• winter term 2022/23: research sabbatical: Visiting Academic at the University of Queensland (Mark lab, School of Chemistry and Molecular Biosciences), Brisbane, Australia
• since Feb 2017: Full professor (W3) for Algorithmic Bioinformatics at Heinrich Heine University Düsseldorf, Germany
• Nov 2015-July 2016: Fulbright Visiting Professor at Brown University (Raphael lab, CS department and CCMB), Providence (RI)
• July 2012-Jan 2017: Professor for Bioinformatics and Operations Research, VU Amsterdam
• 2012: Part-time faculty at the Mathematical Institute, Utrecht University
• Jan 2010-Jan 2017: Group leader (tenured) Life Sciences at CWI
• Sep 2008-Jan 2010: Research group leader (tenure track) computational biology at CWI, member of the Netherlands Institute for Systems Biology (NISB).
• Jan 2004-Sep 2008: Scientific assistant (C1) at Freie Universität Berlin, Mathematics in Life Sciences Group, headed by Alexander Bockmayr and member of the DFG Center Matheon. Habilitation in July 2009, thesis: Discrete Optimization in the Life Sciences.
• 2000-2004: University assistant at Vienna University of Technology, Algorithms and Data Structures group, headed by Petra Mutzel
• 2002-2003: Post-doctoral researcher at the Department of Scientific Computing, Discrete Optimization (headed by Martin Grötschel), Zuse Institute Berlin (ZIB)
• 2001: Post-doctoral researcher at Mitsubishi Electric Research Laboratories, Cambridge Research Lab, Massachusetts, U.S.A., with Neal Lesh and Joe Marks, cooperation with Harvard University.
• 2002: Dissertation prize of the German Operations Research Society (GOR), founded by SAP AG
• 1997-2001: PhD studies at the Max-Planck-Institut für Informatik, Saarbrücken, Germany in the Algorithms and Complexity group, headed by Kurt Mehlhorn. Thesis: A Combinatorial Approach to Orthogonal Placement Problems
• 1997: German Student Research Prize (Deutscher Studienpreis) by the Körber Foundation
• 1994-1997: Studies of computer science (diploma) at Universität des Saarlandes, Saarbrücken, Germany
• 1994: Exchange student (computer science) at Università degli Studi di Padova, Italy
• 1991-1994: Studies in computer science (minor: linguistics) at Julius-Maximilians-Universität, Würzburg, Germany

see Google Scholar profile

since 2017, see Section publications

2016

• Marcel Martin, Murray Patterson, Shilpa Garg, Sarah Fischer, Nadia Pisanti, Gunnar W. Klau, Alexander Schönhuth, Tobias Marschall. WhatsHap: fast and accurate read-based phasing, bioRxiv 085050, 2016, Cold Spring Harbor Labs Journals, under review.
• Theo Knijnenburg, Gunnar W. Klau, Francesco Iorio, Mathew Garnett, Ultan McDermott, Ilya Shmulevich, Lodewyk Wessels. Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy. bioRxiv 036970, 2016, Cold Spring Harbor Labs Journals, accepted for publication in Nature Scientific Reports.
• Tobias Marschall et al. Computational Pan-Genomics: Status, Promises and Challenges. Briefings in Bioinformatics. 2016.
• Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau. CIDANE: comprehensive isoform discovery and abundance estimation. Genome Biology 17:16, 2016. DOI: 10.1186/s13059-015-0865-0.
• Gunnar W. Klau. Networks to the Rescue – from Big “Omics” Data to Targeted Hypotheses. ERCIM News 104:17-18. 2016.

