Gunnar W. Klau

According to our database, Gunnar W. Klau authored at least 94 papers between 1998 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

OFraMP: a fragment-based tool to facilitate the parametrization of large molecules.

Martin Stroet, Bertrand Caron, Martin S. Engler, Jimi van der Woning, Aude Kauffmann, Marc van Dijk, Mohammed El-Kebir, Koen Visscher, Josef Holownia, Callum Macfarlane, Brian J. Bennion, Svetlana Gelpi-Dominguez, Felice C. Lightstone, Tijs van der Storm, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau

J. Comput. Aided Mol. Des., August, 2023

2021

Using the longest run subsequence problem within homology-based scaffolding.

Sven Schrinner, Manish Goel, Michael Wulfert, Philipp Spohr, Korbinian Schneeberger, Gunnar W. Klau

Algorithms Mol. Biol., 2021

2020

The Longest Run Subsequence Problem.

Sven Schrinner, Manish Goel, Michael Wulfert, Philipp Spohr, Korbinian Schneeberger, Gunnar W. Klau

Proceedings of the 20th International Workshop on Algorithms in Bioinformatics, 2020

The Lost Recipes from the Four Schools of Amathus.

Gunnar W. Klau

Proceedings of the SOFSEM 2020: Theory and Practice of Computer Science, 2020

2019

Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach.

Martin S. Engler, Bertrand Caron, Lourens E. Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau

Algorithms Mol. Biol., 2019

2018

Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.

Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael

J. Comput. Biol., 2018

eXamine: Visualizing annotated networks in Cytoscape.

Philipp Spohr, Kasper Dinkla, Gunnar W. Klau, Mohammed El-Kebir

F1000Research, 2018

Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules.

Martin S. Engler, Bertrand Caron, Lourens E. Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau

Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

2017

The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data.

Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael

Proceedings of the Research in Computational Molecular Biology, 2017

A Guided Tour to Computational Haplotyping.

Gunnar W. Klau, Tobias Marschall

Proceedings of the Unveiling Dynamics and Complexity, 2017

2016

On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes.

Paola Bonizzoni, Riccardo Dondi, Gunnar W. Klau, Yuri Pirola, Nadia Pisanti, Simone Zaccaria

J. Comput. Biol., 2016

Networks to the Rescue - From Big "Omics" Data to Targeted Hypotheses.

Gunnar W. Klau

ERCIM News, 2016

HapCol: accurate and memory-efficient haplotype assembly from long reads.

Yuri Pirola, Simone Zaccaria, Riccardo Dondi, Gunnar W. Klau, Nadia Pisanti, Paola Bonizzoni

Bioinform., 2016

metaModules identifies key functional subnetworks in microbiome-related disease.

Ali May, Bernd W. Brandt, Mohammed El-Kebir, Gunnar W. Klau, Egija Zaura, Wim Crielaard, Jaap Heringa, Sanne Abeln

Bioinform., 2016

2015

Next generation cluster editing.

Thomas Bellitto, Tobias Marschall, Alexander Schönhuth, Gunnar W. Klau

PeerJ Prepr., 2015

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.

Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth

J. Comput. Biol., 2015

Genome sequence analysis with MonetDB - A case study on Ebola virus diversity.

Robin Cijvat, Stefan Manegold, Martin L. Kersten, Gunnar W. Klau, Alexander Schönhuth, Tobias Marschall, Ying Zhang

Datenbank-Spektrum, 2015

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.

Mohammed El-Kebir, Hayssam Soueidan, Thomas Hume, Daniela Beisser, Marcus T. Dittrich, Tobias Müller, Guillaume Blin, Jaap Heringa, Macha Nikolski, Lodewyk F. A. Wessels, Gunnar W. Klau

Bioinform., 2015

Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment.

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

Algorithms, 2015

Automatic Classification of Protein Structure Using the Maximum Contact Map Overlap Metric.

Rumen Andonov, Hristo N. Djidjev, Gunnar W. Klau, Mathilde Le Boudic-Jamin, Inken Wohlers

Algorithms, 2015

On Tree-Constrained Matchings and Generalizations.

Stefan Canzar, Khaled M. Elbassioni, Gunnar W. Klau, Julián Mestre

Algorithmica, 2015

CIDANE: Comprehensive Isoform Discovery and Abundance Estimation.

Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau

Proceedings of the Research in Computational Molecular Biology, 2015

On the Fixed Parameter Tractability and Approximability of the Minimum Error Correction Problem.

