Seminar: Regulatory Networks
58307308 Seminar: Regulatory Networks (3 cr, 2 cu)Instructors: Teemu Kivioja, Professor Juho Rousu
Time and place: 07.09-12.10 Friday 12-14 C220, 02.11-07.12 Friday 12-14 C220
Note! We will start the seminar at 12.30 on November 9. The following two sessions will also start at 12.30 unless this is not suitable for some participants.
Note 1: I will sent the seminar reports by email. If you have not received them, please send me an email. Teemu
Note 2: Format your reports according the general format (cover etc.) used on the Scientifc Writing course, example layout
A cell of a living organism has be able to respond to diverse changes in its environment such as rise in temperature, lack of nutrients, or signals from other cells. Cells do complex information processing to integrate the different signals (input) to an internal description of the environment (state) and to produce appropriate response (output). This control system is implemented by networks of interacting genes and proteins. The aim of the seminar is to understand how these fascinating biological circuits emerge from the interactions of the individual components.
The seminar will be based on a new book by Uri Alon:
An
Introduction to Systems Biology: Design Principles of Biological
Circuits.
Original research articles will be used as
additional material. The emphasis will be on understanding general
principles using simplified mathematical models on the level that
hopefully is useful for anyone interested in bioinformatics and
systems biology. The goal is neither to understand any particular
biological system in detail nor to go deep into theory of
dynamical systems.
Schedule
Sept. 14 and Sept 21, no meeting, office hour 13-14 at B218
2 Basic concepts of transcription networks, Sept. 28, Cheng Lu
3 Negative autoregulation: A network motif, Oct. 5, Sari Bombino
4.1 - 4.6 The feed-forward loop network motif, Oct. 12, Jaakko Juvonen
7 Robustness of Protein circuits: The example of bacterial chemotaxis, Nov. 2, Lauri Lyly
6.1 - 6.4 Network motifs in developmental and signal transduction networks, Nov. 9, Vera Mönter
8 Robust patterning in development, Nov. 16, Sirkku Karinen
9 Kinetic Proofreading, Nov. 23, Thekla Hemstedt
10 Optimal gene circuit design, Nov. 30, Sanna Sipilä
5 or 11, Dec 7, Xuan Hung Ta
Prerequisites
The course Introduction to bioinformatics or equivalent background knowledge of the topic.
Teemu J Kivioja Last modified: Wed May 2 15:33:26 EEST 2007