Gunnar W. Klau

107 papers A* 1A 9B 10C 7Misc 1Journal 56Unranked 19
YearRankTypeTitle / Venue / Authors
2026 J jnl
Drug response prediction: A critical systematic review of current datasets and methods.
Pattern Recognit. Lett.
Nguyen Khoa Tran, Gunnar W. Klau
2026 J jnl
VUScope: a mathematical model for evaluating image-based drug response measurements and predicting long-term incubation outcomes.
Bioinform.
Nguyen Khoa Tran, My Ky Huynh, Alexander D. Kotman, Martin Jürgens, Thomas Kurz, Sascha Dietrich, Gunnar W. Klau, Nan Qin
2024 J jnl
A critical review of multi-output support vector regression.
Pattern Recognit. Lett.
Nguyen Khoa Tran, Laura C. Kühle, Gunnar W. Klau
2023 J jnl
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules.
J. Comput. Aided Mol. Des.
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
2021 J jnl
Using the longest run subsequence problem within homology-based scaffolding.
Algorithms Mol. Biol.
Sven Schrinner, Manish Goel, Michael Wulfert, Philipp Spohr, Korbinian Schneeberger, Gunnar W. Klau
2020 C conf
The Longest Run Subsequence Problem.
WABI
Sven Schrinner, Manish Goel, Michael Wulfert, Philipp Spohr, Korbinian Schneeberger, Gunnar W. Klau
2020 B conf
The Lost Recipes from the Four Schools of Amathus.
SOFSEM
Gunnar W. Klau
2019 J jnl
Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach.
Algorithms Mol. Biol.
Martin S. Engler, Bertrand Caron, Lourens E. Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau
2019 — ed.
Computational Intelligence Methods for Bioinformatics and Biostatistics - 14th International Meeting, CIBB 2017, Cagliari, Italy, September 7-9, 2017, Revised Selected Papers
CIBB
Massimo Bartoletti, Annalisa Barla, Andrea Bracciali, Gunnar W. Klau, Leif E. Peterson, Alberto Policriti, Roberto Tagliaferri
2018 C conf
Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules.
WABI
Martin S. Engler, Bertrand Caron, Lourens E. Veen, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau
2018 J jnl
Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.
J. Comput. Biol.
Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael
2018 J jnl
eXamine: Visualizing annotated networks in Cytoscape.
F1000Research
Philipp Spohr, Kasper Dinkla, Gunnar W. Klau, Mohammed El-Kebir
2017 C conf
A Guided Tour to Computational Haplotyping.
CiE
Gunnar W. Klau, Tobias Marschall
2017 B conf
The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data.
RECOMB
Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael
2016 J jnl
HapCol: accurate and memory-efficient haplotype assembly from long reads.
Bioinform.
Yuri Pirola, Simone Zaccaria, Riccardo Dondi, Gunnar W. Klau, Nadia Pisanti, Paola Bonizzoni
2016 J jnl
Networks to the Rescue - From Big "Omics" Data to Targeted Hypotheses.
ERCIM News
Gunnar W. Klau
2016 J jnl
On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes.
J. Comput. Biol.
Paola Bonizzoni, Riccardo Dondi, Gunnar W. Klau, Yuri Pirola, Nadia Pisanti, Simone Zaccaria
2016 J jnl
metaModules identifies key functional subnetworks in microbiome-related disease.
Bioinform.
Ali May, Bernd W. Brandt, Mohammed El-Kebir, Gunnar W. Klau, Egija Zaura, Wim Crielaard, Jaap Heringa, Sanne Abeln
2015 J jnl
Automatic Classification of Protein Structure Using the Maximum Contact Map Overlap Metric.
Algorithms
Rumen Andonov, Hristo N. Djidjev, Gunnar W. Klau, Mathilde Le Boudic-Jamin, Inken Wohlers
2015 B conf
CIDANE: Comprehensive Isoform Discovery and Abundance Estimation.
