Publications

2017

Synthetic Biology: Engineering Living Systems from Biophysical Principles. Bryan A. Bartley, Kyung Kim, J. Kyle Medley, Herbert M. Sauro, Biophysical Journal, Volume 112, Issue 6, p1050–1058, 28 March 2017, DOI: http://dx.doi.org/10.1016/j.bpj.2017.02.013

Synthetic biology: Enter the living machine
 H. M Sauro Nature 543 (7644), 178-178

A Visual Language for Protein Design RS Cox III, JA McLaughlin, R Gruenberg, J Beal, A Wipat, H Sauro ACS Synthetic Biology

Control and regulation of pathways via negative feedback HM Sauro Journal of The Royal Society Interface 14 (127), 20160848

2016

BBF RFC 112: Synthetic Biology Open Language (SBOL) Version 2.1. 0 Jacob Beal, Robert Sidney Cox, Raik Grünberg, James McLaughlin, Tramy Nguyen, Anil Wipat, Chris Macklin, Michael Bissell, Curtis Madsen, Nicholas Roehner, Ernst Oberortner, Goksel Misirli, Kevin Clancy, Matthew Pocock, Zhen Zhang, Chris Myers, Michael Zhang, Meher Samineni, Zach Zundel, Bryan Bartley, Kiri Choi, John H Gennari, Herbert Sauro, Douglas Densmore, Paolo Missier, Jacqueline Quinn, Guy-Bart Stan.

A portable library to support the SBML Layout Extension JK Medley, K Choi, HM Sauro bioRxiv, 035725

phraSED-ML: A paraphrased, human-readable adaptation of SED-ML K Choi, LP Smith, JK Medley, HM Sauro Journal of Bioinformatics and Computational Biology, 1650035

Data Integration and Mining for Synthetic Biology Design G Mısırlı, J Hallinan, M Pocock, P Lord, JA McLaughlin, H Sauro, A Wipat ACS synthetic biology 5 (10), 1086-1097

Sharing structure and function in biological design with SBOL 2.0 N Roehner, J Beal, K Clancy, B Bartley, G Misirli, R Grünberg, … ACS synthetic biology 5 (6), 498-506

Synthetic Biology Open Language (SBOL) Version 2.1. 0 T Nguyen, B Bartley, M Bissell, K Choi, K Clancy, C Macklin, C Madsen, … Journal of Integrative Bioinformatics 13 (3), 291

Tellurium: A Python Based Modeling and Reproducibility Platform for Systems Biology HM Sauro, K Choi, JK Medley, C Cannistra, M Konig, L Smith, K Stocking bioRxiv, 054601

2015

Smith L and Sauro HM (2015) The Use of Distributions in SBML Models. bioRxiv doi: http://dx.doi.org/10.1101/015503

SBOL Visual: A Graphical Language for Genetic Designs. PLoS Biol. 2015 Dec 3;13(12):e1002310. doi: 10.1371/journal.pbio.1002310. eCollection 2015. Quinn JY, Cox RS 3rd, Adler A, Beal J, Bhatia S, Cai Y, Chen J, Clancy K, Galdzicki M, Hillson NJ, Le Novère N, Maheshwari AJ, McLaughlin JA, Myers CJ, P U, Pocock M, Rodriguez C, Soldatova L, Stan GB, Swainston N, Wipat A, Sauro HM.

Synthetic Biology Open Language (SBOL) Version 2.0. Bartley B, Beal J, Clancy K, Misirl Gi, Roehner, N, E Oberortner E, Pocock M et al, … J. Int. Bioinformatics 12, 272

Stochastic Modular Analysis for Gene Circuits: Interplay Among Retroactivity, Nonlinearity, and Stochasticity
KH Kim, HM Sauro Computational Methods in Synthetic Biology, 287-297

The Synthetic Biology Open Language C Myers, K Clancy, G Misirli, E Oberortner, M Pocock, J Quinn, N Roehner, … Computational Methods in Synthetic Biology, 323-336

Intellectual property issues and synthetic biology standards reply M Galdzicki, LJ Kahl, D Endy, HM Sauro
NATURE BIOTECHNOLOGY 33 (1), 25-25

libRoadRunner: a high performance SBML simulation and analysis libraryET Somogyi, JM Bouteiller, G JA, M König, JK Medley, MH Swat, Sauro HM Bioinformatics 31 (20), 3315-21

SimpleSBML: A Python package for creating and editing SBML models C Cannistra, K Medley, H Sauro bioRxiv, 030312

