Pro-/Seminar: Computational Methods for Spatial Transcriptomics (Winter term 2022/2023)

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
Presentations	March 16 and 17, 2023 (place/time: see below)
Summary submission deadline	March 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

Topics

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

Nr.	Presentation	Topic	Participant
1	Seminar	Spatial Multi-Omic Map of Human Myocardial Infarction	Leen Ajjan Alhadid
2	Proseminar	SpotClean adjusts for spot swapping in spatial transcriptomics data
3	Seminar	Spatial transcriptomics at subspot resolution with BayesSpace	Sili Vettiyara Sunil
4	Seminar	Cell2location Maps Fine-Grained Cell Types in Spatial Transcriptomics	Alaa Bakry
5	Seminar	Deep Learning and Alignment of Spatially Resolved Single-Cell Transcriptomes with Tangram	Ali Hassan
6	Proseminar	SpatialDE: Identification of Spatially Variable Genes
7	Seminar	Statistical Analysis of Spatial Expression Patterns for Spatially Resolved Transcriptomic Studies	Midhuna I. Joseph Maran
8	Seminar	Alignment and integration of spatial transcriptomics data	Amila Beganovic
9	Seminar	Deciphering Spatial Domains from Spatially Resolved Transcriptomics with an Adaptive Graph Attention Auto-Encoder	Tobias Wolff
10	Seminar	Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk	Ritika 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:

Method of the Year: spatially resolved transcriptomics [Technology Feature – short overview and outlook]
Current Best Practices in Single-Cell RNA-Seq Analysis: A Tutorial [Single cell analysis – Many concepts are identical in spatial transcriptomics]
Exploring Tissue Architecture Using Spatial Transcriptomics [Review of spatial transcriptomics analyses]
The expanding vistas of spatial transcriptomics [Another recent review of spatial transcriptomics analyses]
Squidpy: a scalable framework for spatial omics analysis [Commonly used framework – preprocessing, visualization, downstream analyses]
Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution [Benchmark of integration and deconvolution methods, including single-cell to spatial data]