Published Papers

F.T. Bergmann, R.R. Vallabhajosyula and H.M. Sauro . Computational Tools for Modeling Protein Networks. Current Proteomics Pp. 181-197 Volume 3(3),(2006)

Ravishankar R. Vallabhajosyula, Herbert M. Sauro . Computational systems biology: complexity reduction: Complexity reduction of biochemical networks Ravishankar R. Vallabhajosyula, Herbert M. Sauro December 2006 Proceedings of the 37th conference on Winter simulation WSC '06 Publisher: Winter Simulation Conference Pages: 1690 - 1697

Frank T. Bergmann, Herbert M. Sauro . Computational systems biology: modularity and composition: SBW - a modular framework for systems biology. Frank T. Bergmann, Herbert M. Sauro December 2006 Proceedings of the 37th conference on Winter simulation WSC '06 Publisher: Winter Simulation Conference Pages: 1637 - 1645

Herbert M. Sauro, David Harel, Marta Kwiatkowska, Clifford A. Shaffer, Adelinde M. Uhrmacher, Michael Hucka, Pedro Mendes, Lena Strömback, John J. Tyson . Computational systems biology: panel discussion: challenges for modeling and simulation in computional biology: Challenges for modeling and simulation methods in systems biology Herbert M. Sauro, David Harel, Marta Kwiatkowska, Clifford A. Shaffer, Adelinde M. Uhrmacher, Michael Hucka, Pedro Mendes, Lena Strömback, John J. Tyson December 2006 Proceedings of the 37th conference on Winter simulation WSC '06 Pages: 1720 - 1730

Deckard A, Bergmann FT, Sauro HM. Supporting the SBML layout extension. Bioinformatics. 2006 Oct 11;

Paladugu SR, Chickarmane V, Deckard A, Frumkin JP, McCormack M, Sauro HM. In silico evolution of functional modules in biochemical networks. Syst Biol (Stevenage). 2006 Jul;153(4):223-35.

Chickarmane V, Troein C, Nuber UA, Sauro HM, Peterson C. Transcriptional Dynamics of the Embryonic Stem Cell Switch. PLoS Comput Biol. 2006 Sep 15;2(9)

Chickarmane V, Kholodenko BN, Sauro HM. Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation.J Theor Biol. 2006 May 23;

Le Novere N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 2006 Jan 1;34

Le Novere N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, Wanner BL. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol. 2005 Dec;23(12):1509-15.

Vallabhajosyula RR, Chickarmane V, Sauro HM  Conservation analysis of large biochemical networks. Bioinformatics. 2005 Nov 29;

Sauro H. M The Next Frontier in Cellular Networking  The Scientist 2005, 19(15):20

Chickarmane V, Paladugu SR, Bergmann F, Sauro HM. Bifurcation discovery tool. Bioinformatics. 2005 Sep 15;21(18):3688-90.

Wellock C, Chickarmane V, Sauro HM. The SBW-MATLAB Interface. Bioinformatics. 2004 Nov 5

Deckard A, Sauro HM. Preliminary studies on the in silico evolution of biochemical networks. Chembiochem. 2004 Oct 4;5(10):1423-31.

Sauro HM, Kholodenko BN. Quantitative analysis of signaling networks. Prog Biophys Mol Biol. 2004 Sep;86(1):5-43. Review.

Sauro. H M and Ingalls B (2004) Conservation analysis in biochemical networks: computational issues for software writers. Biophys Chem. 2004 Apr 1;109(1):1-15.

Sauro. H M (2004 The Computational Versatility of Proteomic Signaling Networks. Current Proteomics, 2004, 1, 67-81 (pdf)

Aguda, B., and Sauro, H, M (2004) Computer Simulation of MAPK Signal Transduction in Methods Mol Biol. MAPK Signalling (R. Seger, Ed.), Humana Press, New Jersey, 2004; 250: 167-76. (link)

Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J and Kitano H. (2003) Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. OMICS. 2003 Winter;7(4):355-72.

Ingalls BP and Sauro H M. (2003) Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories. J Theor Biol. 2003 May 7;222(1):23-36.(pdf)

Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novere N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J; SBML Forum.(2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003 Mar 1;19(4):524-31. (pdf)

HUCKA M, FINNEY A, SAURO HM, BOLOURI H, DOYLE J, KITANO H. (2002) The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology. Pac Symp Biocomput. 2002;:450-61.

