Goals:

  1. Understanding of basics of how a biological system works at molecular level
  2. Enable students to browse current literature and gain exposure to research in this field
  3. Familiarise with main topics using available Sumilation Tools

Textbook:

  • 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

Pre-requisite:

  • Probability and Statistics, Signals and Systems

Syllabus:

  1. Introduction and Applications in Synthetic Biology
  2. Brief review of Cell Biology and Quantitative Biochemistry
  3. Gene Expression Modeling
  4. Autoregulation, Feedback and Bistability
  5. Feed-forward loop Network Motifs
  6. Graph Properties of Transcription Networks
  7. Temporal Programs
  8. Stability Analysis in the Synthetic Toggle Switch
  9. How to turn genes into oscillators?
  10. Cell Signaling Networks
  11. Robustness and Bacterial Chemotaxis
  12. Robustness in Development, Pattern Formation and DNA Proofreading Optimal Gene Circuit Design
  13. Introduction to Stochastic Gene Expression
  14. Synthetic Biology: Current Status and Key Challenges

Grade Distribution (Tentative):

  •   Final 35%
  •   Midterm 25%
  •   Quiz and HW 15-25%
  •   Project 15-25%

Homework:

Course Handouts: By Amitis Shidani

To be uploaded.

Projects:

  • 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.