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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)

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)

Systems of stochastic chemical kinetics are modeled as infinite level-dependent quasibirth-and-death (LDQBD) processes. For these systems, in contrast to many other applications, levels have an increasing number of states as the level number increases and the probability mass may reside arbitrarily far away from lower levels. Ideas from Lyapunov theory are… (More)

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

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 to derive… (More)

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

- David Spieler
- QEST
- 2013

- 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, 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 infinitestate 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