2015

• Paola Bonizzoni, Riccardo Dondi, Gunnar W. Klau, Yuri Pirola, Nadia Pisant, Simone Zaccaria. On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes. To appear in Journal of Computational Biology.
• Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau. Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment. Algorithms 8(4), 1035-1051, Special issue Algorithmic Themes in Bioinformatics, 2015.
• Rumen Andonov, Hristo Djidjev, Gunnar W. Klau, Mathilde Le Boudic-Jamin, Inken Wohlers. Automatic Classification of Protein Structure Using the Maximum Contact Map Overlap Metric. Algorithms 8(4), 850-869, Special issue Algorithmic Themes in Bioinformatics, 2015.
• Guohua Wang, Yunlong Liu, Dongxiao Zhu, Gunnar W. Klau, and Weixing Feng. Bioinformatics Methods and Biological Interpretation for Next-Generation Sequencing Data. Editorial in BioMed Research International, vol. 2015, Article ID 690873, 2 pages, 2015. doi:10.1155/2015/690873
• Robin Cijvat, Stefan Manegold, Martin Kersten, Gunnar W. Klau, Alexander Schönhuth, Tobias Marschall, Ying Zhang. Genome sequence analysis with MonetDB: a case
• Rumen Andonov, Hristo Djidjev, Gunnar W. Klau, Mathilde Le Boudic-Jamin, Inken Wohlers. Automatic Classification of Protein Structure Using the Maximum Contact Map Overlap Metric. Algorithms 8(4), 850-869, Special issue Algorithmic Themes in Bioinformatics, 2015.
• Guohua Wang, Yunlong Liu, Dongxiao Zhu, Gunnar W. Klau, and Weixing Feng. Bioinformatics Methods and Biological Interpretation for Next-Generation Sequencing Data. Editorial in BioMed Research International, vol. 2015, Article ID 690873, 2 pages, 2015. doi:10.1155/2015/690873
• Robin Cijvat, Stefan Manegold, Martin Kersten, Gunnar W. Klau, Alexander Schönhuth, Tobias Marschall, Ying Zhang. Genome sequence analysis with MonetDB: a case study on Ebola virus diversity. Datenbank-Spektrum, Springer, 2015, DOI 10.1007/s13222-015-0198-x.
• Ali May, Bernd Brandt, Mohammed El-Kebir, Gunnar W. Klau, Egija Zaura, Wim Crielaard, Jaap Heringa, Sanne Abeln. metaModules identifies key functional subnetworks in microbiome-related disease. Bioinformatics. To appear, 2015.
• Yuri Pirola, Simone Zaccaria, Riccardo Dondi, Gunnar W. Klau, Nadia Pisanti, and Paola Bonizzoni. HapCol: Accurate and Memory-efficient Haplotype Assembly from Long Reads. Bioinformatics 32(11): 1610-1617. DOI 10.1093/bioinformatics/btv495, 2016.
• Thomas Bellitto, Tobias Marschall, Alexander Schönhuth, Gunnar W. Klau. Next Generation Cluster Editing. In Proc. GCB 2015 (German Conference on Bioinformatics). PeerJ PrePrints 3:e1599, DOI link, 2015.
• Mohammed El-Kebir, Hayssam Soueidan, Thomas Hume, Daniela Beisser, Marcus Dittrich, Tobias Müller, Guillaume Blin, Jaap Heringa, Macha Nikolski, Lodewyk Wessels and Gunnar W. Klau. xHeinz: An algorithm for mining cross-species network modules under a flexible conservation model. Bioinformatics, advance access, 2015.
• Paola Bonizzoni, Ricardo Dondi, Gunnar W. Klau, Yuri Pirola, Nadia Pisanti, Simone Zaccaria. On the fixed parameter tractability and approximability of the minimum error correction problem. In Proc. CPM 2015 (26th Annual Symposium on Combinatorial Pattern Matching). Springer, LNCS 9133, pp. 100-113, 2015.
• Sebastian Böcker, Gunnar W. Klau, Hon Wai Leong (editors). Towards the ground truth: Exact algorithms for bioinformatics research, NII Shonan Meeting Report No. 2014-2. ISSN 2186-7437.
• Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth. WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. Journal of Computational Biology 22(6): 498-509, 2015. DOI: 10. 1089/cmb.2014.0157i, 2015.
• Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert and Gunnar W. Klau. CIDANE: Comprehensive isoform discovery and abundance estimation. To appear as 2-page abstract in Proc. RECOMB 2015 (19th Annual International Conference on Research in Computational Molecular Biology, 12-15 April 2015, Warsaw, Poland), Lecture Notes in Bioinformatics, Springer, 2015. Preprint on bioRxiv.
• Robin Cijvat, Stefan Manegold, Martin Kersten, Gunnar W. Klau, Alexander Schönhuth, Tobias Marschall, Ying Zhang. Genome sequence analysis with MonetDB: a case study on Ebola virus diversity. To appear in Proc. of Workshop on Data Management for Life Sciences at BTW 2015, the 16th conference on Database Systems for Business, Technology, and Web, March 2015, Hamburg, Germany.

