Single-cell Omics for Systems Immunology

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)	TBD
Deliverable 1: Summary of the assigned paper	TBD
Deadline to (de-)register in HISPOS OR de-register from seminar * [mandatory]	TBD
Deadline for slide feedback (Further information can be found below)	TBD
Deliverable 2: Final Slides	Day before Session 2 (until 23:59)
Session 2 (Presentations, mandatory)	TBD
Deliverable 3: Feedback for the assigned talks	Day after Session 2 (until 23:59)
Session 3 (Critique & rebuttal, mandatory)	TBD

*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

TBD