Measuring the Degree of Modularity from Gene Expression Noise in Gene Regulatory Circuits (2009)
Kim, Kyung Hyuk, Sauro, Herbert M.
Gene regulatory circuits show significant stochastic fluctuations in their circuit signals due to the low copy number of transcription factors. When a gene circuit component is connected to an...
TinkerCell: modular CAD tool for synthetic biology (2009)
Chandran, Deepak, Bergmann, Frank T, Sauro, Herbert M
Abstract Background Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between...
TinkerCell: Modular CAD Tool for Synthetic Biology (2009)
Chandran, Deepak, Bergmann, Frank T., Sauro, Herbert M.
Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational...
An Optimization Algorithm for Finding Parameters for Bistability (2009)
Chandran, Deepak, Sauro, Herbert M.
Motivation: Many biochemical pathways are known, but the numerous parameters required to correctly explore the dynamics of the pathways are not known. For this reason, algorithms that can make...
Stochastic Control Analysis for Biochemical Reaction Systems (2009)
Kim, Kyung Hyuk, Sauro, Herbert M.
In this paper, we investigate how stochastic reaction processes are affected by external perturbations. We describe an extension of the deterministic metabolic control analysis (MCA) to the...
Athena: Modular CAM/CAD Software for Synthetic Biology (2009)
Chandran, Deepak, Bergmann, Frank T., Sauro, Herbert M.
Synthetic biology is the engineering of cellular networks. It combines principles of engineering and the knowledge of biological networks to program the behavior of cells. Computational modeling...
Enumeration and Online Library of Mass-Action Reaction Networks (2009)
Deckard, Anastasia C., Bergmann, Frank T., Sauro, Herbert M.
The aim of this work is to make available to the community a large collection of mass-action reaction networks of a given size for further research. The set is limited to what can be computed on a...
Transcriptional Dynamics of the Embryonic Stem Cell Switch (2008)
Vijay Chickarmane, Carl Troein, Ulrike A. Nuber, Herbert M. Sauro, Carsten Peterson
Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the...
BIOINFORMATICS Supporting the SBML Layout Extension (2008)
Anastasia Deckard, Frank T. Bergmann, Herbert M. Sauro, Nikolaus Rajewsky
Motivation: Researchers studying large or complex biochemical networks would benefit from the ability to automatically create lucid visualizations and store them in a portable and widely accepted...
Sensitivity Regulation based on Noise Propagation in Stochastic Reaction Networks (2008)
Kim, Kyung Hyuk, Qian, Hong, Sauro, Herbert M.
In this work we focus on how noise propagates in biochemical reaction networks and affects sensitivities of the system. We discover that the stochastic fluctuations can enhance sensitivities in one...
Abstract CAD/CAM Software for Synthetic Biology (2008)
Frank T. Bergmann, Deepak Ch, Herbert M. Sauro
This poster describes a novel software application that we are developing that will help researchers in Synthetic Biology to design, simulate and fabricate biological systems. The software system is...
Comparing simulation results of SBML capable simulators (2008)
Bergmann, Frank T., Sauro, Herbert M.
Motivation: Simulations are an essential tool when analyzing biochemical networks. Researchers and developers seeking to refine simulation tools or develop new ones would benefit greatly from being...
MAPK Cascades as Feedback Amplifiers (2007)
Sauro, Herbert M, Ingalls, Brian
Interconvertible enzyme cascades, exemplified by the mitogen activated protein kinase (MAPK) cascade, are a frequent mechanism in signal transduction pathways. There has been much speculation as to...
Stochastic simulation GUI for biochemical networks (2007)
Vallabhajosyula, Ravishankar Rao, Sauro, Herbert M.
Motivation: This article describes the development of a useful graphical user interface for stochastic simulation of biochemical networks which allows model builders to run stochastic simulations of...
Transcriptional Dynamics of the Embryonic Stem Cell Switch (2006)
Vijay Chickarmane, Carl Troein, Ulrike A. Nuber, Herbert M. Sauro, Carsten Peterson
Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the...
Transcriptional Dynamics of the Embryonic Stem Cell Switch (2006)
Vijay Chickarmane, Carl Troein, Ulrike Nuber, Herbert M Sauro, Carsten Peterson
Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the...
BIOINFORMATICS APPLICATIONS NOTE Systems biology Supporting the SBML layout extension (2006)
Anastasia Deckard, Frank T. Bergmann, Herbert M. Sauro
Motivation: Researchers studying large or complex biochemical networks would benefit from the ability to automatically create lucid visualizations and store them in a portable and widely accepted...
Supporting the SBML layout extension (2006)
Deckard, Anastasia, Bergmann, Frank T., Sauro, Herbert M.
Motivation: Researchers studying large or complex biochemical networks would benefit from the ability to automatically create lucid visualizations and store them in a portable and widely accepted...
Conservation analysis of large biochemical networks (2006)
Vallabhajosyula, Ravishankar Rao, Chickarmane, Vijay, Sauro, Herbert M.
Motivation: Large biochemical networks pose a unique challenge from the point of view of evaluating conservation laws. The computational problem in most cases exceeds the capability of available...
A p53 Oscillator Model of DNA Break Repair Control (2005)
Chickarmane, Vijay, Nadim, Ali, Ray, Animesh, Sauro, Herbert M.