RECOMB
Stefan Canzar, Sandro Andreotti, David Weese, Knut Reinert, Gunnar W. Klau
2015 J jnl
Genome sequence analysis with MonetDB - A case study on Ebola virus diversity.
Datenbank-Spektrum
Robin Cijvat, Stefan Manegold, Martin L. Kersten, Gunnar W. Klau, Alexander Schönhuth, Tobias Marschall, Ying Zhang
2015 — conf
Genome sequence analysis with monetdb: a case study on ebola virus diversity.
BTW Workshops
Robin Cijvat, Stefan Manegold, Martin L. Kersten, Gunnar W. Klau, Alexander Schönhuth, Tobias Marschall, Ying Zhang
2015 J jnl
Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment.
Algorithms
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
2015 J jnl
Next generation cluster editing.
PeerJ Prepr.
Thomas Bellitto, Tobias Marschall, Alexander Schönhuth, Gunnar W. Klau
2015 J jnl
On Tree-Constrained Matchings and Generalizations.
Algorithmica
Stefan Canzar, Khaled M. Elbassioni, Gunnar W. Klau, Julián Mestre
2015 B conf
On the Fixed Parameter Tractability and Approximability of the Minimum Error Correction Problem.
CPM
Paola Bonizzoni, Riccardo Dondi, Gunnar W. Klau, Yuri Pirola, Nadia Pisanti, Simone Zaccaria
2015 J jnl
WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.
J. Comput. Biol.
Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth
2015 J jnl
xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.
Bioinform.
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
2014 J jnl
A web server for protein-protein interaction network querying.
BMC Syst. Biol.
Mohammed El-Kebir, Bernd W. Brandt, Jaap Heringa, Gunnar W. Klau
2014 — conf
Exact Protein Structure Classification Using the Maximum Contact Map Overlap Metric.
AlCoB
Inken Wohlers, Mathilde Le Boudic-Jamin, Hristo N. Djidjev, Gunnar W. Klau, Rumen Andonov
2014 J jnl
Solving the Maximum-Weight Connected Subgraph Problem to Optimality.
CoRR
Mohammed El-Kebir, Gunnar W. Klau
2014 J jnl
Towards the ground truth: Exact algorithms for bioinformatics research (NII Shonan Meeting 2014-2).
NII Shonan Meet. Rep.
Sebastian Böcker, Gunnar W. Klau, Veli Mäkinen, Hon Wai Leong
2014 B conf
WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads.
RECOMB
Murray Patterson, Tobias Marschall, Nadia Pisanti, Leo van Iersel, Leen Stougie, Gunnar W. Klau, Alexander Schönhuth
2014 J jnl
eXamine: Exploring annotated modules in networks.
BMC Bioinform.
Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine J. Smit, Michel A. Westenberg, Gunnar W. Klau
2014 J jnl
eXamine: Exploring annotated modules in networks.
CoRR
Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine J. Smit, Michel A. Westenberg, Gunnar W. Klau
2013 J jnl
Charge Group Partitioning in Biomolecular Simulation.
J. Comput. Biol.
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
2013 J jnl
DALIX: Optimal DALI Protein Structure Alignment.
IEEE ACM Trans. Comput. Biol. Bioinform.
Inken Wohlers, Rumen Andonov, Gunnar W. Klau
2013 J jnl
Mapping proteins in the presence of paralogs using units of coevolution.
BMC Bioinform.
Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth, Gunnar W. Klau
2013 J jnl
Next Generation Cluster Editing.
CoRR
Thomas Bellitto, Tobias Marschall, Alexander Schönhuth, Gunnar W. Klau
2013 — conf
Reconstructing Consensus Bayesian Network Structures with Application to Learning Molecular Interaction Networks.
GCB
Holger Fröhlich, Gunnar W. Klau
2013 C conf
The Generalized Robinson-Foulds Metric.
WABI
Sebastian Böcker, Stefan Canzar, Gunnar W. Klau
2013 — ch.
The Open Graph Drawing Framework (OGDF).