HUCKA, M., FINNEY, A., SAURO, H., BOLOURI, H., DOYLE, J., KITANO, H. The ERATO Systems Biology Workbench: An Integrated Environment for Multiscale and Multitheoretic Simulations in Systems Biology. Foundations in System Biology, ed, Hiroaki Kitano, MIT Press, 2001

WOODS J. H and SAURO H. M. (1997) Elasticities in Metabolic Control Analysis: algebraic derivation of simplified expressions. CABIOS (now BioInformatics) 13 (2), 123-130

SAURO H. M (1997) Exploring Mathematical Functions using vExplorer. Future Skill Software

SAURO H. M (1997) Introduction to Error Analysis in Experimentation using EasyGraph professional. Future Skill Software

SAURO H. M. (1997) The Periodic Table. Published by: Future Skill Software

SAURO H. M. (1996) Creatures and Population Modelling. Published by: Future Skill Software

SAURO H. M (1996) Introduction to Mathematical Modelling using Fplot. Published by: Future Skill Software

SAURO H. M (1995) User Reference Manual EasyGraph. Published by: Future Skill Software

KHOLODENKO B. N, SAURO H. M. and WESTERHOFF H V. (1995) Coenzyme Cycles and Metabolic Control Analysis: The Determination of the Elasticity Coefficients from the Generalised Connectivity Theorem. Biochemistry and Molecular Biology, 33 (3), 615-625

SAURO, H. M. and BARRETT, J., (1995) in vitro Control Analysis of Metabolic Pathways; experimental and analytical developments. Molecular and Cellular Biochemistry, 145, 141-150

SAURO, H. M., KHOLODENKO, B. N., and WESTERHOFF, H. (1994) Metabolic Control Analysis of Linked Moiety-conserved Cycles. Responses to perturbations of internal variables and conservation totals. Eur. J. Biochem, 225, 179-186

SAURO, H. M., (1994) Moiety-Conserved Cycles and Metabolic Control Analysis. Analysis of Sequestration and Metabolic Channelling. Biosystems, 33, 55-67

SAURO, H. M., (1994) Analyses and Simulators: a brief description of two computer programs SCAMP and iMAP. Biothermokinetics. Ed: Westerhoff, H, Plenum Press, New York, 213-223

SAURO, H. M., (1993) A Biochemical ‘NAND’ Gate and Assorted Circuits. Modern Trends in Biothermokinetics. Ed: Schuster S. et al, Plenum Press, New York, 133-140

KELL D. B, DAVEY C. L, GOODACRE R and SAURO, H. M., (1993) When Going Backwards Means Progress: On the solution of biochemical inverse problems using artificial neural networks. Modern Trends in Biothermokinetics. Ed: Schuster S. et al, Plenum Press, New York, 109-114

SAURO, H. M., (1993) SCAMP: a general-purpose simulator and metabolic control analysis program. CABIOS, 9 (4), 441-450

SAURO H. M. and KELL, D., (1992) Evaluation of Steady-state Kinetic Parameters of Metabolic Pathways using Neural Networks. Binary, 4, 189-190

SAURO, H.M and FELL, D.A. (1991), SCAMP: A metabolic simulator and control analysis program., Mathl. Comput. Modelling, 15, 15-28

FELL D. A. and SAURO H. M., (1990) Metabolic Control Analysis: the effect of high enzyme concentrations. Eur. J. Biochem., 192, 183-187

FELL, D. A. and SAURO, H. M., (1990) Metabolic Control Analysis by Computer: Progress and prospects., Biomed. Biochem. Acta, 8/9, 811-816

SAURO H. M. and KACSER H., (1989) Enzyme-enzyme interactions and control analysis 2. The case of nonindependence: heterologous associations. Eur. J. Biochem., 187, 493-500

KACSER H., SAURO H. M., ACERENZA L., (1989) Enzyme-enzyme interactions and control analysis 1. The case of non-additivity: monomer-oligomer associations. Eur. J. Biochem., 187, 481-491

ACERENZA L., SAURO H. M and KACSER H., (1989) Control Analysis of Time-dependent Metabolic Systems. J. Theor. Biol., 137, 423-444

SAURO H. M., SMALL J. R., FELL D. A., (1987) Metabolic control and its analysis: Extensions to the theory and matrix method. Eur. J. Biochem. 1987, 165, 215-221

SAURO H. M., (1986) Control Analysis and Simulation of Metabolism Ph.D. Thesis, Oxford Polytechnic.

