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Mohammed El-Kebir
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2020 – today
- 2024
- [j23]Xinyu Gu, Yuanyuan Qi
, Mohammed El-Kebir
DERNA Enables Pareto Optimal RNA Design. J. Comput. Biol. 31(3): 179-196 (2024) - [j22]Mrinmoy Saha Roddur, Sagi Snir, Mohammed El-Kebir
Enforcing Temporal Consistency in Migration History Inference. J. Comput. Biol. 31(5): 396-415 (2024) - [c16]Leah L. Weber
TRIBAL: Tree Inference of B Cell Clonal Lineages. RECOMB 2024: 364-367 - [c15]Yuanyuan Qi, Mohammed El-Kebir:
Sapling: Inferring and Summarizing Tumor Phylogenies from Bulk Data Using Backbone Trees. WABI 2024: 7:1-7:19 - 2023
- [j21]Martin Stroet
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. J. Comput. Aided Mol. Des. 37(8): 357-371 (2023) - [j20]Leah L. Weber, Chuanyi Zhang
Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors. PLoS Comput. Biol. 19(10) (2023) - [c14]Mrinmoy Saha Roddur, Sagi Snir, Mohammed El-Kebir:
Inferring Temporally Consistent Migration Histories. WABI 2023: 9:1-9:22 - [c13]Xinyu Gu, Yuanyuan Qi
Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design. WABI 2023: 21:1-21:20 - 2022
- [j19]Palash Sashittal, Simone Zaccaria, Mohammed El-Kebir:
Parsimonious Clone Tree Integration in cancer. Algorithms Mol. Biol. 17(1): 3 (2022) - [j18]Zubair Lalani, Gillian Chu
CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data. PLoS Comput. Biol. 18(10): 1010614 (2022) - [c12]Chuanyi Zhang
CORSID Enables de novo Identification of Transcription Regulatory Sequences and Genes in Coronaviruses. RECOMB 2022: 360-362 - 2021
- [j17]Leah L. Weber
Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors. Algorithms Mol. Biol. 16(1): 14 (2021) - [j16]Leah L. Weber
doubletD: detecting doublets in single-cell DNA sequencing data. Bioinform. 37(Supplement): 214-221 (2021) - [c11]Palash Sashittal, Simone Zaccaria, Mohammed El-Kebir:
Parsimonious Clone Tree Reconciliation in Cancer. WABI 2021: 9:1-9:21 - [e1]Alessandra Carbone
21st International Workshop on Algorithms in Bioinformatics, WABI 2021, August 2-4, 2021, Virtual Conference. LIPIcs 201, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2021, ISBN 978-3-95977-200-6 [contents] - 2020
- [j15]Jiaqi Wu, Mohammed El-Kebir:
ClonArch: visualizing the spatial clonal architecture of tumors. Bioinform. 36(Supplement-1): i161-i168 (2020) - [j14]Palash Sashittal, Mohammed El-Kebir:
Sampling and summarizing transmission trees with multi-strain infections. Bioinform. 36(Supplement-1): i362-i370 (2020) - [j13]Leah L. Weber
PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors. PLoS Comput. Biol. 16(10) (2020) - [c10]Sarah A. Christensen, Mark D. M. Leiserson, Mohammed El-Kebir:
PhySigs: Phylogenetic Inference of Mutational Signature Dynamics. PSB 2020: 226-237 - [c9]Leah L. Weber, Mohammed El-Kebir:
Phyolin: Identifying a Linear Perfect Phylogeny in Single-Cell DNA Sequencing Data of Tumors. WABI 2020: 5:1-5:14
2010 – 2019
- 2019
- [j12]Nuraini Aguse, Yuanyuan Qi
Summarizing the solution space in tumor phylogeny inference by multiple consensus trees. Bioinform. 35(14): i408-i416 (2019) - 2018
- [j11]Mohammed El-Kebir
SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error. Bioinform. 34(17): i671-i679 (2018) - [j10]Simone Zaccaria
Phylogenetic Copy-Number Factorization of Multiple Tumor Samples. J. Comput. Biol. 25(7): 689-708 (2018) - [c8]Dikshant Pradhan, Mohammed El-Kebir
On the Non-uniqueness of Solutions to the Perfect Phylogeny Mixture Problem. RECOMB-CG 2018: 277-293 - [c7]Mohammed El-Kebir
Parsimonious Migration History Problem: Complexity and Algorithms. WABI 2018: 24:1-24:14 - [i6]Philipp Spohr, Kasper Dinkla, Gunnar W. Klau
eXamine: Visualizing annotated networks in Cytoscape. F1000Research 7: 519 (2018) - 2017
- [j9]Mohammed El-Kebir
Complexity and algorithms for copy-number evolution problems. Algorithms Mol. Biol. 12(1): 13:1-13:11 (2017) - [c6]Simone Zaccaria
The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data. RECOMB 2017: 318-335 - 2016
- [j8]Ali May, Bernd W. Brandt
metaModules identifies key functional subnetworks in microbiome-related disease. Bioinform. 32(11): 1678-1685 (2016) - [c5]Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael:
Multi-state Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. RECOMB 2016: 251 - [c4]Mohammed El-Kebir
Copy-Number Evolution Problems: Complexity and Algorithms. WABI 2016: 137-149 - [i5]Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael:
Multi-State Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. CoRR abs/1604.02605 (2016) - 2015
- [j7]Mohammed El-Kebir
Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment. Algorithms 8(4): 1035-1051 (2015) - [j6]Mohammed El-Kebir
Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. Bioinform. 31(12): 62-70 (2015) - [j5]Mohammed El-Kebir
xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. Bioinform. 31(19): 3147-3155 (2015) - 2014
- [j4]Kasper Dinkla, Mohammed El-Kebir
eXamine: Exploring annotated modules in networks. BMC Bioinform. 15: 201 (2014) - [j3]Mohammed El-Kebir
A web server for protein-protein interaction network querying. BMC Syst. Biol. 8: 40 (2014) - [i4]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 abs/1407.2101 (2014) - [i3]Mohammed El-Kebir, Gunnar W. Klau:
Solving the Maximum-Weight Connected Subgraph Problem to Optimality. CoRR abs/1409.5308 (2014) - 2013
- [j2]Mohammed El-Kebir
Mapping proteins in the presence of paralogs using units of coevolution. BMC Bioinform. 14(S-15): S18 (2013) - [j1]Stefan Canzar
Charge Group Partitioning in Biomolecular Simulation. J. Comput. Biol. 20(3): 188-198 (2013) - [i2]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 abs/1312.4490 (2013) - 2012
- [c3]Stefan Canzar
Charge Group Partitioning in Biomolecular Simulation. RECOMB 2012: 29-43 - 2011
- [c2]Mohammed El-Kebir
Lagrangian Relaxation Applied to Sparse Global Network Alignment. PRIB 2011: 225-236 - [c1]Stefan Canzar
A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding. WABI 2011: 26-38 - [i1]Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau:
Lagrangian Relaxation Applied to Sparse Global Network Alignment. CoRR abs/1108.4358 (2011)
Coauthor Index
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