Systems biology

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

External links

• SBML Definition and homepage
• SBML documents
• Systems Biology Portal
• HOT : Highly Optimized/Organized Tradeoffs/Tolerance, A unified theory of complex networks
• SOSTOOLS : Software for analysis of complex systems