Publications
Publications
L.P. Smith, F.T. Bergmann, A. Garny, T. Helikar, J. Karr, D. Nickerson, H. Sauro, D. Waltemath, M. König
Journal of integrative bioinformatics, (0), p.20240008
H.V. Jakubowski, H. Agnew, B. Jardine, and H.M. Sauro
Biochemistry and Molecular Biology Education
First-order ultrasensitivity in phosphorylation cycles
M.A. Kochen, J.L. Hellerstein, H.M. Sauro, H.V. Jakubowski
Interface Focus, 14(1), p.20230045
50 Years of metabolic control analysis
H.M. Sauro
Interface Focus, 14(1), p.20230080
Design patterns of biological cells
S.S. Andrews, H.S. Wiley, H.M. Sauro
BioEssays, p.2300188
VSCode-Antimony: a source editor for building, analyzing, and translating antimony models
S. Ma, L. Fan, S.A. Konanki, E. Liu, J.H. Gennari, L.P. Smith, J.L. Hellerstein, H.M. Sauro
Bioinformatics, 39(12), p.btad753
Whole-cell metabolic control analysis
F.J. Bruggeman, M. Remeijer, M. Droste, L. Salinas, M. Wortel, R. Planqué, H.M. Sauro, B. Teusink, H.V. Westerhoff
Biosystems, 234, p.105067.
An automated model annotation system (AMAS) for SBML models
W. Shin, J.H. Gennari, J.L. Hellerstein, H.M. Sauro
Bioinformatics, 39(11), p.btad658
Tissue forge: interactive biological and biophysics simulation environment
T.J. Sego, J.P. Sluka, H.M. Sauro, J.A. Glazier
PLOS Computational Biology, 19(10), p.e1010768
SBcoyote: An extensible Python-based reaction editor and viewer
J. Xu, G. Geng, N.D. Nguyen, C. Perena-Cortes, C. Samuels, H.M. Sauro
Biosystems, 232, p.105001
SBbadger: Biochemical Reaction Networks with Definable Degree Distributions
M.A. Kochen, H.S. Wiley, S. Feng, H.M. Sauro
Bioinformatics, 39(1)
Adapting modeling and simulation credibility standards to computational systems biology
L.T. Tatka, L.P. Smith, J.L. Hellerstein, H.M. Sauro
Journal of Translational Medicine, 21(1), p.501
Standards, dissemination, and best practices in systems biology
J. Shin, V. Porubsky, J. Carothers, H.M. Sauro
Current Opinion in Biotechnology, 81, p.102922
A Practical Guide to Reproducible Modeling for Biochemical Networks
V.L. Porubsky, H.M. Sauro
Computational Modeling of Signaling Networks New York, NY: Springer US. (pp. 107-138)
Addressing the genetic/nongenetic duality in cancer with systems biology
P. Kulkarni, H.S. Wiley, H. Levine, H. Sauro, A. Anderson, S.T.C. Wong, A.S. Meyer, P. Iyengar, K. Corlette, K. Swanson, A. Mohanty, S. Bhattacharya, A. Patel, V. Jain, R. Salgia
Trends in Cancer, 9(3), pp.185-187
Cesium: a public database of evolved oscillatory reaction networks
L.T. Tatka, W. Luk, T.C. Elston, J.L. Hellerstein, H.M. Sauro
Biosystems, 224, p.104836
SBMLDiagrams: a python package to process and visualize SBML layout and render
J. Xu, J. Jiang, H.M. Sauro
Bioinformatics, 39(1), p.btac730
libRoadRunner 2.0: a high performance SBML simulation and analysis library
C. Welsh, J. Xu, L. Smith, M. König, K. Choi, H.M. Sauro
Bioinformatics, 39(1), p.btac770
BioSimulators: a central registry of simulation engines and services for recommending specific tools
B.Shaikh, L.P. Smith, D. Vasilescu, G. Marupilla, M. Wilson, E. Agmon, H. Agnew, S. S. Andrews, A. Anwar, M. E. Beber, F. T. Bergmann, D. Brooks, L. Brusch, L. Calzone, K. Choi, J. Cooper, J. Detloff, B. Drawert, M. Dumontier, G. B. Ermentrout, J. R. Faeder, A. P. Freiburger, F. Fröhlich, A. Funahashi, A. Garny, J. H. Gennari, P. Gleeson, A. Goelzer, Z. Haiman, J. Hasenauer, J. L. Hellerstein, H. Hermjakob, S. Hoops, J. C. Ison, D. Jahn, H. V. Jakubowski, R. Jordan, M. Kalaš, M. König, W. Liebermeister, R. S. Malik Sheriff, S. Mandal, R. McDougal, J. K. Medley, P. Mendes, R. Müller, C. J. Myers, A. Naldi, T. V. N. Nguyen, D. P. Nickerson, B. G. Olivier, D. Patoliya, L. Paulevé, L. R. Petzold, A. Priya, A. K. Rampadarath, J. M. Rohwer, A. S. Saglam, D. Singh, A. Sinha, J. Snoep, H. Sorby, R. Spangler, J. Starruß, P. J. Thomas, D. Van Niekerk, D. Weindl, F. Zhang, A. Zhukova, A. P. Goldberg, J. C. Schaff, M. L. Blinov, H. M. Sauro, I. I. Moraru, J. R. Karr
