Boyer-Moore Strategy to Efficient Approximate String Matching. - Nadia El-Mabrouk; Maxime Crochemore (CPM, 1996)

Genome Halving. - Nadia El-Mabrouk; Joseph H. Nadeau; David Sankoff (CPM, 1998)

Hybridization and Genome Rearrangement. - Nadia El-Mabrouk; David Sankoff (CPM, 1999)

Reconstructing the pre-doubling genome. - Nadia El-Mabrouk; David Bryant; David Sankoff (RECOMB, 1999)

Genome Rearrangement by Reversals and Insertions/Deletions of Contiguous Segments. - Nadia El-Mabrouk (CPM, 2000)

Approximate matching of secondary structures. - Nadia El-Mabrouk; Mathieu Raffinot (RECOMB, 2002)

Exploring the Set of All Minimal Sequences of Reversals - An Application to Test the Replication-Directed Reversal Hypothesis. - Yasmine Ajana; Jean-François Lefebvre; Elisabeth R. M. Tillier; Nadia El-Mabrouk (WABI, 2002)

Reconstructing an ancestral genome using minimum segments duplications and reversals. - Nadia El-Mabrouk (J. Comput. Syst. Sci., 2002)

Detection and validation of single gene inversions. - Jean-François Lefebvre; Nadia El-Mabrouk; Elisabeth R. M. Tillier; David Sankoff (ISMB (Supplement of Bioinformatics), 2003)

The Reconstruction of Doubled Genomes. - Nadia El-Mabrouk; David Sankoff (SIAM J. Comput., 2003)

The Distribution of Inversion Lengths in Bacteria. - David Sankoff; Jean-François Lefebvre; Elisabeth R. M. Tillier; Adrian Maler; Nadia El-Mabrouk (Comparative Genomics, 2004)

Haplotypes histories as pathways of recombinations. - Nadia El-Mabrouk; Damian Labuda (Bioinform., 2004)

Deriving Haplotypes through Recombination and Gene Conversion Pathways. - Nadia El-Mabrouk (J. Bioinform. Comput. Biol., 2004)

Recovering haplotype structure through recombination and gene conversion. - Mathieu Lajoie; Nadia El-Mabrouk (ECCB/JBI, 2005)

Maximizing Synteny Blocks to Identify Ancestral Homologs. - Guillaume Bourque; Yasmine Yacef; Nadia El-Mabrouk (Comparative Genomics, 2005)

Approximate Matching of Structured Motifs in Dna Sequences. - Nadia El-Mabrouk; Mathieu Raffinot; Jean-Eudes Duchesne; Mathieu Lajoie; Nicolas Luc (J. Bioinform. Comput. Biol., 2005)

Evolution of Tandemly Repeated Sequences Through Duplication and Inversion. - Denis Bertrand; Mathieu Lajoie; Nadia El-Mabrouk; Olivier Gascuel (Comparative Genomics, 2006)

Inferring Gene Orders from Gene Maps Using the Breakpoint Distance. - Guillaume Blin; Eric Blais; Pierre Guillon 001; Mathieu Blanchette; Nadia El-Mabrouk (Comparative Genomics, 2006)

Genome rearrangement with gene families. - Nadia El-Mabrouk (Mathematics of Evolution and Phylogeny, 2007)

Seed-Based Exclusion Method for Non-coding RNA Gene Search. - Jean-Eudes Duchesne; Mathieu Giraud; Nadia El-Mabrouk (COCOON, 2007)

Inferring a Duplication, Speciation and Loss History from a Gene Tree (Extended Abstract). - Cédric Chauve; Jean-Philippe Doyon; Nadia El-Mabrouk (RECOMB-CG, 2007)

Evolution of Tandemly Arrayed Genes in Multiple Species. - Mathieu Lajoie; Denis Bertrand; Nadia El-Mabrouk (RECOMB-CG, 2007)

Gene Maps Linearization Using Genomic Rearrangement Distances. - Guillaume Blin; Eric Blais; Danny Hermelin; Pierre Guillon 001; Mathieu Blanchette; Nadia El-Mabrouk (J. Comput. Biol., 2007)

Duplication and Inversion History of a Tandemly Repeated Genes Family. - Mathieu Lajoie; Denis Bertrand; Nadia El-Mabrouk; Olivier Gascuel (J. Comput. Biol., 2007)

A Phylogenetic Approach to Genetic Map Refinement. - Denis Bertrand; Mathieu Blanchette; Nadia El-Mabrouk (RECOMB-CG, 2008)

Inferring Ancestral Gene Orders for a Family of Tandemly Arrayed Genes. - Denis Bertrand; Mathieu Lajoie; Nadia El-Mabrouk (J. Comput. Biol., 2008)

