A computational algebra approach to the reverse engineering of gene regulatory networks

Journal of Theoretical Biology
Reinhard Laubenbacher, B Stigler

Abstract

This paper proposes a new method to reverse engineer gene regulatory networks from experimental data. The modeling framework used is time-discrete deterministic dynamical systems, with a finite set of states for each of the variables. The simplest examples of such models are Boolean networks, in which variables have only two possible states. The use of a larger number of possible states allows a finer discretization of experimental data and more than one possible mode of action for the variables, depending on threshold values. Furthermore, with a suitable choice of state set, one can employ powerful tools from computational algebra, that underlie the reverse-engineering algorithm, avoiding costly enumeration strategies. To perform well, the algorithm requires wildtype together with perturbation time courses. This makes it suitable for small to meso-scale networks rather than networks on a genome-wide scale. An analysis of the complexity of the algorithm is performed. The algorithm is validated on a recently published Boolean network model of segment polarity development in Drosophila melanogaster.

References

Mar 1, 1969·Journal of Theoretical Biology·S A Kauffman
Sep 25, 1997·Trends in Biochemical Sciences·P Mendes
Aug 14, 1998·Molecular Cell·R J ChoR W Davis
Sep 17, 1999·Bioinformatics·L MendozaE R Alvarez-Buylla
Dec 7, 2000·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·N FriedmanD Pe'er
Dec 4, 2001·Genes & Development·P W Ingham, A P McMahon
Mar 2, 2002·Science·Hiroaki Kitano
Mar 26, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Hidde de Jong
May 2, 2002·Proceedings of the National Academy of Sciences of the United States of America·M K Stephen YeungJames J Collins
May 23, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Vladimir FilkovJizu Zhi
Jul 27, 2002·Trends in Genetics : TIG·Alberto de la FuentePedro Mendes
Oct 10, 2003·Bioinformatics·Pedro MendesKeying Ye

❮ Previous
Next ❯

Citations

Mar 15, 2011·Bulletin of Mathematical Biology·Reinhard Laubenbacher
Dec 8, 2005·Nature Biotechnology·Nicolas Le NovèreBarry L Wanner
Apr 4, 2006·Nature Reviews. Drug Discovery·Stephen F Kingsmore
Jun 27, 2007·IET Systems Biology·K H ChoJ Kim
Oct 26, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Winfried Just
Jun 30, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Elena S DimitrovaReinhard Laubenbacher
Jun 10, 2009·Briefings in Bioinformatics·Wei-Po Lee, Wen-Shyong Tzou
Feb 4, 2009·Bioinformatics·Brian C Haynes, Michael R Brent
Apr 30, 2009·Bioinformatics·Janis Dingel, Olgica Milenkovic
Mar 23, 2010·Bioinformatics·Riccardo PorrecaGiancarlo Ferrari-Trecate
May 8, 2010·Bioinformatics·Alan Veliz-CubaReinhard Laubenbacher
Dec 17, 2009·Journal of Bioinformatics and Computational Biology·Graham J Hickman, T Charlie Hodgman
Feb 16, 2008·EURASIP Journal on Bioinformatics & Systems Biology·Dorothy BollmanEdusmildo Orozco
Jul 31, 2007·BMC Bioinformatics·Robert D ZeiglerBarak A Cohen
Sep 14, 2011·EURASIP Journal on Bioinformatics & Systems Biology·Elena S DimitrovaAbdul Salam Jarrah
Jul 23, 2009·BMC Systems Biology·Johannes WollboldUlrike Gausmann
Nov 5, 2013·BMC Systems Biology·Finja BüchelNicolas Le Novère
Sep 3, 2010·CBE Life Sciences Education·Raina RobevaAlexander Enyedi
Feb 4, 2010·PLoS Computational Biology·Shakti GuptaShankar Subramaniam
Sep 24, 2010·PLoS Computational Biology·Clare E Giacomantonio, Geoffrey J Goodhill
Apr 13, 2012·PLoS Computational Biology·Rachael Hageman BlairGary A Churchill
Sep 20, 2008·PloS One·Brett CalcottPaul A Hohenlohe
Feb 11, 2010·Future Microbiology·Steven Watterson, Peter Ghazal
Feb 27, 2014·Biological cybernetics·Clare E Giacomantonio, Geoffrey J Goodhill
Jan 22, 2014·Neural Networks : the Official Journal of the International Neural Network Society·Meng YangTianguang Chu
Mar 29, 2014·BMC Systems Biology·Paola Vera-LiconaReinhard Laubenbacher
May 13, 2008·Drug Discovery Today·Steven WattersonPeter Ghazal
Apr 26, 2008·Physica D. Nonlinear Phenomena·Abdul Salam JarrahReinhard Laubenbacher
Oct 5, 2014·Bulletin of Mathematical Biology·Elena Dimitrova, Brandilyn Stigler
Oct 11, 2007·Annals of the New York Academy of Sciences·Diogo CamachoReinhard Laubenbacher
Oct 11, 2007·Annals of the New York Academy of Sciences·B StiglerR Laubenbacher
Apr 8, 2009·Annals of the New York Academy of Sciences·Tejaswi GowdaSeungchan Kim
Apr 8, 2009·Annals of the New York Academy of Sciences·Fabio ParisiFelix Naef
Oct 10, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jeong-Rae KimKwang-Hyun Cho
Oct 5, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yi Ming Zou
Mar 1, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Kristopher L PattonGloria K Muday
Mar 11, 2009·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Xiaohua HuBahrad A Sokhansanj
Feb 24, 2011·IEEE Transactions on Neural Networks·Daizhan ChengZhiqiang Li
Jul 9, 2005·Journal of Theoretical Biology·Edward E AllenDavid J John

❮ Previous
Next ❯

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.

Related Papers

Annals of the New York Academy of Sciences
B StiglerReinhard Laubenbacher
Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Elena S DimitrovaReinhard Laubenbacher
© 2022 Meta ULC. All rights reserved