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, 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, 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, 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), 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


  • Evolutionary dynamics on graphs, Lieberman, Hauert and Nowak, letters to Nature, Vol. 433, January 2005.