Herbert M. Sauro

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All published works

Action	Title	Year	Authors
+ PDF Chat	EFECT -- A Method and Metric to Assess the Reproducibility of Stochastic Simulation Studies	2024	T. J. Sego Matthias König Luís L. Fonseca Baylor Fain Ádám Knapp Krishna Kumar Tiwari Henning Hermjakob Herbert M. Sauro James A. Glazier Reinhard Laubenbacher
+ PDF Chat	COMPUTING THE FREQUENCY RESPONSE OF BIOCHEMICAL NETWORKS: A PYTHON MODULE.	2024	Herbert M. Sauro
+ PDF Chat	An Update to the SBML Human-Readable Antimony Language.	2024	Lucian P. Smith Herbert M. Sauro
+ PDF Chat	A Simple Comparison of Biochemical Systems Theory and Metabolic Control Analysis	2024	Herbert M. Sauro
+ PDF Chat	MakeSBML: a tool for converting between Antimony and SBML	2024	Bartholomew Jardine Lucian P. Smith Herbert M. Sauro
+ PDF Chat	50 Years of metabolic control analysis	2024	Herbert M. Sauro
+ PDF Chat	Design patterns of biological cells	2024	Steven S. Andrews H Wiley Herbert M. Sauro
+	Use of Interactive Simulations in Fundamentals of Biochemistry, a LibreText Online Educational Resource, to Promote Understanding of Dynamic Reactions.	2023	Henry V. Jakubowski Henry Agnew Bartholomew Jardine Herbert M. Sauro
+ PDF Chat	SBcoyote: An extensible Python-based reaction editor and viewer	2023	Jin Xu Gary Geng Nhan D. Nguyen Carmen Perena-Cortes Claire Samuels Herbert M. Sauro
+ PDF Chat	Adapting modeling and simulation credibility standards to computational systems biology	2023	Lillian T. Tatka Lucian P. Smith Joseph L. Hellerstein Herbert M. Sauro
+	Adapting Modeling and Simulation Credibility Standards to Computational Systems Biology	2023	Lillian T. Tatka Lucian P. Smith Joseph L. Hellerstein Herbert M. Sauro
+	SBcoyote: An Extensible Python-Based Reaction Editor and Viewer	2023	Jin Xu Gary Geng Nhan D. Nguyen Carmen Perena-Cortes Claire Samuels Herbert M. Sauro
+	MakeSBML: A tool for converting between Antimony and SBML	2023	Bartholomew Jardine Lucian P. Smith Herbert M. Sauro
+	Use of Interactive Simulations in Fundamentals of Biochemistry, a LibreText Online Educational Resource, to Promote Understanding of Dynamic Reactions	2023	Henry V. Jakubowski Henry Agnew Bartholomew Jardine Herbert M. Sauro
+	Design Patterns of Biological Cells	2023	Steven S. Andrews H Wiley Herbert M. Sauro
+ PDF Chat	libRoadRunner 2.0: a high performance SBML simulation and analysis library	2022	Ciaran Welsh Jin Xu Lucian P. Smith Matthias König Kiri Choi Herbert M. Sauro
+ PDF Chat	SBMLDiagrams: a python package to process and visualize SBML layout and render	2022	Jin Xu J. Jiang Herbert M. Sauro
+	SBbadger: biochemical reaction networks with definable degree distributions	2022	Michael A. Kochen H Wiley Song Feng Herbert M. Sauro
+ PDF Chat	BioSimulators: a central registry of simulation engines and services for recommending specific tools	2022	Bilal Shaikh Lucian P. Smith Dan Vasilescu Gnaneswara Marupilla Michael Wilson Eran Agmon Henry Agnew Steven S. Andrews Azraf Anwar Moritz Emanuel Beber
+	SBbadger: Biochemical Reaction Networks with Definable Degree Distributions	2022	Michael A. Kochen H Wiley Song Feng Herbert M. Sauro
+	SBMLDiagrams: A python package to process and visualize SBML layout and render	2022	Jin Xu Jessie Jiang Herbert M. Sauro
+	BioSimulators: a central registry of simulation engines and services for recommending specific tools	2022	Bilal Shaikh Lucian P. Smith Dan Vasilescu Gnaneswara Marupilla Michael A. Wilson Eran Agmon Henry Agnew Steven S. Andrews Azraf Anwar Moritz Emanuel Beber
