John C. Doyle - User contributions [en]

2005-2009

2011-07-04T19:07:51Z

Vanessa: /* Conferences */

John Doyle's [[papers]] from 2005-2009

==2009==
===Conferences===
[http://www.nt.ntnu.no/users/skoge/prost/proceedings/acc09/data/papers/0207.pdf ''Linear control analysis of the autocatalytic glycolysis system''] 
Fiona Chandra, Gentian Buzi, John Doyle 
In Proc. American Control Conf, 319-324 JUN 2009

Javad Lavaei, John C. Doyle and Steven Low, "Congestion Control Algorithms
from Optimal Control Perspective," in Proc. 48th IEEE Conference on
Decision and Control, Shanghai, China, 2009.

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "Solving
Large-Scale Linear Circuit Problems via Convex Optimization," in Proc. 48th
IEEE Conference on Decision and Control, Shanghai, China, 2009.

==2007==
===Journals===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/3/36/IEEEProc_NetsLayer.pdf'' Layering as optimization decomposition: A Mathematical Theory of Network Architectures''] (invited), 
Mung Chiang, Steven H. Low, A. Robert Calderbank, John C. Doyle 
in Proc. IEEE 95(1) Jan 2007. (3.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f5/PRE06.pdf ''Diversity of graphs with highly variable connectivity''] 
David Alderson and Lun Li 
Phys. Rev. E 75, 046102, 2007. (3.9MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f3/IEEETACSideInfo07.pdf ''Fundamental Limitations of Disturbance Attenuation in the Presence of Side Information''] 
Martins, N. C.; Dahleh, M. A.; Doyle, J. C.; 
IEEE Trans Auto Control, 52(1):56 - 66, Jan 2007 (389K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/Nature_Connections07.pdf ''Rules of engagement''] 
John Doyle and Marie Csete 
Nature Vol 446:860 April 19 2007 (142K)

===Conferences===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/6/6e/CSMC2007.pdf ''Can complexity science support the engineering of critical network infrastructures?''] 
Alderson, D.L. and Doyle, J.C.; 
IEEE International Conference on Systems, Man and Cybernetics, pp 44 - 51 , 7-10 Oct. 2007

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/3/38/Ragmac07.pdf Contention Control: A Game-Theoretic Approach] (invited) 
Lijun Chen, Steven H. Low and John C. Doyle 
in Proc. IEEE CDC pp3428 - 3434, New Orleans, LA, 12-14 Dec 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/6/6b/Oscor_mass.pdf ''Opportunistic Source Coding for Data Gathering in Wireless Sensor Networks''] 
Tao Cui, Lijun Chen, Tracey Ho, Steven H. Low and Lachlan H. Andrew 
in Proc. IEEE MASS (Mobile Ad-hoc and Sensor Systems) pp1-11, Pisa, Italy, Oct 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/71/Rag07.pdf ''Game-Theoretic Model for Medium Access Control''] 
Lijun Chen, Tao Cui, Steven H. Low and John C. Doyle 
in Proc. WICON, Austin,Texas, Oct 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/96/Netcod-info07.pdf ''Optimization Based Rate Control for Multi-cast with Network Coding''] 
Lijun Chen, Tracey Ho, Steven H. Low, Mung Chiang and John C. Doyle. 
in Proc. IEEE Infocom, Anchorage, Alaska, May 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/CDC2005.pdf Linear-quadratic-gaussian heat engines], 
H. Sandberg, J.-Ch. Delvenne, and J. C. Doyle, 
in Proc. IEEE CDC, pp:3102 - 3107, New Orleans, LA, USA 12-14 Dec. 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f6/ACC2007.pdf ''The Statistical Mechanics of Fluctuation-Dissipation and Measurement Back Action.''] 
Henrik Sandberg, J.-Ch. Delvenne, and John C. Doyle, 
in Proc. of the American Control Conference, NYC, NY, July 11-13 2007.

* Thermodynamics of linear systems, 
J.-Ch. DDelvenne, H. Sandberg, and J. C. Doyle, 
in Proc. of the European Control Conference, Kos, Greece, July 2007.

===Book Chapter===
[http://www.springerlink.com/content/qp4x0125v16p2g83/?p=cd9b949b2ef14cef910ce160b6ead5c2&pi=6 ''Dual scheduling algorithm in a generalized switch: asymptotic optimality and throughput optimality''], 
L. Chen and S. H. Low and J. C. Doyle, 
in [http://www.springer.com/west/home?SGWID=4-102-22-92732347-0&changeHeader=true ''High-Performance Packet Switching Architectures''], Itamar Elhanany and Mounir Hamdi (Eds), Springer, 2007.

==2006==
===Journals===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1f/PlosCompBio_HS06.pdf ''Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System ''] 
Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash, 
[http://compbiol.plosjournals.org/ PLoS Comput Biol] 2(7): July 2006 (1.1MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1d/InternetMath06.pdf ''Towards a Theory of Scale-Free Graphs: Definition, Properties, and Implications''] 
L. Li, D. Alderson, J. C. Doyle and W. Willinger, 
Internet Mathematics, 2(4): 431-523, Mar 2006 (1.8MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/IEEEProc_Bio.pdf ''Advanced Methods and Algorithms for Biological Networks Analysis''], 
H El-Samad , A Papachristodoulou, S Prajna, J Doyle, and M Khammash 
In Proc. IEEE, 94 (4): 832-853 APR 2006 (900K)
===Conferences===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/ae/Wireless-Chen-infocom06.pdf ''Cross-layer congestion control, routing and scheduling design in ad hoc wireless network''], 
L. Chen and S. H. Low and M. Chiang and J. C. Doyle, 
in Proc. IEEE Infocom, pp1-13; Barcelona, Spain, Apr 2006. (431K)

[http://www.cds.caltech.edu/~doyle2/wiki/index.php?title=Image:WiOpt2006.pdf ''On Asymptotic Optimality of Dual Scheduling Algorithm in A Generalized Switch''] 
L. Chen, S. H. Low and J. C. Doyle 
in Proc. WiOpt, pp1 - 7, Boston, MA, 3-6 April 2006.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/fe/Hotnets06.pdf ''Discovering Dependencies for Network Management''], 
Victor Bahl, Paul Barham, Richard Black, Ranveer Chandra, Moises Goldszmidt, Rebecca Isaacs, Srikanth Kandula, Lun Li, John MacCormick, David A. Maltz, Richard Mortier, Mike Wawrzoniak, and Ming Zhang, 
In Proc. ACM/SIGCOMM HotNets,Irvine, CA, Sept 2006.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/af/CDC2006.pdf ''Complexity in Automation of SOS Proofs: An Illustrative Example''] 
Gayme, D.; Fazel, M.; Doyle, J.C. 
in Proc. IEEE CDC, pp5851 - 5856, San Diego, CA, 13-15 Dec 2006.

===Book===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/5/58/Informs-tc04-chap6.pdf ''The Optimization-based Approach to Modeling Internet Topology''] 
D. Alderson, W. Willinger, L. Li, and J. Doyle, 
[http://www.springer.com/west/home/engineering/electronics?SGWID=4-191-22-81597755-detailsPage=ppmmedia|aboutThisBook Telecommunications Planning: Innovations in Pricing, Network Design and Management.] 
S. Raghavan and G. Anandlingham, eds. Springer. 2006.

===Technical report===
[http://www.cds.caltech.edu/~chen/papers/ramac.pdf ''Random Access Game and Medium Access Control Design''] 
L. Chen, S. H. Low and J. C. Doyle, 
(Caltech) Technical Report, March 2006.

==2005==
===Journals===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/a7/PLOS_Primer05.pdf ''Motifs, control, and stability''] (including ''Supplementary Notes: Elementary Feedback Concepts'') 
Doyle J and Csete M 
[http://www.plosbiology.org PLoS Biol] 3(11): e392; 2005. (387K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/Ton_topology.pdf ''Understanding Internet Topology: Principles, Models, and Validation,''] 
D. Alderson, L. Li, W. Willinger, J. C. Doyle, 
IEEE/ACM ToN, 13(6), Dec. 2005. (1.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/6/64/Fast-network05.pdf ''FAST TCP: From Theory to Experiments''], 
C. Jin, D. X. Wei, S. H. Low, G. Buhrmaster, J. Bunn, D. H. Choe, R. L. A. Cottrell, J. C. Doyle, W. Feng, O. Martin, H. Newman, F. Paganini, S. Ravot and S. Singh, 
IEEE Network, 19(1):4-11, Jan/Feb 2005.(638k)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/02/Tcpip-ton2004-2005.pdf ''Cross-layer optimization in TCP/IP networks''] 
J. Wang, L. Li, S. H. Low and J. C. Doyle. 
IEEE/ACM ToN, 13(3):582-568, Jun 2005 (409k)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/e/e5/Paganini-fast-jour-2005.pdf ''Congestion control for high performance, stability and fairness in general networks''] 
F. Paganini, Z. Wang, J. C. Doyle and S. H. Low. 
IEEE/ACM ToN, 13(1):43-56, Feb 2005 (444k)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/16/PNAS_Internet05.pdf ''The ‘‘robust yet fragile’’ nature of the Internet''] 
John C. Doyle, David L. Alderson, Lun Li, Steven Low, Matthew Roughan, Stanislav Shalunov, Reiko Tanaka, and Walter Willinger 
Proc. Natl. Acad. Sci. USA, 102(41):14497-14502, Oct 11 2005. (635K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/b/b4/PNAS_HeatShock05.pdf ''Surviving Heat Shock: Control Strategies for Robustness and Performance''], 
H. El-Samad, H. Kurata , J.C. Doyle , C.A. Gross, and M. Khammash, 
Proc. Natl. Acad. Sci. USA 102(8): 2736-2741 Feb 22, 2005. (390K)

*''Highly optimized tolerance and power laws in dense and sparse resource regimes'', 
Manning M, Carlson JM, Doyle J, 
Phys. Rev. E 72 (1): Art. No. 016108 Part 2 Jul 2005

*''Three mechanisms for power laws on the Cayley tree'',
T Brookings, JM Carlson, and J Doyle 
Phys. Rev. E 72, 056120

*''Evolutionary dynamics and highly optimized tolerance'', 
Zhou T, Carlson JM, Doyle J 
Journal of Theoretical Biology 236 (4): 438-447 Oct 21 2005

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/98/FEBS_PPI05.pdf ''Some protein interaction data do not exhibit power law statistics''], 
R. Tanaka, T-M Yi, and J. Doyle 
FEBS letters, 579 (23): 5140-5144 Sept 26 2005 (221K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/PNAS_HOTFire05.pdf ''Wildfires, complexity, and highly optimized tolerance''], 
MA Moritz, ME Morais, LA Summerell, JM Carlson, J Doyle 
Proc. Natl. Acad. Sci. USA, December 13, 2005; 102 (50):17912–17917 (403K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f2/IEESysBio05.pdf ''Highly optimised global organisation of metabolic networks''], 
R. Tanaka, M. Csete and J. Doyle, 
IEE Proc.-Syst. Biol. 152(4): 179, Dec 2005 (820K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f6/Li-SFGraph-IM-0508-2005.pdf ''Towards a theory of scale-free graphs: definitions, properties, and implications''] 
L. Li, D. Alderson, J. C. Doyle and W. Willinger 
Internet Mathematics, 2005 (909k).

===Conferences===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1b/Tcpmac-infocom05.pdf ''Joint congestion control and media access control design for wireless ad hoc networks''] 
Lijun Chen, Steven H. Low and John C. Doyle. 
in Proc. IEEE Infocom, Miami, FL, Mar 2005 (193k).

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/d/dd/Sigmetrics05.pdf ''Optimization model of internet protocols''] 
Steven H. Low, John Doyle, Lun Li, Ao Tang and Jiantao Wang 
in Proceedings of SIGMETRICS, pp277 - 277, Banff, Alberta, Canada, June 6-10, 2005.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/CDC2005.pdf ''Fundamental Limitations of Disturbance Attenuation in the Presence of Side Information''] 
Martins, N.C.; Dahleh, M.A.; Doyle, J.C.; 
IEEE CDC - ECC pp2523 - 2529, Seville, Spain, 12-15 Dec 2005.

===Book===
''[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/4e/Part1_vers4.pdf Robustness and the Internet: Design and evolution]'', 
W. Willinger, J Doyle, 
in Robust Design: A Repertoire of Biological, Ecological, and Engineering Case Studies 
(Santa Fe Institute Studies on the Sciences of Complexity), 
Erica Jen, Editor 2005
[[Category:Papers]][[Category:Papers by year]]

2010-2011

2011-07-04T19:07:28Z

Vanessa: /* 2010 */

==2011==
===Journals===
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and nonlinear mechanisms in plane Couette flow.] 
D Gayme, B McKeon, B Bamieh, A Papachristodolou, and J Doyle. 
Physics of Fluids v23:6:065108 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology] 
G Buzi, U Topcu, J Doyle 
Automatica 47:1123-1130 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/c/c4/2.IEEE_TransAutoCtrl_Feb_2011_.pdf On Lossless Approximations, the Fluctuation-Dissipation Theorem, and Limitations of Measurements] 
H Sandberg, JC Delvenne, JC Doyle 
IEE Trans Auto Control, v56:2, 293-308 (2011)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/6/62/9.ComputerNetworksFeb2011.pdf Cross-layer design in multihop wireless networks] 
L Chen, SH Low, and JC Doyle 
Computer Networks 55:480–496 (2011)

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "Solving
Large-Scale Hybrid Circuit-Antenna Problems," IEEE Transactions on Circuits
and Systems I, vol. 58, no. 2, pp. 374-387, Feb. 2011.

==2010==
===Journals===
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/ab/8.IEEETransNetworkingAug2010.pdf Random access game and medium access control design] 
Lijun Chen, Steven Low, and John Doyle 
IEEE Trans Networking 18:4:1303-1316, AUG 2010.

