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List of works by Herbert M. Sauro

A Portable Structural Analysis Library for Reaction Networks

A Visual Language for Protein Design.

scientific article published on 7 February 2017

A brief note on the properties of linear pathways

scientific article published on 24 August 2020

A compiler for biological networks on silicon chips

scientific article published on 23 September 2020

A portable structural analysis library for reaction networks

scientific article published on 30 May 2018

A reappraisal of how to build modular, reusable models of biological systems.

scientific article

Adjusting phenotypes by noise control

scientific article

Antimony: a modular model definition language

scientific article

Best Practices for Making Reproducible Biochemical Models

scientific article published on 01 August 2020

Bifurcation discovery tool

scientific article published on 4 August 2005

BioBrick™ assembly using the In-Fusion PCR Cloning Kit.

scientific article published in January 2013

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

scientific article

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

scientific article

Challenges for Modeling and Simulation Methods in Systems Biology

Communicating Structure and Function in Synthetic Biology Diagrams

scientific article published on 05 August 2019

Comparing simulation results of SBML capable simulators

scientific article published on 25 June 2008

Computational Tools for Modeling Protein Networks

Computational tools for metabolic engineering.

scientific article published on May 2012

Computer simulation of MAPK signal transduction

scientific article published on 01 January 2004

Computer-aided design of biological circuits using tinkercell ⬇️

scientific article published on July 1, 2010

Conservation analysis in biochemical networks: computational issues for software writers

scientific article published on April 2004

Conservation analysis of large biochemical networks

scientific article published on 29 November 2005

Control and regulation of pathways via negative feedback

scientific article published on February 2017

Control by Enzymes, Coenzymes and Conserved Moieties. A Generalisation of the Connectivity Theorem of Metabolic Control Analysis

article

Controlling E. coli Gene Expression Noise.

scientific article

Correction to 'Control and regulation of pathways via negative feedback'.

scientific article published on April 2017

Data Integration and Mining for Synthetic Biology Design

scientific article

Design and implementation of three incoherent feed-forward motif based biological concentration sensors

scientific article

Designing and engineering evolutionary robust genetic circuits.

scientific article

Editorial Reproducibility of Computational Models

scientific article published on 22 September 2016

Erratum: The Systems Biology Graphical Notation

scholarly article published in Nature Biotechnology

Essential information for synthetic DNA sequences

scientific article published on 01 January 2011

Fan-out in gene regulatory networks.

scientific article

Harmonizing semantic annotations for computational models in biology

Harmonizing semantic annotations for computational models in biology

scientific article published on 01 March 2019

Hierarchical modeling for synthetic biology

scientific article published on 10 August 2012

Improving reproducibility in computational biology research

scientific article published on 19 May 2020

In search of noise-induced bimodality

scientific article

In silico evolution of functional modules in biochemical networks.

scientific article

In vitro control analysis of an enzyme system: experimental and analytical developments

scientific article published on 01 April 1995

In-Fusion BioBrick assembly and re-engineering

scientific article (publication date: 10 April 2010)

Introduction to the Special Issue on Computational Synthetic Biology

scholarly article by Chris J. Myers et al published 30 December 2014 in ACM Journal on Emerging Technologies in Computing Systems

Mathematical modeling and synthetic biology.

scientific article published on January 2008

Measuring retroactivity from noise in gene regulatory networks

scientific article

Mechanistic and modular approaches to modeling and inference of cellular regulatory networks

article

Metabolic control analysis. The effects of high enzyme concentrations

article

Minimum Information About a Simulation Experiment (MIASE)

scientific article

Minimum information requested in the annotation of biochemical models (MIRIAM)

scientific article

Modularity defined

scientific article published on 12 February 2008

Moiety-conserved cycles and metabolic control analysis: problems in sequestration and metabolic channelling

scientific article published in January 1994

Network dynamics

scientific article published on January 2009

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

scientific article

Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration

scientific article

Nonlinear biochemical signal processing via noise propagation

scientific article published in October 2013

Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation

article

Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology

scientific article published in September 2021

Preliminary studies on the in silico evolution of biochemical networks.

scientific article published in October 2004

Proposed data model for the next version of the synthetic biology open language

scientific article

Publishing reproducible dynamic kinetic models

scientific article published on 14 August 2020

PyBioNetFit and the Biological Property Specification Language

scientific article published on 28 August 2019

Quantitative analysis of signaling networks.

