Research Theme:
Molecular and Cellular Engineering
Systems, Synthetic and Quantitative Biology

Education

PhD (computational biochemistry), Oxford Brooks University, UK,1986
MSc (biological computation), University of York, York, UK, 1982
BSc honors (biochemistry/microbiology), University of Kent, Canterbury, UK, 1981

Research Interests

• Metabolic and systems transduction networks
• Simulation
• Non-linear dynamics
• Control analysis
• Software development

Contact Information

Department of Bioengineering
University of Washington
Box 355061
William H. Foege Building, Room N410A
Phone: 206-685-2119
Fax: 206-685-3300
E-mail
Lab Web site: http://www.sys-bio.org/

Honors and Awards

• Award for Outstanding Technical Achievement: DARPA 2005
  
• Deputy Editor in Chief: PLoS Computational Biology
  
• Associate Editor: Systems and Synthetic Biology

Selected Publications

• Bergmann F, T., Sauro H. M. (2008) Comparing Simulation Results of SBML Capable Simulators. Bioinformatics, Jun 30.
• Sauro, H. M. (2008) Modularity Defined. Molecular Systems Biology vol 4 (166) Feb 2008.
• 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.
• 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.
• 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.
• 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
• 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;
• 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 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.
• 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.
• 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., (1994) Moiety-Conserved Cycles and Metabolic Control Analysis. Analysis of Sequestration and Metabolic Channelling. Biosystems, 33, 55–67.
• 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.
• 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.
• 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.
• Acerenza L., Sauro H. M and Kacser H., (1989) Control Analysis of Time-dependent Metabolic Systems. J. Theor. Biol., 137, 423–444.
• 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.