arXiv preprint arXiv:2203.06732
SBbadger: Biochemical Reaction Networks with Definable Degree Distributions
MA Kochen, HS Wiley, S Feng, HM Sauro
arXiv preprint arXiv:2202.13004
Dynamics and sensitivity of signaling pathways
B Shaikh, LP Smith, ML Blinov, HM Sauro, II Moraru, JR Karr
Biophysical Journal 121 (3), 127a
Integrated models, model languages, model repositories, simulation experiments, simulation tools and data visualizations enable facile model reuse with biosimulations
B Shaikh, LP Smith, ML Blinov, HM Sauro, II Moraru, JR Karr
Biophysical Journal 121 (3), 127a
libOmexMeta: enabling semantic annotation of models to support FAIR principles
C. Welsh, D.P. Nickerson, A. Rampadarath, M.L. Neal, H.M. Sauro, J.H. Gennari
Bioinformatics 37 (24), 4898-4900
Computing Sensitivities in Reaction Networks Using Finite Difference Methods
E. Yip, H.M. Sauro
preprint arXiv:2110.04335
Simulation experiment description makup language (SED-ML): level 1 version 4
L.P. Smith, F.T. Bergmann, A. Garny, T. Helikar, J. Karr, D. Nickerson, H. Sauro, D. Waltemath, M. König
Journal of Integrative Bioinformatics 18, 2021-0021
Synthetic biology open language visual (SBOL Visual) version 2.3
H. Baig, P. Fontanarossa, V. Kulkarni, J. McLaughlin, P. Vaidyanathan, B. Bartley, S. Bhakta, S. Bhatia, M. Bissell, K. Clancy, R.S. Cox, A. Goñi Moreno, T. Gorochowski, R. Grunberg, J. Lee, A. Luna, C. Madsen, G. Misirli, T. Nguyen, N. Le Novere, Z. Palchick, M. Pocock, N. Roehner, H. Sauro, J. Scott-Brown, J.T. Sexton, G.-B. Stan, J.J. Tabor, L. Terry, M. Vazquez Vilar, C.A. Voigt, A. Wipat, D. Zong, Z. Zundel, J. Beal, C. Myers
Journal of Integrative Bioinformatics 18 (3)
Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology
M.L. Blinov, J.H. Gennari, J.R. Karr, I.I. Moraru, D.P. Nickerson, H.M. Sauro
Current Opinion in Systems Biology 27, 100350
The Practice of Ensuring Repeatable and Reproducible Computational Models
H.M. Sauro
arXiv preprint arXiv:2107.05386
Dynamics and Sensitivity of Signaling Pathways
M.A. Kochen, S.S. Andrews, H.S. Wiley, S. Feng, H.M. Sauro
arXiv preprint arXiv:2106.06929
SED-ML Validator: tool for debugging simulation experiments
B. Shaikh, A.P. Freiburger, M. König, F.T. Bergmann, D.P. Nickerson, H.M. Sauro, M.L. Blinov, L.P. Smith, I.I. Moraru, J.R. Karr
arXiv preprint arXiv:2106.00844
Real-Time Interactive Modeling and Simulation in Biological Physics and Active Matter with Mechanica
E.T. Somogyi, J. Coulter, F. Sun, H.M. Sauro, J.A. Glazier
arXiv preprint arXiv:2105.02476
Publishing reproducible dynamic kinetic models
V. Porubsky, L. Smith, H.M. Sauro
Briefings in Bioinformatics 22 (3), bbaa152
SBMate: A Framework for Evaluating Quality of Annotations in Systems Biology Models
W. Shin, J.L. Hellerstein, Y. Munarko, M.L. Neal, D.P. Nickerson, A.K. Rampadarath, H.M. Sauro, J.H. Gennari
bioRxiv
Status and Challenges of Reproducibility in Computational Systems and Synthetic Biology
K. Choi, J.R. Karr, H.M. Sauro
Academic Press
SimpleSBML: A Python package for creating, editing, and interrogating SBML models: Verison 2.0
H.M. Sauro
arXiv preprint arXiv:2009.01969
A brief note on the properties of linear pathways
H.M. Sauro
Biochemical Society Transactions 48 (4), 1379-1395
Best Practices for Making Reproducible Biochemical Models
V.L. Porubsky, A.P. Goldberg, A.K. Rampadarath, D.P. Nickerson, J.R. Karr, H.M. Sauro
Cell Systems 11 (2), 109-120
