2010
Kim HK and Sauro HM. Sensitivity Summation Theorems for Stochastic Biochemical Reaction Systems 2010, Mathematical Biosciences, in press
Sleight SC, Bartley BA, Lieviant JA, and Sauro HM. In-Fusion BioBrick Assembly and Re-engineering. Nucleic Acids Research, 2010, gkq179. http://nar.oxfordjournals.org/cgi/content/full/gkq179
2009
Sauro HM, and Song, Y Sauro H, Song Y. Fundamental Dynamic Units: Feedforward Networks and Adjustable Gates. arXiv:0907.2005v1 [q-bio.MN]
Chandran D, Bergmann FT and Sauro HM TinkerCell: modular CAD tool for synthetic biology. Journal of Biological Engineering 2009, 3:19doi:10.1186/1754-1611-3-19
Sauro HM [Biological Models of Molecular Network Dynamics|http://www.springer.com/physics/complexity/book/978-0-387-75888-6] in Encyclopedia of Complexity and Systems Science Ed: Editor-in-chief: Meyers, Robert A. ISBN: 978-0-387-75888-6, 2009
Chandran D, Copeland, WB, Sleight SC and Sauro, HM Mathematical modeling and synthetic biology. Drug Discovery Today: Disease Models Volume 5, Issue 4, 2009, Pages 299-309
Kim, KH., and Sauro, HM. Stochastic Control Analysis for Biochemical Reaction Systems. arXiv:0904.3124 [q-bio.QM] (2009).
Le Novère, Nicolas, et al. “The Systems Biology Graphical Notation” Nature Biotechnology. August 2009.
Smith LP, Bergmann FT, Chandran D and Herbert M. Sauro Antimony: A modular model definition language. Bioinformatics. July 2009 (doi:10.1093/bioinformatics/btp401).
Network Dynamics Sauro, H M. (2009) Computational Systems Biology Series: Methods in Molecular Biology , Vol. 541 McDermott, J.; Samudrala, R.; Bumgarner, R.; Montgomery, K.; Ireton, R. (Eds.) ISBN: 978-1-58829-905-5 Link to Humana
Deckard A. C, Bergmann, F. T and Sauro H. M (2009) Enumeration and Online Library of Mass-Action Reaction Networks. eprint arXiv:0901.3067v1 [q-bio.MN].
2008
Sauro H. M and Bergmann F. T (2008) Essays in Biochemistry, volume 45, Systems Biology, Edited by Olaf Wolkenhauer, Peter Wellstead and Kwang-Hyun Cho. Standards and ontologies in computational systems biology, p 211
Kholodenko B. N and Sauro H. M (2008) Spatio-temporal dynamics of protein modification cascades. SEB Exp Biol Ser. 2008;61:141-59.
Bergmann F, T., Sauro H. M. (2008) Comparing Simulation Results of SBML Capable Simulators. Bioinformatics, Jun 30.
Kim, K. H., Qian, H., and Sauro, H. M. (2008) Sensitivity Regulation Based on Noise Propagation in Stochastic Reaction Networks. eprint arXiv:0805.4455v1 [q-bio.MN].
Sauro, H. M. (2008) Modularity Defined. Molecular Systems Biology vol 4 (166) Feb 2008.
2007
Sauro, H. M (2007) A simple Binary Search Tree written in C#, CodeProject Site.
Sauro, H. M and Ingalls, B (2007) MAPK Cascades as Feedback Amplifiers. eprint arXiv:0710.5195v1.
Entus, R, Aufderheide, B., Sauro, H. M. (2007) Design and implementation of three incoherent feed-forward motif based biological concentration sensors. Systems and Synthetic Biology. Volume 1, 119-128. Copy of Paper as PDF
Chickarmane, V; Ray, A; Sauro, H.M, and Nadim A (2007) A Model for p53 Dynamics Triggered by DNA Damage. SIAM Journal on Applied Dynamical Systems. Volume 6(1), 61-78.
Sauro, H. M. Simulation of biochemical networks - Cellular networks as dynamic control systems. (2007) Conf Proc IEEE Eng Med Biol Soc, volume 1.
2006
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
2005
Chickarmane, V; Nadim, A; Ray A; Sauro H. M (2005) A p53 Oscillator Model of DNA Break Repair Control eprint arXiv:q-bio/0510002
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.
2004
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.
Rao, C.V., Sauro, H.M., Arkin, A.P., Putting the “Control” in Metabolic Control Analysis, 7th International Symposium on Dynamics and Control of Process Systems (2004)
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)
2003
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. pdf
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.
2002
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.
2001
Hucka, M., Finney, A., Sauro , H., Bolouri, H., Dolye, 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
1997
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
1996
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
1995
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
1994
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 Moiety-Conserved Cycles
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
1993
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
1992
Sauro H. M. and Kell, D., (1992) Evaluation of Steady-state Kinetic Parameters of Metabolic Pathways using Neural Networks. Binary, 4, 189-190
1991
Sauro , H.M and Fell, D.A. (1991), SCAMP: A metabolic simulator and control analysis program., Mathl. Comput. Modelling, 15, 15-28
1990
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
1989
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
1987
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
1986
Sauro H. M., (1986) Control Analysis and Simulation of Metabolism Ph.D. Thesis, Oxford Polytechnic.
1985
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
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
Sean Sleight, Bryan Bartley, Jane Lieviant, and Herbert Sauro. Designing and Engineering Evolutionary Robust Genetic Circuits. SB4.0 Synthetic Biology Conference in Hong Kong, 2008, and Institute For Systems Biology Symposium in Seattle, 2010.
Michal Galdzicki and Herbert M. Sauro. Building Ontologies and Standards in the Systems Biology Community. NIGMS Cell Behavior Ontology Workshop, 2009.
Michal Galdzicki, Daniel Cook, Benjamin Zaitlen, Ryan Roper, Herbert Sauro, John Gennari. Building the Cell Behavior Ontology (CBO): An Illustrated Guide. Biocomplexity X, Bloomington, Indiana October 2009.
Michal Galdzicki, Deepak Chandran, Herbert Sauro, Daniel Cook, John Gennari. Bridging Synthetic Biology Models and Experiments using PoBoL. First International Workshop on Bio-Design Automation (IWBDA), San Francisco, CA 2009
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.