Several of our projects apply network analysis to evaluate systems such as epidemics, microbiomes, and seed systems. Following are some examples.
JOURNAL ARTICLES
Bold = Member of Garrett Lab / Asterisk = *Equivalent contributions
Alcalá Briseño, R. I., O. Batuman, J. Brawner, W. J. Cuellar, E. Delaquis, B. A. Etherton, R. D. French-Monar, J. F. Kreuze, I. Navarrete, K. Ogero, A. I. Plex Sulá, S. Yilmaz, and K. A. Garrett. 2023. Translating virome analyses to support biosecurity, on-farm management, and crop breeding. Frontiers in Plant Science 14:1056603. [open access link]
Etherton, B. A., R. A. Choudhury, R. I. Alcalá-Briseño, Y. Xing, A. I. Plex Sulá, D. Carrillo, J. Wasielewski, L. Stelinski, K. A. Grogan, F. Ballen, T. Blare, J. Crane, and K. A. Garrett. 2023. Are avocados toast? A framework to analyze decision-making for emerging epidemics, applied to laurel wilt. Agricultural Systems 206:103615. [open access link]
Martins, S. J., J. Pasche, H. A. O. Silva, G. Selten, N. Savastano, L. M. Abreu, H. Bais, K. A. Garrett, N. Kraisitudomsook, C. M. J. Pieterse, and T. Cernava. 2023. The use of synthetic microbial communities (SynComs) for plant health. Phytopathology 113:1369-1379. [open access link]
Poudel, R., A. Jumpponen, M. M. Kennelly, C. Rivard, L. Gomez-Montano, and K. A. Garrett. 2023. Integration of phenotypes in microbiome networks for designing synthetic communities: a study of mycobiomes in the grafted tomato system. Applied and Environmental Microbiology 89:e01843-22. [open access link]
Rich, S. N., R. L. Cook, C. N. Mavian, K. Garrett, E. C. Spencer, M. Salemi, and M. Prosperi. 2023. Network typologies predict future molecular linkages in the network of HIV transmission in Florida. AIDS 37:1739-1746. [open access link]
Buddenhagen*, C. E., Y. Xing*, J. Andrade Piedra, G. A. Forbes, P. Kromann, I. Navarrete, S. Thomas-Sharma, R. A. Choudhury, K. F. Andersen, E. Schulte-Geldermann, B. A. Etherton, A. I. Plex Sulá, and K. A. Garrett. 2022. Where to invest project efforts for greater benefit: A framework for management performance mapping with examples for potato seed health. Phytopathology. [open access link]
Garrett, K. A., D. P. Bebber, B. A. Etherton, K. M. Gold, A. I. Plex Sulá, and M. G. Selvaraj. 2022. Climate change effects on pathogen emergence: artificial intelligence to translate big data for mitigation. Annual Review of Phytopathology 60:357-378. [open access link]
Klein-Gordon, J. M., S. Timilsina, Y. Xing, P. Abrahamian, K. A. Garrett, J. B. Jones, G. E. Vallad, and E. M. Goss. 2022. Whole genome sequences reveal the Xanthomonas perforans population is shaped by the tomato production system. ISME Journal 16:591-601. [open access link]
Nduwimana, I., S. Sylla, Y. Xing, A. Simbare, C. Niyongere , K. A. Garrett, B. A. Omondi. 2022. Banana seed exchange systems in Burundi – linking formal and informal systems. Outlook on Agriculture 51:334-348. [open access link]
Andersen Onofre, K. F., G. A. Forbes, J. Andrade-Piedra, C. E. Buddenhagen, J. C. Fulton, M. Gatto, Z. Khidesheli, R. Mdivani, Y. Xing, K. A. Garrett. 2021. An integrated seed health strategy and phytosanitary risk assessment: potato in the Republic of Georgia. Agricultural Systems 191:103144. [open access link]
Garrett, K. A. 2021. Impact network analysis and the INA R package: Decision support for regional management interventions. Methods in Ecology and Evolution 12:1634-1647. [open access link]
Klein-Gordon, J., Y. Xing, K. A. Garrett, P. Abrahamian, M. L. Paret, G. V. Minsavage, A. L. Strayer-Scherer, J. Fulton, S. Timilsina, J. B. Jones, E. M. Goss, and G. E. Vallad. 2021. Assessing changes and associations in the Xanthomonas perforans population across Florida commercial tomato fields via a state-wide survey. Phytopathology 111:1029-1041. [open access link]
McEwan, M. A., C. J. M. Almekinders, J.L. Andrade-Piedra, E. Delaquis, K. A. Garrett, L. Kumar, S. Mayanja, B. A. Omondi, S. Rajendran, and G. Thiele. 2021. “Breaking through the 40% adoption ceiling: Mind the seed system gaps.” A perspective on seed systems research for development in One CGIAR. Outlook on Agriculture [open access link]
