A bibliography for stochastic systems biology
(Somewhat out of date)
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).
- 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)
- 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.
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.
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