Team:UC Davis/Attributions


Noah Husband

  • As head of Wiki Design, Noah wrote the code and much of the content for the team’s wiki. He also had a hand in software development, building a program to compare motif-finding softwares, processing fungal genome data, investingating the fungal phylogenies, and editing/testing Lastly, he had an early role in experimental design, reviewing literature used to make our protocols.
  • (Head of Wiki Design; worked in software and experimental design)

Lily Karim

  • Lily wrote the majority of the programs found in the GitHub repository. With the help of Ian Korf, she wrote a python function library which was used to extract and analyze the fungal and motif data generated in the experiments. She helped create and interpret software outputs to determine the optimal parameters that were used to execute the workflow. She processed the first 12 fungal clusters to find their binding sites and candidate transcription factors.
  • (Head of Software Development; planned/implemented analysis and processing of theoretical data and fungal genomic data)

Jason Hu

  • Jason was in charge of all media production ranging from the promotional video to presentations. He created the look and feel of Spore_Core and ensured that all our deliverables were presentable. He also has a strong interest in breaking down the theoretical concepts of the project for the general audience in the presentation and promotion
  • (Head of Videography/Editing; worked in experimental design, wiki design, and branding)

Alejandra Wilson

  • Ali designed a system for inducible production of a desired transcription factor, consisting of a DNA construct and p502 from the Fungal Genetics Stock Center. She also developed a system for visualizing the binding of a transcription factor with a predicted binding site, via the targeted inhibition of a reporter gene sgfp. She also developed a culturing and transformation protocol in Aspergillus niger. In the human practices sector, Ali helped interview members from the biotechnology industry.
  • (Head of Experimental Design; worked in human practices and outreach)

Paul Osuna-Kleist

  • Paul spearheaded Human Practices by researching prominent community members, setting up and facilitating meetings, integrating their suggestions throughout the project, and continuously thinking of how to improve the ethics of the project. In addition, he looked for the next steps for how the project could be implemented down the line. He aided in development and presentation of the project for Science Communication. He also worked alongside Ali to develop the protocol for experimental design including protocol design, design of the reporter gene construct using sGFP, finding an improved gpdA promoter, gpdA3B, and locating and annotating gene sequences and constructs. Administrative tasks such as the safety form, team information and parts submission were also overseen and executed by Paul.
  • (Head of Human Practices and Outreach; worked in fundraising/administration, experimental design, and implementation)

Daniel Labolle

  • Daniel did foundational background research for the groundwork of the project. He took the lead on data discovery and developed a large part of the ideas behind our methodology and data testing. Working alongside Lily and Dr. Ian Korf, he helped design algorithms and software for the processing and analysis of both real and theoretical data. He also took the lead in international outreach and directed collaborations with Team IISER berhampur in India and Team Moscow-Russia.
  • (Head of Data Analysis and International Outreach; worked in software)

Dr. Marc Faciotti

  • Dr. Marc Facciotti was our primary advisor in addition to our experimental advisor. He met with us weekly, and whenever there was a gap in our knowledge he graciously provided us with sources to further our investigation.
  • (Head Instructor and Experimental Advisor)

Dr. Ian Korf

  • Dr. Ian Korf supported all bioinformatics research and programming. He helped with conceptual and coding issues. We met with Dr. Korf weekly for discussion sessions where we would work through thought processes and issues with our code to determine the best methods for quantifying the predictive binding sites.
  • (Computational Advisor, Python Coach, Literally Wrote the Book on BLAST)

Andrew Yao

  • Andrew Yao helped with various administrative tasks such as the safety form and parts submissions. Specifically he demonstrated ways of reworking our gene sequences to best fit the parts criteria as a well as broadening our views of the safety necessities.
  • (Administrative Advisor, Safety and Parts Coach)

Special Thanks

  1. UC Davis College of Biological Sciences Dean Winey for the generous donation of $1,000 for Jamboree Fee
  2. UC Davis Genome Center/Marc Facciotti for the generous donation of $1,500 towards Jamboree fee and $5,500 for team registration.
  3. Mr. Mayer and Mrs. McDowell for hosting our presentations at Nevada Union High School
  4. Dr. Sirulnik for hosting our presentation at Saddleback College
  5. Dr. Asaf Salamov and Dr. Igor Grigoriev of JGI for allowing us to study their fungal genomes and for answering our questions
  6. Dr. Mark Yarborough for speaking with us about bioethics
  7. Dr. C. Titus Brown for speaking with us about computational ethics
  8. Ms. Trina Kleist for speaking with us about effective communication for our science communication medal requirement
  9. Dr. Vasavada and Dr. Pierce of Marrone BioInnovations for discussing industry practices with us
  10. Dr. Amanda Fischer of Novozymes for answering our questions about indusrty and experimental design
  11. Cooper Houston of Fever Boys for creating the music in our presentation video