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Single-cell Omics for Systems Immunology
This is a block Seminar for Bioinformatics Bachelor and Master students.
Overview
Systems Immunology links cell-resolved measurements to immune function across tissues and time. We focus on single-cell omics (scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics) and how they reveal immune states, clonality, cell–cell communication, niches, and clinical response. We read and discuss recent papers that apply robust analysis and ML/AI tools (e.g., label transfer, scVI/totalVI, spatial deconvolution, perturbation modeling), always asking: What’s the biological claim? What supports it? What are the limits?
Participation requirements
Proseminar (Bachelor)
- Only Bachelor students • 5 ECTS
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Prerequisites: ≥ 3rd semester; Bioinformatics I & II passed
Seminar (Master)
- Master students • 7 ECTS
- Prerequisites: Basic knowledge in machine learning required
Good command of English is expected; all talks are in English.
Key dates
| Registration | From October 20 to November 5, 2025 in the CMS system |
| Topic selection | From October 20 to November 5, 2025 in the CMS system |
| Session 1 (Kick-off, mandatory) | November 17, 2025, 10am |
| Deliverable 1: Summary of the assigned paper | January 7, 2026 |
| Deadline to (de-)register in HISPOS OR de-register from seminar * [mandatory] | January 12, 2026 |
| Deadline for slide feedback (Further information can be found below) | February 13, 2026 |
| Deliverable 2: Final Slides | Day before Session 2 (until 23:59) |
| Session 2 (Presentations, mandatory) | March 2 and March 3, 2026 |
| Deliverable 3: Feedback for the assigned talks | Day after Session 2 (until 23:59) |
| Session 3 (Critique & rebuttal, mandatory) | March 9, 2026 |
*To de-register, email the tutor even if you (de)registered in HISPOS.
Certificate requirements:
- Session 1: Kick-off Meeting
- Topic distribution and Seminar requirements
- Do's and don'ts of a successful Presentation
- Deliverable 1: Summary of the assigned paper
- Approx. 1 page of text excluding title (page), section titles and the references
- Main structure: Title (page), 3 key messages, main text (5-7 subsections), references
- Figures, tables and formulas are not required and only accepted if they have been created completely by yourself
- Deliverable 2: Final Slides
- Hand in your final slides (as PDF) one day before the presentation session
- Check and hand in a digital copy of the completed guidelines checklist
- Session 2: Presentation session
- Talk: 30 minutes for a Proseminar and 40 minutes for a Seminar
- Discussion: 10 minutes during which you should be able to answer questions from the tutor(s)/audience
- Each talk will have two assigned Discussants that are required to ask questions and fill out a feedback form
- Deliverable 3: Feedback for the assigned talks
- Feedback to the talk: 3 strengths; 3 prioritized improvements
- "Peer review" of the paper: 2 method critiques
- Session 3: Critique & rebuttal
- Presentation of a short rebuttal (address one revised slide and one clarified/improved method)
- Group discussion and overall feedback
Please be advised that the utilization of language models, including but not limited to ChatGPT, for the creation of slides and/or textual content is strictly prohibited. All suspected instances will be subject to a personal interview to investigate the matter further.
Grading
- Slides + Talk — 70%
- One-pager — 15%
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Peer review — 15%
Your slides weigh heavily in the grade. Use the presentation guidelines and checklist.
Slides & feedback
We offer feedback on near-final PDFs submitted by the Slides upload deadline (at least one round; two if requested before the deadline).
Registration & topic assignment
After course registration in CMS, register for specific topics (multiple selections allowed) during the topic-selection window. After the deadline, topics will be auto-assigned; selected students receive a kick-off invite, others a rejection email. All papers are open-access or available via campus/VPN.
Topics
| Nr. | Topic | Literature | Type |
| 1 | Cell-type annotation | Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage | Proseminar |
| 2 | Immune states and cell states in GEX data | Precise identification of cell states altered in disease using healthy single-cell references | Proseminar |
| 3 | Cell-cell communication | Inference and analysis of cell-cell communication using CellChat | Proseminar |
| 4 | TCR/BCR repertoire | scRepertoire: An R-based toolkit for single-cell immune receptor analysis | Seminar |
| 5 | CITE-seq | Simultaneous epitope and transcriptome measurement in single cells | Seminar |
| 6 | Deconvolution | Whole genome deconvolution unveils Alzheimer’s resilient epigenetic signature | Seminar |
| 7 | Data integration | Integrating DNA methylation and gene expression data in a single gene network using the iNETgrate package | Seminar |
| 8 | Perturb-seq | Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens | Seminar |
Questions to answer in your presentation (if applicable)
- What exact task or hypothesis are you addressing (inputs → outputs), and what would count as “success”?
- How does the method work end-to-end (major steps, data flow), and what are the key assumptions?
- Which core equations or probabilistic assumptions define the method, and what’s the intuitive story behind them?
- Which datasets/cohorts (n cells, donors, conditions) were use, and how were they split (train/val/test or discovery/validation) to avoid leakage?
- Which metrics are appropriate here, why, and what do they show?
- What are the main limitations of the method/data (theoretical, computational, or experimental), and how do they affect conclusions?
- Which two are most relevant here (e.g., batch effects, class imbalance, donor confounding, clonal expansion, ambient RNA/ADT), how to diagnose them, and how to mitigate them?
- What concrete improvements or validations would you do next to strengthen the claim?