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ORCIDMarie-France Sagot
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- affiliation: INRIA, France
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Journal Articles
- 2023
[j74]Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri
:
A General Framework for Enumerating Equivalence Classes of Solutions. Algorithmica 85(10): 3003-3023 (2023)- 2022
- [j73]Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri:
Efficiently sparse listing of classes of optimal cophylogeny reconciliations. Algorithms Mol. Biol. 17(1): 2 (2022) - 2021
- [j72]Vicente Acuña, Leandro Ishi Soares de Lima, Giuseppe F. Italiano, Luca Pepè Sciarria, Marie-France Sagot, Blerina Sinaimeri:
A family of tree-based generators for bubbles in directed graphs. J. Graph Algorithms Appl. 25(1): 563-580 (2021) - 2020
- [j71]Vicente Acuña, Roberto Grossi, Giuseppe Francesco Italiano, Leandro Lima, Romeo Rizzi, Gustavo Sacomoto, Marie-France Sagot, Blerina Sinaimeri:
On Bubble Generators in Directed Graphs. Algorithmica 82(4): 898-914 (2020) - [j70]Tiziana Calamoneri, Mattia Gastaldello, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri:
Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility. Algorithms Mol. Biol. 15(1): 14 (2020) - [j69]Taneli Pusa, Mariana Galvao Ferrarini, Ricardo Andrade, Arnaud Mary, Alberto Marchetti-Spaccamela, Leen Stougie, Marie-France Sagot:
MOOMIN - Mathematical explOration of 'Omics data on a MetabolIc Network. Bioinform. 36(2): 514-523 (2020) - [j68]Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri:
Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions. Bioinform. 36(14): 4197-4199 (2020) - [j67]Ricardo Andrade, Mahdi Doostmohammadi, João L. Santos, Marie-France Sagot, Nuno P. Mira, Susana Vinga:
MOMO - multi-objective metabolic mixed integer optimization: application to yeast strain engineering. BMC Bioinform. 21(1): 69 (2020) - 2019
- [j66]Taneli Pusa, Martin Wannagat, Marie-France Sagot:
Metabolic Games. Frontiers Appl. Math. Stat. 5: 18 (2019) - [j65]Laura Urbini, Blerina Sinaimeri, Catherine Matias, Marie-France Sagot:
Exploring the Robustness of the Parsimonious Reconciliation Method in Host-Symbiont Cophylogeny. IEEE ACM Trans. Comput. Biol. Bioinform. 16(3): 738-748 (2019) - 2018
- [j64]Katharina T. Huber, Vincent Moulton, Marie-France Sagot, Blerina Sinaimeri:
Geometric medians in reconciliation spaces of phylogenetic trees. Inf. Process. Lett. 136: 96-101 (2018) - [j63]Katerina Böhmová, Luca Häfliger, Matús Mihalák, Tobias Pröger, Gustavo Sacomoto, Marie-France Sagot:
Computing and Listing st-Paths in Public Transportation Networks. Theory Comput. Syst. 62(3): 600-621 (2018) - 2017
- [j62]Leandro Lima, Blerina Sinaimeri, Gustavo Sacomoto, Hélène Lopez-Maestre, Camille Marchet, Vincent Miele, Marie-France Sagot, Vincent Lacroix:
Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads. Algorithms Mol. Biol. 12(1): 2:1-2:19 (2017) - 2016
- [j61]Ricardo Andrade, Martin Wannagat, Cecilia Coimbra Klein, Vicente Acuña, Alberto Marchetti-Spaccamela, Paulo Vieira Milreu, Leen Stougie, Marie-France Sagot:
Enumeration of minimal stoichiometric precursor sets in metabolic networks. Algorithms Mol. Biol. 11: 25 (2016) - [j60]André Veríssimo, Arlindo Limede Oliveira, Marie-France Sagot, Susana Vinga:
