Gascon, Mathieu; Dondi, Riccardo; El-Mabrouk, Nadia MUL-tree pruning for consistency and optimal reconciliation – complexity and algorithms. (English) Zbl 07605942 Theor. Comput. Sci. 937, 22-38 (2022). MSC: 68Qxx PDFBibTeX XMLCite \textit{M. Gascon} et al., Theor. Comput. Sci. 937, 22--38 (2022; Zbl 07605942) Full Text: DOI
Anselmetti, Yoann; Delabre, Mattéo; El-Mabrouk, Nadia Reconciliation with segmental duplication, transfer, loss and gain. (English) Zbl 1496.92047 Jin, Lingling (ed.) et al., Comparative genomics. 19th international conference, RECOMB-CG 2022, La Jolla, CA, USA, May 20–21, 2022. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 13234, 124-145 (2022). MSC: 92D10 PDFBibTeX XMLCite \textit{Y. Anselmetti} et al., Lect. Notes Comput. Sci. 13234, 124--145 (2022; Zbl 1496.92047) Full Text: DOI
Gascon, Mathieu; Dondi, Riccardo; El-Mabrouk, Nadia Complexity and algorithms for MUL-tree pruning. (English) Zbl 07495032 Flocchini, Paola (ed.) et al., Combinatorial algorithms. 32nd international workshop, IWOCA 2021, Ottawa, ON, Canada, July 5–7, 2021. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 12757, 324-339 (2021). MSC: 68Rxx 68Wxx PDFBibTeX XMLCite \textit{M. Gascon} et al., Lect. Notes Comput. Sci. 12757, 324--339 (2021; Zbl 07495032) Full Text: DOI
Lafond, M.; El-Mabrouk, N.; Huber, K. T.; Moulton, V. The complexity of comparing multiply-labelled trees by extending phylogenetic-tree metrics. (English) Zbl 1410.68172 Theor. Comput. Sci. 760, 15-34 (2019). MSC: 68Q25 05C05 92D15 PDFBibTeX XMLCite \textit{M. Lafond} et al., Theor. Comput. Sci. 760, 15--34 (2019; Zbl 1410.68172) Full Text: DOI arXiv Link
Nøjgaard, Nikolai; El-Mabrouk, Nadia; Merkle, Daniel; Wieseke, Nicolas; Hellmuth, Marc Partial homology relations – satisfiability in terms of di-cographs. (English) Zbl 1512.92056 Wang, Lusheng (ed.) et al., Computing and combinatorics. 24th international conference, COCOON 2018, Qing Dao, China, July 2–4, 2018. Proceedings. Cham: Springer. Lect. Notes Comput. Sci. 10976, 403-415 (2018). MSC: 92D15 05C90 05C85 PDFBibTeX XMLCite \textit{N. Nøjgaard} et al., Lect. Notes Comput. Sci. 10976, 403--415 (2018; Zbl 1512.92056) Full Text: DOI arXiv
El-Mabrouk, Nadia; Ouangraoua, Aïda A general framework for gene tree correction based on duplication-loss reconciliation. (English) Zbl 1443.92128 Schwartz, Russell (ed.) et al., 17th international workshop on algorithms in bioinformatics, WABI 2017, Boston, MA, USA, August 21–23, 2017. Proceedings. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik. LIPIcs – Leibniz Int. Proc. Inform. 88, Article 8, 14 p. (2017). MSC: 92D15 92D10 PDFBibTeX XMLCite \textit{N. El-Mabrouk} and \textit{A. Ouangraoua}, LIPIcs -- Leibniz Int. Proc. Inform. 88, Article 8, 14 p. (2017; Zbl 1443.92128) Full Text: DOI
Dondi, Riccardo; El-Mabrouk, Nadia; Lafond, Manuel Correction of weighted orthology and paralogy relations – complexity and algorithmic results. (English) Zbl 1383.92054 Frith, Martin (ed.) et al., Algorithms in bioinformatics. 16th international workshop, WABI 2016, Aarhus, Denmark, August 22–24, 2016. Proceedings. Cham: Springer (ISBN 978-3-319-43680-7/pbk; 978-3-319-43681-4/ebook). Lecture Notes in Computer Science 9838. Lecture Notes in Bioinformatics, 121-136 (2016). MSC: 92D15 92D10 05C90 05C22 PDFBibTeX XMLCite \textit{R. Dondi} et al., Lect. Notes Comput. Sci. 9838, 121--136 (2016; Zbl 1383.92054) Full Text: DOI Link
