Bradford Condon, PhD
Guide technology decisions across all client projects in CABEM. Piloted automated testing, documentation, and publish harnesses (PHPUnit, Jest, Jest-axe, react-styleguidist, doxygen, selenium, gitlab's npm/composer package registry). Gather requirements from clients, write and manage jira tickets to lead launching two custom, enterprise level applications, while implementing the most critical frontend, backend, and infrastructure components.
Develop and implement OAS 3.0 compliant API using PHP Slim and custom frameworks. Design and build UIs with React. Manage support and development workflow with gitlab and Jira. Pioneer transition from manual to automated deployments using AWS CodeBuild, CodeDeploy, via CodePipelines.
See academic section below for archived technology expertise and language (such as R, Perl, and Ruby).
Tripal core developer. Collaborative Tripal developer for the Hardwood Genomics Web and the USDA-NAL I5K project.
I develop the Hardwood Genomics Web (HWG), a web site that houses genetic and genomic data from a variety of hardwood tree species. I contribute to Tripal, an open source genomic database and website framework. I also authored the mobile app TreeSnap, which allows citizens to partner with scientists to track and study trees. I serve as the biological point person for undergraduate and graduate lab programmers to help them understand the underlying database model.
Performed bioinformatic analyses for whole-genome alignment and phylogenetics of the rice blast pathogen magnaporthe oryzae. Developed and implemented a mentoring program in bioinformatics for undergraduate biologists, UK-BLAST.
Planned and implemented a large-scale metagenomic study of bacterial and fungal endophytes for over 1,000 native prairie grass leaves. Designed a metagenomic sequencing and analysis pipeline.
Performed genetic and genomic studies using the model fungal phytopathogen Cochliobolus heterostrophus. Acted as lab co-manager in charge of ordering and hiring/training/managing undergraduate students.
Lead developer for TreeSnap, a citizen science mobile app. Find out more: https://treesnap.org/
Code:
Proficient with UNIX/LINUX systems, command-line programming, querying and managing big data/databases
Developer for cross-platform (iOS and Android) apps in React-Native, and genomics websites using Tripal and Drupal.
Experience designing experiments and analyzing data for a wide variety of bioinformatic projects, including
Programming languages: R, Perl, javascript, PHP, CSS,SASS, Ruby, Python, SQL
Frameworks: Laravel, Drupal, Wordpress, React, React Native
Trained and certified as a Data Carpentry and Software Carpentry Instructor.
Hosted Workshops
Instructor and web developer. Implemented and maintained the (Drupal-based workshop website)[https://ngs.csr.uky.edu/] and REDCap registration/survey system. Poster publication link.
UK-BLAST is an extracurricular support group for undergraduates performing genomics research at the University of Kentucky. In addition to advising students on their projects, I designed and implemented workshops on topics in genomics.
workshops (1 hour) developed & implemented:
Full day workshops developed & implemented:
Crocker, E, Condon, B, Almsaeed, A, Jarret, B, Nelson, C D, Abbot, A, Main, D, Staton, M (2019) TreeSnap: A citizen science app connecting tree enthusiasts and forest scientists Plants, People, Planet https://doi.org/10.1002/ppp3.41
Spoor, S, Cheng, C, Sanderson, L-A, Condon, B, et al. (2019) Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. Database, baz077, https://doi.org/10.1093/database/baz077
Condon, B, Almsaeed, A, West, J, Chen, M, Staton, M (2018). Tripal Developer Toolkit. Database, bay099 DOI: https://doi.org/10.1093/database/bay099
Lumibao, C, Condon, B, Kinkel , L, May, G, Seabloom, E, Borer, E Site‐specific responses of foliar fungal microbiomes to nutrient addition and herbivory at different spatial scales. Ecology and Evolution, October 2019. https://doi.org/10.1002/ece3.5711
Seabloom, E, Condon, B, Kinkel, L, Komatsu, K, Lumibao, C, May, G, McCulley, R, Borer, E.(2019) Effects of nutrient supply, herbivory, and host community on fungal endophyte diversity. Ecology, . https://doi.org/10.1002/ecy.2758
Condon, B., Elliott, C, Gonzalez, J, Yun, S, Akagi, Y, Wiesner-Hanks, T, Kodama, M, Turgeon, G (2018). Clues to an evolutionary mystery: the genes for T-toxin, enabler of the devastating 1970 Southern Corn Leaf Blight epidemic, are present in ancestral species, suggesting an ancient origin. MPMI Molecular Plant-Microbe Interactions 2018 31:11, 1154-1165. DOI: https://doi.org/10.1094/MPMI-03-18-0070-R