DegreeCox - a network-based regularization method for survival analysis. BMC Bioinform. 17(S-16): 109-121 (2016) - 2015
- [j59]Beatrice Donati, Christian Baudet, Blerina Sinaimeri, Pierluigi Crescenzi, Marie-France Sagot:
EUCALYPT: efficient tree reconciliation enumerator. Algorithms Mol. Biol. 10: 3 (2015) - [j58]Gustavo Sacomoto, Vincent Lacroix, Marie-France Sagot:
A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs. Algorithms Mol. Biol. 10: 20 (2015) - [j57]Emanuele Bosi, Beatrice Donati, Marco Galardini, Sara Brunetti, Marie-France Sagot, Pietro Liò, Pierluigi Crescenzi, Renato Fani, Marco Fondi:
MeDuSa: a multi-draft based scaffolder. Bioinform. 31(15): 2443-2451 (2015) - [j56]Susan Higashi, Cyril Fournier, Christian Gautier, Christine Gaspin, Marie-France Sagot:
Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data. BMC Bioinform. 16: 179:1-179:14 (2015) - 2014
- [j55]Paulo Vieira Milreu, Cecilia Coimbra Klein, Ludovic Cottret, Vicente Acuña, Etienne Birmelé, Michele Borassi, Christophe Junot, Alberto Marchetti-Spaccamela, Andrea Marino, Leen Stougie, Fabien Jourdan, Pierluigi Crescenzi, Vincent Lacroix, Marie-France Sagot:
Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure. Bioinform. 30(1): 61-70 (2014) - [j54]Maria Federico, Pierre Peterlongo, Nadia Pisanti, Marie-France Sagot:
Rime: Repeat identification. Discret. Appl. Math. 163: 275-286 (2014) - 2012
- [j53]Julien Allali, Cédric Saule, Cédric Chauve, Yves D'Aubenton-Carafa, Alain Denise, Christine Drevet, Pascal Ferraro, Daniel Gautheret, Claire Herrbach, Fabrice Leclerc, Antoine de Monte, Aïda Ouangraoua, Marie-France Sagot, Michel Termier, Claude Thermes, Hélène Touzet:
BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms. Adv. Bioinformatics 2012: 893048:1-893048:5 (2012) - [j52]Christian Baudet, Zanoni Dias, Marie-France Sagot:
Sampling solution traces for the problem of sorting permutations by signed reversals. Algorithms Mol. Biol. 7: 18 (2012) - [j51]Vicente Acuña, Paulo Vieira Milreu, Ludovic Cottret, Alberto Marchetti-Spaccamela, Leen Stougie, Marie-France Sagot:
Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks. Bioinform. 28(19): 2474-2483 (2012) - [j50]Nuno D. Mendes, Steffen Heyne, Ana T. Freitas, Marie-France Sagot, Rolf Backofen:
Navigating the unexplored seascape of pre-miRNA candidates in single-genome approaches. Bioinform. 28(23): 3034-3041 (2012) - [j49]Gustavo Akio Tominaga Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo, Vincent Lacroix:
KISSPLICE: de-novo calling alternative splicing events from RNA-seq data. BMC Bioinform. 13(S-6): S5 (2012) - [j48]Igor Nor, Danny Hermelin, Sylvain Charlat, Jan Engelstadter, Max Reuter, Olivier Duron, Marie-France Sagot:
Mod/Resc Parsimony Inference: Theory and application. Inf. Comput. 213: 23-32 (2012) - [j47]Marie-France Sagot:
EIC Editorial. IEEE ACM Trans. Comput. Biol. Bioinform. 9(6): 1553-1557 (2012) - [j46]Vicente Acuña, Etienne Birmelé, Ludovic Cottret, Pierluigi Crescenzi, Fabien Jourdan, Vincent Lacroix, Alberto Marchetti-Spaccamela, Andrea Marino, Paulo Vieira Milreu, Marie-France Sagot, Leen Stougie:
Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets. Theor. Comput. Sci. 457: 1-9 (2012) - 2011
