2000-2004

John Doyle's papers from 2000-2004.

2004

Journals

Bow ties, metabolism, and disease,
Csete M.E. and J.C. Doyle,
Trends in Biotechnology 22(9):446-50 Sept 2004. (121K)

Robustness of cellular functions,
J. Stelling, U. Sauer, Z. Szallasi, F. J. Doyle III, and J. Doyle,
Cell 118: 675–685, Sept 17 2004. (244K)

• MathSBML: a package for manipulating SBML-based biological models,
  

Shapiro BE, Hucka M, Finney A, Doyle J.
Bioinformatics, Nov 1, 2004

Methodological Frameworks for Large-scale Network Analysis and Design
Antonis Papachristodoulou, Lun Li and John C. Doyle,
CCR (Computer Communication Review), 34(3), Jul 2004 (828Kk)

Metabolic Syndrome and Robustness Tradeoffs,
Kitano H, Oda K, Kimura T, Matsuoka Y, Csete M, Doyle J, Muramatsu M.
Diabetes 53: S6-S15 Supply. 3, Dec 2004

Evolving a lingua franca and associated software infrastructure for computational systems biology: theSystemsBiologyMarkupLanguage(SBML) project,
M. Hucka; A. Finney; B.J. Bornstein; S.M. Keating; B.E. Shapiro; J. Matthews; B.L. Kovitz; M.J. Schilstra; A. Funahashi; J.C. Doyle; and H. Kitano
IEE Systems Biology. 1:41-53, 2004

Conferences

Analysis of non-linear differential equation model of TCP/AQM protocols using sums of squares.
A. Papachristodoulou, J. C. Doyle and Steven H. Low.
in Proc. IEEE CDC (Conference on Decision and Control), Paradise Island, Bahamas, Dec 2004 (140k)

A First-principles Approach to Understanding the Internet's Router-level Topology Abstract
Lun Li, David Alderson, W. Willinger and John C. Doyle,
in Proc. ACM SIGCOMM, Portland, OR, Aug 2004 (1.5MB)
CCR (Computer Communication Review), Oct. 2004.

Winner of Best Student paper award

The Role of Optimization in Understanding and Modeling Internet Topology,
D. Alderson, W. Willinger, L. Li and J. C. Doyle,
In Proc. 7th INFORMS Tele-communications Conference, Boca Raton, FL, Mar 2004.

More 'Normal' Than Normal: Scaling Distributions and Complex Systems,
W. Willinger, D. Alderson, J. C. Doyle and L. Li,
WSC (Winter Simulation Conference), Washington D. C., 2004.

A Pragmatic Approach to Dealing with High-variability in Network Measurements,
W. Willinger, D. Alderson, and L. Li,
In Proc. Internet Measurement Conference (ACM SIGCOMM), Scicily, Italy, Oct 2004.

• Managing complexity and uncertainty (chair person for plenary lecture)
  

Doyle, J.C.
SICE 2004 Annual Conference vol. 3; ppxlvii - l; 4-6 Aug. 2004.

2003

Journals

Linear stability of TCP/RED and a Scalable Control
S. H. Low, F. Paganini, J. Wang and J. C. Doyle
Computer Networks Journal, 43(5):633-647, Dec 2003 (465k).

• The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models,
  

Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC,
Bioinformatics 19 (4): 524-531, Mar 1 2003.

Conferences

FAST Kernel: Background Theory and Experimental Results
C. Jin, D. X. Wei, S. H. Low, G. Buhrmaster, J. Bunn, D. H. Choe, R. L. A. Cottrell, J. C. Doyle, H. Newman, F. Paganini, S. Ravot and S. Singh.
presented at PFLDnet 2003 (International Workshop on Protocols for Fast Long-Distance Networks), CERN, Geneva, Switzerland, 3-4 Feb 2003 (431k)

A Control Theoretical Look at Internet Congestion Control
F. Paganini, J. C. Doyle and S. H. Low.
in Multidisciplinary Research in Control: The Mohammed Dahleh Symposium 2002.
Springer Lecture Notes in Control and Information Sciences, Vol. 289 L. Giarre' and B. Bamieh (eds.), Springer-Verlag, 2003 (283k).

Can Shortest Path Routing and TCP Maximize Utility
J. Wang, L. Li, S. H. Low and J. C. Doyle.
in Proc.IEEE Infocom, San Francisco, CA, Apr 2003 (157k)

A new TCP/AQM for Stable Operation In Fast Networks
F. Paganini, Z. Wang, S. H. Low and J. C. Doyle.
in Proc. IEEE Infocom, San Francisco, CA, Apr 2003 (1.4MB)

Model validation and robust stability analysis of the bacterial heat shock response using SOSTOOLS.
H. El-Samad, S. Prajna, A. Papachristodoulou, M. Khammash and J. C. Doyle
in Proc. IEEE CDC, vol. 4:3766 - 3771; Maui, Hawaii, 9-12 Dec. 2003.