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/d/de/1.IEEE_TransSysMCyber_AldersonDoyle-July2010.pdf Contrasting views of complexity and their implications for network-centric infrastructures] 
David Alderson and John Doyle 
IEEE Trans Systems Man Cybernetics—Part A: Syst Humans 40:839-852, JUL 2010.

[http://www.cds.caltech.edu/~dennice/PublishedVersionJFM2010.pdf A streamwise constant model of turbulence in plane Couette flow] 
Gayme DF, McKeon BJ, Papachristodoulou A, Bamieh B, and Doyle JC 
Journal of Fluid Mechanics 665:99-119 (2010)

===Conferences===
Performance Limitations in Autocatalytic Networks in Biology 
Motee N, Chandra F, Bamieh B, Khammash M, and Doyle J 
In Proc 49th IEEE Conf Decision and Control, 4715-4720, Dec 2010.

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "'Passively
Controllable Smart Antennas," in IEEE Global Communications Conference
(GLOBECOM), Miami, Florida, 2010.

Aydin Babakhani, Javad Lavaei, John C. Doyle and Ali Hajimiri, "Finding
Globally Optimum Solutions in Antenna Optimization Problems," in IEEE
International Symposium on Antennas and Propagation, Toronto, Canada, 2010.

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "Programmable
Antenna Design Using Convex Optimization," in 19th International Symposium
on Mathematical Theory of Networks and Systems, Budapest, Hungary, 2010.

Javad Lavaei, Aydin Babakhani, Ali Hajimiri and John C. Doyle, "A Study of
Near-Field Direct Antenna Modulation Systems Using Convex Optimization," in
American Control Conference, Baltimore, 2010.

Javad Lavaei, John C. Doyle and Steven Low, "Utility Functionals Associated
With Available Congestion Control Algorithms," IEEE International
Conference on Computer Communications (INFOCOM), San Diego, California,
2010.

2010-2011

2011-07-04T19:06:43Z

Vanessa: /* Journals */

Research

2011-07-04T16:54:48Z

Vanessa: /* Current Projects */

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics." <http://www.cds.caltech.edu/people/> Aug 2008

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology." <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 2008

==Current Projects==
*Systems Biology
*Fluids: Turbulence Modeling
*[http://openwetware.org/wiki/Doyle Physiology]
*Internet and Networking

==Research Grants==
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Richard Murray] (with links to his wiki below)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

*Some joint grants with [http://netlab.caltech.edu/~slow/ Prof. Steven Low]:
**MURI Analysis and modeling of networks with long range dependence (LRD) characteristics (PI - Jean Walrand, UC Berkeley; Co-PIs - John Doyle, Steven Low, R. Srikanth (UIUC), V. Anantharam & A. Zakhor (UC Berkeley), D. Towsley & W. Gong (U. Mass. Amherst)2008
**NSF RI WAN in Lab (Newman, Psaltis, Yip) 2003-08
**NSF NeTS Collaborative Research: Optimization and Games in Interdomain Routing 2006
**NSF STI Multi-Gbps TCP: Data Intensive Networks for Science & Engineering (Bunn, Newman) 2002-05
**NSF ITR Optimal and Robust TCP Congestion Control 2001-04
**ARO DURIP Hybrid WAN in Lab (Newman, Psaltis, Yip) 2004-05
**ARO Network Research Analytical Theory of Protocols 2002-05
**ARO Network Science Networked control systems (Murray, Parrilo (MIT)) 2005-2006
(Note that other Co-PI are noted in brackets on these joint grants with Prof. Low and Prof. Doyle)

== Past Projects ==
Caltech
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* Lee Center for Networking
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Murray's projects]
*[http://netlab.caltech.edu/projects.php Prof. Low's projects]
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/theory.html Lee Center]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]

Systems biology

2011-07-04T16:53:56Z

Vanessa: /* 2011 */

Intro:

Keywords: '''systems biology''', SBML mark-up, robustness, complexity, networks, biology, proteins.

A few papers were copied from <http://www.cds.caltech.edu/~doyle/RecentPapers/ >

==Systems biology==
Keywords: '''systems biology''', biological networks, complexity, control, heat-shock, protein, robustness, metabolism...

===2011===
Glycolytic Oscillations and Limits on Robust Efficiency 
Fiona Chandra, Gentian Buzi, and John Doyle 
Science (In Press)

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology] 
G Buzi, U Topcu, J Doyle 
Automatica 47:1123-1130 (2011)

===2009===
[http://www.nt.ntnu.no/users/skoge/prost/proceedings/acc09/data/papers/0207.pdf ''Linear control analysis of the autocatalytic glycolysis system''] 
Fiona Chandra, Gentian Buzi, John Doyle 
In Proc. American Control Conf, 319-324 JUN 2009

===2007===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/Nature_Connections07.pdf ''Rules of engagement''] 
John Doyle and Marie Csete 
Nature Vol 446:860 April 19 2007 (142K)

===2006===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/IEEEProc_Bio.pdf ''Advanced Methods and Algorithms for Biological Networks Analysis''], 
H El-Samad , A Papachristodoulou, S Prajna, J Doyle, and M Khammash 
In Proc. IEEE, 94 (4): 832-853 APR 2006 (900K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1f/PlosCompBio_HS06.pdf ''Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System ''] 
Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash, 
[http://compbiol.plosjournals.org/ PLoS Comput Biol] 2(7): July 2006 (1.1MB)

===2005===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/98/FEBS_PPI05.pdf ''Some protein interaction data do not exhibit power law statistics''], 
R. Tanaka, T-M Yi, and J. Doyle 
FEBS letters, 579 (23): 5140-5144 Sept 26 2005 (221K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f2/IEESysBio05.pdf ''Highly optimised global organisation of metabolic networks''], 
R. Tanaka, M. Csete and J. Doyle, 
IEE Proc.-Syst. Biol. 152(4): 179, Dec 2005 (820K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/a7/PLOS_Primer05.pdf ''Motifs, control, and stability''] (including ''Supplementary Notes: Elementary Feedback Concepts'') 
Doyle J and Csete M 
[http://www.plosbiology.org PLoS Biol] 3(11): e392; 2005. (387K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/b/b4/PNAS_HeatShock05.pdf ''Surviving Heat Shock: Control Strategies for Robustness and Performance''] 
H. El-Samad, H. Kurata , J.C. Doyle , C.A. Gross, and M. Khammash, 
Proc. Natl. Acad. Sci. USA 102(8): 2736-2741 Feb 22, 2005. (390K)

===2004===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/13/Cell04.pdf ''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)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/82/Trends04.pdf ''Bow ties, metabolism, and disease''], 
Csete M.E. and J.C. Doyle, 
Trends in Biotechnology 22(9):446-50 Sept 2004. (121K)

===2002===
[http://www.cds.caltech.edu/~doyle2/wiki/skins/common/images/icons/fileicon-pdf.png ''Reverse Engineering of Biological Complexity''] 
Csete M and Doyle J, 
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/12/JtheorBiol2002.pdf ''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.

==SBML==
Keywords: '''SBML''', systems biology mark-up language, computer software, biochemical reaction networks

===2004===
[http://scitation.aip.org/dbt/dbt.jsp?KEY=IPSBDJ&Volume=1 '' 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

*''MathSBML: a package for manipulating SBML-based biological models'', 
Shapiro BE, Hucka M, Finney A, Doyle J. 
Bioinformatics, Nov 1, 2004

===2002===
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11928498&dopt=Abstract ''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.

===2001===
*''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.

==More Biology==
Keywords: '''biology''', cell, HOT (highly optimized tolerance), SOSTOOLS (sums of squares optimization), robustness
===2005===
''Evolutionary dynamics and highly optimized tolerance,''
Zhou T, Carlson JM, Doyle J 
Journal of Theoretical Biology 236 (4): 438-447 Oct 21 2005

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/PNAS_HOTFire05.pdf ''Wildfires, complexity, and highly optimized tolerance''], 
MA Moritz, ME Morais, LA Summerell, JM Carlson, J Doyle 
Proc. Natl. Acad. Sci. USA, December 13, 2005; 102 (50):17912–17917 (403K)

===2003===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f8/CDC2003.pdf ''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.

===2002===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/72/PNAS2538-2002.full.pdf ''Complexity and robustness''], 
Carlson JM, Doyle J, 
Proc. Natl. Acad. Sci. USA 99: 2538-2545 Suppl. 1 Feb 19, 2002.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/85/PNAS2049-2002.full.pdf ''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.

===2001===
*''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

===2000===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f0/PNAS4649-2000.full.pdf ''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.

==Related reading==
[[Papers]]

[[Research]]

[[Tips: Research papers, Publishing and Other Trivia]]

===Other===

===External links===
*[http://sbml.org/Main_Page SBML Definition and homepage]
*[http://sbml.org/Documents SBML documents]
*[http://www.systems-biology.org/ Systems Biology Portal]
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]

[[Category:Research]]
[[Category:Papers by topic]]
[[Category:Papers]]

2010-2011

2011-07-04T16:53:27Z

Vanessa:

Systems biology

2011-07-04T16:51:58Z

Vanessa: /* Systems biology */

Intro:

Keywords: '''systems biology''', SBML mark-up, robustness, complexity, networks, biology, proteins.

A few papers were copied from <http://www.cds.caltech.edu/~doyle/RecentPapers/ >

==Systems biology==
Keywords: '''systems biology''', biological networks, complexity, control, heat-shock, protein, robustness, metabolism...

===2011===
Glycolytic Oscillations and Limits on Robust Efficiency 
Fiona Chandra, Gentian Buzi, and John Doyle 
Science (In Press)

===2009===
[http://www.nt.ntnu.no/users/skoge/prost/proceedings/acc09/data/papers/0207.pdf ''Linear control analysis of the autocatalytic glycolysis system''] 
Fiona Chandra, Gentian Buzi, John Doyle 
In Proc. American Control Conf, 319-324 JUN 2009

===2007===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/Nature_Connections07.pdf ''Rules of engagement''] 
John Doyle and Marie Csete 
Nature Vol 446:860 April 19 2007 (142K)

===2006===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/IEEEProc_Bio.pdf ''Advanced Methods and Algorithms for Biological Networks Analysis''], 
H El-Samad , A Papachristodoulou, S Prajna, J Doyle, and M Khammash 
In Proc. IEEE, 94 (4): 832-853 APR 2006 (900K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1f/PlosCompBio_HS06.pdf ''Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System ''] 
Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash, 
[http://compbiol.plosjournals.org/ PLoS Comput Biol] 2(7): July 2006 (1.1MB)

===2005===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/98/FEBS_PPI05.pdf ''Some protein interaction data do not exhibit power law statistics''], 
R. Tanaka, T-M Yi, and J. Doyle 
FEBS letters, 579 (23): 5140-5144 Sept 26 2005 (221K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f2/IEESysBio05.pdf ''Highly optimised global organisation of metabolic networks''], 
R. Tanaka, M. Csete and J. Doyle, 
IEE Proc.-Syst. Biol. 152(4): 179, Dec 2005 (820K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/a7/PLOS_Primer05.pdf ''Motifs, control, and stability''] (including ''Supplementary Notes: Elementary Feedback Concepts'') 
Doyle J and Csete M 
[http://www.plosbiology.org PLoS Biol] 3(11): e392; 2005. (387K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/b/b4/PNAS_HeatShock05.pdf ''Surviving Heat Shock: Control Strategies for Robustness and Performance''] 
H. El-Samad, H. Kurata , J.C. Doyle , C.A. Gross, and M. Khammash, 
Proc. Natl. Acad. Sci. USA 102(8): 2736-2741 Feb 22, 2005. (390K)

===2004===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/13/Cell04.pdf ''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)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/82/Trends04.pdf ''Bow ties, metabolism, and disease''], 
Csete M.E. and J.C. Doyle, 
Trends in Biotechnology 22(9):446-50 Sept 2004. (121K)

===2002===
[http://www.cds.caltech.edu/~doyle2/wiki/skins/common/images/icons/fileicon-pdf.png ''Reverse Engineering of Biological Complexity''] 
Csete M and Doyle J, 
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/12/JtheorBiol2002.pdf ''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.

==SBML==
Keywords: '''SBML''', systems biology mark-up language, computer software, biochemical reaction networks

===2004===
[http://scitation.aip.org/dbt/dbt.jsp?KEY=IPSBDJ&Volume=1 '' 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

*''MathSBML: a package for manipulating SBML-based biological models'', 
Shapiro BE, Hucka M, Finney A, Doyle J. 
Bioinformatics, Nov 1, 2004

===2002===
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11928498&dopt=Abstract ''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.

===2001===
*''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.

==More Biology==
Keywords: '''biology''', cell, HOT (highly optimized tolerance), SOSTOOLS (sums of squares optimization), robustness
===2005===
''Evolutionary dynamics and highly optimized tolerance,''
Zhou T, Carlson JM, Doyle J 
Journal of Theoretical Biology 236 (4): 438-447 Oct 21 2005

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/PNAS_HOTFire05.pdf ''Wildfires, complexity, and highly optimized tolerance''], 
MA Moritz, ME Morais, LA Summerell, JM Carlson, J Doyle 
Proc. Natl. Acad. Sci. USA, December 13, 2005; 102 (50):17912–17917 (403K)

===2003===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f8/CDC2003.pdf ''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.

===2002===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/72/PNAS2538-2002.full.pdf ''Complexity and robustness''], 
Carlson JM, Doyle J, 
Proc. Natl. Acad. Sci. USA 99: 2538-2545 Suppl. 1 Feb 19, 2002.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/85/PNAS2049-2002.full.pdf ''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.

===2001===
*''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

===2000===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f0/PNAS4649-2000.full.pdf ''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.

