Herbert M. Sauro | Academic Influence

Herbert M. Sauro's AcademicInfluence.com Rankings

Herbert M. Sauro

Engineering

#7765

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#9181

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Bioengineering

#89

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#91

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Electrical Engineering

#2473

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#2592

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engineering Degrees

Herbert M. Sauro

Computer Science

#10702

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#11254

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#7672

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#7970

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computer-science Degrees

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Engineering
Computer Science

Herbert M. Sauro's Degrees

PhD Bioengineering University of Washington
Masters Computer Science University of Washington
Bachelors Electrical Engineering University of Washington

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Why Is Herbert M. Sauro Influential?

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According to Wikipedia, Herbert M. Sauro works in the field of metabolic control analysis and systems biology. Education and early life Sauro was born July 19, 1960, in Dyfed, Wales. He grew up in the village of Llangolman in Pembrokeshire and attended the Welsh comprehensive school Ysgol y Preseli.

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Herbert M. Sauro's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models (2003) (3236)
The Systems Biology Graphical Notation (2009) (894)
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems (2005) (806)
Minimum information requested in the annotation of biochemical models (MIRIAM) (2005) (617)
Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. (2003) (315)
Transcriptional Dynamics of the Embryonic Stem Cell Switch (2006) (269)
Metabolic control and its analysis (1985) (267)
The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology (2014) (249)
Quantitative analysis of signaling networks. (2004) (229)
TinkerCell: modular CAD tool for synthetic biology (2009) (200)
Designing and engineering evolutionary robust genetic circuits (2010) (161)
Minimum Information About a Simulation Experiment (MIASE) (2011) (150)
Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories. (2003) (150)
SBML Level 3: an extensible format for the exchange and reuse of biological models (2020) (137)
SCAMP: a general-purpose simulator and metabolic control analysis program (1993) (136)
In-Fusion BioBrick assembly and re-engineering (2010) (136)
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project (2014) (123)
Metabolic control and its analysis. Extensions to the theory and matrix method. (1987) (120)
libRoadRunner: A High Performance SBML Simulation and Analysis Library (2015) (116)
Antimony: a modular model definition language (2009) (115)
33 JARNAC: a system for interactive metabolic analysis (2000) (109)
The ERATO Systems Biology Workbench: Enabling Interaction and Exchange Between Software Tools for Computational Biology (2001) (101)
Computational tools for metabolic engineering. (2012) (99)
Metabolic control analysis. The effects of high enzyme concentrations. (1990) (99)
Programmer's Manual (2004) (93)
Conservation analysis in biochemical networks: computational issues for software writers. (2004) (93)
Standard Biological Parts Knowledgebase (2011) (92)
Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation. (2007) (88)
Enzyme Kinetics for Systems Biology (2012) (86)
Sharing Structure and Function in Biological Design with SBOL 2.0. (2016) (83)
Metabolic control and its analysis. Additional relationships between elasticities and control coefficients. (1985) (82)
Control analysis of time-dependent metabolic systems. (1989) (82)
Enzyme-enzyme interactions and control analysis. 1. The case of non-additivity: monomer-oligomer associations. (1990) (80)
SBOL Visual: A Graphical Language for Genetic Designs (2015) (79)
In silico evolution of functional modules in biochemical networks. (2006) (79)
Preliminary Studies on the In Silico Evolution of Biochemical Networks (2004) (79)
Conservation analysis of large biochemical networks (2006) (79)
Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach (2014) (76)
