Next Generation Sequencing Competence Network

Next Generation Sequencing Competence Network

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Gunnar W. Klau

Prof. Dr.
Heinrich-Heine-University Duesseldorf
Computer Science, Algorithmic Bioinformatics
Universitätsstraße 1, 40225 Düsseldorf, Germany
Düsseldorf 40225
+49 211 8110427
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Bergkamp ND, van Senten JR, Brink HJ, Bebelman MP, van den Bor J, ?obanoglu TS, Dinkla K, K?ster J, Klau G, Siderius M, Smit MJ. A virally encoded GPCR drives glioblastoma through feed-forward activation of the SK1-S1P1 signaling axis. Sci Signal. 2023 08 15; 16(798):eade6737. PMID: 37582160.
      Citations:    Fields:    Translation:HumansCells
    2. Stroet M, Caron B, Engler MS, van der Woning J, Kauffmann A, van Dijk M, El-Kebir M, Visscher KM, Holownia J, Macfarlane C, Bennion BJ, Gelpi-Dominguez S, Lightstone FC, van der Storm T, Geerke DP, Mark AE, Klau GW. OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. J Comput Aided Mol Des. 2023 08; 37(8):357-371. PMID: 37310542; PMCID: PMC10315351.
      Citations:    Fields:    
    3. McGuinness KN, Klau GW, Morrison SM, Moore EK, Seipp J, Falkowski PG, Nanda V. Evaluating Mineral Lattices as Evolutionary Proxies for Metalloprotein Evolution. Orig Life Evol Biosph. 2022 Nov 16. PMID: 36383289.
      Citations: 1     Fields:    
    4. Finkers R, Arens P, Schrinner S, Serra Mari R, Usadel B, Marschall T, Klau GW. Genetic polyploid phasing from low-depth progeny samples. iScience. 2022 Jun 17; 25(6):104461. PMID: 35692633; PMCID: PMC9184567.
      Citations:    
    5. Park TY, Leiserson MDM, Raphael BJ, Klau GW. SuperDendrix algorithm integrates genetic dependencies and genomic alterations across pathways and cancer types. Cell Genom. 2022 Feb 09; 2(2). PMID: 35382456; PMCID: PMC8979493.
      Citations: 2     
    6. Goel M, Schrinner S, Wulfert M, Spohr P, Schneeberger K, Klau GW. Using the longest run subsequence problem within homology-based scaffolding. Algorithms Mol Biol. 2021 Jun 28; 16(1):11. PMID: 34183036; PMCID: PMC8240273.
      Citations:    
    7. Dieterich C, Hesse J, Owenier C, Lautwein T, Zalfen R, Weber JF, Ding Z, Alter C, Lang A, Grandoch M, Gerdes N, Fischer JW, Klau GW, K?hrer K, Schrader J. Single-cell transcriptomics defines heterogeneity of epicardial cells and fibroblasts within the infarcted murine heart. Elife. 2021 06 21; 10. PMID: 34152268; PMCID: PMC8216715.
      Citations: 26     Fields:    Translation:AnimalsCells
    8. Seillier L, Reimer JJ, Schrinner SD, Mari RS, Ebler J, Rautiainen M, Usadel B, Marschall T, Klau GW. Haplotype threading: accurate polyploid phasing from long reads. Genome Biol. 2020 09 21; 21(1):252. PMID: 32951599; PMCID: PMC7504856.
      Citations: 27     Fields:    Translation:Animals
    9. Papenberg M, Klau GW. Using anticlustering to partition data sets into equivalent parts. Psychol Methods. 2020 Jun 22. PMID: 32567870.
      Citations: 3     Fields:    
    10. Caron B, Veen L, Mark AE, Engler MS, Geerke DP, Klau GW. Automated partial atomic charge assignment for drug-like molecules: a fast knapsack approach. Algorithms Mol Biol. 2019; 14:1. PMID: 30839948; PMCID: PMC6364451.
      Citations: 4     
    11. Dinkla K, El-Kebir M, Spohr P, Klau GW. eXamine: Visualizing annotated networks in Cytoscape. F1000Res. 2018; 7:519. PMID: 29983924; PMCID: PMC6013758.
      Citations: 2     Fields:    
    12. Zaccaria S, El-Kebir M, Raphael BJ, Klau GW. Phylogenetic Copy-Number Factorization of Multiple Tumor Samples. J Comput Biol. 2018 07; 25(7):689-708. PMID: 29658782; PMCID: PMC6067108.
      Citations: 12     Fields:    Translation:Humans
    13. 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. Probing the Genome-Scale Metabolic Landscape of Bordetella pertussis, the Causative Agent of Whooping Cough. Appl Environ Microbiol. 2017 Nov 01; 83(21). PMID: 28842544; PMCID: PMC5648915.
      Citations: 13     Fields:    
    14. Knijnenburg TA, Klau GW, Iorio F, Garnett MJ, McDermott U, Shmulevich I, Wessels LF. Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy. Sci Rep. 2016 11 23; 6:36812. PMID: 27876821; PMCID: PMC5120272.