==Related reading==
[[Papers]]

[[Research]]

[[Tips: Research papers, Publishing and Other Trivia]]

===Other===

===External links===
*[http://sbml.org/Main_Page SBML Definition and homepage]
*[http://sbml.org/Documents SBML documents]
*[http://www.systems-biology.org/ Systems Biology Portal]
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]

[[Category:Research]]
[[Category:Papers by topic]]
[[Category:Papers]]

Systems biology

2011-07-04T16:51:30Z

Vanessa: /* =2011 */

Intro:

Keywords: '''systems biology''', SBML mark-up, robustness, complexity, networks, biology, proteins.

A few papers were copied from <http://www.cds.caltech.edu/~doyle/RecentPapers/ >

==Systems biology==
Keywords: '''systems biology''', biological networks, complexity, control, heat-shock, protein, robustness, metabolism...

===2009===
[http://www.nt.ntnu.no/users/skoge/prost/proceedings/acc09/data/papers/0207.pdf ''Linear control analysis of the autocatalytic glycolysis system''] 
Fiona Chandra, Gentian Buzi, John Doyle 
In Proc. American Control Conf, 319-324 JUN 2009

===2007===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/Nature_Connections07.pdf ''Rules of engagement''] 
John Doyle and Marie Csete 
Nature Vol 446:860 April 19 2007 (142K)

===2006===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/IEEEProc_Bio.pdf ''Advanced Methods and Algorithms for Biological Networks Analysis''], 
H El-Samad , A Papachristodoulou, S Prajna, J Doyle, and M Khammash 
In Proc. IEEE, 94 (4): 832-853 APR 2006 (900K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1f/PlosCompBio_HS06.pdf ''Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System ''] 
Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash, 
[http://compbiol.plosjournals.org/ PLoS Comput Biol] 2(7): July 2006 (1.1MB)

===2005===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/98/FEBS_PPI05.pdf ''Some protein interaction data do not exhibit power law statistics''], 
R. Tanaka, T-M Yi, and J. Doyle 
FEBS letters, 579 (23): 5140-5144 Sept 26 2005 (221K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f2/IEESysBio05.pdf ''Highly optimised global organisation of metabolic networks''], 
R. Tanaka, M. Csete and J. Doyle, 
IEE Proc.-Syst. Biol. 152(4): 179, Dec 2005 (820K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/a7/PLOS_Primer05.pdf ''Motifs, control, and stability''] (including ''Supplementary Notes: Elementary Feedback Concepts'') 
Doyle J and Csete M 
[http://www.plosbiology.org PLoS Biol] 3(11): e392; 2005. (387K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/b/b4/PNAS_HeatShock05.pdf ''Surviving Heat Shock: Control Strategies for Robustness and Performance''] 
H. El-Samad, H. Kurata , J.C. Doyle , C.A. Gross, and M. Khammash, 
Proc. Natl. Acad. Sci. USA 102(8): 2736-2741 Feb 22, 2005. (390K)

===2004===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/13/Cell04.pdf ''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)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/82/Trends04.pdf ''Bow ties, metabolism, and disease''], 
Csete M.E. and J.C. Doyle, 
Trends in Biotechnology 22(9):446-50 Sept 2004. (121K)

===2002===
[http://www.cds.caltech.edu/~doyle2/wiki/skins/common/images/icons/fileicon-pdf.png ''Reverse Engineering of Biological Complexity''] 
Csete M and Doyle J, 
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/12/JtheorBiol2002.pdf ''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.

==SBML==
Keywords: '''SBML''', systems biology mark-up language, computer software, biochemical reaction networks

===2004===
[http://scitation.aip.org/dbt/dbt.jsp?KEY=IPSBDJ&Volume=1 '' 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

*''MathSBML: a package for manipulating SBML-based biological models'', 
Shapiro BE, Hucka M, Finney A, Doyle J. 
Bioinformatics, Nov 1, 2004

===2002===
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11928498&dopt=Abstract ''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.

===2001===
*''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.

==More Biology==
Keywords: '''biology''', cell, HOT (highly optimized tolerance), SOSTOOLS (sums of squares optimization), robustness
===2005===
''Evolutionary dynamics and highly optimized tolerance,''
Zhou T, Carlson JM, Doyle J 
Journal of Theoretical Biology 236 (4): 438-447 Oct 21 2005

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/PNAS_HOTFire05.pdf ''Wildfires, complexity, and highly optimized tolerance''], 
MA Moritz, ME Morais, LA Summerell, JM Carlson, J Doyle 
Proc. Natl. Acad. Sci. USA, December 13, 2005; 102 (50):17912–17917 (403K)

===2003===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f8/CDC2003.pdf ''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.

===2002===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/72/PNAS2538-2002.full.pdf ''Complexity and robustness''], 
Carlson JM, Doyle J, 
Proc. Natl. Acad. Sci. USA 99: 2538-2545 Suppl. 1 Feb 19, 2002.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/85/PNAS2049-2002.full.pdf ''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.

===2001===
*''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

===2000===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f0/PNAS4649-2000.full.pdf ''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.

==Related reading==
[[Papers]]

[[Research]]

[[Tips: Research papers, Publishing and Other Trivia]]

===Other===

===External links===
*[http://sbml.org/Main_Page SBML Definition and homepage]
*[http://sbml.org/Documents SBML documents]
*[http://www.systems-biology.org/ Systems Biology Portal]
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]

[[Category:Research]]
[[Category:Papers by topic]]
[[Category:Papers]]

Systems biology

2011-07-04T16:51:03Z

Vanessa:

Intro:

Keywords: '''systems biology''', SBML mark-up, robustness, complexity, networks, biology, proteins.

A few papers were copied from <http://www.cds.caltech.edu/~doyle/RecentPapers/ >

==Systems biology==
Keywords: '''systems biology''', biological networks, complexity, control, heat-shock, protein, robustness, metabolism...

===2011==
Glycolytic Oscillations and Limits on Robust Efficiency 
Fiona Chandra, Gentian Buzi, and John Doyle 
Science (In Press)

===2009===
[http://www.nt.ntnu.no/users/skoge/prost/proceedings/acc09/data/papers/0207.pdf ''Linear control analysis of the autocatalytic glycolysis system''] 
Fiona Chandra, Gentian Buzi, John Doyle 
In Proc. American Control Conf, 319-324 JUN 2009

===2007===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/Nature_Connections07.pdf ''Rules of engagement''] 
John Doyle and Marie Csete 
Nature Vol 446:860 April 19 2007 (142K)

===2006===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/IEEEProc_Bio.pdf ''Advanced Methods and Algorithms for Biological Networks Analysis''], 
H El-Samad , A Papachristodoulou, S Prajna, J Doyle, and M Khammash 
In Proc. IEEE, 94 (4): 832-853 APR 2006 (900K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1f/PlosCompBio_HS06.pdf ''Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System ''] 
Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash, 
[http://compbiol.plosjournals.org/ PLoS Comput Biol] 2(7): July 2006 (1.1MB)

===2005===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/98/FEBS_PPI05.pdf ''Some protein interaction data do not exhibit power law statistics''], 
R. Tanaka, T-M Yi, and J. Doyle 
FEBS letters, 579 (23): 5140-5144 Sept 26 2005 (221K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f2/IEESysBio05.pdf ''Highly optimised global organisation of metabolic networks''], 
R. Tanaka, M. Csete and J. Doyle, 
IEE Proc.-Syst. Biol. 152(4): 179, Dec 2005 (820K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/a7/PLOS_Primer05.pdf ''Motifs, control, and stability''] (including ''Supplementary Notes: Elementary Feedback Concepts'') 
Doyle J and Csete M 
[http://www.plosbiology.org PLoS Biol] 3(11): e392; 2005. (387K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/b/b4/PNAS_HeatShock05.pdf ''Surviving Heat Shock: Control Strategies for Robustness and Performance''] 
H. El-Samad, H. Kurata , J.C. Doyle , C.A. Gross, and M. Khammash, 
Proc. Natl. Acad. Sci. USA 102(8): 2736-2741 Feb 22, 2005. (390K)

===2004===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/13/Cell04.pdf ''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)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/82/Trends04.pdf ''Bow ties, metabolism, and disease''], 
Csete M.E. and J.C. Doyle, 
Trends in Biotechnology 22(9):446-50 Sept 2004. (121K)

===2002===
[http://www.cds.caltech.edu/~doyle2/wiki/skins/common/images/icons/fileicon-pdf.png ''Reverse Engineering of Biological Complexity''] 
Csete M and Doyle J, 
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/12/JtheorBiol2002.pdf ''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.

==SBML==
Keywords: '''SBML''', systems biology mark-up language, computer software, biochemical reaction networks

===2004===
[http://scitation.aip.org/dbt/dbt.jsp?KEY=IPSBDJ&Volume=1 '' 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

*''MathSBML: a package for manipulating SBML-based biological models'', 
Shapiro BE, Hucka M, Finney A, Doyle J. 
Bioinformatics, Nov 1, 2004

===2002===
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11928498&dopt=Abstract ''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.

===2001===
*''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.

==More Biology==
Keywords: '''biology''', cell, HOT (highly optimized tolerance), SOSTOOLS (sums of squares optimization), robustness
===2005===
''Evolutionary dynamics and highly optimized tolerance,''
Zhou T, Carlson JM, Doyle J 
Journal of Theoretical Biology 236 (4): 438-447 Oct 21 2005

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/PNAS_HOTFire05.pdf ''Wildfires, complexity, and highly optimized tolerance''], 
MA Moritz, ME Morais, LA Summerell, JM Carlson, J Doyle 
Proc. Natl. Acad. Sci. USA, December 13, 2005; 102 (50):17912–17917 (403K)

===2003===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f8/CDC2003.pdf ''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.

===2002===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/72/PNAS2538-2002.full.pdf ''Complexity and robustness''], 
Carlson JM, Doyle J, 
Proc. Natl. Acad. Sci. USA 99: 2538-2545 Suppl. 1 Feb 19, 2002.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/85/PNAS2049-2002.full.pdf ''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.

===2001===
*''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

===2000===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f0/PNAS4649-2000.full.pdf ''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.

==Related reading==
[[Papers]]

[[Research]]

[[Tips: Research papers, Publishing and Other Trivia]]

===Other===

===External links===
*[http://sbml.org/Main_Page SBML Definition and homepage]
*[http://sbml.org/Documents SBML documents]
*[http://www.systems-biology.org/ Systems Biology Portal]
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]

[[Category:Research]]
[[Category:Papers by topic]]
[[Category:Papers]]

Turbulence

2011-07-04T16:48:46Z

Vanessa:

[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/8/87/PhysFluids_23_065108.pdf Amplification and nonlinear mechanisms in plane Couette flow.] 
D Gayme, B McKeon, B Bamieh, A Papachristodolou, and J Doyle. 
Physics of Fluids v23:6:065108 (2011)

[http://www.cds.caltech.edu/~dennice/PublishedVersionJFM2010.pdf A streamwise constant model of turbulence in plane Couette flow] 
Gayme DF, McKeon BJ, Papachristodoulou A, Bamieh B, and Doyle JC 
Journal of Fluid Mechanics 665:99-119 (2010)

2010-2011

2011-07-04T16:48:31Z

Vanessa: /* Journals */

Turbulence

2011-07-04T16:46:53Z

Vanessa:

Papers

2011-07-04T16:41:51Z

Vanessa: /* Topic */

'''Papers''' span many years and cover a diverse range of topics, from understanding the internet to financial market analysis, control theory and also covering certain aspects of biology, physics and physiology. '''Papers''' have been sorted by topic and year (see below.) These pages list some of Doyle's papers and related reading in these areas!



==Year==
[[2010-2011]]

[[2005-2009]]

[[2000-2004]]

[[1995-1999]]

[[1990-1994]]

[[1985-1989]]

==Topic==
*[[General complexity]]
*[[Networking]]
*[[Network architecture and protocols]]
*[[Wildfire ecology]]
*[[Systems biology]]
*[[Physiology]]
*[[Turbulence]]

==Older topics==
*[[Complex networks]]
*[[Complexity and robustness]]

==See also==
[[Tips: Research papers, Publishing and Other Trivia]]

[[Research]]

See [[DoyleWiki:Copyrights|Copyright statment]] before downloading or viewing papers.

[[Category:Papers]]
[[Category:Papers by year]]
[[Category:Papers by topic]]

Papers

2011-07-04T16:36:06Z

Vanessa: /* Topic */

'''Papers''' span many years and cover a diverse range of topics, from understanding the internet to financial market analysis, control theory and also covering certain aspects of biology, physics and physiology. '''Papers''' have been sorted by topic and year (see below.) These pages list some of Doyle's papers and related reading in these areas!



==Year==
[[2010-2011]]

[[2005-2009]]

[[2000-2004]]

[[1995-1999]]

[[1990-1994]]

[[1985-1989]]

==Topic==
*[[General complexity]]
*[[Networking]]
*[[Network architecture and protocols]]
*[[Internet]]
*[[Wildfire ecology]]
*[[Systems biology]]
*[[Physiology]]

==Older topics==
*[[Complex networks]]
*[[Complexity and robustness]]

==See also==
[[Tips: Research papers, Publishing and Other Trivia]]

[[Research]]

See [[DoyleWiki:Copyrights|Copyright statment]] before downloading or viewing papers.