Lafond, Manuel; Noutahi, Emmanuel; El-Mabrouk, Nadia Efficient non-binary gene tree resolution with weighted reconciliation cost. (English) Zbl 1380.68484 Grossi, Roberto (ed.) et al., 27th annual symposium on combinatorial pattern matching, CPM 2016, Tel Aviv, Israel, June 27–29, 2016. Proceedings. Wadern: Schloss Dagstuhl – Leibniz Zentrum für Informatik (ISBN 978-3-95977-012-5). LIPIcs – Leibniz International Proceedings in Informatics 54, Article 14, 12 p. (2016). MSC: 68W40 92D10 92D15 PDFBibTeX XMLCite \textit{M. Lafond} et al., LIPIcs -- Leibniz Int. Proc. Inform. 54, Article 14, 12 p. (2016; Zbl 1380.68484) Full Text: DOI
Lafond, Manuel; El-Mabrouk, Nadia Orthology relation and gene tree correction: complexity results. (English) Zbl 1367.92086 Pop, Mihai (ed.) et al., Algorithms in bioinformatics. 15th international workshop, WABI 2015, Atlanta, GA, USA, September 10–12, 2015. Proceedings. Berlin: Springer (ISBN 978-3-662-48220-9/pbk; 978-3-662-48221-6/ebook). Lecture Notes in Computer Science 9289. Lecture Notes in Bioinformatics, 66-79 (2015). MSC: 92D15 92D10 92-08 68Q17 68Q25 PDFBibTeX XMLCite \textit{M. Lafond} and \textit{N. El-Mabrouk}, Lect. Notes Comput. Sci. 9289, 66--79 (2015; Zbl 1367.92086) Full Text: DOI
Dondi, Riccardo; El-Mabrouk, Nadia; Swenson, Krister M. Gene tree correction for reconciliation and species tree inference: complexity and algorithms. (English) Zbl 1284.68694 J. Discrete Algorithms 25, 51-65 (2014). MSC: 68W32 92D20 68Q17 PDFBibTeX XMLCite \textit{R. Dondi} et al., J. Discrete Algorithms 25, 51--65 (2014; Zbl 1284.68694) Full Text: DOI
Lafond, Manuel; Swenson, Krister M.; El-Mabrouk, Nadia Error detection and correction of gene trees. (English) Zbl 1462.92040 Chauve, Cedric (ed.) et al., Models and algorithms for genome evolution. Selected contributions based on the presentations at the MAGE conference, Montréal, Canada, August 23–26, 2013. London: Springer. Comput. Biol. 19, 261-285 (2013). MSC: 92D10 92D15 PDFBibTeX XMLCite \textit{M. Lafond} et al., Comput. Biol. 19, 261--285 (2013; Zbl 1462.92040) Full Text: DOI
Chauve, Cedric (ed.); El-Mabrouk, Nadia (ed.); Tannier, Eric (ed.) Models and algorithms for genome evolution. Selected contributions based on the presentations at the MAGE conference, Montréal, Canada, August 23–26, 2013. (English) Zbl 1274.92002 Computational Biology 19. London: Springer (ISBN 978-1-4471-5297-2/hbk; 978-1-4471-5298-9/ebook). xii, 328 p. (2013). MSC: 92-06 92-04 92D15 92D10 92D20 00B25 PDFBibTeX XMLCite \textit{C. Chauve} (ed.) et al., Models and algorithms for genome evolution. Selected contributions based on the presentations at the MAGE conference, Montréal, Canada, August 23--26, 2013. London: Springer (2013; Zbl 1274.92002) Full Text: DOI
Dondi, Riccardo; El-Mabrouk, Nadia Aligning and labeling genomes under the duplication-loss model. (English) Zbl 1387.68123 Bonizzoni, Paola (ed.) et al., The nature of computation. Logic, algorithms, applications. 9th conference on computability in Europe, CiE 2013, Milan, Italy, July 1–5, 2013. Proceedings. Berlin: Springer (ISBN 978-3-642-39052-4/pbk). Lecture Notes in Computer Science 7921, 97-107 (2013). MSC: 68Q17 92D10 PDFBibTeX XMLCite \textit{R. Dondi} and \textit{N. El-Mabrouk}, Lect. Notes Comput. Sci. 7921, 97--107 (2013; Zbl 1387.68123) Full Text: DOI