scientific article published in September 2004

Randomized BioBrick assembly: a novel DNA assembly method for randomizing and optimizing genetic circuits and metabolic pathways

scientific article published on 22 July 2013

Rationally designed bidirectional promoter improves the evolutionary stability of synthetic genetic circuits

scientific article published on 23 October 2012

Recent advances in biomedical simulations: a manifesto for model engineering

scientific article published on 05 March 2019

Reply to Intellectual property issues and synthetic biology standards

scientific article published in January 2015

SBML Level 3: an extensible format for the exchange and reuse of biological models

scientific article published on 01 August 2020

SBML and CellML translation in antimony and JSim.

scientific article

SBML2TikZ: supporting the SBML render extension in LaTeX.

scientific article

SBMLDiagrams: a python package to process and visualize SBML layout and render

scientific article published in 2022

SBOL Visual: A Graphical Language for Genetic Designs

scientific article published on 3 December 2015

SBW - A Modular Framework for Systems Biology

SCAMP: A metabolic simulator and control analysis program

article

Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories.

scientific article published in May 2003

Sensitivity summation theorems for stochastic biochemical reaction systems

scientific article published on 4 May 2010

Sharing Structure and Function in Biological Design with SBOL 2.0.

scientific article published on 25 April 2016

Simulation of biochemical networks--cellular networks as dynamic control systems

scientific article

Software Tools for Systems Biology

scholarly article published 2010

Spatio-temporal dynamics of protein modification cascades.

scientific article published on January 2008

Standard biological parts knowledgebase

scientific article

Standards and ontologies in computational systems biology

scientific article

Stochastic modular analysis for gene circuits: interplay among retroactivity, nonlinearity, and stochasticity

scientific article published on January 2015

Stochastic simulation GUI for biochemical networks

scientific article published on 22 June 2007

Supporting the SBML layout extension

scientific article published on 11 October 2006

Synthetic Biology Open Language (SBOL) Version 2.0.0.

scientific article published on 04 September 2015

Synthetic Biology Open Language (SBOL) Version 2.0.0.

scientific article published in June 2015

Synthetic Biology Open Language (SBOL) Version 2.1.0.

scientific article published in September 2016

Synthetic Biology Open Language (SBOL) Version 2.1.0.

scientific article published on 18 December 2016

Synthetic Biology Open Language (SBOL) Version 2.2.0.

scientific article published on 2 April 2018

Synthetic Biology Open Language (SBOL) Version 2.3.

scientific article published on 13 June 2019

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0.

scientific article published on 17 March 2018

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1.

scientific article published on 13 June 2019

Synthetic Biology: Engineering Living Systems from Biophysical Principles

scientific article published on March 2017

Synthetic biology open language visual (SBOL visual) version 2.2.

scientific article published on 10 June 2020

Synthetic biology: Enter the living machine

scientific article published in Nature

Synthetic biology: How best to build a cell

scientific article published in May 2014

Synthetic biology: It's an analog world

scientific article published on 15 May 2013

Tellurium Notebooks - An Environment for Dynamical Model Development, Reproducibility, and Reuse

article

Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology.

scientific article published on 15 June 2018

Tellurium: An extensible python-based modeling environment for systems and synthetic biology

scientific article published on 25 July 2018

The SBW-MATLAB interface

scientific article published on 05 November 2004

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

scientific article

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)

scientific article published on 29 June 2020

The simulation experiment description markup language (SED-ML): language specification for level 1 version 5

scientific article published in March 2024

The synthetic biology open language

scientific article published on January 2015

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

scientific article (publication date: March 2003)

TinkerCell: modular CAD tool for synthetic biology

scientific article published on 29 October 2009

Transcriptional dynamics of the embryonic stem cell switch

scientific article

Visualization of evolutionary stability dynamics and competitive fitness of Escherichia coli engineered with randomized multigene circuits

scientific article published on 4 September 2013

libRoadRunner 2.0: a high performance SBML simulation and analysis library

scientific article published in 2022

libRoadRunner: a high performance SBML simulation and analysis library

scientific article published on 17 June 2015

libsbmljs-Enabling web-based SBML tools

scientific article published on 24 April 2020

phraSED-ML: A paraphrased, human-readable adaptation of SED-ML.

scientific article

pySBOL: A Python Package for Genetic Design Automation and Standardization

scientific article published on 06 December 2018

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