Handbook of Graph Drawing and Visualization
Markus Chimani, Carsten Gutwenger, Michael Jünger, Gunnar W. Klau, Karsten Klein, Petra Mutzel
2013 J jnl
The generalized Robinson-Foulds metric.
CoRR
Sebastian Böcker, Stefan Canzar, Gunnar W. Klau
2013 J jnl
eXamine: a Cytoscape app for exploring annotated modules in networks.
CoRR
Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine J. Smit, Michel A. Westenberg, Gunnar W. Klau
2012 J jnl
Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem.
IEEE ACM Trans. Comput. Biol. Bioinform.
Sandro Andreotti, Gunnar W. Klau, Knut Reinert
2012 J jnl
CLEVER: clique-enumerating variant finder.
Bioinform.
Tobias Marschall, Ivan G. Costa, Stefan Canzar, Markus Bauer, Gunnar W. Klau, Alexander Schliep, Alexander Schönhuth
2012 J jnl
CSA: comprehensive comparison of pairwise protein structure alignments.
Nucleic Acids Res.
Inken Wohlers, Noël Malod-Dognin, Rumen Andonov, Gunnar W. Klau
2012 B conf
Charge Group Partitioning in Biomolecular Simulation.
RECOMB
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
2012 J jnl
Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum.
BMC Syst. Biol.
Daniela Beisser, Markus A. Grohme, Joachim Kopka, Marcus Frohme, Ralph O. Schill, Steffen Hengherr, Thomas Dandekar, Gunnar W. Klau, Marcus T. Dittrich, Tobias Müller
2012 J jnl
Robustness and accuracy of functional modules in integrated network analysis.
Bioinform.
Daniela Beisser, Stefan Brunkhorst, Thomas Dandekar, Gunnar W. Klau, Marcus T. Dittrich, Tobias Müller
2011 J jnl
A critical evaluation of network and pathway based classifiers for outcome prediction in breast cancer
CoRR
Christine Staiger, Sidney Cadot, R. Kooter, Marcus T. Dittrich, Tobias Müller, Gunnar W. Klau, Lodewyk F. A. Wessels
2011 J jnl
Algorithm engineering for optimal alignment of protein structure distance matrices.
Optim. Lett.
Inken Wohlers, Rumen Andonov, Gunnar W. Klau
2011 J jnl
An Exact Algorithm for Side-Chain Placement in Protein Design
CoRR
Stefan Canzar, Nora C. Toussaint, Gunnar W. Klau
2011 J jnl
An exact algorithm for side-chain placement in protein design.
Optim. Lett.
Stefan Canzar, Nora C. Toussaint, Gunnar W. Klau
2011 J jnl
Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem
CoRR
Sandro Andreotti, Gunnar W. Klau, Knut Reinert
2011 J jnl
Exact Algorithms for Cluster Editing: Evaluation and Experiments.
Algorithmica
Sebastian Böcker, Sebastian Briesemeister, Gunnar W. Klau
2011 J jnl
Lagrangian Relaxation Applied to Sparse Global Network Alignment
CoRR
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
2011 — conf
Lagrangian Relaxation Applied to Sparse Global Network Alignment.
PRIB
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
2011 — conf
On Tree-Constrained Matchings and Generalizations.
ICALP (1)
Stefan Canzar, Khaled M. Elbassioni, Gunnar W. Klau, Julián Mestre
2011 C conf
Sparsifying Distance Matrices for Protein-Protein Structure Alignments.
CTW
Antonio Mucherino, Inken Wohlers, Gunnar W. Klau, Rumen Andonov
2010 J jnl
BioNet: an R-Package for the functional analysis of biological networks.
Bioinform.
Daniela Beisser, Gunnar W. Klau, Thomas Dandekar, Tobias Müller, Marcus T. Dittrich
2010 J jnl
Human-guided search.
J. Heuristics
Gunnar W. Klau, Neal Lesh, Joe Marks, Michael Mitzenmacher
2010 J jnl
Introduction to the Special Theme: Computational Biology.
