CSC 7991 - Advanced Topics in Computer Science: Bioinformatics II
Winter 2012 Mon/Wed 13:00-14:20 Room 0318 State Hall
Instructor: Hamidreza Chitsaz
Office Hours: Mon 11:00-12:00, Wed 15:00-16:00

Course announcement



Lecture 1: Introduction to modeling biological systems

Lecture 2: Biochemical reaction networks

Lecture 3: Thermodynamics of biochemical reactions at equilibrium

Lecture 4: Introduction to control theory in systems biology

Lecture 5: Lyapunov stability theory

Lecture 6: Optimal control in systems biology, Part I: Pontryagin Maximum Principle

Lecture 7: Optimal control in systems biology, Part II: Hamilton-Jacobi-Bellman Equation

Lecture 8: Linear Quadratic Regulator (LQR)


Papers to present (to be announced)


  1. Terzer M, Maynard ND, Covert MW, Stelling J, Genome-scale metabolic networks. Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 2009. 1(3): 285 - 297.

  2. Roger Brockett, Dynamical systems that sort lists, diagonalize matrices and solve linear programming problems. Linear Algebra and its Applications. 1991. 146: 79-91.

  3. Sean M. Cory, Theodore J. Perkins, Implementing Arithmetic and Other Analytic Operations By Transcriptional Regulation. PLoS Computational Biology. 2008. 4(5): e1000064. doi:10.1371/journal.pcbi.1000064.

  4. Carl Song et al., Estimating the Stochastic Bifurcation Structure of Cellular Networks. PLoS Computational Biology. 2010. 6(3): e1000699. doi:10.1371/journal.pcbi.1000699.

  5. Daniel G. Gibson et al., Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science. 2010. Vol. 329 no. 5987 pp. 52-56. doi:10.1126/science.1190719.

  6. Jiguo Cao and Hongyu Zhao, Estimating Dynamic Models for Gene Regulation Networks. Bioinformatics. 2008. 24 (14): 1619-1624. doi:10.1093/bioinformatics/btn246.

  7. Chris P. Barnes et al., Bayesian design of synthetic biological systems. PNAS. 2011, doi:10.1073/pnas.1017972108

  8. Michael W Sneddon, James R Faeder, Thierry Emonet, Efficient modeling, simulation and coarse-graining of biological complexity with NFsim. Nature Methods. 2011. 8: 177-183. doi:10.1038/nmeth.1546.

  9. Jeffrey Tabor et al., A Synthetic Genetic Edge Detection Program. Cell. 2009. doi:10.1016/j.cell.2009.04.048.

  10. Keller Rinaudo et al., A universal RNAi-based logic evaluator that operates in mammalian cells. Nature Biotechnology. 2007. 25: 795 - 801. doi:10.1038/nbt1307.

  11. Ari E. Friedland et al., Synthetic Gene Networks That Count. Science. 2009. Vol. 324 no. 5931 pp. 1199-1202. doi:10.1126/science.1172005.

  12. Peng Jiang et al., Load-Induced Modulation of Signal Transduction Networks. Science Signal. 2011. Vol. 4, Issue 194, p. ra67. doi:10.1126/scisignal.2002152.

  13. Cooper, Nicholas, Belta, Calin, Julius, A. Agung, Genetic regulatory network identification using multivariate monotone functions. IEEE CDC. 2011. pp 2208 - 2213. doi:10.1109/CDC.2011.6161460.

  14. Priscilla E. M. Purnick, Ron Weiss, The second wave of synthetic biology: from modules to systems Nature Reviews Mol. Cell. Bio., 10, 410-422 (June 2009) doi:10.1038/nrm2698

  15. J.M. Buescher et al., Global Network Reorganization During Dynamic Adaptations of Bacillus subtilis Metabolism Science, March 2012, Vol. 335 no. 6072 pp. 1099-1103, doi: 10.1126/science.1206871



Projects

iGEM



Recommended Books

  1. Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Systems biology: a textbook. Wiley-VCH, 2009

  2. Pablo A. Iglesias and Brian P. Ingalls, Control Theory and Systems Biology. MIT Press, 2009

  3. Bernhard Palsson, Systems Biology : Simulation of Dynamic Network States. Cambridge University Press, 2011