| 2025 | RECOMB | 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 |
| 2025 | RECOMB | 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 |
| 2025 | WABI | Dolphyin: A Combinatorial Algorithm for Identifying 1-Dollo Phylogenies in Cancer. | Daniel W. Feng, Mohammed El-Kebir |
| 2024 | RECOMB | TRIBAL: Tree Inference of B Cell Clonal Lineages. | Leah L. Weber, Derek Reiman, Mrinmoy Saha Roddur, Yuanyuan Qi, Mohammed El-Kebir, Aly A. Khan |
| 2024 | WABI | Sapling: Inferring and Summarizing Tumor Phylogenies from Bulk Data Using Backbone Trees. | Yuanyuan Qi, Mohammed El-Kebir |
| 2023 | WABI | Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design. | Xinyu Gu, Yuanyuan Qi, Mohammed El-Kebir |
| 2023 | WABI | Inferring Temporally Consistent Migration Histories. | Mrinmoy Saha Roddur, Sagi Snir, Mohammed El-Kebir |
| 2022 | RECOMB | CORSID Enables de novo Identification of Transcription Regulatory Sequences and Genes in Coronaviruses. | Chuanyi Zhang, Palash Sashittal, Mohammed El-Kebir |
| 2021 | WABI | Parsimonious Clone Tree Reconciliation in Cancer. | Palash Sashittal, Simone Zaccaria, Mohammed El-Kebir |
| 2020 | PSB | PhySigs: Phylogenetic Inference of Mutational Signature Dynamics. | Sarah A. Christensen, Mark D. M. Leiserson, Mohammed El-Kebir |
| 2020 | WABI | Phyolin: Identifying a Linear Perfect Phylogeny in Single-Cell DNA Sequencing Data of Tumors. | Leah L. Weber, Mohammed El-Kebir |
| 2018 | RECOMB | On the Non-uniqueness of Solutions to the Perfect Phylogeny Mixture Problem. | Dikshant Pradhan, Mohammed El-Kebir |
| 2018 | WABI | Parsimonious Migration History Problem: Complexity and Algorithms. | Mohammed El-Kebir |
| 2017 | RECOMB | 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 |
| 2016 | RECOMB | Multi-state Perfect Phylogeny Mixture Deconvolution and Applications to Cancer Sequencing. | Mohammed El-Kebir, Gryte Satas, Layla Oesper, Benjamin J. Raphael |
| 2016 | WABI | Copy-Number Evolution Problems: Complexity and Algorithms. | Mohammed El-Kebir, Benjamin J. Raphael, Ron Shamir, Roded Sharan, Simone Zaccaria, Meirav Zehavi, Ron Zeira |
| 2012 | RECOMB | Charge Group Partitioning in Biomolecular Simulation. | Stefan Canzar, Mohammed El-Kebir, Ren Pool, Khaled M. Elbassioni, Alpeshkumar K. Malde, Alan E. Mark, Daan P. Geerke, Leen Stougie, Gunnar W. Klau |
| 2011 | WABI | A Mathematical Programming Approach to Marker-Assisted Gene Pyramiding. | Stefan Canzar, Mohammed El-Kebir |