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Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification

 Laurent Marsan , Marie-France Sagot
Journal of Computational Biology, 2001, 7 (1), pp.345-360
Article dans une revue hal-00619684v1

Les réseaux métaboliques et génétiques

 H. Charles , G. Beslon , Federica Calevro , Jean-François Boulicaut , J.M. Fayard , et al.
Journée INSA de Lyon "BioIngénierie / Sciences et Ingénierie du Vivant", 2008, Villeurbanne (France), juillet 2008, France. pp.1-1
Communication dans un congrès hal-00391271v1

Caractérisation et modélisation de la « fonction symbiotique » de Buchnera aphidicola chez le puceron du pois Acyrthosiphon pisum

 Hubert Charles , Federica Calevro , Stefano Colella , Jean-Michel Fayard , Gérard Febvay , et al.
Séminaire INRA AgroBI, 2008, Bordeaux, décembre 2008, France
Communication dans un congrès hal-02824972v1
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Absence of a core metabolic network common to symbiotic bacteria

 Cecilia Coimbra Klein , Ludovic Cottret , Hubert Charles , Christian Gautier , Ana Tereza Ribeiro de Vasconcelos , et al.
6. Meeting GDRE-RA Comparative genomics, Nov 2011, Lyon, France. 33 diapositives
Communication dans un congrès hal-02806316v1

Development of the Acyrthosiphon pisum Cyc database (ApsCyc) : from genome sequence to metabolic network analyses

 Augusto Vellozo , Stefano Colella , Ludovic Cottret , Gérard Febvay , Federica Calevro , et al.
Integrative Post-Genomics - IPG'08, 2008, Lyon, novembre 2008, France
Communication dans un congrès hal-02821711v1
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Biosynthesis of vitamins and cofactors in bacterium-harbouring trypanosomatids depends on the symbiotic association as revealed by genomic analyses

 Cecilia C Klein , João M P Alves , Myrna G Serrano , Gregory A Buck , Ana Tereza R Vasconcelos , et al.
PLoS ONE, 2013, 8 (11), pp.e79786. ⟨10.1371/journal.pone.0079786⟩
Article dans une revue hal-00922587v1
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Reaction Motifs in Metabolic Networks

 Vincent Lacroix , Cristina Gomes Fernandes , Marie-France Sagot
RR-5563, INRIA. 2005, pp.14
Rapport inria-00070443v1
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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

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data

 Gustavo Akio Tominaga Sacomoto , Vincent Lacroix , Marie-France Sagot
Workshop on Algorithms in Bioinformatics (WABI), Sep 2013, Nice, France
Communication dans un congrès hal-00842982v1

Motif search in graphs: application to metabolic networks.

 Vincent Lacroix , C.G. Fernandes , M.-F. Sagot
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2006, 3 - n°4, pp.360-368
Article dans une revue hal-00427984v1

A Double Combinatorial Approach to Discovering Patterns in Biological Sequences

 M.-F. Sagot , Alain Viari
incollection, 1996, 1075, pp.186-208
Article dans une revue hal-00435048v1
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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, 2015, pp.10. ⟨10.1186/s13015-015-0046-4⟩
Article dans une revue hal-01170399v1
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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 , et al.
GigaScience, 2022, 11, ⟨10.1093/gigascience/giac093⟩
Article dans une revue hal-03831360v1
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A Comparative Study of Bases for Motif Inference

 Nadia Pisanti , Maxime Crochemore , Roberto Grossi , Marie-France Sagot
String Algorithmics, 2005, Londres, United Kingdom. pp.195-225
Communication dans un congrès hal-00620115v1
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A basis of tiling motifs for generating repeated patterns and its complexity for higher quorum

 Nadia Pisanti , Maxime Crochemore , Roberto Grossi , Marie-France Sagot
International Symposium on Mathematical Foundations of Computer Science 2003, Aug 2003, Bratislava, Slovakia. pp.622-632, ⟨10.1007/978-3-540-45138-9_56⟩
Communication dans un congrès hal-00620116v1
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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

Systemic analysis of the symbiotic function of Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum.

 Lilia Brinza , José Viñuelas , Ludovic Cottret , Federica Calevro , Yvan Rahbé , et al.
Comptes Rendus Biologies, 2009, 332 (11), pp.1034-49. ⟨10.1016/j.crvi.2009.09.007⟩
Article dans une revue istex hal-00445861v1
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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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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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An asymmetric approach to preserve common intervals while sorting by reversals

 Marília D.V. Braga , Christian Gautier , Marie-France Sagot
Algorithms for Molecular Biology, 2009, 4 (1), pp.16. ⟨10.1186/1748-7188-4-16⟩
Article dans une revue hal-00784445v1
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Lossless filter for multiple repeats with bounded edit distance

 Pierre Peterlongo , Gustavo Akio Tominaga Sacomoto , Alair Pereira Do Lago , Nadia Pisanti , Marie-France Sagot
Algorithms for Molecular Biology, 2009, 4 (1), pp.3. ⟨10.1186/1748-7188-4-3⟩
Article dans une revue hal-00784457v1
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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 , et al.
Algorithms for Molecular Biology, 2016, 11 (1), pp.25. ⟨10.1186/s13015-016-0087-3⟩
Article dans une revue hal-01368653v1
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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, 2018, 7 (5), pp.1 - 15. ⟨10.1093/gigascience/giy048⟩
Article dans une revue hal-01842462v1
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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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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

SymBioCyc: Metabolic data on endosymbiotic, parasitic and free bacteria

 L. Cottret , H. Charles , M.F. Sagot
Integrative Post-Genomics - IPG'07, 2007, Lyon (France), novembre 2007, France. pp.1-1
Communication dans un congrès hal-00391290v1

AcypiCyc (Acyrthosiphon pisum Cyc database) : a model database to visualize and study the metabolic network underlying the pea aphid-Buchnera symbiosis

 Stefano Colella , Augusto Vellozo , Ludovic Cottret , Gérard Febvay , Federica Calevro , et al.
6. International Symbiosis Society (ISS) Congress, 2009, Madison, août 2009, United States
Communication dans un congrès hal-02814342v1

AcypiCyc (Acyrthosiphon pisum Cyc database) and CycADS (Cyc Annotation Database System): moving from genome sequence annotation to metabolic network analyses

 Stefano Colella , A. Vellozo , L. Cottret , G. Febvay , Federica Calevro , et al.
8th International Symposium on Aphids (8 ISA 2009), 2009, Catania (Italie), juin 2009, France. pp.1-1
Communication dans un congrès hal-00391280v1

Development of the Acyrthosiphon pisum Cyc database (ApsCyc): from genome sequence to metabolic network analyses

 A. Vellozo , Stefano Colella , L. Cottret , G. Febvay , Federica Calevro , et al.
Integrative Post-Genomics - IPG'08, 2008, Lyon (France), novembre 2008, France. pp.1-1
Communication dans un congrès hal-00391519v1

CycADS: an annotation management system for the development and update of BioCyc metabolic network databases

 A. Vellozo , Patrice Baa-Puyoulet , A. Veron , Jaime Huerta-Cepas , Ludovic Cottret , et al.
1st International Workshop on Information Systems for Insect Pests, Rennes, FRANCE, 2009, France
Communication dans un congrès hal-00496032v1
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