Kansas State University

• 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.

• Veerendra Sharma, Fellow (Post Doc)
• Wenguang Zhang, Fellow (Post-Doc)
• Wei Zheng, Fellow (Post-Doc)
• Jun Huang, Ph.D. Graduate Research Assistant
• Jamika Jefferson, Ph.D. Graduate Research Assistant (Fall 2018)

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