ERCIM News
Gunnar W. Klau, Jacques Nicolas
2010 J jnl
Towards optimal alignment of protein structure distance matrices.
Bioinform.
Inken Wohlers, Francisco S. Domingues, Gunnar W. Klau
2009 J jnl
A new graph-based method for pairwise global network alignment.
BMC Bioinform.
Gunnar W. Klau
2009 — conf
Aligning Protein Structures Using Distance Matrices and Combinatorial Optimization.
GCB
Inken Wohlers, Lars Petzold, Francisco S. Domingues, Gunnar W. Klau
2009 J jnl
Fighting Lymph Cancer with Mathematics.
ERCIM News
Annette Kik, Gunnar W. Klau
2009 — conf
Integer Linear Programming in Computational Biology.
Efficient Algorithms
Ernst Althaus, Gunnar W. Klau, Oliver Kohlbacher, Hans-Peter Lenhof, Knut Reinert
2009 J jnl
On optimal comparability editing with applications to molecular diagnostics.
BMC Bioinform.
Sebastian Böcker, Sebastian Briesemeister, Gunnar W. Klau
2009 J jnl
PAUL: protein structural alignment using integer linear programming and Lagrangian relaxation.
BMC Bioinform.
Inken Wohlers, Lars Petzold, Francisco S. Domingues, Gunnar W. Klau
2008 J jnl
A branch-and-cut approach to the crossing number problem.
Discret. Optim.
Christoph Buchheim, Markus Chimani, Dietmar Ebner, Carsten Gutwenger, Michael Jünger, Gunnar W. Klau, Petra Mutzel, René Weiskircher
2008 J jnl
An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment.
Algorithmic Oper. Res.
Markus Bauer, Gunnar W. Klau, Knut Reinert
2008 — conf
Exact Algorithms for Cluster Editing: Evaluation and Experiments.
WEA
Sebastian Böcker, Sebastian Briesemeister, Gunnar W. Klau
2008 A conf
Identifying functional modules in protein-protein interaction networks: an integrated exact approach.
ISMB
Marcus T. Dittrich, Gunnar W. Klau, Andreas Rosenwald, Thomas Dandekar, Tobias Müller
2007 — conf
A General Paradigm for Fast, Adaptive Clustering of Biological Sequences.
German Conference on Bioinformatics
Knut Reinert, Markus Bauer, Andreas Döring, Gunnar W. Klau, Aaron L. Halpern
2007 J jnl
Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.
BMC Bioinform.
Markus Bauer, Gunnar W. Klau, Knut Reinert
2007 J jnl
Integer linear programming approaches for non-unique probe selection.
Discret. Appl. Math.
Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert
2006 — conf
Accelerated microRNA-Precursor Detection Using the Smith-Waterman Algorithm on FPGAs.
GCCB
Patrick May, Gunnar W. Klau, Markus Bauer, Thomas Steinke
2006 J jnl
An Algorithmic Framework for the Exact Solution of the Prize-Collecting Steiner Tree Problem.
Math. Program.
Ivana Ljubic, René Weiskircher, Ulrich Pferschy, Gunnar W. Klau, Petra Mutzel, Matteo Fischetti
2006 A conf
Graph-Drawing Contest Report.
GD
Christian A. Duncan, Gunnar W. Klau, Stephen G. Kobourov, Georg Sander
2006 C conf
Integer Linear Programs for Discovering Approximate Gene Clusters.
WABI
Sven Rahmann, Gunnar W. Klau
2005 A conf
Exact Crossing Minimization.
GD
Christoph Buchheim, Dietmar Ebner, Michael Jünger, Gunnar W. Klau, Petra Mutzel, René Weiskircher
2005 — conf
Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Optimization.
CompLife
Markus Bauer, Gunnar W. Klau, Knut Reinert
2005 C conf
Multiple Structural RNA Alignment with Lagrangian Relaxation.