2014


A Proposed Data Model for the Next Version of the Synthetic Biology Open Language (2014) Nicholas Roehner, Ernst Oberortner, Matthew Pocock, Jacob Beal, Kevin Clancy, Curtis Madsen, Goksel Misirli, Anil Wipat, Herbert Sauro, Chris J Myers, ACS Synthetic Biology

Synthetic biology: How best to build a cell. JJ Collins, M Maxon, A Ellington, M Fussenegger, R Weiss, HM Sauro Nature(2014) 509 (7499), 155-157

Galdzicki et al (2014) The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology 32, 545–550 doi:10.1038/nbt.2891

Sauro (2014), Essentials of Biochemical Modeling, Ambrosius Publishing; ISBN-10: 0982477325

ML Neal, M Galdzicki, JT Gallimore, HM Sauro (2014) A C library for retrieving specific reactions from the BioModels database Bioinformatics, 30 (1): 129-130.

Mayer P et al (2014) Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Systems Biology, 2014, 8:13

Maarleveld T,Ng, BK, Sauro H , Kim K (2014) In Silico Design of Self-Optimizing Integrated Metabolic and Gene Regulatory Networks doi: http://dx.doi.org/10.1101/007658

2013

ET Somogyi, MT Karlsson, M Swat, M Galdzicki, HM Sauro (2013), biorxiv.org libRoadRunner: A High Performance SBML Compliant Simulator

Galdzicki M et al (2013) SBOL: A community standard for communicating designs in synthetic biology Figshare

Sauro H M, Enzyme Kinetics for Systems Biology, Second Edition, Ambrosius Publishing (2013), ISBN-10: 0-9824773-3-3

Kim, Kyung Hyuk and Qian, Hong and Sauro, Herbert M., (2013) Nonlinear biochemical signal processing via noise propagation The Journal of Chemical Physics, 139, 144108,

Lucian Smith, Erik Butterworth, James Bassingthwaighte, Herbert Sauro (2013) SBML and CellML translation in Antimony and JSim, Bioinformatics, (2013) doi: 10.1093/bioinformatics/btt641First published online: November 8, 2013

Sauro HM and Kim K (2013) Synthetic biology: It’s an analog world Nature. 497(7451):572-573

Sleight CS and Sauro HM (2013) BioBrick™ Assembly Using the In-Fusion PCR Cloning Kit, Synthetic Biology Methods in Molecular Biology Volume 1073, 2013, pp 19-30


Sleight CS and Sauro HM (2013) Visualization of Evolutionary Stability Dynamics and Competitive Fitness of Escherichia coli Engineered with Randomized Multigene Circuits ACS synthetic biology, 2 (9), pp 519–528, DOI: 10.1021/sb400055h


Sleight SC and Sauro HM, 2013 Randomized BioBrick Assembly: A Novel DNA Assembly Method for Randomizing and Optimizing Genetic Circuits and Metabolic Pathways. ACS Synthetic Biology, DOI: 10.1021/sb4000542 Publication Date (Web): July 10

2012

In search of noise-induced bimodality, Kyung Hyuk Kim, and Herbert M Sauro
Kim and Sauro BMC Biology 2012, 10:89, http://www.biomedcentral.com/1741-7007/10/89

Yang S, Sleight SC and Sauro HM Rationally designed bidirectional promoter improves the evolutionary stability of synthetic genetic circuits, Nucl. Acids Res. (2012), doi:10.1093/nar/gks972

Chandran D and Sauro HM Hierarchical Modeling for Synthetic Biology ACS Synth. Biol., pp 353–364 July 23, 2012 (Research Article) DOI: 10.1021/sb300033q

Kim KH and Sauro HM. Adjusting Phenotypes by Noise Control. PLoS Computational Biology 8:e1002344 (2012)

Kim KH and Sauro HM. Measuring the degree of modularity in gene regulatory networks from the relaxation of finite perturbations. Proc. IEEE Conf. on Decision and Control (2012) (Invited Paper)


Sleight SC and Sauro HM, 2012, Design and construction of a prototype CMY (Cyan-Magenta-Yellow) genetic circuit as a mutational readout device to measure evolutionary stability dynamics and determine design principles for robust synthetic systems, Artificial Life 13, 481-488

Sleight CS and Sauro HM Design and construction of a prototype CMY (Cyan-Magenta-Yellow) genetic circuit as a mutational readout device to measure evolutionary stability dynamics and determine design principles for robust synthetic systems July 2012, doihttp://dx.doi.org/10.7551/978-0-262-31050-5-ch063

Neal ML and Sauro HM SBML Reaction Finder: Retrieve and extract specific reactions from the BioModels database, 2012, doi:10.1038/npre.2012.7028.1

