Office: Foege N410A
My research group is developing the next generation of high performance software that can simulate human disease states such as cancer or heart disease. In the future we anticipate that doctors will have detailed computer simulations of their patients enabling doctors to try out therapies on the patient simulation first before actually treating to the patient.
Biological Control Systems
High Performance Simulation
I am interested in the nature and operation of cellular control systems. Within this interest, I develop simulation software, control systems theory, and engineer control systems in vivo to understand more fully how biological control systems operate and how noise within biological systems behave. I also have side projects related to developing tools for in vivo real time monitoring of biological systems, the evolutionary robustness of synthetic systems, novel approaches to engineering metabolic pathways, developing standards for synthetic biology, and novel visualization and simulation software for multi-scale modeling of subcellular and multicellular systems.
Postgraduate Certificate in Education (6th to 12th grade high school teaching degree), University of Aberystwyth, Wales, 1993
Ph.D. Computational Biochemistry, Oxford Brookes University (UK), 1985
MS Biological Computation, University of York (UK), 1982
BS Biochemistry/Microbiology, University of Canterbury (UK), 1981
Postdoctoral Fellow 1987-1990, University of Edinburgh, Genetics, Quantitative Systems Biology
Postdoctoral Fellow 1990-1992, University of Aberystwyth, Wales, Neural Networks and Model Fitting
2013 University of Washington College of Engineering, Community of Innovators Awards, Faculty Innovator: Teaching & Learning
2005 Award for Outstanding Technical Achievement: DARPA
BIOEN 336: BIOE Systems & Controls
BIOEN 423/523: Introduction to Synthetic Biology
It’s an Analog World. Sauro HM and Kim K. Nature 497, 572–573 (30 May 2013) doi:10.1038/nature12246
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 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
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
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)
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
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