SubjectsSubjects(version: 954)
Course, academic year 2023/2024
Systems Biology - P143002
Title: Systémová biologie
Guaranteed by: Department of Informatics and Chemistry (143)
Faculty: Faculty of Chemical Technology
Actual: from 2023
Semester: winter
Points: winter s.:0
E-Credits: winter s.:0
Examination process: winter s.:
Hours per week, examination: winter s.:3/0, other [HT]
Capacity: unlimited / unknown (unknown)
Min. number of students: unlimited
State of the course: taught
Language: Czech
Teaching methods: full-time
Teaching methods: full-time
Note: course is intended for doctoral students only
can be fulfilled in the future
Guarantor: Kolář Michal Mgr. Ph.D.
Is interchangeable with: AP143002
Annotation -
This is an introductory course of systems biology. We will focus on the structure of regulatory networks, their global properties and enrichment of regulatory motifs. We will study commonly repeating motifs, and will explain their function and reason for their evolutionary conservation.
Last update: Kubová Petra (11.04.2018)
Aim of the course -

Students will be able to:

  • characterize biological regulatory networks and their network motifs
  • describe biological causes of the enrichment of individual network motifs (e.g., autoregulatory motifs, feed-forward loops)
  • mathematically describe important regulatory motifs and discuss their robustness and optimality
Last update: Kubová Petra (11.04.2018)
Literature -

R: Alon U, An introduction to systems biology. Design principles of biological circuits, Chapman & Hall/CRC 2007, ISBN: 978-1584886426

R: Klipp E, Liebermeister W, Wierling C, Kowald A, Lehrach H, Herwig R, Systems Biology: A textbook, Wiley-VCH Verlag 2009, 978-3527318742

Last update: Kubová Petra (11.04.2018)
Learning resources -


Last update: Kubová Petra (11.04.2018)
Syllabus -

1. How cells perceive a world. Regulatory networks.

2. Transcription networks and their properties. Network motifs.

3. Autoregulation: SOS DNA repair system in E. coli.

4. Coherent feed-forward loop: protection against random fluctuations. Arabinosis system in E. coli.

5. Noncoherent feed-forward loop: quick response to the environment change. Galactosis system in E. coli.

6. Regulatory networks in embryonal development: bistable switch. Sonic Hedgehog and the limb development in vertebrae.

7. Neural networks: multilayer perceptron in C. elegans.

8. Other network motifs and global structure of regulatory networks. Project assignment.

9. Robustness of protein circuits: chemotaxion in E. coli.

10. Robustness in embryonal development: body segmentation in D. melanogaster.

11. Kinetic proofreading: antigenu T recognition by the cell.

12. Optimality of gene circuits, relationship with a biological fitness: LacZ protein in E. coli.

13. Optimality of gene circuits, rule of the demand.

14. Project presentations.

Last update: Kubová Petra (11.04.2018)
Registration requirements -

Biochemistry, Molecular genetics

Last update: Kubová Petra (11.04.2018)
Course completion requirements -

Oral exam

Last update: Svozil Daniel (23.05.2018)