2014

• 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.

2013

• 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.

2012

• Tobias Marschall, Ivan Costa, Stefan Canzar, Markus Bauer, Gunnar W. Klau, Alexander Schliep, Alexander Schönhuth. CLEVER: Clique-Enumerating Variant Finder. Bioinformatics, 28(22):2875-2882, 2012
• Inken Wohlers, Noël Malod-Dognin, Rumen Andonov, and Gunnar W. Klau. CSA: Comprehensive comparison of pairwise protein structure alignments. Nucleic Acids Research, Vol. 40, Nr. W1, pp. 303 - 309, 2012; doi: 10.1093/nar/gks362.
• Daniela Beisser, Markus Grohme, Joachim Kopka, Marcus Frohme, Ralph O. Schill, Steffen Hengherr, Thomas Dandekar, Gunnar W. Klau, Marcus Dittrich, Tobias Müller. Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. BMC Systems Biology 2012, 6:72
• Daniela Beisser, Stefan Brunkhorst, Thomas Dandekar, Gunnar W. Klau, Marcus T. Dittrich, Tobias Müller. Robustness and accuracy of functional modules in integrated network analysis. Bioinformatics 28(14):1887-1894, 2012.
• Christine Staiger, Sidney Cadot, Raul Kooter, Marcus Dittrich, Tobias Müller, Gunnar W. Klau, Lodewyk F. A. Wessels. A critical evaluation of network and pathway based classifiers for outcome prediction in breast cancer. PLoS ONE 7(4): e34796. doi:10.1371/journal.pone.0034796
• Tobias Marschall, Ivan Costa, Stefan Canzar, Markus Bauer, Gunnar W. Klau, Alexander Schliep, Alexander Schoenhuth. CLEVER: Clique-Enumerating Variant Finder. Short abstract in Proceedings of RECOMB-Seq. Preprint on arXiv. 2012
• 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. In B. Chor (Ed.): RECOMB 2012, Proc. of the 16th Annual International Conference on Research in Computational Molecular Biology, LNBI 7262, pp. 29-43. Springer, Heidelberg, 2012
• Sandro Andreotti, Gunnar W. Klau, Knut Reinert. Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9(2):385-394, 2012. Preprint
• Christina Backes, Alexander Rurainski, Gunnar W. Klau, Oliver Müller, Daniel Stöckel, Andreas Gerasch, Jan Küntzer, Daniela Maisel, Nicole Ludwig, Matthias Hein, Andreas Keller, Helmut Burtscher, Michael Kaufmann, Eckart Meese, Hans-Peter Lenhof. An integer linear programming approach for finding deregulated subgraphs in regulatory networks. Nucleic Acids Research, 40(6):e43, 2012

2011

• 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 arXiv.org.
• 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

2010

• Inken Wohlers, Francisco S. Domingues, Gunnar W. Klau. Towards optimal alignment of protein structure distance matrices. Bioinformatics 26(18):2273-2280, 2010.
• Gunnar W. Klau, Jacques Nicolas. Introduction to the Special Theme Computational Biology. ERCIM News, July 2010.
• Daniela Beißer, Gunnar W. Klau, Thomas Dandekar, Tobias Müller, Marcus Dittrich. BioNet: an R-package for the functional analysis of biological networks. Application note. Bioinformatics, 2010.
• Marcus Dittrich, Daniela Beißer, Gunnar W. Klau, Tobias Müller. Functional Modules in Protein-Protein Interaction Networks. Book chapter in: Systems Biology for Signaling Networks. S. Choi (ed.). Springer, 2010.
• Gunnar W. Klau, Neal Lesh, Joe Marks, and Michael Mitzenmacher. Human-guided search, Journal of Heuristics. Vol. 16, No. 3, pp. 289-310, 2010