[[Category:Papers]]
[[Category:Papers by year]]
[[Category:Papers by topic]]

2010-2011

2011-07-04T06:13:52Z

Vanessa: /* 2011 */

File:6.AutomaticaJune2011.pdf

2011-07-04T06:11:03Z

Vanessa:

2010-2011

2011-07-04T06:01:35Z

Vanessa: /* 2011 */

File:9.ComputerNetworksFeb2011.pdf

2011-07-04T05:59:25Z

Vanessa:

2010-2011

2011-07-04T05:57:06Z

Vanessa: /* 2011 */

File:2.IEEE TransAutoCtrl Feb 2011 .pdf

2011-07-04T05:54:03Z

Vanessa:

Research

2011-07-04T05:46:30Z

Vanessa: /* Current Projects */

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics." <http://www.cds.caltech.edu/people/> Aug 2008

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology." <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 2008

==Current Projects==
*Systems Biology
*Fluids: Turbulence Modeling
*[http://openwetware.org/wiki/Doyle Physiology]

==Research Grants==
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Richard Murray] (with links to his wiki below)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

*Some joint grants with [http://netlab.caltech.edu/~slow/ Prof. Steven Low]:
**MURI Analysis and modeling of networks with long range dependence (LRD) characteristics (PI - Jean Walrand, UC Berkeley; Co-PIs - John Doyle, Steven Low, R. Srikanth (UIUC), V. Anantharam & A. Zakhor (UC Berkeley), D. Towsley & W. Gong (U. Mass. Amherst)2008
**NSF RI WAN in Lab (Newman, Psaltis, Yip) 2003-08
**NSF NeTS Collaborative Research: Optimization and Games in Interdomain Routing 2006
**NSF STI Multi-Gbps TCP: Data Intensive Networks for Science & Engineering (Bunn, Newman) 2002-05
**NSF ITR Optimal and Robust TCP Congestion Control 2001-04
**ARO DURIP Hybrid WAN in Lab (Newman, Psaltis, Yip) 2004-05
**ARO Network Research Analytical Theory of Protocols 2002-05
**ARO Network Science Networked control systems (Murray, Parrilo (MIT)) 2005-2006
(Note that other Co-PI are noted in brackets on these joint grants with Prof. Low and Prof. Doyle)

== Past Projects ==
Caltech
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* Lee Center for Networking
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Murray's projects]
*[http://netlab.caltech.edu/projects.php Prof. Low's projects]
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/theory.html Lee Center]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]

2010-2011

2011-07-04T05:30:08Z

Vanessa: /* Journals */

File:1.IEEE TransSysMCyber AldersonDoyle-July2010.pdf

2011-07-04T05:27:40Z

Vanessa:

2010-2011

2011-07-04T05:24:49Z

Vanessa: /* 2010 */

File:8.IEEETransNetworkingAug2010.pdf

2011-07-04T05:22:54Z

Vanessa:

2010-2011

2011-07-04T05:21:58Z

Vanessa:

2005-2009

2011-07-04T05:18:18Z

Vanessa: /* 2007 */

John Doyle's [[papers]] from 2005-2009

==2009==
===Conferences===
[http://www.nt.ntnu.no/users/skoge/prost/proceedings/acc09/data/papers/0207.pdf ''Linear control analysis of the autocatalytic glycolysis system''] 
Fiona Chandra, Gentian Buzi, John Doyle 
In Proc. American Control Conf, 319-324 JUN 2009

==2007==
===Journals===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/3/36/IEEEProc_NetsLayer.pdf'' Layering as optimization decomposition: A Mathematical Theory of Network Architectures''] (invited), 
Mung Chiang, Steven H. Low, A. Robert Calderbank, John C. Doyle 
in Proc. IEEE 95(1) Jan 2007. (3.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f5/PRE06.pdf ''Diversity of graphs with highly variable connectivity''] 
David Alderson and Lun Li 
Phys. Rev. E 75, 046102, 2007. (3.9MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f3/IEEETACSideInfo07.pdf ''Fundamental Limitations of Disturbance Attenuation in the Presence of Side Information''] 
Martins, N. C.; Dahleh, M. A.; Doyle, J. C.; 
IEEE Trans Auto Control, 52(1):56 - 66, Jan 2007 (389K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/Nature_Connections07.pdf ''Rules of engagement''] 
John Doyle and Marie Csete 
Nature Vol 446:860 April 19 2007 (142K)

===Conferences===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/6/6e/CSMC2007.pdf ''Can complexity science support the engineering of critical network infrastructures?''] 
Alderson, D.L. and Doyle, J.C.; 
IEEE International Conference on Systems, Man and Cybernetics, pp 44 - 51 , 7-10 Oct. 2007

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/3/38/Ragmac07.pdf Contention Control: A Game-Theoretic Approach] (invited) 
Lijun Chen, Steven H. Low and John C. Doyle 
in Proc. IEEE CDC pp3428 - 3434, New Orleans, LA, 12-14 Dec 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/6/6b/Oscor_mass.pdf ''Opportunistic Source Coding for Data Gathering in Wireless Sensor Networks''] 
Tao Cui, Lijun Chen, Tracey Ho, Steven H. Low and Lachlan H. Andrew 
in Proc. IEEE MASS (Mobile Ad-hoc and Sensor Systems) pp1-11, Pisa, Italy, Oct 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/71/Rag07.pdf ''Game-Theoretic Model for Medium Access Control''] 
Lijun Chen, Tao Cui, Steven H. Low and John C. Doyle 
in Proc. WICON, Austin,Texas, Oct 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/96/Netcod-info07.pdf ''Optimization Based Rate Control for Multi-cast with Network Coding''] 
Lijun Chen, Tracey Ho, Steven H. Low, Mung Chiang and John C. Doyle. 
in Proc. IEEE Infocom, Anchorage, Alaska, May 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/CDC2005.pdf Linear-quadratic-gaussian heat engines], 
H. Sandberg, J.-Ch. Delvenne, and J. C. Doyle, 
in Proc. IEEE CDC, pp:3102 - 3107, New Orleans, LA, USA 12-14 Dec. 2007.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f6/ACC2007.pdf ''The Statistical Mechanics of Fluctuation-Dissipation and Measurement Back Action.''] 
Henrik Sandberg, J.-Ch. Delvenne, and John C. Doyle, 
in Proc. of the American Control Conference, NYC, NY, July 11-13 2007.

* Thermodynamics of linear systems, 
J.-Ch. DDelvenne, H. Sandberg, and J. C. Doyle, 
in Proc. of the European Control Conference, Kos, Greece, July 2007.

===Book Chapter===
[http://www.springerlink.com/content/qp4x0125v16p2g83/?p=cd9b949b2ef14cef910ce160b6ead5c2&pi=6 ''Dual scheduling algorithm in a generalized switch: asymptotic optimality and throughput optimality''], 
L. Chen and S. H. Low and J. C. Doyle, 
in [http://www.springer.com/west/home?SGWID=4-102-22-92732347-0&changeHeader=true ''High-Performance Packet Switching Architectures''], Itamar Elhanany and Mounir Hamdi (Eds), Springer, 2007.

==2006==
===Journals===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1f/PlosCompBio_HS06.pdf ''Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System ''] 
Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash, 
[http://compbiol.plosjournals.org/ PLoS Comput Biol] 2(7): July 2006 (1.1MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1d/InternetMath06.pdf ''Towards a Theory of Scale-Free Graphs: Definition, Properties, and Implications''] 
L. Li, D. Alderson, J. C. Doyle and W. Willinger, 
Internet Mathematics, 2(4): 431-523, Mar 2006 (1.8MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/IEEEProc_Bio.pdf ''Advanced Methods and Algorithms for Biological Networks Analysis''], 
H El-Samad , A Papachristodoulou, S Prajna, J Doyle, and M Khammash 
In Proc. IEEE, 94 (4): 832-853 APR 2006 (900K)
===Conferences===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/ae/Wireless-Chen-infocom06.pdf ''Cross-layer congestion control, routing and scheduling design in ad hoc wireless network''], 
L. Chen and S. H. Low and M. Chiang and J. C. Doyle, 
in Proc. IEEE Infocom, pp1-13; Barcelona, Spain, Apr 2006. (431K)

[http://www.cds.caltech.edu/~doyle2/wiki/index.php?title=Image:WiOpt2006.pdf ''On Asymptotic Optimality of Dual Scheduling Algorithm in A Generalized Switch''] 
L. Chen, S. H. Low and J. C. Doyle 
in Proc. WiOpt, pp1 - 7, Boston, MA, 3-6 April 2006.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/fe/Hotnets06.pdf ''Discovering Dependencies for Network Management''], 
Victor Bahl, Paul Barham, Richard Black, Ranveer Chandra, Moises Goldszmidt, Rebecca Isaacs, Srikanth Kandula, Lun Li, John MacCormick, David A. Maltz, Richard Mortier, Mike Wawrzoniak, and Ming Zhang, 
In Proc. ACM/SIGCOMM HotNets,Irvine, CA, Sept 2006.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/af/CDC2006.pdf ''Complexity in Automation of SOS Proofs: An Illustrative Example''] 
Gayme, D.; Fazel, M.; Doyle, J.C. 
in Proc. IEEE CDC, pp5851 - 5856, San Diego, CA, 13-15 Dec 2006.

===Book===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/5/58/Informs-tc04-chap6.pdf ''The Optimization-based Approach to Modeling Internet Topology''] 
D. Alderson, W. Willinger, L. Li, and J. Doyle, 
[http://www.springer.com/west/home/engineering/electronics?SGWID=4-191-22-81597755-detailsPage=ppmmedia|aboutThisBook Telecommunications Planning: Innovations in Pricing, Network Design and Management.] 
S. Raghavan and G. Anandlingham, eds. Springer. 2006.

===Technical report===
[http://www.cds.caltech.edu/~chen/papers/ramac.pdf ''Random Access Game and Medium Access Control Design''] 
L. Chen, S. H. Low and J. C. Doyle, 
(Caltech) Technical Report, March 2006.

==2005==
===Journals===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/a7/PLOS_Primer05.pdf ''Motifs, control, and stability''] (including ''Supplementary Notes: Elementary Feedback Concepts'') 
Doyle J and Csete M 
[http://www.plosbiology.org PLoS Biol] 3(11): e392; 2005. (387K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/Ton_topology.pdf ''Understanding Internet Topology: Principles, Models, and Validation,''] 
D. Alderson, L. Li, W. Willinger, J. C. Doyle, 
IEEE/ACM ToN, 13(6), Dec. 2005. (1.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/6/64/Fast-network05.pdf ''FAST TCP: From Theory to Experiments''], 
C. Jin, D. X. Wei, S. H. Low, G. Buhrmaster, J. Bunn, D. H. Choe, R. L. A. Cottrell, J. C. Doyle, W. Feng, O. Martin, H. Newman, F. Paganini, S. Ravot and S. Singh, 
IEEE Network, 19(1):4-11, Jan/Feb 2005.(638k)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/02/Tcpip-ton2004-2005.pdf ''Cross-layer optimization in TCP/IP networks''] 
J. Wang, L. Li, S. H. Low and J. C. Doyle. 
IEEE/ACM ToN, 13(3):582-568, Jun 2005 (409k)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/e/e5/Paganini-fast-jour-2005.pdf ''Congestion control for high performance, stability and fairness in general networks''] 
F. Paganini, Z. Wang, J. C. Doyle and S. H. Low. 
IEEE/ACM ToN, 13(1):43-56, Feb 2005 (444k)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/16/PNAS_Internet05.pdf ''The ‘‘robust yet fragile’’ nature of the Internet''] 
John C. Doyle, David L. Alderson, Lun Li, Steven Low, Matthew Roughan, Stanislav Shalunov, Reiko Tanaka, and Walter Willinger 
Proc. Natl. Acad. Sci. USA, 102(41):14497-14502, Oct 11 2005. (635K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/b/b4/PNAS_HeatShock05.pdf ''Surviving Heat Shock: Control Strategies for Robustness and Performance''], 
H. El-Samad, H. Kurata , J.C. Doyle , C.A. Gross, and M. Khammash, 
Proc. Natl. Acad. Sci. USA 102(8): 2736-2741 Feb 22, 2005. (390K)

*''Highly optimized tolerance and power laws in dense and sparse resource regimes'', 
Manning M, Carlson JM, Doyle J, 
Phys. Rev. E 72 (1): Art. No. 016108 Part 2 Jul 2005

*''Three mechanisms for power laws on the Cayley tree'',
T Brookings, JM Carlson, and J Doyle 
Phys. Rev. E 72, 056120

*''Evolutionary dynamics and highly optimized tolerance'', 
Zhou T, Carlson JM, Doyle J 
Journal of Theoretical Biology 236 (4): 438-447 Oct 21 2005

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/98/FEBS_PPI05.pdf ''Some protein interaction data do not exhibit power law statistics''], 
R. Tanaka, T-M Yi, and J. Doyle 
FEBS letters, 579 (23): 5140-5144 Sept 26 2005 (221K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/PNAS_HOTFire05.pdf ''Wildfires, complexity, and highly optimized tolerance''], 
MA Moritz, ME Morais, LA Summerell, JM Carlson, J Doyle 
Proc. Natl. Acad. Sci. USA, December 13, 2005; 102 (50):17912–17917 (403K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f2/IEESysBio05.pdf ''Highly optimised global organisation of metabolic networks''], 
R. Tanaka, M. Csete and J. Doyle, 
IEE Proc.-Syst. Biol. 152(4): 179, Dec 2005 (820K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f6/Li-SFGraph-IM-0508-2005.pdf ''Towards a theory of scale-free graphs: definitions, properties, and implications''] 
L. Li, D. Alderson, J. C. Doyle and W. Willinger 
Internet Mathematics, 2005 (909k).

===Conferences===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1b/Tcpmac-infocom05.pdf ''Joint congestion control and media access control design for wireless ad hoc networks''] 
Lijun Chen, Steven H. Low and John C. Doyle. 
in Proc. IEEE Infocom, Miami, FL, Mar 2005 (193k).

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/d/dd/Sigmetrics05.pdf ''Optimization model of internet protocols''] 
Steven H. Low, John Doyle, Lun Li, Ao Tang and Jiantao Wang 
in Proceedings of SIGMETRICS, pp277 - 277, Banff, Alberta, Canada, June 6-10, 2005.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/CDC2005.pdf ''Fundamental Limitations of Disturbance Attenuation in the Presence of Side Information''] 
Martins, N.C.; Dahleh, M.A.; Doyle, J.C.; 
IEEE CDC - ECC pp2523 - 2529, Seville, Spain, 12-15 Dec 2005.

