SCAMP: a general-purpose simulator and metabolic control analysis program. - Herbert M. Sauro (Comput. Appl. Biosci., 1993)

Elasticities in Metabolic Control Analysis: algebraic derivation of simplified expressions. - J. H. Woods; Herbert M. Sauro (Comput. Appl. Biosci., 1997)

The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology. - Michael Hucka; Andrew Finney; Herbert M. Sauro; H. Bolouri; John C. Doyle 001; Hiroaki Kitano (Pacific Symposium on Biocomputing, 2002)

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. - Michael Hucka; Andrew Finney; Herbert M. Sauro; H. Bolouri; John C. Doyle 001; Hiroaki Kitano; Adam P. Arkin; Benjamin J. Bornstein; Dennis Bray; Athel Cornish-Bowden; Autumn A. Cuellar; Serge Dronov; et al. (Bioinform., 2003)

Bifurcation discovery tool. - Vijay Chickarmane; Sri R. Paladugu; Frank T. Bergmann; Herbert M. Sauro (Bioinform., 2005)

The SBW-CMATLAB interface. - Cameron Wellock; Vijay Chickarmane; Herbert M. Sauro (Bioinform., 2005)

Simulation of biochemical networks - Cellular networks as dynamic control systems. - Herbert M. Sauro (EMBC, 2006)

SBW - a modular framework for systems biology. - Frank T. Bergmann; Herbert M. Sauro (WSC, 2006)

Innovation in software for systems biology: is there any? - Herbert M. Sauro (WSC, 2006)

Challenges for modeling and simulation methods in systems biology. - Herbert M. Sauro; David Harel; Marta Z. Kwiatkowska; Clifford A. Shaffer; Adelinde M. Uhrmacher; Michael Hucka; Pedro Mendes 001; Lena Strömbäck; John J. Tyson (WSC, 2006)

Complexity reduction of biochemical networks. - Ravishankar Rao Vallabhajosyula; Herbert M. Sauro (WSC, 2006)

Supporting the SBML layout extension. - Anastasia Deckard; Frank T. Bergmann; Herbert M. Sauro (Bioinform., 2006)

Conservation analysis of large biochemical networks. - Ravishankar Rao Vallabhajosyula; Vijay Chickarmane; Herbert M. Sauro (Bioinform., 2006)

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. - Nicolas Le Novère; Benjamin J. Bornstein; Alexander Broicher; Mélanie Courtot; Marco Donizelli; Harish Dharuri; Lu Li 002; Herbert M. Sauro; Maria J. Schilstra; Bruce E. Shapiro; Jacky L. Snoep; Michael Hucka (Nucleic Acids Res., 2006)

Transcriptional Dynamics of the Embryonic Stem Cell Switch. - Vijay Chickarmane; Carl Troein; Ulrike A. Nuber; Herbert M. Sauro; Carsten Peterson (PLoS Comput. Biol., 2006)

Stochastic simulation GUI for biochemical networks. - Ravishankar Rao Vallabhajosyula; Herbert M. Sauro (Bioinform., 2007)

A Model for p53 Dynamics Triggered by DNA Damage. - Vijay Chickarmane; Animesh Ray; Herbert M. Sauro; Ali Nadim (SIAM J. Appl. Dyn. Syst., 2007)

Comparing simulation results of SBML capable simulators. - Frank T. Bergmann; Herbert M. Sauro (Bioinform., 2008)

Antimony: a modular model definition language. - Lucian P. Smith; Frank T. Bergmann; Deepak Chandran; Herbert M. Sauro (Bioinform., 2009)

Biological Models of Molecular Network Dynamics. - Herbert M. Sauro (Encyclopedia of Complexity and Systems Science, 2009)

SBML2TikZ: supporting the SBML render extension in LaTeX. - Si Yuan Shen; Frank T. Bergmann; Herbert M. Sauro (Bioinform., 2010)

Minimum Information About a Simulation Experiment (MIASE). - Dagmar Waltemath; Richard R. Adams; Daniel A. Beard; Frank T. Bergmann; Upinder S. Bhalla; Randall Britten; Vijayalakshmi Chelliah; Mike T. Cooling; Jonathan Cooper; Edmund J. Crampin; Alan Garny; Stefan Hoops; et al. (PLoS Comput. Biol., 2011)