+	libRoadRunner 2.0: A High-Performance SBML Simulation and Analysis Library	2022	Ciaran Welsh Jin Xu Lucian P. Smith Matthias König Kiri Choi Herbert M. Sauro
+	Computing Sensitivities in Reaction Networks using Finite Difference Methods	2021	Evan Yip Herbert M. Sauro
+ PDF Chat	Practical resources for enhancing the reproducibility of mechanistic modeling in systems biology	2021	Michael L. Blinov John H. Gennari Jonathan R. Karr Ion I. Moraru David Nickerson Herbert M. Sauro
+	Practical Resources for Enhancing the Reproducibility of Mechanistic Modeling in Systems Biology	2021	Michael L. Blinov John H. Gennari Jonathan R. Karr Ion I. Moraru David Nickerson Herbert M. Sauro
+	Real-Time Interactive Modeling and Simulation in Biological Physics and Active Matter with Mechanica	2021	Endre Somogyi Jeffery Coulter Fanbo Sun Herbert M. Sauro James A. Glazier
+	SED-ML Validator: tool for debugging simulation experiments	2021	Bilal Shaikh Andrew Freiburger Matthias König Frank Bergmann David Nickerson Herbert M. Sauro Michael L. Blinov Lucian P. Smith Ion I. Moraru Jonathan R. Karr
+	The Practice of Ensuring Repeatable and Reproducible Computational Models	2021	Herbert M. Sauro
+	Computing Sensitivities in Reaction Networks using Finite Difference Methods	2021	Evan Yip Herbert M. Sauro
+	Dynamics and Sensitivity of Signaling Pathways	2021	Michael A. Kochen Steven S. Andrews H Wiley Song Feng Herbert M. Sauro
+	Practical Resources for Enhancing the Reproducibility of Mechanistic Modeling in Systems Biology	2021	Michael L. Blinov John H. Gennari Jonathan R. Karr Ion I. Moraru David Nickerson Herbert M. Sauro
+	SimpleSBML: A Python package for creating, editing, and interrogating SBML models: Version 2.0	2020	Herbert M. Sauro
+	SimpleSBML: A Python package for creating, editing, and interrogating SBML models: Version 2.0	2020	Herbert M. Sauro
+ PDF Chat	PyBioNetFit and the Biological Property Specification Language	2019	Eshan D. Mitra Ryan Suderman Joshua Colvin Alexander Ionkov Andrew Hu Herbert M. Sauro Richard G. Posner William S. Hlavacek
+	PyBioNetFit and the Biological Property Specification Language	2019	Eshan D. Mitra Ryan Suderman Joshua Colvin Alexander Ionkov Andrew Hu Herbert M. Sauro Richard G. Posner William S. Hlavacek
+	A Commentary on the Linearity and Time-Invariance of ODE-Based Systems	2019	Parker S. Ruth Herbert M. Sauro
+ PDF Chat	PyBioNetFit and the Biological Property Specification Language	2019	Eshan D. Mitra Ryan Suderman Joshua Colvin Alexander Ionkov Andrew Hu Herbert M. Sauro Richard G. Posner William S. Hlavacek
+	PyBioNetFit and the Biological Property Specification Language	2019	Eshan D. Mitra Ryan Suderman Joshua Colvin Alexander Ionkov Andrew Hu Herbert M. Sauro Richard G. Posner William S. Hlavacek
+ PDF Chat	libRoadRunner: a high performance SBML simulation and analysis library	2015	Endre Somogyi Jean-Marie C. Bouteiller James A. Glazier Matthias König Kyle Medley Maciej Swat Herbert M. Sauro
+	libRoadRunner: A High Performance SBML Simulation and Analysis Library	2015	Endre Somogyi Jean-Marie C. Bouteiller James A. Glazier Matthias König Kyle Medley Maciej Swat Herbert M. Sauro
+ PDF Chat	COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project	2014	Frank Bergmann Richard R. Adams Stuart Moodie Jonathan Cooper Mihai Glont Martin Golebiewski Michael Hucka Camille Laibe Andrew K. Miller David Nickerson