      Citations: 19     Fields:    Translation:HumansCells
    15. Bonizzoni P, Dondi R, Klau GW, Pirola Y, Pisanti N, Zaccaria S. On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes. J Comput Biol. 2016 Sep; 23(9):718-36. PMID: 27280382.
      Citations: 14     Fields:    Translation:Humans
    16. Canzar S, Klau GW, Andreotti S, Weese D, Reinert K. CIDANE: comprehensive isoform discovery and abundance estimation. Genome Biol. 2016 Jan 30; 17:16. PMID: 26831908; PMCID: PMC4734886.
      Citations: 15     Fields:    Translation:Cells
    17. Wang G, Liu Y, Zhu D, Klau GW, Feng W. Bioinformatics Methods and Biological Interpretation for Next-Generation Sequencing Data. Biomed Res Int. 2015; 2015:690873. PMID: 26436095; PMCID: PMC4576002.
      Citations: 5     Fields:    Translation:HumansAnimalsCells
    18. May A, Brandt BW, El-Kebir M, Klau GW, Zaura E, Crielaard W, Heringa J, Abeln S. metaModules identifies key functional subnetworks in microbiome-related disease. Bioinformatics. 2016 06 01; 32(11):1678-85. PMID: 26342232.
      Citations: 12     Fields:    Translation:Humans
    19. Pirola Y, Zaccaria S, Dondi R, Klau GW, Pisanti N, Bonizzoni P. HapCol: accurate and memory-efficient haplotype assembly from long reads. Bioinformatics. 2016 06 01; 32(11):1610-7. PMID: 26315913.
      Citations: 15     Fields:    
    20. El-Kebir M, Soueidan H, Hume T, Beisser D, Blin G, Heringa J, Nikolski M, Wessels LF, Klau GW, Dittrich M, M?ller T. xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. Bioinformatics. 2015 Oct 01; 31(19):3147-55. PMID: 26023104.
      Citations:    Fields:    Translation:HumansAnimalsCells
    21. Pisanti N, van Iersel L, Stougie L, Klau GW, Patterson M, Marschall T, Sch?nhuth A. WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads. J Comput Biol. 2015 Jun; 22(6):498-509. PMID: 25658651.
      Citations: 140     Fields:    Translation:Humans
    22. Dinkla K, El-Kebir M, Bucur CI, Siderius M, Smit MJ, Westenberg MA, Klau GW. eXamine: exploring annotated modules in networks. BMC Bioinformatics. 2014 Jul 10; 15:201. PMID: 25002203; PMCID: PMC4084410.
      Citations: 7     Fields:    
    23. Boyanova D, Nilla S, Klau GW, Dandekar T, M?ller T, Dittrich M. Functional module search in protein networks based on semantic similarity improves the analysis of proteomics data. Mol Cell Proteomics. 2014 Jul; 13(7):1877-89. PMID: 24807868; PMCID: PMC4083122.
      Citations: 2     Fields:    Translation:HumansCells
    24. El-Kebir M, Brandt BW, Heringa J, Klau GW. NatalieQ: a web server for protein-protein interaction network querying. BMC Syst Biol. 2014 Apr 01; 8:40. PMID: 24690407; PMCID: PMC3998945.
      Citations: 3     Fields:    Translation:HumansCells
    25. Staiger C, Cadot S, Wessels LF, Klau GW, Gy?rffy B. Current composite-feature classification methods do not outperform simple single-genes classifiers in breast cancer prognosis. Front Genet. 2013; 4:289. PMID: 24391662; PMCID: PMC3870302.
      Citations: 28     
    26. El-Kebir M, Marschall T, Wohlers I, Patterson M, Heringa J, Klau GW, Sch?nhuth A. Mapping proteins in the presence of paralogs using units of coevolution. BMC Bioinformatics. 2013; 14 Suppl 15:S18. PMID: 24564758; PMCID: PMC3852051.
      Citations: 2     Fields:    Translation:Cells
    27. Hagen F, Ceresini PC, Polacheck I, Ma H, van Nieuwerburgh F, Kagan S, Pursall ER, Hoogveld HL, van Iersel LJ, Klau GW, Kelk SM, Stougie L, Bartlett KH, Voelz K, Pryszcz LP, Lazera M, Meyer W, Deforce D, Meis JF, May RC, Boekhout T, Gabald?n T, Casta?eda E, Klaassen CH. Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest. PLoS One. 2013; 8(8):e71148. PMID: 23940707; PMCID: PMC3737135.
      Citations: 66     Fields:    Translation:HumansAnimalsCellsPHPublic Health
    28. van der Gulik PT, Klau GW, Schaffner C, Speijer D, Stougie L, Buhrman H. A realistic model under which the genetic code is optimal. J Mol Evol. 2013 Oct; 77(4):170-84. PMID: 23877342.