2009

• Inken Wohlers, Lars Petzold, Francisco S. Domingues, and Gunnar W. Klau. PAUL: protein structural alignment using integer linear programming and Lagrangian relaxation. Selected abstract. BMC Bioinformatics 2009, 10(Suppl 13):P2
• Ernst Althaus, Gunnar W. Klau, Oliver Kohlbacher, Hans-Peter Lenhof, and Knut Reinert. Integer Linear Programming in Computational Biology. In Efficient Algorithms, LNCS 5760, Springer, 2009:199-218
• Inken Wohlers, Lars Petzold, Francisco S. Domingues, and Gunnar W. Klau. Aligning protein structures using distance matrices and combinatorial optimization. In Proc. of GCB 2009 (German Conference on Bioinformatics, Halle (Saale), Germany, 28-30 Sep 2009), I. Grosse et al. (eds.), Lecture Notes in Informatics, 2009
• Gunnar W. Klau. Diskrete Optimierung in den Lebenswissenschaften. Habilitation thesis. Department of Mathematics and Computer Science, Freie Universität Berlin, Germany.
• Annette Kik and Gunnar W. Klau. Fighting lymph cancer with mathematics. ERCIM News 77. 2009.
• Gunnar W. Klau. A new graph-based method for pairwise global network alignment. BMC Bioinformatics 10(Suppl. 1):S59, 2009
• Sebastian Böcker, Sebastian Briesemeister, and Gunnar W. Klau. On optimal comparability editing with applications to molecular diagnostics. BMC Bioinformatics 10 (Suppl. 1):S61, 2009.

2008

• Marcus T. Dittrich, Gunnar W. Klau, Andreas Rosenwald, Thomas Dandekar, Tobias Müller. Identifying functional modules in protein-protein interaction networks: an integrated exact approach, Bioinformatics, Special Issue on ISMB 2008 (16th International Conference Intelligent Systems for Molecular Biology, Toronto, Canada, July 2008), Vol. 24, pp. i223-i231, Oxford University Press, 2008. Preprint. Awarded the outstanding paper award.
• Markus Bauer, Gunnar W. Klau and Knut Reinert. An exact mathematical programming approach to multiple RNA sequence-structure alignment. Algorithmic Operations Research, Vol. 3, No. 2, 2008. Preprint.
• Sebastian Böcker, Sebastian Briesemeister, and Gunnar W. Klau. Exact algorithms for cluster editing: evaluation and experiments, in Proc. of WEA 2008 (7th International Workshop on Experimental Algorithms, Provincetown, Cape Cod, MA, USA, 30 May - 2 June 2008), LNCS 5038, C. C. McGeogh (ed.), Springer, Berlin, 2008, pp. 289-302.
• Sven Rahmann and Gunnar W. Klau. Integer linear programming models for approximate gene cluster detection, chapter in Bioinformatics Algorithms: Techniques and Applications, I. I. Mandoiu and A. Z. Zelikovsky (eds.), Wiley Book Series on Bioinformatics. John Wiley & Sons. March 2008.
• Christoph Buchheim, Markus Chimani, Dietmar Ebner, Carsten Gutwenger, Michael Jünger, Gunnar W. Klau, Petra Mutzel, and René Weiskircher. A branch-and-cut approach to the crossing number problem. Discrete Optimization, Vol. 5, Issue 2, Special Issue in memory of George B. Dantzig, pp. 373-388, 2008. Preprint.