Publishing reproducible dynamic kinetic models
V.L. Porubsky, L.P. Smith, H.M. Sauro,
Briefings in Bioinformatics
SBML Level 3: an extensible format for the exchange and reuse of biological models
S.M. Keating, D. Waltemath, M. König, F. Zhang, A. Dräger, C. Chaouiya, F.T. Bergmann, A. Finney, C.S. Gillespie, T. Helikar, S. Hoops, R.S. Malik-Sheriff, S.L. Moodie, I.I. Moraru, C.J. Myers, A. Naldi, B.G. Olivier, S. Sahle, J.C. Schaff, L.P. Smith, M.J. Swat, D. Thieffry, L. Watanabe, D.J. Wilkinson, M.L. Blinov, K. Begley, J.R. Faeder, H.F. Gómez, T.M. Hamm, Y. Inagaki, W. Liebermeister, A.L. Lister, D. Lucio, E. Mjolsness, C.J. Proctor, K. Raman, N. Rodriguez, C.A. Shaffer, B.E. Shapiro, J. Stelling, N. Swainston, N. Tanimura, J. Wagner, M. Meier-Schellersheim, H.M. Sauro, B. Palsson, H. Bolouri, H. Kitano, A. Funahashi, H. Hermjakob, J.C. Doyle, M. Hucka, R.R. Adams, N.A. Allen, B.R. Angermann, M. Antoniotti, G.D. Bader, J. Červený, M. Courtot, C.D. Cox, P. Dalle Pezze, E. Demir, W.S. Denney, H. Dharuri, J. Dorier, D. Drasdo, A. Ebrahim, J. Eichner, J. Elf, L. Endler, C.D. Evelo, C. Flamm, R.M.T. Fleming, M. Fröhlich, M. Glont, E. Gonçalves, M. Golebiewski, H. Grabski, A. Gutteridge, D. Hachmeister, L.A. Harris, B.D. Heavner, R. Henkel, W.S. Hlavacek, B. Hu, D.R. Hyduke, H. de Jong, N. Juty, P.D. Karp, J.R. Karr, D.B. Kell, R. Keller, I. Kiselev, S. Klamt, E. Klipp, C. Knüpfer, F. Kolpakov, F. Krause, M. Kutmon, C. Laibe, C. Lawless, L. Li, L.M. Loew, R. Machne, Y. Matsuoka, P. Mendes, H. Mi, F. Mittag, P.T. Monteiro, K.N. Natarajan, P.M.F. Nielsen, T. Nguyen, A. Palmisano, J.-B. Pettit, T. Pfau, R.D. Phair, T. Radivoyevitch, J.M. Rohwer, O.A. Ruebenacker, J. Saez-Rodriguez, M. Scharm, H. Schmidt, F. Schreiber, M. Schubert, R. Schulte, S.C. Sealfon, K. Smallbone, S. Soliman, M.I. Stefan, D.P. Sullivan, K. Takahashi, B. Teusink, D. Tolnay, I. Vazirabad, A. von Kamp, U. Wittig, C. Wrzodek, F. Wrzodek, I. Xenarios, A. Zhukova, J. Zucker
Molecular Systems Biology 16 (8), e9110
The first 10 years of the International Coordination Network for standards in systems and synthetic biology (COMBINE)
D. Waltemath, M. Golebiewski, M.L. Blinov, P. Gleeson, H. Hermjakob, M. Hucka, E.T. Inau, S.M. Keating, M. König, O. Krebs, R.S. Malik-Sheriff, D. Nickerson, E. Oberortner, H.M. Sauro, F. Schreiber, L. Smith, M.I. Stefan, U. Wittig, C.J. Myers
Journal of Integrative Bioinformatics 17 (2-3)
Synthetic biology open language visual (SBOL visual) Version 2.2
H. Baig, P. Fontanarossa, V. Kulkarni, J. McLaughlin, P. Vaidyanathan, B. Bartley, S. Bhakta, S. Bhatia, M. Bissell, K. Clancy, R.S. Cox, A. Goñi Moreno, T. Gorochowski, R. Grunberg, J. Lee, A. Luna, C. Madsen, G. Misirli, T. Nguyen, N. Le Novere, Z. Palchick, M. Pocock, N. Roehner, H. Sauro, J. Scott-Brown, J.T. Sexton, G.-B. Stan, J.J. Tabor, L. Terry, M. Vazquez Vilar, C.A. Voigt, A. Wipat, D. Zong, Z. Zundel, J. Beal, C. Myers
Journal of Integrative Bioinformatics 17 (2-3)
Improving reproducibility in computational biology research
J.A. Papin, F. Mac Gabhann, H.M. Sauro, D. Nickerson, A. Rampadarath
PLOS Computational Biology 16 (5), e1007881
libsbmljs—Enabling web–based SBML tools
J.K. Medley, J. Hellerstein, H.M. Sauro
Biosystems, 1041501
Generating Synthetic Signaling Networks for in Silico Modeling Studies
J. Xu, H.S. Wiley, H.M. Sauro
bioRxiv
A Commentary on the Linearity and Time-Invariance of ODE-Based Systems
P.S. Ruth, H.M. Sauro
arXiv preprint arXiv:1912.07830
Class notes on oscillators: Systems and Synthetic Biology
H.M. Sauro
PyBioNetFit and the biological property specification language
E.D. Mitra, R. Suderman, J. Colvin, A. Ionkov, A. Hu, H.M. Sauro, R.G. Posner, W.S. Hlavacek