===Book===
''[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/4e/Part1_vers4.pdf Robustness and the Internet: Design and evolution]'', 
W. Willinger, J Doyle, 
in Robust Design: A Repertoire of Biological, Ecological, and Engineering Case Studies 
(Santa Fe Institute Studies on the Sciences of Complexity), 
Erica Jen, Editor 2005
[[Category:Papers]][[Category:Papers by year]]

2010-2011

2011-07-04T05:16:25Z

Vanessa:

File:PhysFluids 23 065108.pdf

2011-07-04T05:11:31Z

Vanessa:

Group

2011-07-04T05:08:21Z

Vanessa: /* Postdocs */

John Doyle's research '''group''' is part of [http://www.cds.caltech.edu/people/ CDS department] at Caltech.

==Current Group==

===Faculty===
John Doyle

===Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/~chen/ Lijun Chen]
[http://www.cds.caltech.edu/people/portal/?id=331 Dennice Maynard Gayme]
|[http://www.cs.caltech.edu/~krister/ Krister Jacobsson]
|[http://www.ist.caltech.edu/~brecht/ Ben Recht]
|}

===Graduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/?id=4 Aristotelis Asimakopoulos]
|[http://www.cds.caltech.edu/people/portal/?id=384 Gentian Buzi]
|[http://www.cds.caltech.edu/people/portal/?id=758 Vanessa Jönsson]
|-
|[http://www.its.caltech.edu/~fiona Fiona Chandra]
|[http://www.cds.caltech.edu/~andyl/ Andrew Lamperski]
|-
|[http://www.cds.caltech.edu/~lavaei/ Javad Lavaei-Yanesi]
|[http://www.cds.caltech.edu/people/portal/?id=753 Na Li]
|[http://www.cds.caltech.edu/people/portal/?id=522 Marcos Nahmad Bensusan]
|-
|[http://www.cds.caltech.edu/people/portal/index.php?id=797 Somayeh Sojoudi]
|Jerry Cruz||
|}

===Undergraduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/index.php?id=772 George Hines]||[http://www.cds.caltech.edu/people/portal/?id=803 Nicholas Fette]
|}
===Admin===
Anissa Scott

===Visitors===
[http://www.cds.caltech.edu/~lun/ Lun Li, also alumni]
====Students====
{| class="wikitable" border="1"
|-
|''SURF 2008''||''Other''
|-
|Jackson Wang Ji Young Lee||Paul Fang, student from Temple City High School
|}

==Past Group==
===Alumni===
{| class="wikitable" border="0" width="80%"
|-
|'''2007'''||'''2000-2006'''||'''1990-1999'''
|-
|[http://www.cds.caltech.edu/~chen/ Lijun Chen]

[http://www.cds.caltech.edu/~lun Lun Li]

[http://www.cds.caltech.edu/people/portal/?id=6 Xin Liu]

[http://www.cds.caltech.edu/~alfredo/ Alfredo Martinez]

[http://www.cds.caltech.edu/people/portal/?id=184 Oluwatosin Otitoju]
|
[http://faculty.nps.edu/dlalders/ David Alderson]

Nizar Batada

[http://www.cds.caltech.edu/~xlfeng/ Xiaolin Feng]

Irene Gregory

[http://www.seas.upenn.edu/~jadbabai/ Ali Jadbabaie]

[http://webfiles.uci.edu/yjing/www/ Yindi Jing]

Sven Khatri

[http://users.ox.ac.uk/~engs0587/ Antonis Papachristodoulou]

[http://www.mit.edu/~parrilo/ Pablo Parrilo]

[http://www.cds.caltech.edu/~prajna/ Stephen Prajna]

[http://www.cds.caltech.edu/~jiantao/ Jiantao Wang]

[http://www.cds.caltech.edu/~jyu/ Jie Yu]

[http://www.cds.caltech.edu/~xyzhu/ Xiaoyun Zhu]

|Carolyn Beck

Raff D'Andrea

Sonja Glavaski

Irene Gregory

Yun Huang

Michael Kantner

[http://www.ee.ucla.edu/~paganini/ Fernando Paganini]

[http://www.stanford.edu/dept/MSandE/people/faculty/primbs/index.html James Primbs]

Stefano Soatto

Jorge Tierno
|}

===Past Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|'''2007-2008'''||'''2000-2006'''||'''1990-1999'''
|-
|
[http://www.cds.caltech.edu/people/portal/?id=662 Aaron D. Ames]

[http://www.cds.caltech.edu/~dtarraf/ Danielle C.Tarraf]

[http://www.cds.caltech.edu/~maryam/ Maryam Fazel, Research scientist]
|
Masahiro Yanagisawa

[http://www-control.eng.cam.ac.uk/~jmg77/ Jorge Goncalves]

[http://devcell.bio.uci.edu/faculty/yi.htm Tau-Mu Yi]
|
[http://www.nps.navy.mil/orfacpag/resumePages/alderson.htm David Alderson]

[http://www.bmc.riken.jp/~reiko/index.htm Reiko Tanaka]
|}
===Past Admin===

?-2008 Gloria Bain

===Past Visitors===
{| class="wikitable" border="0" width="80%"
|-
|'''2007'''
|'''2000-2006
|'''1990-1999'''
|-
|Panagiota Stratou
|?
|?
|}

==MURF and SURF Students==
{| class="wikitable" border="0" width="80%"
|'''2008'''||'''2007''' ||'''2000-2006'''
|-
|Jackson Wang Ji Young Lee ||[http://www.cds.caltech.edu/people/portal/?id=722 Chinwendu Enyioha]||
|-
| ||
|}

==Other collaborators==
{| class="wikitable" border="0" width="80%"
|-
|[[Image:3profs07.jpg|200px]]||[[Image:John-and-marie.jpg]]
|-
|2007 Commencement: Prof.'s John Doyle, Richard Murray & Steven Low. ||John Doyle and Marie Csete
|}

[[Image:JCDgraph.jpg]]

Some collaborators at John Doyle's 50th birthday Connections Workshop, 2004:

*[http://userwww.service.emory.edu/~mcsete/ Marie Csete, Lab] at [http://www.emory.edu/change_mode.cfm?mode=text Emory University], Atlanta.
**[http://www.emory.edu/PROVOST/greatscholars/MarieCsete.htm About Marie Csete's work.]

==See also==
*[[Group Meetings]]
*[[Calendar]]
*<http://www.cds.caltech.edu/people/portal/?un=doyle>

Group

2011-07-04T05:07:25Z

Vanessa: /* Graduate students */

John Doyle's research '''group''' is part of [http://www.cds.caltech.edu/people/ CDS department] at Caltech.

==Current Group==

===Faculty===
John Doyle

===Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/~chen/ Lijun Chen]
|[http://www.cs.caltech.edu/~krister/ Krister Jacobsson]
|[http://www.ist.caltech.edu/~brecht/ Ben Recht]
|}

===Graduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/?id=4 Aristotelis Asimakopoulos]
|[http://www.cds.caltech.edu/people/portal/?id=384 Gentian Buzi]
|[http://www.cds.caltech.edu/people/portal/?id=758 Vanessa Jönsson]
|-
|[http://www.its.caltech.edu/~fiona Fiona Chandra]
|[http://www.cds.caltech.edu/~andyl/ Andrew Lamperski]
|-
|[http://www.cds.caltech.edu/~lavaei/ Javad Lavaei-Yanesi]
|[http://www.cds.caltech.edu/people/portal/?id=753 Na Li]
|[http://www.cds.caltech.edu/people/portal/?id=522 Marcos Nahmad Bensusan]
|-
|[http://www.cds.caltech.edu/people/portal/index.php?id=797 Somayeh Sojoudi]
|Jerry Cruz||
|}

===Undergraduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/index.php?id=772 George Hines]||[http://www.cds.caltech.edu/people/portal/?id=803 Nicholas Fette]
|}
===Admin===
Anissa Scott

===Visitors===
[http://www.cds.caltech.edu/~lun/ Lun Li, also alumni]
====Students====
{| class="wikitable" border="1"
|-
|''SURF 2008''||''Other''
|-
|Jackson Wang Ji Young Lee||Paul Fang, student from Temple City High School
|}

==Past Group==
===Alumni===
{| class="wikitable" border="0" width="80%"
|-
|'''2007'''||'''2000-2006'''||'''1990-1999'''
|-
|[http://www.cds.caltech.edu/~chen/ Lijun Chen]

[http://www.cds.caltech.edu/~lun Lun Li]

[http://www.cds.caltech.edu/people/portal/?id=6 Xin Liu]

[http://www.cds.caltech.edu/~alfredo/ Alfredo Martinez]

[http://www.cds.caltech.edu/people/portal/?id=184 Oluwatosin Otitoju]
|
[http://faculty.nps.edu/dlalders/ David Alderson]

Nizar Batada

[http://www.cds.caltech.edu/~xlfeng/ Xiaolin Feng]

Irene Gregory

[http://www.seas.upenn.edu/~jadbabai/ Ali Jadbabaie]

[http://webfiles.uci.edu/yjing/www/ Yindi Jing]

Sven Khatri

[http://users.ox.ac.uk/~engs0587/ Antonis Papachristodoulou]

[http://www.mit.edu/~parrilo/ Pablo Parrilo]

[http://www.cds.caltech.edu/~prajna/ Stephen Prajna]

[http://www.cds.caltech.edu/~jiantao/ Jiantao Wang]

[http://www.cds.caltech.edu/~jyu/ Jie Yu]

[http://www.cds.caltech.edu/~xyzhu/ Xiaoyun Zhu]

|Carolyn Beck

Raff D'Andrea

Sonja Glavaski

Irene Gregory

Yun Huang

Michael Kantner

[http://www.ee.ucla.edu/~paganini/ Fernando Paganini]

[http://www.stanford.edu/dept/MSandE/people/faculty/primbs/index.html James Primbs]

Stefano Soatto

Jorge Tierno
|}

===Past Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|'''2007-2008'''||'''2000-2006'''||'''1990-1999'''
|-
|
[http://www.cds.caltech.edu/people/portal/?id=662 Aaron D. Ames]

[http://www.cds.caltech.edu/~dtarraf/ Danielle C.Tarraf]

[http://www.cds.caltech.edu/~maryam/ Maryam Fazel, Research scientist]
|
Masahiro Yanagisawa

[http://www-control.eng.cam.ac.uk/~jmg77/ Jorge Goncalves]

[http://devcell.bio.uci.edu/faculty/yi.htm Tau-Mu Yi]
|
[http://www.nps.navy.mil/orfacpag/resumePages/alderson.htm David Alderson]

[http://www.bmc.riken.jp/~reiko/index.htm Reiko Tanaka]
|}
===Past Admin===

?-2008 Gloria Bain

===Past Visitors===
{| class="wikitable" border="0" width="80%"
|-
|'''2007'''
|'''2000-2006
|'''1990-1999'''
|-
|Panagiota Stratou
|?
|?
|}

==MURF and SURF Students==
{| class="wikitable" border="0" width="80%"
|'''2008'''||'''2007''' ||'''2000-2006'''
|-
|Jackson Wang Ji Young Lee ||[http://www.cds.caltech.edu/people/portal/?id=722 Chinwendu Enyioha]||
|-
| ||
|}

==Other collaborators==
{| class="wikitable" border="0" width="80%"
|-
|[[Image:3profs07.jpg|200px]]||[[Image:John-and-marie.jpg]]
|-
|2007 Commencement: Prof.'s John Doyle, Richard Murray & Steven Low. ||John Doyle and Marie Csete
|}

[[Image:JCDgraph.jpg]]

Some collaborators at John Doyle's 50th birthday Connections Workshop, 2004:

*[http://userwww.service.emory.edu/~mcsete/ Marie Csete, Lab] at [http://www.emory.edu/change_mode.cfm?mode=text Emory University], Atlanta.
**[http://www.emory.edu/PROVOST/greatscholars/MarieCsete.htm About Marie Csete's work.]

==See also==
*[[Group Meetings]]
*[[Calendar]]
*<http://www.cds.caltech.edu/people/portal/?un=doyle>

Group

2011-07-04T05:07:01Z

Vanessa: /* Graduate students */

John Doyle's research '''group''' is part of [http://www.cds.caltech.edu/people/ CDS department] at Caltech.

