Gunnar W. Klau

According to our database1, Gunnar W. Klau authored at least 85 papers between 1998 and 2019.

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Bibliography

2019
Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach.
Algorithms for Molecular Biology, 2019

2018
Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules.
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.
Proceedings of the Research in Computational Molecular Biology, 2017

A Guided Tour to Computational Haplotyping.
Proceedings of the Unveiling Dynamics and Complexity, 2017

2016
On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes.
Journal of Computational Biology, 2016

Networks to the Rescue - From Big "Omics" Data to Targeted Hypotheses.
ERCIM News, 2016

HapCol: accurate and memory-efficient haplotype assembly from long reads.
Bioinformatics, 2016

metaModules identifies key functional subnetworks in microbiome-related disease.
Bioinformatics, 2016

2015
Next generation cluster editing.
PeerJ PrePrints, 2015

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads.
Journal of Computational Biology, 2015

Genome sequence analysis with MonetDB - A case study on Ebola virus diversity.
Datenbank-Spektrum, 2015

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.
Bioinformatics, 2015

Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment.
Algorithms, 2015

Automatic Classification of Protein Structure Using the Maximum Contact Map Overlap Metric.
Algorithms, 2015

CIDANE: Comprehensive Isoform Discovery and Abundance Estimation.
Proceedings of the Research in Computational Molecular Biology, 2015

On the Fixed Parameter Tractability and Approximability of the Minimum Error Correction Problem.
Proceedings of the Combinatorial Pattern Matching - 26th Annual Symposium, 2015

Genome sequence analysis with monetdb: a case study on ebola virus diversity.
Proceedings of the Datenbanksysteme für Business, Technologie und Web (BTW 2015), 2015

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

A web server for protein-protein interaction network querying.
BMC Systems Biology, 2014

eXamine: Exploring annotated modules in networks.
BMC Bioinformatics, 2014

WhatsHap: Haplotype Assembly for Future-Generation Sequencing Reads.
Proceedings of the Research in Computational Molecular Biology, 2014

Exact Protein Structure Classification Using the Maximum Contact Map Overlap Metric.
Proceedings of the Algorithms for Computational Biology - First International Conference, 2014

2013
The Open Graph Drawing Framework (OGDF).
Proceedings of the Handbook on Graph Drawing and Visualization., 2013

DALIX: Optimal DALI Protein Structure Alignment.
IEEE/ACM Trans. Comput. Biology Bioinform., 2013

Charge Group Partitioning in Biomolecular Simulation.
Journal of Computational Biology, 2013

Mapping proteins in the presence of paralogs using units of coevolution.
BMC Bioinformatics, 2013

The Generalized Robinson-Foulds Metric.
Proceedings of the Algorithms in Bioinformatics - 13th International Workshop, 2013

Reconstructing Consensus Bayesian Network Structures with Application to Learning Molecular Interaction Networks.
Proceedings of the German Conference on Bioinformatics 2013, 2013

2012
Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem.
IEEE/ACM Trans. Comput. Biology Bioinform., 2012

CSA: comprehensive comparison of pairwise protein structure alignments.
Nucleic Acids Research, 2012

Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum.
BMC Systems Biology, 2012

CLEVER: clique-enumerating variant finder.
Bioinformatics, 2012

Robustness and accuracy of functional modules in integrated network analysis.
Bioinformatics, 2012

Charge Group Partitioning in Biomolecular Simulation.
Proceedings of the Research in Computational Molecular Biology, 2012

2011
Algorithm engineering for optimal alignment of protein structure distance matrices.
Optimization Letters, 2011

An exact algorithm for side-chain placement in protein design.
Optimization Letters, 2011

Lagrangian Relaxation Applied to Sparse Global Network Alignment.
Proceedings of the Pattern Recognition in Bioinformatics, 2011

On Tree-Constrained Matchings and Generalizations.
Proceedings of the Automata, Languages and Programming - 38th International Colloquium, 2011

Sparsifying Distance Matrices for Protein-Protein Structure Alignments.
Proceedings of the 10th Cologne-Twente Workshop on graphs and combinatorial optimization. Extended Abstracts, 2011

2010
Human-guided search.
J. Heuristics, 2010

Introduction to the Special Theme: Computational Biology.
ERCIM News, 2010

Towards optimal alignment of protein structure distance matrices.
Bioinformatics, 2010

BioNet: an R-Package for the functional analysis of biological networks.
Bioinformatics, 2010

