Mohammed El-Kebir

55 papers B 7C 10Misc 1Journal 34Unranked 3
YearRankTypeTitle / Venue / Authors
2026 J jnl
Inferring and summarizing tumor phylogenies from bulk DNA data.
Algorithms Mol. Biol.
Yuanyuan Qi, Henri Schmidt, Mohammed El-Kebir
2026 J jnl
Pharming: Joint Clonal Tree Reconstruction of Single-Nucleotide Variant and Copy Number Aberration Evolution from Single-Cell DNA Sequencing of Tumors.
J. Comput. Biol.
Leah L. Weber, Anna Hart, Idoia Ochoa, Mohammed El-Kebir
2025 B conf
Characterizing the Solution Space of Migration Histories of Metastatic Cancers with MACH2.
RECOMB
Mrinmoy Saha Roddur, Vikram Ramavarapu, Abigail Bunkum, Ariana Huebner, Roman Mineyev, Nicholas McGranahan, Simone Zaccaria, Mohammed El-Kebir
2025 C conf
Dolphyin: A Combinatorial Algorithm for Identifying 1-Dollo Phylogenies in Cancer.
WABI
Daniel W. Feng, Mohammed El-Kebir
2025 J jnl
Fast tumor phylogeny regression via tree-structured dual dynamic programming.
Bioinform.
Henri Schmidt, Yuanyuan Qi, Benjamin J. Raphael, Mohammed El-Kebir
2025 B conf
Pharming: Joint Clonal Tree Reconstruction of SNV and CNA Evolution from Single-Cell DNA Sequencing of Tumors.
RECOMB
Leah L. Weber, Anna Hart, Idoia Ochoa, Mohammed El-Kebir
2024 — conf
Bayesian Optimization for Crop Genetics with Scalable Probabilistic Models.
AABI
Ruhana Azam, Sang T. Truong, Samuel B. Fernandes, Andrew D. B. Leakey, Alexander E. Lipka, Mohammed El-Kebir, Sanmi Koyejo
2024 J jnl
Consensus Tree Under the Ancestor-Descendant Distance is NP-Hard.
J. Comput. Biol.
Yuanyuan Qi, Mohammed El-Kebir
2024 J jnl
DERNA Enables Pareto Optimal RNA Design.
J. Comput. Biol.
Xinyu Gu, Yuanyuan Qi, Mohammed El-Kebir
2024 J jnl
Enforcing Temporal Consistency in Migration History Inference.
J. Comput. Biol.
Mrinmoy Saha Roddur, Sagi Snir, Mohammed El-Kebir
2024 C conf
Sapling: Inferring and Summarizing Tumor Phylogenies from Bulk Data Using Backbone Trees.
WABI
Yuanyuan Qi, Mohammed El-Kebir
2024 B conf
TRIBAL: Tree Inference of B Cell Clonal Lineages.
RECOMB
Leah L. Weber, Derek Reiman, Mrinmoy Saha Roddur, Yuanyuan Qi, Mohammed El-Kebir, Aly A. Khan
2023 C conf
Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design.
WABI
Xinyu Gu, Yuanyuan Qi, Mohammed El-Kebir
2023 C conf
Inferring Temporally Consistent Migration Histories.
WABI
Mrinmoy Saha Roddur, Sagi Snir, Mohammed El-Kebir
2023 J jnl
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules.
J. Comput. Aided Mol. Des.
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
2023 J jnl
Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors.
PLoS Comput. Biol.
Leah L. Weber, Chuanyi Zhang, Idoia Ochoa, Mohammed El-Kebir
2022 J jnl
CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data.
PLoS Comput. Biol.
Zubair Lalani, Gillian Chu, Silas Hsu, Shaw Kagawa, Michael Xiang, Simone Zaccaria, Mohammed El-Kebir
2022 B conf
CORSID Enables de novo Identification of Transcription Regulatory Sequences and Genes in Coronaviruses.
RECOMB
Chuanyi Zhang, Palash Sashittal, Mohammed El-Kebir
2022 J jnl
Parsimonious Clone Tree Integration in cancer.
Algorithms Mol. Biol.
Palash Sashittal, Simone Zaccaria, Mohammed El-Kebir
2021 C ed.
21st International Workshop on Algorithms in Bioinformatics, WABI 2021, Virtual Conference, August 2-4, 2021
WABI
Alessandra Carbone, Mohammed El-Kebir
2021 J jnl
Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors.
Algorithms Mol. Biol.
Leah L. Weber, Mohammed El-Kebir
2021 C conf
Parsimonious Clone Tree Reconciliation in Cancer.
WABI
Palash Sashittal, Simone Zaccaria, Mohammed El-Kebir
2021 J jnl
doubletD: detecting doublets in single-cell DNA sequencing data.
Bioinform.