WABI
Markus Bauer, Gunnar W. Klau, Knut Reinert
2005 B conf
Non-planar Orthogonal Drawings with Fixed Topology.
SOFSEM
Markus Chimani, Gunnar W. Klau, René Weiskircher
2005 — conf
Solving the Prize-Collecting Steiner Tree Problem to Optimality.
ALENEX/ANALCO
Ivana Ljubic, René Weiskircher, Ulrich Pferschy, Gunnar W. Klau, Petra Mutzel, Matteo Fischetti
2004 — ch.
AGD - A Library of Algorithms for Graph Drawing.
Graph Drawing Software
Michael Jünger, Gunnar W. Klau, Petra Mutzel, René Weiskircher
2004 — conf
Combining a Memetic Algorithm with Integer Programming to Solve the Prize-Collecting Steiner Tree Problem.
GECCO (1)
Gunnar W. Klau, Ivana Ljubic, Andreas Moser, Petra Mutzel, Philipp Neuner, Ulrich Pferschy, Günther R. Raidl, René Weiskircher
2004 A conf
Label Number Maximization in the Slider Model.
GD
Dietmar Ebner, Gunnar W. Klau, René Weiskircher
2004 — conf
Optimal robust non-unique probe selection using Integer Linear Programming.
ISMB/ECCB (Supplement of Bioinformatics)
Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, Knut Reinert
2004 — conf
Robustness and Resilience.
Network Analysis
Gunnar W. Klau, René Weiskircher
2004 B conf
Structural Alignment of Two RNA Sequences with Lagrangian Relaxation.
ISAAC
Markus Bauer, Gunnar W. Klau
2003 J jnl
Optimal labeling of point features in rectangular labeling models.
Math. Program.
Gunnar W. Klau, Petra Mutzel
2003 A conf
The Fractional Prize-Collecting Steiner Tree Problem on Trees: Extended Abstract.
ESA
Gunnar W. Klau, Ivana Ljubic, Petra Mutzel, Ulrich Pferschy, René Weiskircher
2002 — conf
A Combinatorial Approach to Orthogonal Placement Problems.
OR
Gunnar W. Klau
2002 — —
A combinatorial approach to orthogonal placement problems.
Gunnar W. Klau
2002 — conf
Human-Guided Tabu Search.
AAAI/IAAI
Gunnar W. Klau, Neal Lesh, Joe Marks, Michael Mitzenmacher
2002 A* conf
Investigating human-computer optimization.
CHI
Stacey D. Scott, Neal Lesh, Gunnar W. Klau
2002 B conf
The HuGS platform: a toolkit for interactive optimization.
AVI
Gunnar W. Klau, Neal Lesh, Joe Marks, Michael Mitzenmacher, Guy T. Schafer
2001 A conf
AGD: A Library of Algorithms for Graph Drawing.
GD
Carsten Gutwenger, Michael Jünger, Gunnar W. Klau, Sebastian Leipert, Petra Mutzel, René Weiskircher
2001 — conf
Graph Drawing Algorithm Engineering with AGD.
Software Visualization
Carsten Gutwenger, Michael Jünger, Gunnar W. Klau, Sebastian Leipert, Petra Mutzel
2000 A conf
An Experimental Comparison of Orthogonal Compaction Algorithms (Extended Abstract).
GD
Gunnar W. Klau, Karsten Klein, Petra Mutzel
2000 Misc conf
Optimal Labelling of Point Features in the Slider Model.
COCOON
Gunnar W. Klau, Petra Mutzel
1999 A conf
Combining Graph Labeling and Compaction.
GD
Gunnar W. Klau, Petra Mutzel
1999 B conf
Optimal Compaction of Orthogonal Grid Drawings.
IPCO
Gunnar W. Klau, Petra Mutzel
1999 — conf
Orthogonal Graph Drawing.
Drawing Graphs
Markus Eiglsperger, Sándor P. Fekete, Gunnar W. Klau
1998 A conf
A Library of Algorithms for Graph Drawing.
GD
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