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- 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)

- 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)

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)

- 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)

- 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)

- 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)

- Markus Chimani, Carsten Gutwenger, Michael Jünger, Gunnar W. Klau, Karsten Klein, Petra Mutzel
- Handbook of Graph Drawing and Visualization
- 2013

- C. Staiger, Sidney Cadot, +4 authors Lodewyk F. A. Wessels
- PloS one
- 2012

Recently, several classifiers that combine primary tumor data, like gene expression data, and secondary data sources, such as protein-protein interaction networks, have been proposed for predicting outcome in breast cancer. In these approaches, new composite features are typically constructed by aggregating the expression levels of several genes. The… (More)

- Ferry Hagen, Paulo C. Ceresini, +21 authors Teun Boekhout
- PloS one
- 2013

Over the past two decades, several fungal outbreaks have occurred, including the high-profile 'Vancouver Island' and 'Pacific Northwest' outbreaks, caused by Cryptococcus gattii, which has affected hundreds of otherwise healthy humans and animals. Over the same time period, C. gattii was the cause of several additional case clusters at localities outside of… (More)