2007

• Markus Bauer, Gunnar W. Klau and Knut Reinert. Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics, Vol. 8, No. 271, BioMed Central, 2007.
• Knut Reinert, Markus Bauer, Andreas Döring, Gunnar W. Klau, and Aaron L. Halpern. A general paradigm for fast, adaptive clustering of biological sequences, in Proc. of GCB 2007 (German Conference on Bioinformatics, Potsdam, Germany, September 26-28, 2007), M. Vingron et al. (ed.), GI-Edition, Lecture Notes in Informatics, pp. 15-29.
• Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert. Integer linear programming approaches for non-unique probe selection, Discrete Applied Mathematics, Vol. 155, Issues 6-7, pp. 840-856, Computational Molecular Biology Series, Issue V, Elsevier Publishers, 2007
• Christian A. Duncan, Gunnar W. Klau, Stephen G. Kobourov, and Georg Sander. Graph drawing contest report, in Proc. of GD 2006 (14th International Symposium on Graph Drawing, Karlsruhe, Germany, September 2006), Lecture Notes in Computer Science 4372, Springer, Berlin, 2007, pp. 448-452.
• Patrick May, Gunnar W. Klau, Markus Bauer, and Thomas Steinke. Accelerated microRNA precursor detection using the Smith-Waterman algorithm on FPGAs, in Proc. of GCCB 2006 (International Workshop on Distributed, High-Performance, and Grid Computing in Computational Biology, Eilat, Israel, January 21-24, 2007), W. Dubitzky et al. (eds.), Lecture Notes in Bioinformatics, Vol. 4360, pp. 19-32, Springer, Berlin, 2007

2006

• Ivana Ljubic, René Weiskircher, Ulrich Pferschy, Gunnar W. Klau, Petra Mutzel, and Matteo Fischetti. An algorithmic framework for the exact solution of the prize-collecting Steiner tree problem, Mathematical Programming, Series B, Vol. 105, No. 2-3, pp. 427-449, Special Issue on the 7th Aussois Meeting on Combinatorial Optimization (2003), Springer, 2006. Preprint.
• Sven Rahmann and Gunnar W. Klau. Integer linear programs for discovering approximate gene clusters, in Proc. of WABI 2006 (6th Workshop on Algorithms in Bioinformatics, Zurich, Switzerland, September 11-13, 2006), B. Moret and P. Bucher (eds.), Lecture Notes in Bioinformatics, Vol. 4175, pp. 298-309, Springer, Berlin, 2006
• Patrick May, Markus Bauer, Christian Köberle, and Gunnar W. Klau. A computational approach to microRNA detection. Technical Report TR-06-44, Zuse Institute Berlin, December 2006
• Christoph Buchheim, Dietmar Ebner, Michael Jünger, Gunnar W. Klau, Petra Mutzel, and René Weiskircher. Exact crossing minimization, in Proc. of GD 2005 (13th International Symposium on Graph Drawing, Limerick, Ireland, September 12-14, 2005), P. Healy and N. S. Nikolov (eds.), Lecture Notes in Computer Science, Vol. 3843, pp. 37-48, Springer, Berlin, 2006

2005

• Markus Bauer, Gunnar W. Klau, and Knut Reinert. Fast and accurate structural RNA alignment by progressive Lagrangian relaxation, in Proc. of CompLife 2005 (First International Symposium on Computational Life Science, Konstanz, Germany, September 25-27, 2005), M. R. Berthold et al. (eds.), Lecture Notes in Bioinformatics, Vol. 3695, pp. 217-228, Springer, Berlin, 2005. Preprint.
• Markus Bauer, Gunnar W. Klau, and Knut Reinert. Multiple structural RNA alignment with Lagrangian relaxation, extended abstract in Proc. of WABI 2005 (Fifth Workshop on Algorithms in Bioinformatics, Mallorca, Spain, October 3-6, 2005), R. Casadio and G. Myers (eds.), Lecture Notes in Bioinformatics, Vol. 3692, pp. 303-314, Springer, Berlin, 2005. Preprint.
• Ivana Ljubic, René Weiskircher, Ulrich Pferschy, Gunnar W. Klau, Petra Mutzel, and Matteo Fischetti. Solving the prize-collecting Steiner tree problem to optimality, in Proc. of ALENEX/ANALCO 2005 (Seventh Workshop on Algorithm Engineering and Experiments and the Second Workshop on Analytic Algorithmics and Combinatorics, Vancouver, British Columbia, Canada, January 22, 2005), C. Demetrescu, R. Tamassia, and R. Sedgewick (eds.), ISBN 0-89871-596-2, SIAM, 2005
• Gunnar W. Klau and René Weiskircher. Robustness and resilience, chapter in "Network Analysis: Methodological Foundations", Ulrik Brandes and Thomas Erlebach (eds.), Lecture Notes in Computer Science, Vol. 3418, Springer, Berlin, 2005, pp.417-437. Preprint.
• Markus Chimani and Gunnar W. Klau and René Weiskircher. Non-planar orthogonal drawings with fixed topology, extended abstract in Proc. of SOFSEM 2005 (31st Annual Conference on Current Trends in Theory and Practice of Informatics, January 22-28, 2005, Liptovsky Jan, Slovak Republic), M. Bieliková et al. (eds.), Lecture Notes in Computer Science, Vol. 3381, pp. 96-105, Springer, 2005. Preprint.
• Dietmar Ebner, Gunnar W. Klau, and René Weiskircher. Label number maximization in the slider model, in Proc. of GD 2004 (12th International Symposium on Graph Drawing, New York, U.S.A., September 2004), J. Pach (ed.), Lecture Notes in Computer Science, Vol. 3383, pp. 144-154, Springer, Berlin, 2005. Preprint.

2004

• Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert. Optimal robust non-unique probe selection using integer linear programming, Bioinformatics, Volume 20, Special Issue on ISMB/ECCB 2004 (Twelfth International Conference on Intelligent Systems for Molecular Biology and Third European Conference on Computational Biology, Glasgow, Scotland, August 2004), pp. i186-i193, Oxford University Press, 2004. Preprint.
• Markus Bauer and Gunnar W. Klau. Structural alignment of two RNA sequences with Lagrangian relaxation, in Proc. of ISAAC 2004 (15th Annual International Symposium on Algorithms and Computation, Hong Kong, China, December 2004), R. Fleischer and G. Trippen (eds.), Lecture Notes in Computer Science, Vol. 3341, pp. 113-123, Springer, Berlin, 2004. Preprint.
• Dietmar Ebner, Gunnar W. Klau and René Weiskircher. Computational Study of Label Number Maximization Algorithms in the Slider Model. Research Report TR-186-1-04-03. Vienna University of Technology, Institute of Computer Graphics and Algorithms, Austria, July 2004.
• Gunnar W. Klau, Ivana Ljubic, Andreas Moser, Petra Mutzel, Philipp Neuner, Ulrich Pferschy, Günther Raidl, and René Weiskircher. Combining a memetic algorithm with integer linear programming to solve the prize-collecting Steiner tree problem, in Proc. of GECCO 2004 (Genetic and Evolutionary Computation Conference, Seattle, United States of America, June 2004), K. Deb et al. (eds.), Lecture Notes in Computer Science, Vol. 3102, pp. 1304-1315, Springer, Berlin, 2004. Preprint.

2003

• Gunnar W. Klau and Petra Mutzel. Optimal labeling of point features in rectangular labeling models, Mathematical Programming, Series B, Vol. 94, Special Issue on the 4th Aussois Meeting on Combinatorial Optimization (2000), Springer, 2003. Preprint.
• Gunnar W. Klau, Ivana Ljubic, Petra Mutzel, Ulrich Pferschy and René Weiskircher. The fractional prize-collecting Steiner tree problem on trees, in Proc. of ESA 2003 (European Symposium on Algorithms, Budapest, Hungary, September 2003), G. Di Battista and U. Zwick (eds.), Lecture Notes in Computer Science, Vol. 2832, pp.691-702, Springer, Berlin, 2003. Preprint.
• Michael Jünger, Gunnar W. Klau, Petra Mutzel and René Weiskircher. AGD: A library of algorithms for graph drawing, chapter in "Graph Drawing Software", Springer Series "Mathematics and Visualization", Berlin, 2003, pp.149-172. Preprint.
• Gunnar W. Klau. A combinatorial approach to orthogonal placement problems, in Proc. of Operations Research 2002 (International Conference on Operations Research, Klagenfurt, Austria, September 2002), U. Leopold-Wildburger et al. (eds.), Springer, Berlin, 2003. Preprint.
• Gunnar W. Klau and Petra Mutzel. Automatic layout and labelling of state diagrams, chapter in "Mathematics - Key Technology for the Future", Springer, Berlin, 2003, pp.584-608. Preprint.