==Current Group==

===Faculty===
John Doyle

===Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/~chen/ Lijun Chen]
|[http://www.cs.caltech.edu/~krister/ Krister Jacobsson]
|[http://www.ist.caltech.edu/~brecht/ Ben Recht]
|}

===Graduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/?id=4 Aristotelis Asimakopoulos]
|[http://www.cds.caltech.edu/people/portal/?id=384 Gentian Buzi]
|[http://www.cds.caltech.edu/people/portal/?id=758 Vanessa Jönsson]
|-
|[http://www.its.caltech.edu/~fiona Fiona Chandra]
|[http://www.cds.caltech.edu/people/portal/?id=331 Dennice Maynard Gayme]
|[http://www.cds.caltech.edu/~andyl/ Andrew Lamperski]
|-
|[http://www.cds.caltech.edu/~lavaei/ Javad Lavaei-Yanesi]
|[http://www.cds.caltech.edu/people/portal/?id=753 Na Li]
|[http://www.cds.caltech.edu/people/portal/?id=522 Marcos Nahmad Bensusan]
|-
|[http://www.cds.caltech.edu/people/portal/index.php?id=797 Somayeh Sojoudi]
|Jerry Cruz||
|}

===Undergraduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/index.php?id=772 George Hines]||[http://www.cds.caltech.edu/people/portal/?id=803 Nicholas Fette]
|}
===Admin===
Anissa Scott

===Visitors===
[http://www.cds.caltech.edu/~lun/ Lun Li, also alumni]
====Students====
{| class="wikitable" border="1"
|-
|''SURF 2008''||''Other''
|-
|Jackson Wang Ji Young Lee||Paul Fang, student from Temple City High School
|}

==Past Group==
===Alumni===
{| class="wikitable" border="0" width="80%"
|-
|'''2007'''||'''2000-2006'''||'''1990-1999'''
|-
|[http://www.cds.caltech.edu/~chen/ Lijun Chen]

[http://www.cds.caltech.edu/~lun Lun Li]

[http://www.cds.caltech.edu/people/portal/?id=6 Xin Liu]

[http://www.cds.caltech.edu/~alfredo/ Alfredo Martinez]

[http://www.cds.caltech.edu/people/portal/?id=184 Oluwatosin Otitoju]
|
[http://faculty.nps.edu/dlalders/ David Alderson]

Nizar Batada

[http://www.cds.caltech.edu/~xlfeng/ Xiaolin Feng]

Irene Gregory

[http://www.seas.upenn.edu/~jadbabai/ Ali Jadbabaie]

[http://webfiles.uci.edu/yjing/www/ Yindi Jing]

Sven Khatri

[http://users.ox.ac.uk/~engs0587/ Antonis Papachristodoulou]

[http://www.mit.edu/~parrilo/ Pablo Parrilo]

[http://www.cds.caltech.edu/~prajna/ Stephen Prajna]

[http://www.cds.caltech.edu/~jiantao/ Jiantao Wang]

[http://www.cds.caltech.edu/~jyu/ Jie Yu]

[http://www.cds.caltech.edu/~xyzhu/ Xiaoyun Zhu]

|Carolyn Beck

Raff D'Andrea

Sonja Glavaski

Irene Gregory

Yun Huang

Michael Kantner

[http://www.ee.ucla.edu/~paganini/ Fernando Paganini]

[http://www.stanford.edu/dept/MSandE/people/faculty/primbs/index.html James Primbs]

Stefano Soatto

Jorge Tierno
|}

===Past Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|'''2007-2008'''||'''2000-2006'''||'''1990-1999'''
|-
|
[http://www.cds.caltech.edu/people/portal/?id=662 Aaron D. Ames]

[http://www.cds.caltech.edu/~dtarraf/ Danielle C.Tarraf]

[http://www.cds.caltech.edu/~maryam/ Maryam Fazel, Research scientist]
|
Masahiro Yanagisawa

[http://www-control.eng.cam.ac.uk/~jmg77/ Jorge Goncalves]

[http://devcell.bio.uci.edu/faculty/yi.htm Tau-Mu Yi]
|
[http://www.nps.navy.mil/orfacpag/resumePages/alderson.htm David Alderson]

[http://www.bmc.riken.jp/~reiko/index.htm Reiko Tanaka]
|}
===Past Admin===

?-2008 Gloria Bain

===Past Visitors===
{| class="wikitable" border="0" width="80%"
|-
|'''2007'''
|'''2000-2006
|'''1990-1999'''
|-
|Panagiota Stratou
|?
|?
|}

==MURF and SURF Students==
{| class="wikitable" border="0" width="80%"
|'''2008'''||'''2007''' ||'''2000-2006'''
|-
|Jackson Wang Ji Young Lee ||[http://www.cds.caltech.edu/people/portal/?id=722 Chinwendu Enyioha]||
|-
| ||
|}

==Other collaborators==
{| class="wikitable" border="0" width="80%"
|-
|[[Image:3profs07.jpg|200px]]||[[Image:John-and-marie.jpg]]
|-
|2007 Commencement: Prof.'s John Doyle, Richard Murray & Steven Low. ||John Doyle and Marie Csete
|}

[[Image:JCDgraph.jpg]]

Some collaborators at John Doyle's 50th birthday Connections Workshop, 2004:

*[http://userwww.service.emory.edu/~mcsete/ Marie Csete, Lab] at [http://www.emory.edu/change_mode.cfm?mode=text Emory University], Atlanta.
**[http://www.emory.edu/PROVOST/greatscholars/MarieCsete.htm About Marie Csete's work.]

==See also==
*[[Group Meetings]]
*[[Calendar]]
*<http://www.cds.caltech.edu/people/portal/?un=doyle>

Systems biology

2011-07-04T05:03:25Z

Vanessa: /* Systems biology */

Intro: ...'''systems biology'''...

....the development of machine-readable language to discuss biological systems '''SBML''' has resulted from a collaborative effort between many other diverse research groups...this has opended up...

Keywords: '''systems biology''', SBML mark-up, robustness, complexity, networks, biology, proteins.

A few papers were copied from <http://www.cds.caltech.edu/~doyle/RecentPapers/ >

==Systems biology==
Keywords: '''systems biology''', biological networks, complexity, control, heat-shock, protein, robustness, metabolism...

===2009===
[http://www.nt.ntnu.no/users/skoge/prost/proceedings/acc09/data/papers/0207.pdf ''Linear control analysis of the autocatalytic glycolysis system''] 
Fiona Chandra, Gentian Buzi, John Doyle 
In Proc. American Control Conf, 319-324 JUN 2009

===2007===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/4/43/Nature_Connections07.pdf ''Rules of engagement''] 
John Doyle and Marie Csete 
Nature Vol 446:860 April 19 2007 (142K)

===2006===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/IEEEProc_Bio.pdf ''Advanced Methods and Algorithms for Biological Networks Analysis''], 
H El-Samad , A Papachristodoulou, S Prajna, J Doyle, and M Khammash 
In Proc. IEEE, 94 (4): 832-853 APR 2006 (900K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/1f/PlosCompBio_HS06.pdf ''Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System ''] 
Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash, 
[http://compbiol.plosjournals.org/ PLoS Comput Biol] 2(7): July 2006 (1.1MB)

===2005===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/98/FEBS_PPI05.pdf ''Some protein interaction data do not exhibit power law statistics''], 
R. Tanaka, T-M Yi, and J. Doyle 
FEBS letters, 579 (23): 5140-5144 Sept 26 2005 (221K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f2/IEESysBio05.pdf ''Highly optimised global organisation of metabolic networks''], 
R. Tanaka, M. Csete and J. Doyle, 
IEE Proc.-Syst. Biol. 152(4): 179, Dec 2005 (820K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/a/a7/PLOS_Primer05.pdf ''Motifs, control, and stability''] (including ''Supplementary Notes: Elementary Feedback Concepts'') 
Doyle J and Csete M 
[http://www.plosbiology.org PLoS Biol] 3(11): e392; 2005. (387K)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/b/b4/PNAS_HeatShock05.pdf ''Surviving Heat Shock: Control Strategies for Robustness and Performance''] 
H. El-Samad, H. Kurata , J.C. Doyle , C.A. Gross, and M. Khammash, 
Proc. Natl. Acad. Sci. USA 102(8): 2736-2741 Feb 22, 2005. (390K)

===2004===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/13/Cell04.pdf ''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)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/82/Trends04.pdf ''Bow ties, metabolism, and disease''], 
Csete M.E. and J.C. Doyle, 
Trends in Biotechnology 22(9):446-50 Sept 2004. (121K)

===2002===
[http://www.cds.caltech.edu/~doyle2/wiki/skins/common/images/icons/fileicon-pdf.png ''Reverse Engineering of Biological Complexity''] 
Csete M and Doyle J, 
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB)

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/12/JtheorBiol2002.pdf ''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.

==SBML==
Keywords: '''SBML''', systems biology mark-up language, computer software, biochemical reaction networks

===2004===
[http://scitation.aip.org/dbt/dbt.jsp?KEY=IPSBDJ&Volume=1 '' 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

*''MathSBML: a package for manipulating SBML-based biological models'', 
Shapiro BE, Hucka M, Finney A, Doyle J. 
Bioinformatics, Nov 1, 2004

===2002===
[http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11928498&dopt=Abstract ''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.

===2001===
*''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.

==More Biology==
Keywords: '''biology''', cell, HOT (highly optimized tolerance), SOSTOOLS (sums of squares optimization), robustness
===2005===
''Evolutionary dynamics and highly optimized tolerance,''
Zhou T, Carlson JM, Doyle J 
Journal of Theoretical Biology 236 (4): 438-447 Oct 21 2005

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/0/01/PNAS_HOTFire05.pdf ''Wildfires, complexity, and highly optimized tolerance''], 
MA Moritz, ME Morais, LA Summerell, JM Carlson, J Doyle 
Proc. Natl. Acad. Sci. USA, December 13, 2005; 102 (50):17912–17917 (403K)

===2003===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f8/CDC2003.pdf ''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.

===2002===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/72/PNAS2538-2002.full.pdf ''Complexity and robustness''], 
Carlson JM, Doyle J, 
Proc. Natl. Acad. Sci. USA 99: 2538-2545 Suppl. 1 Feb 19, 2002.

[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/8/85/PNAS2049-2002.full.pdf ''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.

===2001===
*''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

===2000===
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f0/PNAS4649-2000.full.pdf ''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.

==Related reading==
[[Papers]]

[[Research]]

[[Tips: Research papers, Publishing and Other Trivia]]

===Other===

===External links===
*[http://sbml.org/Main_Page SBML Definition and homepage]
*[http://sbml.org/Documents SBML documents]
*[http://www.systems-biology.org/ Systems Biology Portal]
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]

[[Category:Research]]
[[Category:Papers by topic]]
[[Category:Papers]]

2010-2011

2011-07-04T04:44:58Z

Vanessa:

D. Gayme, B. McKeon, J. C. Doyle and B. Bamieh, Amplification and Nonlinear Mechanisms in Plane Couette Flow. Physics of Fluids vol. 23, Issue 6, 065108 (2011)

Papers

2011-07-04T04:44:33Z

Vanessa: /* Year */

'''Papers''' span many years and cover a diverse range of topics, from understanding the internet to financial market analysis, control theory and also covering certain aspects of biology, physics and physiology. '''Papers''' have been sorted by topic and year (see below.) These pages list some of Doyle's papers and related reading in these areas!



==Year==
[[2010-2011]]

[[2005-2009]]

[[2000-2004]]

[[1995-1999]]

[[1990-1994]]

[[1985-1989]]

==Topic==
*[[General complexity]]
*[[Networking]]
*[[Network architecture and protocols]]
*[[Wildfire ecology]]
*[[Systems biology]]
*[[Physiology]]

==Older topics==
*[[Complex networks]]
*[[Complexity and robustness]]

==See also==
[[Tips: Research papers, Publishing and Other Trivia]]

[[Research]]

See [[DoyleWiki:Copyrights|Copyright statment]] before downloading or viewing papers.

[[Category:Papers]]
[[Category:Papers by year]]
[[Category:Papers by topic]]

Research

2011-07-04T04:41:19Z

Vanessa: /* Current Projects */

"Professor Doyle's current '''research''' interests are in theoretical foundations for complex networks, primarily in network engineering and biology." He is also "interested in multiscale physics and financial markets, and the interplay between robustness, feedback, control, dynamical systems, computation, communications, and statistical physics." <http://www.cds.caltech.edu/people/> Aug 2008

Prof. Doyle has "applied complex ideas of robust design and control to many fields and is working on a unified theory of control in engineering, physics and biology." <http://www.ieee.org/portal/pages/about/awards/bios/2004controlsystems.html> Aug 2008

==Current Projects==
*Fluids: Turbulence Modeling
*[http://openwetware.org/wiki/Doyle Physiology]

==Research Grants==
*[http://www.nsf.gov/index.jsp NSF] award: [http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0326635 ITR COLLAB: Theory and Software Infrastructure for a Scalable Systems Biology], 2003-present

*Some joint projects with [http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Richard Murray] (with links to his wiki below)
**[http://www.cds.caltech.edu/~murray/VaVmuri/index.php?title=Main_Page Specification, Design and Verification of Distributed Embedded Systems] (MURI/AFOSR)
**Networked Feedback Systems in Biology (ARO ICB)
**[http://www.cds.caltech.edu/~murray/wiki/Model-Based_Design_and_Qualification_of_Complex_Systems Model-Based Design and Qualification of Complex Systems] (Boeing)

*Some joint grants with [http://netlab.caltech.edu/~slow/ Prof. Steven Low]:
**MURI Analysis and modeling of networks with long range dependence (LRD) characteristics (PI - Jean Walrand, UC Berkeley; Co-PIs - John Doyle, Steven Low, R. Srikanth (UIUC), V. Anantharam & A. Zakhor (UC Berkeley), D. Towsley & W. Gong (U. Mass. Amherst)2008
**NSF RI WAN in Lab (Newman, Psaltis, Yip) 2003-08
**NSF NeTS Collaborative Research: Optimization and Games in Interdomain Routing 2006
**NSF STI Multi-Gbps TCP: Data Intensive Networks for Science & Engineering (Bunn, Newman) 2002-05
**NSF ITR Optimal and Robust TCP Congestion Control 2001-04
**ARO DURIP Hybrid WAN in Lab (Newman, Psaltis, Yip) 2004-05
**ARO Network Research Analytical Theory of Protocols 2002-05
**ARO Network Science Networked control systems (Murray, Parrilo (MIT)) 2005-2006
(Note that other Co-PI are noted in brackets on these joint grants with Prof. Low and Prof. Doyle)

== Past Projects ==
Caltech
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]
*[http://www.cds.caltech.edu/~doyle/MURI.html "Mathematical Infrastructure for Robust Virtual Engineering"] MURI award 1996
*Past projects with Prof Murray (links to his wiki)
**[http://www.cds.caltech.edu/~murray/projects/afosr95-vehicles/ Robust Nonlinear Control Theory with Application to Aerospace Vehicles] (AFOSR)
**[http://www.cds.caltech.edu/~murray/cdspanel/ Panel on Future Directions in Control, Dynamics, and Systems]
**[http://www.cds.caltech.edu/~murray/projects/nsf93-crcd/index.html Curriculum in Control and Dynamical Systems] (NSF)

Other

==Collaborative groups==
*[http://www.cimms.caltech.edu/whatiscimms.html CIMMS: Center for Integrative Multiscale Modeling and Simulation]
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page Prof. Richard Murray]
* Lee Center for Networking
*[http://netlab.caltech.edu/ Netlab]
**[http://netlab.caltech.edu/FAST/FAST: Fast AQM Scalable TCP, new internet protocol design.]

