GECO Evolutionary and Computational Genomics

Baobab Group

Sagot Marie-France

Directrice de recherche

INRIA

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

Tel: 33 04 72 44 82 38

Email

Publications

Display of 1 to 30 publications on 209 in total

A General Framework for Enumerating Equivalence Classes of Solutions

Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri

Algorithmica . 85 ( 10 ) : 3003-3023

DOI: 10.1007/s00453-023-01131-1

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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 . : syad058

DOI: 10.1093/sysbio/syad058

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BrumiR: A toolkit for de novo discovery of microRNAs from sRNA-seq data

Carol Moraga, Evelyn Sanchez, Mariana Galvão Ferrarini, Rodrigo A Gutierrez, Elena A Vidal, Marie-France Sagot

GigaScience . 11

DOI: 10.1093/gigascience/giac093

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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

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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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A General Framework for Enumerating Equivalence Classes of Solutions

Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri

ESA 2021 - 29th Annual European Symposium on Algorithms . : 1-14

DOI: 10.4230/LIPIcs.ESA.2021.80

Conference paper

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Dichloroacetate and Pyruvate Metabolism: Pyruvate Dehydrogenase Kinases as Targets Worth Investigating for Effective Therapy of Toxoplasmosis

Mariana Galvão Ferrarini, Lindice Mitie Nisimura, Richard Marcel Bruno Moreira Girard, Mayke Bezerra Alencar, Mariana Sayuri Ishikawa Fragoso, Carlla Assis Araújo-Silva...

MSphere . 6 ( 1 )

DOI: 10.1128/mSphere.01002-20

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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, Blerina Sinaimeri

Journal of Graph Algorithms and Applications . 25 ( 1 ) : 549-562

DOI: 10.7155/jgaa.00572

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A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog

Marianne Borderes, Cyrielle Gasc, Emmanuel Prestat, Mariana Galvão Ferrarini, Susana Vinga, Lilia Boucinha...

NAR Genomics and Bioinformatics . 3 ( 1 )

DOI: 10.1093/nargab/lqab009

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Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations

Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri

WABI 2021 - 21st International Workshop on Algorithms in Bioinformatics . : 1-18

DOI: 10.4230/LIPIcs.WABI.2021.3

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Efficient hybrid de novo assembly of human genomes with WENGAN

Alex Di Genova, Elena Buena-Atienza, Stephan Ossowski, Marie-France Sagot

Nature Biotechnology . 39 : 422–430

DOI: 10.1038/s41587-020-00747-w

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MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering

Ricardo Andrade, Mahdi Doostmohammadi, João Santos, Marie-France Sagot, Nuno P Mira, Susana Vinga

BMC Bioinformatics . 21 ( 1 ) : 1-13

DOI: 10.1186/s12859-020-3377-1

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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, Blerina Sinaimeri

IWOCA 2020 - 31st International Workshop on Combinatorial Algorithms . 12126 : 17-29

DOI: 10.1007/978-3-030-48966-3_2

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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

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Mycoplasma hyopneumoniae J elicits an antioxidant response and decreases the expression of ciliary genes in infected swine epithelial cells

Scheila Gabriele Mucha, Mariana G. Ferrarini, Carol Moraga, Alex Di Genova, Laurent Guyon, Florence Tardy...

Scientific Reports . 10 ( 13707 )

DOI: 10.1038/s41598-020-70040-y

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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

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Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions

Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri

Bioinformatics . 36 ( 14 ) : 4197-4199

DOI: 10.1093/bioinformatics/btaa498

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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 . : 1-11

DOI: 10.1109/TCBB.2018.2838667

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A Distance-based block searching algorithm

M-F. Sagot, Alain Viari, H. Soldano

Third International Conference on Intelligent Systems for Molecular Biology (ISMB-95) . 3 : 322-331

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On Bubble Generators in Directed Graphs

Vicente Acuña, Roberto Grossi, Giuseppe F. Italiano, Leandro Lima, Romeo Rizzi, Gustavo Sacomoto...

Algorithmica . : 1-19

DOI: 10.1007/s00453-019-00619-z

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Hydrogen peroxide production and myo-inositol metabolism as important traits for virulence of Mycoplasma hyopneumoniae

Mariana G. Ferrarini, Scheila Gabriele Mucha, Delphine Parrot, Guillaume Meiffren, José Fernando Ruggiero Bachega, Gilles Comte...

Molecular Microbiology . : 1-45

DOI: 10.1111/mmi.13957

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Exploring and Visualising Spaces of Tree Reconciliations

Katharina Huber, Vincent Moulton, Marie-France Sagot, Blerina Sinaimeri

Systematic Biology . : 1-36

DOI: 10.1093/sysbio/syy075

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Pierce's Disease of Grapevines: A Review of Control Strategies and an Outline of an Epidemiological Model

Ifigeneia Kyrkou, Taneli Pusa, Lea Ellegaard-Jensen, Marie-France Sagot, Lars Hestbjerg Hansen

Frontiers in Microbiology . 9 : 1-23

DOI: 10.3389/fmicb.2018.02141

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Geometric medians in reconciliation spaces

Katharina Huber, Vincent Moulton, Marie-France Sagot, Blerina Sinaimeri

Information Processing Letters . 136 : 96 - 101

DOI: 10.1016/j.ipl.2018.04.001

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Fast-SG: an alignment-free algorithm for hybrid assembly

Alex Di Genova, Gonzalo A Ruz, Marie-France Sagot, Alejandro Maass

GigaScience . 7 ( 5 ) : 1 - 15

DOI: 10.1093/gigascience/giy048

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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

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OptPipe - a pipeline for optimizing metabolic engineering targets

András Hartmann, Ana Vila-Santa, Nicolai Kallscheuer, Michael Vogt, Alice Julien-Laferrière, Marie-France Sagot...

BMC Systems Biology . 11 : 1-9

DOI: 10.1186/s12918-017-0515-0

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On Bubble Generators in Directed Graphs

Vicente Acuna, Roberto Grossi, Giuseppe F Italiano, Leandro Lima, Romeo Rizzi, Gustavo Sacomoto...

WG 2017 - 43rd International Workshop on Graph-Theoretic Concepts in Computer Science . 10520 : 18-31

DOI: 10.1007/978-3-319-68705-6_2

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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, Vincent Miele...

Algorithms for Molecular Biology . 12 ( 1 ) : 2

DOI: 10.1186/s13015-017-0091-2

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