FELL D. A. and SAURO H. M., (1985) Metabolic Control and its Analysis: Additional Relationships between Elasticities and Control Coefficients. Eur. J. Biochem., 148, 555-561

Conference Proceedings

FELL D. A. and SAURO H. M., (1985) Substrate cycles: do they really cause amplification? Biochem. Soc. Trans., 13, 762-763

FELL D. A. and SAURO H. M., (1986) Non-equilibrium/equilibrium reactions: which controls? Biochem. Soc. Trans., 14, 624-625

SAURO H. M. and FELL D. A., (1987) The role of co-operativity in metabolism. Biochem. Soc. Trans. 1987, 15, 234-235

FELL, D. A., SAURO, H. M. and SMALL, J R., (1988) “Le calcul des coefficients de controle parl’algebre matricielle.” Le controle du metabolisme Ed: Mazat, J.P. and Reder C., Published by Universite de Bordeaux II, Bordeaux.

FELL D. A., SAURO H. M., and SMALL J. R. (1990) Ch. 9, 139-148, Control coefficients and the matrix method.

Control of Metabolic Processes. (Cornish-Bowden, A. & Cardenas, M.L. eds.) NATO ASI Series, plenum Press, New York.

SAURO H. M., (1990) Ch. 17, 225-230, Quantification of metabolic regulation by effectors. Control of Metabolic Processes. (Cornish-Bowden, A.& Cardenas, M.L. eds.) NATO ASI Series, plenum Press, New York.

KACSER H., SAURO H. M., and ACERENZA L., (1990) Ch. 20, 251-257, Control analysis of systems with enzyme-enzyme interactions. Control of Metabolic Processes. (Cornish-Bowden, A.& Cardenas, M.L. eds.) NATO ASI Series, plenum Press, New York.

SAURO, H. M., (2000) Ch. 33, 221- 228, Jarnac: a system for interactive metabolic analysis. Animating the Cellular Map 9th International BioThermoKinetics Meeting (eds: Hofmeyr, J-H. S, Rohwer, J. M, Snoep J. L) Stellenbosch University Press, ISBN 0-7972-0776-7

SAURO, H. M., (2000) Ch. 4, Jarnac: An Interactive Metabolic Systems Language in Computation in Cells: Proceedings of an EPSRC Emerging Computing Paradigms Workshop Bolouri, Hamid & Paton, Raymond C (Editors), Dept. of Computer Science Technical Report No. 345, University of Hertfordshire, UK, April 2000

Presentation at The First International Conference on Systems Biology (ICSB2000), Tokyo, Japan, November 2000, put together by Herbert Sauro, Michael Hucka, Andrew Finney and presented by Hamid Bolouri

Michael Hucka, Herbert Sauro, Andrew Finney, Hamid Bolouri, John Doyle, Hiroaki Kitano, Foundations of Systems Biology, ed. Hiroaki Kitano, MIT Press, Cambridge, Massachusetts, 2001 Presentation at the First International Symposium on Computational Cell Biology, Lenox, Massachussetts, USA, March 2001

Andrew Finney, Michael Hucka, Herbert Sauro, Hamid Bolouri, John Doyle, Hiroaki Kitano. First presented at the First International Symposium on Computational Cell Biology, Lenox, Massachussetts, USA, March 2001.

Herbert M Sauro. A Rationale for the ‘Design’ of the MAP Kinase Pathway, Presention at the second internation conference on systems biology, 2001, Caltech

Workshops

Workshop on modelling cellular processes at University of Stellenbosch, 10-14 April 2000, see http://www.sun.ac.za/biochem/btk/workshop.html

Second Workshop on Software Platforms for Systems Biology, May 2000, ERATO Kitano Systems Biology Project. Held at Caltech.

Third Workshop on Software Platforms for Systems Biology, June 2001, ERATO Kitano Systems Biology Project. Held at Caltech.

Fourth Workshop on Software Platforms for Systems Biology, November 2001, ERATO Kitano Systems Biology Project. Held at Caltech.