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ORCIDBibTeX records: Marie-France Sagot
@article{DBLP:journals/algorithmica/WangMSS23,
author = {Yishu Wang and
Arnaud Mary and
Marie{-}France Sagot and
Blerina Sinaimeri},
title = {A General Framework for Enumerating Equivalence Classes of Solutions},
journal = {Algorithmica},
volume = {85},
number = {10},
pages = {3003--3023},
year = {2023},
url = {https://doi.org/10.1007/s00453-023-01131-1},
doi = {10.1007/S00453-023-01131-1},
timestamp = {Wed, 06 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/algorithmica/WangMSS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/WangMSS22,
author = {Yishu Wang and
Arnaud Mary and
Marie{-}France Sagot and
Blerina Sinaimeri},
title = {Efficiently sparse listing of classes of optimal cophylogeny reconciliations},
journal = {Algorithms Mol. Biol.},
volume = {17},
number = {1},
pages = {2},
year = {2022},
url = {https://doi.org/10.1186/s13015-022-00206-y},
doi = {10.1186/S13015-022-00206-Y},
timestamp = {Wed, 06 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/WangMSS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jgaa/AcunaLISSS21,
author = {Vicente Acu{\~{n}}a and
Leandro Ishi Soares de Lima and
Giuseppe F. Italiano and
Luca Pep{\`{e}} Sciarria and
Marie{-}France Sagot and
Blerina Sinaimeri},
title = {A family of tree-based generators for bubbles in directed graphs},
journal = {J. Graph Algorithms Appl.},
volume = {25},
number = {1},
pages = {563--580},
year = {2021},
url = {https://doi.org/10.7155/jgaa.00572},
doi = {10.7155/JGAA.00572},
timestamp = {Mon, 14 Feb 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jgaa/AcunaLISSS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/esa/WangMSS21,
author = {Yishu Wang and
Arnaud Mary and
Marie{-}France Sagot and
Blerina Sinaimeri},
editor = {Petra Mutzel and
Rasmus Pagh and
Grzegorz Herman},
title = {A General Framework for Enumerating Equivalence Classes of Solutions},
booktitle = {29th Annual European Symposium on Algorithms, {ESA} 2021, September
6-8, 2021, Lisbon, Portugal (Virtual Conference)},
series = {LIPIcs},
volume = {204},
pages = {80:1--80:14},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2021},
url = {https://doi.org/10.4230/LIPIcs.ESA.2021.80},
doi = {10.4230/LIPICS.ESA.2021.80},
timestamp = {Wed, 06 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/esa/WangMSS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/WangMSS21,
author = {Yishu Wang and
Arnaud Mary and
Marie{-}France Sagot and
Blerina Sinaimeri},
editor = {Alessandra Carbone and
Mohammed El{-}Kebir},
title = {Making Sense of a Cophylogeny Output: Efficient Listing of Representative
Reconciliations},
booktitle = {21st International Workshop on Algorithms in Bioinformatics, {WABI}
2021, August 2-4, 2021, Virtual Conference},
series = {LIPIcs},
volume = {201},
pages = {3:1--3:18},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2021},
url = {https://doi.org/10.4230/LIPIcs.WABI.2021.3},
doi = {10.4230/LIPICS.WABI.2021.3},
timestamp = {Wed, 06 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wabi/WangMSS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithmica/AcunaGILRSSS20,
author = {Vicente Acu{\~{n}}a and
Roberto Grossi and
Giuseppe Francesco Italiano and
Leandro Lima and
Romeo Rizzi and
Gustavo Sacomoto and
Marie{-}France Sagot and
Blerina Sinaimeri},
title = {On Bubble Generators in Directed Graphs},
journal = {Algorithmica},
volume = {82},
number = {4},
pages = {898--914},
year = {2020},
url = {https://doi.org/10.1007/s00453-019-00619-z},
doi = {10.1007/S00453-019-00619-Z},
timestamp = {Thu, 19 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/algorithmica/AcunaGILRSSS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/CalamoneriGMSS20,
author = {Tiziana Calamoneri and
Mattia Gastaldello and
Arnaud Mary and
Marie{-}France Sagot and
Blerina Sinaimeri},
title = {Algorithms for the quantitative Lock/Key model of cytoplasmic incompatibility},
journal = {Algorithms Mol. Biol.},
volume = {15},
number = {1},
pages = {14},
year = {2020},
url = {https://doi.org/10.1186/s13015-020-00174-1},
doi = {10.1186/S13015-020-00174-1},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/CalamoneriGMSS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PusaFAMMSS20,
author = {Taneli Pusa and
Mariana Galvao Ferrarini and
Ricardo Andrade and
Arnaud Mary and
Alberto Marchetti{-}Spaccamela and
Leen Stougie and
Marie{-}France Sagot},
title = {{MOOMIN} - Mathematical explOration of 'Omics data on a MetabolIc
Network},
journal = {Bioinform.},
volume = {36},
number = {2},
