Nadia El-Mabrouk

Département d'informatique et de recherche opérationnelle (DIRO)

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List of Publications

  • Gene Tree and Species Tree Reconciliation with Endosymbiotic Gene Transfer (preview)
    Y. Anselmetti, N. El-Mabrouk, M. Lafond and A. Ouangraoua
    ISMB/ECCB , Submitted, 2021
  • Reconstructing the history of syntenies through Super-Reconciliation (preview)
    M. Delabre, N. El-Mabrouk, K. Huber, M. Lafond, V. Moulton, E. Noutahi and M. Sautie Castellanos
    RECOMB-CG , 2018
  • A general framework for gene tree correction based on duplication-loss reconciliation (preview)
    N. El-Mabrouk and A. Ouangraoua
    WABI 2017, Algorithms in Bioinformatics, LIPIcs 88, pp. 8:1-8:14, 2017
  • Orthology Relation and Gene Tree Correction: Complexity Results (preview)
    M. Lafond and N. El-Mabrouk
    WABI 2015, Algorithms in Bioinformatics, Vol. 9289 of LNCS, pp 66-79, 2015.
  • Orthology and paralogy constraints: satisfiability and consistency
    (preview) Please take this version. The journal version is full of errors and mathematical style problems.
    Manuel Lafond and Nadia El-Mabrouk,
    BMC-Genomics, 15(Suppl 6):S12, special issue for RECOMB-CG, 2014.
  • Gene order alignment on trees with multiOrthoAlign
    (preview) Please take this version. The journal version is full of errors and mathematical style problems.
    Billel Benzaid and Nadia El-Mabrouk,
    BMC-Genomics, 15(Suppl 6):S5, special issue for RECOMB-CG, 2014.
  • Gene Tree Correction for Reconciliation and Species Tree Inference: Complexity and Algorithms
    Riccardo Dondi, Nadia El-Mabrouk, and Krister M. Swenson.
    Journal of Discrete Algorithms , Vol. 25, pp. 51 - 65, 2014
  • Gene tree correction guided by orthology
    Manuel Lafond, Magalie Semeria, Krister M. Swenson, Eric Tannier and Nadia El-Mabrouk
    BMC Bioinformatics, Vol. 14, Suppl 15, S5, 2013.
  • Gene Tree Correction for Reconciliation and Species Tree Inference
    K. M. Swenson, A. Doroftei and N. El-Mabrouk
    Algorithms for Molecular Biology, 7(1):31. doi: 10.1186/1748-7188-7-31, 2012.
  • Gene Trees and Species Trees: Irreconcilable Differences
    K. M. Swenson and N. El-Mabrouk
    BMC Bioinformatics 13 (Suppl 19): S15, 2012.
  • A Flexible Ancestral Genome Reconstruction Method based on Gapped Adjacencies
    Y. Gagnon, M. Blanchette and N. El-Mabrouk
    BMC Bioinformatics, 13 (Suppl 19): S4, 2012.
  • An Optimal Reconciliation Algorithm for Gene Trees with Polytomies (preview)
    M. Lafond, K.M. Swenson and N. El-Mabrouk
    WABI 2012, Algorithms in Bioinformatics, LNCS/LNBI 7534, pp.106-122, 2012.
  • Evolution of Genome Organization by Duplication and Loss: an Alignment Approach (preview)
    P. Holloway, K. Swenson, D. Ardell and N. El-Mabrouk
    RECOMB, LNCS/LNBI 7262, 94-112, 2012.
    RECOMB 2012 Best Paper Award
  • Analysis of Gene Order Evolution beyond Single-Copy Genes (preview)
    N. El-Mabrouk and D. Sankoff
    Methods in Molecular Biology, Vol. 855, Evolutionary Genomics: statistical and computational methods, pp. 397 - 429, Springer (Humana), 2012.
  • Evolution of orthologous tandemly arrayed gene clusters
    O. Tremblay-Savard, D. Bertrand and N. El-Mabrouk
    BMC Bioinformatics, 12(Suppl 9):S2 doi:10.1186/1471-2105-12-S9-S2, 2011.
  • Removing Noise from Gene Trees (preview)
    A. Doroftei and N. El-Mabrouk
    WABI 2011, Algorithms in Bioinformatics, LNCS/LNBI 6833, pp.76-91, 2011.
  • Reconstruction of Ancestral Genome subject to Whole Genome Duplication, Speciation, Rearrangement and Loss (preview)
    D. Bertrand, Y. Gagnon, M. Blanchette and N. El-Mabrouk
