Parameter optimization in S-system models.

BMC Systems Biology
Marco VilelaJonas S Almeida

Abstract

The inverse problem of identifying the topology of biological networks from their time series responses is a cornerstone challenge in systems biology. We tackle this challenge here through the parameterization of S-system models. It was previously shown that parameter identification can be performed as an optimization based on the decoupling of the differential S-system equations, which results in a set of algebraic equations. A novel parameterization solution is proposed for the identification of S-system models from time series when no information about the network topology is known. The method is based on eigenvector optimization of a matrix formed from multiple regression equations of the linearized decoupled S-system. Furthermore, the algorithm is extended to the optimization of network topologies with constraints on metabolites and fluxes. These constraints rejoin the system in cases where it had been fragmented by decoupling. We demonstrate with synthetic time series why the algorithm can be expected to converge in most cases. A procedure was developed that facilitates automated reverse engineering tasks for biological networks using S-systems. The proposed method of eigenvector optimization constitutes an advancement ov...Continue Reading

References

Apr 1, 1992·Mathematical Biosciences·E O Voit
Feb 1, 1970·Journal of Theoretical Biology·M A Savageau
Jan 12, 1996·Journal of Molecular Biology·W S Hlavacek, M A Savageau
Mar 26, 2003·Bioinformatics·Shinichi KikuchiMasaru Tomita
Feb 28, 2004·Bioinformatics·Eberhard O Voit, Jonas Almeida
Jan 31, 2006·Theoretical Biology & Medical Modelling·Pradeep K PolisettyEdward P Gatzke
Apr 29, 2006·BMC Bioinformatics·Yoshiya MatsubaraMasaru Tomita
Jun 13, 2006·Proceedings of the National Academy of Sciences of the United States of America·Eberhard VoitHelena Santos
Jul 21, 2006·Theoretical Biology & Medical Modelling·I-Chun ChouEberhard O Voit
Oct 14, 2006·Bioinformatics·Orland R GonzalezEduardo Mendoza
Aug 23, 2007·BMC Bioinformatics·Marco VilelaJonas S Almeida
Oct 10, 2007·PLoS Computational Biology·Ryan N GutenkunstJames P Sethna
Jul 22, 2008·Mathematical Biosciences·Masahiko NakatsuiMasahiro Okamoto
Jan 12, 2010·Journal of Biotechnology·Anna MachinaEberhard O Voit

❮ Previous
Next ❯

Citations

Nov 30, 2010·Bioprocess and Biosystems Engineering·Kazuhiro MaedaHiroyuki Kurata
Oct 24, 2009·Annals of Biomedical Engineering·Weiwei YinEberhard O Voit
Jan 17, 2014·Systems and Synthetic Biology·Fatma A AlazabiSusmit Suvas
Dec 2, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Riccardo PorrecaGiancarlo Ferrari-Trecate
Feb 4, 2012·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Xinyi YangChristine Nardini
Sep 6, 2008·Bioinformatics·Gautam GoelEberhard O Voit
Oct 6, 2010·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·S VingaS A L M Kooijman
Oct 7, 2011·Journal of Bioinformatics and Computational Biology·Dulce CalçadaArlindo L Oliveira
Aug 30, 2012·Source Code for Biology and Medicine·Kentaro InoueHiroyuki Kurata
May 7, 2009·BMC Systems Biology·Marco VilelaJonas S Almeida
Sep 4, 2012·BMC Systems Biology·Nishanth ChemmangattuvalappilIpsita Banerjee
Jul 11, 2012·BMC Systems Biology·I-Chun Chou, Eberhard O Voit
Dec 3, 2014·Computational Biology and Chemistry·Shinq-Jen Wu, Cheng-Tao Wu
Dec 2, 2009·IET Systems Biology·E O VoitL L Fonseca
Feb 24, 2016·Frontiers in Genetics·Sepideh Dolatshahi, Eberhard O Voit
Jun 12, 2012·Biochimica Et Biophysica Acta·Nguyen Xuan VinhPramod P Wangikar
Sep 8, 2010·Mathematical Biosciences·Yun Lee, Eberhard O Voit
Jan 20, 2009·Bio Systems·Michael HeckerReinhard Guthke
Oct 5, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Li-Zhi LiuW J Zhang
May 18, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Kyriakos Kentzoglanakis, Matthew Poole
Nov 13, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Delphine RopersHidde de Jong
Oct 7, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yu-Ting HsiaoPhilipp Kügler
Nov 2, 2013·Mathematical Biosciences·George Michailidis, Florence d'Alché-Buc
Aug 10, 2013·Mathematical Biosciences·Shinq-Jen Wu, Cheng-Tao Wu
Jul 21, 2006·Theoretical Biology & Medical Modelling·I-Chun ChouEberhard O Voit
Aug 16, 2016·Methods : a Companion to Methods in Enzymology·Junbai WangTianhai Tian
May 18, 2016·Molecular Biology Reports·José Eduardo VargasPaulo Márcio Pitrez
Nov 23, 2018·BMC Systems Biology·Jenny E Jeong, Peng Qiu
May 26, 2017·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Eberhard O Voit

❮ Previous
Next ❯

Software Mentioned

MATLAB
JSA
Mathworks Extraction Toolbox
Matlab m code

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.