Lagrangian Relaxation Applied to Sparse Global Network Alignment. - Mohammed El-Kebir; Jaap Heringa; Gunnar W. Klau (PRIB, 2011)

A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding. - Stefan Canzar; Mohammed El-Kebir (WABI, 2011)

Charge Group Partitioning in Biomolecular Simulation. - Stefan Canzar; Mohammed El-Kebir; René Pool; Khaled M. Elbassioni; Alpeshkumar K. Malde; Alan E. Mark; Daan P. Geerke; Leen Stougie; Gunnar W. Klau (RECOMB, 2012)

Mapping proteins in the presence of paralogs using units of coevolution. - Mohammed El-Kebir; Tobias Marschall; Inken Wohlers; Murray Patterson; Jaap Heringa; Alexander Schönhuth; Gunnar W. Klau (BMC Bioinform., 2013)

eXamine: a Cytoscape app for exploring annotated modules in networks. - Kasper Dinkla; Mohammed El-Kebir; Cristina-Iulia Bucur; Marco Siderius; Martine J. Smit; Michel A. Westenberg; Gunnar W. Klau (CoRR, 2013)

Charge Group Partitioning in Biomolecular Simulation. - Stefan Canzar; Mohammed El-Kebir; René Pool; Khaled M. Elbassioni; Alan E. Mark; Daan P. Geerke; Leen Stougie; Gunnar W. Klau (J. Comput. Biol., 2013)

eXamine: Exploring annotated modules in networks. - Kasper Dinkla; Mohammed El-Kebir; Cristina-Iulia Bucur; Marco Siderius; Martine J. Smit; Michel A. Westenberg; Gunnar W. Klau (BMC Bioinform., 2014)

A web server for protein-protein interaction network querying. - Mohammed El-Kebir; Bernd W. Brandt; Jaap Heringa; Gunnar W. Klau (BMC Syst. Biol., 2014)

Solving the Maximum-Weight Connected Subgraph Problem to Optimality. - Mohammed El-Kebir; Gunnar W. Klau (CoRR, 2014)

Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment. - Mohammed El-Kebir; Jaap Heringa; Gunnar W. Klau (Algorithms, 2015)

Reconstruction of clonal trees and tumor composition from multi-sample sequencing data. - Mohammed El-Kebir; Layla Oesper; Hannah Acheson-Field; Benjamin J. Raphael (Bioinform., 2015)

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. - Mohammed El-Kebir; Hayssam Soueidan; Thomas Hume; Daniela Beisser; Marcus T. Dittrich; Tobias Müller 001; Guillaume Blin; Jaap Heringa; Macha Nikolski; Lodewyk F. A. Wessels; Gunnar W. Klau (Bioinform., 2015)

Multi-state Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. - Mohammed El-Kebir; Gryte Satas; Layla Oesper; Benjamin J. Raphael (RECOMB, 2016)

Copy-Number Evolution Problems: Complexity and Algorithms. - Mohammed El-Kebir; Benjamin J. Raphael; Ron Shamir; Roded Sharan; Simone Zaccaria; Meirav Zehavi; Ron Zeira (WABI, 2016)

metaModules identifies key functional subnetworks in microbiome-related disease. - Ali May; Bernd W. Brandt; Mohammed El-Kebir; Gunnar W. Klau; Egija Zaura; Wim Crielaard; Jaap Heringa; Sanne Abeln (Bioinform., 2016)

The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data. - Simone Zaccaria; Mohammed El-Kebir; Gunnar W. Klau; Benjamin J. Raphael (RECOMB, 2017)

Complexity and algorithms for copy-number evolution problems. - Mohammed El-Kebir; Benjamin J. Raphael; Ron Shamir; Roded Sharan; Simone Zaccaria; Meirav Zehavi; Ron Zeira (Algorithms Mol. Biol., 2017)

On the Non-uniqueness of Solutions to the Perfect Phylogeny Mixture Problem. - Dikshant Pradhan; Mohammed El-Kebir (RECOMB-CG, 2018)

Parsimonious Migration History Problem: Complexity and Algorithms. - Mohammed El-Kebir (WABI, 2018)

SPhyR: tumor phylogeny estimation from single-cell sequencing data under loss and error. - Mohammed El-Kebir (Bioinform., 2018)

eXamine: Visualizing annotated networks in Cytoscape. - Philipp Spohr; Kasper Dinkla; Gunnar W. Klau; Mohammed El-Kebir (F1000Research, 2018)

Phylogenetic Copy-Number Factorization of Multiple Tumor Samples. - Simone Zaccaria; Mohammed El-Kebir; Gunnar W. Klau; Benjamin J. Raphael (J. Comput. Biol., 2018)

Summarizing the solution space in tumor phylogeny inference by multiple consensus trees. - Nuraini Aguse; Yuanyuan Qi; Mohammed El-Kebir (Bioinform., 2019)