Enzyme-enzyme interactions and control analysis. 2. The case of non-independence: heterologous associations. (1990) (73)
Visualization of evolutionary stability dynamics and competitive fitness of Escherichia coli engineered with randomized multigene circuits. (2013) (73)
Tellurium: An extensible python-based modeling environment for systems and synthetic biology (2018) (68)
Design and implementation of three incoherent feed-forward motif based biological concentration sensors (2007) (68)
Bifurcation discovery tool (2005) (62)
SCAMP: A metabolic simulator and control analysis program (1991) (56)
SBW - A Modular Framework for Systems Biology (2006) (56)
Modularity defined (2008) (55)
Rationally designed bidirectional promoter improves the evolutionary stability of synthetic genetic circuits (2012) (52)
A Reappraisal of How to Build Modular, Reusable Models of Biological Systems (2014) (50)
Mathematical modeling and synthetic biology. (2008) (48)
Essential information for synthetic DNA sequences (2011) (47)
Comparing simulation results of SBML capable simulators (2008) (42)
Harmonizing semantic annotations for computational models in biology (2018) (42)
A Model for p53 Dynamics Triggered by DNA Damage (2007) (39)
Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology (2018) (38)
Fan-out in gene regulatory networks (2010) (38)
Challenges for Modeling and Simulation Methods in Systems Biology (2006) (37)
Synthetic Biology Open Language (SBOL) Version 2.2.0 (2018) (37)
Control and regulation of pathways via negative feedback (2017) (35)
Computer-aided design of biological circuits using tinkercell (2010) (34)
Synthetic Biology Open Language (SBOL) Version 2.3 (2019) (33)
Measuring retroactivity from noise in gene regulatory networks. (2011) (33)
Synthetic biology: It's an analog world (2013) (32)
Synthetic Biology Open Language (SBOL) Version 2.0.0 (2015) (31)
PyBioNetFit and the Biological Property Specification Language (2019) (31)
Supporting the SBML layout extension (2006) (30)
Standards and ontologies in computational systems biology. (2008) (29)
Adjusting Phenotypes by Noise Control (2012) (29)
Control by enzymes, coenzymes and conserved moieties (1994) (29)
Proposed data model for the next version of the synthetic biology open language. (2015) (27)
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0 (2018) (27)
Synthetic biology: How best to build a cell (2014) (27)
Synthetic Biology Open Language (SBOL) Version 2.0.0. (2015) (27)
Randomized BioBrick assembly: a novel DNA assembly method for randomizing and optimizing genetic circuits and metabolic pathways. (2013) (26)
Communicating Structure and Function in Synthetic Biology Diagrams. (2019) (25)
The Computational Versatility of Proteomic Signaling Networks (2004) (25)
A p53 Oscillator Model of DNA Break Repair Control (2005) (24)
The ERATO Systems Biology Workbench: An Integrated Environment for Multiscale and Multitheoretic Simulations in Systems Biology (2001) (23)
Synthetic Biology: Engineering Living Systems from Biophysical Principles. (2017) (23)
Synthetic Biology Open Language (SBOL) Version 2.1.0 (2012) (22)
Tellurium: A Python Based Modeling and Reproducibility Platform for Systems Biology (2016) (22)
Quantitative Biology: Theory, Computational Methods, and Models (2018) (21)
Data Integration and Mining for Synthetic Biology Design. (2016) (21)
Best Practices for Making Reproducible Biochemical Models. (2020) (20)
Erratum: The Systems Biology Graphical Notation (2009) (20)
Regulatory Responses and Control Analysis: Assessment of the Relative Importance of Internal Effectors (1990) (20)
MAPK Cascades as Feedback Amplifiers (2007) (20)
Synthetic biology open language (SBOL) version 3.1.0 (2016) (19)
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE) (2020) (18)
Computational Tools for Modeling Protein Networks (2006) (17)
Moiety-conserved cycles and metabolic control analysis: problems in sequestration and metabolic channelling. (1994) (17)
SBML and CellML translation in Antimony and JSim (2014) (17)
Improving reproducibility in computational biology research (2020) (17)
Synthetic biology open language (SBOL) (2015) (17)
Mechanistic and modular approaches to modeling and inference of cellular regulatory networks (2005) (17)
Computer algebra approaches to enzyme kinetics (1991) (16)
Hierarchical modeling for synthetic biology. (2012) (15)
phraSED-ML: A paraphrased, human-readable adaptation of SED-ML (2016) (14)
