Sagot Marie-France

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

2017

Journal article

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How Long Does Wolbachia Remain on Board?

Marc Bailly-Bechet, Patricia Martins-Simões, Gergely Szöllősi, Gladys Mialdea, Marie-France Sagot, Sylvain Charlat

Molecular Biology and Evolution . 34 ( 5 ) : 1183 - 1193

DOI: 10.1093/molbev/msx073

2017

Journal article

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Metabolic Investigation of the Mycoplasmas from the Swine Respiratory Tract

Mariana G Ferrarini, Franciele Maboni Siqueira, Scheila G Mucha, Tony L Palama, Elodie E Jobard, Bénédicte Elena-Herrmann...

JOBIM 2016 .

DOI: 10.1186/s12864-016-2644-z

2016

Poster

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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

2016

Journal article

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Introduction to the Special Theme - Tackling Big Data in the Life Sciences

Roeland M.H. Merks, Marie-France Sagot

2016

Other publication

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Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling

Mariana G. Ferrarini, Franciele M. Siqueira, Scheila G. Mucha, Tony Lionel Palama, Elodie Jobard, Bénédicte Elena-Herrmann...

BMC Genomics . 17 ( 1 ) : 353

DOI: 10.1186/s12864-016-2644-z

2016

Journal article

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SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

Hélène Lopez-Maestre, Lilia Brinza, Camille Marchet, Janice Kielbassa, Sylvère Bastien, Mathilde Boutigny...

Nucleic Acids Research .

DOI: 10.1093/nar/gkw655

2016

Journal article

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DegreeCox – a network-based regularization method for survival analysis

André Veríssimo, Arlindo Limede Oliveira, Marie-France Sagot, Susana Vinga

BMC Bioinformatics . 17 ( Suppl 16 ) : 109-121

DOI: 10.1186/s12859-016-1310-4

2016

Journal article

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Enumeration of minimal stoichiometric precursor sets in metabolic networks

Ricardo Andrade, Martin Wannagat, Cecilia C. Klein, Vicente Acuña, Alberto Marchetti-Spaccamela, Paulo V. Milreu...

Algorithms for Molecular Biology . 11 ( 1 ) : 25

DOI: 10.1186/s13015-016-0087-3

2016

Journal article

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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 . 9702 : 12

DOI: 10.1007/978-3-319-38827-4_10

2016

Journal article

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Computing and Listing st-Paths in Subway Networks

Kateřina Böhmová, Matúš Mihalák, Tobias Pröger, Gustavo Sacomoto, Marie-France Sagot, Peter Widmayer

CSR 2016 - 11th International Computer Science Symposium in Russia . 9691 : 102-116

DOI: 10.1007/978-3-319-34171-2_8

2016

Conference paper

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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 .

2016

Poster

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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

2016

Conference paper

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Mycoplasma non-coding RNA: identification of small RNAs and targets

Franciele Maboni Siqueira, Guilherme Loss de Morais, Susan Higashi, Laura Scherer Beier, Gabriela Merker Breyer, Caio Padoan de Sá Godinho...

BMC Genomics . 23 : 1289 - 26

DOI: 10.1186/s12864-016-3061-z

2016

Journal article

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MeDuSa: A multi-draft based scaffolder.

Emanuele Bosi, Beatrice Donati, Marco Galardini, Sara Brunetti, Marie-France Sagot, Pietro Lió...

Bioinformatics . : pii: btv171 [Epub ahead of print]

DOI: 10.1093/bioinformatics/btv171

2015

Journal article

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A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs

Gustavo Sacomoto, Vincent Lacroix, Marie‑france Sagot

Algorithms for Molecular Biology . : 10

DOI: 10.1186/s13015-015-0046-4

2015

Journal article

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Mitochondrial respiration and genomic analysis provide insight into the influence of the symbiotic bacterium on host trypanosomatid oxygen consumption.

Allan C. Azevedo-Martins, A. C. L. Machado, Cecilia Coimbra Klein, L. Ciapina, Luiz Gonzaga, Ana Tereza Ribeiro Vasconcelos...

Parasitology . 142 ( 2 ) : 352-362

DOI: 10.1017/S0031182014001139

2015

Journal article

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Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci

Qiong Rao, Pierre-Antoine Rollat-Farnier, Dan-Tong Zhu, Diego Santos-Garcia, Francisco J Silva, Andrés Moya...

BMC Genomics . 16 : 226

DOI: 10.1186/s12864-015-1379-6

2015

Journal article

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Two Host Clades, Two Bacterial Arsenals: Evolution through Gene Losses in Facultative Endosymbionts.

Pierre-Antoine Rollat-Farnier, Diego Santos-Garcia, Qiong Rao, Marie-France Sagot, Francisco J Silva, Hélène Henri...

Genome Biology and Evolution . 7 ( 3 ) : 839-855

DOI: 10.1093/gbe/evv030

2015

Journal article

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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

2015

Conference paper

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EUCALYPT: efficient tree reconciliation enumerator

Beatrice Donati, Christian Baudet, Blerina Sinaimeri, Pierluigi Crescenzi, Marie-France Sagot

Algorithms for Molecular Biology . 10 ( 1 ) : 11

DOI: 10.1186/s13015-014-0031-3

2015

Journal article

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Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data

Susan Higashi, Cyril Fournier, Christian Gautier, Christine Gaspin, Marie-France Sagot

BMC Bioinformatics . 16 ( 1 ) : 179

DOI: 10.1186/s12859-015-0594-0

2015

Journal article

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Cophylogeny Reconstruction via an Approximate Bayesian Computation

Christian Baudet, Béatrice Donati, Blerina Sinaimeri, Pierluigi Crescenzi, Christian Gautier, Catherine Matias...

Systematic Biology . 64 ( 3 ) : 416-431

DOI: 10.1093/sysbio/syu129

2015

Journal article

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Annotating arthropods genome to study and compare their metabolism: the ArthropodaCyc collection of Cyc databases powered by CycADS

Patrice Baa-Puyoulet, Augusto Vellozo, Jaime Huerta-Cepas, Gérard Febvay, Federica Calevro, Marie-France Sagot...

13. European Conference on Computational Biology (ECCB) . : 1 p.

2014

Poster

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Amortized Õ(\textbarV)-Delay Algorithm for Listing Chordless Cycles in Undirected Graphs

R. Ferreira, R. Grossi, R. Rizzi, Gustavo Sacomoto, Marie-France Sagot

Lecture Notes in Computer Science . 8737 : 418-429

2014

Journal article

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Efficiently listing bounded length st-paths

Romeo Rizzi, Gustavo Sacomoto, Marie-France Sagot

Twenty-Fifth International Workshop on Combinatorial Algorithms (IWOCA 2014) . : in press

2014

Conference paper

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

Gustavo Sacomoto, Blerina Sinaimeri, Camille Marchet, Vincent Miele, Marie-France Sagot, Vincent Lacroix

WABI 2014 - 14th International Workshop on Algorithms in Bioinformatics . 8701 : 82-96

DOI: 10.1007/978-3-662-44753-6_7

2014

Conference paper

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Rime: Repeat identification

Maria Federico, Pierre Peterlongo, Nadia Pisanti, Marie-France Sagot

Discrete Applied Mathematics . 163 ( 3 ) : 275–286

DOI: 10.1016/j.dam.2013.02.016

2014

Journal article

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Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure

Paulo Vieira Milreu, Cecilia Coimbra Klein, Ludovic Cottret, Vicente Acuña, Etienne E. Birmelé, Michele Borassi...

Bioinformatics . 30 ( 1 ) : 61-70

DOI: 10.1093/bioinformatics/btt597

2014

Journal article

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Amortized Õ(|V|) -Delay Algorithm for Listing Chordless Cycles in Undirected Graphs

Rui Ferreira, Roberto Grossi, Romeo Rizzi, Gustavo Sacomoto, Marie-France Sagot

22th Annual European Symposium on Algorithms . 8737 : 418-429

DOI: 10.1007/978-3-662-44777-2_35

2014

Conference paper

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Publications

Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads

How Long Does Wolbachia Remain on Board?

Metabolic Investigation of the Mycoplasmas from the Swine Respiratory Tract

A Combinatorial Algorithm for Microbial Consortia Synthetic Design

Introduction to the Special Theme - Tackling Big Data in the Life Sciences

Insights on the virulence of swine respiratory tract mycoplasmas through genome-scale metabolic modeling

SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

DegreeCox – a network-based regularization method for survival analysis

Enumeration of minimal stoichiometric precursor sets in metabolic networks

Robustness of the Parsimonious Reconciliation Method in Cophylogeny

Computing and Listing st-Paths in Subway Networks

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

On Maximal Chain Subgraphs and Covers of Bipartite Graphs

Mycoplasma non-coding RNA: identification of small RNAs and targets

MeDuSa: A multi-draft based scaffolder.

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs

Mitochondrial respiration and genomic analysis provide insight into the influence of the symbiotic bacterium on host trypanosomatid oxygen consumption.

Genome reduction and potential metabolic complementation of the dual endosymbionts in the whitefly Bemisia tabaci

Two Host Clades, Two Bacterial Arsenals: Evolution through Gene Losses in Facultative Endosymbionts.

Incremental complexity of a bi-objective hypergraph transversal problem

EUCALYPT: efficient tree reconciliation enumerator

Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data

Cophylogeny Reconstruction via an Approximate Bayesian Computation

Annotating arthropods genome to study and compare their metabolism: the ArthropodaCyc collection of Cyc databases powered by CycADS

Amortized Õ(\textbarV)-Delay Algorithm for Listing Chordless Cycles in Undirected Graphs

Efficiently listing bounded length st-paths

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

Rime: Repeat identification

Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure

Amortized Õ(|V|) -Delay Algorithm for Listing Chordless Cycles in Undirected Graphs