Science 19, 1012-1036
Communicating structure and function in synthetic biology diagrams
J. Beal, T. Nguyen, T.E. Gorochowski, A. Goni-Moreno, J. Scott-Brown, J.A. McLaughlin, C. Madsen, B. Aleritsch, B. Bartley, S. Bhakta, M. Bissell, S.C. Hair, K. Clancy, A. Luna, N. Le Novere, Z. Palchick, M. Pocock, H. Sauro, J.T. Sexton, J.J. Tabor, C.A. Voigt, Z. Zundel, C. Myers, A. Wipat
Synthetic Biology 8 (8), 1818-1825
Synthetic biology open language visual (SBOL visual) version 2.1
C. Madsen, A.G. Moreno, Z. Palchick, U. P, N. Roehner, B. Bartley, S. Bhatia, S. Bhakta, M. Bissell, K. Clancy, R.S. Cox, T. Gorochowski, R. Grunberg, A. Luna, J. McLaughlin, T. Nguyen, N. Le Novere, M. Pocock, H. Sauro, J. Scott-Brown, J.T. Sexton, G.-B. Stan, J.J. Tabor, C.A. Voigt, Z. Zundel, C. Myers, J. Beal, A. Wipat
Journal of Integrative Bioinformatics 16 (2)
Synthetic biology open language (SBOL) version 2.3
C. Madsen, A. Goñi Moreno, U. P., Z. Palchick, N. Roehner, C. Atallah, B. Bartley, K. Choi, R.S. Cox, T. Gorochowski, R. Grünberg, C. Macklin, J. McLaughlin, X. Meng, T. Nguyen, M. Pocock, M. Samineni, J. Scott-Brown, Y. Tarter, M. Zhang, Z. Zhang, Z. Zundel, J. Beal, M. Bissell, K. Clancy, J.H. Gennari, G. Misirli, C. Myers, E. Oberortner, H. Sauro, A. Wipat
Journal of Integrative Bioinformatics 16 (2)
Methods in Computational Biology
R.P. Carlson, H.M. Sauro
Processes 7 (4), 205
Application of Parameter Optimization to Search for Oscillatory Mass-Action Networks Using Python
V.L. Porubsky, H.M. Sauro
Processes
Recent advances in biomedical simulations: a manifesto for model engineering
J.L. Hellerstein, S. Gu, K, Choi, H.M. Sauro
F1000Research (8)
Harmonizing semantic annotations for computational models in biology
M.L. Neal, M. König, D. Nickerson, G. Mısırlı, R. Kalbasi, A. Dräger, K. Atalag, V. Chelliah, M.C. Cooling, D.L. Cook, S. Crook, M. De Alba, S.H. Friedman, A. Garny, J.H. Gennari, P. Gleeson, M. Golebiewski, M. Hucka, N. Juty, C. Myers, B.G. Olivier, H.M. Sauro, M. Scharm, J.L. Snoep, V. Touré, A. Wipat, O. Wolkenhauer, D. Waltemath
Briefings in Bioinformatics 20 (2), 540-550
pySBOL: a python package for genetic design automation and standardization
B.A. Bartley, K. Choi, M. Samineni, Z. Zundel, T. Nguyen, C.J. Myers, H.M. Sauro
pySBOL: ACS synthetic biology
Tellurium: An extensible python-based modeling environment for systems and synthetic biology
K. Choi, J.K. Medley, M. König, K. Stocking, L. Smith, S. Gu, H.M. Sauro
Biosystems, 171, 74-79
Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology
J.K. Medley, K. Choi, M. König, L. Smith, S. Gu, J. Hellerstein, S.C. Sealfon, H.M. Sauro
PLoS Computational Biology Vol. 14 (6) e1006220
A Portable Structural Analysis Library for Reaction Networks
Y. Bedaso, F.T. Bergmann, K. Choi, K. Medley, H.M. Sauro
Biosystems Vol. 169-170, p20-25
Quantitative Biology: Theory, Computational Methods, and Models
K.T. Tuzman, D. Fey, M. Dobrzynski, B.N. Kholodenko, S. Olson, J. Huang, H.M. Sauro, et al
MIT Press
Synthetic biology open language (SBOL) version 2.2. 0
R.S. Cox III, C. Madsen, J.A. McLaughlin, T. Nguyen, N. Roehner, B. Bartley, J. Beal, M. Bissell, K. Choi, K. Clancy, R. Grünberg, C. Macklin, G. Mısırlı, E. Oberortner, M. Pocock, M. Samineni, M. Zhang, Z. Zhang, Z. Zundel, J.H. Gennari, C. Myers, H. Sauro, A. Wipat
Journal of Integrative Bioinformatics 15(1)
Harmonizing semantic annotations for computational models in biology
M.L. Neal, M. König, D. Nickerson, G. Mısırlı, R. Kalbasi, A. Dräger, K. Atalag, V. Chelliah, M.T. Cooling, D.L. Cook, S. Crook, M. De Alba, S.H. Friedman, A. Garny, J.H. Gennari, P. Gleeson, M. Golebiewski, M. Hucka, N. Juty, C. Myers, B.G. Olivier, H.M. Sauro, M. Scharm, J.L. Snoep, V. Touré, A. Wipat, O. Wolkenhauer, D. Waltemath
