SubjectsSubjects(version: 949)
Course, academic year 2023/2024
Systems Biology - AP143002
Title: Systems Biology
Guaranteed by: Department of Informatics and Chemistry (143)
Faculty: Faculty of Chemical Technology
Actual: from 2019
Semester: both
Points: 0
E-Credits: 0
Examination process:
Hours per week, examination: 3/0, other [HT]
Capacity: winter:unlimited / unknown (unknown)
summer:unknown / unknown (unknown)
Min. number of students: unlimited
Language: English
Teaching methods: full-time
Teaching methods: full-time
For type: doctoral
Note: course is intended for doctoral students only
can be fulfilled in the future
you can enroll for the course in winter and in summer semester
Guarantor: Kolář Michal Mgr. Ph.D.
Interchangeability : N143048, P143002
Annotation -
Last update: Pátková Vlasta (08.06.2018)
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.
Aim of the course -
Last update: Pátková Vlasta (08.06.2018)

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
Literature -
Last update: Pátková Vlasta (08.06.2018)

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

Learning resources -
Last update: Pátková Vlasta (08.06.2018)


Syllabus -
Last update: Pátková Vlasta (08.06.2018)

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.

Registration requirements -
Last update: Pátková Vlasta (08.06.2018)

Biochemistry, Molecular genetics

Course completion requirements -
Last update: Pátková Vlasta (08.06.2018)

Oral exam