- [j45]Augusto F. Vellozo, Amélie S. Véron, Patrice Baa-Puyoulet, Jaime Huerta-Cepas, Ludovic Cottret, Gérard Febvay, Federica Calevro, Yvan Rahbé, Angela E. Douglas, Toni Gabaldón, Marie-France Sagot, Hubert Charles, Stefano Colella:
CycADS: an annotation database system to ease the development and update of BioCyc databases. Database J. Biol. Databases Curation 2011 (2011) - [j44]Yves-Pol Deniélou, Marie-France Sagot, Frédéric Boyer, Alain Viari:
Bacterial syntenies: an exact approach with gene quorum. BMC Bioinform. 12: 193 (2011) - [j43]Marie-France Sagot:
EIC Editorial. IEEE ACM Trans. Comput. Biol. Bioinform. 8(1): 1 (2011) - [j42]Marie-France Sagot:
EIC Editorial. IEEE ACM Trans. Comput. Biol. Bioinform. 8(2): 289-291 (2011) - 2010
- [j41]Christian Baudet, Claire Lemaitre, Zanoni Dias, Christian Gautier, Eric Tannier, Marie-France Sagot:
Cassis: detection of genomic rearrangement breakpoints. Bioinform. 26(15): 1897-1898 (2010) - [j40]Vicente Acuña, Alberto Marchetti-Spaccamela, Marie-France Sagot, Leen Stougie:
A note on the complexity of finding and enumerating elementary modes. Biosyst. 99(3): 210-214 (2010) - [j39]Said Sadique Adi, Marília D. V. Braga, Cristina G. Fernandes, Carlos Eduardo Ferreira, Fábio Viduani Martinez, Marie-France Sagot, Marco Aurelio Stefanes, Christian Tjandraatmadja, Yoshiko Wakabayashi:
Repetition-free longest common subsequence. Discret. Appl. Math. 158(12): 1315-1324 (2010) - [j38]Ludovic Cottret, David Wildridge, Florence Vinson, Michael P. Barrett, Hubert Charles, Marie-France Sagot, Fabien Jourdan:
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Res. 38(Web-Server-Issue): 132-137 (2010) - [j37]Ludovic Cottret, Paulo Vieira Milreu, Vicente Acuña, Alberto Marchetti-Spaccamela, Leen Stougie, Hubert Charles, Marie-France Sagot:
Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri, with Their Insect Host, Homalodisca coagulata. PLoS Comput. Biol. 6(9) (2010) - [j36]Marie-France Sagot:
EIC Editorial. IEEE ACM Trans. Comput. Biol. Bioinform. 7(2): 193-194 (2010) - 2009
- [j35]Marília D. V. Braga, Christian Gautier, Marie-France Sagot:
An asymmetric approach to preserve common intervals while sorting by reversals. Algorithms Mol. Biol. 4: 16 (2009) - [j34]Pierre Peterlongo, Gustavo Akio Tominaga Sacomoto, Alair Pereira do Lago, Nadia Pisanti, Marie-France Sagot:
Lossless filter for multiple repeats with bounded edit distance. Algorithms Mol. Biol. 4 (2009) - [j33]Marie-France Sagot, B. J. Morrison McKay, Gene Myers:
ISMB/ECCB 2009 Stockholm. Bioinform. 25(12): 1570-1573 (2009) - [j32]Vicente Acuña, Flavio Chierichetti, Vincent Lacroix, Alberto Marchetti-Spaccamela, Marie-France Sagot, Leen Stougie:
Modes and cuts in metabolic networks: Complexity and algorithms. Biosyst. 95(1): 51-60 (2009) - [j31]Sophie Schbath, Vincent Lacroix, Marie-France Sagot:
Assessing the Exceptionality of Coloured Motifs in Networks. EURASIP J. Bioinform. Syst. Biol. 2009 (2009) - [j30]Marie-France Sagot:
New EIC Editorial. IEEE ACM Trans. Comput. Biol. Bioinform. 6(1): 3 (2009) - [j29]Marie-France Sagot:
EIC Editorial. IEEE ACM Trans. Comput. Biol. Bioinform. 6(2): 177 (2009) - [j28]Marie-France Sagot:
EIC Editorial: Introducing New Associate Editors. IEEE ACM Trans. Comput. Biol. Bioinform. 6(3): 369 (2009) - 2008
- [j27]Claire Lemaitre, Eric Tannier, Christian Gautier, Marie-France Sagot:
