STOCHASTIC SYSTEMS SEMINAR
SOME SAMPLE PAPERS: BIOLOGY
Science Magazine, Special Issue on Systems Biology, March 2002.
Systems Biology: From Physiology to Gene Regulation, H. El Samad
and M. Khammash, IEEE Control Systems Magazine, 2004, Vol 24, 62-76.
Reverse engineering of biological complexity, M. Csete and J. Doyle,
Science, 2002, 295, 1664-1669.
Chemical reaction network theory for
Jeremy Gunawardena, 2003.
Lecture Notes of Martin Feinberg on Chemical Reaction Networks (especially for mathematicians).
Sniffers, buzzers, toggles and blinkers: dynamics of regulatory
and signaling pathways in the cell,
John J Tyson, Katherine C Chen, and Bela Novak.
Molecular Motors, Brownian Ratchets, and Reflected Diffusions', Amarjit Budhiraja and John Fricks,
Submitted for Publication.
Deterministic and Stochastic Models of Biochemical Reactions
Biochemical clocks and molecular noise: theoretical study
of robustness factors, D. Gonze, J. Halloy and P. Gaspard, J. Chemical Physics,
Vol. 116, No. 24, 2002, 10997-11010.
Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics, J. Chem. Phys. 117 (15), 2002,
Stochastic vs. deterministic modeling of intracellular virus kinetics,
R. Srivastava, L. You, J. Summers and J. Yin, J. Theoretical Biology,
218(3), 2002, 309--321.
Asymptotic analysis of multiscale approximations to reaction networks,
Karen Ball, Tom Kurtz, Lea Popovic, Greg Rempala, preprint.
Gene Structure and Expression and a Queueing Model
Guanosine tetraphosphate as a
global regulator of bacterial RNA synthesis: a model involving RNA polymerase pausing and queuing,
Hans Bremer and Mans Ehrenberg, Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression,
Volume 1262, Issue 1, (17 May 1995),
Summing up the noise in gene networks,
Nature, vol. 427, 29 jan 2004,
Arazi, Ben-Jacob, Yechiali, Bridging genetic networks and queueing theory, Physica A, 332 (2004), 585-616.
Kinetic Analysis of Pausing and Fidelity of Human Immunodeficiency Virus
Type 1 Reverse Transcription, Pop and Biebricher, Biochemistry, 35 (1996), 5054-5062.
Stability and Control
Intrinsic noise rejection in gene networks by regulation of stability,
H. El Samad and M. Khammash,
Control, Communications and Signal Processing, 2004. First International Symposium on,
Pages:187 - 190.
Model validation and robust stability analysis of the bacterial heat shock response using SOSTOOLS
El-Samad, H.; Prajna, S.; Papachristodoulou, A.; Khammash, M.; Doyle, J.C.;
Decision and Control, 2003. Proceedings. 42nd IEEE Conference on ,Volume: 4 , 9-12 Dec. 2003.
Robustness analysis of the heat shock response in E. coli
El-Samad, H.; Khammash, M.; Kurata, H.; Doyle, J.;
American Control Conference, 2002. Proceedings of the 2002 ,Volume: 3 , 8-10 May 2002
Pages:1742 - 1747 vol.3.
Feedback regulation of the heat shock response in E. coli
Kurata, H.; El-Samad, H.; Yi, T.-M.; Khammash, M.; Doyle, J.;
Decision and Control, 2001. Proceedings of the 40th IEEE Conference on ,Volume: 1 , 4-7 Dec. 2001
Pages:837 - 842 vol.1
Calcium Homeostasis, H. El Samad, M. Khammash, J. Goff,
Proc. American Control Conference, Chicago, 2000.
Feedback analysis of calcium homeostasis and parturient paresis
El-Samad, H.; Khammash, M.;
Bio-Informatics and Biomedical Engineering, 2000. Proceedings. IEEE International Symposium on , 8-10 Nov. 2000
Pages:365 - 369
Evolutionary dynamics on graphs, Lieberman, Hauert and Nowak,
letters to Nature, Vol. 433, January 2005.