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 61 to 90 publications on 211 in total

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

Conference paper

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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) .

Conference paper

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Telling Stories Fast

Michele Borassi, Pierluigi Crescenzi, Vincent Lacroix, Andrea Marino, Marie-France Sagot, Paulo Vieira Milreu

12th International Symposium Experimental Algorithms (SEA) . 7933 : 200-211

Conference paper

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Predicting the proteins of Angomonas deanei, Strigomonas culicis and their respective endosymbionts reveals new aspects of the trypanosomatidae family

Maria Cristina Machado Motta, Allan Cezar de Azevedo Martins, Silvana Sant'Anna de Souza, Carolina Moura Costa Catta-Preta, Rosane Silva, Cecilia Coimbra Klein...

PLoS ONE . 8 ( 4 ) : e60209

DOI: 10.1371/journal.pone.0060209

Journal article

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On the genetic architecture of cytoplasmic incompatibility: inference from phenotypic data

Igor Nor, Jan Engelstädter, Olivier Duron, Max Reuter, Marie-France Sagot, Sylvain Charlat

The American Naturalist . 182 ( 1 ) : 15-24

DOI: 10.1086/670612

Journal article

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« ArthropodaCyc » : une collection de bases de données enrichies à l’aide de CycADS pour étudier et comparer le métabolisme des arthropodes.

Patrice Baa-Puyoulet, Stefano Colella, Augusto Vellozo, Jaime Huerta-Cepas, Gérard Febvay, Federica Calevro...

17. Colloque de Biologie de l’Insecte - CBI-2013 .

Poster

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New developments in KisSplice: Combining local and global transcriptome assemblers to decipher splicing in RNA-seq data

Alice Julien-Laferriere, Gustavo Sacomoto, Rayan Chikhi, Erwan Scaon, David P. Parsons, Marie-France Sagot...

Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) .

Conference paper

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Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers

João Alves, Cecilia Klein, Flávia Maia da Silva, André Costa-Martins, Myrna Serrano, Gregory Buck...

BMC Evolutionary Biology . 13 ( 1 ) : 190

DOI: 10.1186/1471-2148-13-190

Journal article

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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, Marie-France Sagot...

PLoS ONE . 8 ( 11 ) : e79786

DOI: 10.1371/journal.pone.0079786

Journal article

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Short and long-term genome stability analysis of prokaryotic genomes

Matteo Brilli, Pietro Liò, Vincent Lacroix, Marie-France Sagot

BMC Genomics . 14 ( 1 ) : 309

DOI: 10.1186/1471-2164-14-309

Journal article

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KISSPLICE: de-novo calling alternative splicing events from RNA-seq data

Gustavo Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot...

BMC Bioinformatics . 13 ( Suppl 6 ) : S5

DOI: 10.1186/1471-2105-13-S6-S5

Journal article

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Efficient Bubble Enumeration in Directed Graphs

Etienne E. Birmelé, Pierluigi Crescenzi, Rui Ferreira, Roberto Grossi, Vincent Lacroix, Andrea Marino...

String Processing and Information Retrieval (SPIRE) . 7608 : 118-129

DOI: 10.1007/978-3-642-34109-0_13

Conference paper

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Minimum ratio cover of matrix columns by extreme rays of its induced cone

Alexandre da Silva Freire, Vicente Acuña, Pierluigi Crescenzi, Carlos Eduardo Ferreira, Vincent Lacroix, Paulo Vieira Milreu...

Proceedings of the Second international Symposium on Combinatorial Optimization (ISCO) . 7422 : 165--177

DOI: 10.1007/978-3-642-32147-4_16

Conference paper

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Sampling solution traces for the problem of sorting permutations by signed reversals

Christian Baudet, Zanoni Dias, Marie-France Sagot

Algorithms for Molecular Biology . 7 ( 1 ) : 18

DOI: 10.1186/1748-7188-7-18

Journal article

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The CycADS annotation database system to support the development and update of enriched BioCyc databases. Development of ad hoc BioCyc DB : AcypiCyc, ArthopodaCyc

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

5. Réunion Réseau BAPOA .

Poster

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Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches.

