- Understanding of basics of how a biological system works at molecular level
- Enable students to browse current literature and gain exposure to research in this field
- Familiarise with main topics using available Sumilation Tools
- Alon, U. An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman and Hall / CRC, 2006Additional References:
- Strogatz, Steven H. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering. Westview Press, 2014.
- Alberts, B., et al. Essential Cell Biology. 3rd ed. Garland Science, 2009
- Probability and Statistics, Signals and Systems
- Introduction and Applications in Synthetic Biology
- Brief review of Cell Biology and Quantitative Biochemistry
- Gene Expression Modeling
- Autoregulation, Feedback and Bistability
- Feed-forward loop Network Motifs
- Graph Properties of Transcription Networks
- Temporal Programs
- Stability Analysis in the Synthetic Toggle Switch
- How to turn genes into oscillators?
- Cell Signaling Networks
- Robustness and Bacterial Chemotaxis
- Robustness in Development, Pattern Formation and DNA Proofreading Optimal Gene Circuit Design
- Introduction to Stochastic Gene Expression
- Synthetic Biology: Current Status and Key Challenges
Grade Distribution (Tentative):
- Final 35%
- Midterm 25%
- Quiz and HW 15-25%
- Project 15-25%
Course Handouts: By Amitis Shidani
To be uploaded.
- Students: Naghmeh Sadat Nazer, Kamyar Akbar, Menua Keshishian
- Topic: Cancer Systems Biology
- Paper 1: Werner, Henrica MJ, Gordon B. Mills, and Prahlad T. Ram. “Cancer systems biology: a peek into the future of patient care?.” Nature reviews clinical oncology 11.3 (2014): 167-176
- Students: Behrooz Tahmasebi, Maliheh Mahlooji, Masoumeh Sadat Hosseini
- Topic: Evolutionary Systems Biology
- Paper 1: Soyer, Orkun S., and Maureen A. O’Malley. “Evolutionary systems biology: what it is and why it matters.” Bioessays 35.8 (2013): 696-705.
- Students: Arash Asghari, Ali Mohammad Mehr, Mojtaba Nikahd
- Topic: Analog Computing with cells
- Paper 1: Daniel, Ramiz, et al. “Synthetic analog computation in living cells.” Nature 497.7451 (2013): 619-623.
- Students: Seyed Amir Hossein Saberi, Damoon Nashtaali, Parsa Moradi, Seyed Navid Madani
- Topic: Optimal Circuit Design
- Paper 1:
- Students: Elaheh Vedadi, Hosein Fouladi, Amitis shidani
- Topic: Stochastic Modeling of dynamical systems
- Paper 1: Wilkinson, Darren J. “Stochastic modelling for quantitative description of heterogeneous biological systems.” Nature Reviews Genetics 10.2 (2009): 122-133.
- Paper 2: Lei, Jinzhi. “Stochastic modeling in systems biology.” J. Adv. Math. Appl 1.1 (2012): 76-88.
- Students: Mobin Asri, Hirad Aalipanah, Sina Al Ahmad
- Topic: Personalised medicine and systems biology
- Paper 1: Gonzalez-Angulo, Ana Maria, Bryan TJ Hennessy, and Gordon B. Mills. “Future of personalized medicine in oncology: a systems biology approach.” Journal of Clinical Oncology 28.16 (2010): 2777-2783.
- Students: Milad Kazemi, Mobina Kazemi
- Topic: Biological Networks
- Paper 1: Liu, Yang-Yu, Jean-Jacques Slotine, and Albert-László Barabási. “Controllability of complex networks.” Nature 473.7346 (2011): 167-173.