Recent advances in biomedical simulations: a manifesto for model engineering (2019) (14)
BioBrick™ assembly using the In-Fusion PCR Cloning Kit. (2013) (14)
Putting the “Control” in Metabolic Control Analysis (2004) (14)
The ERATO Systems Biology Workbench: Architectural Evolution (2001) (13)
Complexity Reduction of Biochemical Networks (2006) (13)
Enumeration and Online Library of Mass-Action Reaction Networks (2009) (13)
PyCoTools: a Python toolbox for COPASI (2018) (13)
Synthetic Biology Open Language Visual (SBOL Visual) Version 2.1 (2019) (13)
Computer-Aided Design for Synthetic Biology (2011) (13)
The SBW-MATLAB interface. (2005) (12)
Controlling E. coli gene expression noise (2015) (12)
Control by enzymes, coenzymes and conserved moieties. A generalisation of the connectivity theorem of metabolic control analysis. (1994) (12)
Nonlinear biochemical signal processing via noise propagation. (2013) (12)
pySBOL: A Python Package for Genetic Design Automation and Standardization. (2018) (11)
Sensitivity summation theorems for stochastic biochemical reaction systems. (2010) (11)
Elasticities in Metabolic Control Analysis: algebraic derivation of simplified expressions (1997) (11)
In search of noise-induced bimodality (2012) (11)
Synthetic biology open language visual (SBOL visual) version 2.2 (2020) (11)
Drug Discovery Today : Disease Models (2009) (10)
Stochastic simulation GUI for biochemical networks (2007) (10)
Sensitivity Analysis of Stoichiometric Networks: An Extension of Metabolic Control Analysis to Non-equilibrium Trajectories (2002) (9)
‘Molecular habituation’ as a potential mechanism of gradual homeostatic loss with age (2017) (9)
Systems modelling ageing: from single senescent cells to simple multi-cellular models (2017) (9)
SimpleSBML: A Python package for creating and editing SBML models (2015) (9)
Metabolic control analysis by computer: progress and prospects. (1990) (8)
libRoadRunner: A High Performance SBML Compliant Simulator (2013) (8)
Synthetic biology open language visual (SBOL Visual) version 2.3 (2021) (8)
Publishing reproducible dynamic kinetic models (2020) (7)
The synthetic biology open language. (2015) (7)
Solution of Some Equations in Biochemistry (1988) (7)
SBML2TikZ: supporting the SBML render extension in LaTeX (2010) (7)
Introduction to the Systems Biology Workbench (2003) (6)
Athena: Modular CAM/CAD Software for Synthetic Biology (2009) (6)
Software Tools for Systems Biology (2010) (6)
Sensitivity Regulation based on Noise Propagation in Stochastic Reaction Networks (2008) (6)
A C library for retrieving specific reactions from the BioModels database (2014) (6)
Control Analysis of Systems with Enzyme-Enzyme Interactions (1990) (6)
A Biochemical “NAND” Gate and Assorted Circuits (1993) (6)
libOmexMeta: enabling semantic annotation of models to support FAIR principles (2021) (6)
libOmexMeta: enabling semantic annotation of models to support FAIR principles (2021) (6)
Inferring Reaction Networks using Perturbation Data (2018) (5)
The SBW-CMATLAB interface (2005) (5)
Non-equilibrium/equilibrium reactions: which controls? (1986) (5)
Quantitative analysis ofsignaling networks (2004) (5)
libRoadRunner 2.0: a high performance SBML simulation and analysis library (2022) (5)
Provisional BioBrick Language (PoBoL) (2009) (5)
Control Coefficients and the Matrix Method (1990) (5)
A compiler for biological networks on silicon chips (2020) (4)
One file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project (2014) (4)
A Portable Structural Analysis Library for Reaction Networks (2018) (4)
Application of Parameter Optimization to Search for Oscillatory Mass-Action Networks Using Python (2019) (4)
The role of co-operativity in metabolism (1987) (4)
The simulation experiment description markup language (SED-ML): language specification for level 1 version 4 (2021) (4)
An Overview of the ERATO Systems Biology Workbench Project (2001) (4)
Spatio-temporal dynamics of protein modification cascades. (2008) (4)
Practical Resources for Enhancing the Reproducibility of Mechanistic Modeling in Systems Biology (2021) (4)
BBF RFC 31 : Provisional BioBrick Language ( PoBoL ) (2009) (3)
Systems Biology Workbench C++ Programmer's Manual (2002) (3)
BioSimulators: a central registry of simulation engines and services for recommending specific tools (2022) (3)
Toward Modularity in Synthetic Biology: Design Patterns and Fan-out (2011) (3)
