2000-2004

John Doyle's papers from 2000-2004.

2004

Journals

Methodological Frameworks for Largescale Network Analysis and Design

Antonis Papachristodoulou, Lun Li and John C. Doyle

Computer Communication Review, 34(3), Jul 2004 (566k)

Metabolic Syndrome and Robustness Tradeoffs,

Kitano, H., Oda, K., Kimura, T., Matsuoka, Y., Csete, M., Doyle, J., Muramatsu, M..

Diabetes 53, S6-S15, 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 Proceedings of IEEE Conference on Decision and Control (CDC), Paradise Island, Bahamas, Dec 2004 (140k)

A First-principles Approach to Understanding the Internet's Router-level Topology

Lun Li, David Alderson, W. Willinger and John C. Doyle

in Proceedings of ACM SIGCOMM, Portland, OR, Aug 2004 (1.5MB)

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 Proceedings of the 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 Proceedings of Internet Measurement Conference (ACM SIGCOMM), Scicily, Italy, Oct 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).

• Computational complexity of μ calculation

R.P. Braatz, P. M. Young, J. C. Doyle, M. Morari Automatic Control, IEEE Transactions 39(5):1000-1002, May 1994.

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.

in Presented at International Workshop on Protocols for Fast Long-Distance Networks (PFLDnet), 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 Proceedings of 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 Proceedings of IEEE Infocom, San Francisco, CA, Apr 2003 (1.4MB)

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

Internet Congestion Control

S. H. Low, F. Paganini and J. C. Doyle

IEEE Control Systems Magazine, 22(1):28-43, Feb 2002 (225k)

• Reverse Engineering of Biological Complexity

Marie E. Csete, John C. Doyle

Science 1 295(5560):1664 - 1669, March 2002

Robustness as a measure of plausibility in models of biochemical networks (abstract),

Morohashi, M., Winn, A. E., Borisuk, M. T., Bolouri, H., Doyle, J., and Kitano, H.

J Theor Biol. 2002 May 7;216(1):19-30.

Conferences

A new TCP/AQM for Stability and Performance in Fast Networks, Fernando Paganini, Zhikui Wang, Steven H. Low and John C. Doyle

in Proceedings of 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 Proceedings of IEEE Infocom, New York, NY, Jun 2002 (435k).

Extensions of Jump Markov System Estimation,

K. Sun, L. Li, G. Panayotopoulos and A. Packard,

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 Proceedings of Pac Symp Biocomput. 450-61, 2002.

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• 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

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 Proceedings of Allerton Conference on Communication, Control, and Computing, Monticello, IL, Oct 2001.