BioRxiv p.246470
Synthetic biology open language visual (SBOL visual) version 2.0
R.S. Cox, C. Madsen, J. McLaughlin, T. Nguyen, N. Roehner, B. Bartley, S. Bhatia, M. Bissell, K. Clancy, T. Gorochowski, R. Grünberg, A. Luna, N. Le Novère, M. Pocock, H. Sauro, J.T. Sexton, G.-B. Stan, J.J. Tabor, C.A. Voigt, Z. Zundel, C. Myers, J. Beal, A. Wipat
Journal of Integrative Bioinformatics, 15(1)
Inferring Reaction Networks using Perturbation Data
K. Choi, J. Hellerstein, H.S. Wiley, H.M. Sauro
BioRxiv, 351767
Synthetic biology open language (SBOL) version 2.2
R.S. Cox III, C. Madsen, J.A. McLaughlin, T. Nguyen, N. Roehner, B. Bartley, J. Beal, M. Bissell, K. Choi, K. Clancy, R. Grünberg, C. Macklin, G. Misirli, E. Oberortner, M. Pocock, M. Samineni, M. Zhang, Z. Zhang, Z. Zundel, J.H. Gennari, C. Myers, H. Sauro, A. Wipat
Journal of Integrative Bioinformatics, Vol. 15 (1) p. 20180001
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
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 Get pdf here
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
The Use of Distributions in SBML Models.
Smith L and Sauro HM
bioRxiv doi: http://dx.doi.org/10.1101/015503
SBOL Visual: A Graphical Language for Genetic Designs
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.
PLoS Biol. 2015 Dec 3;13(12):e1002310. doi: 10.1371/journal.pbio.1002310. eCollection 2015
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
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
A Proposed Data Model for the Next Version of the Synthetic Biology Open Language
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
The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.
Galdzicki et al (2014)
Nature Biotechnology 32, 545–550 (2014) doi:10.1038/nbt.2891
Essentials of Biochemical Modeling
Sauro (2014),
Ambrosius Publishing; ISBN-10: 0982477325
A C library for retrieving specific reactions from the BioModels database
ML Neal, M Galdzicki, JT Gallimore, HM Sauro
Bioinformatics, 30 (1): 129-130.
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
Mayer P et al
BMC Systems Biology, 2014, 8:13
In Silico Design of Self-Optimizing Integrated Metabolic and Gene Regulatory Networks
Maarleveld T,Ng, BK, Sauro H , Kim K
doi: http://dx.doi.org/10.1101/007658
libRoadRunner: A High Performance SBML Compliant Simulator
ET Somogyi, MT Karlsson, M Swat, M Galdzicki, HM Sauro
biorxiv.org
SBOL: A community standard for communicating designs in synthetic biology
Galdzicki M et al
Figshare
Enzyme Kinetics for Systems Biology,
Sauro H M,
Second Edition, Ambrosius Publishing (2013), ISBN-10: 0-9824773-3-3
Nonlinear biochemical signal processing via noise propagation
Kim, Kyung Hyuk and Qian, Hong and Sauro, Herbert M., (2013)
The Journal of Chemical Physics, 139, 144108
SBML and CellML translation in Antimony and JSim,
Lucian Smith, Erik Butterworth, James Bassingthwaighte, Herbert Sauro
Bioinformatics doi: 10.1093/bioinformatics/btt641First published online: November 8, 2013
Synthetic biology: It’s an analog world
Sauro HM and Kim K (2013)
Nature. 497(7451):572-573
BioBrick™ Assembly Using the In-Fusion PCR Cloning Kit
Sleight CS and Sauro HM (2013)
Synthetic Biology Methods in Molecular Biology Volume 1073, 2013, pp 19-30
Visualization of Evolutionary Stability Dynamics and Competitive Fitness of Escherichia coli Engineered with Randomized Multigene Circuits
Sleight CS and Sauro HM (2013)
ACS synthetic biology, 2 (9), pp 519–528, DOI: 10.1021/sb400055h
Randomized BioBrick Assembly: A Novel DNA Assembly Method for Randomizing and Optimizing Genetic Circuits and Metabolic Pathways.
