This is a block Pro-/Seminar for Bioinformatics students.

Overview: Spatial Transcriptomics describes methods that capture RNA transcripts at near single-cell resolution while preserving the spatial context of the cells. Named Method of the Year 2021 by Nature, the field has seen a growing number of computational tools to analyze spatial patterns of genes and the distribution and interaction of different cell types. This allows to characterize complex and heterogeneous microenvironments like developing organs and tissue diseases with much more insight than using single-cell sequencing alone. We will focus on analyzing in situ capturing based assays that provide an unbiased detection of transcripts without prior knowledge.

The current seminar is designed to provide students with a varied overview of Bioinformatics methods for the analysis of spatial transcriptomics data as well as some applications that highlight its usefulness in biomedical research.

Depending on the current pandemic situation, we will try to have the presentations in presence. If it is not possible, we will do remote meetings via Microsoft Teams conferences instead of personal meetings.

Tutors: Dr. Fabian Kern, M. Sc. Jérémy Amand
Key Dates

Registration *from November 7 to November 20, 2022 HERE
Kick-off meeting [mandatory]November 29, 2022 – 10:15 am (Download slides)
Deadline to (de-)register in HISPOS OR de-register from seminar *December 20, 2022
Deadline for feedback ** [optional]March 2, 2023
PresentationsMarch 16 and 17, 2023 (place/time: see below)
Summary submission deadlineMarch 24, 2023
* If you want to de-register from the seminar, please send the tutor an email irrespectively whether you (de)registered in HISPOS or not.

**If you would like to get feedback about your slides, e.g. to improve your presentation before the talk, send your slides to the tutor before the feedback deadline. We strongly encourage you to take this opportunity. When asking for feedback the more complete the submitted presentation the more helpful our feedback can be. Thus, try to avoid submitting half-finished slides. Feedback will be provided at least once but at most twice per participant. Also, before sending in the slides, check out our support materials (presentation guidelines, presentation guidelines checklist).

Please note: Your slides will make up a substantial part of the final grade. Reading and paying attention to the provided presentation guidelines will help you to get an impression of which aspects are relevant for the evaluation. Disregarding many of the points listed in the guidelines may negatively affect your grade.

Place and Time for Presentations (Bioinformatics)

  • E2 1, R206, time TBA

Requirements for participation

  • Proseminar: at least in 3rd semester, Bioinformatics I
  • Seminar: no pre-requisites.

Participation in a lecture similar to Single Cell Bioinformatics can be helpful but is not a pre-requisite.
Good language skills are presumed as all talks will be held in English.

Certificate requirements

  • Successful presentation:
    • Talk: 30 minutes for a Pro-seminar and 40 minutes for a Seminar
    • Discussion: 5 minutes during which you should be able to answer questions from the tutor(s)/audience
  • Attendance to all presentations is mandatory
  • Submitting a summary (may have an impact on the final grade):
    • Short description of the presented topic(s)
    • Ca. 2 pages of text, excluding title (page), references, figures, tables etc.
    • Main structure: title page, main text (with or without subsections), references
    • It is recommended to write the report using LaTeX in order to train scientific writing

Final grade

  • Primarily based on the given presentation, slides & follow-up discussion
  • Might be influenced by the quality of the submitted summary report


All manuscript files are either open-access or available via the university network using a secure VPN connection.

1SeminarSpatial Multi-Omic Map of Human Myocardial InfarctionLeen Ajjan Alhadid
2ProseminarSpotClean adjusts for spot swapping in spatial transcriptomics data
3SeminarSpatial transcriptomics at subspot resolution with BayesSpaceSili Vettiyara Sunil
4SeminarCell2location Maps Fine-Grained Cell Types in Spatial TranscriptomicsAlaa Bakry
5SeminarDeep Learning and Alignment of Spatially Resolved Single-Cell Transcriptomes with TangramAli Hassan
6ProseminarSpatialDE: Identification of Spatially Variable Genes
7SeminarStatistical Analysis of Spatial Expression Patterns for Spatially Resolved Transcriptomic StudiesMidhuna I. Joseph Maran
8SeminarAlignment and integration of spatial transcriptomics dataAmila Beganovic
9SeminarDeciphering Spatial Domains from Spatially Resolved Transcriptomics with an Adaptive Graph Attention Auto-EncoderTobias Wolff
10SeminarKnowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalkRitika Bansal

Recommended readings

Students who either have a shallow understanding on the topic and / or want to prepare for the course should consider reading the following papers: