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Efficiently sparse listing of classes of optimal cophylogeny reconciliations

 Yishu Wang , Marie-France Sagot , Arnaud Mary , Blerina Sinaimeri
Algorithms for Molecular Biology, 2022, 17 (1), pp.1-16. ⟨10.1186/s13015-022-00206-y⟩
Article dans une revue hal-03576371v1
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A General Framework for Enumerating Equivalence Classes of Solutions

 Yishu Wang , Arnaud Mary , Marie-France Sagot , Blerina Sinaimeri
Algorithmica, 2023, 85 (10), pp.3003-3023. ⟨10.1007/s00453-023-01131-1⟩
Article dans une revue hal-04365403v1
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A Family of Tree-Based Generators for Bubbles in Directed Graphs

 Vicente Acuña , Leandro Ishi Soares de Lima , Giuseppe F Italiano , Luca Pepè Sciarria , Marie-France Sagot , et al.
IWOCA 2020 - 31st International Workshop on Combinatorial Algorithms, Jun 2020, Bordeaux, France. pp.17-29, ⟨10.1007/978-3-030-48966-3_2⟩
Communication dans un congrès hal-02971154v1
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On Cancellative Set Families

 János Körner , Blerina Sinaimeri
Combinatorics, Probability and Computing, 2007, 16 (5), pp.767-773. ⟨10.1017/S0963548307008413⟩
Article dans une revue hal-00681899v1
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Computing an Evolutionary Ordering is Hard

 Laurent Bulteau , Gustavo Sacomoto , Blerina Sinaimeri
Electronic Notes in Discrete Mathematics, 2015, ⟨10.1016/j.endm.2015.07.043⟩
Article dans une revue hal-01249259v1
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On Bubble Generators in Directed Graphs

 Vicente Acuna , Roberto Grossi , Giuseppe F Italiano , Leandro Lima , Romeo Rizzi , et al.
WG 2017 - 43rd International Workshop on Graph-Theoretic Concepts in Computer Science, Jun 2017, Eindhoven, Netherlands. pp.18-31, ⟨10.1007/978-3-319-68705-6_2⟩
Communication dans un congrès hal-01647516v1
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On Maximal Chain Subgraphs and Covers of Bipartite Graphs

 Tiziana Calamoneri , Mattia Gastaldello , Arnaud Mary , Marie-France Sagot , Blerina Sinaimeri
Combinatorial Algorithms - 27th International Workshop, IWOCA 2016, Aug 2016, Helsinki, Finland. pp.137-150, ⟨10.1007/978-3-319-44543-4_11⟩
Communication dans un congrès hal-01388546v1
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Pairwise Compatibility Graphs: A Survey

 Tiziana Calamoneri , Blerina Sinaimeri
SIAM Review, 2016, 58 (3), pp.445 - 460. ⟨10.1137/140978053⟩
Article dans une revue hal-01388533v1
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A family of tree-based generators for bubbles in directed graphs

 Vicente Acuña , Leandro Ishi Soares de Lima , Giuseppe F Italiano , Luca Pepè Sciarria , Marie-France Sagot , et al.
Journal of Graph Algorithms and Applications, 2021, 25 (1), pp.549-562. ⟨10.7155/jgaa.00572⟩
Article dans une revue hal-03504540v1
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STARGATE-X: a Python package for statistical analysis on the REACTOME network

 Andrea Marino , Blerina Sinaimeri , Enrico Tronci , Tiziana Calamoneri
Journal of Integrative Bioinformatics, 2023, ⟨10.1515/jib-2022-0029⟩
Article dans une revue hal-04365656v1
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Exploring and Visualising Spaces of Tree Reconciliations

 Katharina Huber , Vincent Moulton , Marie-France Sagot , Blerina Sinaimeri
Systematic Biology, 2018, pp.1-36. ⟨10.1093/sysbio/syy075⟩
Article dans une revue hal-01964682v1
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EUCALYPT: efficient tree reconciliation enumerator

 Beatrice Donati , Christian Baudet , Blerina Sinaimeri , Pierluigi Crescenzi , Marie-France Sagot
Algorithms for Molecular Biology, 2015, 10 (1), pp.11. ⟨10.1186/s13015-014-0031-3⟩
Article dans une revue hal-01092977v1
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Cophylogeny Reconstruction via an Approximate Bayesian Computation

 Christian Baudet , Béatrice Donati , Blerina Sinaimeri , Pierluigi Crescenzi , Christian Gautier , et al.
Systematic Biology, 2015, 64 (3), pp.416-431. ⟨10.1093/sysbio/syu129⟩
Article dans une revue hal-01092972v1
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Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny

 Laura Urbini , Blerina Sinaimeri , Catherine Matias , Marie-France Sagot
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2019, pp.1-11. ⟨10.1109/TCBB.2018.2838667⟩
Article dans une revue hal-01842451v1
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On types of growth for graph-different permutations

 János Körner , Gábor Simonyi , Blerina Sinaimeri
J. Comb. Theory, Ser. A, 2009, 116 (3), pp.713-723. ⟨10.1016/j.jcta.2008.11.003⟩
Article dans une revue hal-00681907v1
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Cophylogeny Reconstruction Allowing for Multiple Associations Through Approximate Bayesian Computation

 Blerina Sinaimeri , Laura Urbini , Marie-France Sagot , Catherine Matias
Systematic Biology, 2023, pp.syad058. ⟨10.1093/sysbio/syad058⟩
Article dans une revue hal-03673256v4
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Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions

 Yishu Wang , Arnaud Mary , Marie-France Sagot , Blerina Sinaimeri
Bioinformatics, 2020, 36 (14), pp.4197-4199. ⟨10.1093/bioinformatics/btaa498⟩
Article dans une revue hal-02917341v1
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Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility

 Tiziana Calamoneri , Mattia Gastaldello , Arnaud Mary , Marie-France Sagot , Blerina Sinaimeri
Algorithms for Molecular Biology, 2020, pp.1-16. ⟨10.1186/s13015-020-00174-1⟩
Article dans une revue hal-02917569v1

On variants of Vertex Geography on undirected graphs

 Angelo Monti , Blerina Sinaimeri
Discrete Applied Mathematics, 2018, 251, pp.268-275. ⟨10.1016/j.dam.2018.05.044⟩
Article dans une revue hal-01965197v1

Navigating in a Sea of Repeats in RNA-seq without Drowning

 Gustavo Sacomoto , Blerina Sinaimeri , Camille Marchet , Vincent Miele , Marie-France Sagot , et al.
WABI 2014 - 14th International Workshop on Algorithms in Bioinformatics, Sep 2014, Wroclaw, Poland. pp.82-96, ⟨10.1007/978-3-662-44753-6_7⟩
Communication dans un congrès hal-01079947v1
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Geometric medians in reconciliation spaces

 Katharina Huber , Vincent Moulton , Marie-France Sagot , Blerina Sinaimeri
Information Processing Letters, 2018, 136, pp.96 - 101. ⟨10.1016/j.ipl.2018.04.001⟩
Article dans une revue hal-01842439v2
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Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

 Leandro Lima , Blerina Sinaimeri , Gustavo Sacomoto , Helene Lopez-Maestre , Camille Marchet , et al.
Algorithms for Molecular Biology, 2017, 12 (1), pp.2. ⟨10.1186/s13015-017-0091-2⟩
Article dans une revue hal-01474524v1
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On the domination number of t-constrained de Bruijn graphs

 Tiziana Calamoneri , Angelo Monti , Blerina Sinaimeri
Discrete Mathematics and Theoretical Computer Science, 2022, 24 (2), ⟨10.46298/dmtcs.8879⟩
Article dans une revue hal-03832873v1
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Robustness of the Parsimonious Reconciliation Method in Cophylogeny

 Laura Urbini , Blerina Sinaimeri , Catherine Matias , Marie-France Sagot
Lecture Notes in Computer Science, 2016, Algorithms for Computational Biology, 9702, pp.12. ⟨10.1007/978-3-319-38827-4_10⟩
Article dans une revue hal-01349773v1
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Co-divergence and tree topology

 Tiziana Calamoneri , Angelo Monti , Blerina Sinaimeri
Journal of Mathematical Biology, 2019, 79 (3), pp.1149-1167. ⟨10.1007/s00285-019-01385-w⟩
Article dans une revue hal-02298643v1
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