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. - Sean C. Sleight; Herbert M. Sauro (ALIFE, 2012)

Measuring the degree of modularity in gene regulatory networks from the relaxation of finite perturbations. - Kyung Hyuk Kim; Herbert M. Sauro (CDC, 2012)

Modeling and design automation of biological circuits and systems. - Natasa Miskov-Zivanov; James R. Faeder; Chris J. Myers; Herbert M. Sauro (ICCAD, 2012)

Adjusting Phenotypes by Noise Control. - Kyung Hyuk Kim; Herbert M. Sauro (PLoS Comput. Biol., 2012)

A C library for retrieving specific reactions from the BioModels database. - Maxwell Lewis Neal; Michal Galdzicki; J. T. Gallimore; Herbert M. Sauro (Bioinform., 2014)

SBML and CellML translation in Antimony and JSim. - Lucian P. Smith; Erik Butterworth; James B. Bassingthwaighte; Herbert M. Sauro (Bioinform., 2014)

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. - Frank T. Bergmann; Richard R. Adams; Stuart L. Moodie; Jonathan Cooper; Mihai Glont; Martin Golebiewski; Michael Hucka; Camille Laibe; Andrew K. Miller; David P. Nickerson; Brett G. Olivier; Nicolas Rodriguez 001; et al. (BMC Bioinform., 2014)

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. - Pablo Meyer 001; Thomas Cokelaer; Deepak Chandran; Kyung Hyuk Kim; Po-Ru Loh; George Tucker; Mark Lipson; Bonnie Berger; Clemens Kreutz; Andreas Raue; Bernhard Steiert; Jens Timmer; et al. (BMC Syst. Biol., 2014)

COMBINE archive: One File To Share Them All. - Frank T. Bergmann; Richard Adams; Stuart L. Moodie; Jonathan Cooper; Mihai Glont; Martin Golebiewski; Michael Hucka; Camille Laibe; Andrew K. Miller; David P. Nickerson; Brett G. Olivier; Nicolas Rodriguez 001; et al. (CoRR, 2014)

Introduction to the Special Issue on Computational Synthetic Biology. - Chris J. Myers; Herbert M. Sauro; Anil Wipat (ACM J. Emerg. Technol. Comput. Syst., 2014)

A Reappraisal of How to Build Modular, Reusable Models of Biological Systems. - Maxwell Lewis Neal; Michael T. Cooling; Lucian P. Smith; Christopher T. Thompson; Herbert M. Sauro; Brian E. Carlson; Daniel L. Cook; John H. Gennari (PLoS Comput. Biol., 2014)

libRoadRunner: a high performance SBML simulation and analysis library. - Endre T. Somogyi; Jean-Marie Bouteiller; James A. Glazier; Matthias König 003; J. Kyle Medley; Maciej H. Swat; Herbert M. Sauro (Bioinform., 2015)

Synthetic Biology Open Language (SBOL) Version 2.0.0. - Bryan Bartley; Jacob Beal; Kevin Clancy; Goksel Misirli; Nicholas Roehner; Ernst Oberortner; Matthew R. Pocock; Michael Bissell; Curtis Madsen; Tramy Nguyen; Zhen Zhang 006; John H. Gennari; et al. (J. Integr. Bioinform., 2015)

Controlling E. coli Gene Expression Noise. - Kyung Hyuk Kim; Kiri Choi; Bryan Bartley; Herbert M. Sauro (IEEE Trans. Biomed. Circuits Syst., 2015)

phraSED-ML: A paraphrased, human-readable adaptation of SED-ML. - Kiri Choi; Lucian P. Smith; J. Kyle Medley; Herbert M. Sauro (J. Bioinform. Comput. Biol., 2016)

Synthetic Biology Open Language (SBOL) Version 2.1.0. - Jacob Beal; Robert Sidney Cox III; Raik Grünberg; James Alastair McLaughlin; Tramy Nguyen; Bryan Bartley; Michael Bissell; Kiri Choi; Kevin Clancy; Chris Macklin; Curtis Madsen; Goksel Misirli; et al. (J. Integr. Bioinform., 2016)