Sleight SC and Sauro HM
ACS Synthetic Biology, DOI: 10.1021/sb4000542
In search of noise-induced bimodality
Kyung Hyuk Kim, and Herbert M Sauro
BMC Biology 2012, 10:89,
Kim and Sauro
http://www.biomedcentral.com/1741-7007/10/89
Rationally designed bidirectional promoter improves the evolutionary stability of synthetic genetic circuits,
Yang S, Sleight SC and Sauro HM
Nucl. Acids Res., doi:10.1093/nar/gks972
Hierarchical Modeling for Synthetic Biology
Chandran D and Sauro HM
ACS Synth. Biol., pp 353–364 (Research Article) DOI: 10.1021/sb300033q
Adjusting Phenotypes by Noise Control
Kim KH and Sauro HM.
PLoS Computational Biology 8:e1002344
Measuring the degree of modularity in gene regulatory networks from the relaxation of finite perturbations.
Kim KH and Sauro HM.
Proc. IEEE Conf. on Decision and Control (Invited Paper)
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
Sleight SC and Sauro HM
Artificial Life 13, 481-488
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
Sleight CS and Sauro HM
doihttp://dx.doi.org/10.7551/978-0-262-31050-5-ch063
SBML Reaction Finder: Retrieve and extract specific reactions from the BioModels database
Neal ML and Sauro HM
doi:10.1038/npre.2012.7028.1
Computational tools for metabolic engineering
Copeland WB, Bartley BA, Chandran D, Galdzicki M, Kim KH, Sleight S, Maranas CD, Sauro HM,
Metabolic Engineering 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
Enzyme Kinetics for Systems Biology
Sauro H M,
Ambrosius Publishing ISBN-10: 0982477317
Data Model Standardization for Synthetic Biomolecular Circuits and Systems. In Heinz Koeppl, et al, Design and Analysis of Bio-molecular Circuits
Michal Galdzicki, Deepak Chandran, John H. Gennari, and Herbert M. Sauro.
Springer-Verlag. pp 281-294
Computer-Aided Design for Synthetic Biology. In Heinz Koeppl, et al, Design and Analysis of Bio-molecular Circuits.
Deepak Chandran, Frank T. Bergmann, Herbert M. Sauro, and Douglas Densmore
Springer-Verlag. pp 203-224
Minimum Information About a Simulation Experiment (MIASE) Author(s):
Waltemath Dagmar; Adams Richard; Beard Daniel A.; et al. Source:
PLOS Computation 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.
K.H. Kim, D. Chandran, and H.M. Sauro. T
Springer-Verlag. pp 117-138 (2011)
Standard Biological Parts Knowledgebase
Galdzicki, M., Rodriguez, C., Chandran, D., Sauro, H.M., and Gennari, J.H. 2011,
PLoS ONE, e17005. doi:10.1371/journal.pone.0017005
Measuring Retroactivity from Noise in Gene Regulatory Networks
Kim KH and Sauro HM
Biophysical Journal 100:1167-1177, 2011 Article Link
Essential information for synthetic DNA sequences.
Jean Peccoud, J Christopher Anderson, Deepak Chandran, Douglas Densmore, Michal Galdzicki, Matthew W Lux, Cesar A Rodriguez, Guy-Bart Stan & Herbert M Sauro
Nature Biotechnology Volume 29(1)
Designing and engineering evolutionary robust genetic circuits
Sleight SC, Bartley BA, Lieviant JA and Sauro HM.
Journal of Biological Engineering, 4:12
Fan-out in gene regulatory networks
Kim KH and Sauro HM.
Journal of Biological Engineering 4:16, 2010.
Computer-aided design of biological circuits using tinkercell
Chandran, D., Bergmann, FT., and Sauro, HM.
BioengineeredBugs Volume 1(4), 276-283
Sensitivity Summation Theorems for Stochastic Biochemical Reaction Systems
Kim KH and Sauro HM.
Mathematical Biosciences 226:109
In-Fusion BioBrick Assembly and Re-engineering.
Sleight SC, Bartley BA, Lieviant JA, and Sauro HM
Nucleic Acids Research, gkq179. http://nar.oxfordjournals.org/cgi/content/full/gkq179
Software Tools for Systems Biology.
Sauro HM and Bergmann FT.
In Liu and Lauffenburger, Systems biomedicine. Academic Press. pp 289-312
Fundamental Dynamic Units: Feedforward Networks and Adjustable Gates.
Sauro HM, and Song, Y Sauro H, Song Y
arXiv:0907.2005v1 [q-bio.MN]
TinkerCell: modular CAD tool for synthetic biology
Chandran D, Bergmann FT and Sauro HM
Journal of Biological Engineering 2009, 3:19doi:10.1186/1754-1611-3-19
Biological Models of Molecular Network Dynamics
Sauro HM
Encyclopedia of Complexity and Systems Science Ed: Editor-in-chief: Meyers, Robert A. ISBN: 978-0-387-75888-6, 2009
Mathematical modeling and synthetic biology
Chandran D, Copeland, WB, Sleight SC and Sauro, HM
Drug Discovery Today: Disease Models Volume 5, Issue 4, 2009, Pages 299-309
Stochastic Control Analysis for Biochemical Reaction Systems
Kim, KH., and Sauro, HM.
arXiv:0904.3124 [q-bio.QM]
“The Systems Biology Graphical Notation”
Le Novère, Nicolas, et al.
