Herbert M. Sauro

According to our database1, Herbert M. Sauro authored at least 46 papers between 1993 and 2019.

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Bibliography

2019
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1.
J. Integrative Bioinformatics, 2019

Synthetic Biology Open Language (SBOL) Version 2.3.
J. Integrative Bioinformatics, 2019

A Commentary on the Linearity and Time-Invariance of ODE-Based Systems.
CoRR, 2019

Harmonizing semantic annotations for computational models in biology.
Briefings in Bioinformatics, 2019

2018
Tellurium notebooks - An environment for reproducible dynamical modeling in systems biology.
PLoS Computational Biology, 2018

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0.
J. Integrative Bioinformatics, 2018

Synthetic Biology Open Language (SBOL) Version 2.2.0.
J. Integrative Bioinformatics, 2018

Tellurium: An extensible python-based modeling environment for systems and synthetic biology.
Biosyst., 2018

A portable structural analysis library for reaction networks.
Biosyst., 2018

2016
Synthetic Biology Open Language (SBOL) Version 2.1.0.
J. Integrative Bioinformatics, 2016

phraSED-ML: A paraphrased, human-readable adaptation of SED-ML.
J. Bioinformatics and Computational Biology, 2016

2015
Controlling E. coli Gene Expression Noise.
IEEE Trans. Biomed. Circuits and Systems, 2015

Synthetic Biology Open Language (SBOL) Version 2.0.0.
J. Integrative Bioinformatics, 2015

libRoadRunner: a high performance SBML simulation and analysis library.
Bioinformatics, 2015

2014
A Reappraisal of How to Build Modular, Reusable Models of Biological Systems.
PLoS Computational Biology, 2014

Introduction to the Special Issue on Computational Synthetic Biology.
JETC, 2014

COMBINE archive: One File To Share Them All.
CoRR, 2014

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
BMC Systems Biology, 2014

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.
BMC Bioinformatics, 2014

SBML and CellML translation in Antimony and JSim.
Bioinformatics, 2014

A C library for retrieving specific reactions from the BioModels database.
Bioinformatics, 2014

2012
Adjusting Phenotypes by Noise Control.
PLoS Computational Biology, 2012

Modeling and design automation of biological circuits and systems.
Proceedings of the 2012 IEEE/ACM International Conference on Computer-Aided Design, 2012

Measuring the degree of modularity in gene regulatory networks from the relaxation of finite perturbations.
Proceedings of the 51th IEEE Conference on Decision and Control, 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.
Proceedings of the Artificial Life 13: Proceedings of the Thirteenth International Conference on the Simulation and Synthesis of Living Systems, 2012

2011
Minimum Information About a Simulation Experiment (MIASE).
PLoS Computational Biology, 2011

2010
SBML2TikZ: supporting the SBML render extension in LaTeX.
Bioinformatics, 2010

2009
Biological Models of Molecular Network Dynamics.
Proceedings of the Encyclopedia of Complexity and Systems Science, 2009

Antimony: a modular model definition language.
Bioinformatics, 2009

2008
Comparing simulation results of SBML capable simulators.
Bioinformatics, 2008

2007
A Model for p53 Dynamics Triggered by DNA Damage.
SIAM J. Applied Dynamical Systems, 2007

Stochastic simulation GUI for biochemical networks.
Bioinformatics, 2007

2006
Transcriptional Dynamics of the Embryonic Stem Cell Switch.
PLoS Computational Biology, 2006

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems.
Nucleic Acids Research, 2006

Conservation analysis of large biochemical networks.
Bioinformatics, 2006

Supporting the SBML layout extension.
Bioinformatics, 2006

Complexity reduction of biochemical networks.
Proceedings of the Winter Simulation Conference WSC 2006, 2006

Challenges for modeling and simulation methods in systems biology.
Proceedings of the Winter Simulation Conference WSC 2006, 2006

Innovation in software for systems biology: is there any?
Proceedings of the Winter Simulation Conference WSC 2006, 2006

SBW - a modular framework for systems biology.
Proceedings of the Winter Simulation Conference WSC 2006, 2006

2005
The SBW-CMATLAB interface.
Bioinformatics, 2005

Bifurcation discovery tool.
Bioinformatics, 2005

2003
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Bioinformatics, 2003

2002
The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

1997
Elasticities in Metabolic Control Analysis: algebraic derivation of simplified expressions.
Computer Applications in the Biosciences, 1997

1993
SCAMP: a general-purpose simulator and metabolic control analysis program.
Computer Applications in the Biosciences, 1993


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