Precise detection of rearrangement breakpoints in mammalian chromosomes. BMC Bioinform. 9 (2008) - [j26]Said Sadique Adi, Marília D. V. Braga, Cristina G. Fernandes, Carlos Eduardo Ferreira, Fábio Viduani Martinez, Marie-France Sagot, Marco Aurelio Stefanes, Christian Tjandraatmadja, Yoshiko Wakabayashi:
Repetition-free longest common subsequence. Electron. Notes Discret. Math. 30: 243-248 (2008) - [j25]Pierre Peterlongo, Julien Allali, Marie-France Sagot:
Indexing Gapped-Factors Using a Tree. Int. J. Found. Comput. Sci. 19(1): 71-87 (2008) - [j24]Katia S. Guimarães, Marie-France Sagot:
Editorial. J. Discrete Algorithms 6(2): 163 (2008) - [j23]Pierre Peterlongo, Nadia Pisanti, Frédéric Boyer, Alair Pereira do Lago, Marie-France Sagot:
Lossless filter for multiple repetitions with Hamming distance. J. Discrete Algorithms 6(3): 497-509 (2008) - [j22]Julien Allali, Marie-France Sagot:
A multiple layer model to compare RNA secondary structures. Softw. Pract. Exp. 38(8): 775-792 (2008) - [j21]Marília D. V. Braga, Marie-France Sagot, Céline Scornavacca, Eric Tannier:
Exploring the Solution Space of Sorting by Reversals, with Experiments and an Application to Evolution. IEEE ACM Trans. Comput. Biol. Bioinform. 5(3): 348-356 (2008) - [j20]Vincent Lacroix, Ludovic Cottret, Patricia Thébault, Marie-France Sagot:
An Introduction to Metabolic Networks and Their Structural Analysis. IEEE ACM Trans. Comput. Biol. Bioinform. 5(4): 594-617 (2008) - [j19]Claire Lemaitre, Marie-France Sagot:
A small trip in the untranquil world of genomes: A survey on the detection and analysis of genome rearrangement breakpoints. Theor. Comput. Sci. 395(2-3): 171-192 (2008) - 2007
- [j18]Romain Bourqui, Ludovic Cottret, Vincent Lacroix, David Auber, Patrick Mary, Marie-France Sagot, Fabien Jourdan:
Metabolic network visualization eliminating node redundance and preserving metabolic pathways. BMC Syst. Biol. 1: 29 (2007) - [j17]Eric Tannier, Anne Bergeron, Marie-France Sagot:
Advances on sorting by reversals. Discret. Appl. Math. 155(6-7): 881-888 (2007) - [j16]Emilios Cambouropoulos, Maxime Crochemore, Costas S. Iliopoulos, Manal Mohamed, Marie-France Sagot:
All maximal-pairs in step-leap representation of melodic sequence. Inf. Sci. 177(9): 1954-1962 (2007) - [j15]Yoan Diekmann, Marie-France Sagot, Eric Tannier:
Evolution under Reversals: Parsimony and Conservation of Common Intervals. IEEE ACM Trans. Comput. Biol. Bioinform. 4(2): 301-309 (2007) - [j14]Estela Maris Rodrigues, Marie-France Sagot, Yoshiko Wakabayashi:
The maximum agreement forest problem: Approximation algorithms and computational experiments. Theor. Comput. Sci. 374(1-3): 91-110 (2007) - 2006
- [j13]Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira, Marie-France Sagot:
An Efficient Algorithm for the Identification of Structured Motifs in DNA Promoter Sequences. IEEE ACM Trans. Comput. Biol. Bioinform. 3(2): 126-140 (2006) - [j12]Vincent Lacroix, Cristina G. Fernandes, Marie-France Sagot:
Motif Search in Graphs: Application to Metabolic Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 3(4): 360-368 (2006) - [j11]Maxime Crochemore, Costas S. Iliopoulos, Manal Mohamed, Marie-France Sagot:
Longest repeats with a block of k don't cares. Theor. Comput. Sci. 362(1-3): 248-254 (2006) - 2005
- [j10]Costas S. Iliopoulos, James A. M. McHugh, Pierre Peterlongo, Nadia Pisanti, Wojciech Rytter, Marie-France Sagot:
A first approach to finding common motifs with gaps. Int. J. Found. Comput. Sci. 16(6): 1145-1154 (2005) - [j9]Julien Allali, Marie-France Sagot:
A New Distance for High Level RNA Secondary Structure Comparison. IEEE ACM Trans. Comput. Biol. Bioinform. 2(1): 3-14 (2005) - [j8]Nadia Pisanti, Maxime Crochemore, Roberto Grossi, Marie-France Sagot:
Bases of Motifs for Generating Repeated Patterns with Wild Cards. IEEE ACM Trans. Comput. Biol. Bioinform. 2(1): 40-50 (2005) - 2003
- [j7]Philippe Blayo, Pierre Rouzé, Marie-France Sagot:
Orphan gene finding - an exon assembly approach. Theor. Comput. Sci. 290(3): 1407-1431 (2003) - 2002
- [j6]Nadia Pisanti, Marie-France Sagot:
Further Thoughts on the Syntenic Distance between Genomes. Algorithmica 34(2): 157-180 (2002) - [j5]Stéphane Robin, Jean-Jacques Daudin, Hugues Richard, Marie-France Sagot, Sophie Schbath:
Occurrence Probability of Structured Motifs in Random Sequences. J. Comput. Biol. 9(6): 761-773 (2002) - 2000
- [j4]Laurent Marsan, Marie-France Sagot:
Algorithms for Extracting Structured Motifs Using a Suffix Tree with an Application to Promoter and Regulatory Site Consensus Identification. J. Comput. Biol. 7(3-4): 345-362 (2000) - 1998
- [j3]Marie-France Sagot, Eugene W. Myers:
Identifying Satellites and Periodic Repetitions in Biological Sequences. J. Comput. Biol. 5(3): 539-553 (1998) - 1997
- [j2]Marie-France Sagot, Alain Viari, Henry Soldano:
Multiple Sequence Comparison - A Peptide Matching Approach. Theor. Comput. Sci. 180(1-2): 115-137 (1997) - 1995
- [j1]Marie-France Sagot, Alain Viari, Joël Pothier, Henry Soldano:
Finding flexible patterns in a text: an application to three-dimensional molecular matching. Comput. Appl. Biosci. 11(1): 59-70 (1995)
Conference and Workshop Papers
- 2021
- [c50]Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri:
A General Framework for Enumerating Equivalence Classes of Solutions. ESA 2021: 80:1-80:14 - [c49]Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri:
Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations. WABI 2021: 3:1-3:18 - 2020
- [c48]Vicente Acuña, Leandro Lima, Giuseppe F. Italiano, Luca Pepè Sciarria, Marie-France Sagot, Blerina Sinaimeri:
A Family of Tree-Based Generators for Bubbles in Directed Graphs. IWOCA 2020: 17-29 - 2017
- [c47]Mattia Gastaldello, Tiziana Calamoneri, Marie-France Sagot:
Extracting Few Representative Reconciliations with Host Switches. CIBB 2017: 9-18 - [c46]Vicente Acuña, Roberto Grossi, Giuseppe F. Italiano, Leandro Lima, Romeo Rizzi, Gustavo Sacomoto, Marie-France Sagot, Blerina Sinaimeri:
On Bubble Generators in Directed Graphs. WG 2017: 18-31 - 2016
- [c45]Laura Urbini, Blerina Sinaimeri, Catherine Matias, Marie-France Sagot:
Robustness of the Parsimonious Reconciliation Method in Cophylogeny. AlCoB 2016: 119-130 - [c44]Katerina Böhmová, Matús Mihalák, Tobias Pröger, Gustavo Sacomoto, Marie-France Sagot:
Computing and Listing st-Paths in Public Transportation Networks. CSR 2016: 102-116 - [c43]Tiziana Calamoneri, Mattia Gastaldello, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri:
On Maximal Chain Subgraphs and Covers of Bipartite Graphs. ICTCS 2016: 286-291 - [c42]Tiziana Calamoneri, Mattia Gastaldello, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri:
On Maximal Chain Subgraphs and Covers of Bipartite Graphs. IWOCA 2016: 137-150 - 2015
- [c41]Ricardo Andrade, Etienne Birmelé, Arnaud Mary, Thomas Picchetti, Marie-France Sagot:
Incremental Complexity of a Bi-objective Hypergraph Transversal Problem. FCT 2015: 202-213 - 2014
- [c40]Rui A. Ferreira, Roberto Grossi, Romeo Rizzi, Gustavo Sacomoto, Marie-France Sagot:
Amortized Õ(|V|) -Delay Algorithm for Listing Chordless Cycles in Undirected Graphs. ESA 2014: 418-429 - [c39]Romeo Rizzi, Gustavo Sacomoto, Marie-France Sagot:
Efficiently Listing Bounded Length st-Paths. IWOCA 2014: 318-329 - [c38]Gustavo Sacomoto, Blerina Sinaimeri, Camille Marchet, Vincent Miele, Marie-France Sagot, Vincent Lacroix:
Navigating in a Sea of Repeats in RNA-seq without Drowning. WABI 2014: 82-96 - 2013
- [c37]Gustavo Sacomoto, Vincent Lacroix, Marie-France Sagot:
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. WABI 2013: 99-111 - [c36]Michele Borassi, Pierluigi Crescenzi, Vincent Lacroix, Andrea Marino, Marie-France Sagot, Paulo Vieira Milreu:
Telling Stories Fast. SEA 2013: 200-211 - 2012
- [c35]Alexandre S. Freire, Vicente Acuña, Pilu Crescenzi, Carlos Eduardo Ferreira, Vincent Lacroix, Paulo Vieira Milreu, Eduardo Moreno, Marie-France Sagot:
Minimum Ratio Cover of Matrix Columns by Extreme Rays of Its Induced Cone. ISCO 2012: 165-177 - [c34]Etienne Birmelé, Pierluigi Crescenzi, Rui A. Ferreira, Roberto Grossi, Vincent Lacroix, Andrea Marino, Nadia Pisanti, Gustavo Akio Tominaga Sacomoto, Marie-France Sagot:
Efficient Bubble Enumeration in Directed Graphs. SPIRE 2012: 118-129 - 2011
- [c33]Maria Federico, Pierre Peterlongo, Nadia Pisanti, Marie-France Sagot:
Finding Long and Multiple Repeats with Edit Distance. Stringology 2011: 83-97 - 2010
- [c32]Igor Nor, Danny Hermelin, Sylvain Charlat, Jan Engelstadter, Max Reuter, Olivier Duron, Marie-France Sagot:
Mod/Resc Parsimony Inference. CPM 2010: 202-213 - [c31]Pierre Peterlongo, Nicolas Schnel, Nadia Pisanti, Marie-France Sagot, Vincent Lacroix:
Identifying SNPs without a Reference Genome by Comparing Raw Reads. SPIRE 2010: 147-158 - [c30]Paulo Vieira Milreu, Vicente Acuña, Etienne Birmelé, Pierluigi Crescenzi, Alberto Marchetti-Spaccamela, Marie-France Sagot, Leen Stougie, Vincent Lacroix:
Enumerating Chemical Organisations in Consistent Metabolic Networks: Complexity and Algorithms. WABI 2010: 226-237 - 2009
- [c29]Yves-Pol Deniélou, Frédéric Boyer, Alain Viari, Marie-France Sagot:
Multiple Alignment of Biological Networks: A Flexible Approach. CPM 2009: 263-273 - 2008
- [c28]Paulo G. S. da Fonseca, Katia S. Guimarães, Marie-France Sagot:
Efficient representation and P-value computation for high-order Markov motifs. ECCB 2008: 160-166 - [c27]Ludovic Cottret, Paulo Vieira Milreu, Vicente Acuña, Alberto Marchetti-Spaccamela, Fábio Viduani Martinez, Marie-France Sagot, Leen Stougie:
Enumerating Precursor Sets of Target Metabolites in a Metabolic Network. WABI 2008: 233-244 - 2007
- [c26]Alexandra M. Carvalho, Arlindo L. Oliveira, Marie-France Sagot:
Efficient Learning of Bayesian Network Classifiers. Australian Conference on Artificial Intelligence 2007: 16-25 - [c25]Marília D. V. Braga, Marie-France Sagot, Céline Scornavacca, Eric Tannier:
The Solution Space of Sorting by Reversals. ISBRA 2007: 293-304 - 2006
- [c24]Nadia Pisanti, Alexandra M. Carvalho, Laurent Marsan, Marie-France Sagot:
RISOTTO: Fast Extraction of Motifs with Mismatches. LATIN 2006: 757-768 - [c23]Pierre Peterlongo, Julien Allali, Marie-France Sagot:
The gapped-factor tree. Stringology 2006: 182-196 - 2005
- [c22]Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira, Marie-France Sagot:
A highly scalable algorithm for the extraction of CIS-regulatory regions. APBC 2005: 273-282 - [c21]Marie-France Sagot, Eric Tannier:
Perfect Sorting by Reversals. COCOON 2005: 42-51 - [c20]Emilios Cambouropoulos, Maxime Crochemore, Costas S. Iliopoulos, Manal Mohamed, Marie-France Sagot:
A Pattern Extraction Algorithm for Abstract Melodic Representations that Allow Partial Overlapping of Intervallic Categories. ISMIR 2005: 167-174 - [c19]Pierre Peterlongo, Nadia Pisanti, Frédéric Boyer, Marie-France Sagot:
Lossless Filter for Finding Long Multiple Approximate Repetitions Using a New Data Structure, the Bi-factor Array. SPIRE 2005: 179-190 - [c18]Julien Allali, Marie-France Sagot:
A Multiple Graph Layers Model with Application to RNA Secondary Structures Comparison. SPIRE 2005: 348-359 - [c17]Vincent Lacroix, Cristina G. Fernandes, Marie-France Sagot:
Reaction Motifs in Metabolic Networks. WABI 2005: 178-191 - 2004
- [c16]Eric Tannier, Marie-France Sagot:
Sorting by Reversals in Subquadratic Time. CPM 2004: 1-13 - [c15]Maxime Crochemore, Costas S. Iliopoulos, Manal Mohamed, Marie-France Sagot:
Longest Repeats with a Block of Don't Cares. LATIN 2004: 271-278 - [c14]Alexandra M. Carvalho, Arlindo L. Oliveira, Ana T. Freitas, Marie-France Sagot:
A parallel algorithm for the extraction of structured motifs. SAC 2004: 147-153 - [c13]Alexandra M. Carvalho, Ana T. Freitas, Arlindo L. Oliveira, Marie-France Sagot:
Efficient Extraction of Structured Motifs Using Box-Links. SPIRE 2004: 267-268 - [c12]Maxime Crochemore, Raffaele Giancarlo, Marie-France Sagot:
Longest Motifs with a Functionally Equivalent Central Block. SPIRE 2004: 298-209 - [c11]Costas S. Iliopoulos, James A. M. McHugh, Pierre Peterlongo, Nadia Pisanti, Wojciech Rytter, Marie-France Sagot:
A First Approach to Finding Common Motifs With Gaps. Stringology 2004: 88-97 - [c10]Julien Allali, Marie-France Sagot:
Novel Tree Edit Operations for RNA Secondary Structure Comparison. WABI 2004: 412-425 - 2003
- [c9]Nadia Pisanti, Maxime Crochemore, Roberto Grossi, Marie-France Sagot:
A Basis of Tiling Motifs for Generating Repeated Patterns and Its Complexity for Higher Quorum. MFCS 2003: 622-631 - 2001
- [c8]Estela Maris Rodrigues, Marie-France Sagot, Yoshiko Wakabayashi:
Some Approximation Results for the Maximum Agreement Forest Problem. RANDOM-APPROX 2001: 159-169 - 2000
- [c7]Laurent Marsan, Marie-France Sagot:
Extracting structured motifs using a suffix tree - algorithms and application to promoter consensus identification. RECOMB 2000: 210-219 - 1998
- [c6]Marie-France Sagot:
Spelling Approximate Repeated or Common Motifs Using a Suffix Tree. LATIN 1998: 374-390 - [c5]Marie-France Sagot, Eugene W. Myers:
Identifying satellites in nucleic acid sequences. RECOMB 1998: 234-242 - 1997
- [c4]Marie-France Sagot, Alain Viari:
Flexible Identification of Structural Objects in Nucleic Acid Sequences: Palindromes, Mirror Repeats, Pseudoknots and Triple Helices. CPM 1997: 224-246 - 1996
- [c3]Marie-France Sagot, Alain Viari:
A Double Combinatorial Approach to Discovering Patterns in Biological Sequences. CPM 1996: 186-208 - 1995
- [c2]Marie-France Sagot, Alain Viari, Henry Soldano:
Multiple Sequence Comparison: A Peptide Matching Approach. CPM 1995: 366-385 - [c1]Marie-France Sagot, Alain Viari, Henry Soldano:
A Distance-Based Block Searching Algorithm. ISMB 1995: 322-331
Editorship
- 2011
- [e3]Teresa M. Przytycka, Marie-France Sagot:
Algorithms in Bioinformatics - 11th International Workshop, WABI 2011, Saarbrücken, Germany, September 5-7, 2011. Proceedings. Lecture Notes in Computer Science 6833, Springer 2011, ISBN 978-3-642-23037-0 [contents] - 2007
- [e2]Marie-France Sagot, Maria Emília Telles Walter:
Advances in Bioinformatics and Computational Biology, Second Brazilian Symposium on Bioinformatics, BSB 2007, Angra dos Reis, Brazil, August 29-31, 2007, Proceedings. Lecture Notes in Computer Science 4643, Springer 2007, ISBN 978-3-540-73730-8 [contents] - 2001
- [e1]Olivier Gascuel, Marie-France Sagot:
Computational Biology, First International Conference on Biology, Informatics, and Mathematics, JOBIM 2000, Montpellier, France, May 3-5, 2000, Selected Papers. Lecture Notes in Computer Science 2066, Springer 2001, ISBN 3-540-42242-0 [contents]
Informal and Other Publications
- 2020
- [i11]Yishu Wang, Arnaud Mary, Marie-France Sagot, Blerina Sinaimeri:
Lazy listing of equivalence classes - A paper on dynamic programming and tropical circuits. CoRR abs/2004.12143 (2020) - 2018
- [i10]Henning Fernau, Petr A. Golovach, Marie-France Sagot:
Algorithmic Enumeration: Output-sensitive, Input-Sensitive, Parameterized, Approximative (Dagstuhl Seminar 18421). Dagstuhl Reports 8(10): 63-86 (2018) - 2016
- [i9]Roeland Merks, Marie-France Sagot:
Tackling Big Data in the Life Sciences - Introduction to the Special Theme. ERCIM News 2016(104) (2016) - 2015
- [i8]Ricardo Andrade, Etienne Birmelé, Arnaud Mary, Thomas Picchetti, Marie-France Sagot:
Incremental complexity of a bi-objective hypergraph transversal problem. CoRR abs/1505.06025 (2015) - 2014
- [i7]Gustavo Sacomoto, Blerina Sinaimeri, Camille Marchet, Vincent Miele, Marie-France Sagot, Vincent Lacroix:
Navigating in a sea of repeats in RNA-seq without drowning. CoRR abs/1406.1022 (2014) - [i6]Rui A. Ferreira, Roberto Grossi, Romeo Rizzi, Gustavo Sacomoto, Marie-France Sagot:
Amortized Õ(|V|)-Delay Algorithm for Listing Chordless Cycles in Undirected Graphs. CoRR abs/1408.1265 (2014) - [i5]Romeo Rizzi, Gustavo Sacomoto, Marie-France Sagot:
Efficiently listing bounded length st-paths. CoRR abs/1411.6852 (2014) - 2013
- [i4]Gustavo Sacomoto, Vincent Lacroix, Marie-France Sagot:
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. CoRR abs/1307.7813 (2013) - 2012
- [i3]Etienne Birmelé, Rui A. Ferreira, Roberto Grossi, Andrea Marino, Nadia Pisanti, Romeo Rizzi, Gustavo Akio Tominaga Sacomoto, Marie-France Sagot:
Optimal Listing of Cycles and st-Paths in Undirected Graphs. CoRR abs/1205.2766 (2012) - 2010
- [i2]Igor Nor, Danny Hermelin, Sylvain Charlat, Jan Engelstadter, Max Reuter, Olivier Duron, Marie-France Sagot:
Mod/Resc Parsimony Inference. CoRR abs/1002.1292 (2010) - 2008
- [i1]Julien Allali, Marie-France Sagot:
A new distance for high level RNA secondary structure comparison. CoRR abs/0810.4002 (2008)
Coauthor Index
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