Alexander Lück

Universität des Saarlandes | UKS · Department of Computer Science

DNA methylation is an epigenetic mechanism whose important role in development has been widely recognized. This epigenetic modification results in heritable changes in gene expression not encoded by the DNA sequence. The underlying mechanisms controlling DNA methylation are only partly understood and recently different mechanistic models of enzyme...

Discrete-state stochastic models have become a well-established approach to describe biochemical reac- tion networks that are influenced by the inherent randomness of cellular events. In the last years several methods for accurately approximating the statistical moments of such models have become very popular since they allow an efficient analysis...

A widely used approach to describe the dynamics of gene regulatory networks is based on the chemical master equation, which considers probability distributions over all possible combinations of molecular counts. The analysis of such models is extremely challenging due to their large discrete state space. We therefore propose a hybrid approximation...

In this work we study a microtubule (MT) model , whose length is regulated by the action of processive kinesin motors. We treat the case of infinite processivity, i.e. particle exchange in the bulk is neglected. The exact results can be obtained for model parameters which correspond to a finite length of the MT. In contrast to the model with partic...

The microtubule (MT) motor Kip3p is very processive kinesin that promotes catastrophes and pausing in particular on cortical contact. These properties explain the role of Kip3p in positioning the mitotic spindle in budding yeast and potentially other processes controlled by kinesin-8 family members. We present a theoretical approach to positioning...

DNA methylation is an important biological mechanism to regulate gene expression and control cell development. Mechanistic modeling has become a popular approach to enhance our understanding of the dynamics of methylation pattern formation in living cells. Recent findings suggest that the methylation state of a cytosine base can be influenced by it...

With recent advances in sequencing technologies, large amounts of epigenomic data have become available and computational methods are contributing significantly to the progress of epigenetic research. As an orthogonal approach to methods based on machine learning, mechanistic modeling aims at a description of the mechanisms underlying epigenetic ch...

DNA methylation is an important biological mechanism to regulate gene expression and control cell development. Mechanistic modeling has become a popular approach to enhance our understanding of the dynamics of methylation pattern formation in living cells. Recent findings suggest that the methylation state of a cytosine base can be influenced by it...

The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA methylation can however be subject to specific and fast changes over a short time scale even in non-dividing (i.e. not-r...

DNA methylation is an epigenetic mark whose important role in development has been widely recognized. This epigenetic modification results in heritable information not encoded by the DNA sequence. The underlying mechanisms controlling DNA methylation are only partly understood. Several mechanistic models of enzyme activities responsible for DNA met...

The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA methylation can however be subject to specific and fast changes over a short time scale even in non-dividing (i.e. not-r...

DNA methylation is an epigenetic mechanism whose important role in development has been widely recognized. This epigenetic modification results in heritable changes in gene expression not encoded by the DNA sequence. The underlying mechanisms controlling DNA methylation are only partly understood and recently different mechanistic models of enzyme...

"Automatic Moment-Closure Approximation of Spatially Distributed Collective Adaptive Systems" by Feng, Hilston, and Galpin presents detailed simulation analysis results for three models of spatially distributed collective adaptive systems. In this replicated computational results report, the corresponding implementation together with a documentatio...