Book

Robustness and the Internet: Theoretical foundations
John C. Doyle, Jean Carlson, Steven H. Low, Fernando Paganini, Glenn Vinnicombe, Walter Willinger, Jason Hickey, Pablo Parrilo and Lieven Vandenberghe.
in Robust design: a repertoire from biology, ecology, and engineering. E. Jen (eds.), Oxford University Press, 2003

2002

Journals

Reverse Engineering of Biological Complexity
Csete M and Doyle J,
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB)

Robustness as a measure of plausibility in models of biochemical networks,
Morohashi M, Winn AE, Borisuk MT, Bolouri H, Doyle J, Kitano H,
Journal Of Theoretical Biology 216 (1): 19-30 May 7, 2002 .

Complexity and robustness,
Carlson JM, Doyle J,
Proc. Natl. Acad. Sci. USA 99: 2538-2545 Suppl. 1 Feb 19, 2002.

Mutation, specialization, and hypersensitivity in highly optimized tolerance,
Zhou T, Carlson JM, Doyle J,
Proc. Natl. Acad. Sci. USA 99 (4): 2049-2054 Feb 19, 2002.

Internet Congestion Control
S. H. Low, F. Paganini and J. C. Doyle
IEEE Control Systems Magazine, 22(1):28-43, Feb 2002 (225k)

Conferences

A new TCP/AQM for Stability and Performance in Fast Networks,
Fernando Paganini, Zhikui Wang, Steven H. Low and John C. Doyle
in Proc. 39th Annual Allerton Conference on Communication, Control, and Computing, Monticello, IL, Oct 2002 (1.36M)

Dynamics of TCP/RED and a Scalable Control
S. H. Low, F. Paganini, J. Wang, S. Adlakha and J. C. Doyle.
in Proc. IEEE Infocom, New York, NY, Jun 2002 (435k).

Extensions of Jump Markov System Estimation,
K. Sun, L. Li, G. Panayotopoulos and A. Packard,
in Proc. American Control Conference, 2002.

The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology (Abstract)
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J., and Kitano,H.
in Proc. Pac Symp Biocomput. 450-61, 2002.

?

• A New TCP Congestion Control with Empty Queues and Scalable Stability
  

F. Paganini, S. H. Low, Z. Wang, S. Athuraliya and J. C. Doyle.
2002

2001

Journals

• Oxygen-mediated regulation of skeletal muscle satellite cell proliferation and adipogenesis in culture
  

Csete M, Walikonis J, Slawny N, Wei Y, Korsnes S , Doyle JC, Wold B,
Journal of Cellular Physiology, Volume 189, Issue 2, Nov. 2001. 189-196

• The Systems Biology Markup Language
  

Finney AM, Hucka M, Sauro HM, Doyle J, Kitano H, Bolouri H,
Molecular Biology of the Cell 12: 708 Suppl. S NOV 2001.

Conferences

Scalable Laws for Stable Network Congestion Control
Fernando Paganini, J. C. Doyle and S. H. Low.
in Proceedings of IEEE CDC, Orlando, FL, Dec 2001 (475k).

• Linear stability of TCP/RED and a Scalable Control (invited)
  

S. H. Low, F. Paganini, J. Wang, S. Adlakha and J. C. Doyle.
in Proc. of Allerton Conference on Communication, Control, and Computing, Monticello, IL, Oct 2001.

Heavy Tails, Generalized Coding, and Optimal Web Layout
Zhu X, Yu J, Doyle J,
in Proc. IEEE Infocom joint with CCS, Vol. 3: pp1617 - 1626, Apr 2001

• Feedback regulation of the heat shock response in E. coli
  

Kurata, H. El-Samad, H. Yi, T.-M. Khammash, M. Doyle, J.
IEEE CDC Vol 1 pp 837-842; Orlando, FL, USA 2001

2000

Journal

A receding horizon generalization of pointwise min-norm controllers.
JA Primbs, V Nevistic and JC Doyle,
IEEE Trans. Auto.Control 45(5):898 - 909, May 2000.

Robust perfect adaptation in bacterial chemotaxis through integral feedback control.
Yi T-M, Huang Y, Simon MI, Doyle J.
Proc. Natl. Acad. Sci. USA 97(9):4649-4653, 2000.

Power Laws, Highly Optimized Tolerance and Generalized Source Coding,
J. Doyle and J.M. Carlson,
Phys. Rev. Let., 84(24):5656-5659, 2000.

Highly Optimized Tolerance: Robustness and Design in Complex Systems
JM Carlson, J Doyle
Phys. Rev. Lett. 84, 2529 - 2532 (2000)