A bibliography for stochastic systems biology

(Somewhat out of date)

Stochastic modelling:

Shimizu TS, Aksenov SV, Bray D. A spatially extended stochastic model of the bacterial chemotaxis signalling pathway. J Mol Biol. 2003 May 30;329(2):291-309. (E coli chemotaxis model)
Gillespie. J. Phys. Chem. 81:2340-2361, 1977. Exact stochastic simulation of coupled chemical reactions.
- IanHolmes adds: also J. Comput. Phys. 22:403-434? For citations see e.g...
- Laurenzi IJ, Diamond SL. Monte Carlo simulation of the heterotypic aggregation kinetics of platelets and neutrophils. Biophys J. 1999 Sep;77(3):1733-46.
- Aranyi P, Toth J. A full stochastic description of the Michaelis-Menten reaction for small systems. Acta Biochim Biophys Acad Sci Hung. 1977;12(4):375-88.
- Weinberger LS, Burnett JC, Toettcher JE, Arkin AP, Schaffer DV. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell. 2005 Jul 29;122(2):169-82.
- Lai K, Robertson MJ, Schaffer DV. The sonic hedgehog signaling system as a bistable genetic switch. Biophys J. 2004 May;86(5):2748-57.
Stiles JR, Van Helden D, Bartol TM Jr, Salpeter EE, Salpeter MM. Miniature endplate current rise times less than 100 microseconds from improved dual recordings can be modeled with passive acetylcholine diffusion from a synaptic vesicle. Proc Natl Acad Sci U S A. 1996 Jun 11;93(12):5747-52. (use of MCell for synapse modelling)
Samoilov M, Plyasunov S, Arkin AP. Stochastic amplification and signaling in enzymatic futile cycles through noise-induced bistability with oscillations. Proc Natl Acad Sci U S A. 2005 Feb 15;102(7):2310-5. Epub 2005 Feb 8.

Robustness and sensitivity:

Barkai N, Leibler S. Robustness in simple biochemical networks. Nature. 1997 Jun 26;387(6636):913-7. (E coli chemotaxis robustness)
Bray D, Levin MD, Morton-Firth CJ. Receptor clustering as a cellular mechanism to control sensitivity. Nature. 1998 May 7;393(6680):85-8. (E coli chemotaxis receptor clustering)
Duke TA, Bray D. Heightened sensitivity of a lattice of membrane receptors. Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10104-8. (sensitivity of a receptor lattice)
Ozbudak EM, Thattai M, Kurtser I, Grossman AD, van Oudenaarden A. Regulation of noise in the expression of a single gene. Nat Genet. 2002 May;31(1):69-73. Epub 2002 Apr 22. (gene expression noise)
Yi TM, Huang Y, Simon MI, Doyle J. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc Natl Acad Sci U S A. 2000 Apr 25;97(9):4649-53. (robustness and fragility).

Bacterial motion:

Berg HC, Brown DA. Chemotaxis in Escherichia coli analysed by three-dimensional tracking. Nature. 1972 Oct 27;239(5374):500-4. (tracking of E. coli chemotaxis)

Non-genetic individuality:

Levin MD, Morton-Firth CJ, Abouhamad WN, Bourret RB, Bray D. Origins of individual swimming behavior in bacteria. Biophys J. 1998 Jan;74(1):175-81. (individual swimming behavior in E coli)
Blake WJ, KAErn M, Cantor CR, Collins JJ. Noise in eukaryotic gene expression. Nature. 2003 Apr 10;422(6932):633-7. (noise in gene expression)
Arkin A, Ross J, McAdams HH. Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics. 1998 Aug;149(4):1633-48. (gene expression stochasticity in lambda)

Information transfer:

Schreiber S, Machens CK, Herz AV, Laughlin SB. Energy-efficient coding with discrete stochastic events. Neural Comput. 2002 Jun;14(6):1323-46. (energy required for biological information transfer)

Brownian motion:

Berg HC, Purcell EM. Physics of chemoreception. Biophys J. 1977 Nov;20(2):193-219. (all about Brownian motion and chemotaxis)
Berg. Random Walks in Biology, 1983 (a less technical book that expands on the Berg and Purcell paper)
Futrelle. Trends Neurosci. 7:116-120, 1984 (diffusion of pheremones and capture by receptors)

Game theory:

Kerr B, Riley MA, Feldman MW, Bohannan BJ. Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors. Nature. 2002 Jul 11;418(6894):171-4. (rock-paper-scissors bacterial system)
Wolf DM, Vazirani VV, Arkin AP. Diversity in times of adversity: probabilistic strategies in microbial survival games. J Theor Biol. 2005 May 21;234(2):227-53. Epub 2005 Jan 24. (Stochastic Evolutionary Games)

Review Papers:

Rao CV, Wolf DM, Arkin AP. Control, exploitation and tolerance of intracellular noise. Nature. 2002 Nov 14;420(6912):231-7.

Gene Expression

Elowitz MB, Levine AJ, Siggia ED, Swain PS. Stochastic gene expression in a single cell. Science. 2002 Aug 16;297(5584):1183-6.
Swain PS, Elowitz MB, Siggia ED. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12795-800. Epub 2002 Sep 17.
Blake WJ, KAErn M, Cantor CR, Collins JJ. Noise in eukaryotic gene expression. Nature. 2003 Apr 10;422(6932):633-7.
McAdams HH, Arkin A. Stochastic mechanisms in gene expression. Proc Natl Acad Sci U S A. 1997 Feb 4;94(3):814-9.
Weinberger LS, Burnett JC, Toettcher JE, Arkin AP, Schaffer DV. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell. 2005 Jul 29;122(2):169-82. (Stochastic gene expression in HIV)

Also see the O'Shea paper on yeast stochastics.

Raser JM, O'Shea EK. Control of stochasticity in eukaryotic gene expression. Science. 2004 Jun 18;304(5678):1811-4. Epub 2004 May 27.

The above list was in the most part suggested by AdamArkin:

From: Ian Holmes
Sent: Thursday, August 18, 2005 1:35 PM
To: Adam Arkin
Subject: Re: Langevin biology

After Ted's recent talk on stochastic resonance, you mentioned an example of stability analysis in a Langevin model system.

In my graduate class this fall, I'm hoping to touch on Langevin dynamics (the broad scope is "stochastic computational biology": mainly grammars and trees, but I'd like to mention stochastic biophysics).

Could you recommend one or two pithy biological analogues of the canonical models in classical stochastic physics (Langevin, Smoluchowski, Fokker-Planck etc) or of stochastic differential equations in general (Ito processes, Wiener, superprocesses, etc)?

From: Adam Arkin

Well-- the classical great example is E. coli chemotaxis with examples form Berg's Stochastic processes in Biology Book. Then there is a vast literature in neural stochastics, ion channel stochastics etc. There are spatial stochastic models of calcium waves in T-cells and cardiomyocytes. There are models with the OU process and immune cell motility. And then there is the new literature on stochastic gene expression and signaling.

Are there particular areas you are interested in?

As for the Langevin analysis I mentioned I'm attaching our PNAS paper on the subject and preprint on the "mistakes" made on going from the chemical master equation and the deterministic cellular kinetic equations.

Also-- below is short bibliography covering a number of topics....

Anyway-- tell me if this is what you needed or you want me to be more focused.