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- Julia Arand, David Spieler, +8 authors Jörn Walter
- PLoS genetics
- 2012

The enzymatic control of the setting and maintenance of symmetric and non-symmetric DNA methylation patterns in a particular genome context is not well understood. Here, we describe a comprehensive analysis of DNA methylation patterns generated by high resolution sequencing of hairpin-bisulfite amplicons of selected single copy genes and repetitive elements… (More)

- Christian Eisentraut, David Spieler
- WS-FM
- 2008

We propose a numerical technique for parameter inference in Markov models of biological processes. Based on time-series data of a process we estimate the kinetic rate constants by maximizing the likelihood of the data. The computation of the likelihood relies on a dynamic abstraction of the discrete state space of the Markov model which successfully… (More)

- Tugrul Dayar, Holger Hermanns, David Spieler, Verena Wolf
- Numerical Lin. Alg. with Applic.
- 2011

SUMMARY We propose a bounding technique for the equilibrium probability distribution of continuous-time Markov chains with population structure and infinite state space. We use Lyapunov functions to determine a finite set of states that contains most of the equilibrium probability mass. Then we apply a refinement scheme based on stochastic complementation… (More)

- Aleksandr Andreychenko, Linar Mikeev, David Spieler, Verena Wolf
- EURASIP J. Bioinformatics and Systems Biology
- 2012

: Recent experimental imaging techniques are able to tag and count molecular populations in a living cell. From these data mathematical models are inferred and calibrated. If small populations are present, discrete-state stochastic models are widely-used to describe the discreteness and randomness of molecular interactions. Based on time-series data of the… (More)

- Linar Mikeev, Martin R. Neuhäußer, David Spieler, Verena Wolf
- Formal Methods in System Design
- 2013

- David Spieler
- QEST
- 2013

- David Spieler, Ernst Moritz Hahn, Lijun Zhang
- QAPL
- 2011

—Markov population models (MPMs) are a widely used modelling formalism in the area of computational biology and related areas. The semantics of a MPM is an infinite-state continuous-time Markov chain. In this paper, we use the established continuous stochastic logic (CSL) to express properties of Markov population models. This allows us to express important… (More)

- David Spieler
- 2014