Publications

Please also see my Google Scholar page and my CV.

Peer-reviewed journal

  1. P. Spohr, K. Dinkla, G.W. Klau, M. El-Kebir. eXamine: Visualizing annotated networks in Cytoscape. F1000Research, 7, 519, 2018.
  2. S. Zaccaria*, M. El-Kebir*, G.W. Klau, B.J. Raphael. Phylogenetic Copy-Number Factorization of Multiple Tumor Samples. Journal of Computational Biology, 27(0), 2018.
  3. M. El-Kebir, G. Satas and B.J. Raphael. Inferring parsimonious migration histories for metastatic cancers. Nature Genetics, 2018.
  4. M. El-Kebir, B.J. Raphael, R. Shamir, R. Sharan, S. Zaccaria, M. Zehavi and R. Zeira. Complexity and algorithms for copy-number evolution problems. Algorithms for Molecular Biology, 12(1), 2017.
  5. The Computational Pan-Genomics Consortium. Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics, 19(1):118-135, 2016.
  6. M. El-Kebir*, G. Satas* , L. Oesper, B.J. Raphael. Inferring the Mutational History of a Tumor using Multi-State Perfect Phylogeny Mixtures. Cell Systems, 3(1):43-53, 2016.
  7. A. May, B. W. Brandt, M. El-Kebir, G. W. Klau, E. Zaura, W. Crielaard, J. Heringa and S. Abeln. metaModules identifies key functional subnetworks in microbiome-related disease. Bioinformatics, 32(11):1678-85, 2016.
  8. M. El-Kebir, J. Heringa and G. W. Klau. Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment. Algorithms, 8 (4), 1035-1051, 2015.
  9. M. El-Kebir*, H. Soueidan*, T. Hume*, D. Beisser, M. Dittrich, T. Mueller, G. Blin, J. Heringa, M. Nikolski, L. F. A. Wessels, G. W. Klau. xHeinz: An algorithm for mining cross-species network modules under a flexible conservation model. Bioinformatics, 31(19):3147-55, 2015.
  10. M. El-Kebir*, L. Oesper*, H. Acheson-Field, B. J. Raphael. Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. Bioinformatics (Special Issue: Proceedings of ISMB), 31(12):i62-i70, 2015.
  11. K. Dinkla*, M. El-Kebir*, C.-I. Bucur, M. Siderius, M. J. Smit, M. A. Westenberg, and G. W. Klau. eXamine: Exploring annotated modules in networks. BMC Bioinformatics, 15(1):201, 2014.
  12. M. El-Kebir*, B. W. Brandt*, J. Heringa, and G. W. Klau. NatalieQ: A web server for protein-protein interaction network querying. BMC Systems Biology, 8(1):40, 2014.
  13. M. El-Kebir*, T. Marschall*, I. Wohlers*, M. Patterson, J. Heringa, A. Schoenhuth, and G. W. Klau. Mapping proteins in the presence of paralogs using units of coevolution. BMC Bioinformatics, 14(Suppl 15):S18, 2013.
  14. M. El-Kebir*, M. van der Kuip*, A. M. van Furth, and D. E. Kirschner. Computational modeling of tuberculous meningitis reveals an important role for tumor necrosis factor-alpha. Journal of Theoretical Biology, 328(C):43-53, 2013.
  15. S. Canzar* , M. El-Kebir*, R. Pool, K. Elbassioni, A. K. Malde, A. E. Mark, D. P. Geerke, L. Stougie, and G. W. Klau. Charge Group Partitioning in Biomolecular Simulation. Journal of Computational Biology, 20(3):188-198, 2013.
  16. S. Marino, M. El-Kebir, and D. Kirschner. A hybrid multi-compartment model of granuloma formation and T cell priming in Tuberculosis. Journal of Theoretical Biology, 280(1):50-62, 2011.
  17. Fallahi-Sichani, M. El-Kebir, S. Marino, D. E. Kirschner, and J. J. Linderman. Multiscale Computational Modeling Reveals a Critical Role for TNF-Receptor 1 Dynamics in Tuberculosis Granuloma Formation. The Journal of Immunology, 186(6):3472-3483, 2011.


Peer-reviewed conference

  1. M.S. Engler, M. El-Kebir, A. E. Mark, D. P. Geerke and G. W. Klau. Enumerating common molecular substructures. GCB 2017, German Conference on Bioinformatics, Tuebingen, Germany, September 18-20, 2017.
  2. S. Zaccaria*, M. El-Kebir*, G. W. Klau, B. J. Raphael. The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-Sample Bulk Sequencing Tumor Data. RECOMB 2017, Annual International Conference on Research in Computational Molecular Biology, Hong Kong, China, May 3-7, 2017.
  3. M. El-Kebir, B.J. Raphael, R. Shamir, R. Sharan, S. Zaccaria, M. Zehavi, R. Zeira. Copy-Number Evolution Problems: Complexity and Algorithms. WABI 2016, Workshop on Algorithms in Bioinformatics, Aarhus, Denmark, August 22-24, 2016.
  4. M. El-Kebir, G. Satas, L. Oesper, B. J. Raphael. Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. RECOMB 2016, Annual International Conference on Research in Computational Molecular Biology, Santa Monica, CA, April 18-21 2016.
  5. M. El-Kebir*, L. Oesper*, H. Acheson-Field, B. J. Raphael. Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. ISMB 2015, Annual International Conference on Intelligent Systems for Molecular Biology, Dublin, Ireland, July 10-14, 2015.
  6. K. Dinkla*, M. El-Kebir*, C.-I. Bucur, M. Siderius, M. J. Smit, M. A. Westenberg, and G. W. Klau. eXamine: Exploring annotated modules in networks. BIOVIS 2014, Symposium on Biological Data Visualization, Boston, MA, 11-12 July, 2014.
  7. M. El-Kebir*, T. Marschall*, I. Wohlers*, M. Patterson, J. Heringa, A. Schoenhuth, and G. W. Klau. Mapping proteins in the presence of paralogs using units of coevolution. RECOMB-CG 2013, RECOMB Comparative Genomics, Lyon, France, October 17-19, 2013.
  8. S. Canzar*, M. El-Kebir*, R. Pool, K. Elbassioni, A. K. Malde, A. E. Mark, D. P. Geerke, L. Stougie, and G. W. Klau. Charge Group Partitioning in Biomolecular Simulation. RECOMB 2012, Annual International Conference on Research in Computational Molecular Biology, Barcelona, Spain, April 21-24, 2012.
  9. M. El-Kebir, J. Heringa and G. W. Klau. Lagrangian relaxation applied to sparse global network alignment. PRIB 2011, International Conference on Pattern Recognition in Bioinformatics, Delft, The Netherlands, November 2-4, 2011.
  10. S. Canzar* and M. El-Kebir*. A mathematical programming approach to marker-assisted gene pyramiding. WABI 2011, Workshop on Algorithms in Bioinformatics, Saarbruecken, Germany, September 5-7, 2011.
  11. S. Schlobach, E. Blaauw, M. El Kebir, A. ten Teije, F. Van Harmelen, et al. Anytime classification by ontology approximation. NFRSW 2007, New forms of reasoning for the Semantic Web: Scalable, Tolerant and Dynamic, Busan, South Korea, 2007.
*joint first authorship