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Issues with Registrations

Written on 06.11.25 by Friederike Grandke

Dear students,

Due to a technical issue in the registration system, some registrations were not captured correctly.
If you had already registered for the seminar and selected a topic, but your registration was removed from the course, please send us an email by tomorrow with your name and chosen… Read more

Dear students,

Registrations are closed

Written on 06.11.25 by Friederike Grandke

The registration period has now ended. As announced, we will remove all students from the course who did not select at least one topic. Everyone else will receive an email with the final decision within the next few days.

Seminar Registration Now Open

Written on 20.10.25 by Friederike Grandke

Seminar registration is now open. Please remember that you need to register twice: once for the seminar itself and once for the seminar topics. Both can be accessed under Registration.

Students who are not registered for at least one topic by the end of the registration period will not be… Read more

Students who are not registered for at least one topic by the end of the registration period will not be considered for a place in the seminar.

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
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%
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
9	RNA velocity	Generalizing RNA velocity to transient cell states through dynamical modeling	Proseminar
10	Enhancer and GRN inference	SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks	Seminar

Questions to answer in your presentation (if applicable)

- What core concepts and prior work does a newcomer need to understand this topic, and why does it matter for systems immunology?
- 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?