Adaptive Immune Receptor Repertoires (AIRRs) refer to the diverse collection of antigen-specific receptors expressed by T cells and B cells. These receptors are crucial for the immune system's ability to recognize and respond to pathogens and other foreign molecules. The diversity of AIRRs arises from complex genetic recombination processes, enabling the immune system to identify virtually any antigen it encounters.
Studying AIRRs is essential for understanding how the immune system generates and maintains its remarkable ability to recognize and respond to diverse antigens. Changes in AIRR profiles are associated with various diseases, including autoimmune disorders, infections, and cancer, and can serve as valuable biomarkers for diagnosis and monitoring. AIRR analysis also plays a critical role in the development of targeted therapies such as monoclonal antibodies and personalized immunotherapies. Additionally, it contributes to vaccine design by revealing how the immune system responds to specific pathogens. Research in this area drives the creation of advanced computational tools to manage and analyze complex immune repertoire data, supporting innovation in biomedical science.
The Computational Immunology Summer School offers an in depth exploration of Adaptive Receptor Repertoire (AIRR) data analysis, with a primary focus on T cells. Participants will develop both theoretical knowledge and practical skills in cutting-edge bioinformatics tools and lab techniques used to study immune system diversity. This program is designed for MSc and PhD researchers, as well as those at higher academic levels, with a basic understanding of R and command-line tools. Introductory courses will be provided to help build foundational practical skills.
Course Focus:
Mechanisms of generating diverse immune repertoires in T cells
Wet-lab protocols for generating AIRR data
Computational tools for understanding immune repertoire diversity
Hands-On Learning:
Running analyses in HPC environment and interactive notebooks
Project-based workshops to design and execute independent analyses.
Practical sessions with tools like MICXR, GLIPH2, ALICE, and others.
Information about the course
Focus area:
Biomedicine
Coordinating unit:
Institute of Biomedicine and Translational Medicine
Study Field:
Immunology
Course Leaders:
Igor Filippov, Alexandra Elsakova
Format:
Summer Course
Location:
Biomedicum (Ravila 19, Tartu)
Course dates:
28 July - 6 August 2025
Language:
English
ECTS:
3
Study group:
MA/PhD
Lecturers
Alexandra Elsakova
PhD student and Junior Research Fellow at the University of Tartu's Institute of Biomedicine and Translational Medicine, specializing in molecular immunology.
Igor Filippov
Doctoral student and Junior Research Fellow in Molecular Immunology at the University of Tartu's Institute of Biomedicine and Translational Medicine.
Prof Pärt Peterson
Molecular immunologist at the University of Tartu, Estonia. He serves as the Head of the Institute of Biomedicine and Translational Medicine and leads the Molecular Pathology Research Group.
Prof Kai Kisand
Immunologist at the University of Tartu, serving as a Research Professor of Cellular Immunology at the Institute of Biomedicine and Translational Medicine.
Chinna Susan Phillip
PhD student and Junior Research Fellow in Molecular Immunology at the University of Tartu's Institute of Biomedicine and Translational Medicine.
Dawit A. Yohannes
University of Helsinki
Victor Greiff
University of Oslo
Application deadline: 30 April 2025
Application period: 1 April - 30 April 2025 NB! All of the applicants are required to pay a non-refundable application fee of EUR 25. Your application will only be processed after the University has received the fee. The application fee is required to facilitate the admissions process and will not be refunded, regardless of the admission result.
Course fee: 600EUR
Includes: Study materials 8 days of academic work with lecturers Certificate of completion (3 ECTS) 4 cultural events in the evenings Ticket to University of Tartu museums
NB! Transportation and accommodation costs are not included. The course fee does not cover participant's lunch during the summer school.
Week 1: Foundations and Practical Tools
July 28: Introduction to AIRR and T Cells
13:00–14:00 Course Introduction and Networking, 3 min presentation of participants' own work
14:00–15:30 Session 1: What Are T Cells? Why Study AIRR? Introduction to T cell subsets (CD4+ , CD8+ ), immune roles, and significance of diversity.
15:45–17:00 Session 2: Introduction to AIRR Analysis Overview of AIRR, sequencing technologies, and the role of high-throughput sequencing.
13:00–17:00 Session 2: Introduction to MICXR Tool Hands-on exploration of AIRR data using MICXR. Group discussion: Common challenges in data quality
July 30: Diversity Analysis in Bulk AIRR Data (Guest lecture)
09:00–12:00 Session 1: Bulk AIRR Data Exploration Analysis of diversity metrics Task: Explore a full dataset to identify patterns and anomalies.
13:00–17:00 Session 2: Repositories and Data Formats Introduction to AIRR repositories and bulk vs. singlecell data. Task: searching for datasets on specific conditions in public repositories.
July 31: Single-Cell AIRR Analysis
09:00–12:00 Session 1: Single-Cell Data Overview Technologies, datasets, and unique challenges. Introduction to 10x Genomics, Parse Biosciences, and other single-cell technologies. Paired TCR and BCR sequencing. Data exchange formats and software workflows for processing single-cell data. Downstream analysis of immune repertoire diversity in single-cell.
13:00–17:00 Session 2: Single-Cell Data Analysis Task: Compare TCR repertoires across cell types and conditions.
August 1: Disease Associations and Predictions (Guest lecture)
09:00–12:00 Session 1: Disease-Specific Repertoires data Overview of tools for predicting disease associations.
13:00–17:00 Session 2: Application of Predictive Tools Task: Use datasets to identify disease correlations
August 2, August 3 Weekend/free day
August 4: Independent Projects
Morning: Guidance on project topics. 24-second elevator pitches with 1-slide presentations.
All Day: Independent or paired project work with instructor support.
August 5: Presentations and Wrap-Up
09:00–12:00 Project Presentations and final notes
By the end of the course, participants will:
• Understand the mechanisms behind adaptive immunity
• Understand the principles of bulk and single-cell immune repertoire assays
• Analyze diversity metrics, clonal distributions, and antigen specificity
• Conduct independent analyses of immune repertoire data
During the course: Students must complete given tasks and practical exercises
By the end of the course: Participants will engage in group work throughout the whole course. The final assignment is presenting the group project.
Which previous knowledge is required?
Basic understanding of cellular and molecular immunology
Basic programming skills (R or Python), familiarity with command line
Entry requirements:
Online application form (application period April 1 - April 30 2025)
Motivation letter (up to 1 page) that demonstrates the applicant’s motivation to participate, his/her expectations about the programme, how participation in the summer programme relates to his/her studies and interests, and how the applicant plans to use the gained experience and knowledge in the future.
Transcript of academic records
Copy of passport
PS: Only complete applications including all annexes submitted by the deadline will be considered for selection.
Are you wondering how to get to Tartu and where to stay? Tartu is the second biggest city in Estonia and is, therefore, quite easily reachable. Tartu is famous for its sustainable transportation methods which make moving around the city very quick, cheap and convenient. In the City of Education there are many options of accommodation. You'll get to choose between a cheap stay at the dormitory with other international students or pick a fancier option in a hotel or apartment.
While the academic course is broaden your knowledge and learning skills, the cultural programme offers a range of fun and engaging cultural activities, introducing you to Estonia and the opportunity to interact and network with other participants in a lively environment. Students will have the opportunity to enjoy a range of day trips and events offered through the programmes and their experience in Tartu! Please scroll down to see the information about the social programme events, fees, refund policy, etc.