Paola Bonizzoni, Riccardo Dondi, Gunnar W. Klau, Yuri Pirola, Nadia Pisanti, Simone Zaccaria

Proceedings of the Combinatorial Pattern Matching - 26th Annual Symposium, 2015

2014

Towards the ground truth: Exact algorithms for bioinformatics research (NII Shonan Meeting 2014-2).

Sebastian Böcker, Gunnar W. Klau, Veli Mäkinen, Hon Wai Leong

NII Shonan Meet. Rep., 2014

Solving the Maximum-Weight Connected Subgraph Problem to Optimality.

Mohammed El-Kebir, Gunnar W. Klau

CoRR, 2014

A web server for protein-protein interaction network querying.

Mohammed El-Kebir, Bernd W. Brandt, Jaap Heringa, Gunnar W. Klau

BMC Syst. Biol., 2014

eXamine: Exploring annotated modules in networks.

Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine J. Smit, Michel A. Westenberg, Gunnar W. Klau

BMC Bioinform., 2014

WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads.

Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth

Proceedings of the Research in Computational Molecular Biology, 2014

Exact Protein Structure Classification Using the Maximum Contact Map Overlap Metric.

Inken Wohlers, Mathilde Le Boudic-Jamin, Hristo N. Djidjev, Gunnar W. Klau, Rumen Andonov

Proceedings of the Algorithms for Computational Biology - First International Conference, 2014

2013

The Open Graph Drawing Framework (OGDF).

Markus Chimani, Carsten Gutwenger, Michael Jünger, Gunnar W. Klau, Karsten Klein, Petra Mutzel

Proceedings of the Handbook on Graph Drawing and Visualization., 2013

DALIX: Optimal DALI Protein Structure Alignment.

Inken Wohlers, Rumen Andonov, Gunnar W. Klau

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Charge Group Partitioning in Biomolecular Simulation.

Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau

J. Comput. Biol., 2013

eXamine: a Cytoscape app for exploring annotated modules in networks.

Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine J. Smit, Michel A. Westenberg, Gunnar W. Klau

CoRR, 2013

Mapping proteins in the presence of paralogs using units of coevolution.

Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth, Gunnar W. Klau

BMC Bioinform., 2013

The Generalized Robinson-Foulds Metric.

Sebastian Böcker, Stefan Canzar, Gunnar W. Klau

Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

Reconstructing Consensus Bayesian Network Structures with Application to Learning Molecular Interaction Networks.

Holger Fröhlich, Gunnar W. Klau

Proceedings of the German Conference on Bioinformatics 2013, 2013

2012

Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem.

Sandro Andreotti, Gunnar W. Klau, Knut Reinert

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

CSA: comprehensive comparison of pairwise protein structure alignments.

Inken Wohlers, Noël Malod-Dognin, Rumen Andonov, Gunnar W. Klau

Nucleic Acids Res., 2012

Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum.

Daniela Beisser, Markus A. Grohme, Joachim Kopka, Marcus Frohme, Ralph O. Schill, Steffen Hengherr, Thomas Dandekar, Gunnar W. Klau, Marcus T. Dittrich, Tobias Müller

BMC Syst. Biol., 2012

CLEVER: clique-enumerating variant finder.

Tobias Marschall, Ivan G. Costa, Stefan Canzar, Markus Bauer, Gunnar W. Klau, Alexander Schliep, Alexander Schönhuth

Bioinform., 2012

Robustness and accuracy of functional modules in integrated network analysis.

Daniela Beisser, Stefan Brunkhorst, Thomas Dandekar, Gunnar W. Klau, Marcus T. Dittrich, Tobias Müller

Bioinform., 2012

Charge Group Partitioning in Biomolecular Simulation.

Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau

Proceedings of the Research in Computational Molecular Biology, 2012

2011

Algorithm engineering for optimal alignment of protein structure distance matrices.

Inken Wohlers, Rumen Andonov, Gunnar W. Klau

Optim. Lett., 2011

An exact algorithm for side-chain placement in protein design.

Stefan Canzar, Nora C. Toussaint, Gunnar W. Klau

Optim. Lett., 2011

A critical evaluation of network and pathway based classifiers for outcome prediction in breast cancer

Christine Staiger, Sidney Cadot, R. Kooter, Marcus T. Dittrich, Tobias Müller, Gunnar W. Klau, Lodewyk F. A. Wessels

CoRR, 2011

Exact Algorithms for Cluster Editing: Evaluation and Experiments.

Sebastian Böcker, Sebastian Briesemeister, Gunnar W. Klau

Algorithmica, 2011

Lagrangian Relaxation Applied to Sparse Global Network Alignment.

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

Proceedings of the Pattern Recognition in Bioinformatics, 2011

Sparsifying Distance Matrices for Protein-Protein Structure Alignments.

