GECO Evolutionary and Computational Genomics

Baobab Group

Mary Arnaud

Maître de conférences

UCBL

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

Tel: 04 72 43 15 52

Email

Publications

Display of 1 to 26 publications on 26 in total

Efficient enumeration of maximal split subgraphs and induced sub-cographs and related classes

Caroline Brosse, Aurélie Lagoutte, Vincent Limouzy, Arnaud Mary, Lucas Pastor

Discrete Applied Mathematics . 345 : 34-51

DOI: 10.1016/j.dam.2023.10.025

Journal article

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Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues

Rita Rebollo, Pierre Gerenton, Eric Cumunel, Arnaud Mary, François Sabot, Nelly Burlet...

Peer Community Journal . 4 ( e89 )

DOI: 10.24072/pcjournal.457

Journal article

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Polynomial Delay Algorithm for Minimal Chordal Completions

Caroline Brosse, Vincent Limouzy, Arnaud Mary

49th International Colloquium on Automata, Languages, and Programming (ICALP) .

DOI: 10.4230/LIPIcs.ICALP.2022.33

Conference paper

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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 . 17 ( 1 ) : 1-16

DOI: 10.1186/s13015-022-00206-y

Journal article

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Totoro: Identifying Active Reactions During the Transient State for Metabolic Perturbations

Mariana Galvão Ferrarini, Irene Ziska, Ricardo Andrade, Alice Julien-Laferrière, Louis Duchemin, Roberto Marcondes César...

Frontiers in Genetics . 13 : 1-12

DOI: 10.3389/fgene.2022.815476

Journal article

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CALDERA: Finding all significant de Bruijn subgraphs for bacterial GWAS

Hector Roux de Bézieux, Leandro Lima, Fanny Perraudeau, Arnaud Mary, Sandrine Dudoit, Laurent Jacob

Bioinformatics .

DOI: 10.1093/bioinformatics/btac238

Journal article

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MOOMIN – Mathematical explOration of ’Omics data on a MetabolIc Network

Taneli Pusa, Mariana G. Ferrarini, Ricardo Andrade, Arnaud Mary, Alberto Marchetti-Spaccamela, Leen Stougie...

Bioinformatics . 36 ( 2 ) : 514-523

DOI: 10.1093/bioinformatics/btz584

Journal article

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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 . : 1-16

DOI: 10.1186/s13015-020-00174-1

Journal article

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The Perfect Matching Reconfiguration Problem

Marthe Bonamy, Nicolas Bousquet, Marc Heinrich, Takehiro Ito, Yusuke Kobayashi, Arnaud Mary...

MFCS 2019 - 44th International Symposium on Mathematical Foundations of Computer Science . : 1-14

DOI: 10.4230/LIPIcs.MFCS.2019.80

Conference paper

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Efficient enumeration of solutions produced by closure operations

Arnaud Mary, Yann Strozecki

Discrete Mathematics and Theoretical Computer Science . : 1-30

DOI: 10.23638/DMTCS-21-3-22

Journal article

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Bounding the Order of a Graph Using Its Diameter and Metric Dimension: A Study Through Tree Decompositions and VC Dimension

Laurent Beaudou, Peter Dankelmann, Florent Foucaud, Michael Antony Henning, Arnaud Mary, Aline Parreau

SIAM Journal on Discrete Mathematics . 32 ( 2 ) : 902 - 918

DOI: 10.1137/16M1097833

Journal article

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Reconfiguration of graphs with connectivity constraints

Nicolas Bousquet, Arnaud Mary

WAOA 2018 - International Workshop on Approximation and Online Algorithms . 11312 : 295-309

DOI: 10.1007/978-3-030-04693-4_18

Conference paper

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BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

Alexey Dudnik, Filipa Almeida, Ricardo Andrade, Barbara Avila, Pilar Bañados, Barbay Diane...

Phytochemistry Reviews . : 1-36

DOI: 10.1007/s11101-017-9532-2

Journal article

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Token Jumping in minor-closed classes

Nicolas Bousquet, Arnaud Mary, Aline Parreau

International symposium on fundamentals of computer theory (FCT 2017) . 10472 : 136-149

DOI: 10.1007/978-3-662-55751-8_12

Conference paper

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A Combinatorial Algorithm for Microbial Consortia Synthetic Design

Alice Julien-Laferrière, Laurent Bulteau, Delphine Parrot, Alberto Marchetti-Spaccamela, Leen Stougie, Susana Vinga...

Scientific Reports .

DOI: 10.1038/srep29182

Journal article

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A Polynomial Delay Algorithm for Enumerating Minimal Dominating Sets in Chordal Graphs

Mamadou Moustapha Kanté, Vincent Limouzy, Arnaud Mary, Lhouari Nourine, Takeaki Uno

WG 2015: Graph-Theoretic Concepts in Computer Science . : 138-153

DOI: 10.1007/978-3-662-53174-7_11

Book chapter

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MultiPus: Conception de communautés microbiennes pour la production de composés d'intérêt

A Julien-Laferrière, Laurent Bulteau, D Parrot, A Marchetti-Spaccamela, L Stougie, S Vinga...

Jobim .

Poster

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Efficient Enumeration of Solutions Produced by Closure Operations

Arnaud Mary, Yann Strozecki

33rd Symposium on Theoretical Aspects of Computer Science, STACS 2016 . 47

DOI: 10.4230/LIPIcs.STACS.2016.52

Conference paper

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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 . 9843 : 137-150

DOI: 10.1007/978-3-319-44543-4_11

Conference paper

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Polynomial Delay Algorithm for Listing Minimal Edge Dominating Sets in Graphs

Mamadou Moustapha Kanté, Vincent Limouzy, Arnaud Mary, Lhouari Nourine, Takeaki Uno

Algorithms and Data Structures (WADS) . 9214 : 446-457

Conference paper

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Incremental complexity of a bi-objective hypergraph transversal problem

Ricardo Andrade, Etienne E. Birmelé, Arnaud Mary, Thomas Picchetti, Marie-France Sagot

Fundamentals of Computation Theory (FCT2015) . 9210 : 202-213

DOI: 10.1007/978-3-319-22177-9_16

Conference paper

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An average study of hypergraphs and their minimal transversals

Julien David, Loïck Lhote, Arnaud Mary, François Rioult

Theoretical Computer Science . 596 : 124-141

DOI: 10.1016/j.tcs.2015.06.052

Journal article

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On the Enumeration of Minimal Dominating Sets and Related Notions

Mamadou Moustapha Kanté, Vincent Limouzy, Arnaud Mary, Lhouari Nourine

SIAM Journal on Discrete Mathematics . 28 ( 4 ) : 1916 - 1929

DOI: 10.1137/120862612

Journal article

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