Course Details for A.Y. 2017/2018

The information on this page refer to the academic year 2017/2018. Therefore, several links are not available and data may be incomplete. To read the current information on the course, if it is still available, go to the university course catalogue . To read information relating other academic years, use the list at the bottom of this page.

A. Year:

2017/2018

Name:

Systems Biology / Systems biology

Type:

Course

Basic information

Code:

I0549

Sector:

ING-INF/04

Credits:

: Master Degree in Mathematical Engineering 6 CFU (b)

Term:

1^st semester

Degree(s):

Master Degree in Mathematical Engineering 1^st anno curriculum Comune Compulsory

Language:

English

Teacher(s):

Pasquale Palumbo

Course Objectives

Systems biology is an emerging research area, which aims to provide mathematical models helping to understand the dynamic interactions occurring within and between cells. This course gives the mathematical tools to model and analyze gene transcription networks as well as signal transduction and metabolic networks: most important network motifs are investigated and data-based identification algorithms are also provided.

Course Content

Transcription networks. The rules of transcription: promoters and transcriptor factors, activators and repressors. Graph properties of a transcription network: in/out degree distribution, clustering coeffcients and modularity, scale-free distributions and hubs. ODE approach: modeling the clearance and production rate, Hill functions and logic input functions, dynamics of gene regulation. Network motifs emerging by comparison to randomized networks: negative/positive autoregulation, coherent/incoherent Feed-Forward Loops (FFL), Single-Input-Modules (SIM), Multi-Output Feed-Forward Loops (MO-FFL), bi-fan, diamonds, Dense-Overlapping-Regulons (DOR). Possible functions of network motifs in transcription networks: speed up of the response time, increase robustness, produce oscillations, introduce sign-sensitive delays, generate pulses or temporal programs of expression. Biological examples from the E. Coli: the arabinose system, the lactose system, the galactose system; temporal programs and assembly steps of the flagella motor.
Mathematical tools to identify gene networks. State observers for linear and nonlinear systems. The Ackerman formula. Asymptotic observers: the Luenberger observer. Applications to gene transcription networks: a case study on the FFL.
Growth and cell cycle models. Models of the cell growth: the case of eukaryotic cells. Cell cycle models: balanced exponential growth. Modelling the cell cycle of the budding yeast Saccharomyces cerevisiae: asymmetrical division. Age and protein distribution functions for daughter and parent cells.

Assessment Methods and Criteria

A case study on a scientific paper + Oral exams

Textbooks

Uri Alon, An introduction to systems biology: design principles of biological circuits , Chapman & Hall/CRC, Taylor & Francis Group. 2007.

Notes

Si veda anche la pagina sul vecchio sito di ingegneria: http://www.ing.univaq.it/cdl/scheda_corso.php?codice=I2W031

Course page updates

This course page is available (with possible updates) also for the following academic years:

To read the current information on this course, if it is still available, go to the university course catalogue .

Course information last updated on: 10 maggio 2016, 17:11