Cellular Programs WS 26/27

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 three mini-tests, and students must achieve at least half of the points from the three mini tests to be eligible to take the final exam. The tests will take place on Nov. 5, Nov. 26, and Dec. 17, 12:30 – 13:30, in E2 2 (Günter Hotz lecture hall).
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

Circadian Rhythms:

1. Yan et al. (2025) Science Advances, 11. TOC1 phosphorylation disproportionally enhances chromatin binding at rhythmic gene promoters, doi:10.1126/sciadv.adx7804
2. Zhao et al. (2026) Cell, 189, p2007-2023.e20. Restoring circadian rhythms in the hypothalamic paraventricular nucleus reverses aging biomarkers and extends lifespan in male mice, doi:10.1016/j.cell.2026.01.016
3. Zhu et al. (2025) Science Advances, 11. Immunomodulatory role of the stem cell circadian clock in muscle repair, doi:10.1126/sciadv.adq8538
   
   Cell Cycle:
4. Forey et al. (2025) Cell Genomics, 5, 100923. Evolutionarily recent transcription factors partake in human cell cycle regulation, doi: 10.1016/j.xgen.2025.100923
5. Chen et al. (2026) Journal of Advanced Research, 82.367-379. Bombyx mori Jun gene is involved in endoreplication of silk gland cells by regulating S-phase cell cycle genes, doi: 10.1016/j.jare.2025.07.029.
6. Niño et al. (2026) Cancer Cell, 1, 166-186.e16. Tumor-infiltrating bacteria disrupt cancer epithelial cell interactions and induce cell-cycle arrest, doi:10.1016/j.ccell.2025.09.010
7. Nie et al. (2025) Advanced Science, 12, e05823. Mitigating cell cycle effects in multi-omics data: solutions and analytical frameworks, doi:10.1002/advs.202505823
   
   Differentiation:
8. Colgan et al. (2026) Cell (in press). Comprehensive lineage tracing maps the landscape of cell fate decisions in mouse embryogenesis, doi:10.1016/j.cell.2026.09.050; see also: https://www.science.org/content/article/two-teams-map-development-mammal-embryos-cell-cell?utm_source=sfmc&utm_medium=email&utm_content=alert&utm_campaign=WeeklyLatestNews&et_rid=41139936&et_cid=6092690
9. Ayushman et al. (2025) Nature, 24, 312–322. Cell tumbling enhances stem cell differentiation in hydrogels via nuclear mechanotransduction, doi:10.1038/s41563-024-02038-0
10. Lu et al. (2026) Advanced Science, 13, e76329. Single-cell and spatial transcriptomics unveil key regulators governing cell differentiation for Schistosoma japonicum sexual development, doi:10.1002/advs.76329
    
    Cancerogenesis:
11. Lee et al. (2026) Nature, 653, 1184–1195. Androgen loss accelerates brain tumour growth via HPA axis activation, doi:10.1038/s41586-026-10451-5
12. Sahin et al. (2026) Nature, 651, pages 1088–1096. Individualized mRNA vaccines evoke durable T cell immunity in adjuvant TNBC, doi:10.1038/s41586-025-10004-2
13. Lai et al. (2025) The EMBO Journal, 44, 5860-5889. Resistance to CDK7 inhibitors directed by acquired mutation of a conserved residue in cancer cells, doi:10.1038/s44318-025-00554-6