A portable structural analysis library for reaction networks. - Yosef Bedaso; Frank T. Bergmann; Kiri Choi; Kyle Medley; Herbert M. Sauro (Biosyst., 2018)

Tellurium: An extensible python-based modeling environment for systems and synthetic biology. - Kiri Choi; J. Kyle Medley; Matthias König 003; Kaylene Stocking; Lucian P. Smith; Stanley Gu; Herbert M. Sauro (Biosyst., 2018)

Synthetic Biology Open Language (SBOL) Version 2.2.0. - Robert Sidney Cox III; Curtis Madsen; James Alastair McLaughlin; Tramy Nguyen; Nicholas Roehner; Bryan Bartley; Jacob Beal; Michael Bissell; Kiri Choi; Kevin Clancy; Raik Grünberg; Chris Macklin; et al. (J. Integr. Bioinform., 2018)

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0. - Robert Sidney Cox III; Curtis Madsen; James Alastair McLaughlin; Tramy Nguyen; Nicholas Roehner; Bryan Bartley; Swapnil Bhatia; Mike Bissell; Kevin Clancy; Thomas E. Gorochowski; Raik Grünberg; Augustin Luna; et al. (J. Integr. Bioinform., 2018)

Tellurium notebooks - An environment for reproducible dynamical modeling in systems biology. - J. Kyle Medley; Kiri Choi; Matthias König 003; Lucian P. Smith; Stanley Gu; Joseph L. Hellerstein; Stuart C. Sealfon; Herbert M. Sauro (PLoS Comput. Biol., 2018)

Harmonizing semantic annotations for computational models in biology. - Maxwell Lewis Neal; Matthias König 003; David P. Nickerson; Goksel Misirli; Reza Kalbasi; Andreas Dräger; Koray Atalag; Vijayalakshmi Chelliah; Michael T. Cooling; Daniel L. Cook; Sharon M. Crook; Miguel de Alba; et al. (Briefings Bioinform., 2019)

A Commentary on the Linearity and Time-Invariance of ODE-Based Systems. - Parker S. Ruth; Herbert M. Sauro (CoRR, 2019)

Synthetic Biology Open Language (SBOL) Version 2.3. - Curtis Madsen; Ángel Goñi-Moreno; Umesh P; Zachary Palchick; Nicholas Roehner; Christian Atallah; Bryan Bartley; Kiri Choi; Robert Sidney Cox III; Thomas E. Gorochowski; Raik Grünberg; Chris Macklin; et al. (J. Integr. Bioinform., 2019)

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1. - Curtis Madsen; Ángel Goñi-Moreno; Zachary Palchick; Umesh P; Nicholas Roehner; Bryan Bartley; Swapnil Bhatia; Shyam Bhakta; Mike Bissell; Kevin Clancy; Robert Sidney Cox III; Thomas E. Gorochowski; et al. (J. Integr. Bioinform., 2019)

libsbmljs - Enabling web-based SBML tools. - J. Kyle Medley; Joseph L. Hellerstein; Herbert M. Sauro (Biosyst., 2020)

Synthetic biology open language visual (SBOL visual) version 2.2. - Hasan Baig; Pedro Fontanarrosa; Vishwesh Kulkarni 002; James Alastair McLaughlin; Prashant Vaidyanathan; Bryan Bartley; Swapnil Bhatia; Shyam Bhakta; Michael Bissell; Kevin Clancy; Robert Sidney Cox III; Ángel Goñi-Moreno; et al. (J. Integr. Bioinform., 2020)

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). - Dagmar Waltemath; Martin Golebiewski; Michael L. Blinov; Padraig Gleeson; Henning Hermjakob; Michael Hucka; Esther Thea Inau; Sarah M. Keating; Matthias König 003; Olga Krebs; Rahuman S. Malik-Sheriff; David P. Nickerson; et al. (J. Integr. Bioinform., 2020)

A compiler for biological networks on silicon chips. - J. Kyle Medley; Jonathan J. Y. Teo; Sung Sik Woo; Joseph L. Hellerstein; Rahul Sarpeshkar; Herbert M. Sauro (PLoS Comput. Biol., 2020)

Improving reproducibility in computational biology research. - Jason A. Papin; Feilim Mac Gabhann; Herbert M. Sauro; David P. Nickerson; Anand K. Rampadarath (PLoS Comput. Biol., 2020)