Nature Biotechnology
Antimony: A modular model definition language.
Smith LP, Bergmann FT, Chandran D and Herbert M. Sauro
Bioinformatics 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
Enumeration and Online Library of Mass-Action Reaction Networks
Deckard A. C, Bergmann, F. T and Sauro H. M (2009)
eprint arXiv:0901.3067v1 [q-bio.MN]
Essays in Biochemistry, volume 45, Systems Biology,
Sauro H. M and Bergmann F. T
Edited by Olaf Wolkenhauer, Peter Wellstead and Kwang-Hyun Cho.
Standards and ontologies in computational systems biology, p 211
Spatio-temporal dynamics of protein modification cascades
Kholodenko B. N and Sauro H. M
SEB Exp Biol Ser. 2008;61:141-59
Comparing Simulation Results of SBML Capable Simulators
Bergmann F, T., Sauro H. M.
Bioinformatics
Sensitivity Regulation Based on Noise Propagation in Stochastic Reaction Networks
Kim, K. H., Qian, H., and Sauro, H. M.
eprint arXiv:0805.4455v1 [q-bio.MN]
Modularity Defined
Sauro, H. M.
Molecular Systems Biology vol 4 (166)
A simple Binary Search Tree written in C#
Sauro, H. M (2007)
CodeProject Site
MAPK Cascades as Feedback Amplifiers
Sauro, H. M and Ingalls, B (2007)
eprint arXiv:0710.5195v1.
Design and implementation of three incoherent feed-forward motif based biological concentration sensors
Entus, R, Aufderheide, B., Sauro, H. M.
Systems and Synthetic Biology. Volume 1, 119-128. Copy of Paper as PDF
A Model for p53 Dynamics Triggered by DNA Damage
Chickarmane, V; Ray, A; Sauro, H.M, and Nadim A
SIAM Journal on Applied Dynamical Systems. Volume 6(1), 61-78
Simulation of biochemical networks – Cellular networks as dynamic control systems
Sauro, H. M.
Conf Proc IEEE Eng Med Biol Soc, volume 1
Computational Tools for Modeling Protein Networks.
F.T. Bergmann, R.R. Vallabhajosyula, H.M. Sauro
Current Proteomics Pp. 181-197 Volume 3(3),(2006)
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
Computational systems biology: modularity and composition: SBW – a modular framework for systems biology
Frank T. Bergmann, Herbert M. Sauro
Proceedings of the 37th conference on Winter simulation WSC ’06 Publisher: Winter Simulation Conference Pages: 1637 – 1645
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
Proceedings of the 37th conference on Winter simulation WSC ’06 Pages: 1720 – 1730
Supporting the SBML layout extension
Deckard A, Bergmann FT, Sauro HM.
Bioinformatics
In silico evolution of functional modules in biochemical networks.
Paladugu SR, Chickarmane V, Deckard A, Frumkin JP, McCormack M, Sauro HM.
Syst Biol (Stevenage) 153(4):223-35.
Transcriptional Dynamics of the Embryonic Stem Cell Switch.
Chickarmane V, Troein C, Nuber UA, Sauro HM, Peterson C.
PLoS Comput Biol.;2(9)
Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation.
Chickarmane V, Kholodenko BN, Sauro HM.
J Theor Biol. 2007, Jan 7;244(1):68-76
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.
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
Nucleic Acids Res. 2006 Jan 1;34
Oscillator Model of DNA Break Repair Control
Chickarmane, V; Nadim, A; Ray A; Sauro H. M
A p53 eprint arXiv:q-bio/0510002
Minimum information requested in the annotation of biochemical models (MIRIAM)
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.
Nat Biotechnol (12):1509-15
Conservation analysis of large biochemical networks
Vallabhajosyula RR, Chickarmane V, Sauro HM.
Bioinformatics. 2005 Nov 29; 22 (3): 346-353
The Next Frontier in Cellular Networking
Sauro H. M.
The Scientist 19(15):20
Bifurcation discovery tool
Chickarmane V, Paladugu SR, Bergmann F, Sauro HM.
Bioinformatics 21(18):3688-90
The SBW-MATLAB Interface
Wellock C, Chickarmane V, Sauro HM
Bioinformatics. 2004 Nov 5
Preliminary studies on the in silico evolution of biochemical networks
Chembiochem. 2004 Oct 4;5(10):1423-31
Deckard A, Sauro HM.
Quantitative analysis of signaling networks.
Sauro HM, Kholodenko BN.
Prog Biophys Mol Biol. 2004 Sep;86(1):5-43. Review
Putting the “Control” in Metabolic Control Analysis
Rao, C.V., Sauro, H.M., Arkin, A.P.
