Mohammed El-Kebir

melkebir[AT]illinois[DOT]edu

Publications

Group members are indicated in boldface, ‘†’ indicates corresponding author(s) and ‘*’ indicates joint first authors. Many of the papers listed below first appeared in a conference and later in a journal. Only the journal version (with an additional indication of the conference) is listed if the two versions are very similar in content. Please also see my Google Scholar page and my CV.

Preprints

Edited conference proceedings

  1. 21st International Workshop on Algorithms in Bioinformatics, WABI 2021, August 2–4, 2021, Virtual Conference. Edited by Alessandra Carbone and Mohammed El-Kebir.

Peer-reviewed journal

  1. X. Gu, Y. Qi and M. El-Kebir†. DERNA Enables Pareto Optimal RNA Design. Journal of Computational Biology, ahead of print, 1-18. Extended version of WABI 2023 paper.
  2. Y. Qi and M. El-Kebir†. Consensus Tree Under the Ancestor–Descendant Distance is NP-Hard. Journal of Computational Biology, ahead of print, 1-14.
  3. L.L. Weber*, C. Zhang*, I. Ochoa† and M. El-Kebir†. Phertilizer: growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors. PLOS Computational Biology 19, no. 10: e1011544, 2023. Extended version of RECOMB-CCB 2023 paper.
  4. S. Ivanovic and M. El-Kebir†. Modeling and Predicting Cancer Clonal Evolution with Reinforcement Learning. Genome Research 33: 1078-1088 (2023). Extended version of selected papers that appeared in RECOMB 2023.
  5. M. Stroet, B. Caron, M.S. Engler, J. van der Woning, A. Kauffmann, M. van Dijk, M. El-Kebir, K.M. Visscher, J. Holownia, C. Macfarlane, B.J. Bennion, S. Gelpi‑Dominguez, F.C. Lightstone, T. van der Storm, D.P. Geerke, A.E. Mark, G.W. Klau. OFraMP: A Fragment-Based Tool to Facilitate the Parametrization of Large Molecules. Journal of Computer-Aided Molecular Design, June 13, 2023.
  6. Z. Lalani*, G. Chu*, S. Hsu, S. Kagawa, M. Xiang, S. Zaccaria† and M. El-Kebir†. CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data. PLOS Computational Biology 18, no. 10 (October 13, 2022): e1010614, 2022. Extended version of RECOMB-CCB 2022 paper.
  7. C. Zhang*, P. Sashittal*, M. Xiang, Y. Zhang, A. Kazi, M. El-Kebir†. Accurate Identification of Transcription Regulatory Sequences and Genes in Coronaviruses. Molecular Biology and Evolution, 2022. Extended version of RECOMB 2022 paper.
  8. P. Sashittal, S. Zaccaria, and M. El-Kebir†. Parsimonious Clone Tree Integration in Cancer. Algorithms for Molecular Biology 17, no. 1 (2022): 3. Extended version of WABI 2021 paper.
  9. C. Oh*, P. Sashittal*, A. Zhou, L. Wang, M. El-Kebir†, and Thanh H. Nguyen†. Design of SARS-CoV-2 Variant-Specific PCR Assays Considering Regional and Temporal Characteristics. Applied and Environmental Microbiology, March 14, 2022, e02289-21.
  10. P. Sashittal, C. Zhang, J. Peng, and M. El-Kebir†. Jumper Enables Discontinuous Transcript Assembly in Coronaviruses. Nature Communications 12, no. 1 (December 2021): 6728.
  11. G. Satas*, S. Zaccaria*, M. El-Kebir*†, B.J. Raphael†. DeCiFering the elusive cancer cell fraction in tumor heterogeneity and evolution. Cell Systems, 12:1004–1018, 2021. Extended version of selected papers that appeared in RECOMB 2021.
  12. L.L. Weber*, P. Sashittal* and M. El-Kebir†. doubletD: detecting doublets in single-cell DNA sequencing data. Bioinformatics (ISMB/ECCB 2021), 37:i214-i221, 2021
  13. L.L. Weber and M. El-Kebir†. Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors. Algorithms for Molecular Biology, 16(1):14, 2021. Extended version of WABI 2021 paper.
  14. C. Zhang, M. El-Kebir† and I. Ochoa†. Moss enables high sensitivity single-nucleotide variant calling from multiple bulk DNA tumor samples. Nature Communications, 12(1):2204, 2021.
  15. S.S. Patel, A. Sandur, M. El-Kebir, R.C. Gaba, L.B. Schook and K.M. Schachtschneider. Transcriptional Profiling of Porcine HCC Xenografts Provides Insights Into Tumor Cell Microenvironment Signaling. Frontiers in Genetics, 12, 2021.
  16. S. Christensen, J. Kim, N. Chia, O. Koyejo and M. El-Kebir†. Detecting Evolutionary Patterns of Cancers using Consensus Trees. Bioinformatics (ECCB 2020), 36:i362–i370, 2020.
  17. L.L. Weber*, N. Aguse*, N. Chia and M. El-Kebir†. PhyDOSE: Design of Follow-up Single-cell Sequencing Experiments of Tumors. PLOS Computational Biology, 16(10):e1008240, 2020. Invited journal version of RECOMB-CCB 2020 conference paper.
  18. R. C. Gaba, L. Elkhadragy, F.E. Boas, S. Chaki, H.H. Chen, M. El-Kebir, K.D. Garcia, E.F. Giurini, G. Guzman, F.V. LoBianco, M.F. Neto, J.L. Newson, A. Qazi, M. Regan, L.A. und, R.M. Schwind, M.C. Stewart, F.M. Thomas, H.E. Whiteley, J. Wu, L.B. Schook and K.M. Schachtschneider. Development and comprehensive characterization of porcine hepatocellular carcinoma for translational liver cancer investigation. Oncotarget 11:2686-–2701, 2020.
  19. J. Wu and M. El-Kebir†. ClonArch: Visualizing the Spatial Clonal Architecture of Tumors. Bioinformatics (ISMB 2020), 36:i161–i168, 2020.
  20. P. Sashittal and M. El-Kebir†. Sampling and Summarizing Transmission Trees with Multi-strain Infections. Bioinformatics (ISMB 2020), 36:i362–i370, 2020.
  21. Y. Qi, D. Pradhan and M. El-Kebir†. Implications of non-uniqueness in phylogenetic deconvolution of bulk DNA samples of tumors. Algorithms for Molecular Biology, 14:19, 2019. Extended version of RECOMB-CG 2018 paper.
  22. N. Aguse*, Y. Qi* and M. El-Kebir†. Summarizing the Solution Space in Tumor Phylogeny Inference using Multiple Consensus Trees. Bioinformatics (ISMB/ECCB 2019), 35:i408-i146, 2019.
  23. M. El-Kebir†. SPhyR: Tumor Phylogeny Estimation from Single-Cell Sequencing Data under Loss and Error. Bioinformatics (ECCB 2018), 34(17):i671-679, 2018.
  24. P. Spohr, K. Dinkla, G.W. Klau and M. El-Kebir†. eXamine: Visualizing annotated networks in Cytoscape. F1000Research, 7, 519, 2018.
  25. S. Zaccaria*, M. El-Kebir*, G.W. Klau and B.J. Raphael. Phylogenetic Copy-Number Factorization of Multiple Tumor Samples. Journal of Computational Biology, 27(0), 2018. Extended version of RECOMB 2017 paper.
  26. M. El-Kebir, G. Satas and B.J. Raphael. Inferring parsimonious migration histories for metastatic cancers. Nature Genetics, 50:718-726, 2018.
  27. 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. Extended version of selected papers that appeared in WABI 2016.
  28. The Computational Pan-Genomics Consortium. Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics, 19(1):118-135, 2016.
  29. M. El-Kebir*, G. Satas* , L. Oesper and B.J. Raphael. Inferring the Mutational History of a Tumor using Multi-State Perfect Phylogeny Mixtures. Cell Systems, 3(1):43-53, 2016. Extended version of selected papers that appeared in RECOMB 2016.
  30. 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.
  31. 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.
  32. M. El-Kebir*, H. Soueidan*, T. Hume*, D. Beisser, M. Dittrich, T. Mueller, G. Blin, J. Heringa, M. Nikolski, L. F. A. Wessels and G. W. Klau. xHeinz: An algorithm for mining cross-species network modules under a flexible conservation model. Bioinformatics, 31(19):3147-55, 2015.
  33. M. El-Kebir*, L. Oesper*, H. Acheson-Field and 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.
  34. 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. Extended version of selected papers that appeared in Symposium on Biological Data Visualization (BioVis) 2014.
  35. 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.
  36. 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. Special issue for RECOMB Comparative Genomics (RECOMB-CG) 2013.
  37. 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.
  38. 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. Extended version of RECOMB 2013 paper.
  39. 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.
  40. 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 conferences