pages = {514--523},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btz584},
doi = {10.1093/BIOINFORMATICS/BTZ584},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PusaFAMMSS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangMSS20,
author = {Yishu Wang and
Arnaud Mary and
Marie{-}France Sagot and
Blerina Sinaimeri},
title = {Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed
ReconciliAtions},
journal = {Bioinform.},
volume = {36},
number = {14},
pages = {4197--4199},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa498},
doi = {10.1093/BIOINFORMATICS/BTAA498},
timestamp = {Wed, 06 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangMSS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AndradeDSSMV20,
author = {Ricardo Andrade and
Mahdi Doostmohammadi and
Jo{\~{a}}o L. Santos and
Marie{-}France Sagot and
Nuno P. Mira and
Susana Vinga},
title = {{MOMO} - multi-objective metabolic mixed integer optimization: application
to yeast strain engineering},
journal = {{BMC} Bioinform.},
volume = {21},
number = {1},
pages = {69},
year = {2020},
url = {https://doi.org/10.1186/s12859-020-3377-1},
doi = {10.1186/S12859-020-3377-1},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/AndradeDSSMV20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwoca/AcunaLISSS20,
author = {Vicente Acu{\~{n}}a and
Leandro Lima and
Giuseppe F. Italiano and
Luca Pep{\`{e}} Sciarria and
Marie{-}France Sagot and
Blerina Sinaimeri},
editor = {Leszek Gasieniec and
Ralf Klasing and
Tomasz Radzik},
title = {A Family of Tree-Based Generators for Bubbles in Directed Graphs},
booktitle = {Combinatorial Algorithms - 31st International Workshop, {IWOCA} 2020,
Bordeaux, France, June 8-10, 2020, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12126},
pages = {17--29},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-48966-3\_2},
doi = {10.1007/978-3-030-48966-3\_2},
timestamp = {Fri, 29 May 2020 16:43:36 +0200},
biburl = {https://dblp.org/rec/conf/iwoca/AcunaLISSS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2004-12143,
author = {Yishu Wang and
Arnaud Mary and
Marie{-}France Sagot and
Blerina Sinaimeri},
title = {Lazy listing of equivalence classes - {A} paper on dynamic programming
and tropical circuits},
journal = {CoRR},
volume = {abs/2004.12143},
year = {2020},
url = {https://arxiv.org/abs/2004.12143},
eprinttype = {arXiv},
eprint = {2004.12143},
timestamp = {Wed, 06 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2004-12143.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fams/PusaWS19,
author = {Taneli Pusa and
Martin Wannagat and
Marie{-}France Sagot},
title = {Metabolic Games},
journal = {Frontiers Appl. Math. Stat.},
volume = {5},
pages = {18},
year = {2019},
url = {https://doi.org/10.3389/fams.2019.00018},
doi = {10.3389/FAMS.2019.00018},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/fams/PusaWS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/UrbiniSMS19,
author = {Laura Urbini and
Blerina Sinaimeri and
Catherine Matias and
Marie{-}France Sagot},
title = {Exploring the Robustness of the Parsimonious Reconciliation Method
in Host-Symbiont Cophylogeny},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {16},
number = {3},
pages = {738--748},
year = {2019},
url = {https://doi.org/10.1109/TCBB.2018.2838667},
doi = {10.1109/TCBB.2018.2838667},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/UrbiniSMS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/HuberMSS18,
author = {Katharina T. Huber and
Vincent Moulton and
Marie{-}France Sagot and
Blerina Sinaimeri},
title = {Geometric medians in reconciliation spaces of phylogenetic trees},
journal = {Inf. Process. Lett.},
volume = {136},
pages = {96--101},
year = {2018},
url = {https://doi.org/10.1016/j.ipl.2018.04.001},
doi = {10.1016/J.IPL.2018.04.001},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ipl/HuberMSS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mst/BohmovaHMPSS18,
author = {Katerina B{\"{o}}hmov{\'{a}} and
Luca H{\"{a}}fliger and
Mat{\'{u}}s Mihal{\'{a}}k and
Tobias Pr{\"{o}}ger and
Gustavo Sacomoto and
Marie{-}France Sagot},
title = {Computing and Listing st-Paths in Public Transportation Networks},
journal = {Theory Comput. Syst.},
volume = {62},
number = {3},
pages = {600--621},
year = {2018},
url = {https://doi.org/10.1007/s00224-016-9747-4},
doi = {10.1007/S00224-016-9747-4},
timestamp = {Thu, 15 Mar 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/mst/BohmovaHMPSS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dagstuhl-reports/FernauGS18,
author = {Henning Fernau and
Petr A. Golovach and
Marie{-}France Sagot},
title = {Algorithmic Enumeration: Output-sensitive, Input-Sensitive, Parameterized,
