Cellular Programs SS 2025

Information

The course will take place in person only.

Please send an email to Kerstin Gronow-Pudelek if you want to be added to the MS Teams group of the course.

This course can be used as a “Spezialvorlesung der Biowissenschaften/Special-topic Lecture Biosciences”.

Requirements

There are no formal requirements, but solid prior knowledge about the following topics is enocuraged:

• cellular networks
• genetics
• cell biology
• omics technologies

Content

1. biological content
   • circadian rhythms
   • cell cycle
   • cell differentiation/cell reprogramming
   • development of cancer
2. bioinformatics content
   • gene expression analysis
   • DNA methylation analysis
   • time series analysis
   • gene ontology and pathway annotation
   • interaction networks
   • application of clustering techniques
   • construction of gene-regulatory networks

Conditions for Certification

1. There will be n=6 biweekly assignments. Students need to answer questions and write short essays about topics covered in the lecture and in assigned research papers. There are three possible grades: excellent, pass, failed. Students need to get a “pass” grade on at least n-1 assignments or n-3 “pass” and one “excellent” grade.
2. A written final exam of 120 min. will be offered at the end of the semester.
3. Students need to present at least once during the lecture in a group of up to 3 students on the content of an assigned research paper (20 min. presentation and 10 min. discussion).

Certification (Schein)

An averaged score will be computed from the mark of the final exam (counts 2/3) and the graded presentation (counts 1/3). This yields the grade of certification (“Schein”).

Lectures

Lectures take place on Tuesdays from 10:15 am to 11:45 am in building E2.1 room 001. The lecture slides are available in the Microsoft Teams group in the “General” channel under “Files”.

Tutorials

Biweekly, to be announced

Topics for Student Presentations

Here you can find the topics for your presentations:

Circadian Clock

1. Seinkmane et al. (2024) EMBO Journal, 43, 2813-2833. Circadian regulation of macromolecular complex turnover and proteome renewal, DOI:10.1038/s44318-024-00121-5
2. March et al. (2024) Science Advances, 10, eadm9281. Autonomous circadian rhythms in the human hepatocyte regulate hepatic drug metabolism and inflammatory responses, DOI: 10.1126/sciadv.adm9281
3. Hui et al. (2024) EMBO Journal, 43, 5667-5689. O-GlcNAcylation of circadian clock protein Bmal1 impairs cognitive function in diabetic mice, DOI: 10.1038/s44318-024-00263-6
   
   Cell Cycle
4. Choksi et al. (2024) Nature, 630, 214-221. An alternative cell cycle coordinates multiciliated cell differentiation, DOI: s41586-024-07476-z
5. Lam et al. (2024) Nature Genetics, 56, 1938-1952. YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle, DOI: s41588-024-01871-y
6. Fukushima et al. (2024) EMBO Reports, 25, 3300-3323. Cell cycle length governs heterochromatin reprogramming during early development in non-mammalian vertebrates, DOI:10.1038/s44319-024-00188-5
   
   Differentiation / Development
7. Sun et al. (2024) EMBO Journal, 43, 4752-4785. The global phosphorylation landscape of mouse oocytes during meiotic maturation, DOI: 10.1038/s44318-024-00222-1
8. Li et al. (2023) Science, 382. Multifaceted SOX2-chromatin interaction underpins pluripotency progression in early embryos, DOI: 10.1126/science.adi5516
9. Yao et al. (2023) Nature, 624, 317-332. A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain, DOI: s41586-023-06812-z
10. Han et al. (2024) Advanced Sciences, 12, 2406849. Deficiency of FABP7 triggers premature neural differentiation in idiopathic normocephalic autism organoids, DOI: 10.1002/advs.202406849
    
    Cancerogenesis
11. Pillai et al. (2024) Science Advances, 10. Single-cell chemoproteomics identifies metastatic activity signatures in breast cancer, DOI: 10.1126/sciadv.adp2622
12. Gardner et al. (2024) Science, 383. Lineage-specific intolerance to oncogenic drivers restricts histological transformation, DOI: 10.1126/science.adj1415