Modelling cellular signalling systems.
Cell signalling pathways and networks are complex and often non-linear. Signalling pathways can be represented as systems of biochemical reactions that can be modelled using differential equations. Computational modelling of cell signalling pathways is emerging as a tool that facilitates mechanistic understanding of complex biological systems. Mathematical models are also used to generate predictions that may be tested experimentally. In the present chapter, the various steps involved in building models of cell signalling pathways are discussed. Depending on the nature of the process being modelled and the scale of the model, different mathematical formulations, ranging from stochastic representations to ordinary and partial differential equations are discussed. This is followed by a brief summary of some recent modelling successes and the state of future models.
Rangamani
Padmini
P
Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, U.S.A. padmini.rangamani@mssm.edu
Iyengar
Ravi
R
D000818:Animals; D002477:Cells / Q000378:metabolism*; D006801:Humans; D008954:Models, Biological; D015203:Reproducibility of Results; D015398:Signal Transduction
Nat Biotechnol. 2002 Apr;20(4):370-5
11923843
Biophys J. 2004 Nov;87(5):L01-2
15454405
Biophys J. 2007 Oct 1;93(7):2279-88
17526574
Biophys J. 2003 Mar;84(3):1591-605
12609863
Biophys J. 1996 Dec;71(6):3030-45
8968574
Bioessays. 2004 Jan;26(1):68-72
14696042
Biochem J. 2005 Dec 1;392(Pt 2):249-61
16293107
FEBS Lett. 2005 Mar 21;579(8):1891-5
15763569
Biophys J. 2004 Jan;86(1 Pt 1):599-608
14695304
Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2310-5
15701703
J Theor Biol. 2006 Aug 7;241(3):617-27
16473373
Nat Rev Mol Cell Biol. 2003 Sep;Suppl:SS16-21
14587522
Annu Rev Biophys Biomol Struct. 2002;31:151-75
11988466
Science. 2002 Aug 9;297(5583):1018-23
12169734
Annu Rev Phys Chem. 2007;58:35-55
17037977
Science. 1999 Apr 2;284(5411):92-6
10102825
Biophys J. 2002 Sep;83(3):1237-58
12202352
Science. 2002 Aug 9;297(5583):948-9
12169717
Biophys J. 2004 Jan;86(1 Pt 1):589-98
14695303
Science. 1999 Jan 15;283(5400):381-7
9888852
Curr Biol. 2003 Feb 18;13(4):315-20
12593797
Bioinformatics. 2004 Jan 1;20(1):78-84
14693812
Science. 2005 Apr 22;308(5721):523-9
15845847
Biotechnol Prog. 2001 Mar-Apr;17(2):227-39
11312698
J Cell Biol. 2000 Dec 11;151(6):1269-80
11121441
Biophys Chem. 2007 Feb;125(2-3):286-97
17014949
Trends Biochem Sci. 1996 Dec;21(12):460-6
9009826
Comput Biol Chem. 2006 Aug;30(4):280-91
16880117
Biophys J. 2007 Feb 1;92(3):744-68
17098793
Methods. 2007 Feb;41(2):238-47
17189866
Science. 2005 Sep 16;309(5742):1857-61
16166517
Curr Opin Neurobiol. 2000 Jun;10(3):416-21
10851181
Biotechnol Bioeng. 2007 Aug 1;97(5):1216-29
17171720
Proc Natl Acad Sci U S A. 1996 Sep 17;93(19):10078-83
8816754
Biophys J. 2007 Feb 1;92(3):808-15
17098795
Mol Pharmacol. 2004 Jul;66(1):70-5
15213297
Trends Biochem Sci. 1997 Aug;22(8):288-9
9270299
Biophys J. 2005 Aug;89(2):1389-97
15908579
Nature. 2005 Dec 1;438(7068):605-11
16319880
Science. 1999 Jan 15;283(5400):339-40
9925495