SBML Reaction Finder: Retrieve and extract specific reactions from the BioModels database (2012) (3)
A Visual Language for Protein Design. (2017) (3)
Coenzyme cycles and metabolic control analysis: the determination of the elasticity coefficients from the generalised connectivity theorem. (1995) (3)
COMBINE archive: One File To Share Them All (2014) (3)
The next frontier in cellular networking (2005) (3)
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 (2012) (3)
Computer simulation of MAPK signal transduction. (2004) (3)
Network dynamics. (2009) (2)
Correction to ‘Control and regulation of pathways via negative feedback’ (2017) (2)
Systems Biology Workbench Delphi/Kylix Programmer's Manual (2002) (2)
Stochastic modular analysis for gene circuits: interplay among retroactivity, nonlinearity, and stochasticity. (2015) (2)
libsbmljs — Enabling Web–Based SBML Tools (2019) (2)
When Going Backwards Means Progress: On the Solution of Biochemical Inverse Problems Using Artificial Neural Networks (1993) (2)
Standards, Platforms, and Applications (2014) (2)
Fundamental Dynamic Units: Feedforward Networks and Adjustable Gates (2009) (2)
Standard for the Electronic Distribution of SBOLv Diagrams (2010) (2)
SimpleSBML: A Python package for creating, editing, and interrogating SBML models: Verison 2.0 (2020) (2)
Biological Models of Molecular Network Dynamics (2009) (1)
Synthetic biology: Enter the living machine (2017) (1)
Simulation of biochemical networks - Cellular networks as dynamic control systems (2006) (1)
A portable library to support the SBML Layout Extension (2016) (1)
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project (2014) (1)
In search of noise-induced bimodality (2012) (1)
Reply to Intellectual property issues and synthetic biology standards (2015) (1)
Reply to Essential information for synthetic DNA sequences (2011) (1)
Chapter 6 – Standards, Platforms, and Applications (2006) (1)
SYNTHETIC SYSTEMS AS MICROBIAL THREATS: PREDICTABILITY OF LOSS-OF-FUNCTION MUTATIONS IN ENGINEERED SYSTEMS (2011) (1)
An Optimization Algorithm for Finding Parameters for Bistability (2009) (1)
Faculty Opinions recommendation of BioNetGen 2.2: advances in rule-based modeling. (2019) (1)
Faculty Opinions recommendation of Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. (2019) (1)
Tissue Forge: Interactive Biological and Biophysics Simulation Environment (2022) (1)
Addressing the genetic/nongenetic duality in cancer with systems biology. (2023) (1)
SBMate: A Framework for Evaluating Quality of Annotations in Systems Biology Models (2021) (1)
The Systems Biology Markup Language ( SBML ) : A Standard for the Exchange of Biochemical Network Models (2001) (1)
DYNAMIC INTEGRATION: DYNAMICS | Metabolism (2016) (1)
Substrate cycles: do they really cause amplification? (1985) (1)
The Practice of Ensuring Repeatable and Reproducible Computational Models (2021) (1)
Tellurium Notebooks - An Environment for Dynamical Model Development, Reproducibility, and Reuse (2017) (1)
Modeling and design automation of biological circuits and systems (2012) (1)
Data Model Standardization for Synthetic Biomolecular Circuits and Systems (2011) (1)
Measuring the degree of modularity in gene regulatory networks from the relaxation of finite perturbations (2012) (1)
In vitro control analysis of an enzyme system: Experimental and analytical developments (1995) (1)
Measuring the Degree of Modularity from Gene Expression Noise in Gene Regulatory Circuits (2009) (1)
Cell Senescence-Independent Ageing of Human Skin (2022) (1)
WikiDust: a TinkerCell Plugin to Annotate and Share Network Models (2011) (1)
Faculty Opinions recommendation of Emerging whole-cell modeling principles and methods. (2019) (0)
Book reviews (2001) (0)
Editorial Reproducibility of Computational Models. (2016) (0)
Faculty Opinions recommendation of Integrating systems biology models and biomedical ontologies. (2019) (0)
Systems Biology Workbench Standard Modules and Menus (2002) (0)
Members of the SBOL development group (2015) (0)
Status and Challenges of Reproducibility in Computational Systems and Synthetic Biology (2021) (0)
Adapting Modeling and Simulation Credibility Standards to Computational Systems Biology (2023) (0)
Context-Dependent Genetic Regulation (2017) (0)
Faculty Opinions recommendation of Toward Community Standards and Software for Whole-Cell Modeling. (2019) (0)
Faculty Opinions recommendation of A universal biomolecular integral feedback controller for robust perfect adaptation. (2021) (0)
