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Items: 17

1.

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

El-Kebir M.

Bioinformatics. 2018 Sep 1;34(17):i671-i679. doi: 10.1093/bioinformatics/bty589.

2.

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.

3.

Inferring parsimonious migration histories for metastatic cancers.

El-Kebir M, Satas G, Raphael BJ.

Nat Genet. 2018 May;50(5):718-726. doi: 10.1038/s41588-018-0106-z. Epub 2018 Apr 26.

4.

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.

PMID:
29658782
5.

Complexity and algorithms for copy-number evolution problems.

El-Kebir M, Raphael BJ, Shamir R, Sharan R, Zaccaria S, Zehavi M, Zeira R.

Algorithms Mol Biol. 2017 May 16;12:13. doi: 10.1186/s13015-017-0103-2. eCollection 2017.

6.

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

El-Kebir M, Satas G, Oesper L, Raphael BJ.

Cell Syst. 2016 Jul;3(1):43-53. doi: 10.1016/j.cels.2016.07.004.

7.

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.

PMID:
26342232
8.

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

El-Kebir M, Oesper L, Acheson-Field H, Raphael BJ.

Bioinformatics. 2015 Jun 15;31(12):i62-70. doi: 10.1093/bioinformatics/btv261.

9.

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.

PMID:
26023104
10.

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.

11.

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.

12.

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.

13.

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

El-Kebir M, van der Kuip M, van Furth AM, Kirschner DE.

J Theor Biol. 2013 Jul 7;328:43-53. doi: 10.1016/j.jtbi.2013.03.008. Epub 2013 Mar 26.

14.

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.

15.

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

Marino S, El-Kebir M, Kirschner D.

J Theor Biol. 2011 Jul 7;280(1):50-62. doi: 10.1016/j.jtbi.2011.03.022. Epub 2011 Apr 1.

16.

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 DE, Linderman JJ.

J Immunol. 2011 Mar 15;186(6):3472-83. doi: 10.4049/jimmunol.1003299. Epub 2011 Feb 14.

17.

Free and bound cinnamic acid derivatives in corsica sweet blond oranges.

Carrera E, El Kebir MV, Jacquemond C, Luro F, Lozano Y, Gaydou EM.

Nat Prod Commun. 2010 Mar;5(3):435-40.

PMID:
20420324

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