As noted, conference papers that have a corresponding journal version are not listed below.

  1. L.L. Weber, Derek Reiman, M.S. Roddur, Y. Qi, M. El-Kebir† and A.A. Khan†. TRIBAL: Tree Inference of B cell Clonal Lineages. RECOMB 2024. Annual International Conference on Research in Computational Molecular Biology, Boston, MA, April 29 - May 2, 2024.
  2. M.S. Roddur, S. Snir and M. El-Kebir†. Inferring Temporally Consistent Migration Histories. WABI 2023, Workshop on Algorithms in Bioinformatics, Houston, TX, September 3-6, 2023.
  3. M. El-Kebir†, Q. Morris, L. Oesper, and S.C. Sahinalp. Emerging Topics in Cancer Evolution. PSB 2022, Pacific Symposium on Biocomputing. The Big Island of Hawaii, January 3-7, 2022.
  4. S. Christensen, M.D.M. Leiserson, M. El-Kebir†. PhySigs: Phylogenetic Inference of Mutational Signature Dynamics. PSB 2020, Pacific Symposium on Biocomputing, 25:226-237, 2020.
  5. P. Sashittal and M. El-Kebir†. SharpTNI: Counting and Sampling Parsimonious Transmission Networks under a Weak Bottleneck. RECOMB-CG 2019, RECOMB Comparative Genomics, Montpellier, France, October 1-4, 2019.
  6. M. El-Kebir†. Parsimonious Migration History Problem: Complexity and Algorithms. WABI 2018, Workshop on Algorithms in Bioinformatics, Helsinki, Finland, August 20-22, 2018.
  7. 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.
  8. 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.
  9. 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.
  10. 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.

Peer-reviewed workshop

  1. M. El-Kebir†, J. Oh, Y. Qi and P. Sashittal. Counting and Sampling Problems in Computational Biology. Model Counting Workshop (MCW) 2020, part of the International Conference on Theory and Applications of Satisfiability Testing (SAT) 2020, July 9th, 2020, virtual.

Other (opinions, editorials, etc.)

  1. B. Berger, D. Tian, W.V. Li, M. El-Kebir, A.I. Tomescu, R. Singh, N. Beerenwinkel, Y. Li, C. Boucher, and Z. Bar-Joseph. What Are the Keys to Succeeding as a Computational Biologist in Today’s Research Climate? Cell Systems 13, no. 10 (October 2022): 781–85.