PhySigs: Phylogenetic Inference of Mutational Signature Dynamics. - Sarah A. Christensen; Mark D. M. Leiserson; Mohammed El-Kebir (PSB, 2020)

Phyolin: Identifying a Linear Perfect Phylogeny in Single-Cell DNA Sequencing Data of Tumors. - Leah L. Weber; Mohammed El-Kebir (WABI, 2020)

Detecting evolutionary patterns of cancers using consensus trees. - Sarah A. Christensen; Juho Kim; Nicholas Chia; Oluwasanmi Koyejo; Mohammed El-Kebir (Bioinform., 2020)

Sampling and summarizing transmission trees with multi-strain infections. - Palash Sashittal; Mohammed El-Kebir (Bioinform., 2020)

ClonArch: visualizing the spatial clonal architecture of tumors. - Jiaqi Wu; Mohammed El-Kebir (Bioinform., 2020)

PhyDOSE: Design of follow-up single-cell sequencing experiments of tumors. - Leah L. Weber; Nuraini Aguse; Nicholas Chia; Mohammed El-Kebir (PLoS Comput. Biol., 2020)

Parsimonious Clone Tree Reconciliation in Cancer. - Palash Sashittal; Simone Zaccaria; Mohammed El-Kebir (WABI, 2021)

Distinguishing linear and branched evolution given single-cell DNA sequencing data of tumors. - Leah L. Weber; Mohammed El-Kebir (Algorithms Mol. Biol., 2021)

doubletD: detecting doublets in single-cell DNA sequencing data. - Leah L. Weber; Palash Sashittal; Mohammed El-Kebir (Bioinform., 2021)

CORSID Enables de novo Identification of Transcription Regulatory Sequences and Genes in Coronaviruses. - Chuanyi Zhang; Palash Sashittal; Mohammed El-Kebir (RECOMB, 2022)

Parsimonious Clone Tree Integration in cancer. - Palash Sashittal; Simone Zaccaria; Mohammed El-Kebir (Algorithms Mol. Biol., 2022)

CNAViz: An interactive webtool for user-guided segmentation of tumor DNA sequencing data. - Zubair Lalani; Gillian Chu; Silas Hsu; Shaw Kagawa; Michael Xiang; Simone Zaccaria; Mohammed El-Kebir (PLoS Comput. Biol., 2022)

Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design. - Xinyu Gu; Yuanyuan Qi; Mohammed El-Kebir (WABI, 2023)

Inferring Temporally Consistent Migration Histories. - Mrinmoy Saha Roddur; Sagi Snir; Mohammed El-Kebir (WABI, 2023)

OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. - 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; et al. (J. Comput. Aided Mol. Des., 2023)

Phertilizer: Growing a clonal tree from ultra-low coverage single-cell DNA sequencing of tumors. - Leah L. Weber; Chuanyi Zhang; Idoia Ochoa; Mohammed El-Kebir (PLoS Comput. Biol., 2023)

Bayesian Optimization for Crop Genetics with Scalable Probabilistic Models. - Ruhana Azam; Sang T. Truong; Samuel B. Fernandes; Andrew D. B. Leakey; Alexander E. Lipka; Mohammed El-Kebir; Sanmi Koyejo (AABI, 2024)

TRIBAL: Tree Inference of B Cell Clonal Lineages. - Leah L. Weber; Derek Reiman; Mrinmoy Saha Roddur; Yuanyuan Qi; Mohammed El-Kebir; Aly A. Khan (RECOMB, 2024)

Sapling: Inferring and Summarizing Tumor Phylogenies from Bulk Data Using Backbone Trees. - Yuanyuan Qi; Mohammed El-Kebir (WABI, 2024)

DERNA Enables Pareto Optimal RNA Design. - Xinyu Gu; Yuanyuan Qi; Mohammed El-Kebir (J. Comput. Biol., 2024)

Enforcing Temporal Consistency in Migration History Inference. - Mrinmoy Saha Roddur; Sagi Snir; Mohammed El-Kebir (J. Comput. Biol., 2024)

Consensus Tree Under the Ancestor-Descendant Distance is NP-Hard. - Yuanyuan Qi; Mohammed El-Kebir (J. Comput. Biol., 2024)

Characterizing the Solution Space of Migration Histories of Metastatic Cancers with MACH2. - Mrinmoy Saha Roddur; Vikram Ramavarapu; Abigail Bunkum; Ariana Huebner; Roman Mineyev; Nicholas McGranahan; Simone Zaccaria; Mohammed El-Kebir (RECOMB, 2025)

Pharming: Joint Clonal Tree Reconstruction of SNV and CNA Evolution from Single-Cell DNA Sequencing of Tumors. - Leah L. Weber; Anna Hart; Idoia Ochoa; Mohammed El-Kebir (RECOMB, 2025)

Dolphyin: A Combinatorial Algorithm for Identifying 1-Dollo Phylogenies in Cancer. - Daniel W. Feng; Mohammed El-Kebir (WABI, 2025)