+	One file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project	2014	Frank Bergmann Richard Adams Stuart Moodie Jonathan Cooper Mihai Glont Martin Golebiewski Michael Hucka Camille Laibe Andrew K. Miller David Nickerson
+ PDF Chat	Nonlinear biochemical signal processing via noise propagation	2013	Kyung Hyuk Kim Hong Qian Herbert M. Sauro
+	C Library for Simulated Evolution of Biological Networks	2010	Deepak Chandran Herbert M. Sauro
+ PDF Chat	Fan-out in gene regulatory networks	2010	Kyung H. Kim Herbert M. Sauro
+	Athena: Modular CAM/CAD Software for Synthetic Biology	2009	Deepak Chandran Frank Bergmann Herbert M. Sauro
+	Enumeration and Online Library of Mass-Action Reaction Networks	2009	Anastasia Deckard Frank Bergmann Herbert M. Sauro
+	Fundamental Dynamic Units: Feedforward Networks and Adjustable Gates	2009	Herbert M. Sauro Song Yang
+	Measuring the Degree of Modularity from Gene Expression Noise in Gene Regulatory Circuits	2009	Kyung Hyuk Kim Herbert M. Sauro
+	Stochastic Control Analysis for Biochemical Reaction Systems	2009	Kyung Hyuk Kim Herbert M. Sauro
+	An Optimization Algorithm for Finding Parameters for Bistability	2009	Deepak Chandran Herbert M. Sauro
+ PDF Chat	TinkerCell: modular CAD tool for synthetic biology	2009	Deepak Chandran Frank Bergmann Herbert M. Sauro
+	TinkerCell: Modular CAD Tool for Synthetic Biology	2009	Deepak Chandran Frank Bergmann Herbert M. Sauro
+	Sensitivity Regulation based on Noise Propagation in Stochastic Reaction Networks	2008	Kyung Hyuk Kim Hong Qian Herbert M. Sauro
+	MAPK Cascades as Feedback Amplifiers	2007	Herbert M. Sauro Brian Ingalls
+	Simulation of biochemical networks - Cellular networks as dynamic control systems	2006	Herbert M. Sauro
+	A p53 Oscillator Model of DNA Break Repair Control	2005	Vijay Chickarmane Ali Nadim Animesh Ray Herbert M. Sauro
+	Sensitivity Analysis of Stoichiometric Networks: An Extension of Metabolic Control Analysis to Non-equilibrium Trajectories	2002	Brian Ingalls Herbert M. Sauro

Common Coauthors

Coauthor	Papers Together
Lucian P. Smith	10
Frank Bergmann	9
David Nickerson	8
Matthias König	7
Jonathan R. Karr	6
Ion I. Moraru	6
Michael L. Blinov	6
John H. Gennari	5
Deepak Chandran	5
Steven S. Andrews	5
H Wiley	5
Richard G. Posner	4
Henry V. Jakubowski	4
Alexander Ionkov	4
Henry Agnew	4
Bartholomew Jardine	4
Kiri Choi	4
Eshan D. Mitra	4
Kyung Hyuk Kim	4
Joshua Colvin	4
James A. Glazier	4
Brett G. Olivier	4
Ryan Suderman	4
William S. Hlavacek	4
Jin Xu	4
Song Feng	3
Endre Somogyi	3
Joseph L. Hellerstein	3
Michael A. Kochen	3
Kyle Medley	3
Andrew Hu	3
Bilal Shaikh	3
Jacky L. Snoep	2
James R. Faeder	2
Padraig Gleeson	2
Moritz Emanuel Beber	2
Lillian T. Tatka	2
Jean-Marie C. Bouteiller	2
Brian Drawert	2
Michael Hucka	2
Akira Funahashi	2
Nicolás Rodríguez	2
Matúš Kalaš	2
Zachary B. Haiman	2
Wolfram Liebermeister	2
Diego Jahn	2
Daniel Weindl	2
Stian Soiland‐Reyes	2
Tung V N Nguyen	2
Martin Golebiewski	2

Commonly Cited References

Action	Title	Year	Authors	# of times referenced
+	Exact stochastic simulation of coupled chemical reactions	1977	Daniel T. Gillespie	9
+ PDF Chat	libRoadRunner: a high performance SBML simulation and analysis library	2015	Endre Somogyi Jean-Marie C. Bouteiller James A. Glazier Matthias König Kyle Medley Maciej Swat Herbert M. Sauro	7
+	SUNDIALS	2005	A.C. Hindmarsh Peter N. Brown Keith Eric Grant Steven L. Lee Radu Serban Dan Shumaker Carol S. Woodward	7
+ PDF Chat	COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project	2014	Frank Bergmann Richard R. Adams Stuart Moodie Jonathan Cooper Mihai Glont Martin Golebiewski Michael Hucka Camille Laibe Andrew K. Miller David Nickerson	6
