Bradford Condon PhD

Bioinformatics, Web & Mobile Development


Bradford Condon, PhD

Education

August 2013, PhD in Plant Pathology & Plant-Microbe Interactions, Cornell University, Ithaca, NY

May 2007, BA in Biology and Religion, Oberlin College, Oberlin, OH

Employment

February 2017 to present: Postdoctoral associate, Department of Entomology and Plant Pathology, University of Tennessee, Knoxville.

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.

January 2016 to January 2017: Postdoctoral associate, Department of Plant Pathology, University of Kentucky.

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.

June 2014 to December 2015: Postdoctoral associate, Department of Ecology, Evolution, and Behavior, University of Minnesota.

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.

August 2007 to June 2014: Graduate Student and Post-Doctoral fellow, Department of Plant Pathology & Plant-Microbe Interactions, Cornell University, advised by Dr. B Gillian Turgeon

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.

Accomplishments

  • Tripal project manager.
    • Established testing protocols and continuous integration testing.
    • Formed a governance structure with contribution guidelines and requirements.
  • Upgraded HardwoodGenomics to Tripal 3, performed bioinformatic analyses and uploaded new data to site.
  • Co-developer of TreeSnap, mobile citizen science app.

Software

Tripal

  • Tripal Analysis Expression Module
    • For loading and display of RNASeq data, from biological source material to gene expression data
    • DOI: 10.5281/zenodo.1115662
  • Tripal ElasticSearch Module
    • For installing and managing sitewide search, customized search forms, and cross-Tripal-site queries via ElasticSearch
    • DOI: 10.5281/zenodo.1193925
  • Tripal Fields Generator
    • Developer CLI tool to automate Tripal field creation for Tripal v3 development
    • DOI: 10.5281/zenodo.1200662
  • Tripal TestSuite
    • A composer package that handles common test practices such as bootstrapping Drupal before running the tests, creating test file, and creating and managing database seeders.
    • DOI: 10.5281/zenodo.1209904
  • Tripal Alchemist
    • Enables bulk transformation of Tripal entities from one type to another
    • DOI: 10.5281/zenodo.1187120

TreeSnap

Skills

Bioinformatics and programming

  • 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
    • Metagenomics
    • RNA-seq and transcriptomics
    • Genome assembly and annotation
    • Phylogenetics
  • Programming languages: R, Perl, javascript, PHP, CSS, Ruby, SQL
  • Frameworks: Laravel, Drupal, Wordpress, React, React Native

Molecular biology

  • Fungal and bacterial culture, transformation, and phenotyping
  • Molecular bio bench skills include DNA extraction, PCR, southern/northern blotting, light and confocal microscopy
  • Next-gen (illumina) library preparation
  • Greenhouse management

Communication and mentorship

  • Formed UK-BLAST, the undergraduate bioinformatics mentorship group at the University of Kentucky
    • Leading and designing workshops in bioinformatics
    • Co-mentoring and advising students on their bioinformatics projects
  • Strong track record of supervising undergraduates in the laboratory and integrating their work into complex workflows
  • Co-PI awardee for bringing Expanding Your Horizons, a STEM conference for young girls, to the University of Kentucky
  • Community outreach and education on fungi includes presentations at Floracliff Nature Sanctuary and the Kentucky Food Retail Safety conference

Awards and honors

  • 2006 Oberlin College Norman H Wright Prize for undergraduate research
  • 2007-2008 Presidential Life Science Fellow
  • 2009 NSF graduate research fellowship honorable mention
  • 2010 NSF EAPSI fellow (New Zealand)
  • 2011 Plant Sciences outstanding TA award
  • 2012 McClintock Outstanding Plant Sciences Graduate Student Award
  • 2011-2012 Center For Teaching Excellence Graduate Teaching Associate Fellow
  • 2012-2013 Center For Teaching Excellence Graduate Teaching Associate Fellow
  • 2017 NSF EPSCoR grant, Expanding Your Horizons
  • 2017 UKY SOPS research symposium postdoc poster award (second place)

Teaching and leadership

Data and Software Carpentry Certified Instructor 2017

Trained and certified as a Data Carpentry and Software Carpentry Instructor.

Blog posts regarding SWC/DC.

Hosted Workshops

KBRIN Next Generation Sequencing and Data Analysis Workshop, University of Kentucky 2017

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: University of Kentucky 2016

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.

Departmental teaching: Cornell University 2008-2013
  • Spring 2008: PLPA 2010 TA: Magical Mushrooms & Mischievous Molds.
  • Spring 2010: PLPA 2015 TA: Mushrooms, Molds and Molecules.
  • Spring 2011 PLPA 2015 TA: Mushrooms, Molds, and Molecules.
  • Spring 2012 PLPA 2015 TA:  Mushrooms, Molds, and Molecules.
  • Spring 2013 PLPA 2015 TA:  Mushrooms, Molds, and Molecules.

 

Center for Teaching Excellence: Cornell University 2011-2013

workshops (1 hour) developed & implemented:

  • Classical teaching models and the psychology of learning
  • What do I want my students to learn? Identifying learning outcomes as the basis for instruction and assessment
  • Using library resources to enhance student’s research skills
  • Creating effective questions for iClickers and online quizzes
  • Establishing a professional electronic online identity

Full day workshops developed & implemented:

  • 2012 Chemistry TA training instructor
  • 2012 Teaching Excellence Practicum Instructor, CTE summer Institute

Presentations

Workshops
Talks
  • Joint Genome Institute Dothideomycete jamboree. Walnut Creek, CA (2008)
  • Fungal Genetics Conference, secondary metabolism session. Asilomar, CA (2013)
  • Kentucky Food Retail Safety Conference, invited speaker on wild mushroom safety. Frankfort, KY (2016)
Posters

Publications

Accepted, In Review

Harper, Lisa, Agbiodata consortium, 2018. AgBioData Consortium Recommendations for Sustainable Genomics and Genetics Databases for Agriculture. Database, In Review.

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, In Review.

In Review

Lumibao, C, Condon, B, Kinkel , L, May, G, Seabloom, E, Borer, E 2018. Where you are matters: site-specific responses of fungal endophyte communities in Andropogon gerardii to fertilization and herbivory. Ecology, In Review.

Condon, B, Almsaeed, A, West, J, Chen, M, Staton, M 2018. Tripal Developer Toolkit. BioRxiv preprint, in review. doi: https://doi.org/10.1101/328641

Peer-reviewed

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

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 (digital preprint). 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