Benzaid, Billel; Dondi, Riccardo; El-Mabrouk, Nadia Duplication-loss genome alignment: complexity and algorithm. (English) Zbl 1377.92027 Dediu, Adrian-Horia (ed.) et al., Language and automata theory and applications. 7th international conference, LATA 2013, Bilbao, Spain, April 2–5, 2013. Proceedings. Berlin: Springer (ISBN 978-3-642-37063-2/pbk). Lecture Notes in Computer Science 7810, 116-127 (2013). MSC: 92C40 68Q17 90C39 90C59 92-08 PDFBibTeX XMLCite \textit{B. Benzaid} et al., Lect. Notes Comput. Sci. 7810, 116--127 (2013; Zbl 1377.92027) Full Text: DOI
Dondi, Riccardo; El-Mabrouk, Nadia Minimum leaf removal for reconciliation: complexity and algorithms. (English) Zbl 1358.68114 Kärkkäinen, Juha (ed.) et al., Combinatorial pattern matching. 23rd annual symposium, CPM 2012, Helsinki, Finland, July 3–5, 2012. Proceedings. Berlin: Springer (ISBN 978-3-642-31264-9/pbk). Lecture Notes in Computer Science 7354, 399-412 (2012). MSC: 68Q17 05C05 05C85 92D15 PDFBibTeX XMLCite \textit{R. Dondi} and \textit{N. El-Mabrouk}, Lect. Notes Comput. Sci. 7354, 399--412 (2012; Zbl 1358.68114) Full Text: DOI
Duchesne, Jean-Eudes; Giraud, Mathieu; El-Mabrouk, Nadia Seed-based exclusion method for non-coding RNA gene search. (English) Zbl 1206.92007 Lin, Guohui (ed.), Computing and combinatorics. 13th annual international conference, COCOON 2007, Banff, Canada, July 16–19, 2007. Proceedings. Berlin: Springer (ISBN 978-3-540-73544-1/pbk). Lecture Notes in Computer Science 4598, 27-39 (2007). MSC: 92C40 92C42 PDFBibTeX XMLCite \textit{J.-E. Duchesne} et al., Lect. Notes Comput. Sci. 4598, 27--39 (2007; Zbl 1206.92007) Full Text: DOI
Sankoff, David; Lefebvre, Jean-François; Tillier, Elisabeth; Maler, Adrian; El-Mabrouk, Nadia The distribution of inversion lengths in bacteria. (English) Zbl 1117.92321 Lagergren, Jens (ed.), Comparative genomics. RECOMB 2004 international workshop, RCG 2004, Bertinoro, Italy, October 16–19, 2004. Revised selected papers. Berlin: Springer (ISBN 3-540-24455-7/pbk). Lecture Notes in Computer Science 3388. Lecture Notes in Bioinformatics, 97-108 (2005). MSC: 92D10 92D15 PDFBibTeX XMLCite \textit{D. Sankoff} et al., Lect. Notes Comput. Sci. 3388, 97--108 (2005; Zbl 1117.92321) Full Text: DOI
El-Mabrouk, Nadia Genome rearrangements with gene families. (English) Zbl 1090.92029 Gascuel, Olivier (ed.), Mathematics of evolution and phylogeny. Oxford: Oxford University Press (ISBN 0-19-856610-7/hbk). 291-320 (2005). MSC: 92D15 05C90 05C05 PDFBibTeX XMLCite \textit{N. El-Mabrouk}, in: Mathematics of evolution and phylogeny. Oxford: Oxford University Press. 291--320 (2005; Zbl 1090.92029)
El-Mabrouk, Nadia; Sankoff, David The reconstruction of doubled genomes. (English) Zbl 1046.68056 SIAM J. Comput. 32, No. 3, 754-792 (2003). MSC: 68Q25 05C90 92D10 05C85 PDFBibTeX XMLCite \textit{N. El-Mabrouk} and \textit{D. Sankoff}, SIAM J. Comput. 32, No. 3, 754--792 (2003; Zbl 1046.68056) Full Text: DOI
