This is an archived file from the Spring 2022 version of the course.
See the current course website for a more recent version.

Fall 2022 Course

This course will be offered again in in Fall 2022. The course will be somewhat similar to the Spring 2022 course (which you can explore here, including the Syllabus and Schedule, but with some changes based on what we learned last spring and new versions of these will be posted soon.

The Fall 2022 course is scheduled for Tuesdays and Thursdays, 12:30-1:45pm in Olsson Hall 120.

Final Projects

Here are final projects with public websites available.

Final Project Presentations

Wednesday, 27 April

Monday, 2 May

Project Presentations Schedule

Project Presentations

Each team will have an opportunity to present your project to the class on either Wednesday, 27 April or Monday, 2 May. You will have 5 minutes maximum for your presentation (which will need to be enforced strictly to be able to complete all the presentations within the schedule class period). It is fine if your presentation is shorter (which might even allow time for questions), but you should keep the time limit in mind in planning your presentation.

Teams presenting should submit your slides as either a PDF file, a link to a (publicly-visible) URL, or a PowerPoint file by sending a slack message in your team channel to me no later than 10:29am on the date of your presentation.

Wednesday, 27 April

  • Emily Buckley, Investigating Heart Disease in Cavalier King Charles Spaniels
  • Joshita Gullanki, Sindhu Mente, Shruthi Nyshadham, The Role of Computational Biology in Prenatal Testing
  • Anna Williamson, An Introduction to Connectomics
  • Joshua Devine, Ian Switzer, Ronith Ranjan, New DNA/RNA/Amino Acid File Formats with Biopython Support and a Standalone Python Library
  • Davis Garwood, Kevin Wen, Identifying Genes in DNA Sequences
  • Mohit Srivastav, Trying to re-create the fractal evolution of gene promoter networks using aggregation
  • Meghan Anderson, Kathia Crawford, Izzy Shehan, Visualizing and Understanding Olfaction
  • Marvin Cheng, Computer Vision and Human Vision
  • Brenna Courtney, On Christian Bök’s The Xenotext (Book 1)
  • Shreyas Gullapalli, Zachary Heidel, Nikhil Aluru, An Analysis of COVID Variants
  • Alyce Hong, Ife Adetunji, Faisal Refai, David Kim, Eugene Lee, Rachel Lee, Synthesizing Covid Test Information
  • Yanjin Chen, Gene network analysis
  • Caroline Linkous, Taylor Brooks, GAPDH Primer Selection: Finding the best primers for targeting the GAPDH gene
  • Medhini Rachamallu, Anna Brower, Creation of Synthetic Patient Data
  • Sion Kim, Sequencing my own genome

Monday, 2 May

  • Jason Calem, Will Pemble, Gabriel Silliman, Cooper Scher, DNA Profiling with Incomplete Databases
  • Lily Roark, Allison Branch, Toy CODIS: Loci Variation, Matching and Encryption
  • Yuchen Sun, Nafisa Amrula, SARS-CoV-2 Sequence Analysis
  • Harshita Pathipati, Noor Rafiq, Scientific Exploration of Popular American COVID-19 Vaccines and Other Novel Vaccines
  • Ho Yeon Jeong, Pawan Jayakumar, A Survey of CRISPR and its Newest Variations and Applications
  • Sid Chauhan, Aging and Reversing Aging
  • Justin Ngo, Emily Franklin, The Ethics of Gene Editing on Intellectual Disability
  • Riley Heck, Trophic web modeling using weighted directed graphs
  • Raymond Wen, DIY DNA Extraction and Education
  • Neil Phan, Alip Arslan, Emil Diaz, Evolve
  • Zachery Boner, Jason Yu, Grant Matteo, SmartSleep
  • Tatiana Kennedy, DNA Encoded Library Enumeration
  • Jacob Hilliard, MRI Data Pipeline Builder
  • Ethan Gahm, Peptide Sequencing: A New Project for Computational Biology Students
  • Colin Crowe, The Mystery of Chargaff’s Second Parity Rule

Class 25: Computational Biology: Ensembles of Trees (Guest: Kristen Naegle)


Our guest speaker today was Kristen Naegle, Professor of Biomedical Engineering. Her slides are here: Computational Biology: Ensembles of Trees.