Antonio Mucherino, Inken Wohlers, Gunnar W. Klau, Rumen Andonov

Proceedings of the 10th Cologne-Twente Workshop on graphs and combinatorial optimization. Extended Abstracts, 2011

2010

Human-guided search.

Gunnar W. Klau, Neal Lesh, Joe Marks, Michael Mitzenmacher

J. Heuristics, 2010

Introduction to the Special Theme: Computational Biology.

Gunnar W. Klau, Jacques Nicolas

ERCIM News, 2010

Towards optimal alignment of protein structure distance matrices.

Inken Wohlers, Francisco S. Domingues, Gunnar W. Klau

Bioinform., 2010

BioNet: an R-Package for the functional analysis of biological networks.

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

Bioinform., 2010

2009

Fighting Lymph Cancer with Mathematics.

Annette Kik, Gunnar W. Klau

ERCIM News, 2009

PAUL: protein structural alignment using integer linear programming and Lagrangian relaxation.

Inken Wohlers, Lars Petzold, Francisco S. Domingues, Gunnar W. Klau

BMC Bioinform., 2009

A new graph-based method for pairwise global network alignment.

Gunnar W. Klau

BMC Bioinform., 2009

On optimal comparability editing with applications to molecular diagnostics.

Sebastian Böcker, Sebastian Briesemeister, Gunnar W. Klau

BMC Bioinform., 2009

Aligning Protein Structures Using Distance Matrices and Combinatorial Optimization.

Inken Wohlers, Lars Petzold, Francisco S. Domingues, Gunnar W. Klau

Proceedings of the German Conference on Bioinformatics 2009, 2009

Integer Linear Programming in Computational Biology.

Ernst Althaus, Gunnar W. Klau, Oliver Kohlbacher, Hans-Peter Lenhof, Knut Reinert

Proceedings of the Efficient Algorithms, 2009

2008

A branch-and-cut approach to the crossing number problem.

Christoph Buchheim, Markus Chimani, Dietmar Ebner, Carsten Gutwenger, Michael Jünger, Gunnar W. Klau, Petra Mutzel, René Weiskircher

Discret. Optim., 2008

An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment.

Markus Bauer, Gunnar W. Klau, Knut Reinert

Algorithmic Oper. Res., 2008

Identifying functional modules in protein-protein interaction networks: an integrated exact approach.

Marcus T. Dittrich, Gunnar W. Klau, Andreas Rosenwald, Thomas Dandekar, Tobias Müller

Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

2007

Integer linear programming approaches for non-unique probe selection.

Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert

Discret. Appl. Math., 2007

Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.

Markus Bauer, Gunnar W. Klau, Knut Reinert

BMC Bioinform., 2007

A General Paradigm for Fast, Adaptive Clustering of Biological Sequences.

Knut Reinert, Markus Bauer, Andreas Döring, Gunnar W. Klau, Aaron L. Halpern

Proceedings of the German Conference on Bioinformatics, 2007

2006

An Algorithmic Framework for the Exact Solution of the Prize-Collecting Steiner Tree Problem.

Ivana Ljubic, René Weiskircher, Ulrich Pferschy, Gunnar W. Klau, Petra Mutzel, Matteo Fischetti

Math. Program., 2006

Integer Linear Programs for Discovering Approximate Gene Clusters.

Sven Rahmann, Gunnar W. Klau

Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

Graph-Drawing Contest Report.

Christian A. Duncan, Gunnar W. Klau, Stephen G. Kobourov, Georg Sander

Proceedings of the Graph Drawing, 14th International Symposium, 2006

Accelerated microRNA-Precursor Detection Using the Smith-Waterman Algorithm on FPGAs.

Patrick May, Gunnar W. Klau, Markus Bauer, Thomas Steinke

Proceedings of the Distributed, 2006

2005

Multiple Structural RNA Alignment with Lagrangian Relaxation.

Markus Bauer, Gunnar W. Klau, Knut Reinert

Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005

Non-planar Orthogonal Drawings with Fixed Topology.

Markus Chimani, Gunnar W. Klau, René Weiskircher

Proceedings of the SOFSEM 2005: Theory and Practice of Computer Science, 2005

Exact Crossing Minimization.

Christoph Buchheim, Dietmar Ebner, Michael Jünger, Gunnar W. Klau, Petra Mutzel, René Weiskircher

Proceedings of the Graph Drawing, 13th International Symposium, 2005

Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Optimization.

Markus Bauer, Gunnar W. Klau, Knut Reinert

Proceedings of the Computational Life Sciences, First International Symposium, 2005

Solving the Prize-Collecting Steiner Tree Problem to Optimality.

