Mohammed El-Kebir

Orcid: 0000-0002-1468-2407

According to our database1, Mohammed El-Kebir authored at least 38 papers between 2011 and 2023.

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Bibliography

2023
Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors.
PLoS Comput. Biol., October, 2023

OFraMP: a fragment-based tool to facilitate the parametrization of large molecules.
J. Comput. Aided Mol. Des., August, 2023

Inferring Temporally Consistent Migration Histories.
Proceedings of the 23rd International Workshop on Algorithms in Bioinformatics, 2023

Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design.
Proceedings of the 23rd International Workshop on Algorithms in Bioinformatics, 2023

2022
CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data.
PLoS Comput. Biol., October, 2022

Parsimonious Clone Tree Integration in cancer.
Algorithms Mol. Biol., 2022

CORSID Enables de novo Identification of Transcription Regulatory Sequences and Genes in Coronaviruses.
Proceedings of the Research in Computational Molecular Biology, 2022

2021
doubletD: detecting doublets in single-cell DNA sequencing data.
Bioinform., 2021

Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors.
Algorithms Mol. Biol., 2021

Parsimonious Clone Tree Reconciliation in Cancer.
Proceedings of the 21st International Workshop on Algorithms in Bioinformatics, 2021

2020
PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors.
PLoS Comput. Biol., 2020

ClonArch: visualizing the spatial clonal architecture of tumors.
Bioinform., 2020

Sampling and summarizing transmission trees with multi-strain infections.
Bioinform., 2020

Phyolin: Identifying a Linear Perfect Phylogeny in Single-Cell DNA Sequencing Data of Tumors.
Proceedings of the 20th International Workshop on Algorithms in Bioinformatics, 2020

PhySigs: Phylogenetic Inference of Mutational Signature Dynamics.
Proceedings of the Pacific Symposium on Biocomputing 2020, 2020

2019
Summarizing the solution space in tumor phylogeny inference by multiple consensus trees.
Bioinform., 2019

2018
Phylogenetic Copy-Number Factorization of Multiple Tumor Samples.
J. Comput. Biol., 2018

eXamine: Visualizing annotated networks in Cytoscape.
F1000Research, 2018

SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error.
Bioinform., 2018

Parsimonious Migration History Problem: Complexity and Algorithms.
Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

On the Non-uniqueness of Solutions to the Perfect Phylogeny Mixture Problem.
Proceedings of the Comparative Genomics - 16th International Conference, 2018

2017
Complexity and algorithms for copy-number evolution problems.
Algorithms Mol. Biol., 2017

The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data.
Proceedings of the Research in Computational Molecular Biology, 2017

2016
metaModules identifies key functional subnetworks in microbiome-related disease.
Bioinform., 2016

Copy-Number Evolution Problems: Complexity and Algorithms.
Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016

Multi-state Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing.
Proceedings of the Research in Computational Molecular Biology - 20th Annual Conference, 2016

2015
xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.
Bioinform., 2015

Reconstruction of clonal trees and tumor composition from multi-sample sequencing data.
Bioinform., 2015

Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment.
Algorithms, 2015

2014
Solving the Maximum-Weight Connected Subgraph Problem to Optimality.
CoRR, 2014

A web server for protein-protein interaction network querying.
BMC Syst. Biol., 2014

eXamine: Exploring annotated modules in networks.
BMC Bioinform., 2014

2013
Charge Group Partitioning in Biomolecular Simulation.
J. Comput. Biol., 2013

eXamine: a Cytoscape app for exploring annotated modules in networks.
CoRR, 2013

Mapping proteins in the presence of paralogs using units of coevolution.
BMC Bioinform., 2013

2012
Charge Group Partitioning in Biomolecular Simulation.
Proceedings of the Research in Computational Molecular Biology, 2012

2011
A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding.
Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

Lagrangian Relaxation Applied to Sparse Global Network Alignment.
Proceedings of the Pattern Recognition in Bioinformatics, 2011


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