Publishing reproducible dynamic kinetic models. - Veronica Porubsky; Lucian P. Smith; Herbert M. Sauro (Briefings Bioinform., 2021)

libOmexMeta: enabling semantic annotation of models to support FAIR principles. - Ciaran M. Welsh; David P. Nickerson; Anand K. Rampadarath; Maxwell Lewis Neal; Herbert M. Sauro; John H. Gennari (Bioinform., 2021)

Synthetic biology open language visual (SBOL Visual) version 2.3. - Hasan Baig; Pedro Fontanarossa; Vishwesh Kulkarni 002; James Alastair McLaughlin; Prashant Vaidyanathan; Bryan Bartley; Shyam Bhakta; Swapnil Bhatia; Mike Bissell; Kevin Clancy; Robert Sidney Cox III; Ángel Goñi-Moreno; et al. (J. Integr. Bioinform., 2021)

The simulation experiment description markup language (SED-ML): language specification for level 1 version 4. - Lucian P. Smith; Frank T. Bergmann; Alan Garny; Tomás Helikar; Jonathan R. Karr; David P. Nickerson; Herbert M. Sauro; Dagmar Waltemath; Matthias König 003 (J. Integr. Bioinform., 2021)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (CoRR, 2022)

BioSimulators: a central registry of simulation engines and services for recommending specific tools. - Bilal Shaikh; Lucian P. Smith; Dan Vasilescu; Gnaneswara Marupilla; Michael Wilson; Eran Agmon; Henry Agnew; Steven S. Andrews; Azraf Anwar; Moritz E. Beber; Frank T. Bergmann; David Brooks 006; et al. (Nucleic Acids Res., 2022)

SBbadger: biochemical reaction networks with definable degree distributions. - Michael A Kochen; H. Steven Wiley; Song Feng; Herbert M. Sauro (Bioinform., 2022)

libRoadRunner 2.0: a high performance SBML simulation and analysis library. - Ciaran M. Welsh; Jin Xu; Lucian P. Smith; Matthias König 003; Kiri Choi; Herbert M. Sauro (Bioinform., 2023)

SBMLDiagrams: a python package to process and visualize SBML layout and render. - Jin Xu; Jessie Jiang; Herbert M. Sauro (Bioinform., 2023)

Cesium: A public database of evolved oscillatory reaction networks. - Lillian T. Tatka; Wesley Luk; Timothy C. Elston; Joseph L. Hellerstein; Herbert M. Sauro (Biosyst., 2023)

An automated model annotation system (AMAS) for SBML models. - Woosub Shin; John H. Gennari; Joseph L. Hellerstein; Herbert M. Sauro (Bioinform., 2023)

SBcoyote: An extensible Python-based reaction editor and viewer. - Jin Xu; Gary Geng; Nhan D. Nguyen; Carmen Perena-Cortes; Claire Samuels; Herbert M. Sauro (Biosyst., 2023)

Tissue Forge: Interactive biological and biophysics simulation environment. - T. J. Sego; James P. Sluka; Herbert M. Sauro; James A. Glazier (PLoS Comput. Biol., 2023)

VSCode-Antimony: a source editor for building, analyzing, and translating antimony models. - Steve Ma; Longxuan Fan; Sai Anish Konanki; Eva Liu; John H. Gennari; Lucian P. Smith; Joseph L. Hellerstein; Herbert M. Sauro (Bioinform., 2023)

Whole-cell metabolic control analysis. - Frank J. Bruggeman; Maaike Remeijer; Maarten Droste; Luis Salinas; Meike T. Wortel; Robert Planqué; Herbert M. Sauro; Bas Teusink; Hans V. Westerhoff (Biosyst., 2023)

MakeSBML: a tool for converting between Antimony and SBML. - Bartholomew E. Jardine; Lucian P. Smith; Herbert M. Sauro (J. Integr. Bioinform., 2024)

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5. - Lucian P. Smith; Frank T. Bergmann; Alan Garny; Tomás Helikar; Jonathan R. Karr; David P. Nickerson; Herbert M. Sauro; Dagmar Waltemath; Matthias König 003 (J. Integr. Bioinform., 2024)