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
Plex Sulá, A. I., V. De Col, B. A. Etherton, Y. Xing, A. Agarwal, L. Ramić, E. Bonaiuti, M. Friedmann, C. Proietti, G. Thiele, and K. A. Garrett. 2024. What traits of collaboration networks are associated with project success? The case of two CGIAR agricultural research programs for development. Agricultural Systems 219:104013. [open access link]
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.