Approximative (Dagstuhl Seminar 18421)},
journal = {Dagstuhl Reports},
volume = {8},
number = {10},
pages = {63--86},
year = {2018},
url = {https://doi.org/10.4230/DagRep.8.10.63},
doi = {10.4230/DAGREP.8.10.63},
timestamp = {Fri, 11 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dagstuhl-reports/FernauGS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/LimaSSLMMSL17,
author = {Leandro Lima and
Blerina Sinaimeri and
Gustavo Sacomoto and
H{\'{e}}l{\`{e}}ne Lopez{-}Maestre and
Camille Marchet and
Vincent Miele and
Marie{-}France Sagot and
Vincent Lacroix},
title = {Playing hide and seek with repeats in local and global de novo transcriptome
assembly of short RNA-seq reads},
journal = {Algorithms Mol. Biol.},
volume = {12},
number = {1},
pages = {2:1--2:19},
year = {2017},
url = {https://doi.org/10.1186/s13015-017-0091-2},
doi = {10.1186/S13015-017-0091-2},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/LimaSSLMMSL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cibb/GastaldelloCS17,
author = {Mattia Gastaldello and
Tiziana Calamoneri and
Marie{-}France Sagot},
editor = {Massimo Bartoletti and
Annalisa Barla and
Andrea Bracciali and
Gunnar W. Klau and
Leif E. Peterson and
Alberto Policriti and
Roberto Tagliaferri},
title = {Extracting Few Representative Reconciliations with Host Switches},
booktitle = {Computational Intelligence Methods for Bioinformatics and Biostatistics
- 14th International Meeting, {CIBB} 2017, Cagliari, Italy, September
7-9, 2017, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {10834},
pages = {9--18},
publisher = {Springer},
year = {2017},
url = {https://doi.org/10.1007/978-3-030-14160-8\_2},
doi = {10.1007/978-3-030-14160-8\_2},
timestamp = {Tue, 14 May 2019 10:00:54 +0200},
biburl = {https://dblp.org/rec/conf/cibb/GastaldelloCS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wg/AcunaGILRSSS17,
author = {Vicente Acu{\~{n}}a and
Roberto Grossi and
Giuseppe F. Italiano and
Leandro Lima and
Romeo Rizzi and
Gustavo Sacomoto and
Marie{-}France Sagot and
Blerina Sinaimeri},
editor = {Hans L. Bodlaender and
Gerhard J. Woeginger},
title = {On Bubble Generators in Directed Graphs},
booktitle = {Graph-Theoretic Concepts in Computer Science - 43rd International
Workshop, {WG} 2017, Eindhoven, The Netherlands, June 21-23, 2017,
Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {10520},
pages = {18--31},
publisher = {Springer},
year = {2017},
url = {https://doi.org/10.1007/978-3-319-68705-6\_2},
doi = {10.1007/978-3-319-68705-6\_2},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wg/AcunaGILRSSS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/AndradeWKAMMSS16,
author = {Ricardo Andrade and
Martin Wannagat and
Cecilia Coimbra Klein and
Vicente Acu{\~{n}}a and
Alberto Marchetti{-}Spaccamela and
Paulo Vieira Milreu and
Leen Stougie and
Marie{-}France Sagot},
title = {Enumeration of minimal stoichiometric precursor sets in metabolic
networks},
journal = {Algorithms Mol. Biol.},
volume = {11},
pages = {25},
year = {2016},
url = {https://doi.org/10.1186/s13015-016-0087-3},
doi = {10.1186/S13015-016-0087-3},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/AndradeWKAMMSS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/VerissimoOSV16,
author = {Andr{\'{e}} Ver{\'{\i}}ssimo and
Arlindo Limede Oliveira and
Marie{-}France Sagot and
Susana Vinga},
title = {DegreeCox - a network-based regularization method for survival analysis},
journal = {{BMC} Bioinform.},
volume = {17},
number = {{S-16}},
pages = {109--121},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-1310-4},
doi = {10.1186/S12859-016-1310-4},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/VerissimoOSV16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alcob/UrbiniSMS16,
author = {Laura Urbini and
Blerina Sinaimeri and
Catherine Matias and
Marie{-}France Sagot},
editor = {Mar{\'{\i}}a Bot{\'{o}}n{-}Fern{\'{a}}ndez and
Carlos Mart{\'{\i}}n{-}Vide and
Sergio Santander{-}Jim{\'{e}}nez and
Miguel A. Vega{-}Rodr{\'{\i}}guez},
title = {Robustness of the Parsimonious Reconciliation Method in Cophylogeny},
booktitle = {Algorithms for Computational Biology - Third International Conference,
AlCoB 2016, Trujillo, Spain, June 21-22, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9702},
pages = {119--130},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-38827-4\_10},
doi = {10.1007/978-3-319-38827-4\_10},
timestamp = {Sat, 05 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/alcob/UrbiniSMS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csr/BohmovaMPSS16,
author = {Katerina B{\"{o}}hmov{\'{a}} and