2002

• Gunnar W. Klau, Neal Lesh, Joe Marks, and Michael Mitzenmacher. Human-guided tabu search, in Proc. of AAAI 2002 (The Eighteenth National Conference on Artificial Intelligence, Edmonton, Alberta, Canada, July/August 2002). Preprint.
• Gunnar W. Klau, Neal Lesh, Joe Marks, Michael Mitzenmacher, and Guy T. Schafer. The HuGS platform: a toolkit for interactive optimization, in Proc. of AVI 2002 (International Working Conference on Advanced Visual Interfaces, Trento, Italy, May 2002). Preprint.
• Carsten Gutwenger, Michael Jünger, Sebastian Leipert, Gunnar W. Klau, Petra Mutzel, and René Weiskircher. AGD: a library of algorithms for graph drawing, in Proc. of GD 2001 (Ninth International Symposium on Graph Drawing, Vienna, Austria, September 2001), Lecture Notes in Computer Science 2265, Springer, Berlin, 2002, pp. 473-474. Preprint.
• Stacey D. Scott, Neal Lesh, and Gunnar W. Klau. Investigating human-computer optimization, in Proc. of CHI 2002 (Conference on Human Factors in Computing Systems, Minneapolis, MS, U.S.A., April 2002). Preprint.
• Carsten Gutwenger, Michael Jünger, Sebastian Leipert, Gunnar W. Klau, and Petra Mutzel. Graph drawing algorithm engineering with AGD, in Software Visualization: State of the Art Survey (Proc. of the Int. Dagstuhl Seminar on Software Visualization, Schloss Dagstuhl, Germany, May 2001), Lecture Notes in Computer Science 2269, Springer, Berlin, 2002, pp. 307-333. Preprint.

2001

• Gunnar W. Klau. A combinatorial approach to orthogonal placement problems. PhD thesis, Universität des Saarlandes, Saarbrücken, September 2001. Preprint (PDF).
• Gunnar W. Klau, Karsten Klein, and Petra Mutzel. An Experimental Comparison of Orthogonal Compaction Algorithms, extended abstract in Proc. of the Eighth International Symposium on Graph Drawing (GD 2000), LNCS 1984, Williamsburg, Virginia, U.S.A., September 20 - 23, 2000, Springer, Berlin, 2001, pp. 37-51. Preprint.
• Markus Eiglsperger, Sándor Fekete, and Gunnar W. Klau. Orthogonal graph drawing. Chapter in "Drawing Graphs: Methods and Models", M. Kaufmann and D. Wagner (eds.), LNCS 2025 (Tutorial), Springer, Berlin, 2001, pp. 121-171. Preprint.

2000

• Gunnar W. Klau and Petra Mutzel. Optimal labelling of point features in the slider model, extended abstract in Proc. of the Sixth Annual International Computing and Combinatorics Conference (COCOON 2000), LNCS 1858, Sydney, Australia, July 26 - 28 2000, Springer, Berlin, 2000, pp. 340-350. Preprint.
• Gunnar W. Klau, Karsten Klein, and Petra Mutzel. An Experimental Comparison of Orthogonal Compaction Algorithms. Research Report TR-186-1-00-03. Vienna University of Technology, Institute of Computer Graphics and Algorithms, Austria, October 2000, 20 pages. Preprint. the Seventh International Symposium on Graph Drawing (GD-99), LNCS 1731, Stirin Castle, Czech Republic, September 15 - 18, 1999, Springer, Berlin, 1999, pp. 27-37. Preprint.
• Gunnar W. Klau and Petra Mutzel. Optimal compaction of orthogonal grid drawings, extended abstract in Proc. of the Seventh International IPCO Conference (Integer Programming and Combinatorial Optimization), LNCS 1610, Graz, Austria, June 9-11, 1999, Springer, Berlin, 1999, pp. 304-319. Preprint.

1998

• 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.

1997

• 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.