Infectious Diseases, Immunology and Within Host Models
Meeting Times:
- Monday, July 20, 9:00 AM – 5:00 PM
- Tuesday July 21, 9:00 AM – 5:00 PM
- Wednesday July 22, 9:00 AM – 12:00 PM
Classroom: TBA
Module Summary:
This module introduces infectious diseases, immunology and modeling on the level of the individual host. We provide an introduction to immunology and modeling of acute and chronic viral infections, bacterial infections and other pathogens of interest. We will discuss how models can be used to analyze pathogen-host interactions, and how to model intervention strategies, such as vaccines and drug treatments. This is an introductory and survey course. We start at the basics but cover a lot of material.
Prerequisites:
While prior immunological or modeling training is not required, prior knowledge in either area will be beneficial. Some familiarity with the R programming language is recommended.
Module Content:
- Simple compartmental deterministic models.
- Basic immunological concepts
- How to use mathematical models to study within-host infection dynamics.
- Using models to analyze interventions such as vaccines or drugs.
Instructors
Andreas Handel, PhD
Professor, Department of Epidemiology and Biostatistics, University of Georgia
Dr. Handel’s main research focus is influenza, with some other work on a variety of pathogens such as SARS-CoV-2, norovirus, tuberculosis, and others. He uses mathematical models, computational simulations and statistical analysis to understand the dynamics of pathogens on different spatial and temporal scales. He works on both the within-host level (the immunology, virology, microbiology scale) and the population level (the epidemiology, ecology, evolution scale). He and his group aim to help design better intervention and control strategies against infectious diseases, both for individual patients and on the population level.
Paul Thomas, PhD
Professor and Program Head, Immunology and Vaccine Development Program Vaccine and Infectious Disease Division, Fred Hutch
Dr. Paul Thomas is a viral immunologist with a focus on respiratory viruses. He integrates quantitative, computational and empirical methods to understand how our immune systems respond to infection. Dr. Thomas focuses immune regulation of health and disease, including tissue injury during infection, cancer development and resolution, and effective anti-pathogen responses. A particular focus of the lab in on T cells, immune cells that can orchestrate immune responses as well as kill target cells. These cells use a specialized molecule called the T-cell receptor, or TCR, to find their targets. Each newly produced T cell creates a unique TCR, and Dr. Thomas works to untangle the relationship between TCR specificity and immune efficacy.
Using a variety of adult and pediatric cohorts, Dr. Thomas studies the immunological signatures that reflect an individual’s immune history and predict their responses to future exposures. He has developed computational tools to create highly detailed maps of TCR repertoires and understand how they reflect immune function and pathogen exposure. Dr. Thomas’ findings will help researchers design more effective vaccines and enhance T-cell or TCR-based cancer therapies.
Required Software:
R software
- DSAIRM R package: https://ahgroup.github.io/DSAIRM/
Recommended Reading:
- Simulation Modeling in Immunology (SMI) website, which contains material from previous iterations of this course: https://andreashandel.github.io/SMIcourse/
- “Simulation modeling for immunologists” a review/tutorial we wrote on the topic a few years ago: https://www.nature.com/articles/s41577-019-0235-3