Gene Family Evolution by Duplication, Speciation, and Loss. - Cédric Chauve; Jean-Philippe Doyon; Nadia El-Mabrouk (J. Comput. Biol., 2008)

New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees. - Cédric Chauve; Nadia El-Mabrouk (RECOMB, 2009)

Genetic Map Refinement Using a Comparative Genomic Approach. - Denis Bertrand; Mathieu Blanchette; Nadia El-Mabrouk (J. Comput. Biol., 2009)

Advances on Genome Duplication Distances. - Yves Gagnon; Olivier Tremblay Savard; Denis Bertrand; Nadia El-Mabrouk (RECOMB-CG, 2010)

Reconstruction of Ancestral Genome Subject to Whole Genome Duplication, Speciation, Rearrangement and Loss. - Denis Bertrand; Yves Gagnon; Mathieu Blanchette; Nadia El-Mabrouk (WABI, 2010)

Removing Noise from Gene Trees. - Andrea Doroftei; Nadia El-Mabrouk (WABI, 2011)

Evolution of orthologous tandemly arrayed gene clusters. - Olivier Tremblay Savard; Denis Bertrand; Nadia El-Mabrouk (BMC Bioinform., 2011)

Genome Halving and Double Distance with Losses. - Olivier Tremblay Savard; Yves Gagnon; Denis Bertrand; Nadia El-Mabrouk (J. Comput. Biol., 2011)

Minimum Leaf Removal for Reconciliation: Complexity and Algorithms. - Riccardo Dondi; Nadia El-Mabrouk (CPM, 2012)

Evolution of Genome Organization by Duplication and Loss: An Alignment Approach. - Patrick Holloway; Krister M. Swenson; David H. Ardell; Nadia El-Mabrouk (RECOMB, 2012)

An Optimal Reconciliation Algorithm for Gene Trees with Polytomies. - Manuel Lafond; Krister M. Swenson; Nadia El-Mabrouk (WABI, 2012)

Gene tree correction for reconciliation and species tree inference. - Krister M. Swenson; Andrea Doroftei; Nadia El-Mabrouk (Algorithms Mol. Biol., 2012)

A flexible ancestral genome reconstruction method based on gapped adjacencies. - Yves Gagnon; Mathieu Blanchette; Nadia El-Mabrouk (BMC Bioinform., 2012)

Gene trees and species trees: irreconcilable differences. - Krister M. Swenson; Nadia El-Mabrouk (BMC Bioinform., 2012)

On the Complexity of Minimum Labeling Alignment of Two Genomes - Riccardo Dondi; Nadia El-Mabrouk (CoRR, 2012)

Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later. - Cédric Chauve; Nadia El-Mabrouk; Laurent Guéguen; Magali Semeria; Eric Tannier (Models and Algorithms for Genome Evolution, 2013)

Error Detection and Correction of Gene Trees. - Manuel Lafond; Krister M. Swenson; Nadia El-Mabrouk (Models and Algorithms for Genome Evolution, 2013)

Aligning and Labeling Genomes under the Duplication-Loss Model. - Riccardo Dondi; Nadia El-Mabrouk (CiE, 2013)

Duplication-Loss Genome Alignment: Complexity and Algorithm. - Billel Benzaid; Riccardo Dondi; Nadia El-Mabrouk (LATA, 2013)

Gene tree correction guided by orthology. - Manuel Lafond; Magali Semeria; Krister M. Swenson; Eric Tannier; Nadia El-Mabrouk (BMC Bioinform., 2013)

Ancestral Genome Organization: An Alignment Approach. - Patrick Holloway; Krister M. Swenson; David H. Ardell; Nadia El-Mabrouk (J. Comput. Biol., 2013)

Polytomy refinement for the correction of dubious duplications in gene trees. - Manuel Lafond; Cédric Chauve; Riccardo Dondi; Nadia El-Mabrouk (Bioinform., 2014)

Gene tree correction for reconciliation and species tree inference: Complexity and algorithms. - Riccardo Dondi; Nadia El-Mabrouk; Krister M. Swenson (J. Discrete Algorithms, 2014)

Orthology Relation and Gene Tree Correction: Complexity Results. - Manuel Lafond; Nadia El-Mabrouk (WABI, 2015)

Reconstructing a SuperGeneTree minimizing reconciliation. - Manuel Lafond; Aïda Ouangraoua; Nadia El-Mabrouk (BMC Bioinform., 2015)

Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost. - Manuel Lafond; Emmanuel Noutahi; Nadia El-Mabrouk (CPM, 2016)

