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MOTIVATION With the exponential growth of expression and protein-protein interaction (PPI) data, the frontier of research in systems biology shifts more and more to the integrated analysis of these large datasets. Of particular interest is the identification of functional modules in PPI networks, sharing common cellular function beyond the scope of(More)
The Prize-Collecting Steiner Tree Problem (PCST) on a graph with edge costs and vertex profits asks for a subtree minimizing the sum of the total cost of all edges in the subtree plus the total profit of all vertices not contained in the subtree. PCST appears frequently in the design of utility networks where profit generating customers and the network(More)
The Prize-Collecting Steiner Tree Problem (PCST) on a graph with edge costs and vertex profits asks for a subtree minimizing the sum of the total cost of all edges in the subtree plus the total profit of all vertices not contained in the subtree. PCST appears in the design of utility networks (eg. fiber optics or district heating) where profit generating(More)
BACKGROUND In addition to component-based comparative approaches, network alignments provide the means to study conserved network topology such as common pathways and more complex network motifs. Yet, unlike in classical sequence alignment, the comparison of networks becomes computationally more challenging, as most meaningful assumptions instantly lead to(More)
BACKGROUND The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA(More)
Data on molecular interactions is increasing at a tremendous pace, while the development of solid methods for analyzing this network data is lagging behind. This holds in particular for the field of comparative network analysis, where one wants to identify commonalities between biological networks. Since biological functionality primarily operates at the(More)
MOTIVATION Next-generation sequencing techniques have facilitated a large-scale analysis of human genetic variation. Despite the advances in sequencing speed, the computational discovery of structural variants is not yet standard. It is likely that many variants have remained undiscovered in most sequenced individuals. RESULTS Here, we present a novel(More)
The CLUSTER EDITING problem is defined as follows: Given an undi-rected, loopless graph, we want to find a set of edge modifications (insertions and deletions) of minimum cardinality, such that the modified graph consists of disjoint cliques. We present empirical results for this problem using exact methods from fixed-parameter algorithmics and linear(More)
The prize-collecting Steiner tree problem on a graph with edge costs and vertex profits asks for a subtree minimizing the sum of the total cost of all edges in the subtree plus the total profit of all vertices not contained in the subtree. For this well-known problem we develop a new algorithmic framework consisting of three main parts: (1) An extensive(More)
We investigate the NP-hard label number maximization problem (LNM): Given a set of rectangular labels Λ, each of which belongs to a point feature in the plane, the task is to find a labeling for a largest subset Λ P of Λ. A labeling is a placement such that none of the labels overlap and each λ ∈ Λ P is placed according to a labeling model: In the discrete(More)