Several of our projects apply network analysis to evaluate systems such as microbiomes, seed systems, and epidemics.  Here are some examples:

Buddenhagen*C. E.,  J. F. Hernandez Nopsa*K. F. Andersen, J. Andrade-Piedra, G. A. Forbes, P. Kromann, S. Thomas-Sharma, P. Useche, and K. A. Garrett. 2017. Epidemic network analysis for mitigation of invasive pathogens in seed systems: Potato in Ecuador.  Phytopathology 107: https://doi.org/10.1094/PHYTO-03-17-0108-FI.

Garrett, K. A.K. F. Andersen, F. Asche, R. L. Bowden, G. A. Forbes, P. A. Kulakow, and B. Zhou. 2017. Resistance genes in global crop breeding networks. Phytopathology 107:  https://doi.org/10.1094/PHYTO-03-17-0082-FI  [interactive interface for exploring model behavior]

Poudel, R., A. Jumpponen, D. C. Schlatter, T. C. Paulitz, B. McSpadden Gardener, L. L. Kinkel, and K. A. Garrett.  2016.  Microbiome networks: A systems framework for identifying candidate microbial assemblages for disease management.  Phytopathology 106:1083-1096. [open access link] [one of the most downloaded papers in Phytopathology]

Sanatkar, M. R., W. N. White, B. Natarajan, C. Scoglio, and K. A. Garrett. 2016. Epidemic threshold of an SIS model in dynamic switching networks. IEEE Transactions on Systems, Man, and Cybernetics 46:345-55. [link]

Hernandez Nopsa, J. F., G. J. Daglish, D. W. Hagstrum, J. F. Leslie, T. W. Phillips, C. Scoglio, S. Thomas-Sharma, G. H. Walter, and K. A. Garrett. 2015. Ecological networks in stored grain: identifying key nodes for emerging pests and mycotoxins in postharvest networks.  BioScience 65:985-1002. [open access link] [UF press release] [UF/IFAS FAES High Impact Award winner]

Sanatkar, M. R., C. Scoglio, B. Natarajan, S. Isard, and K. A. Garrett. 2015. History, epidemic evolution, and model burn-in for a network of annual invasion: Soybean rust. Phytopathology 105:947-955. [open access link]

Cox, C. M., W. W. Bockus, R. D. Holt, L. Fang, and K. A. Garrett. 2013. The spatial connectedness of plant species: Potential links for apparent competition via plant diseases. Plant Pathology 62:1195-1438. [link]

Garrett, K. A. 2012. Information networks for plant disease: Commonalities in human management networks and within-host signaling networks. [Invited] European Journal of Plant Pathology 133:75-88. [link]

Sutrave, S., C. Scoglio, S. A. Isard, J. M. S. Hutchinson, and K. A. Garrett. 2012. Identifying highly connected counties compensates for resource limitations when evaluating national spread of an invasive pathogen. PLoS ONE 7:e37793. [open access link]

Margosian, M. L., K. A. Garrett, J. M. S. Hutchinson, and K. A. With. 2009. Connectivity of the American agricultural landscape: Assessing the national risk of crop pest and disease spread. BioScience 59:141-151. [open access link]

Garrett, K. A., S. Thomas-Sharma, G. A. Forbes, and J. Hernandez Nopsa. 2014. Climate change and plant pathogen invasions. In Invasive Species and Climate Change. L. Ziska and J. Dukes, eds. CABI Publishing.