Mohammed El-Kebir

Publication Activity (10 Years)

Years Active: 2011-2024
Publications (10 Years): 31

Top Topics

Temporally Consistent

Transcriptional Regulation

Perfect Phylogeny

Top Venues

J. Comput. Biol.

Publications

Mrinmoy Saha Roddur, Sagi Snir, Mohammed El-Kebir
Enforcing Temporal Consistency in Migration History Inference. J. Comput. Biol. 31 (5) (2024)
Yuanyuan Qi, Mohammed El-Kebir
Sapling: Inferring and Summarizing Tumor Phylogenies from Bulk Data Using Backbone Trees. WABI (2024)
Leah L. Weber, Derek Reiman, Mrinmoy Saha Roddur, Yuanyuan Qi, Mohammed El-Kebir, Aly A. Khan
TRIBAL: Tree Inference of B Cell Clonal Lineages. RECOMB (2024)
Xinyu Gu, Yuanyuan Qi, Mohammed El-Kebir
DERNA Enables Pareto Optimal RNA Design. J. Comput. Biol. 31 (3) (2024)
Xinyu Gu, Yuanyuan Qi, Mohammed El-Kebir
Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design. WABI (2023)
Martin Stroet, Bertrand Caron, Martin S. Engler, Jimi van der Woning, Aude Kauffmann, Marc van Dijk, Mohammed El-Kebir, Koen Visscher, Josef Holownia, Callum Macfarlane, Brian J. Bennion, Svetlana Gelpi-Dominguez, Felice C. Lightstone, Tijs van der Storm, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. J. Comput. Aided Mol. Des. 37 (8) (2023)
Mrinmoy Saha Roddur, Sagi Snir, Mohammed El-Kebir
Inferring Temporally Consistent Migration Histories. WABI (2023)
Leah L. Weber, Chuanyi Zhang, Idoia Ochoa, Mohammed El-Kebir
Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors. PLoS Comput. Biol. 19 (10) (2023)
Palash Sashittal, Simone Zaccaria, Mohammed El-Kebir
Parsimonious Clone Tree Integration in cancer. Algorithms Mol. Biol. 17 (1) (2022)
Zubair Lalani, Gillian Chu, Silas Hsu, Shaw Kagawa, Michael Xiang, Simone Zaccaria, Mohammed El-Kebir
CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data. PLoS Comput. Biol. 18 (10) (2022)
Chuanyi Zhang, Palash Sashittal, Mohammed El-Kebir
CORSID Enables de novo Identification of Transcription Regulatory Sequences and Genes in Coronaviruses. RECOMB (2022)
Palash Sashittal, Simone Zaccaria, Mohammed El-Kebir
Parsimonious Clone Tree Reconciliation in Cancer. WABI (2021)
Leah L. Weber, Mohammed El-Kebir
Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors. Algorithms Mol. Biol. 16 (1) (2021)
Leah L. Weber, Palash Sashittal, Mohammed El-Kebir
doubletD: detecting doublets in single-cell DNA sequencing data. Bioinform. 37 (Supplement) (2021)
Leah L. Weber, Nuraini Aguse, Nicholas Chia, Mohammed El-Kebir
PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors. PLoS Comput. Biol. 16 (10) (2020)
Jiaqi Wu, Mohammed El-Kebir
ClonArch: visualizing the spatial clonal architecture of tumors. Bioinform. 36 (Supplement-1) (2020)
Sarah Christensen, Mark D. M. Leiserson, Mohammed El-Kebir
PhySigs: Phylogenetic Inference of Mutational Signature Dynamics. PSB (2020)
Palash Sashittal, Mohammed El-Kebir
Sampling and summarizing transmission trees with multi-strain infections. Bioinform. 36 (Supplement-1) (2020)
Leah L. Weber, Mohammed El-Kebir
Phyolin: Identifying a Linear Perfect Phylogeny in Single-Cell DNA Sequencing Data of Tumors. WABI (2020)
Nuraini Aguse, Yuanyuan Qi, Mohammed El-Kebir
Summarizing the solution space in tumor phylogeny inference by multiple consensus trees. Bioinform. 35 (14) (2019)
Mohammed El-Kebir
SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error. Bioinform. 34 (17) (2018)
Dikshant Pradhan, Mohammed El-Kebir
On the Non-uniqueness of Solutions to the Perfect Phylogeny Mixture Problem. RECOMB-CG (2018)
Philipp Spohr, Kasper Dinkla, Gunnar W. Klau, Mohammed El-Kebir
eXamine: Visualizing annotated networks in Cytoscape. F1000Research 7 (2018)
Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael
Phylogenetic Copy-Number Factorization of Multiple Tumor Samples. J. Comput. Biol. 25 (7) (2018)
Mohammed El-Kebir
Parsimonious Migration History Problem: Complexity and Algorithms. WABI (2018)
Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael
The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data. RECOMB (2017)
Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira
Complexity and algorithms for copy-number evolution problems. Algorithms Mol. Biol. 12 (1) (2017)
Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael
Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. CoRR (2016)
Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael
Multi-state Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. RECOMB (2016)
Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira
Copy-Number Evolution Problems: Complexity and Algorithms. WABI (2016)
Ali May, Bernd W. Brandt, Mohammed El-Kebir, Gunnar W. Klau, Egija Zaura, Wim Crielaard, Jaap Heringa, Sanne Abeln
metaModules identifies key functional subnetworks in microbiome-related disease. Bioinform. 32 (11) (2016)
Mohammed El-Kebir, Layla Oesper, Hannah Acheson-Field, Benjamin J. Raphael
Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. Bioinform. 31 (12) (2015)
Mohammed El-Kebir, Hayssam Soueidan, Thomas Hume, Daniela Beisser, Marcus T. Dittrich, Tobias Müller, Guillaume Blin, Jaap Heringa, Macha Nikolski, Lodewyk F. A. Wessels, Gunnar W. Klau
xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. Bioinform. 31 (19) (2015)
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment. Algorithms 8 (4) (2015)
Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine J. Smit, Michel A. Westenberg, Gunnar W. Klau
eXamine: Exploring annotated modules in networks. CoRR (2014)
Mohammed El-Kebir, Gunnar W. Klau
Solving the Maximum-Weight Connected Subgraph Problem to Optimality. CoRR (2014)
Mohammed El-Kebir, Bernd W. Brandt, Jaap Heringa, Gunnar W. Klau
A web server for protein-protein interaction network querying. BMC Syst. Biol. 8 (2014)
Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine J. Smit, Michel A. Westenberg, Gunnar W. Klau
eXamine: Exploring annotated modules in networks. BMC Bioinform. 15 (2014)
Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth, Gunnar W. Klau
Mapping proteins in the presence of paralogs using units of coevolution. BMC Bioinform. 14 (S-15) (2013)
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
Charge Group Partitioning in Biomolecular Simulation. J. Comput. Biol. 20 (3) (2013)
Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine J. Smit, Michel A. Westenberg, Gunnar W. Klau
eXamine: a Cytoscape app for exploring annotated modules in networks. CoRR (2013)
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
Charge Group Partitioning in Biomolecular Simulation. RECOMB (2012)
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
Lagrangian Relaxation Applied to Sparse Global Network Alignment CoRR (2011)
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
Lagrangian Relaxation Applied to Sparse Global Network Alignment. PRIB (2011)
Stefan Canzar, Mohammed El-Kebir
A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding. WABI (2011)