, Phillips T D, Panaccione D G, Farman M L, Schardl C L. (2016) Chromosome-end knockoff strategy to reshape alkaloid profiles of a fungal endophyte. G3 6:2601-2610.


2015

Okagaki L, Nunes C, Sailsbery J, Clay B, Brown D, John T, Oh Y, Young N, Fitzgerald M, Haas B, Zeng Q, Young S, Adiconis X, Fan L, Levin J, Mitchell T, Okubara P, Farman M, Kohn L, Birren B, Ma L-J, Dean R (2015) Genome sequences of three phytopathogenic species of the Magnaporthaceae family of fungi. G3 5:2539-2545.

Minton R L, Martinez Cruz M A, Farman M, Perez K E (2016) Two complete mitochondrial genomes from Praticolella mexicana Perez, 2011 (Polygyridae) and gene order evolution in Helicoidea (Mollusca, Gastropoda). ZooKeys 626: 137-154

Malaker P, Barma N, Tewari T, Collis W, Duveiller E, Singh P, Joshi A, Singh R, Braun H-J, Peterson G, Pedley K, Farman M, Valent B (2016) First report of wheat blast caused by Magnaporthe oryzae pathotype Triticum in Bangladesh. Plant Dis. 100: 2330.

Okagaki L, Nunes C· Sailsbery J, Clay B, Brown D, John T, Oh Y, Young N, Fitzgerald M, Haas B, Zeng Q, Young S, Adiconis X, Fan L, Levin J, Mitchell T, Okubara P, Farman M, Kohn L, Birren B, Ma L-J, Dean R (2015) Genome sequences of three phytopathogenic species of the Magnaporthaceae family of fungi. G3:Genes|Genomes|Genetics doi:10.1534/g3.115020057


2014

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.

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. http://apsjournals.apsnet.org/doi/abs/10.1094/PDIS-06-14-0610-RE


2013

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.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.


2012

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 1000recommended reading.


2010

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 inHelminthosporium (Cochliobolusvictoriae enhances the antifungal activity of culture filtrates. Phytopathology100:890-896.

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.


2009

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.