*[http://www.sisl.caltech.edu/ SISL]

* and more...

==See also==
*[[Papers]]
*[[Special:Allpages|All articles]]
*[[Special:Categories|Pages listed by Categories]]

===More research links===
Caltech
*[http://www.cds.caltech.edu/~murray/wiki/Main_Page#Research Prof. Murray's projects]
*[http://netlab.caltech.edu/projects.php Prof. Low's projects]
*[http://www.cds.caltech.edu/research/ CDS]
*[http://leecenter.caltech.edu/theory.html Lee Center]
*[http://leecenter.caltech.edu/doyle-res.html HOT at Lee Center]
*[http://www.sisl.caltech.edu/people/index.html SISL]

UCSB
*[http://www.physics.ucsb.edu/~complex/ Jean Carlson’s HOT website]
[[Category:Research]]

Group

2011-07-04T01:02:23Z

Vanessa: /* Admin */

John Doyle's research '''group''' is part of [http://www.cds.caltech.edu/people/ CDS department] at Caltech.

==Current Group==

===Faculty===
John Doyle

===Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/~chen/ Lijun Chen]
|[http://www.cs.caltech.edu/~krister/ Krister Jacobsson]
|[http://www.ist.caltech.edu/~brecht/ Ben Recht]
|}

===Graduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/?id=4 Aristotelis Asimakopoulos]
|[http://www.cds.caltech.edu/people/portal/?id=384 Gentian Buzi]
|[http://www.cds.caltech.edu/people/portal/?id=758 Vanessa Jönsson]
|-
|[http://www.cds.caltech.edu/people/portal/?id=760 Fiona Chandra]
|[http://www.cds.caltech.edu/people/portal/?id=331 Dennice Maynard Gayme]
|[http://www.cds.caltech.edu/~andyl/ Andrew Lamperski]
|-
|[http://www.cds.caltech.edu/~lavaei/ Javad Lavaei-Yanesi]
|[http://www.cds.caltech.edu/people/portal/?id=753 Na Li]
|[http://www.cds.caltech.edu/people/portal/?id=522 Marcos Nahmad Bensusan]
|-
|[http://www.cds.caltech.edu/people/portal/index.php?id=797 Somayeh Sojoudi]
|Jerry Cruz||
|}

===Undergraduate students===
{| class="wikitable" border="0" width="80%"
|-
|[http://www.cds.caltech.edu/people/portal/index.php?id=772 George Hines]||[http://www.cds.caltech.edu/people/portal/?id=803 Nicholas Fette]
|}
===Admin===
Anissa Scott

===Visitors===
[http://www.cds.caltech.edu/~lun/ Lun Li, also alumni]
====Students====
{| class="wikitable" border="1"
|-
|''SURF 2008''||''Other''
|-
|Jackson Wang Ji Young Lee||Paul Fang, student from Temple City High School
|}

==Past Group==
===Alumni===
{| class="wikitable" border="0" width="80%"
|-
|'''2007'''||'''2000-2006'''||'''1990-1999'''
|-
|[http://www.cds.caltech.edu/~chen/ Lijun Chen]

[http://www.cds.caltech.edu/~lun Lun Li]

[http://www.cds.caltech.edu/people/portal/?id=6 Xin Liu]

[http://www.cds.caltech.edu/~alfredo/ Alfredo Martinez]

[http://www.cds.caltech.edu/people/portal/?id=184 Oluwatosin Otitoju]
|
[http://faculty.nps.edu/dlalders/ David Alderson]

Nizar Batada

[http://www.cds.caltech.edu/~xlfeng/ Xiaolin Feng]

Irene Gregory

[http://www.seas.upenn.edu/~jadbabai/ Ali Jadbabaie]

[http://webfiles.uci.edu/yjing/www/ Yindi Jing]

Sven Khatri

[http://users.ox.ac.uk/~engs0587/ Antonis Papachristodoulou]

[http://www.mit.edu/~parrilo/ Pablo Parrilo]

[http://www.cds.caltech.edu/~prajna/ Stephen Prajna]

[http://www.cds.caltech.edu/~jiantao/ Jiantao Wang]

[http://www.cds.caltech.edu/~jyu/ Jie Yu]

[http://www.cds.caltech.edu/~xyzhu/ Xiaoyun Zhu]

|Carolyn Beck

Raff D'Andrea

Sonja Glavaski

Irene Gregory

Yun Huang

Michael Kantner

[http://www.ee.ucla.edu/~paganini/ Fernando Paganini]

[http://www.stanford.edu/dept/MSandE/people/faculty/primbs/index.html James Primbs]

Stefano Soatto

Jorge Tierno
|}

===Past Postdocs===
{| class="wikitable" border="0" width="80%"
|-
|'''2007-2008'''||'''2000-2006'''||'''1990-1999'''
|-
|
[http://www.cds.caltech.edu/people/portal/?id=662 Aaron D. Ames]

[http://www.cds.caltech.edu/~dtarraf/ Danielle C.Tarraf]

[http://www.cds.caltech.edu/~maryam/ Maryam Fazel, Research scientist]
|
Masahiro Yanagisawa

[http://www-control.eng.cam.ac.uk/~jmg77/ Jorge Goncalves]

[http://devcell.bio.uci.edu/faculty/yi.htm Tau-Mu Yi]
|
[http://www.nps.navy.mil/orfacpag/resumePages/alderson.htm David Alderson]

[http://www.bmc.riken.jp/~reiko/index.htm Reiko Tanaka]
|}
===Past Admin===

?-2008 Gloria Bain

===Past Visitors===
{| class="wikitable" border="0" width="80%"
|-
|'''2007'''
|'''2000-2006
|'''1990-1999'''
|-
|Panagiota Stratou
|?
|?
|}

==MURF and SURF Students==
{| class="wikitable" border="0" width="80%"
|'''2008'''||'''2007''' ||'''2000-2006'''
|-
|Jackson Wang Ji Young Lee ||[http://www.cds.caltech.edu/people/portal/?id=722 Chinwendu Enyioha]||
|-
| ||
|}

==Other collaborators==
{| class="wikitable" border="0" width="80%"
|-
|[[Image:3profs07.jpg|200px]]||[[Image:John-and-marie.jpg]]
|-
|2007 Commencement: Prof.'s John Doyle, Richard Murray & Steven Low. ||John Doyle and Marie Csete
|}

[[Image:JCDgraph.jpg]]

Some collaborators at John Doyle's 50th birthday Connections Workshop, 2004:

*[http://userwww.service.emory.edu/~mcsete/ Marie Csete, Lab] at [http://www.emory.edu/change_mode.cfm?mode=text Emory University], Atlanta.
**[http://www.emory.edu/PROVOST/greatscholars/MarieCsete.htm About Marie Csete's work.]

==See also==
*[[Group Meetings]]
*[[Calendar]]
*<http://www.cds.caltech.edu/people/portal/?un=doyle>

Main Page

2011-07-04T00:46:42Z

Vanessa: /* Contact */

<table border=1 width=100% style="color:black; " cellpadding="20" cellspacing="0">
<tr>
<td align=center width=20%> [[Image:doyle.jpg]]</td>
<td width=60% align=center>
John C. Doyle 

John G Braun Professor 
of Control and Dynamical Systems 
Electrical Engineering 
and BioEngineering 
Division of Engineering and Applied Science 
California Institute of Technology 

</td>
<td align=center width=20%>


[[J. Doyle’s Bio]]

[[News]]

[[Calendar]]

[[#Contact|Contact]]

[https://www.cds.caltech.edu/squirrelmail/src/login.php CDS Webmail]
</td>
</tr></table>
{| align=center
|[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]||[[Image:Blossoms900strip.jpg]]
|}
<hr>

==News==
*[[Calendar]]
*[[Research|MURI 2008]]
*[http://discovermagazine.com/2007/nov/this-man-wants-to-control-the-internet Discover magazine] interviews Prof. Doyle.

"This man wants to control the internet" by Carl Zimmer, Discover magazine, 10/25/2007.

==Papers==
*[[Papers|'''More Papers''']]

== Research ==
"John Doyle's '''[[research]]''' interests are in theoretical foundations for complex networks in engineering and biology, as well as multiscale physics, and include integrating modeling, ID, analysis and design of uncertain nonlinear systems, and computation in analysis and simulation, including complexity theory to guide algorithm development. Applications interests are motivated by the interplay between: control, dynamical systems, and design and analysis of large, complex systems." <http://www.cds.caltech.edu/people/> Aug 16, 2008

*[[Research|Research projects and grants list]]


== Teaching ==

*[[CDS 213|The Architecture of Robust, Evolvable Networks (Wi10)]]

== Contact ==
{| width=100%
|- valign=top
| width=50% |

'''Mailing Address'''

John Doyle 
California Institute of Technology 
Control and Dynamical Systems, MC 107-81 
1200 E. California Blvd 
Pasadena, CA 91125 USA
| width=50% |

'''Contact information'''

E-mail: doyle AT cds dot caltech dot edu 
Office: 109 Steele, 
Phone: 626.395.4808 Fax: 626.395.6170 

'''Admin Assistant''': Anissa Scott 
Office: 107 Steele, 
Email: anissa AT caltech dot edu 
Phone: 626.395.4140 
Labs: 12 STL, 110 GUG (x2319)
|-
|

===Other Caltech links===

*[http://www.caltech.edu California Institute of Technology]
**[http://www.eas.caltech.edu Engineering and Applied Science Division]
***[http://www.be.caltech.edu/ Bioengineering Department]
***[http://www.cds.caltech.edu Control and Dynamical Systems Department]
***[http://www.ee2.caltech.edu/ Electrical Engineering Department]
|}

Molecular Cell Biology Project

2010-04-18T00:46:02Z

Vanessa: /* Reading */

== Project Description ==

== Reading ==

=== Cell Models ===

* [[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/6/61/Roleofribosomes.pdf ]]

== Participants ==

* Fiona Chandra
* Vanessa Jonsson
* Andy Lamperski
* Shaun Maguire
* Nader Motee

Molecular Cell Biology Project

2010-04-18T00:43:37Z

Vanessa: /* Reading */

== Project Description ==

== Reading ==

=== Cell Models ===

* [[http://www.cds.caltech.edu/~doyle2/wiki/index.php?title=Image:Roleofribosomes.pdf]]

== Participants ==

* Fiona Chandra
* Vanessa Jonsson
* Andy Lamperski
* Shaun Maguire
* Nader Motee

File:Roleofribosomes.pdf

2010-04-18T00:41:58Z

Vanessa:

Molecular Cell Biology Project

2010-04-18T00:21:59Z

Vanessa: /* Cell Models */

== Project Description ==

== Reading ==

=== Cell Models ===

== Participants ==

* Fiona Chandra
* Vanessa Jonsson
* Andy Lamperski
* Shaun Maguire
* Nader Motee

Molecular Cell Biology Project

2010-04-18T00:21:44Z

Vanessa: /* Reading */

== Project Description ==

== Reading ==

= Cell Models =

== Participants ==

* Fiona Chandra
* Vanessa Jonsson
* Andy Lamperski
* Shaun Maguire
* Nader Motee

Molecular Cell Biology Project

2010-04-18T00:20:16Z

Vanessa: /* Participants */

== Project Description ==

== Reading ==

== Participants ==

* Fiona Chandra
* Vanessa Jonsson
* Andy Lamperski
* Shaun Maguire
* Nader Motee

Molecular Cell Biology Project

2010-04-03T17:39:08Z

Vanessa: /* Participants */

== Project Description ==

== Reading ==

== Participants ==

* Fiona Chandra
* Vanessa Jonsson
* Shaun Maguire

Molecular Cell Biology Project

2010-04-03T17:37:56Z

Vanessa:

== Project Description ==

== Reading ==

== Participants ==

* Fiona Chandra
* Vanessa Jonsson
* Shaun McGuire

Molecular Cell Biology Project

2010-04-03T17:37:02Z

Vanessa:

== Project Description ==

== Reading ==

CDS 213

2010-04-03T17:36:15Z

Vanessa:

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> </td>
<td align=center>The Architecture of Robust, Evolvable Networks</td>
<td rowspan=2 align=center> </td></tr>
<tr valign=top><td align=center>Winter 2010</td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>
* Instructor: [http://www.cds.caltech.edu/~doyle2/wiki/index.php?title=J._Doyle’s_Bio John C. Doyle]
<table cellpadding=0 cellspacing=0><tr><td>
* [http://listserv.cds.caltech.edu/mailman/listinfo/cds-213 Course mailing list]
* Lectures: TTh 4-5:30 pm, 107 Annenberg, changes emailed to course mailing list
</td></tr></table>

