Introduction to Systems Biology


Meeting times             : Monday 13:30, 14:30, 15:30

Text                            : Uri Alon, “Introduction to Systems Biology: Design Principles of Biological Circuits,” CRC Press, 2006

Instructor                   : Bilge Karaçalı, PhD

Office                          : EEE Building Room K1-32

Phone                         : 6534

E-mail                         :



This course will begin with a broad description of molecular organization of living cells. The signal transduction networks and the regulation of gene transcription will be studied with regards to molecular circuits modeled by kinetic equations. Mathematical aspects of the development of robustness and functionality will be overviewed.



Midterm          20%

Final                30%

Homework      20%

Project             30%


Warnings to prospective students

This class takes on a computational perspective on the interactions between different molecules in living cells. This means:

1- You must be prepared for a series of crash courses on molecular biology throughout the semester.

2- You will be expected to carry out computations on these interactions and perform simulations of the corresponding systems using a mathematical analysis platform such as Matlab®, Octave, R and so on.

3- Taking this class by your part is a statement indicating that you want to learn about systems biology. Hence, if you are looking to graduate as soon as possible with a minimum of effort, you are strongly discouraged from taking it.


General policy on ‘single course exams’

The school policy allows graduating class students to take a last exam on a class that they have failed at the end of the semester. The acting rules for this class are:

1- You must deserve to pass.

2- The greatest grade one can obtain in passing the course through the single course exam procedure can be no better than the worst passing grade of the class in the regular term.


Homework Assignments


Homework 1 (due 16.3.2020)











Week 1: Introduction to cell biology


Week 2: Molecules of life: Genes and proteins


Week 3: Transcription networks


Week 4: Regulation of gene transcription


Week 5: Network motifs in transcription regulation


Week 6: Network motifs in signaling networks


Week 7: Origins of biological robustness


Week 8: Optimal gene circuits


Week 9: Kinetic modeling of biochemical reactions


Week 10: Kinetic modeling of large scale biomolecular networks


Week 11: Integration of regulatory and metabolic networks


Week 12: Graph theoretic analysis of biological networks


Week 13: Biological networks and drug development


Week 14: Overview