Sort by
Items per page

Send to

Choose Destination

Search results

Items: 35


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

Engler MS, Caron B, Veen L, Geerke DP, Mark AE, Klau GW.

Algorithms Mol Biol. 2019 Feb 5;14:1. doi: 10.1186/s13015-019-0138-7. eCollection 2019.


eXamine: Visualizing annotated networks in Cytoscape.

Spohr P, Dinkla K, Klau GW, El-Kebir M.

Version 2. F1000Res. 2018 Apr 30 [revised 2018 Jan 1];7:519. doi: 10.12688/f1000research.14612.2. eCollection 2018.


Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.

Zaccaria S, El-Kebir M, Klau GW, Raphael BJ.

J Comput Biol. 2018 Jul;25(7):689-708. doi: 10.1089/cmb.2017.0253. Epub 2018 Apr 16.


Probing the Genome-Scale Metabolic Landscape of Bordetella pertussis, the Causative Agent of Whooping Cough.

Branco Dos Santos F, Olivier BG, Boele J, Smessaert V, De Rop P, Krumpochova P, Klau GW, Giera M, Dehottay P, Teusink B, Goffin P.

Appl Environ Microbiol. 2017 Oct 17;83(21). pii: e01528-17. doi: 10.1128/AEM.01528-17. Print 2017 Nov 1.


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

Knijnenburg TA, Klau GW, Iorio F, Garnett MJ, McDermott U, Shmulevich I, Wessels LF.

Sci Rep. 2016 Nov 23;6:36812. doi: 10.1038/srep36812.


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

Bonizzoni P, Dondi R, Klau GW, Pirola Y, Pisanti N, Zaccaria S.

J Comput Biol. 2016 Sep;23(9):718-36. doi: 10.1089/cmb.2015.0220. Epub 2016 Jun 9.


CIDANE: comprehensive isoform discovery and abundance estimation.

Canzar S, Andreotti S, Weese D, Reinert K, Klau GW.

Genome Biol. 2016 Jan 30;17:16. doi: 10.1186/s13059-015-0865-0.


Bioinformatics Methods and Biological Interpretation for Next-Generation Sequencing Data.

Wang G, Liu Y, Zhu D, Klau GW, Feng W.

Biomed Res Int. 2015;2015:690873. doi: 10.1155/2015/690873. Epub 2015 Sep 7. No abstract available.


metaModules identifies key functional subnetworks in microbiome-related disease.

May A, Brandt BW, El-Kebir M, Klau GW, Zaura E, Crielaard W, Heringa J, Abeln S.

Bioinformatics. 2016 Jun 1;32(11):1678-85. doi: 10.1093/bioinformatics/btv526. Epub 2015 Sep 5.


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

Pirola Y, Zaccaria S, Dondi R, Klau GW, Pisanti N, Bonizzoni P.

Bioinformatics. 2016 Jun 1;32(11):1610-7. doi: 10.1093/bioinformatics/btv495. Epub 2015 Aug 26.


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

El-Kebir M, Soueidan H, Hume T, Beisser D, Dittrich M, Müller T, Blin G, Heringa J, Nikolski M, Wessels LF, Klau GW.

Bioinformatics. 2015 Oct 1;31(19):3147-55. doi: 10.1093/bioinformatics/btv316. Epub 2015 May 27.


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

Patterson M, Marschall T, Pisanti N, van Iersel L, Stougie L, Klau GW, Schönhuth A.

J Comput Biol. 2015 Jun;22(6):498-509. doi: 10.1089/cmb.2014.0157. Epub 2015 Feb 6.


eXamine: exploring annotated modules in networks.

Dinkla K, El-Kebir M, Bucur CI, Siderius M, Smit MJ, Westenberg MA, Klau GW.

BMC Bioinformatics. 2014 Jul 10;15:201. doi: 10.1186/1471-2105-15-201.


Functional module search in protein networks based on semantic similarity improves the analysis of proteomics data.

Boyanova D, Nilla S, Klau GW, Dandekar T, Müller T, Dittrich M.

Mol Cell Proteomics. 2014 Jul;13(7):1877-89. doi: 10.1074/mcp.M113.032839. Epub 2014 May 7.


NatalieQ: a web server for protein-protein interaction network querying.

El-Kebir M, Brandt BW, Heringa J, Klau GW.

BMC Syst Biol. 2014 Apr 1;8:40. doi: 10.1186/1752-0509-8-40.


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

El-Kebir M, Marschall T, Wohlers I, Patterson M, Heringa J, Schönhuth A, Klau GW.

BMC Bioinformatics. 2013;14 Suppl 15:S18. doi: 10.1186/1471-2105-14-S15-S18. Epub 2013 Oct 15.


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

Staiger C, Cadot S, Györffy B, Wessels LF, Klau GW.