Alcalá-Briseño, R. I., K. Casarrubias-Castillo, D. López-Ley, K. A. Garrett, L. Silva-Rosales. 2020. Network analysis of the papaya orchard virome from two agroecological regions of Chiapas, Mexico. mSystems 5:e00423-19. [open access link]
Xing*, Y., J. Hernandez Nopsa*, K. F. Andersen, J. Andrade-Piedra, F. Beed, G. Blomme, M. Carvajal Yepes, D. Coyne, W. Cuellar, G. Forbes, J. Kreuze, J. Kroschel, L. Kumar, J. Legg, M. Parker, E. Schulte-Geldermann, K. Sharma, and K. A. Garrett. 2020. Global cropland connectivity: A risk factor for invasion and saturation by emerging pathogens and pests. BioScience 70:744-758. [open access link]
Andersen, K. F., C. E. Buddenhagen, P. Rachkara, R. Gibson, S. Kalule, D. Phillips, and K. A. Garrett. 2019. Modeling epidemics in seed systems and landscapes to guide management strategies: The case of sweetpotato in Northern Uganda. Phytopathology 109:1519-1532. [open access link]
Ascunce, M. S., Keumchul Shin, J. C. Huguet-Tapia, R. Poudel, K. A. Garrett, A. H. C. van Bruggen, E. M. Goss. 2019. Penicillin trunk injection affects bacterial community structure in citrus trees. Microbial Ecology 78:457-469. [link]
Bell, T. H., K. Hockett, R. I. Alcalá-Briseño, M. Barbercheck, G. A. Beattie, M. A. Bruns, J. Carlson, T. Chung, A. Collins, B. Emmett, P. Esker, K. A. Garrett, L. Glenna, B. K. Gugino, M. d. M. Jimenez Gasco, L. Kinkel, J. Kovac, K. Kowalski, G. Kuldau, J. Leveau, M. Michalska-Smith, J. Myrick, K. Peter, M. V. Salazar, A. Shade, N. Stopnisek, X. Tan, A. Welty, K. Wickings, and E. Yergeau. 2019. Manipulating wild and tamed phytobiomes: challenges and opportunities. Phytobiomes 3:3-21. [open access link]
Bennett, A. E., K. Preedy, A. Golubski, J. Umbanhowar, S. R. Borrett, L. Byrne, K. Apostol, J. D. Bever, L. Biederman, A. T. Classen, K. Cuddington, M.-A. de Graaff, K. A. Garrett, L. Gross, A. Hastings, J. D. Hoeksema, V. Hrynkiv, J. Karst, M. Kummel, C. T. Lee, C. Liang, W. Liao, K. Mack, L. Miller, B. Ownley, C. Rojas, E. L. Simms, V. K. Walsh, M. Warren and J. Zhu. 2019. Beyond the black box: promoting mathematical collaborations for elucidating interactions in soil ecology. Ecosphere 10:e02799. [open access link]
Carvajal-Yepes, M., K. Cardwell, A. Nelson, K. A. Garrett, B. Giovani, D. G. O. Saunders, S. Kamoun, J. P. Legg, V. Verdier, J. Lessel, R. A. Neher, R. Day, P. Pardey, M. L. Gullino, A. R. Records, B. Bextine, J. E. Leach, S. Staiger, J. Tohme. 2019. A global surveillance system for crop diseases. Science 364:1237-1239. [link]
Delaquis, E., K. F. Andersen, N. Minato, C. T. L. Thuy, M. E. Karssenberg, S. Sophearith, K. A. G. Wyckhuys, J. Newby, D. D. Burra, P. Srean, I. Phirun, L. D. Niem, P. T. Nhan, K. A. Garrett, C. J. M. Almekinders, P. C. Struik, S. de Haan. 2018. Raising the stakes: cassava seed networks at multiple scales in Cambodia and Vietnam. Frontiers in Sustainable Food Systems 2:73. [open access link]
Garrett, K. A., R. I. Alcalá-Briseño, K. F. Andersen, C. E. Buddenhagen, R. A. Choudhury, J. C. Fulton, J. F. Hernandez Nopsa, R. Poudel, and Y. Xing. 2018. Network analysis: A systems framework to address grand challenges in plant pathology. Annual Review of Phytopathology 56: 559-580. [open access link]
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 107:1209-1218. [open access link]
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 107:1268-1278. [open access link] [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]
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]
BOOK CHAPTER and USER guides
Garrett, K. A. 2021. User guide to impact network analysis (INA). CGIAR Research Program on Roots, Tubers and Bananas (RTB). RTB User Guide. No. 2021-4. Lima, Peru. [open access link]
Andrade-Piedra, J. L., C. J. M. Almekinders, M. A. McEwan, F. B. M. Kilwinger, S. Mayanja, L. Mulugo, E. Delaquis, K.A. Garrett, A. B. Omondi, S. Rajendran, P. L. Kumar and G. Thiele. 2020. User guide to the toolbox for working with root, tuber and banana seed systems. CGIAR Research Program on Roots, Tubers and Bananas (RTB), Lima, Peru. [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.