      Citations: 7     Fields:    Translation:Cells
    29. Canzar S, El-Kebir M, Elbassioni K, Mark AE, Geerke DP, Stougie L, Klau GW, Pool R. Charge group partitioning in biomolecular simulation. J Comput Biol. 2013 Mar; 20(3):188-98. PMID: 23461571; PMCID: PMC3590896.
      Citations: 25     Fields:    Translation:Cells
    30. Andonov R, Klau GW, Wohlers I. DALIX: optimal DALI protein structure alignment. IEEE/ACM Trans Comput Biol Bioinform. 2013 Jan-Feb; 10(1):26-36. PMID: 23702541.
      Citations: 8     Fields:    
    31. Marschall T, Costa IG, Canzar S, Bauer M, Klau GW, Schliep A, Sch?nhuth A. CLEVER: clique-enumerating variant finder. Bioinformatics. 2012 Nov 15; 28(22):2875-82. PMID: 23060616.
      Citations: 29     Fields:    Translation:Humans
    32. Grohme MA, Kopka J, Frohme M, Schill RO, Hengherr S, Dandekar T, Klau GW, Dittrich M, Beisser D, M?ller T. Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. BMC Syst Biol. 2012 Jun 19; 6:72. PMID: 22713133; PMCID: PMC3534414.
      Citations: 5     Fields:    Translation:Animals
    33. Brunkhorst S, Dandekar T, Klau GW, Dittrich MT, Beisser D, M?ller T. Robustness and accuracy of functional modules in integrated network analysis. Bioinformatics. 2012 Jul 15; 28(14):1887-94. PMID: 22581175.
      Citations: 11     Fields:    Translation:Humans
    34. Wohlers I, Andonov R, Klau GW, Malod-Dognin N. CSA: comprehensive comparison of pairwise protein structure alignments. Nucleic Acids Res. 2012 Jul; 40(Web Server issue):W303-9. PMID: 22553365; PMCID: PMC3394275.
      Citations: 5     Fields:    Translation:Cells
    35. Staiger C, Cadot S, Kooter R, Dittrich M, Klau GW, Wessels LF, M?ller T. A critical evaluation of network and pathway-based classifiers for outcome prediction in breast cancer. PLoS One. 2012; 7(4):e34796. PMID: 22558100; PMCID: PMC3338754.
      Citations: 30     Fields:    Translation:Humans
    36. Backes C, Rurainski A, Klau GW, Gerasch A, Maisel D, Ludwig N, Hein M, Keller A, Burtscher H, Kaufmann M, Meese E, Lenhof HP, M?ller O, St?ckel D, K?ntzer J. An integer linear programming approach for finding deregulated subgraphs in regulatory networks. Nucleic Acids Res. 2012 Mar; 40(6):e43. PMID: 22210863; PMCID: PMC3315310.
      Citations: 19     Fields:    Translation:HumansCells
    37. Klau GW, Reinert K, Andreotti S. Antilope--a Lagrangian relaxation approach to the de novo peptide sequencing problem. IEEE/ACM Trans Comput Biol Bioinform. 2012; 9(2):385-94. PMID: 21464512.
      Citations: 2     Fields:    
    38. Wohlers I, Domingues FS, Klau GW. Towards optimal alignment of protein structure distance matrices. Bioinformatics. 2010 Sep 15; 26(18):2273-80. PMID: 20639543.
      Citations: 5     Fields:    Translation:HumansCells
    39. Klau GW, Dandekar T, Dittrich MT, Beisser D, M?ller T. BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics. 2010 Apr 15; 26(8):1129-30. PMID: 20189939.
      Citations: 116     Fields:    
    40. Klau GW. A new graph-based method for pairwise global network alignment. BMC Bioinformatics. 2009 Jan 30; 10 Suppl 1:S59. PMID: 19208162; PMCID: PMC2648773.
      Citations: 27     Fields:    
    41. Briesemeister S, Klau GW, B?cker S. On optimal comparability editing with applications to molecular diagnostics. BMC Bioinformatics. 2009 Jan 30; 10 Suppl 1:S61. PMID: 19208165; PMCID: PMC2648753.
      Citations:    Fields:    Translation:Humans
    42. Klau GW, Rosenwald A, Dandekar T, Dittrich MT, M?ller T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics. 2008 Jul 01; 24(13):i223-31. PMID: 18586718; PMCID: PMC2718639.
      Citations: 189     Fields:    Translation:HumansCells
    43. Bauer M, Klau GW, Reinert K. Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics. 2007 Jul 27; 8:271. PMID: 17662141; PMCID: PMC1955456.
      Citations: 31     Fields:    
    44. Klau GW, Rahmann S, Schliep A, Vingron M, Reinert K. Optimal robust non-unique probe selection using Integer Linear Programming. Bioinformatics. 2004 Aug 04; 20 Suppl 1:i186-93. PMID: 15262798.
      Citations: 6     Fields:    Translation:Cells

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