Proposal for a Minimal SBML Level 2 Definition (2002) (0)
A Portable Software Library that Implements the Gillespie Direct Method (2017) (0)
SBbadger: biochemical reaction networks with definable degree distributions (2022) (0)
Faculty Opinions recommendation of Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases. (2019) (0)
Accelerated Biochemical Kinetic Model Fitting via the Asynchronous, Generalized Island Method (2019) (0)
Faculty Opinions recommendation of A combined experimental and modelling approach for the Weimberg pathway optimisation. (2020) (0)
Recent Advances in the Synthetic Biology Open Language (2013) (0)
Introduction to the Special Issue on Computational Synthetic Biology (2014) (0)
In Silico Design of Self-Optimizing Integrated Metabolic and Gene Regulatory Networks (2014) (0)
Special Issue: Methods in Computational Biology (2019) (0)
SED-ML Validator: tool for debugging simulation experiments (2021) (0)
Design Principles for Constructing Gene Regulatory Networks with Specific Properties : A Modular Approach (2003) (0)
Faculty Opinions recommendation of dCas9 regulator to neutralize competition in CRISPRi circuits. (2021) (0)
Lawrence Berkeley National Laboratory Recent Work Title SBOL Visual : A Graphical Language for Genetic Designs Permalink (2015) (0)
Cesium: A public database of evolved oscillatory reaction networks (2023) (0)
Essentials of Biochemical Modeling (2014) (0)
Computing Sensitivities in Reaction Networks using Finite Difference Methods (2021) (0)
C Library for Simulated Evolution of Biological Networks (2010) (0)
Faculty Opinions recommendation of Contrasting Theories of Life: Historical Context, Current Theories. In search of an ideal theory. (2020) (0)
NEWS AND VIEWS Modularity defined (2013) (0)
SBcoyote: An Extensible Python-Based Reaction Editor and Viewer (2023) (0)
A brief note on the properties of linear pathways. (2020) (0)
Title: Synthetic Biology Open Language (SBOL) Version 1.0.0 (2011) (0)
A Commentary on the Linearity and Time-Invariance of ODE-Based Systems (2019) (0)
Faculty Opinions recommendation of Analysis of network motifs in cellular regulation: Structural similarities, input-output relations and signal integration. (2020) (0)
Model Fitting Tools for BioSPICE and the Systems Biology Workbench (2004) (0)
CAD/CAM Software for Synthetic Biology (2007) (0)
Innovation in Software for Systems Biology. Is There Any? (2006) (0)
Explorer Minimum Information About a Simulation Experiment ( MIASE ) (2017) (0)
SBMLDiagrams: a python package to process and visualize SBML layout and render (2022) (0)
Computational Resources for GTL (2007) (0)
Class notes on oscillators: Systems and Synthetic Biology (2019) (0)
Faculty Opinions recommendation of Reproducibility in computational neuroscience models and simulations. (2019) (0)
Integrated models, model languages, model repositories, simulation experiments, simulation tools and data visualizations enable facile model reuse with biosimulations (2022) (0)
Faculty of 1000 evaluation for Could a neuroscientist understand a microprocessor (2018) (0)
Stochastic Control Analysis for Biochemical Reaction Systems (2009) (0)
Capitalize on evolution (2014) (0)
The Synthetic Biology Open Language Supports Integration of the Engineering Life-Cycle for Synthetic Biologists (2019) (0)
The Use of Distributions in SBML Models (2015) (0)
Dynamics and Sensitivity of Signaling Pathways (2021) (0)
Real-Time Interactive Modeling and Simulation in Biological Physics and Active Matter with Mechanica (2021) (0)
Faculty Opinions recommendation of Boolean modeling in systems biology: an overview of methodology and applications. (2019) (0)
A Practical Guide to Reproducible Modeling for Biochemical Networks. (2023) (0)
Faculty Opinions recommendation of Ten simple rules for reproducible computational research. (2019) (0)
Generating Synthetic Signaling Networks for in Silico Modeling Studies (2020) (0)
A Comparison of Two Alternative Implementations of Message-Passing in the Systems Biology Workbench (2001) (0)
Standards, dissemination, and best practices in systems biology. (2023) (0)
Synthetic Biology Open Language Visual: An Open-Source Graphical Notation for Synthetic Biology (2013) (0)

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What Schools Are Affiliated With Herbert M. Sauro?

Herbert M. Sauro is affiliated with the following schools:

University of Washington