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Genome sequence analysis with MonetDB

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

Journal:

Datenbank-Spektrum

Year:

2015

Language:

english

File:

PDF, 794 KB

english, 2015

[Lecture Notes in Computer Science] Computational Intelligence Methods for Bioinformatics and Biostatistics Volume 10834 (14th International Meeting, CIBB 2017, Cagliari, Italy, September 7-9, 2017, Revised Selected Papers) ||

Bartoletti, Massimo, Barla, Annalisa, Bracciali, Andrea, Klau, Gunnar W., Peterson, Leif, Policriti, Alberto, Tagliaferri, Roberto

Year:

2019

Language:

english

File:

PDF, 20.27 MB

english, 2019

Integer linear programming approaches for non-unique probe selection

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

Journal:

Discrete Applied Mathematics

Year:

2007

Language:

english

File:

PDF, 246 KB

english, 2007

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

Journal:

Discrete Optimization

Year:

2008

Language:

english

File:

PDF, 1.65 MB

english, 2008

Exact Algorithms for Cluster Editing: Evaluation and Experiments

Sebastian Böcker, Sebastian Briesemeister, Gunnar W. Klau

Journal:

Algorithmica

Year:

2011

Language:

english

File:

PDF, 658 KB

english, 2011

Optimal labeling of point features in rectangular labeling models

Gunnar W. Klau, Petra Mutzel

Journal:

Mathematical Programming

Year:

2003

Language:

english

File:

PDF, 1.60 MB

english, 2003

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

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

Journal:

Mathematical Programming

Year:

2006

Language:

english

File:

PDF, 369 KB

english, 2006

Human-guided search

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

Journal:

Journal of Heuristics

Year:

2010

Language:

english

File:

PDF, 2.12 MB

english, 2010

Algorithm engineering for optimal alignment of protein structure distance matrices

Inken Wohlers, Rumen Andonov, Gunnar W. Klau

Journal:

Optimization Letters

Year:

2011

Language:

english

File:

PDF, 303 KB

english, 2011

An exact algorithm for side-chain placement in protein design

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

Journal:

Optimization Letters

Year:

2011

Language:

english

File:

PDF, 205 KB

english, 2011

A new graph-based method for pairwise global network alignment

Gunnar W Klau

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 998 KB

english, 2009

On optimal comparability editing with applications to molecular diagnostics

Sebastian Böcker, Sebastian Briesemeister, Gunnar W Klau

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 427 KB

english, 2009

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

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

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 182 KB

english, 2009

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

Markus Bauer, Gunnar W Klau, Knut Reinert

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 1.17 MB

english, 2007

Integrated pathway modules using time-course metabolic profiles and EST data fromMilnesium tardigradum

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

Journal:

BMC Systems Biology

Year:

2012

Language:

english

File:

PDF, 960 KB

english, 2012

A Realistic Model Under Which the Genetic Code is Optimal

Buhrman, Harry, Gulik, Peter T. S., Klau, Gunnar W., Schaffner, Christian, Speijer, Dave, Stougie, Leen

Journal:

Journal of Molecular Evolution

Year:

2013

Language:

english

File:

PDF, 470 KB

english, 2013

On Tree-Constrained Matchings and Generalizations

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

Journal:

Algorithmica

Year:

2015

Language:

english

File:

PDF, 763 KB

english, 2015

Charge Group Partitioning in Biomolecular Simulation

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

Journal:

Journal of Computational Biology

Year:

2013

Language:

english

File:

PDF, 544 KB

english, 2013

Mapping proteins in the presence of paralogs using units of coevolution

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

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 551 KB

english, 2013

NatalieQ: A web server for protein-protein interaction network querying

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

Journal:

BMC Systems Biology

Year:

2014

Language:

english

File:

PDF, 398 KB

english, 2014

DALIX: Optimal DALI Protein Structure Alignment

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

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 500 KB

english, 2013

[ACM Press the SIGCHI conference - Minneapolis, Minnesota, USA (2002.04.20-2002.04.25)] Proceedings of the SIGCHI conference on Human factors in computing systems Changing our world, changing ourselves - CHI '02 - Investigating human-computer optimization

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

Year:

2002

Language:

english

File:

PDF, 1.50 MB

english, 2002

W hats H ap : Weighted Haplotype Assembly for Future-Generation Sequencing Reads

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

Journal:

Journal of Computational Biology

Year:

2015

Language:

english

File:

PDF, 280 KB

english, 2015

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

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

Journal:

Bioinformatics

Year:

2015

Language:

english

File:

PDF, 253 KB

english, 2015

metaModules identifies key functional subnetworks in microbiome-related disease

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

Journal:

Bioinformatics

Year:

2015

Language:

english

File:

PDF, 1013 KB

english, 2015

CIDANE: comprehensive isoform discovery and abundance estimation

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

Journal:

Genome Biology

Year:

2016

Language:

english

File:

PDF, 1.74 MB

english, 2016

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

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

Journal:

Journal of Computational Biology

Year:

2016

Language:

english

File:

PDF, 579 KB

english, 2016

Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy

Knijnenburg, Theo A., Klau, Gunnar W., Iorio, Francesco, Garnett, Mathew J., McDermott, Ultan, Shmulevich, Ilya, Wessels, Lodewyk F. A.

Journal:

Scientific Reports

Year:

2016

Language:

english

File:

PDF, 678 KB

english, 2016

Probing the genome-scale metabolic landscape of Bordetella pertussis , the causative agent of whooping cough

Branco dos Santos, Filipe, Olivier, Brett G., Boele, Joost, Smessaert, Vincent, De Rop, Philippe, Krumpochova, Petra, Klau, Gunnar W., Giera, Martin, Dehottay, Philippe, Teusink, Bas, Goffin, Philippe

Journal:

Applied and Environmental Microbiology

Year:

2017

Language:

english

File:

PDF, 3.78 MB

english, 2017

Phylogenetic Copy-Number Factorization of Multiple Tumor Samples

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

Journal:

Journal of Computational Biology

Year:

2018

Language:

english

File:

PDF, 2.03 MB

english, 2018

A Critical Evaluation of Network and Pathway-Based Classifiers for Outcome Prediction in Breast Cancer

Staiger, Christine, Cadot, Sidney, Kooter, Raul, Dittrich, Marcus, Müller, Tobias, Klau, Gunnar W., Wessels, Lodewyk F. A., Dopazo, Joaquín

Journal:

PLoS ONE

Year:

2012

Language:

english

File:

PDF, 1.22 MB

english, 2012

Ancient Dispersal of the Human Fungal Pathogen Cryptococcus gattii from the Amazon Rainforest

Hagen, Ferry, Ceresini, Paulo C., Polacheck, Itzhack, Ma, Hansong, Nieuwerburgh, Filip van, Gabaldón, Toni, Kagan, Sarah, Pursall, E. Rhiannon, Hoogveld, Hans L., van Iersel, Leo J. J., Klau, Gunnar W

Journal:

PLoS ONE

Year:

2013

Language:

english

File:

PDF, 1.33 MB

english, 2013

Bioinformatics Methods and Biological Interpretation for Next-Generation Sequencing Data

Wang, Guohua, Liu, Yunlong, Zhu, Dongxiao, Klau, Gunnar W., Feng, Weixing

Journal:

BioMed Research International

Year:

2015

Language:

english

File:

PDF, 1.06 MB

english, 2015

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

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

Journal:

Algorithms

Year:

2015

Language:

english

File:

PDF, 328 KB

english, 2015

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

Andonov, Rumen, Djidjev, Hristo, Klau, Gunnar, Boudic-Jamin, Mathilde, Wohlers, Inken

Journal:

Algorithms

Year:

2015

Language:

english

File:

PDF, 604 KB

english, 2015

Current composite-feature classification methods do not outperform simple single-genes classifiers in breast cancer prognosis

Staiger, Christine, Cadot, Sidney, Györffy, Balázs, Wessels, Lodewyk F. A., Klau, Gunnar W.

Journal:

Frontiers in Genetics

Year:

2013

Language:

english

File:

PDF, 2.57 MB

english, 2013

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

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

Journal:

Algorithms for Molecular Biology

Year:

2019

Language:

english

File:

PDF, 6.59 MB

english, 2019

Haplotype threading: accurate polyploid phasing from long reads

Schrinner, Sven D., Mari, Rebecca Serra, Ebler, Jana, Rautiainen, Mikko, Seillier, Lancelot, Reimer, Julia J., Usadel, BjÃ¶rn, Marschall, Tobias, Klau, Gunnar W.

Journal:

Genome Biology

Year:

2020

File:

PDF, 1.94 MB

2020