Copeland WB, Bartley BA, Chandran D, Galdzicki M, Kim KH, Sleight S, Maranas CD, Sauro HM, Computational tools for metabolic engineering, Metabolic Engineering, (2012) http://dx.doi.org/10.1016/j.ymben.2012.03.001

2011

The Science and Applications of Synthetic and Systems Biology (2011), Ed: Eileen R. Choffnes, David A. Relman, and Leslie Pray, Rapporteurs; Forum on Microbial Threats; Institute of Medicine. Sean and Sauro, Predicability of Loss-of-Function Mutations in Engineered Systems, A18, 394-417

Synthetic Biology Open Language (SBOL) Version 1.0.0, http://hdl.handle.net/1721.1/66172

Sauro H M, Enzyme Kinetics for Systems Biology, Ambrosius Publishing (April 4, 2011), ISBN-10: 0982477317

Michal Galdzicki, Deepak Chandran, John H. Gennari, and Herbert M. Sauro. Data Model Standardization for Synthetic Biomolecular Circuits and Systems. In Heinz Koeppl, et al, Design and Analysis of Bio-molecular Circuits. Springer-Verlag. pp 281-294 (2011)

Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro, and Douglas Densmore. Computer-Aided Design for Synthetic Biology. In Heinz Koeppl, et al, Design and Analysis of Bio-molecular Circuits. Springer-Verlag. pp 203-224 (2011)

Minimum Information About a Simulation Experiment (MIASE) Author(s): Waltemath Dagmar; Adams Richard; Beard Daniel A.; et al. Source: PLOS COMPUTATIONAL BIOLOGY Volume: 7 Issue: 4 Article Number: e1001122 DOI: 10.1371/journal.pcbi.1001122 Published: APR 2011


K.H. Kim, D. Chandran, and H.M. Sauro. Toward Modularity in Synthetic Biology: Design Patterns and Fan-out. In Heinz Koeppl, et al, Design and Analysis of Bio-molecular Circuits. Springer-Verlag. pp 117-138 (2011)

Galdzicki, M., Rodriguez, C., Chandran, D., Sauro, H.M., and Gennari, J.H. 2011, Standard Biological Parts Knowledgebase. PLoS ONE, e17005. doi:10.1371/journal.pone.0017005

Kim KH and Sauro HM. Measuring Retroactivity from Noise in Gene Regulatory Networks. Biophysical Journal 100:1167-1177, 2011 Article Link

Jean Peccoud, J Christopher Anderson, Deepak Chandran, Douglas Densmore, Michal Galdzicki, Matthew W Lux, Cesar A Rodriguez, Guy-Bart Stan & Herbert M Sauro. Essential information for synthetic DNA sequences. volume 29(1), January 2011 Nature Biotechnology

2010

Sleight SC, Bartley BA, Lieviant JA and Sauro HM. Designing and engineering evolutionary robust genetic circuits Journal: Journal of Biological Engineering, 4:12 (2010)

Kim KH and Sauro HM. Fan-out in gene regulatory networks. Journal of Biological Engineering 4:16, 2010.

Chandran, D., Bergmann, FT., and Sauro, HM. Computer-aided design of biological circuits using tinkercell. BioengineeredBugs Volume 1(4), 2010. pages 276-283

Kim KH and Sauro HM. Sensitivity Summation Theorems for Stochastic Biochemical Reaction Systems. Mathematical Biosciences 226:109, 2010.

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

Sauro HM and Bergmann FT. Software Tools for Systems Biology. In Liu and Lauffenburger, Systems biomedicine. Academic Press. pp 289-312 (2009)

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 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. 2007, Jan 7;244(1):68-76.

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; 22 (3): 346-353.

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)

auro. 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


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

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

Smith, Lucian. Tales from the Code Front: Translating Modularity. COMBINE 2010, Edinburgh, UK 2010. http://precedings.nature.com/documents/5132/


Smith, Lucian; Hucka, Mike. SBML Level 3 Hierarchical Model Composition. COMBINE 2010, Edinburgh, UK 2010. http://precedings.nature.com/documents/5133/

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.

Title: Minimum Information About a Simulation Experiment (MIASE)
Author(s): Waltemath Dagmar; Adams Richard; Beard Daniel A.; et al.
Source: PLOS COMPUTATIONAL BIOLOGY Volume: 7 Issue: 4 Article Number: e1001122 DOI: 10.1371/journal.pcbi.1001122 Published: APR 2011
Times Cited: 2 (from Web of Science)