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Research Output 2007 2019

  • 20 Article
  • 7 Conference contribution
  • 1 Conference article
2019

Implications of non-uniqueness in phylogenetic deconvolution of bulk DNA samples of tumors

Qi, Y., Pradhan, D. & El-Kebir, M., Sep 3 2019, In : Algorithms for Molecular Biology. 14, 1, 19.

Research output: Contribution to journalArticle

Open Access
Phylogeny
Nonuniqueness
Deconvolution
Phylogenetics
Tumors

Summarizing the solution space in tumor phylogeny inference by multiple consensus trees

Aguse, N., Qi, Y. & El-Kebir, M., Jul 15 2019, In : Bioinformatics. 35, 14, p. i408-i416 btz312.

Research output: Contribution to journalArticle

Open Access
Phylogeny
Tumors
Tumor
Linear Programming
Cancer
2018

Computational pan-genomics: Status, promises and challenges

The Computational Pan-Genomics Consortium, Jan 1 2018, In : Briefings in bioinformatics. 19, 1, p. 118-135 18 p., bbw089.

Research output: Contribution to journalArticle

Genomics
Genes
Computational Biology
Genome
Bioinformatics

eXamine: Visualizing annotated networks in Cytoscape [version 1; referees: 1 approved, 2 approved with reservations]

El-Kebir, M., Spohr, P., Dinkla, K. & Klau, G. W., Jan 1 2018, In : F1000Research. 7, 519.

Research output: Contribution to journalArticle

Workflow
Automation
Application programs
Social Support
Visualization

Inferring parsimonious migration histories for metastatic cancers

El-Kebir, M., Satas, G. & Raphael, B. J., May 1 2018, In : Nature Genetics. 50, 5, p. 718-726 9 p.

Research output: Contribution to journalArticle

Neoplasm Metastasis
Neoplasms
DNA Sequence Analysis
Cell Movement
Mutation

On the non-uniqueness of solutions to the perfect phylogeny mixture problem

Pradhan, D. & El-Kebir, M., Jan 1 2018, Comparative Genomics - 16th International Conference, RECOMB-CG 2018, Proceedings. Ouangraoua, A. & Blanchette, M. (eds.). Springer-Verlag, p. 277-293 17 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 11183 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Phylogeny
Nonuniqueness
Tumors
Tumor
Phylogenetic Tree

Parsimonious migration history problem: Complexity and algorithms

El-Kebir, M., Aug 1 2018, 18th International Workshop on Algorithms in Bioinformatics, WABI 2018. Parida, L. & Ukkonen, E. (eds.). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, Vol. 113. 24

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Phylogenetic copy-number factorization of multiple tumor samples

Zaccaria, S., El-Kebir, M., Klau, G. W. & Raphael, B. J., Jul 2018, In : Journal of Computational Biology. 25, 7, p. 689-708 20 p.

Research output: Contribution to journalArticle

Phylogenetics
Factorization
Phylogenetic Tree
Tumors
Tumor

SPhyR: Tumor phylogeny estimation from single-cell sequencing data under loss and error

El-Kebir, M., Sep 1 2018, In : Bioinformatics. 34, 17, p. i671-i679

Research output: Contribution to journalArticle

Phylogeny
Sequencing
Tumors
Tumor
Cell
2017

Complexity and algorithms for copy-number evolution problems

El-Kebir, M., Raphael, B. J., Shamir, R., Sharan, R., Zaccaria, S., Zehavi, M. & Zeira, R., May 16 2017, In : Algorithms for Molecular Biology. 12, 1, 13.

Research output: Contribution to journalArticle

Evolution Problems
Chromosomes
Tumors
Inductive logic programming (ILP)
Aberrations

The copy-number tree mixture deconvolution problem and applications to multi-sample bulk sequencing tumor data

Zaccaria, S., El-Kebir, M., Klau, G. W. & Raphael, B. J., Jan 1 2017, Research in Computational Molecular Biology - 21st Annual International Conference, RECOMB 2017, Proceedings. Sahinalp, S. C. (ed.). Springer-Verlag, p. 318-335 18 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 10229 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Deconvolution
Sequencing
Tumors
Tumor
Phylogenetic Tree
2016

Copy-number evolution problems: Complexity and algorithms

El-Kebir, M., Raphael, B. J., Shamir, R., Sharan, R., Zaccaria, S., Zehavi, M. & Zeira, R., Jan 1 2016, Algorithms in Bioinformatics - 16th International Workshop, WABI 2016, Proceedings. Springer-Verlag, p. 137-149 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 9838 LNCS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Evolution Problems
Chromosomes
Tumors
Aberrations
Dynamic programming

Inferring the Mutational History of a Tumor Using Multi-state Perfect Phylogeny Mixtures

El-Kebir, M., Satas, G., Oesper, L. & Raphael, B. J., Jul 27 2016, In : Cell Systems. 3, 1, p. 43-53 11 p.

Research output: Contribution to journalArticle

Phylogeny
History
Neoplasms
Nucleotides
DNA Sequence Analysis

MetaModules identifies key functional subnetworks in microbiome-related disease

May, A., Brandt, B. W., El-Kebir, M., Klau, G. W., Zaura, E., Crielaard, W., Heringa, J. & Abeln, S., Jun 1 2016, In : Bioinformatics. 32, 11, p. 1678-1685 8 p.