Nuno D Mendes, Steffen Heyne, Ana T Freitas, Marie-France Sagot, Rolf Backofen

Bioinformatics . 28 ( 23 ) : 3034-3041

DOI: 10.1093/bioinformatics/bts574

Journal article

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Exploration of the core metabolism of symbiotic bacteria

Cecilia Coimbra Klein, Ludovic Cottret, Janice Kielbassa, Hubert Charles, Christian Gautier, Ana Tereza Ribeiro de Vasconcelos...

BMC Genomics . 13 ( 1 ) : 438

DOI: 10.1186/1471-2164-13-438

Journal article

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Mod/Resc Parsimony Inference: Theory and application

Igor Nor, Danny Hermelin, Sylvain Charlat, Jan Engelstadter, Max Reuter, Olivier Duron...

Information and Computation . 213 : 23-32

DOI: 10.1016/j.ic.2011.03.008

Journal article

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Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks.

Vicente Acuña, Paulo Vieira Milreu, Ludovic Cottret, Alberto Marchetti-Spaccamela, Leen Stougie, Marie-France Sagot

Bioinformatics . 28 ( 19 ) : 2474-2483

DOI: 10.1093/bioinformatics/bts423

Journal article

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The CycADS annotation database system to support the development and update of enriched BioCyc databases. Development of ad hoc BioCyc DB : AcypiCyc, ArthopodaCyc

Patrice Baa-Puyoulet, Augusto F. Vellozo, Jaime Huerta-Cepas, Gérard Febvay, Toni Gabaldon, Marie-France Sagot...

13. Journées Ouvertes en Biologie, Informatique et Mathématiques . 978-2-7261-1301-1 : Pagination multiple

Conference paper

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Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets

Vicente Acuña, Etienne Birmelé, Ludovic Cottret, Pierluigi Crescenzi, Fabien Jourdan, Vincent Lacroix...

Theoretical Computer Science . 457 : 1--9

DOI: 10.1016/j.tcs.2012.07.023

Journal article

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Structural and dynamical analysis of biological networks.

Cecilia C. Klein, Andrea Marino, Marie-France Sagot, Paulo Vieira Milreu, Matteo Brilli

Briefings in Functional Genomics and Proteomics . 14 : 309

DOI: 10.1093/bfgp/els030

Journal article

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BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms

Julien Allali, Cédric Saule, Cedric Chauve, Yves d'Aubenton-Carafa, Alain Denise, Christine Drevet...

Advances in Bioinformatics . 2012 : 1-5

DOI: 10.1155/2012/893048

Journal article

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“ArthropodaCyc”: a BioCyc database powered by CycADS to study and compare the metabolism of arthropods

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

5. Annual Arthropod Genomics Symposium “Arthropod Genomics 2011: Exploring Diversity, Relating Similarity” . : 33 p.

Poster

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kisSplice, détection d'évènements d'épissages alternatifs dans les données RNA-seq

Gustavo Akio Tominaga Sacomoto, J. Kielbassa, Pavlos Antoniou, Rayan Chikhi, Raluca Uricaru, Marie-France Sagot...

: 12

Report

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Metabolic network comparison of bacteria in the context of symbiosis

Cecilia C. Klein, Ludovic Cottret, Hubert Charles, Christian Gautier, Ana T Vasconcelos, Vincent Lacroix...

Otto Warburg International Summer School and Research Symposium on Evolutionary Genomics .

Conference paper

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RNA-seq without a reference genome: a comparison of the mapping and the assembly approaches

M.-C. Carpentier, J. Charif, Vincent Lacroix, Marie-France Sagot, Fabrice Vavre

JOBIM .

Conference paper

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Telling Stories

Vicente Acuña, Etienne Birmele, Ludovic Cottret, Pierluigi Crescenzi, Fabien Jourdan, Vincent Lacroix...

ICALP 2011 satellite workshop: Graph Algorithms and Applications (GA) .

DOI: 10.1016/j.tcs.2012.07.023

Conference paper

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Finding Long and Multiple Repeats with Edit Distance

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

The Prague Stringology Conference 2011 .

Conference paper

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ArthropodaCyc: a BioCyc database powered by CycADS to study and compare the metabolism of arthropods

Patrice Baa-Puyoulet, Augusto F Vellozo, Jaime Huerta-Cepas, Gérard Febvay, T. Gabaldon, Marie-France Sagot...

5th Annual Arthropod Genomics Symposium "Arthropod Genomics 2011: Exploring Diversity, Relating Similarity" .

Conference paper

see the publication