Stochastic Biology

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A bibliography for stochastic systems biology

(Somewhat out of date)

Stochastic modelling:

Robustness and sensitivity:

Bacterial motion:

Non-genetic individuality:

Information transfer:

Brownian motion:

  • Berg & Purcell: Physics of chemoreception. Biophys. J. 1977;20:193-219. (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:

Review Papers:

Gene Expression

Also see the O'Shea paper on yeast stochastics.

The above list was in the most part suggested by Adam Arkin:

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.