Research output: Contribution to journalArticle

Microbiota
Pathway
Mouth Diseases
Sugar Alcohols
Health
2015

Natalie 2.0: Sparse global network alignment as a special case of quadratic assignment

El-Kebir, M., Heringa, J. & Klau, W. G., Jan 1 2015, In : Algorithms. 8, 4, p. 1035-1051 17 p.

Research output: Contribution to journalArticle

Quadratic Assignment
Alignment
Topology
Quadratic Assignment Problem
Molecular interactions

Reconstruction of clonal trees and tumor composition from multi-sample sequencing data

El-Kebir, M., Oesper, L., Acheson-Field, H. & Raphael, B. J., Jun 15 2015, In : Bioinformatics. 31, 12, p. i62-i70

Research output: Contribution to journalArticle

Clonal Evolution
Sequencing
Tumors
Tumor
Factorization

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, L. F. A. & Klau, G. W., Oct 1 2015, In : Bioinformatics. 31, 19, p. 3147-3155 9 p.

Research output: Contribution to journalArticle

T-cells
Conservation
Mining
Genes
Module
2014

EXamine: Exploring annotated modules in networks

Dinkla, K., El-Kebir, M., Bucur, C. I., Siderius, M., Smit, M. J., Westenberg, M. A. & Klau, G. W., Jul 10 2014, In : BMC bioinformatics. 15, 1, 201.

Research output: Contribution to journalArticle

Molecular Sequence Annotation
Electric network analysis
G-Protein-Coupled Receptors
Proteins
Module

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

El-Kebir, M., Brandt, B. W., Heringa, J. & Klau, G. W., Apr 1 2014, In : BMC Systems Biology. 8, 1, 40.

Research output: Contribution to journalArticle

Protein Interaction Maps
Protein Interaction Networks
Web Server
Protein-protein Interaction
Alignment
2013

Charge group partitioning in biomolecular simulation

Canzar, S., El-Kebir, M., Pool, R., Elbassioni, K., Mark, A. E., Geerke, D. P., Stougie, L. & Klau, G. W., Mar 1 2013, In : Journal of Computational Biology. 20, 3, p. 188-198 11 p.

Research output: Contribution to journalArticle

Hardness
Partitioning
Charge
Force Field
Molecules

Computational modeling of tuberculous meningitis reveals an important role for tumor necrosis factor-α

El-Kebir, M., van der Kuip, M., van Furth, A. M. & Kirschner, D. E., Jul 7 2013, In : Journal of Theoretical Biology. 328, p. 43-53 11 p.

Research output: Contribution to journalArticle

Tumor Necrosis Factor
Meningeal Tuberculosis
tumor necrosis factors
meningitis
Computational Modeling

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, G. W., 2013, In : BMC bioinformatics. 14 Suppl 15

Research output: Contribution to journalArticle

Coevolution
Proteins
Protein
Unit
Quantification
2012

Charge group partitioning in biomolecular simulation

Canzar, S., El-Kebir, M., Pool, R., Elbassioni, K., Malde, A. K., Mark, A. E., Geerke, D. P., Stougie, L. & Klau, G. W., May 15 2012, Research in Computational Molecular Biology - 16th Annual International Conference, RECOMB 2012, Proceedings. p. 29-43 15 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7262 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Partitioning
Charge
Force Field
Molecules
Simulation
2011

A hybrid multi-compartment model of granuloma formation and T cell priming in Tuberculosis

Marino, S., El-Kebir, M. & Kirschner, D., Jul 7 2011, In : Journal of Theoretical Biology. 280, 1, p. 50-62 13 p.

Research output: Contribution to journalArticle

Compartment Model
Tuberculosis
T-cells
granuloma
Granuloma

A mathematical programming approach to marker-assisted gene pyramiding

Canzar, S. & El-Kebir, M., Sep 26 2011, Algorithms in Bioinformatics - 11th International Workshop, WABI 2011, Proceedings. p. 26-38 13 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6833 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Mathematical programming
Integer programming
Mathematical Programming
Genes
Mathematical models

Lagrangian relaxation applied to sparse global network alignment

El-Kebir, M., Heringa, J. & Klau, G. W., Nov 9 2011, Pattern Recognition in Bioinformatics - 6th IAPR International Conference, PRIB 2011, Proceedings. p. 225-236 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7036 LNBI).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Lagrangian Relaxation
Alignment
Topology
Molecular interactions
Electric network analysis

Multiscale computational modeling reveals a critical role for TNF-α receptor 1 dynamics in tuberculosis granuloma formation

Fallahi-Sichani, M., El-Kebir, M., Marino, S., Kirschner, D. E. & Linderman, J. J., Mar 15 2011, In : Journal of Immunology. 186, 6, p. 3472-3483 12 p.

Research output: Contribution to journalArticle

Tumor Necrosis Factor Receptors
Granuloma
Tuberculosis
Mycobacterium tuberculosis
Mycobacterium Infections
2007

Anytime classification by ontology approximation

Schlobach, S., Blaauw, E., El-Kebir, M., Ten Teije, A., Van Harmelen, F., Bortoli, S., Hobbelman, M., Millian, K., Ren, Y., Stam, S., Thomassen, P., Van Het Schip, R. & Van Willigem, W., Jan 1 2007, In : CEUR Workshop Proceedings. 291

Research output: Contribution to journalConference article

Ontology
Bottles
Semantics