Correction of Weighted Orthology and Paralogy Relations - Complexity and Algorithmic Results. - Riccardo Dondi; Nadia El-Mabrouk; Manuel Lafond (WABI, 2016)

The link between orthology relations and gene trees: a correction perspective. - Manuel Lafond; Riccardo Dondi; Nadia El-Mabrouk (Algorithms Mol. Biol., 2016)

A General Framework for Gene Tree Correction Based on Duplication-Loss Reconciliation. - Nadia El-Mabrouk; Aïda Ouangraoua (WABI, 2017)

Approximating the correction of weighted and unweighted orthology and paralogy relations. - Riccardo Dondi; Manuel Lafond; Nadia El-Mabrouk (Algorithms Mol. Biol., 2017)

CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes. - Emmanuel Noutahi; Virginie Calderon; Mathieu Blanchette; B. Franz Lang; Nadia El-Mabrouk (Bioinform., 2017)

Partial Orthology, Paralogy and Xenology Relations - Satisfiability in terms of Di-Cographs. - Nikolai Nøjgaard; Nadia El-Mabrouk; Daniel Merkle; Nicolas Wieseke; Marc Hellmuth (CoRR, 2017)

Partial Homology Relations - Satisfiability in Terms of Di-Cographs. - Nikolai Nøjgaard; Nadia El-Mabrouk; Daniel Merkle; Nicolas Wieseke; Marc Hellmuth (COCOON, 2018)

Reconstructing the History of Syntenies Through Super-Reconciliation. - Mattéo Delabre; Nadia El-Mabrouk; Katharina T. Huber; Manuel Lafond; Vincent Moulton; Emmanuel Noutahi; Miguel Sautie Castellanos (RECOMB-CG, 2018)

GATC: a genetic algorithm for gene tree construction under the Duplication-Transfer-Loss model of evolution. - Emmanuel Noutahi; Nadia El-Mabrouk (BMC Genom., 2018)

Gene Tree Construction and Correction Using SuperTree and Reconciliation. - Manuel Lafond; Cédric Chauve; Nadia El-Mabrouk; Aïda Ouangraoua (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

ISMB/ECCB 2019 Proceedings. - Yana Bromberg; Nadia El-Mabrouk; Predrag Radivojac (Bioinform., 2019)

The complexity of comparing multiply-labelled trees by extending phylogenetic-tree metrics. - Manuel Lafond; Nadia El-Mabrouk; Katharina T. Huber; Vincent Moulton (Theor. Comput. Sci., 2019)

Evolution through segmental duplications and losses: a Super-Reconciliation approach. - Mattéo Delabre; Nadia El-Mabrouk; Katharina T. Huber; Manuel Lafond; Vincent Moulton; Emmanuel Noutahi; Miguel Sautie Castellanos (Algorithms Mol. Biol., 2020)

ISMB 2020 proceedings. - Nadia El-Mabrouk; Donna K. Slonim (Bioinform., 2020)

A generalized Robinson-Foulds distance for labeled trees. - Samuel Briand; Christophe Dessimoz; Nadia El-Mabrouk; Manuel Lafond; Gabriela Lobinska (BMC Genom., 2020)

Complexity and Algorithms for MUL-Tree Pruning. - Mathieu Gascon; Riccardo Dondi; Nadia El-Mabrouk (IWOCA, 2021)

Predicting the Evolution of Syntenies - An Algorithmic Review. - Nadia El-Mabrouk (Algorithms, 2021)

Gene tree and species tree reconciliation with endosymbiotic gene transfer. - Yoann Anselmetti; Nadia El-Mabrouk; Manuel Lafond; Aïda Ouangraoua (Bioinform., 2021)

Reconciliation with Segmental Duplication, Transfer, Loss and Gain. - Yoann Anselmetti; Mattéo Delabre; Nadia El-Mabrouk (RECOMB-CG, 2022)

Non-Binary Tree Reconciliation with Endosymbiotic Gene Transfer. - Mathieu Gascon; Nadia El-Mabrouk (WABI, 2022)

MUL-tree pruning for consistency and optimal reconciliation - complexity and algorithms. - Mathieu Gascon; Riccardo Dondi; Nadia El-Mabrouk (Theor. Comput. Sci., 2022)

On the complexity of non-binary tree reconciliation with endosymbiotic gene transfer. - Mathieu Gascon; Nadia El-Mabrouk (Algorithms Mol. Biol., 2023)

Simultaneously Building and Reconciling a Synteny Tree. - Mathieu Gascon; Mattéo Delabre; Nadia El-Mabrouk (SPIRE, 2024)

Synesth: Comprehensive Syntenic Reconciliation with Unsampled Lineages. - Mattéo Delabre; Nadia El-Mabrouk (Algorithms, 2024)