Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art

Simulation and inference algorithms for stochastic biochemical reaction networks: from basic concepts to state-of-the-art

Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterizing stochastic effects in biochemical systems is essential to understand the complex dynamics of living things. Mathematical idealizations of biochemically reacting...

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Xehetasun bibliografikoak
Egile Nagusiak:	Warne, D, Baker, R, Simpson, M
Formatua:	Journal article
Argitaratua:	Royal Society 2019

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nork: Elston Timothy C, et al.
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nork: David Schnoerr, et al.
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