Lisa Harper, Jacqueline Campbell, Ethalinda K S Cannon, Sook Jung, Monica Poelchau, Ramona Walls, Carson Andorf, Elizabeth Arnaud, Tanya Z Berardini, Clayton Birkett, Steve Cannon, James Carson, Bradford Condon, Laurel Cooper, Nathan Dunn, Christine G Elsik, Andrew Farmer, Stephen P Ficklin, David Grant, Emily Grau, Nic Herndon, Zhi-Liang Hu, Jodi Humann, Pankaj Jaiswal, Clement Jonquet, Marie-Angélique Laporte, Pierre Larmande, Gerard Lazo, Fiona McCarthy, Naama Menda, Christopher J Mungall, Monica C Munoz-Torres, Sushma Naithani, Rex Nelson, Daureen Nesdill, Carissa Park, James Reecy, Leonore Reiser, Lacey-Anne Sanderson, Taner Z Sen, Margaret Staton, Sabarinath Subramaniam, Marcela Karey Tello-Ruiz, Victor Unda, Deepak Unni, Liya Wang, Doreen Ware, Jill Wegrzyn, Jason Williams, Margaret Woodhouse, Jing Yu, Doreen Main (2018) AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture, Database, Volume 2018, bay088, DOI: https://doi.org/10.1093/database/bay088
Gladieux, P., Condon, B. J. (co-first author), Ravel, S., Soanes, D., Maciel, J. L. N., Nhani, A., Chen, L., Terauchi, R., Lebrun, M.-H., Tharreau, D., Mitchell, T., Pedley, K. F., Valent, B., Talbot, N. J., Farman, M., and Fournier, E. (2018). Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae. J.W. Taylor, ed. MBio. 9:e01219–17. DOI: 10.1128/mBio.01219-17
Mohd Zainudin, N. A. I., Condon, B. J., De Bruyne, L., Poucke, C. V., Bi, Q., Li, W., et al. (2015). Virulence, host selective toxin production, and development of three Cochliobolus phytopathogens lacking the Sfp-type 4′-phosphopantetheinyl transferase Ppt1. MPMI, 28:10, 1130-1141. DOI: 10.1094/MPMI-03-15-0068-R
Santana, M. F., Silva, J. C. F., Mizubuti, E. S. G., Araújo, E. F., Condon, B. J., Turgeon, B. G., & Queiroz, M. V. (2014). Characterization and potential evolutionary impact of transposable elements in the genome of Cochliobolus heterostrophus. BMC Genomics, 15(1), 536. doi:10.1186/1471-2164-15-536
Condon, B. J., Wu, D., Kraševec, N., Horwitz, B. A., & Turgeon, B. G. (2014). Comparative Genomics of Cochliobolus Phytopathogens. In R. A. Dean, A. Lichens-Park, & C. Kole, Genomics of Plant-Associated Fungi: Monocot Pathogens (pp. 41–67). Berlin, Heidelberg: Springer Berlin Heidelberg. doi:10.1007/978-3-662-44053-7_2
Condon, B. J., Oide, S., Gibson, D. M., Krasnoff, S. B., & Turgeon, B. G. (2014). Reductive iron assimilation and intracellular siderophores assist extracellular siderophore-driven iron homeostasis and virulence. Molecular Plant-Microbe Interactions : MPMI, 27(8), 793–808. doi:10.1094/MPMI-11-13-0328-R
Horwitz, B. A., Condon, B., & Turgeon, B. G. (2013). Cochliobolus heterostrophus: A Dothideomycete Pathogen of Maize. In Genomics of Soil-and Plant-associated Fungi (Vol. 36, pp. 213–228). Berlin, Heidelberg: Springer Berlin Heidelberg. doi:10.1007/978-3-642-39339-6_9
Zhang, N., MohdZainudin, N. A. I., Scher, K., Condon, B. J., Horwitz, B. A., & Turgeon, B. G. (2013). Iron, oxidative stress, and virulence: roles of iron-sensitive transcription factor Sre1 and the redox sensor ChAp1 in the maize pathogen Cochliobolus heterostrophus. Molecular Plant-Microbe Interactions : MPMI, 26(12), 1473–1485. doi:10.1094/MPMI-02-13-0055-R
Condon, B. J., Leng, Y., Wu, D., Bushley, K. E., Ohm, R. A., Otillar, R., et al. (2013). Comparative genome structure, secondary metabolite, and effector coding capacity across Cochliobolus pathogens. PLoS Genetics, 9(1), e1003233. doi:10.1371/journal.pgen.1003233
Xue, C., Wu, D., Condon, B., Bi, Q., Wang, W., & Turgeon, B. G. (2013). Efficient gene knockout in the maize pathogen Setosphaeria turcica using Agrobacterium tumefaciens-mediated transformation. Phytopathology, 103(6), 641–647. doi:10.1094/PHYTO-08-12-0199-R
Ohm, R. A., Feau, N., Henrissat, B., Schoch, C. L., Horwitz, B. A., Barry, K. W., Condon, B. J., et al. (2012). Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathogens, 8(12), e1003037. doi:10.1371/journal.ppat.1003037
Turgeon, B. G., Condon, B. J., Liu, J., & Zhang, N. (2010). Protoplast transformation of filamentous fungi. Methods in Molecular Biology (Clifton, N.J.), 638(Chapter 1), 3–19. doi:10.1007/978-1-60761-611-5_1
Almeida, N. F., Yan, S., Lindeberg, M., Studholme, D. J., Schneider, D. J., Condon, B. J., et al. (2009). A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of Pseudomonas syringae pv. tomato DC3000. Molecular Plant-Microbe Interactions : MPMI, 22(1), 52–62. doi:10.1094/MPMI-22-1-0052