From this course the student will know how to do exact stochastic simulations, delayed stochastic simulations, and how to create models of delayed stochastic gene regulatory networks. Students will become familiar with detailed models and experimental results related to single gene expression and its underlying mechanisms. Also, the student will be introduced to basic concepts of cell type and cell differentiation and learn the latest modeling techniques in these topics.
a) Exercises (Must complete 50% of exercise points. 80% provides a bonus).
b) Final exam (50% of the final grade).
c) Project work (50% of the final grade).
| (Peruttu) SGN-52406 Models of Gene Networks/E/01 |
Fri 02.09.2016 |
12:00 - 14:00 |
| (Peruttu) SGN-52406 Models of Gene Networks/E/01 |
Fri 09.09.2016 |
12:00 - 14:00 |
| SGN-52406 Models of Gene Networks/E/01 (*) |
Mon 12.09.2016 |
10:00 - 12:00 |
| (Peruttu) SGN-52406 Models of Gene Networks/E/01 |
Fri 16.09.2016 |
12:00 - 14:00 |
| SGN-52406 Models of Gene Networks/E/01 (*) |
Mon 19.09.2016 |
10:00 - 12:00 |
| (Peruttu) SGN-52406 Models of Gene Networks/E/01 |
Fri 23.09.2016 |
12:00 - 14:00 |
| SGN-52406 Models of Gene Networks/E/01 (*) |
Mon 26.09.2016 |
10:00 - 12:00 |
| (Peruttu) SGN-52406 Models of Gene Networks/E/01 |
Fri 30.09.2016 |
12:00 - 14:00 |
| SGN-52406 Models of Gene Networks/E/01 (*) |
Mon 03.10.2016 |
10:00 - 12:00 |
| (Peruttu) SGN-52406 Models of Gene Networks/E/01 |
Fri 07.10.2016 |
12:00 - 14:00 |
| SGN-52406 Models of Gene Networks/E/01 (*) |
Mon 10.10.2016 |
10:00 - 12:00 |
| (Peruttu) SGN-52406 Models of Gene Networks/E/01 |
Fri 14.10.2016 |
12:00 - 14:00 |
| Type |
Name |
Author |
ISBN |
Additional information |
Language |
Examination material |
| Journal |
A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics |
Andre S. Ribeiro, R. Zhu, S. A. Kauffman |
|
Andre S. Ribeiro, R. Zhu, S. A. Kauffman, A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics, Journal of Computational Biology, Vol. 13 (9), 1630-1639, 2006. |
English |
Yes |
| Journal |
A general method for numerically simulating the stochastic time evolution of coupled chemical reactions |
Gillespie, D. T. |
|
Gillespie, D. T., A general method for numerically simulating the stochastic time evolution of coupled chemical reactions, J. Comput. Phys., 22, 1976, 403-434. |
English |
No |
| Journal |
Exact stochastic simulation of coupled chemical reactions |
Gillespie, D. T. |
|
Gillespie, D. T., Exact stochastic simulation of coupled chemical reactions, J. Phys. Chem., 81, 1977, 2340-2361 |
English |
Yes |
| Journal |
Modeling and Simulation of Genetic Regulatory Systems: A Literature Review |
Hidde de Jong |
|
Hidde de Jong, Modeling and Simulation of Genetic Regulatory Systems: A Literature Review, Journal of Computational Biology. 2002, 9(1): 67-103. |
English |
No |
| Journal |
Noisy Attractors and Ergodic Sets in Models of Genetic Regulatory Networks |
Andre S. Ribeiro, S. A. Kauffman |
|
Andre S. Ribeiro, S. A. Kauffman, Noisy Attractors and Ergodic Sets in Models of Genetic Regulatory Networks, J. of Theoretical Bio., 247, Issue 4, 2007, Pgs 743-755 |
English |
No |
| Journal |
SGNSim a stochastic gene network simulator |
Andre S. Ribeiro and Jason Lloyd-Price |
|
Bioinformatics |
English |
No |
| Journal |
Studying genetic regulatory networks at the molecular level: Delayed reaction stochastic models |
Rui Zhu, Andre S. Ribeiro, Dennis Salahub, and Stuart A. Kauffman |
|
Rui Zhu, Andre S. Ribeiro, Dennis Salahub, and Stuart A. Kauffman, "Studying genetic regulatory networks at the molecular level: Delayed reaction stochastic models", Journal of Theoretical Biology, 246(4):725-45, 2007. |
English |
Yes |
| Other literature |
A Model of Genetic Networks with Delayed Stochastic Dynamics |
Andre S. Ribeiro |
|
Andre S. Ribeiro, A Model of Genetic Networks with Delayed Stochastic Dynamics, in Analysis of Microarray Data: Network based Approaches, Wiley, Matthias Dehmer and Frank Emmert-Streib (Editors), 2007. |
English |
Yes |
