Systems biology
Keywords: systems biology, SBML mark-up, robustness, complexity, networks, biology, proteins.
Some papers were copied from <http://www.cds.caltech.edu/~doyle/RecentPapers/ >
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)
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
2002
Reverse Engineering of Biological Complexity
Csete M and Doyle J,
Science 295 (5560): 1664-1669 Mar 1, 2002. (1.2MB)
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.
Biology
- 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.