+	A Simplex Method for Function Minimization	1965	J. A. Nelder R. Mead	4
+ PDF Chat	PyDREAM: high-dimensional parameter inference for biological models in python	2017	Erin Shockley Jasper A. Vrugt Carlos F. Lopez	4
+	None	1997	Rainer Storn Kenneth V. Price	4
+ PDF Chat	The simultaneous solution and sensitivity analysis of systems described by ordinary differential equations	1988	Jorge R. Leis Mark Kramer	3
+	Numerical Recipes 3rd Edition: The Art of Scientific Computing	2007	William H. Press Saul A. Teukolsky William T. Vetterling Brian P. Flannery	3
+ PDF Chat	BioNetGen 2.2: advances in rule-based modeling	2016	Leonard A. Harris Justin Hogg José-Juan Tapia John A. P. Sekar Sanjana Gupta Ilya Korsunsky Arshi Arora Dipak Barua Robert P. Sheehan James R. Faeder	3
+ PDF Chat	Evaluation of Parallel Tempering to Accelerate Bayesian Parameter Estimation in Systems Biology	2018	Sanjana Gupta Liam Hainsworth Justin Hogg Robin Lee James R. Faeder	3
+ PDF Chat	A Step-by-Step Guide to Using BioNetFit	2019	William S. Hlavacek Jennifer A. Csicsery-Ronay Lewis R. Baker Maria Del Álamo Alexander Ionkov Eshan D. Mitra Ryan Suderman Keesha E. Erickson Raquel Dias Joshua Colvin	3
+ PDF Chat	Designer gene networks: Towards fundamental cellular control	2001	Jeff Hasty Farren J. Isaacs Miloš Dolnik David R. McMillen James J. Collins	3
+	Prediction of Optimal Drug Schedules for Controlling Autophagy	2019	Afroza Shirin Isaac Klickstein Song Feng Yen Ting Lin William S. Hlavacek Francesco Sorrentino	3
+ PDF Chat	Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems	2015	Andreas Raue Bernhard Steiert Max Schelker Clemens Kreutz T. Maiwald Helge Hass Joep Vanlier Christian Tönsing Lorenz Adlung Raphael Engesser	3
+ PDF Chat	Multi-Scale Modeling of Tissues Using CompuCell3D	2012	Maciej Swat Gilberto L. Thomas Julio M. Belmonte Abbas Shirinifard Dimitrij Hmeljak James A. Glazier	3
+	A robust parallel algorithm of the particle swarm optimization method for large dimensional engineering problems	2014	Antonio de Oliveira Samel Moraes João Felipe Mitre Paulo L.C. Lage Argimiro R. Secchi	3
+ PDF Chat	MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics	2014	José A. Egea David Henriques Thomas Cokelaer Alejandro F. Villaverde Aidan MacNamara Diana-Patricia Danciu Julio R. Banga Julio Sáez-Rodríguez	3
+ PDF Chat	Stochasticity in Transcriptional Regulation: Origins, Consequences, and Mathematical Representations	2001	Thomas B. Kepler Timothy C. Elston	3
+ PDF Chat	Deterministic characterization of stochastic genetic circuits	2007	Matthew P. Scott Terence Hwa Brian Ingalls	2
+ PDF Chat	Signal Detection, Modularity, and the Correlation between Extrinsic and Intrinsic Noise in Biochemical Networks	2006	Sorin Tănase‐Nicola Patrick B. Warren Pieter Rein ten Wolde	2
+	Striking a balance with Recon 2.1	2013	Kieran Smallbone	2
+ PDF Chat	Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology	2020	Lucia Marucci Matteo Barberis Jonathan R. Karr Oliver Ray Paul R. Race Miguel de Souza Andrade Claire Grierson Stefan A. Hoffmann Sophie Landon Elíbio Rech	2
+	An Introduction to the Bootstrap	1994	Bradley Efron Robert Tibshirani	2
+ PDF Chat	Parallel tempering: Theory, applications, and new perspectives	2005	David J. Earl Michael W. Deem	2
+ PDF Chat	SBMLDiagrams: a python package to process and visualize SBML layout and render	2022	Jin Xu J. Jiang Herbert M. Sauro	2