Mat{\'{u}}s Mihal{\'{a}}k and
Tobias Pr{\"{o}}ger and
Gustavo Sacomoto and
Marie{-}France Sagot},
editor = {Alexander S. Kulikov and
Gerhard J. Woeginger},
title = {Computing and Listing st-Paths in Public Transportation Networks},
booktitle = {Computer Science - Theory and Applications - 11th International Computer
Science Symposium in Russia, {CSR} 2016, St. Petersburg, Russia, June
9-13, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9691},
pages = {102--116},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-34171-2\_8},
doi = {10.1007/978-3-319-34171-2\_8},
timestamp = {Tue, 14 May 2019 10:00:51 +0200},
biburl = {https://dblp.org/rec/conf/csr/BohmovaMPSS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ictcs/CalamoneriGMSS16,
author = {Tiziana Calamoneri and
Mattia Gastaldello and
Arnaud Mary and
Marie{-}France Sagot and
Blerina Sinaimeri},
editor = {Vittorio Bil{\`{o}} and
Antonio Caruso},
title = {On Maximal Chain Subgraphs and Covers of Bipartite Graphs},
booktitle = {Proceedings of the 17th Italian Conference on Theoretical Computer
Science, Lecce, Italy, September 7-9, 2016},
series = {{CEUR} Workshop Proceedings},
volume = {1720},
pages = {286--291},
publisher = {CEUR-WS.org},
year = {2016},
url = {https://ceur-ws.org/Vol-1720/short12.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:17 +0100},
biburl = {https://dblp.org/rec/conf/ictcs/CalamoneriGMSS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwoca/CalamoneriGMSS16,
author = {Tiziana Calamoneri and
Mattia Gastaldello and
Arnaud Mary and
Marie{-}France Sagot and
Blerina Sinaimeri},
editor = {Veli M{\"{a}}kinen and
Simon J. Puglisi and
Leena Salmela},
title = {On Maximal Chain Subgraphs and Covers of Bipartite Graphs},
booktitle = {Combinatorial Algorithms - 27th International Workshop, {IWOCA} 2016,
Helsinki, Finland, August 17-19, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9843},
pages = {137--150},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-44543-4\_11},
doi = {10.1007/978-3-319-44543-4\_11},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/iwoca/CalamoneriGMSS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ercim/MerksS16,
author = {Roeland Merks and
Marie{-}France Sagot},
title = {Tackling Big Data in the Life Sciences - Introduction to the Special
Theme},
journal = {{ERCIM} News},
volume = {2016},
number = {104},
year = {2016},
url = {http://ercim-news.ercim.eu/en104/special/tackling-big-data-in-the-life-sciences-introduction-to-the-special-theme},
timestamp = {Wed, 22 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ercim/MerksS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DonatiBSCS15,
author = {Beatrice Donati and
Christian Baudet and
Blerina Sinaimeri and
Pierluigi Crescenzi and
Marie{-}France Sagot},
title = {{EUCALYPT:} efficient tree reconciliation enumerator},
journal = {Algorithms Mol. Biol.},
volume = {10},
pages = {3},
year = {2015},
url = {https://doi.org/10.1186/s13015-014-0031-3},
doi = {10.1186/S13015-014-0031-3},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/DonatiBSCS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/SacomotoLS15,
author = {Gustavo Sacomoto and
Vincent Lacroix and
Marie{-}France Sagot},
title = {A polynomial delay algorithm for the enumeration of bubbles with length
constraints in directed graphs},
journal = {Algorithms Mol. Biol.},
volume = {10},
pages = {20},
year = {2015},
url = {https://doi.org/10.1186/s13015-015-0046-4},
doi = {10.1186/S13015-015-0046-4},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/SacomotoLS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BosiDGBSLCFF15,
author = {Emanuele Bosi and
Beatrice Donati and
Marco Galardini and
Sara Brunetti and
Marie{-}France Sagot and
Pietro Li{\`{o}} and
Pierluigi Crescenzi and
Renato Fani and
Marco Fondi},
title = {MeDuSa: a multi-draft based scaffolder},
journal = {Bioinform.},
volume = {31},
number = {15},
pages = {2443--2451},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btv171},
doi = {10.1093/BIOINFORMATICS/BTV171},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/BosiDGBSLCFF15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HigashiFGGS15,
author = {Susan Higashi and
Cyril Fournier and
Christian Gautier and
Christine Gaspin and
Marie{-}France Sagot},
title = {Mirinho: An efficient and general plant and animal pre-miRNA predictor
for genomic and deep sequencing data},
journal = {{BMC} Bioinform.},
volume = {16},
pages = {179:1--179:14},
year = {2015},
url = {https://doi.org/10.1186/s12859-015-0594-0},
doi = {10.1186/S12859-015-0594-0},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HigashiFGGS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fct/AndradeBMPS15,
author = {Ricardo Andrade and
Etienne Birmel{\'{e}} and
Arnaud Mary and
Thomas Picchetti and
Marie{-}France Sagot},
editor = {Adrian Kosowski and
Igor Walukiewicz},
title = {Incremental Complexity of a Bi-objective Hypergraph Transversal Problem},
booktitle = {Fundamentals of Computation Theory - 20th International Symposium,
{FCT} 2015, Gda{\'{n}}sk, Poland, August 17-19, 2015, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9210},
pages = {202--213},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-22177-9\_16},
doi = {10.1007/978-3-319-22177-9\_16},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/fct/AndradeBMPS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/AndradeBMPS15,
author = {Ricardo Andrade and
Etienne Birmel{\'{e}} and
Arnaud Mary and
Thomas Picchetti and
Marie{-}France Sagot},
title = {Incremental complexity of a bi-objective hypergraph transversal problem},
journal = {CoRR},
volume = {abs/1505.06025},
year = {2015},
url = {http://arxiv.org/abs/1505.06025},
eprinttype = {arXiv},
eprint = {1505.06025},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/AndradeBMPS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MilreuKCABBJMMSJCLS14,
author = {Paulo Vieira Milreu and
Cecilia Coimbra Klein and
Ludovic Cottret and
Vicente Acu{\~{n}}a and
Etienne Birmel{\'{e}} and
Michele Borassi and
Christophe Junot and
Alberto Marchetti{-}Spaccamela and
Andrea Marino and
Leen Stougie and
Fabien Jourdan and
Pierluigi Crescenzi and
Vincent Lacroix and
Marie{-}France Sagot},
title = {Telling metabolic stories to explore metabolomics data: a case study
on the yeast response to cadmium exposure},
journal = {Bioinform.},
volume = {30},
number = {1},
pages = {61--70},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btt597},
doi = {10.1093/BIOINFORMATICS/BTT597},
timestamp = {Sun, 18 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MilreuKCABBJMMSJCLS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/FedericoPPS14,
author = {Maria Federico and
Pierre Peterlongo and
Nadia Pisanti and
Marie{-}France Sagot},
title = {Rime: Repeat identification},
journal = {Discret. Appl. Math.},
volume = {163},
pages = {275--286},
year = {2014},
url = {https://doi.org/10.1016/j.dam.2013.02.016},
doi = {10.1016/J.DAM.2013.02.016},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/FedericoPPS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/esa/FerreiraGRSS14,
author = {Rui A. Ferreira and
Roberto Grossi and
Romeo Rizzi and
Gustavo Sacomoto and
Marie{-}France Sagot},
editor = {Andreas S. Schulz and
Dorothea Wagner},
title = {Amortized {\~{O}}({\(\vert\)}V{\(\vert\)}) -Delay Algorithm for Listing
Chordless Cycles in Undirected Graphs},
booktitle = {Algorithms - {ESA} 2014 - 22th Annual European Symposium, Wroclaw,
Poland, September 8-10, 2014. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8737},
pages = {418--429},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-662-44777-2\_35},
doi = {10.1007/978-3-662-44777-2\_35},
timestamp = {Tue, 14 May 2019 10:00:54 +0200},
biburl = {https://dblp.org/rec/conf/esa/FerreiraGRSS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwoca/RizziSS14,
author = {Romeo Rizzi and
Gustavo Sacomoto and
Marie{-}France Sagot},
editor = {Jan Kratochv{\'{\i}}l and
Mirka Miller and
Dalibor Froncek},
title = {Efficiently Listing Bounded Length st-Paths},
booktitle = {Combinatorial Algorithms - 25th International Workshop, {IWOCA} 2014,
Duluth, MN, USA, October 15-17, 2014, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {8986},
pages = {318--329},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-19315-1\_28},
doi = {10.1007/978-3-319-19315-1\_28},
timestamp = {Tue, 14 May 2019 10:00:53 +0200},
biburl = {https://dblp.org/rec/conf/iwoca/RizziSS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/SacomotoSMMSL14,
author = {Gustavo Sacomoto and
Blerina Sinaimeri and
Camille Marchet and
Vincent Miele and
Marie{-}France Sagot and
Vincent Lacroix},
editor = {Daniel G. Brown and
Burkhard Morgenstern},
title = {Navigating in a Sea of Repeats in RNA-seq without Drowning},
booktitle = {Algorithms in Bioinformatics - 14th International Workshop, {WABI}
2014, Wroclaw, Poland, September 8-10, 2014. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8701},
pages = {82--96},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-662-44753-6\_7},
doi = {10.1007/978-3-662-44753-6\_7},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/SacomotoSMMSL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/SacomotoSMMSL14,
author = {Gustavo Sacomoto and
Blerina Sinaimeri and
Camille Marchet and
Vincent Miele and
Marie{-}France Sagot and
Vincent Lacroix},
title = {Navigating in a sea of repeats in RNA-seq without drowning},
journal = {CoRR},
volume = {abs/1406.1022},
year = {2014},
url = {http://arxiv.org/abs/1406.1022},
eprinttype = {arXiv},
eprint = {1406.1022},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/SacomotoSMMSL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/FerreiraGRSS14,
author = {Rui A. Ferreira and
Roberto Grossi and
Romeo Rizzi and
Gustavo Sacomoto and
Marie{-}France Sagot},
title = {Amortized {\~{O}}({\(\vert\)}V{\(\vert\)})-Delay Algorithm for Listing
Chordless Cycles in Undirected Graphs},
journal = {CoRR},
volume = {abs/1408.1265},
year = {2014},
url = {http://arxiv.org/abs/1408.1265},
eprinttype = {arXiv},
eprint = {1408.1265},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/FerreiraGRSS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/RizziSS14,
author = {Romeo Rizzi and
Gustavo Sacomoto and
Marie{-}France Sagot},
title = {Efficiently listing bounded length st-paths},
journal = {CoRR},
volume = {abs/1411.6852},
year = {2014},
url = {http://arxiv.org/abs/1411.6852},
eprinttype = {arXiv},
eprint = {1411.6852},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/RizziSS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/SacomotoLS13,
author = {Gustavo Sacomoto and
Vincent Lacroix and
Marie{-}France Sagot},
editor = {Aaron E. Darling and
Jens Stoye},
title = {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},
booktitle = {Algorithms in Bioinformatics - 13th International Workshop, {WABI}
2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8126},
pages = {99--111},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-40453-5\_9},
doi = {10.1007/978-3-642-40453-5\_9},
timestamp = {Tue, 21 Mar 2023 21:00:29 +0100},
biburl = {https://dblp.org/rec/conf/wabi/SacomotoLS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wea/BorassiCLMSM13,
author = {Michele Borassi and
Pierluigi Crescenzi and
Vincent Lacroix and
Andrea Marino and
Marie{-}France Sagot and
Paulo Vieira Milreu},
editor = {Vincenzo Bonifaci and
Camil Demetrescu and
Alberto Marchetti{-}Spaccamela},
title = {Telling Stories Fast},
booktitle = {Experimental Algorithms, 12th International Symposium, {SEA} 2013,
Rome, Italy, June 5-7, 2013. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7933},
pages = {200--211},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-38527-8\_19},
doi = {10.1007/978-3-642-38527-8\_19},
timestamp = {Sun, 18 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wea/BorassiCLMSM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/SacomotoLS13,
author = {Gustavo Sacomoto and
Vincent Lacroix and
Marie{-}France Sagot},
title = {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},
journal = {CoRR},
volume = {abs/1307.7813},
year = {2013},
url = {http://arxiv.org/abs/1307.7813},
eprinttype = {arXiv},
eprint = {1307.7813},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/SacomotoLS13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/abi/AllaliSCDDDFGHLMOSTTT12,
author = {Julien Allali and
C{\'{e}}dric Saule and
C{\'{e}}dric Chauve and
Yves D'Aubenton{-}Carafa and
Alain Denise and
Christine Drevet and
Pascal Ferraro and
Daniel Gautheret and
Claire Herrbach and
Fabrice Leclerc and
Antoine de Monte and
A{\"{\i}}da Ouangraoua and
Marie{-}France Sagot and
Michel Termier and
Claude Thermes and
H{\'{e}}l{\`{e}}ne Touzet},
title = {{BRASERO:} {A} Resource for Benchmarking {RNA} Secondary Structure
Comparison Algorithms},
journal = {Adv. Bioinformatics},
volume = {2012},
pages = {893048:1--893048:5},
year = {2012},
url = {https://doi.org/10.1155/2012/893048},
doi = {10.1155/2012/893048},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/abi/AllaliSCDDDFGHLMOSTTT12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BaudetDS12,
author = {Christian Baudet and
Zanoni Dias and
Marie{-}France Sagot},
title = {Sampling solution traces for the problem of sorting permutations by
signed reversals},
journal = {Algorithms Mol. Biol.},
volume = {7},
pages = {18},
year = {2012},
url = {https://doi.org/10.1186/1748-7188-7-18},
doi = {10.1186/1748-7188-7-18},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/BaudetDS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AcunaMCMSS12,
author = {Vicente Acu{\~{n}}a and
Paulo Vieira Milreu and
Ludovic Cottret and
Alberto Marchetti{-}Spaccamela and
Leen Stougie and
Marie{-}France Sagot},
title = {Algorithms and complexity of enumerating minimal precursor sets in
genome-wide metabolic networks},
journal = {Bioinform.},
volume = {28},
number = {19},
pages = {2474--2483},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts423},
doi = {10.1093/BIOINFORMATICS/BTS423},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AcunaMCMSS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MendesHFSB12,
author = {Nuno D. Mendes and
Steffen Heyne and
Ana T. Freitas and
Marie{-}France Sagot and
Rolf Backofen},
title = {Navigating the unexplored seascape of pre-miRNA candidates in single-genome
approaches},
journal = {Bioinform.},
volume = {28},
number = {23},
pages = {3034--3041},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts574},
doi = {10.1093/BIOINFORMATICS/BTS574},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MendesHFSB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SacomotoKCUASPL12,
author = {Gustavo Akio Tominaga Sacomoto and
Janice Kielbassa and
Rayan Chikhi and
Raluca Uricaru and
Pavlos Antoniou and
Marie{-}France Sagot and
Pierre Peterlongo and
Vincent Lacroix},
title = {{KISSPLICE:} de-novo calling alternative splicing events from RNA-seq
data},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-6}},
pages = {S5},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-S6-S5},
doi = {10.1186/1471-2105-13-S6-S5},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SacomotoKCUASPL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/iandc/NorHCERDS12,
author = {Igor Nor and
Danny Hermelin and
Sylvain Charlat and
Jan Engelstadter and
Max Reuter and
Olivier Duron and
Marie{-}France Sagot},
title = {Mod/Resc Parsimony Inference: Theory and application},
journal = {Inf. Comput.},
volume = {213},
pages = {23--32},
year = {2012},
url = {https://doi.org/10.1016/j.ic.2011.03.008},
doi = {10.1016/J.IC.2011.03.008},
timestamp = {Fri, 12 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/iandc/NorHCERDS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/Sagot12,
author = {Marie{-}France Sagot},
title = {{EIC} Editorial},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {9},
number = {6},
pages = {1553--1557},
year = {2012},
url = {https://doi.org/10.1109/TCBB.2012.155},
doi = {10.1109/TCBB.2012.155},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/Sagot12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AcunaBCCJLMMMSS12,
author = {Vicente Acu{\~{n}}a and
Etienne Birmel{\'{e}} and
Ludovic Cottret and
Pierluigi Crescenzi and
Fabien Jourdan and
Vincent Lacroix and
Alberto Marchetti{-}Spaccamela and
Andrea Marino and
Paulo Vieira Milreu and
Marie{-}France Sagot and
Leen Stougie},
title = {Telling stories: Enumerating maximal directed acyclic graphs with
a constrained set of sources and targets},
journal = {Theor. Comput. Sci.},
volume = {457},
pages = {1--9},
year = {2012},
url = {https://doi.org/10.1016/j.tcs.2012.07.023},
doi = {10.1016/J.TCS.2012.07.023},
timestamp = {Sun, 18 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/AcunaBCCJLMMMSS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iscopt/FreireACFLMMS12,
author = {Alexandre S. Freire and
Vicente Acu{\~{n}}a and
Pilu Crescenzi and
Carlos Eduardo Ferreira and
Vincent Lacroix and
Paulo Vieira Milreu and
Eduardo Moreno and
Marie{-}France Sagot},
editor = {Ali Ridha Mahjoub and
Vangelis Markakis and
Ioannis Milis and
Vangelis Th. Paschos},
title = {Minimum Ratio Cover of Matrix Columns by Extreme Rays of Its Induced
Cone},
booktitle = {Combinatorial Optimization - Second International Symposium, {ISCO}
2012, Athens, Greece, April 19-21, 2012, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {7422},
pages = {165--177},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-32147-4\_16},
doi = {10.1007/978-3-642-32147-4\_16},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iscopt/FreireACFLMMS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/spire/BirmeleCFGLMPSS12,
author = {Etienne Birmel{\'{e}} and
Pierluigi Crescenzi and
Rui A. Ferreira and
Roberto Grossi and
Vincent Lacroix and
Andrea Marino and
Nadia Pisanti and
Gustavo Akio Tominaga Sacomoto and
Marie{-}France Sagot},
editor = {Liliana Calder{\'{o}}n{-}Benavides and
Cristina N. Gonz{\'{a}}lez{-}Caro and
Edgar Ch{\'{a}}vez and
Nivio Ziviani},
title = {Efficient Bubble Enumeration in Directed Graphs},
booktitle = {String Processing and Information Retrieval - 19th International Symposium,
{SPIRE} 2012, Cartagena de Indias, Colombia, October 21-25, 2012.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7608},
pages = {118--129},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-34109-0\_13},
doi = {10.1007/978-3-642-34109-0\_13},
timestamp = {Sun, 18 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/spire/BirmeleCFGLMPSS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1205-2766,