    WABI , LNCS/LNBI 6293, pp. 78- 89, 2010.
  • New perspectives on gene family evolution: losses in reconciliation and a link with supertrees. (preview)
    C. Chauve and N. El-Mabrouk.
    RECOMB, LNCS 5541, pp. 46-58, 2009.
  • The artiodactyl APOBEC3 innate immune repertoire shows evidence for a multi-functional domain organization that existed in the ancestor of placental mammals.
    R.S. LaRue, S.R. Jonsson, K.A.T. Silverstein, M. Lajoie, D. Bertrand, N. El-Mabrouk, I. Hotzel, V. Andresdottir, T.P.L. Smith and R.S. Harri
    BMC Molecular Biology, Vol.9, No. 104, 20 pages, 2008.
  • Inferring Ancestral Gene Orders for a Family of Tandemly Arrayed Genes.
    D. Bertrand, M. Lajoie and N. El-Mabrouk.
    Journal of Computational Biology, Vol. 15, No.8, pp 1063-1077, 2008.
  • Gene Family Evolution by Duplication, Speciation and Loss.
    C. Chauve, J.P. Doyon and N. El-Mabrouk.
    Journal of Computational Biology , Vol. 15, No.8, pp 1043-1062, 2008.
  • Gene Maps Linearization using Genomic Rearrangement Distances.
    G. Blin, E. Blais, D. Hermelin, P. Guillon, M. Blanchette and N. El-Mabrouk.
    Journal of Computational Biology, Vol. 14, No. 4, pp.394-407, 2007.
  • Duplication and Inversion History of a Tandemly Repeated Genes Family.
    M. Lajoie, D. Bertrand, N. El-Mabrouk and O. Gascuel.
    Journal of Computational Biology, Vol. 14, Issue 4, pp. 462-478, 2007.
  • Deriving Haplotypes through Recombination and Gene Conversion.
    N. El-Mabrouk.
    Journal of Bioinformatics and Computational Biology, Vol. 2, No. 2, pp. 241-256, June 2004.
  • Detection and Validation of Single Gene Inversions .
    J.F. Lefebvre and N. El-Mabrouk, E. Tillier and D. Sankoff.
    Bioinformatics, Vol. 19, Suppl. 1, special issue, 11th International Conference on Intelligent Systems for Molecular Biology (ISMB), pp 190-196, 2003.
  • Approximate Matching of Secondary Structures - Extended Abstract.
    N. El-Mabrouk and M. Raffinot.
    Proceedings of the sixth annual international conference on computational molecular biology (RECOMB02), pages 156-164, April 2002.
    The algorithm contains a flaw. For the complete and corrected version, consult our paper in Journal of Bioinformatics and Computational Biology above.
  • Computational Methods for Genome Comparison and Applications.
    D. Sankoff, N. El-Mabrouk.
    Current Topics in Computational Biology, Chapter 10, Computational Molecular Biology Series, MIT Press, 2001.
  • N. El-Mabrouk. Recovery of ancestral tetraploids. Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map alignment and the Evolution of Gene Families. Computational Biology Series. Kluwer Academic Publishers. Vol 1. pp. 465-477, 2000.
  • D. Sankoff and N. El-Mabrouk. Duplication, rearrangement and reconciliation. Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map alignment and the Evolution of Gene Families. Computational Biology Series. Kluwer Academic Publishers. Vol. 1, pp. 537-550, 2000.
  • N. El-Mabrouk and D. Bryant and D. Sankoff. Reconstructing the Pre-Doubling Genome. Third annual international conference on computational molecular biology (RECOMB99), to appear in the conference proceedings, ACM press. Lyon, France, April 1999.
  • N. El-Mabrouk and J. Nadeau and D. Sankoff. Genome Halving. In M. Farach editor, Lecture Notes in Computer Science, volume 1448 of CPM, 9th annual symposium, pages 235-250. Piscataway, New-Jersey, USA, July 1998.
  • N. El-Mabrouk and F. Lisacek. Very fast identification of RNA motifs in genomic DNA. Application to tRNA search in the yeast genome. Journal of Molecular Biology, 264:46-55, November 1996.