+ PDF Chat	libRoadRunner 2.0: a high performance SBML simulation and analysis library	2022	Ciaran Welsh Jin Xu Lucian P. Smith Matthias König Kiri Choi Herbert M. Sauro	2
+ PDF Chat	The fluctuation-dissipation theorem	1966	Ryogo Kubo	2
+ PDF Chat	PhysiCell: An open source physics-based cell simulator for 3-D multicellular systems	2018	Ahmadreza Ghaffarizadeh Randy Heiland Samuel H. Friedman Shannon M. Mumenthaler Paul Macklin	2
+ PDF Chat	Ultrasensitivity in the mitogen-activated protein kinase cascade.	1996	Chi‐Ying F. Huang James E. Ferrell	2
+ PDF Chat	Transparency and reproducibility in artificial intelligence	2020	Benjamin Haibe‐Kains George Alexandru Adam Ahmed Hosny Farnoosh Khodakarami Thakkar Shraddha Rebecca Kusko Susanna‐Assunta Sansone Weida Tong Russ Wolfinger Christopher E. Mason	2
+ PDF Chat	Integrating Intracellular Dynamics Using CompuCell3D and Bionetsolver: Applications to Multiscale Modelling of Cancer Cell Growth and Invasion	2012	Vivi Andasari Ryan T. Roper Maciej Swat Mark A. J. Chaplain	2
+	A Family of Newton Codes for Systems of Highly Nonlinear Equations.	1992	U. Nowak Lutz Weimann	2
+ PDF Chat	Structuring research methods and data with the research object model: genomics workflows as a case study	2014	Kristina Hettne Harish Dharuri Jun Zhao Katherine Wolstencroft Khalid Belhajjame Stian Soiland‐Reyes Eleni Mina Mark Thompson Don Cruickshank L. Verdes–Montenegro	2
+	Robust perfect adaptation in bacterial chemotaxis through integral feedback control	2000	Tau‐Mu Yi Yun Huang Melvin I. Simon John C. Doyle	2
+	Dynamic Optimization of Nonlinear Processes with an Enhanced Scatter Search Method	2009	José A. Egea Eva Balsa‐Canto María-Sonia G. García Julio R. Banga	2
+	Understanding the Metropolis-Hastings Algorithm	1995	Siddhartha Chib Edward Greenberg	2
+ PDF Chat	Colored extrinsic fluctuations and stochastic gene expression	2008	Vahid Shahrezaei Julien F. Ollivier Peter S. Swain	2
+ PDF Chat	PEtab—Interoperable specification of parameter estimation problems in systems biology	2021	Leonard Schmiester Yannik Schälte Frank Bergmann Tacio Camba Erika Dudkin Janine Egert Fabian Fröhlich Lara Fuhrmann Adrian L. Hauber Svenja Kemmer	2
+ PDF Chat	Hierarchical Organization of Modularity in Metabolic Networks	2002	Erzsébet Ravasz Regan A. L. Somera D. A. Mongru Zoltán N. Oltvai Albert‐László Barabási	1
+ PDF Chat	Functional cartography of complex metabolic networks	2005	Roger Guimerà Luı́s A. Nunes Amaral	1
+ PDF Chat	Evolution of Complex Modular Biological Networks	2008	Arend Hintze Christoph Adami	1
+ PDF Chat	Python Unleashed on Systems Biology	2007	Christopher R. Myers Ryan N. Gutenkunst James P. Sethna	1
+	Numerical methods and software for sensitivity analysis of differential-algebraic systems	1996	Timothy Maly Linda Petzold	1
+	An Optimization Algorithm for Finding Parameters for Bistability	2009	Deepak Chandran Herbert M. Sauro	1
+ PDF Chat	Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems	2015	Zhen Li Alireza Yazdani Alexandre M. Tartakovsky George Em Karniadakis	1
+ PDF Chat	Scaling Breakdown in Flow Fluctuations on Complex Networks	2008	Sandro Meloni Jesús Gómez‐Gardeñes Vito Latora Yamir Moreno	1
+ PDF Chat	Dynamic screening in a two-species asymmetric exclusion process	2007	Kyung Hyuk Kim Marcel den Nijs	1
+	A p53 Oscillator Model of DNA Break Repair Control	2005	Vijay Chickarmane Ali Nadim Animesh Ray Herbert M. Sauro	1
+	A Local Convergence Theory for Combined Inexact-Newton/Finite-Difference Projection Methods	1987	Peter N. Brown	1