**EE430**

**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** :
bilgekaracali@iyte.edu.tr

**Summary**

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.

**Grading **

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)

**Tests**

**Material**

**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 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**