| 2024 | SPIRE | Simultaneously Building and Reconciling a Synteny Tree. | Mathieu Gascon, Matto Delabre, Nadia El-Mabrouk |
| 2022 | WABI | Non-Binary Tree Reconciliation with Endosymbiotic Gene Transfer. | Mathieu Gascon, Nadia El-Mabrouk |
| 2021 | IWOCA | Complexity and Algorithms for MUL-Tree Pruning. | Mathieu Gascon, Riccardo Dondi, Nadia El-Mabrouk |
| 2018 | COCOON | Partial Homology Relations - Satisfiability in Terms of Di-Cographs. | Nikolai Njgaard, Nadia El-Mabrouk, Daniel Merkle, Nicolas Wieseke, Marc Hellmuth |
| 2018 | RECOMB | Reconstructing the History of Syntenies Through Super-Reconciliation. | Matto Delabre, Nadia El-Mabrouk, Katharina T. Huber, Manuel Lafond, Vincent Moulton, Emmanuel Noutahi, Miguel Sautie Castellanos |
| 2017 | WABI | A General Framework for Gene Tree Correction Based on Duplication-Loss Reconciliation. | Nadia El-Mabrouk, Ada Ouangraoua |
| 2016 | CPM | Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost. | Manuel Lafond, Emmanuel Noutahi, Nadia El-Mabrouk |
| 2016 | WABI | Correction of Weighted Orthology and Paralogy Relations - Complexity and Algorithmic Results. | Riccardo Dondi, Nadia El-Mabrouk, Manuel Lafond |
| 2015 | WABI | Orthology Relation and Gene Tree Correction: Complexity Results. | Manuel Lafond, Nadia El-Mabrouk |
| 2013 | CiE | Aligning and Labeling Genomes under the Duplication-Loss Model. | Riccardo Dondi, Nadia El-Mabrouk |
| 2013 | LATA | Duplication-Loss Genome Alignment: Complexity and Algorithm. | Billel Benzaid, Riccardo Dondi, Nadia El-Mabrouk |
| 2012 | CPM | Minimum Leaf Removal for Reconciliation: Complexity and Algorithms. | Riccardo Dondi, Nadia El-Mabrouk |
| 2012 | RECOMB | Evolution of Genome Organization by Duplication and Loss: An Alignment Approach. | Patrick Holloway, Krister M. Swenson, David H. Ardell, Nadia El-Mabrouk |
| 2012 | WABI | An Optimal Reconciliation Algorithm for Gene Trees with Polytomies. | Manuel Lafond, Krister M. Swenson, Nadia El-Mabrouk |
| 2011 | WABI | Removing Noise from Gene Trees. | Andrea Doroftei, Nadia El-Mabrouk |
| 2010 | RECOMB | Advances on Genome Duplication Distances. | Yves Gagnon, Olivier Tremblay-Savard, Denis Bertrand, Nadia El-Mabrouk |
| 2010 | WABI | Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss. | Denis Bertrand, Yves Gagnon, Mathieu Blanchette, Nadia El-Mabrouk |
| 2009 | RECOMB | New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees. | Cdric Chauve, Nadia El-Mabrouk |
| 2008 | RECOMB | A Phylogenetic Approach to Genetic Map Refinement. | Denis Bertrand, Mathieu Blanchette, Nadia El-Mabrouk |
| 2007 | COCOON | Seed-Based Exclusion Method for Non-coding RNA Gene Search. | Jean-Eudes Duchesne, Mathieu Giraud, Nadia El-Mabrouk |
| 2007 | RECOMB | Inferring a Duplication, Speciation and Loss History from a Gene Tree (Extended Abstract). | Cdric Chauve, Jean-Philippe Doyon, Nadia El-Mabrouk |
| 2007 | RECOMB | Evolution of Tandemly Arrayed Genes in Multiple Species. | Mathieu Lajoie, Denis Bertrand, Nadia El-Mabrouk |
| 2006 | RECOMB | Evolution of Tandemly Repeated Sequences Through Duplication and Inversion. | Denis Bertrand, Mathieu Lajoie, Nadia El-Mabrouk, Olivier Gascuel |
| 2006 | RECOMB | Inferring Gene Orders from Gene Maps Using the Breakpoint Distance. | Guillaume Blin, Eric Blais, Pierre Guillon, Mathieu Blanchette, Nadia El-Mabrouk |
| 2005 | ECCB | Recovering haplotype structure through recombination and gene conversion. | Mathieu Lajoie, Nadia El-Mabrouk |
| 2005 | RECOMB | Maximizing Synteny Blocks to Identify Ancestral Homologs. | Guillaume Bourque, Yasmine Yacef, Nadia El-Mabrouk |
| 2004 | RECOMB | The Distribution of Inversion Lengths in Bacteria. | David Sankoff, Jean-Franois Lefebvre, Elisabeth R. M. Tillier, Adrian Maler, Nadia El-Mabrouk |
| 2003 | ISMB | Detection and validation of single gene inversions. | Jean-Franois Lefebvre, Nadia El-Mabrouk, Elisabeth R. M. Tillier, David Sankoff |
| 2002 | RECOMB | Approximate matching of secondary structures. | Nadia El-Mabrouk, Mathieu Raffinot |
| 2002 | WABI | Exploring the Set of All Minimal Sequences of Reversals - An Application to Test the Replication-Directed Reversal Hypothesis. | Yasmine Ajana, Jean-Franois Lefebvre, Elisabeth R. M. Tillier, Nadia El-Mabrouk |
| 2000 | CPM | Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments. | Nadia El-Mabrouk |
| 1999 | CPM | Hybridization and Genome Rearrangement. | Nadia El-Mabrouk, David Sankoff |
| 1999 | RECOMB | Reconstructing the pre-doubling genome. | Nadia El-Mabrouk, David Bryant, David Sankoff |
| 1998 | CPM | Genome Halving. | Nadia El-Mabrouk, Joseph H. Nadeau, David Sankoff |
| 1996 | CPM | Boyer-Moore Strategy to Efficient Approximate String Matching. | Nadia El-Mabrouk, Maxime Crochemore |