Computational Immunology Summer School
On-site in Tartu 28 July - 6 August 2025
Adaptive Immune Receptor Repertoires (AIRRs) are key to the immune system's ability to recognise and combat diverse pathogens. These antigen-specific receptors, expressed by T and B cells, are generated through intricate genetic recombination processes. Their analysis is critical for understanding immune diversity, discovering disease biomarkers, developing personalised immunotherapies, and designing vaccines.
This programme is tailored for students with a basic knowledge of R and command-line tools, offering a comprehensive foundation in AIRR data analysis while also delving into advanced secondary analysis techniques. Participants will gain both theoretical insights and hands-on experience with cutting-edge computational tools and laboratory protocols.
Highlights:
- Core Topics: T-cell repertoire diversity mechanisms, wet-lab protocols, and computational approaches for AIRR analysis.
- Hands-On Learning: Solve practical challenges using real-world AIRR data through interactive notebooks and project-based workshops.
- Tool Training: Practical sessions with advanced tools such as MICXR, GLIPH2, ALICE, and others.
Application period: 1 April - 30 April 2025
NB! All of the applicants are required to pay a non-refundable application fee (read more here) 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.
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: | MSc/PhD |
Lecturers
| Alexandra Elsakova |
| Igor Filippov |
Junior Research Fellow in Molecular Immunology at the University of Tartu's Institute of Biomedicine and Translational Medicine. His research focuses on studying immune cells at single-cell resolution, aiming to better understand the complexity of immune responses. |
| Prof Pärt Peterson |
| Professor of Molecular Immunology at the University of Tartu, Estonia, since 2008. He holds a PhD in Molecular Immunology from the University of Tampere, Finland. His research focuses on the AIRE gene, DNA methylation, and epigenetic imprinting. Currently, he leads the Institute of Biomedicine and Translational Medicine and the Molecular Pathology Research Group. |
| Prof Kai Kisand |
| Immunologist at the University of Tartu, serving as Research Professor of Cellular Immunology at the Institute of Biomedicine and Translational Medicine. She earned her MD and PhD from the University of Tartu and completed postdoctoral training at Uppsala University, Sweden. Her research focuses on monogenic autoimmunity, self-tolerance, and autoinflammatory disorders. She has contributed to understanding the role of Th17 cytokines in Candida infection protection and type I IFNs in autoimmunity predisposition. |
| 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 |
| A postdoctoral researcher at the University of Helsinki, specialising in inborn and acquired immunodeficiencies. He holds an MSc in Bioinformatics and a PhD in Genomics. His expertise includes TCR repertoire analysis and scRNAseq data for immunological research. Currently, he develops bioinformatics methods and applies machine learning to study immunodeficiencies. |
| Lisa Dratva |
| A final-year PhD student in genomics of immunity under the supervision of Professor Sarah Teichmann at Cambridge University. Her research focuses on constructing a single-cell pan-infection atlas of T cell states and receptors, encompassing multiple viral infections, various tissues, and data from over a thousand donors. The goal is to enhance the understanding of the human immune response to infection and contribute to the development of precision medicine and T cell therapeutics. Originally from Switzerland, she holds a BSc and MSc from EPFL and is eager to explore Estonia for the first time. |
| Juan C. Nieto Sáchica |
| A Senior Postdoctoral Researcher in the Single-Cell Genomics Team at the National Center for Genomic Analysis (CNAG) in Barcelona, Spain. With a strong background in immunology, his expertise lies in interpreting complex biological systems through an immunological perspective. He has vast experience in inflammatory processes, autoimmune disorders, oncology and immunotherapy. |
| Hélène Vantomme |
| Academic Hospital Pharmacist and Postdoctoral Researcher at Sorbonne University. Her research focuses on the T-cell receptor repertoire and selection processes in the thymus. She explores how biological factors, including sex differences, influence early T-cell selection and shape immune responses, potentially contributing to autoimmune disease risk. |
| Martin Pezous |
| PhD student at Sorbonne University studying the T-cell receptor repertoire within the context of immunotherapy development for systemic lupus erythematosus. |
The course is supported by the EU project SysAge
Course fee: 800EUR
Includes:
Study materials
8 days of academic work with lecturers
Certificate of completion (3 ECTS)
4 cultural events in the evenings
Lunch on study days
NB! Transportation and accommodation costs are not included. The course fee does not cover participant's lunch during the summer school.
Please note: This is a preliminary schedule, and the course leaders reserve the right to make changes.
July 27
Arrival
Week 1: Foundations and Practical Tools
July 28: Introduction to AIRR and T Cells
- 9:00–10:00
University Summer School Info Session - 11:00–12:00
Introduction to the Course. - 13:00–14:30
What Are T Cells? Why Study AIRR? (Introduction to T cell subsets [CD4+, CD8+], immune roles, and the significance of diversity). - 14:45–17:00
Introduction to the Computational Environment of the Course.
July 29: Sequencing Protocols and Quality Control
- 09:00–12:00
Session 1: Sequencing Technologies and QC
Tools: FastQC, exploring real-life QC reports.
Task: Analyze sample datasets, identify quality issues. - 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 (e.g., Chao50).
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. - 13:00–16:00
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 DATASET CELIAC DISEASE DATASET, TOOLS GLIPH2, ALICE and REPAN
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
Week 2: Project Work and Synthesis
August 4: Guest Lecture and Independent Projects
- 10:30-12:00 AIRR studies and their application in clinical practice (Guest Lecture)
Lecture and guidance on project topics.
24-second elevator pitches with 1-slide presentations.All Day: Independent or paired project work with instructor support.
August 4-5: Independent Projects
- Morning: Lecture and guidance on project topics.
24-second elevator pitches with 1-slide presentations. - All Day: Independent or paired project work with instructor support.
August 6: Presentations and Wrap-Up
09:00–11:00
Project Presentations11:00–12:00
Group Reflection and Feedback
Final Q&A with instructors and guest speakers.
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
• Analyse 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.