The transcription factor p53 is an important regulator of cell fate. Mutations in p53 gene are associated with many cancers. In response to signals such as DNA damage, p53 controls the transcription...
Bifurcation discovery tool (2005)
Chickarmane, Vijay, Paladugu, Sri R., Bergmann, Frank, Sauro, Herbert M.
Motivation: Biochemical networks often yield interesting behavior such as switching, oscillation and chaotic dynamics. This article describes a tool that is capable of searching for bifurcation...
BIOINFORMATICS APPLICATIONS NOTE Systems biology (2005)
Bifurcation Discovery Tool, Vijay Chickarmane, Sri R. Paladugu, Frank Bergmann, Herbert M. Sauro
Motivation: Biochemical networks often yield interesting behavior such as switching, oscillation and chaotic dynamics. This article describes a tool that is capable of searching for bifurcation...
Bifurcation discovery tool (2005)
Chickarmane, Vijay, Paladugu, Sri R., Bergmann, Frank, Sauro, Herbert M.
Motivation: Biochemical networks often yield interesting behavior such as switching, oscillation and chaotic dynamics. This article describes a tool that is capable of searching for bifurcation...
The SBW-MATLAB interface (2005)
Wellock, Cameron, Chickarmane, Vijay, Sauro, Herbert M.
Summary: The SBW–MATLAB Interface allows MATLAB users to take advantage of the wide variety of tools available through SBW, the Systems Biology Workbench (Sauro et al. (2003) OMICS, 7, 355–372)....
Bifurcation discovery tool (2005)
Chickarmane, Vijay, Paladugu, Sri R., Bergmann, Frank, Sauro, Herbert M.
Motivation: Biochemical networks often yield interesting behavior such as switching, oscillation, and chaotic dynamics. This article describes a tool which is capable of searching for bifurcation...
Conservation analysis of large biochemical networks (2005)
Vallabhajosyula, Ravishankar Rao, Chickarmane, Vijay, Sauro, Herbert M.
Motivation: Large biochemical networks pose a unique challenge from the point of view of evaluating conservation laws. The computational problem in most cases exceeds the capability of available...
Conservation analysis in biochemical networks: computational issues for software writers (2004)
Herbert M. Sauro, Brian Ingalls
Large scale genomic studies are generating significant amounts of data on the structure of cellular networks. This is in contrast to kinetic data which is frequently absent, unreliable or...
The SBW-MATLAB Interface (2004)
Wellock, Cameron, Chickarmane, Vijay, Sauro, Herbert M.
Summary: The SBW-MATLAB Interface allows MATLAB users to take advantage of the wide variety of tools available through SBW, the Systems Biology Workbench [1]. It also enables MATLAB users to...
The SBW-MATLAB Interface (2004)
Wellock, Cameron, Chickarmane, Vijay, Sauro, Herbert M.
Summary: The SBW-MATLAB Interface allows MATLAB users to take advantage of the wide variety of tools available through SBW, the Systems Biology Workbench [1]. It also enables MATLAB users to...
Next generation simulation tools: the systems biology workbench and biospice integration (2003)
Herbert M. Sauro, Michael Hucka, Andrew Finney, Cameron Wellock, Hamid Bolouri, John Doyle, ...
Researchers in quantitative systems biology make use of a large number of different software packages for modelling, analysis, visualization, and general data manipulation. In this paper, we describe...
Brian P. Ingalls, Herbert M. Sauro
A sensitivity analysis of general stoichiometric networks is considered. The results are presented as a generalization of Metabolic Control Analysis, which has been concerned primarily with system...
Ingalls, Brian P., Sauro, Herbert M.
A sensitivity analysis of general stoichiometric networks is considered. The results are presented as a generalization of Metabolic Control Analysis, which has been concerned primarily with system...
Elasticities in Metabolic Control Analysis: algebraic derivation of simplified expressions (1997)
Woods, John H., Sauro, Herbert M.
Motivation Metabolic Control Analysis is one of many disciplines that make use of scaled derivatives. In particular, ‘elasticities’ are used to quantify the effect of an effector or substrate...
The computational versatility of proteomic signaling networks (1993)
Abstract: Almost all proteomic signaling networks in prokaryotes and eukaryotes are based on the simple phosphorylation/dephosporylation cycle; from this simple unit it is possible to construct a...
SCAMP: a general-purpose simulator and metabolic control analysis program (1993)
SCAMP is a general-purpose simulator of metabolic and chemical networks. The program is written in C and is portable to all computer systems that support an ANSI C compiler. SCAMP accepts metabolic...
Transcriptional Dynamics of the Embryonic Stem Cell Switch
Chickarmane, Vijay, Troein, Carl, Nuber, Ulrike A, Sauro, Herbert M, Peterson, Carsten
Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the...
Transcriptional Dynamics of the Embryonic Stem Cell Switch
Chickarmane, Vijay, Troein, Carl, Nuber, Ulrike A, Sauro, Herbert M, Peterson, Carsten
Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the...
Entus, Robert, Aufderheide, Brian, Sauro, Herbert M.
Synthetic biology is a useful tool to investigate the dynamics of small biological networks and to assess our capacity to predict their behavior from computational models. In this work we report the...
Comparing simulation results of SBML capable simulators
Bergmann, Frank T., Sauro, Herbert M.
Motivation: Simulations are an essential tool when analyzing biochemical networks. Researchers and developers seeking to refine simulation tools or develop new ones would benefit greatly from being...