== Course Schedule ==
{| border=1 width=100%
|-
| Week || Date || Topic || Reading
|-
| align=center rowspan=3 | 1
| colspan=3 | '''Introduction to Network Architectures'''
|-
| 12 Jan (T)
| [[IST Seminar: The Architecture of Robust, Evolvable Networks]]
|
|-
| 14 Jan (Th)
| [[Internet Architecture]]
| Network is IPC:[[Media:IPC-arch-rearch08.pdf | Day et al, 2008 (Paper)]];[[Media:IPC-arch.pdf | Matta (Slides)]]; [[Media:DAYIEEECCW2009.pdf | Implications PNA, Day, 2009 (Slides)]];[[Media:Touchccw2009.pdf | Multihop/Multiparty influences on Net. Arch., Touch (Slides)]]
|-
| align=center rowspan=3 | 2
| colspan=3 | '''Network Architectures: Operating Systems and Cell Biology '''
|-
| 19 Jan (T)
| [[Network Architectures: Internet vs. Biology| Internet and Biology Architectures]]
| [[Media:RINA_Security_11209.pdf | Assessing Security of a Clean Slate Internet Architecture , Boddapati, Day]];[[Media:GlycolysisACCFinal.pdf | Linear Control Analysis of the Autocatalytic Glycolysis System , Chandra, Buzi, Doyle]]
|-
| 21 Jan (Th)
| [[Robustness and Fragility, Hard limits and Tradeoffs| Robustness and Fragility, Hard Limits and Tradeoffs]]
| [[Media:TAC-statmech-revised-final.pdf | On Lossless Approximations, Fluctuation-Dissipation and Limitations of Measurements , Sandberg, Doyle]]
|-
| align=center rowspan=3 | 3
| colspan=3 | '''Case Studies: Cell Biology, Clothing and Legos '''
|-
| 26 Jan (T)
| [[Glycolysis | Network architecture and control of glycolysis; Clothing; Legos]]
| [[Media:GlycolysisACCFinal.pdf | Linear Control Analysis of the Autocatalytic Glycolysis System , Chandra, Buzi, Doyle]];[[Media:RedBloodCellsGlycolysis.pdf | Assembly and Regulation of a Glycolytic Enzyme Complex on the Human Erythrocyte Membrane , Campanella et al]]
|-
| 28 Jan (Th)
| [[ Heat Shock| Heat Shock in cells; Clothing; Legos]]
|[[Media: PNASHeatShock.pdf | Surviving Heat Shock: Control strategies for robustness and performance , El-Samad, et al]];[[Media: Cell.pdf | Robustness of Cellular Functions Review, Stelling, et al]];[[Media: ScienceOnlinePDF.pdf | Reverse Engineering of Biological Complexity, Csete, Doyle]]
|-
| align=center rowspan=3 | 4
| colspan=3 | '''Naming, Addressing and Control in Cell Biology '''
|-
| 2 Feb (T)
| [[Naming, Addressing and Control in Cell Biology | Naming, Addressing and Control in Cell Biology ]]
| [http://www.cds.caltech.edu/~doyle/213/Feb02SlidesReading/Final_IEE_SB.pdf Highly optimised global organisation of metabolic networks, R. Tanaka, M. Csete and J. Doyle];[http://www.cds.caltech.edu/~doyle/213/Feb02SlidesReading/ScaleRichMetabolism.pdf Quantitative evaluation of scale-rich metabolic networks, Tanaka, Doyle]
|-
| 4 Feb (Th)
| [[ Signal Transduction | Signal Transduction]]
|[http://www.cds.caltech.edu/~doyle/213/Feb02SlidesReading/YiEtAlPNAS.pdf Robust perfect adaptation in bacterial chemotaxis through integral feedback control, Yi, Huang, Simon and Doyle]; [http://www.amazon.com/Introduction-Systems-Biology-Mathematical-Computational/dp/1584886420 Chapter 7: Robustness of Protein Circuits: The Example of Bacterial Chemotaxis of "An Introduction to Systems Biology", Uri Alon]
|-
| align=center rowspan=3 | 5
| colspan=3 | '''Architecture and Modeling in Cell Biology '''
|-
| 9 Feb (T)
| [[Modeling Biological Systems | Architecture and Layering in Cell Biology]]
|
|-
| 11 Feb (Th)
| [[ Modeling Biological Systems | Modeling Bio Systems, Speaker: James Faeder]]
|[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Faeder_2009.pdf Rule-Based Modeling of Biochemical Systems with BioNetGen, Faeder, Blinov and Hlavacek]; [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Bioinformatics09a_inpress.pdf Simulation of large-scale rule-based models, Colvin et al.]; [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/FaederPerspectives.pdf The Complexity of Cell Signaling and the Need for a New Mechanics, Hlavacek and Faeder];[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/STKE2006.pdf Rules for Modeling Signal-Transduction Systems, Hlavacek et al.]; [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/nri-published.pdf Mathematical and Computational Models of Immune-Receptor Signalling, Goldstein et al.]
|-
| align=center rowspan=3 | 6
| colspan=3 | '''Complexity and Fragility '''
|-
| 16 Feb (T)
| [[Complexity and Fragility | Complexity and Fragility: Examples with NPP and Mandelbrot sets]]
| [http://www.cds.caltech.edu/~doyle/213/Feb16weekSlidesReading/logFinalCDC2006_X.pdf Complexity in Automation of SOS Proofs: An Illustrative Example, Gayme et al.];[http://www.cds.caltech.edu/~doyle/213/Feb16weekSlidesReading/mandel2.pdf Optimization Based Methods for Determining Basins of Attraction in the Logistic Map and Set Membership in the Mandelbrot Set, Gayme et al. ]; [http://www.cds.caltech.edu/~doyle/213/Feb16weekSlidesReading/DenniceConnections2006.pdf Studying the Logistic Map and the Mandelbrot Set Using SOS Methods, Gayme, Fazel, Doyle]
|-
| 18 Feb (Th)
| [[Complexity and Fragility | Complexity and Fragility (continued)]]
| [http://www.cds.caltech.edu/~doyle/213/Feb16weekSlidesReading/AldersonDoyle-SMCA.pdf Contrasting Views of Complexity and Their Implications For Network-Centric Infrastructures, Alderson, Doyle ]
|-
| align=center rowspan=3 | 7
| colspan=3 | '''Power Laws/ TCP IP '''
|-
| 23 Feb (T)
| [[Power Laws | Power Laws]]
| [http://www.cds.caltech.edu/~doyle2/wiki/index.php?title=Power_Laws Reading ]
|-
| 25 Feb (Th)
| [[The Internet | Steven Low guest speaker: TCP IP]]
| [http://www.cds.caltech.edu/~doyle2/wiki/index.php?title=The_Internet Reading ]
|-
|-
|}

== Course Projects ==

There will be a course project to be discussed.

* [[Molecular Cell Biology Project | Molecular Cell Biology Project]]

CDS 213

2010-04-03T17:35:23Z

Vanessa: /* Course Projects */

<table width="100%" cellspacing=0>
<tr valign=top>
<td rowspan=2 align=center> </td>
<td align=center>The Architecture of Robust, Evolvable Networks</td>
<td rowspan=2 align=center> </td></tr>
<tr valign=top><td align=center>Winter 2010</td></tr>
</table>

<table align=right><tr><td>__TOC__</td></tr></table>
<table cellspacing=0 cellpadding=0>
<tr valign=top>
<td width=60%>
* Instructor: [http://www.cds.caltech.edu/~doyle2/wiki/index.php?title=J._Doyle’s_Bio John C. Doyle]
<table cellpadding=0 cellspacing=0><tr><td>
* [http://listserv.cds.caltech.edu/mailman/listinfo/cds-213 Course mailing list]
* Lectures: TTh 4-5:30 pm, 107 Annenberg, changes emailed to course mailing list
</td></tr></table>

== Course Schedule ==
{| border=1 width=100%
|-
| Week || Date || Topic || Reading
|-
| align=center rowspan=3 | 1
| colspan=3 | '''Introduction to Network Architectures'''
|-
| 12 Jan (T)
| [[IST Seminar: The Architecture of Robust, Evolvable Networks]]
|
|-
| 14 Jan (Th)
| [[Internet Architecture]]
| Network is IPC:[[Media:IPC-arch-rearch08.pdf | Day et al, 2008 (Paper)]];[[Media:IPC-arch.pdf | Matta (Slides)]]; [[Media:DAYIEEECCW2009.pdf | Implications PNA, Day, 2009 (Slides)]];[[Media:Touchccw2009.pdf | Multihop/Multiparty influences on Net. Arch., Touch (Slides)]]
|-
| align=center rowspan=3 | 2
| colspan=3 | '''Network Architectures: Operating Systems and Cell Biology '''
|-
| 19 Jan (T)
| [[Network Architectures: Internet vs. Biology| Internet and Biology Architectures]]
| [[Media:RINA_Security_11209.pdf | Assessing Security of a Clean Slate Internet Architecture , Boddapati, Day]];[[Media:GlycolysisACCFinal.pdf | Linear Control Analysis of the Autocatalytic Glycolysis System , Chandra, Buzi, Doyle]]
|-
| 21 Jan (Th)
| [[Robustness and Fragility, Hard limits and Tradeoffs| Robustness and Fragility, Hard Limits and Tradeoffs]]
| [[Media:TAC-statmech-revised-final.pdf | On Lossless Approximations, Fluctuation-Dissipation and Limitations of Measurements , Sandberg, Doyle]]
|-
| align=center rowspan=3 | 3
| colspan=3 | '''Case Studies: Cell Biology, Clothing and Legos '''
|-
| 26 Jan (T)
| [[Glycolysis | Network architecture and control of glycolysis; Clothing; Legos]]
| [[Media:GlycolysisACCFinal.pdf | Linear Control Analysis of the Autocatalytic Glycolysis System , Chandra, Buzi, Doyle]];[[Media:RedBloodCellsGlycolysis.pdf | Assembly and Regulation of a Glycolytic Enzyme Complex on the Human Erythrocyte Membrane , Campanella et al]]
|-
| 28 Jan (Th)
| [[ Heat Shock| Heat Shock in cells; Clothing; Legos]]
|[[Media: PNASHeatShock.pdf | Surviving Heat Shock: Control strategies for robustness and performance , El-Samad, et al]];[[Media: Cell.pdf | Robustness of Cellular Functions Review, Stelling, et al]];[[Media: ScienceOnlinePDF.pdf | Reverse Engineering of Biological Complexity, Csete, Doyle]]
|-
| align=center rowspan=3 | 4
| colspan=3 | '''Naming, Addressing and Control in Cell Biology '''
|-
| 2 Feb (T)
| [[Naming, Addressing and Control in Cell Biology | Naming, Addressing and Control in Cell Biology ]]
| [http://www.cds.caltech.edu/~doyle/213/Feb02SlidesReading/Final_IEE_SB.pdf Highly optimised global organisation of metabolic networks, R. Tanaka, M. Csete and J. Doyle];[http://www.cds.caltech.edu/~doyle/213/Feb02SlidesReading/ScaleRichMetabolism.pdf Quantitative evaluation of scale-rich metabolic networks, Tanaka, Doyle]
|-
| 4 Feb (Th)
| [[ Signal Transduction | Signal Transduction]]
|[http://www.cds.caltech.edu/~doyle/213/Feb02SlidesReading/YiEtAlPNAS.pdf Robust perfect adaptation in bacterial chemotaxis through integral feedback control, Yi, Huang, Simon and Doyle]; [http://www.amazon.com/Introduction-Systems-Biology-Mathematical-Computational/dp/1584886420 Chapter 7: Robustness of Protein Circuits: The Example of Bacterial Chemotaxis of "An Introduction to Systems Biology", Uri Alon]
|-
| align=center rowspan=3 | 5
| colspan=3 | '''Architecture and Modeling in Cell Biology '''
|-
| 9 Feb (T)
| [[Modeling Biological Systems | Architecture and Layering in Cell Biology]]
|
|-
| 11 Feb (Th)
| [[ Modeling Biological Systems | Modeling Bio Systems, Speaker: James Faeder]]
|[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Faeder_2009.pdf Rule-Based Modeling of Biochemical Systems with BioNetGen, Faeder, Blinov and Hlavacek]; [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/Bioinformatics09a_inpress.pdf Simulation of large-scale rule-based models, Colvin et al.]; [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/FaederPerspectives.pdf The Complexity of Cell Signaling and the Need for a New Mechanics, Hlavacek and Faeder];[http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/STKE2006.pdf Rules for Modeling Signal-Transduction Systems, Hlavacek et al.]; [http://www.cds.caltech.edu/~doyle/213/Feb09weekSlidesReading/nri-published.pdf Mathematical and Computational Models of Immune-Receptor Signalling, Goldstein et al.]
|-
| align=center rowspan=3 | 6
| colspan=3 | '''Complexity and Fragility '''
|-
| 16 Feb (T)
| [[Complexity and Fragility | Complexity and Fragility: Examples with NPP and Mandelbrot sets]]
| [http://www.cds.caltech.edu/~doyle/213/Feb16weekSlidesReading/logFinalCDC2006_X.pdf Complexity in Automation of SOS Proofs: An Illustrative Example, Gayme et al.];[http://www.cds.caltech.edu/~doyle/213/Feb16weekSlidesReading/mandel2.pdf Optimization Based Methods for Determining Basins of Attraction in the Logistic Map and Set Membership in the Mandelbrot Set, Gayme et al. ]; [http://www.cds.caltech.edu/~doyle/213/Feb16weekSlidesReading/DenniceConnections2006.pdf Studying the Logistic Map and the Mandelbrot Set Using SOS Methods, Gayme, Fazel, Doyle]
|-
| 18 Feb (Th)
| [[Complexity and Fragility | Complexity and Fragility (continued)]]
| [http://www.cds.caltech.edu/~doyle/213/Feb16weekSlidesReading/AldersonDoyle-SMCA.pdf Contrasting Views of Complexity and Their Implications For Network-Centric Infrastructures, Alderson, Doyle ]
|-
| align=center rowspan=3 | 7
| colspan=3 | '''Power Laws/ TCP IP '''
|-
| 23 Feb (T)
| [[Power Laws | Power Laws]]
| [http://www.cds.caltech.edu/~doyle2/wiki/index.php?title=Power_Laws Reading ]
|-
| 25 Feb (Th)
| [[The Internet | Steven Low guest speaker: TCP IP]]
| [http://www.cds.caltech.edu/~doyle2/wiki/index.php?title=The_Internet Reading ]
|-
|-
|}

== Course Projects ==

There will be a course project to be discussed.

* [ Molecular Cell Biology Project | Molecular Cell Biology Project]

CDS 213

2010-04-03T17:34:58Z

Vanessa: