Publications of Gunnar W. Klau

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  • Mohammed El-Kebir and Gunnar W. Klau. Solving the Maximum-Weight Connected Subgraph Problem to Optimality. Accepted for presentation at the 11th DIMACS Challenge workshop, 4/5 Dec 2014, Providence (RI), U.S.A. Preprint available on arXiv.
  • Desislava Boyanova, Santosh Nilla, Gunnar W. Klau, Thomas Dandekar, Tobias Mueller, Marcus Dittrich. Functional module search in protein networks based on semantic similarity improves the analysis of proteomics data. Molecular & Cellular Proteomics 13:1877-1889, 2014.
  • Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine Smit, Michel Westenberg, Gunnar W. Klau. eXamine: Exploring annotated modules in networks. BMC Bioinformatics 15:201, 2014. (Proc. 4th Symposium on Biological Data Visualization, BioVis 2014). Honorary mention best paper award.
  • Mohammed El-Kebir, Bernd Brandt, Jaap Heringa, Gunnar W. Klau. NatalieQ: A web server for protein-protein interaction network querying. BMC Systems Biology 8:40, 2014.
  • Inken Wohlers, Mathilde Le Boudic-Jamin, Hristo Djidjev, Gunnar W. Klau, Rumen Andonov. Exact protein structure classification using the maximum contact map overlap metric. In Proc. AlCoB 2014 (1st International Conference on Algorithms for Computational Biology, Tarragona, Spain, July 1-3, 2014), LNBI 8542, pp. 262-273, Springer, 2014. Extended version available as Research Report LA-UR-14-20815, Los Alamos National Laboratory, 2014.
  • Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth. WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads. In Proc. RECOMB 2014 (18th Annual International Conference on Research in Computational Molecular Biology), Lecture Notes in Computer Science, Volume 8394, pp. 237-249, 2014.


  • Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine J. Smit, Michel A. Westenberg and Gunnar W. Klau. eXamine: a Cytoscape app for exploring annotated modules in networks. Submitted. arXiv:1312.4490, 2013
  • Christine Staiger, Sidney Cadot, Balàzs Györffy, Lodewyk F. A. Wessels, Gunnar W. Klau. Current composite-feature classification methods do not outperform simple single-genes classifiers in breast cancer prognosis. Frontiers in Genetics 4:289, 2013
  • Thomas Bellitto, Tobias Marschall, Alexander Schönhuth, Gunnar W. Klau. Next Generation Cluster Editing. arXiv:1310.3353, 2013
  • Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth, Gunnar W. Klau. Mapping proteins in the presence of paralogs using units of coevolution. BMC Bioinformatics 14(Suppl 15):S18 (Special issue RECOMB Comparative Genomics), 2013
  • Holger Fröhlich, Gunnar W. Klau. Reconstructing Consensus Bayesian Network Structures with Application to Learning Molecular Interaction Networks. In T. Beissbarth et al. (Eds.), Proc. of German Conference on Bioinformatics, Open Access Series in Informatics, Vol. 34, pp. 46-55, 2013.
  • Harry Buhrman, Peter van der Gulik, Gunnar W. Klau, Chris Schaffner, Dave Speijer, Leen Stougie. A Realistic Model Under Which the Genetic Code is Optimal. Journal of Molecular Evolution, Vol. 77, Issue 4 (2013), pp. 170-184 (doi 10.1007/s00239-013-9571-2), 2013
  • Ferry Hagen, Paulo C. Ceresini, Itzhack Polacheck, Hansong Ma, Filip van Nieuwerburgh, Toni Gabaldon, Sarah Kagan, E. Rhiannon Pursall, Hans L. Hoogveld, Leo J. J. van Iersel, Gunnar W. Klau, Steven M. Kelk, Leen Stougie, Karen H. Bartlett, Kerstin Voelz, Leszek P. Pryszcz, Elizabeth Castaneda, Marcia Lazera, Wieland Meyer, Dieter Deforce, Jacques F. Meis, Robin C. May, Corne H. W. Klaassen, Teun Boekhout. Ancient Dispersal of the Human Fungal Pathogen Cryptococcus gattii from the Amazon Rainforest. PLoS ONE 8(8):e71148. doi:10.1371/journal.pone.0071148
  • Sebastian Böcker, Stefan Canzar, and Gunnar W. Klau. The Generalized Robinson-Foulds Metric. In A. Darling and J. Stoye (Eds.): WABI 2013, Proc. of the 13th Annual International Workshop on Algorithms in Bioinformatics, LNCS 8126, pp. 156-169, 2013
  • Stefan Canzar, Khaled Elbassioni, Gunnar W. Klau, Julián Mestre. On Tree-Constrained Matchings and Generalizations. Algorithmica, 2013.
  • Inken Wohlers, Rumen Andonov, and Gunnar W. Klau. DALIX: Optimal DALI protein structure alignment. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10(1):26-36, 2013.
  • Stefan Canzar, Mohammed El-Kebir, Rene Pool, Khaled Elbassioni, Alpesh Malde, Alan Mark, Daan Geerke, Leen Stougie and Gunnar W. Klau. Charge Group Partitioning in Biomolecular Simulation. Journal of Computational Biology 20(3):188-198. 2013
  • Markus Chimani, Carsten Gutwenger, Michael Juenger, Gunnar W. Klau, Karsten Klein, Petra Mutzel. Open Graph Drawing Framework (OGDF). In Handbook of Graph Drawing and Visualization. Roberto Tamassia (ed.), CRC Press. 2013.



  • Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau. Lagrangian Relaxation Applied to Sparse Global Network Alignment. In Proc. 6th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2011), Delft, The Netherlands, November 2-4 2011. LNCS 7036, pp.225-236, Springer, 2011. Full version available on
  • Gunnar W. Klau. Operations Resarch and the Life Sciences - A Healthy Combination. In Liber Amicorum for Jan Karel Lenstra, CWI, 2011.
  • Antonio Mucherino, Inken Wohlers, Gunnar W. Klau, Rumen Andonov. Sparsifying Distance Matrices for Protein-Protein Structure Alignments. Extended abstract, to be presented at 10th Cologne-Twente Workshop on Graphs and Combinatorial Optimization. Frascati, Italy, 14-16 June 2011.
  • Stefan Canzar, Khaled Elbassioni, Gunnar W. Klau, Julián Mestre. On Tree-Constrained Matchings and Generalizations. In Proc. 38th International Colloquium on Automata, Languages and Programming (ICALP 2011), Lecture Notes in Computer Science, Vol. 6755, pp. 98 - 109, Springer, 2011. Full version available as CWI technical report MAC1102.
  • Sebastian Böcker, Sebastian Briesemeister, and Gunnar W. Klau. Exact algorithms for cluster editing: evaluation and experiments. Algorithmica 60(2):316-334, 2011
  • Stefan Canzar, Nora Toussaint, and Gunnar W. Klau. An Exact Algorithm for Side-Chain Placement in Protein Design, Optimization Letters 5(3): 393-406, 2011. Preprint.
  • Inken Wohlers, Rumen Andonov, and Gunnar W. Klau. Algorithm Engineering for Optimal Alignment of Protein Structure Distance Matrices, Optimization Letters 5(3):421-433, 2011













  • Petra Mutzel, Carsten Gutwenger, Ralf Brockenauer, Sergej Fialko, Gunnar W. Klau, Michael Krüger, Thomas Ziegler, Stefan Näher, David Alberts, Dirk Ambras, Gunter Koch, Michael Jünger, Christoph Buchheim, and Sebastian Leipert. AGD: a library of algorithms for graph drawing, in Proc. of the Sixth International Symposium on Graph Drawing (GD-98), LNCS 1547, Montréal, Canada, August 13 - 15, Springer, Berlin, 1998, pp. 456-457. Preprint.
  • Gunnar W. Klau and Petra Mutzel. Optimal Compaction of Orthogonal Grid Drawings. Technical Report No. MPI-I-98-1-031. Max-Planck-Institut für Informatik, Saarbrücken, Germany, December 1998, 20 pages. Preprint.
  • Gunnar W. Klau and Petra Mutzel. Quasi Orthogonal Drawing of Planar Graphs. Technical Report No. MPI-I-98-1-013. Max-Planck-Institut für Informatik, Saarbrücken, Germany, May 1998, 15 pages. Link.


  • Gunnar W. Klau. Visuelle Zeitenwende: Bilder - Technik - Reflexionen. Quasi-orthogonales Zeichnen. Participation in the competition German Student Research Price (Deutscher Studienpreis) by the Körber Foundation, awarded 2nd. Leipzig, 1997.
  • Gunnar W. Klau. Quasi-orthogonales Zeichnen planarer Graphen mit wenigen Knicken. Diploma thesis, Universität des Saarlandes, Saarbrücken, January 1997. Link.
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