7th International Symposium on Dynamics and Control of Process Systems
Conservation analysis in biochemical networks: computational issues for software writers.
Sauro. H M and Ingalls B (2004)
Biophys Chem. 2004 Apr 1;109(1):1-15
The Computational Versatility of Proteomic Signaling Networks
Sauro. H M (2004
Current Proteomics, 2004, 1, 67-81 pdf
Computer Simulation of MAPK Signal Transduction
Aguda, B., and Sauro, H, M (2004)
in Methods Mol Biol. MAPK Signalling (R. Seger, Ed.), Humana Press, New Jersey, 2004; 250: 167-76. (link)
Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration
Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J and Kitano H. (2003)
OMICS. 2003 Winter;7(4):355-72. pdf
Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories
Ingalls BP and Sauro H M. (2003)
J Theor Biol. 2003 May 7;222(1):23-36. pdf
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
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)
Bioinformatics. 2003 Mar 1;19(4):524-31
The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle J, Kitano H.
Pac Symp Biocomput. 2002;:450-61.
Exploring Mathematical Functions using vExplorer
H.M. Sauro
Future Skill Software
Introduction to Error Analysis in Experimentation using EasyGraph professional
H.M. Sauro
Future Skill Software
The Periodic Table
H.M. Sauro
Published by: Future Skill Software
Creatures and Population Modelling
H.M. Sauro
Published by: Future Skill Software
Introduction to Mathematical Modelling using Fplot
H.M. Sauro
Published by: Future Skill Software
User Reference Manual EasyGraph
H.M. Sauro
Published by: Future Skill Software
Coenzyme Cycles and Metabolic Control Analysis: The Determination of the Elasticity Coefficients from the Generalised Connectivity Theorem
B.N. Kholodenko, H.M. Sauro, H.V. Westerhoff
Biochemistry and Molecular Biology, 33 (3), 615-625
in vitro Control Analysis of Metabolic Pathways; experimental and analytical developments
H.M. Sauro, J. Barrett
Molecular and Cellular Biochemistry, 145, 141-150
Control by enzymes, coenzymes and conserved moieties: A generalisation of the connectivity theorem of metabolic control analysis
H.M. Sauro, B.N. Kholodenko, H. Westerhoff
European Journal of Biochemistry, 225, 179-186
Moiety-conserved cycles and metabolic control analysis: problems in sequestration and metabolic channelling
H.M. Sauro
Biosystems, 33, 55-67 Moiety-Conserved Cycles
Analyses and Simulators: a brief description of two computer programs SCAMP and iMAP
H.M. Sauro
Biothermokinetics. Ed: Westerhoff, H, Plenum Press, New York, 213-223
A Biochemical ‘NAND’ Gate and Assorted Circuits. Modern Trends in Biothermokinetics
H.M. Sauro
Modern Trends in Biothermokinetics, Ed: Schuster S. et al, Plenum Press, New York, 133-140
When Going Backwards Means Progress: On the solution of biochemical inverse problems using artificial neural networks
D.B. Kell D. B, C.L. Davey, R. Goodacre, H.M. Sauro
Modern Trends in Biothermokinetics. Ed: Schuster S. et al, Plenum Press, New York, 109-114
SCAMP: a general-purpose simulator and metabolic control analysis program
H.M. Sauro
Bioinformatics, 9 (4), 441-450
Evaluation of Steady-state Kinetic Parameters of Metabolic Pathways using Neural Networks
H.M. Sauro, D.B. Kell
Binary Computing in Microbiology, 4, 189-190
SCAMP: A metabolic simulator and control analysis program
H.M. Sauro, D.A. Fell
Mathematical and computer modelling, 15, 15-28
Metabolic Control Analysis: the effect of high enzyme concentrations
H.M. Sauro, D.A. Fell
European Journal of Biochemistry, 192, 183-187
Metabolic Control Analysis by Computer: Progress and prospects
H.M. Sauro, D.A. Fell
Biomed. Biochem. Acta, 8/9, 811-816
Metabolic control and its analysis: Extensions to the theory and matrix method
H.M. Sauro, J.R. Small, D.A. Fell
European Journal of Biochemistry, 165, 215-221
Control Analysis and Simulation of Metabolism: Ph.D. Thesis
H.M. Sauro
Oxford Polytechnic
Metabolic Control and its Analysis: Additional Relationships between Elasticities and Control Coefficients
D.A. Fell, H.M. Sauro
European Journal of Biochemistry, 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)
Control coefficients and the matrix method. Ch. 9, 139-148,
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.
Control analysis of systems with enzyme-enzyme interactions. Control of Metabolic Processes.
KACSER H., SAURO H. M., and ACERENZA L., (1990),
Cornish-Bowden, A.& Cardenas, M.L. eds.) NATO ASI Series, plenum Press, New York. Ch. 20, 251-257
Jarnac: a system for interactive metabolic analysis. Animating the Cellular Map 9th International BioThermoKinetics Meeting
SAURO, H. M., (2000) Ch. 33, 221- 228, (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)