STOCHASTIC SYSTEMS SEMINAR
SOME SAMPLE PAPERS: BIOLOGY
General Articles
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
in-silico biologists,
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.
Diffusion Approximations
Molecular Motors, Brownian Ratchets, and Reflected Diffusions', Amarjit Budhiraja and John Fricks,
2005.
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,
6959-6969.
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, 2007.
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),
pp. 15-36.
Gene Networks
Summing up the noise in gene networks,
Johan Paulsson,
Nature, vol. 427, 29 jan 2004,
415-418.
Arazi, Ben-Jacob, Yechiali, Bridging genetic networks and queueing theory, Physica A, 332 (2004), 585-616.
Biochemical Reactions-Background
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
Evolution
Evolutionary dynamics on graphs, Lieberman, Hauert and Nowak,
letters to Nature, Vol. 433, January 2005.