Ivana Ljubic, René Weiskircher, Ulrich Pferschy, Gunnar W. Klau, Petra Mutzel, Matteo Fischetti

Proceedings of the Seventh Workshop on Algorithm Engineering and Experiments and the Second Workshop on Analytic Algorithmics and Combinatorics, 2005

2004

Optimal robust non-unique probe selection using Integer Linear Programming.

Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert

Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

Structural Alignment of Two RNA Sequences with Lagrangian Relaxation.

Markus Bauer, Gunnar W. Klau

Proceedings of the Algorithms and Computation, 15th International Symposium, 2004

Combining a Memetic Algorithm with Integer Programming to Solve the Prize-Collecting Steiner Tree Problem.

Gunnar W. Klau, Ivana Ljubic, Andreas Moser, Petra Mutzel, Philipp Neuner, Ulrich Pferschy, Günther R. Raidl, René Weiskircher

Proceedings of the Genetic and Evolutionary Computation, 2004

Label Number Maximization in the Slider Model.

Dietmar Ebner, Gunnar W. Klau, René Weiskircher

Proceedings of the Graph Drawing, 12th International Symposium, 2004

Robustness and Resilience.

Gunnar W. Klau, René Weiskircher

Proceedings of the Network Analysis: Methodological Foundations [outcome of a Dagstuhl seminar, 2004

AGD - A Library of Algorithms for Graph Drawing.

Michael Jünger, Gunnar W. Klau, Petra Mutzel, René Weiskircher

Proceedings of the Graph Drawing Software, 2004

2003

Optimal labeling of point features in rectangular labeling models.

Gunnar W. Klau, Petra Mutzel

Math. Program., 2003

The Fractional Prize-Collecting Steiner Tree Problem on Trees: Extended Abstract.

Gunnar W. Klau, Ivana Ljubic, Petra Mutzel, Ulrich Pferschy, René Weiskircher

Proceedings of the Algorithms, 2003

2002

A combinatorial approach to orthogonal placement problems.

Gunnar W. Klau

PhD thesis, 2002

A Combinatorial Approach to Orthogonal Placement Problems.

Gunnar W. Klau

Proceedings of the Operations Research Proceedings 2002, 2002

Investigating human-computer optimization.

Stacey D. Scott, Neal Lesh, Gunnar W. Klau

Proceedings of the CHI 2002 Conference on Human Factors in Computing Systems: Changing our World, 2002

The HuGS platform: a toolkit for interactive optimization.

Gunnar W. Klau, Neal Lesh, Joe Marks, Michael Mitzenmacher, Guy T. Schafer

Proceedings of the Working Conference on Advanced Visual Interfaces, 2002

Human-Guided Tabu Search.

Gunnar W. Klau, Neal Lesh, Joe Marks, Michael Mitzenmacher

Proceedings of the Eighteenth National Conference on Artificial Intelligence and Fourteenth Conference on Innovative Applications of Artificial Intelligence, July 28, 2002

2001

AGD: A Library of Algorithms for Graph Drawing.

Carsten Gutwenger, Michael Jünger, Gunnar W. Klau, Sebastian Leipert, Petra Mutzel, René Weiskircher

Proceedings of the Graph Drawing, 9th International Symposium, 2001

Graph Drawing Algorithm Engineering with AGD.

Carsten Gutwenger, Michael Jünger, Gunnar W. Klau, Sebastian Leipert, Petra Mutzel

Proceedings of the Software Visualization, 2001

2000

An Experimental Comparison of Orthogonal Compaction Algorithms (Extended Abstract).

Gunnar W. Klau, Karsten Klein, Petra Mutzel

Proceedings of the Graph Drawing, 8th International Symposium, 2000

Optimal Labelling of Point Features in the Slider Model.

Gunnar W. Klau, Petra Mutzel

Proceedings of the Computing and Combinatorics, 6th Annual International Conference, 2000

1999

Optimal Compaction of Orthogonal Grid Drawings.

Gunnar W. Klau, Petra Mutzel

Proceedings of the Integer Programming and Combinatorial Optimization, 1999

Combining Graph Labeling and Compaction.

Gunnar W. Klau, Petra Mutzel

Proceedings of the Graph Drawing, 7th International Symposium, 1999

Orthogonal Graph Drawing.

Markus Eiglsperger, Sándor P. Fekete, Gunnar W. Klau

Proceedings of the Drawing Graphs, 1999

1998

A Library of Algorithms for Graph Drawing.

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, Sebastian Leipert

Proceedings of the Graph Drawing, 6th International Symposium, 1998