Parameter estimation for Boolean models of biological networks

DOI10.1016/J.TCS.2010.04.034zbMATH Open1215.92020DBLPjournals/tcs/DimitrovaGHJLSSV11arXiv0908.3037OpenAlexW2024769762WikidataQ61714555 ScholiaQ61714555MaRDI QIDQ548478FDOQ548478

Authors: Luis David Garcia Puente, Franziska Hinkelmann, Brandilyn Stigler, Mike Stillman, Paola Vera-Licona, Elena S. Dimitrova, Abdul Salam Jarrah, Reinhard Laubenbacher 

Publication date: 28 June 2011

Published in: Theoretical Computer Science (Search for Journal in Brave)

Abstract: Boolean networks have long been used as models of molecular networks and play an increasingly important role in systems biology. This paper describes a software package, Polynome, offered as a web service, that helps users construct Boolean network models based on experimental data and biological input. The key feature is a discrete analog of parameter estimation for continuous models. With only experimental data as input, the software can be used as a tool for reverse-engineering of Boolean network models from experimental time course data.

Full work available at URL: https://arxiv.org/abs/0908.3037

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zbMATH Keywords

parameter estimationcomputer algebraBoolean networkbiological modelreverse-engineering

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Systems biology, networks (92C42) Software, source code, etc. for problems pertaining to biology (92-04) Theory of software (68N99)

Cites Work

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• Reverse-engineering of polynomial dynamical systems
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Cited In (16)

• Title not available (Why is that?)
• Structural properties of continuous representations of Boolean functions for gene network modelling
• ModRev -- model revision tool for Boolean logical models of biological regulatory networks
• Transactions on Computational Systems Biology III
• On persistent excitations for the identification of switched linear dynamical systems over finite fields
• Unfolding of parametric Boolean networks
• Bistability and asynchrony in a Boolean model of the \textsc{L}-arabinose operon in \textit{Escherichia coli}
• Fitting Boolean networks from steady state perturbation data
• Polynome
• Efficient synthesis of a class of Boolean programs from I-O data: application to genetic networks
• Boolean biology: introducing Boolean networks and finite dynamical systems models to biology and mathematics courses
• Data identification for improving gene network inference using computational algebra
• Estimating the volumes of the cones in a Gröbner fan
• Proper orthogonal decomposition for parameter estimation in oscillating biological networks
• Parallelized Parameter Estimation of Biological Pathway Models
• Algebraic Models and Their Use in Systems Biology

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