Ferhat Ay

Bioinformatics for Immunologists
(BGGN 239, Spring 2023)

Course Director
Prof. Ferhat Ay (Email: fay@health.ucsd.edu)
Prof. Mitchell Kronenberg (Email: mitch@lji.org)
Course Coordinator
Donaldo Sosa (Email: donaldo@lji.org)
Course Syllabus
Spring 2023 (PDF)

Overview

Bioinformatics is conceptualizing biology in terms of macromolecules and then applying “informatics” techniques derived from disciplines such as applied mathematics, computer science, and statistics to understand and organize the information associated with these molecules, on a large-scale.

Among many other discoveries, bioinformatics approaches coupled with sequencing of RNA and DNA molecules have enabled the discovery of new immune cell types and previously uncharacterized functions for known immune cells in the context of different diseases.

This course has an integrated lecture/exercise structure with a strong lineup of faculty and instructors who are renowned experts in their respective fields, who are committed to teach bioinformatics with a specific focus on its applications to important problems in immunology through practical and hands-on training likely to impact students’ overall success in their research

Major topics include:

  • Gene expression analysis;
  • Human genetics;
  • Epigenomics in immune cells;
  • Epitopes;
  • Neoantigens;
  • Proteomics;
  • Metabolomics; and
  • Imaging analysis.

Students completing this course will be able to:

  • Understand main computational concepts underlying commonly used bioinformatics tools;
  • Be familiar with online databases and resources (e.g., GWAS catalog, IEDB, DICE, ImmGen, ENCODE, IHEC) and efficient ways to query them;
  • Be able to utilize existing tools to perform data analysis for several different sequencing and imaging techniques; and
  • Learn and actively utilize best practices for reproducible research and collaboration related to bioinformatics (project organization, version control, online lab notebooks).

For further details please see our complete list of course objectives and specific learning goals.

Audience:

Bioinformatics graduate students and others familiar with

Accessibility:

We are committed to making this course accessible to everybody. Please contact Dr. Ferhat Ay ferhatay@lji.org if you have questions regarding room accessibility

Requirements:

To fully participate in this course students will be expected to use their own laptop computers with specific freely available software installed. A limited number of classroom computers are also available should the need arise. Participants must bring a laptop with specific software installed.

Schedule:

Lectures are on Monday and Wednesday at 4:30 - 6:20 pm in Tata Hall 2501. Map. These lectures will include lectures and exercise work sessions. A detailed schedule with class related material is provided online.

Class announcements:

All announcements regarding the course will be by email to your UCSD address and will also be updated on the class website.

Office hours & location:

We will use Zoom on a weekly basis at a time to be determined from student polling. Please email me if you are interested in meeting to discuss course related content at any point.

Syllabus:

A detailed syllabus with topic outlines and learning goals is available for download.