Front Genet. 2013 Dec 23;4:289. doi: 10.3389/fgene.2013.00289. eCollection 2013.


Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest.

Hagen F, Ceresini PC, Polacheck I, Ma H, van Nieuwerburgh F, Gabaldón T, Kagan S, Pursall ER, Hoogveld HL, van Iersel LJ, Klau GW, Kelk SM, Stougie L, Bartlett KH, Voelz K, Pryszcz LP, Castañeda E, Lazera M, Meyer W, Deforce D, Meis JF, May RC, Klaassen CH, Boekhout T.

PLoS One. 2013 Aug 7;8(8):e71148. doi: 10.1371/journal.pone.0071148. Print 2013.


A realistic model under which the genetic code is optimal.

Buhrman H, van der Gulik PT, Klau GW, Schaffner C, Speijer D, Stougie L.

J Mol Evol. 2013 Oct;77(4):170-84. doi: 10.1007/s00239-013-9571-2. Epub 2013 Jul 23.


DALIX: optimal DALI protein structure alignment.

Wohlers I, Andonov R, Klau GW.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jan-Feb;10(1):26-36. doi: 10.1109/TCBB.2012.143.


Charge group partitioning in biomolecular simulation.

Canzar S, El-Kebir M, Pool R, Elbassioni K, Mark AE, Geerke DP, Stougie L, Klau GW.

J Comput Biol. 2013 Mar;20(3):188-98. doi: 10.1089/cmb.2012.0239.


CLEVER: clique-enumerating variant finder.

Marschall T, Costa IG, Canzar S, Bauer M, Klau GW, Schliep A, Schönhuth A.

Bioinformatics. 2012 Nov 15;28(22):2875-82. doi: 10.1093/bioinformatics/bts566. Epub 2012 Oct 11.


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

Beisser D, Grohme MA, Kopka J, Frohme M, Schill RO, Hengherr S, Dandekar T, Klau GW, Dittrich M, Müller T.

BMC Syst Biol. 2012 Jun 19;6:72. doi: 10.1186/1752-0509-6-72.


Robustness and accuracy of functional modules in integrated network analysis.

Beisser D, Brunkhorst S, Dandekar T, Klau GW, Dittrich MT, Müller T.

Bioinformatics. 2012 Jul 15;28(14):1887-94. doi: 10.1093/bioinformatics/bts265. Epub 2012 May 11.


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

Staiger C, Cadot S, Kooter R, Dittrich M, Müller T, Klau GW, Wessels LF.

PLoS One. 2012;7(4):e34796. doi: 10.1371/journal.pone.0034796. Epub 2012 Apr 27.


CSA: comprehensive comparison of pairwise protein structure alignments.

Wohlers I, Malod-Dognin N, Andonov R, Klau GW.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W303-9. doi: 10.1093/nar/gks362. Epub 2012 May 2.


An integer linear programming approach for finding deregulated subgraphs in regulatory networks.

Backes C, Rurainski A, Klau GW, Müller O, Stöckel D, Gerasch A, Küntzer J, Maisel D, Ludwig N, Hein M, Keller A, Burtscher H, Kaufmann M, Meese E, Lenhof HP.

Nucleic Acids Res. 2012 Mar;40(6):e43. doi: 10.1093/nar/gkr1227. Epub 2011 Dec 30.


Antilope--a Lagrangian relaxation approach to the de novo peptide sequencing problem.

Andreotti S, Klau GW, Reinert K.

IEEE/ACM Trans Comput Biol Bioinform. 2012;9(2):385-94. doi: 10.1109/TCBB.2011.59. Epub 2011 Mar 22.


Towards optimal alignment of protein structure distance matrices.

Wohlers I, Domingues FS, Klau GW.

Bioinformatics. 2010 Sep 15;26(18):2273-80. doi: 10.1093/bioinformatics/btq420. Epub 2010 Jul 17.


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

Beisser D, Klau GW, Dandekar T, Müller T, Dittrich MT.

Bioinformatics. 2010 Apr 15;26(8):1129-30. doi: 10.1093/bioinformatics/btq089. Epub 2010 Feb 25.


On optimal comparability editing with applications to molecular diagnostics.

Böcker S, Briesemeister S, Klau GW.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S61. doi: 10.1186/1471-2105-10-S1-S61.


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

Klau GW.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S59. doi: 10.1186/1471-2105-10-S1-S59.


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

Dittrich MT, Klau GW, Rosenwald A, Dandekar T, Müller T.

Bioinformatics. 2008 Jul 1;24(13):i223-31. doi: 10.1093/bioinformatics/btn161.


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

Klau GW, Rahmann S, Schliep A, Vingron M, Reinert K.

Bioinformatics. 2004 Aug 4;20 Suppl 1:i186-93.


Supplemental Content

Support Center