Ajana, Yasmine; Lefebvre, Jean-François; Tillier, Elisabeth R. M.; El-Mabrouk, Nadia Exploring the set of all minimal sequences of reversals – an application to test the replication-directed reversal hypothesis. (English) Zbl 1016.68690 Guigó, Roderic (ed.) et al., Algorithms in bioinformatics. Second international workshop, WABI 2002, Rome, Italy, September 17-21, 2002, Proceedings. Berlin: Springer. Lect. Notes Comput. Sci. 2452, 300-315 (2002). MSC: 68U99 68W05 92D10 PDFBibTeX XMLCite \textit{Y. Ajana} et al., Lect. Notes Comput. Sci. 2452, 300--315 (2002; Zbl 1016.68690) Full Text: Link
El-Mabrouk, Nadia Reconstructing an ancestral genome using minimum segments duplications and reversals. (English) Zbl 1058.68529 J. Comput. Syst. Sci. 65, No. 3, 442-464 (2002). MSC: 68P10 92D20 PDFBibTeX XMLCite \textit{N. El-Mabrouk}, J. Comput. Syst. Sci. 65, No. 3, 442--464 (2002; Zbl 1058.68529) Full Text: DOI
Sankoff, David; El-Mabrouk, Nadia Duplication, rearrangement, and reconciliation. (English) Zbl 1138.92362 Sankoff, David (ed.) et al., Comparative genomics. Empirical and analytical approaches to gene order dynamics, map alignment and the evolution of gene families. Papers at the DCAF workshop, Québec, Canada, September 22–25, 2000. Dordrecht: Kluwer Academic Publishers (ISBN 0-7923-6583-6/hbk; 0-7923-6584-4/pbk). Computational Biology Series 1, 537-550 (2000). MSC: 92D15 92D10 PDFBibTeX XMLCite \textit{D. Sankoff} and \textit{N. El-Mabrouk}, in: Comparative genomics. Empirical and analytical approaches to gene order dynamics, map alignment and the evolution of gene families. Papers at the DCAF workshop, Québec, Canada, September 22--25, 2000. Dordrecht: Kluwer Academic Publishers. 537--550 (2000; Zbl 1138.92362)
El-Mabrouk, Nadia Recovery of ancestral tetraploids. (English) Zbl 1137.92353 Sankoff, David (ed.) et al., Comparative genomics. Empirical and analytical approaches to gene order dynamics, map alignment and the evolution of gene families. Papers at the DCAF workshop, Québec, Canada, September 22–25, 2000. Dordrecht: Kluwer Academic Publishers (ISBN 0-7923-6583-6/hbk; 0-7923-6584-4/pbk). Computational Biology Series 1, 465-477 (2000). MSC: 92D15 05C90 92-08 PDFBibTeX XMLCite \textit{N. El-Mabrouk}, in: Comparative genomics. Empirical and analytical approaches to gene order dynamics, map alignment and the evolution of gene families. Papers at the DCAF workshop, Québec, Canada, September 22--25, 2000. Dordrecht: Kluwer Academic Publishers. 465--477 (2000; Zbl 1137.92353)
El-Mabrouk, Nadia Genome rearrangement by reversals and insertions/deletions of contiguous segments. (English) Zbl 0964.92030 Giancarlo, Raffaele (ed.) et al., Combinatorial pattern matching. 11th annual symposium, CPM 2000. Montréal, Canada, June 21-23, 2000. Proceedings. Berlin: Springer. Lect. Notes Comput. Sci. 1848, 222-234 (2000). MSC: 92D10 68W05 PDFBibTeX XMLCite \textit{N. El-Mabrouk}, Lect. Notes Comput. Sci. 1848, 222--234 (2000; Zbl 0964.92030)
El-Mabrouk, Nadia; Sankoff, David Hybridization and genome rearrangement. (English) Zbl 1063.68615 Crochemore, Maxime (ed.) et al., Combinatorial pattern matching. 10th annual symposium, CPM 99, Warwick University, UK, July 22–24, 1999. Proceedings. Berlin: Springer (ISBN 3-540-66278-2/pbk). Lecture Notes in Computer Science 1645, 78-87 (1999). MSC: 68R15 92D10 68W05 PDFBibTeX XMLCite \textit{N. El-Mabrouk} and \textit{D. Sankoff}, Lect. Notes Comput. Sci. 1645, 78--87 (1999; Zbl 1063.68615)