Modeling and simulation of genetic regulatory systems: a literature review

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Hidde de Jong

Abstract

In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools for the modeling and simulation of genetic regulatory networks will be indispensable. This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations, ordinary and partial differential equations, qualitative differential equations, stochastic equations, and rule-based formalisms. In addition, the paper discusses how these formalisms have been used in the simulation of the behavior of actual regulatory systems.

References

Jan 20, 1978·Science·S A KauffmanK Trabert
Mar 1, 1976·Biophysical Chemistry·M Sanglier, G Nicolis
Dec 1, 1976·European Journal of Biochemistry·R ThomasL Lambert
Apr 29, 1976·Journal of Mathematical Biology·H G Othmer
Oct 1, 1975·Journal of Theoretical Biology·L Glass
Apr 30, 1992·Biochemical and Biophysical Research Communications·M N ObeyesekereS O Zimmerman
May 1, 1992·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·M S Ko
Jan 16, 1992·Nature·J Maddox
Oct 21, 1991·Journal of Theoretical Biology·E MjolsnessJ Reinitz
Nov 21, 1991·Journal of Theoretical Biology·M S Ko
Aug 9, 1990·Journal of Theoretical Biology·A HundingB C Goodwin
Feb 22, 1989·Journal of Theoretical Biology·J Collado-Vides
Jan 20, 1985·Journal of Molecular Biology·M A Shea, G K Ackers
Apr 21, 1986·Journal of Theoretical Biology·E R JacksonW G Nash
Jan 1, 1985·Journal of Mathematical Biology·S Busenberg, J Mahaffy
Dec 1, 1973·Journal of Theoretical Biology·R Thomas
Dec 1, 1972·Kybernetik·A Gierer, H Meinhardt
Apr 1, 1973·Journal of Theoretical Biology·L Glass, S A Kauffman
Jun 1, 1974·Journal of Theoretical Biology·J Bard, I Lauder
Jan 1, 1971·Current Topics in Developmental Biology·S Kauffman
Feb 1, 1972·Journal of Theoretical Biology·L Glass, S A Kauffman
Jan 1, 1971·Proceedings of the National Academy of Sciences of the United States of America·S A Newman, S A Rice
Dec 1, 1969·The Bulletin of Mathematical Biophysics·H D Landahl
Aug 1, 1968·Journal of Theoretical Biology·J S Griffith
Aug 1, 1968·Journal of Theoretical Biology·J S Griffith
Mar 1, 1969·Journal of Theoretical Biology·S A Kauffman
Jan 1, 1965·Advances in Enzyme Regulation·B C Goodwin
May 1, 1967·Journal of Theoretical Biology·C WalterM Ycas
Jan 11, 1984·Nucleic Acids Research·S Meyers, P Friedland
Feb 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·G K AckersM A Shea
Jul 21, 1982·Journal of Theoretical Biology·R D BlissA G Marr
Jan 1, 1981·Progress in Biophysics and Molecular Biology·A Gierer
Sep 21, 1995·Journal of Theoretical Biology·T MestlS W Omholt

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Citations

Nov 26, 2002·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Hamid Bolouri, Eric H Davidson
Jul 17, 2008·Comparative and Functional Genomics·Ilya ShmulevichWei Zhang
Jul 17, 2008·Comparative and Functional Genomics·Sergio Nasi
Oct 1, 2005·Journal of Mathematical Biology·Richard CaseyJean-Luc Gouzé
Mar 8, 2006·Journal of Mathematical Biology·R CoutinhoA Meyroneinc
May 26, 2009·Journal of Mathematical Biology·Linghong Lu, Roderick Edwards
Dec 2, 2010·Journal of Mathematical Biology·Adrien Richard, Jean-Paul Comet
Feb 12, 2013·Acta Biotheoretica·Ibrahima Ndiaye, Jean-Luc Gouzé
Jan 31, 2013·Bulletin of Mathematical Biology·Luis Mendoza
Jun 1, 2013·Bulletin of Mathematical Biology·Claudine Chaouiya, Elisabeth Remy
Nov 13, 2008·Cognitive Neurodynamics·Wangli He, Jinde Cao
Jul 31, 2009·Cognitive Neurodynamics·Zhengxia WangHongli Wu
May 28, 2010·Journal of Genetics·Luwen ZhangWu Zhang
Aug 10, 2012·Journal of the American Society for Mass Spectrometry·Xingchuang XiongZheng Ouyang
Oct 15, 2013·Bio Systems·Ravie Chandren MuniyandiJ W Sanders
Feb 12, 2004·Bulletin of Mathematical Biology·Hidde De JongMichel Page
Feb 12, 2004·Bulletin of Mathematical Biology·Hidde De JongJohannes Geiselmann
Apr 23, 2004·Current Opinion in Biotechnology·Markus J HerrgårdBernhard Ø Palsson
Jun 14, 2005·Comptes rendus biologies·Filipa Alves, Rui Dilão
Jan 21, 2004·Current Opinion in Plant Biology·Przemyslaw Prusinkiewicz
Apr 27, 2010·Physics of Life Reviews·Timothy S Gardner, Jeremiah J Faith
Jan 19, 2008·Theory in Biosciences = Theorie in Den Biowissenschaften·M J Gagen, J S Mattick
Oct 31, 2003·Trends in Genetics : TIG·Yuk Fai Leung, Duccio Cavalieri
Nov 15, 2003·Journal of Theoretical Biology·Thomas MacCarthyAndrew Pomiankowski
Nov 11, 2003·Bulletin of Mathematical Biology·Vincent DevlooMartine Labbé
Nov 5, 2002·Trends in Biotechnology·Larry D Greller, Roland Somogyi
Nov 5, 2002·Trends in Biotechnology·Paul BrazhnikPedro Mendes
Jul 3, 2003·Trends in Biotechnology·Jaroslav StarkMichael Hubank
Jul 31, 2003·Current Opinion in Genetics & Development·Denis Thieffry, Lucas Sanchez
Mar 29, 2003·Trends in Plant Science·Mark G M Aarts, Mark W E J Fiers
Nov 1, 2008·Genomics, Proteomics & Bioinformatics·Wei-Po Lee, Kung-Cheng Yang
Aug 12, 2009·Nature Reviews. Genetics·Matthew R Bennett, Jeff Hasty
Oct 30, 2010·IET Systems Biology·S RoyT Lane
Jul 16, 2009·Médecine sciences : M/S·Emmanuel BarillotAndrei Zinovyev
Mar 9, 2004·Chaos·Asa Ben-Hur, Hava T Siegelmann
Jun 25, 2010·Journal of Toxicology and Environmental Health. Part B, Critical Reviews·Imran Shah, John Wambaugh
Dec 20, 2003·Omics : a Journal of Integrative Biology·Daniel E ZakFrancis J Doyle
Jan 22, 2005·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mathäus Dejori, Martin Stetter
Mar 16, 2005·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Lei M Li, Henry Horng-Shing Lu
Oct 26, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Winfried Just
Dec 7, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Peter C Y Chen
Sep 7, 2007·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Réka AlbertKelly Westbrooks
Dec 2, 2008·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Riccardo PorrecaGiancarlo Ferrari-Trecate

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