Leah L. Weber, Palash Sashittal, Mohammed El-Kebir
2020 J jnl
ClonArch: visualizing the spatial clonal architecture of tumors.
Bioinform.
JiaQi Wu, Mohammed El-Kebir
2020 J jnl
Detecting evolutionary patterns of cancers using consensus trees.
Bioinform.
Sarah A. Christensen, Juho Kim, Nicholas Chia, Oluwasanmi Koyejo, Mohammed El-Kebir
2020 J jnl
PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors.
PLoS Comput. Biol.
Leah L. Weber, Nuraini Aguse, Nicholas Chia, Mohammed El-Kebir
2020 Misc conf
PhySigs: Phylogenetic Inference of Mutational Signature Dynamics.
PSB
Sarah A. Christensen, Mark D. M. Leiserson, Mohammed El-Kebir
2020 C conf
Phyolin: Identifying a Linear Perfect Phylogeny in Single-Cell DNA Sequencing Data of Tumors.
WABI
Leah L. Weber, Mohammed El-Kebir
2020 J jnl
Sampling and summarizing transmission trees with multi-strain infections.
Bioinform.
Palash Sashittal, Mohammed El-Kebir
2019 J jnl
Summarizing the solution space in tumor phylogeny inference by multiple consensus trees.
Bioinform.
Nuraini Aguse, Yuanyuan Qi, Mohammed El-Kebir
2018 — conf
On the Non-uniqueness of Solutions to the Perfect Phylogeny Mixture Problem.
RECOMB-CG
Dikshant Pradhan, Mohammed El-Kebir
2018 C conf
Parsimonious Migration History Problem: Complexity and Algorithms.
WABI
Mohammed El-Kebir
2018 J jnl
Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.
J. Comput. Biol.
Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael
2018 J jnl
SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error.
Bioinform.
Mohammed El-Kebir
2018 J jnl
eXamine: Visualizing annotated networks in Cytoscape.
F1000Research
Philipp Spohr, Kasper Dinkla, Gunnar W. Klau, Mohammed El-Kebir
2017 J jnl
Complexity and algorithms for copy-number evolution problems.
Algorithms Mol. Biol.
Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira
2017 B conf
The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data.
RECOMB
Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael
2016 C conf
Copy-Number Evolution Problems: Complexity and Algorithms.
WABI
Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira
2016 J jnl
Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing.
CoRR
Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael
2016 B conf
Multi-state Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing.
RECOMB
Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael
2016 J jnl
metaModules identifies key functional subnetworks in microbiome-related disease.
Bioinform.
Ali May, Bernd W. Brandt, Mohammed El-Kebir, Gunnar W. Klau, Egija Zaura, Wim Crielaard, Jaap Heringa, Sanne Abeln
2015 J jnl
Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment.
Algorithms
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
2015 J jnl
Reconstruction of clonal trees and tumor composition from multi-sample sequencing data.
Bioinform.
Mohammed El-Kebir, Layla Oesper, Hannah Acheson-Field, Benjamin J. Raphael
2015 J jnl
xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.
Bioinform.
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
2014 J jnl
A web server for protein-protein interaction network querying.
BMC Syst. Biol.
Mohammed El-Kebir, Bernd W. Brandt, Jaap Heringa, Gunnar W. Klau
2014 J jnl
Solving the Maximum-Weight Connected Subgraph Problem to Optimality.
CoRR
Mohammed El-Kebir, Gunnar W. Klau
2014 J jnl
eXamine: Exploring annotated modules in networks.
BMC Bioinform.
Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine J. Smit, Michel A. Westenberg, Gunnar W. Klau
2014 J jnl
eXamine: Exploring annotated modules in networks.
CoRR
Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine J. Smit, Michel A. Westenberg, Gunnar W. Klau
2013 J jnl
Charge Group Partitioning in Biomolecular Simulation.
J. Comput. Biol.
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
2013 J jnl
Mapping proteins in the presence of paralogs using units of coevolution.
BMC Bioinform.
Mohammed El-Kebir, Tobias Marschall, Inken Wohlers, Murray Patterson, Jaap Heringa, Alexander Schönhuth, Gunnar W. Klau
2013 J jnl
eXamine: a Cytoscape app for exploring annotated modules in networks.
CoRR
Kasper Dinkla, Mohammed El-Kebir, Cristina-Iulia Bucur, Marco Siderius, Martine J. Smit, Michel A. Westenberg, Gunnar W. Klau
2012 B conf
Charge Group Partitioning in Biomolecular Simulation.
RECOMB
Stefan Canzar, Mohammed El-Kebir, René Pool, Khaled M. Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau
2011 C conf
A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding.
WABI
Stefan Canzar, Mohammed El-Kebir
2011 J jnl
Lagrangian Relaxation Applied to Sparse Global Network Alignment
CoRR
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau
2011 — conf
Lagrangian Relaxation Applied to Sparse Global Network Alignment.
PRIB
Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau