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Biology is the broad study of life, with many fields ...
Intro: We study fundamental constraints and trade-offs in biological systems using analytical tools from control theory, information theory, and graph theory. There are hard trade-offs between complexity and robustness in every system, which is worse in systems with particular architecture. We are interested in pinpointing these problems and analyzing how nature manages these trade-offs.


Systems biology in this research group concerns... :
Keywords: '''systems biology''', SBML mark-up, robustness, complexity, networks, biology, proteins.


- their molecular components and biochemistry
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.


- function, structure and interactions of each component or system
===2011===
[http://www.cds.caltech.edu/~doyle/wiki/images/8/82/OnlineFinalPNASSackler2011.pdf Architecture, constraints, and behavior]<br>
JC Doyle, MC Csete <br>
P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630 (2011)


- dynamics...
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/b/b6/Science-2011-Chandra-187-92.pdf Glycolytic Oscillations and Limits on Robust Efficiency]<br>
Fiona Chandra, Gentian Buzi, and John Doyle<br>
Science 333(6039):187-192, July 2011


==Recent papers==
[http://cds-web1.cds.caltech.edu/~doyle2/wiki/images/a/a2/6.AutomaticaJune2011.pdf Analysis of autocatalytic networks in biology]<br>
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/13/Cell04.pdf ''Robustness of cellular functions''],<br>
G Buzi, U Topcu, J Doyle<br>
J. Stelling, U. Sauer, Z. Szallasi, F. J. Doyle III, and J. Doyle,<br>
Automatica 47:1123-1130 (2011)
Cell 118: 675–685, Sept 17 2004 (244K)


[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/9/98/FEBS_PPI05.pdf ''Some protein interaction data do not exhibit power law statistics''],<br>
===2009===
R. Tanaka, T-M Yi, and J. Doyle<br>
[http://www.nt.ntnu.no/users/skoge/prost/proceedings/acc09/data/papers/0207.pdf ''Linear control analysis of the autocatalytic glycolysis system'']<br>
FEBS letters, 579 (23): 5140-5144 Sept 26 2005 (221K)
Fiona Chandra, Gentian Buzi, John Doyle<br>
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'']<br>
John Doyle and Marie Csete<br>
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''],<br>
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/7/74/IEEEProc_Bio.pdf ''Advanced Methods and Algorithms for Biological Networks Analysis''],<br>
H El-Samad , A Papachristodoulou, S Prajna, J Doyle, and M Khammash<br>
H El-Samad , A Papachristodoulou, S Prajna, J Doyle, and M Khammash<br>
In Proc. IEEE, 94 (4): 832-853 APR 2006 (900K)
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 '']<br>
Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash,<br>
[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''],<br>
R. Tanaka, T-M Yi, and J. Doyle<br>
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''],<br>
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/f/f2/IEESysBio05.pdf ''Highly optimised global organisation of metabolic networks''],<br>
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Proc. Natl. Acad. Sci. USA 102(8): 2736-2741 Feb 22, 2005. (390K)
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''],<br>
J. Stelling, U. Sauer, Z. Szallasi, F. J. Doyle III, and J. Doyle,<br>
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''],<br>
Csete M.E. and J.C. Doyle,<br>
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'']<br>
[http://www.cds.caltech.edu/~doyle2/wiki/skins/common/images/icons/fileicon-pdf.png ''Reverse Engineering of Biological Complexity'']<br>
Csete M and Doyle J,<br>
Csete M and Doyle J,<br>
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB)
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB)


[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 '']<br>
[http://www.cds.caltech.edu/%7Edoyle2/wiki/images/1/12/JtheorBiol2002.pdf ''Robustness as a measure of plausibility in models of biochemical networks''],<br>
Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash,<br>
Morohashi M, Winn AE, Borisuk MT, Bolouri H, Doyle J, Kitano H,<br>
[http://compbiol.plosjournals.org/ PLoS Comput Biol] 2(7): July 2006 (1.1MB)
Journal Of Theoretical Biology 216 (1): 19-30 May 7, 2002.
 
===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.'']<br>
Yi T-M, Huang Y, Simon MI, Doyle J.<br>
Proc. Natl. Acad. Sci. USA 97(9):4649-4653, 2000.
 
==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''],<br>
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<br>
IEE Systems Biology. 1:41-53, 2004
 
*''MathSBML: a package for manipulating SBML-based biological models'',<br>
Shapiro BE, Hucka M, Finney A, Doyle J.<br>
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)]<br>
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J., and Kitano,H.<br>
in Proc. Pac Symp Biocomput. 450-61, 2002.
 
===2001===
*''The Systems Biology Markup Language''<br>
Finney AM, Hucka M, Sauro HM, Doyle J, Kitano H, Bolouri H, <br>
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<br>
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''],<br>
MA Moritz, ME Morais, LA Summerell, JM Carlson, J Doyle<br>
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.'']<br>
H. El-Samad, S. Prajna, A. Papachristodoulou, M. Khammash and J. C. Doyle<br>
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''],<br>
Carlson JM, Doyle J,<br>
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''],<br>
Zhou T, Carlson JM, Doyle J,<br>
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''<br>
Csete M, Walikonis J, Slawny N, Wei Y, Korsnes S , Doyle JC, Wold  B,<br>
Journal of Cellular Physiology, Volume 189, Issue 2, Nov. 2001. 189-196
 
==Related reading==
[[Papers]]


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


==External links==
[[Tips: Research papers, Publishing and Other Trivia]]


*[http://sbml.org/contacts/ Systems Biology Mark up Language]
===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.systems-biology.org/ Systems Biology Portal]
 
*[http://www.hot.caltech.edu/ HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks ]
==Additional references==
*[http://www.cds.caltech.edu/sostools/ SOSTOOLS : Software for analysis of complex systems]


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

Latest revision as of 16:39, 4 May 2012

Intro: We study fundamental constraints and trade-offs in biological systems using analytical tools from control theory, information theory, and graph theory. There are hard trade-offs between complexity and robustness in every system, which is worse in systems with particular architecture. We are interested in pinpointing these problems and analyzing how nature manages these trade-offs.

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

Architecture, constraints, and behavior
JC Doyle, MC Csete
P Natl Acad Sci USA, vol. 108, Sup 3 15624-15630 (2011)

Glycolytic Oscillations and Limits on Robust Efficiency
Fiona Chandra, Gentian Buzi, and John Doyle
Science 333(6039):187-192, July 2011

Analysis of autocatalytic networks in biology
G Buzi, U Topcu, J Doyle
Automatica 47:1123-1130 (2011)

2009

Linear control analysis of the autocatalytic glycolysis system
Fiona Chandra, Gentian Buzi, John Doyle
In Proc. American Control Conf, 319-324 JUN 2009

2007

Rules of engagement
John Doyle and Marie Csete
Nature Vol 446:860 April 19 2007 (142K)

2006

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)

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,
PLoS Comput Biol 2(7): July 2006 (1.1MB)

2005

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)

Highly optimised global organisation of metabolic networks,
R. Tanaka, M. Csete and J. Doyle,
IEE Proc.-Syst. Biol. 152(4): 179, Dec 2005 (820K)

Motifs, control, and stability (including Supplementary Notes: Elementary Feedback Concepts)
Doyle J and Csete M
PLoS Biol 3(11): e392; 2005. (387K)

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

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)

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

2002

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

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

2000

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

SBML

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

2004

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

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

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

2002

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

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

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

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

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

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

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

Related reading

Papers

Research

Tips: Research papers, Publishing and Other Trivia

Other

External links

Retrieved from "https://doyle.caltech.edu/index.php?title=Systems_biology&oldid=3358"