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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)

- Gunnar W. Klau
- BMC Bioinformatics
- 2009

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 NP-hard… (More)

- Daniela Beisser, Gunnar W. Klau, Thomas Dandekar, Tobias Müller, Marcus T. Dittrich
- Bioinformatics
- 2010

MOTIVATION
Increasing quantity and quality of data in transcriptomics and interactomics create the need for integrative approaches to network analysis. Here, we present a comprehensive R-package for the analysis of biological networks including an exact and a heuristic approach to identify functional modules.
RESULTS
The BioNet package provides an… (More)

- Ivana Ljubic, René Weiskircher, Ulrich Pferschy, Gunnar W. Klau, Petra Mutzel, Matteo Fischetti
- Math. Program.
- 2006

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)

- Markus Bauer, Gunnar W. Klau, Knut Reinert
- BMC Bioinformatics
- 2007

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 alignment… (More)

- Ivana Ljubic, René Weiskircher, Ulrich Pferschy, Gunnar W. Klau, Petra Mutzel, Matteo Fischetti
- ALENEX/ANALCO
- 2005

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)

- Sebastian Böcker, Sebastian Briesemeister, Gunnar W. Klau
- Algorithmica
- 2008

The Cluster Editing problem is defined as follows: Given an undirected, 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)

- Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert
- ISMB/ECCB
- 2004

MOTIVATION
Besides their prevalent use for analyzing gene expression, microarrays are an efficient tool for biological, medical and industrial applications due to their ability to assess the presence or absence of biological agents, the targets, in a sample. Given a collection of genetic sequences of targets one faces the challenge of finding short… (More)

- Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
- PRIB
- 2011

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)

- Tobias Marschall, Ivan G. Costa, +4 authors Alexander Schönhuth
- Bioinformatics
- 2012

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)