Nadia El-Mabrouk

Département d'informatique et de recherche opérationnelle (DIRO)
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Despite the remarkable unity of the basic components of the living world (DNA, RNA, the genetic code), we are probably still not aware of the diversity of genome structures nor of the diversity of means genomes use to evolve. In addition to local mutations affecting genome sequences, various global mutations also affect their overall gene order and content: rearrangements, horizontal gene transfer, hybridization, losses, duplications ranging from single genes to the whole genome. By comparing complete or partial genomes it is possible to infer evolutionary scenarios for gene families, gene clusters or entire genomes, and to predict ancestral characteristics. This has important consequences, not only for documenting the evolutionary history of life on earth, but also for answering many fundamental biological questions regarding gene function, adaptation processes and variations on the genetic and physiological specificities of species. Each problem, each type of mutation (or set of mutations), has its own model and gives rise to specific algorithmic, combinatorial, statistical and mathematical developments. Our research projects are related to these computational biology aspects of comparative genomics.


Publications

  • Reconciliation with Segmental Duplication, Transfer, Loss and Gain (preview)
    M. Delabre, Y. Anselmetti and N. El-Mabrouk
    RECOMB-CG, LNCS, Vol. 13234, pp. 124-145, Springer, 2022
  • Complexity and Algorithms for MUL-Tree Pruning
    M. Gascon, R. Dondi and N. El-Mabrouk
    IWOCA , LNCS, Vol. 12757, pp 324\--339, 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.