2009
Fighting Lymph Cancer with Mathematics.
ERCIM News, 2009

PAUL: protein structural alignment using integer linear programming and Lagrangian relaxation.
BMC Bioinformatics, 2009

A new graph-based method for pairwise global network alignment.
BMC Bioinformatics, 2009

On optimal comparability editing with applications to molecular diagnostics.
BMC Bioinformatics, 2009

Aligning Protein Structures Using Distance Matrices and Combinatorial Optimization.
Proceedings of the German Conference on Bioinformatics 2009, 2009

Integer Linear Programming in Computational Biology.
Proceedings of the Efficient Algorithms, 2009

2008
A branch-and-cut approach to the crossing number problem.
Discrete Optimization, 2008

An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment.
Algorithmic Operations Research, 2008

Exact Algorithms for Cluster Editing: Evaluation and Experiments.
Proceedings of the Experimental Algorithms, 7th International Workshop, 2008

Identifying functional modules in protein-protein interaction networks: an integrated exact approach.
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.
Discrete Applied Mathematics, 2007

Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.
BMC Bioinformatics, 2007

A General Paradigm for Fast, Adaptive Clustering of Biological Sequences.
Proceedings of the German Conference on Bioinformatics, 2007

2006
An Algorithmic Framework for the Exact Solution of the Prize-Collecting Steiner Tree Problem.
Math. Program., 2006

Integer Linear Programs for Discovering Approximate Gene Clusters.
Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

Graph-Drawing Contest Report.
Proceedings of the Graph Drawing, 14th International Symposium, GD 2006, Karlsruhe, 2006

Accelerated microRNA-Precursor Detection Using the Smith-Waterman Algorithm on FPGAs.
Proceedings of the Distributed, 2006

2005
Multiple Structural RNA Alignment with Lagrangian Relaxation.
Proceedings of the Algorithms in Bioinformatics, 5th International Workshop, 2005

Non-planar Orthogonal Drawings with Fixed Topology.
Proceedings of the SOFSEM 2005: Theory and Practice of Computer Science, 2005

Exact Crossing Minimization.
Proceedings of the Graph Drawing, 13th International Symposium, 2005

Fast and Accurate Structural RNA Alignment by Progressive Lagrangian Optimization.
Proceedings of the Computational Life Sciences, First International Symposium, 2005

Solving the Prize-Collecting Steiner Tree Problem to Optimality.
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.
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.
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.
Proceedings of the Genetic and Evolutionary Computation, 2004

Label Number Maximization in the Slider Model.
Proceedings of the Graph Drawing, 12th International Symposium, 2004

Robustness and Resilience.
Proceedings of the Network Analysis: Methodological Foundations [outcome of a Dagstuhl seminar, 2004

AGD - A Library of Algorithms for Graph Drawing.
Graph Drawing Software, 2004

2003
Optimal labeling of point features in rectangular labeling models.
Math. Program., 2003

The Fractional Prize-Collecting Steiner Tree Problem on Trees: Extended Abstract.
Proceedings of the Algorithms, 2003

2002
A Combinatorial Approach to Orthogonal Placement Problems.
Proceedings of the Operations Research Proceedings 2002, 2002

Investigating human-computer optimization.
Proceedings of the CHI 2002 Conference on Human Factors in Computing Systems: Changing our World, 2002

The HuGS platform: a toolkit for interactive optimization.
Proceedings of the Working Conference on Advanced Visual Interfaces, 2002

Human-Guided Tabu Search.
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.
Graph Drawing, 2001

Graph Drawing Algorithm Engineering with AGD.
Proceedings of the Software Visualization, 2001

2000
An Experimental Comparison of Orthogonal Compaction Algorithms (Extended Abstract).
Proceedings of the Graph Drawing, 8th International Symposium, 2000

Optimal Labelling of Point Features in the Slider Model.
Proceedings of the Computing and Combinatorics, 6th Annual International Conference, 2000

1999
Optimal Compaction of Orthogonal Grid Drawings.
Proceedings of the Integer Programming and Combinatorial Optimization, 1999

Combining Graph Labeling and Compaction.
Proceedings of the Graph Drawing, 7th International Symposium, 1999

Orthogonal Graph Drawing.
Proceedings of the Drawing Graphs, 1999

1998
A Library of Algorithms for Graph Drawing.
Proceedings of the Graph Drawing, 6th International Symposium, 1998


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