In 2021-22, the COI instituted a new track for doctoral trainees in immunology – the Computational and Systems Immunology Track (CSI). Genomic technologies are greatly expanding how we study and understand immune functions in health and disease. Yet, leveraging large-scale, high-dimensional genomic data to decipher the complexity of the immune system remains a major challenge. Effective collection, integration, analysis, and interpretation of these data promises to provide new insights into the genetic contributions and molecular pathways at the root of human immunological diseases. The goal of the CSI track is to instill students with the conceptual and technical training needed to tackle immunological questions using quantitative and systems-level genomic approaches, and to think about immunological questions from an evolutionary perspective. The CSI Track is supported by two new graduate courses, Immunogenomics I & II (described below) that are specifically designed for Immunology trainees.
Immunogenomics I: Evolutionary and Genomic Approaches to Immunology (IMMU 48000). This course will train students to tackle immunological questions using quantitative and systems-level approaches, and think about the immune system from an evolutionary perspective. The topics covered will include: (i) introduction of innate and adaptive immunity, (ii) evolution of the different arms of the immune system, (iii) Population variation in immune responses, (iv) genomic technologies and applications, (v) study design in genomic studies, and paper-based discussion of key immunological concepts and how we can study them using systems immunology approaches. Barreiro, Roy Chowdhury. Autumn. (**Required for students on the COI-CSI track**)
Immunogenomics II: Data Science in Systems Immunology (IMMU 48900). This course teaches fundamental concepts in genomic data science and trains students to apply them critically in immunological contexts. Students will gain an understanding of how to use basic statistics, linear algebra, and computation to explore, analyze, and interpret published RNA-sequencing data (bulk and single-cell) and immune-cell receptor sequencing data. Student performance will be assessed through in-class discussions, take-home assignments and exams, and an end-of-term final project of the student’s choice. Basic R or Python programming skills are prerequisite. Riesenfeld, Weinstein. Spring. (**Required for students on the COI-CSI track**)