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Department of Plant Pathology

Dr. David Cook

Dr. David Cook

Associate Professor

Director - Plant Pathology Graduate Program

Email Dr. Cook

Kansas State University
4004 Throckmorton PSC
1712 Claflin Road
Manhattan, KS 66506

Ph: +1-785-532-1362
Fx: +1-785-532-5692


  • Ph.D. University of Wisconsin-Madison, 2013
  • M.S. Virginia Tech, 2008
  • B.S. Virginia Tech, 2005


Selected Publications (*corresponding author)

  • Zhao P, Garcia-Oliveira E, Guifang L, Ying H, Dalby M, Migeon P, Tang Haibao, Farman M, Cook DE, White F, Valent B, Liu S. 2018. Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus. BioRxiv. DOI: https://doi.org/10.1101/359455
  • Thomma BPHJ and Cook DE. 2018. Targeting microbial pathogens. Science 360: 1070-1071.
  • Cook DE*, Valle-Inclan JE*, Pajoro A, Rovenich H, Thomma BPHJ, Faino L. 2017. Long-Read Annotation (LoReAn): automated eukaryotic genome annotation based on long-read cDNA sequencing. BioRxiv. DOI: https://doi.org/10.1101/230359
  • Seidl MF*, Cook DE*, Thomma BPHJ. 2016. Chromatin biology impacts adaptive evolution of filamentous plant pathogens. PLoS Pathogens, 12 (11) e1005920
  • Cook DE, Mesarich CH, Thomma BPHJ. 2015 Understanding plant immunity as a surveillance system to detect invasion. Annual Review of Phytopathology 53:25.1-25.23.
  • Cook DE*, TG Lee*, Guo X, Melito S, Wang K, Bayless A, Wang J, Hughes TJ, Willis DK, Clemente T, Diers BW, Jiang J, Hudson ME, Bent AF. 2012. Copy number variation of multiple genes at Rhg1 mediates nematode resistant in soybean. Science 338:1206-1209.


The Cook lab has two broad areas of research.

Genome Dynamics during plant-fungal interactions

Fungal Plant pathogens have evolved many strategies to facilitate the successful infection of host plants. How these fungi grow when interacting with a host is quite different than how they grow in the soil or under lab conditions. We are interested in determining how they achieve these differences in growth to precisely control the infection process. We use a variety of experimental and computation approaches to understand genome regulation and chromatin dynamics using the Magnaporthe oryzae - Rice pathosystem. We are additionally interested in how genome structure influences function, and how spatial organization of the genome influences adaptation.

Novel biotech approaches to improve agronomic defense, response and performance

The Cook lab is developing new tools and approaches to deliver biotech solutions for difficult food production and food security challenges of the 21st century. The technology we are developing can address a range of crop and plant science challenges and can impact Kansas, national and international growers.

Staff & Students

  • David Rowe, Ph.D
  • Wei Zheng, Fellow (Post-Doc)
  • Jun Huang, Ph.D. 
  • Divya Mishra. Fellow Post Doc
  • Pratima Subedi, Ph.D


  • PLPTH870 - Thesis Proposal Seminar
  • PLPTH910 - Molecular Plant-Microbe Interactions