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
PNAS, in press, July 2011
Glycolytic Oscillations and Limits on Robust Efficiency
Fiona Chandra, Gentian Buzi, and John Doyle
Science (In Press)
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
Tips: Research papers, Publishing and Other Trivia