author = {Etienne Birmel{\'{e}} and
Rui A. Ferreira and
Roberto Grossi and
Andrea Marino and
Nadia Pisanti and
Romeo Rizzi and
Gustavo Akio Tominaga Sacomoto and
Marie{-}France Sagot},
title = {Optimal Listing of Cycles and st-Paths in Undirected Graphs},
journal = {CoRR},
volume = {abs/1205.2766},
year = {2012},
url = {http://arxiv.org/abs/1205.2766},
eprinttype = {arXiv},
eprint = {1205.2766},
timestamp = {Sun, 18 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1205-2766.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/VellozoVBHCFCRDGSCC11,
author = {Augusto F. Vellozo and
Am{\'{e}}lie S. V{\'{e}}ron and
Patrice Baa{-}Puyoulet and
Jaime Huerta{-}Cepas and
Ludovic Cottret and
G{\'{e}}rard Febvay and
Federica Calevro and
Yvan Rahb{\'{e}} and
Angela E. Douglas and
Toni Gabald{\'{o}}n and
Marie{-}France Sagot and
Hubert Charles and
Stefano Colella},
title = {CycADS: an annotation database system to ease the development and
update of BioCyc databases},
journal = {Database J. Biol. Databases Curation},
volume = {2011},
year = {2011},
url = {https://doi.org/10.1093/database/bar008},
doi = {10.1093/DATABASE/BAR008},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/VellozoVBHCFCRDGSCC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DenielouSBV11,
author = {Yves{-}Pol Deni{\'{e}}lou and
Marie{-}France Sagot and
Fr{\'{e}}d{\'{e}}ric Boyer and
Alain Viari},
title = {Bacterial syntenies: an exact approach with gene quorum},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {193},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-193},
doi = {10.1186/1471-2105-12-193},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/DenielouSBV11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/Sagot11,
author = {Marie{-}France Sagot},
title = {{EIC} Editorial},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {8},
number = {1},
pages = {1},
year = {2011},
url = {https://doi.org/10.1109/TCBB.2011.7},
doi = {10.1109/TCBB.2011.7},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/Sagot11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/Sagot11a,
author = {Marie{-}France Sagot},
title = {{EIC} Editorial},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {8},
number = {2},
pages = {289--291},
year = {2011},
url = {https://doi.org/10.1109/TCBB.2011.15},
doi = {10.1109/TCBB.2011.15},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/Sagot11a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stringology/FedericoPPS11,
author = {Maria Federico and
Pierre Peterlongo and
Nadia Pisanti and
Marie{-}France Sagot},
editor = {Jan Holub and
Jan Zd{\'{a}}rek},
title = {Finding Long and Multiple Repeats with Edit Distance},
booktitle = {Proceedings of the Prague Stringology Conference 2011, Prague, Czech
Republic, August 29-31, 2011},
pages = {83--97},
publisher = {Prague Stringology Club, Department of Theoretical Computer Science,
Faculty of Information Technology, Czech Technical University in Prague},
year = {2011},
url = {http://www.stringology.org/event/2011/p08.html},
timestamp = {Wed, 10 Feb 2021 08:42:18 +0100},
biburl = {https://dblp.org/rec/conf/stringology/FedericoPPS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/wabi/2011,
editor = {Teresa M. Przytycka and
Marie{-}France Sagot},
title = {Algorithms in Bioinformatics - 11th International Workshop, {WABI}
2011, Saarbr{\"{u}}cken, Germany, September 5-7, 2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6833},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-23038-7},
doi = {10.1007/978-3-642-23038-7},
isbn = {978-3-642-23037-0},
timestamp = {Tue, 14 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/2011.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BaudetLDGTS10,
author = {Christian Baudet and
Claire Lemaitre and
Zanoni Dias and
Christian Gautier and
Eric Tannier and
Marie{-}France Sagot},
title = {Cassis: detection of genomic rearrangement breakpoints},
journal = {Bioinform.},
volume = {26},
number = {15},
pages = {1897--1898},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq301},
doi = {10.1093/BIOINFORMATICS/BTQ301},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/BaudetLDGTS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biosystems/AcunaMSS10,
author = {Vicente Acu{\~{n}}a and
Alberto Marchetti{-}Spaccamela and
Marie{-}France Sagot and
Leen Stougie},
title = {A note on the complexity of finding and enumerating elementary modes},
journal = {Biosyst.},
volume = {99},
number = {3},
pages = {210--214},
year = {2010},
url = {https://doi.org/10.1016/j.biosystems.2009.11.004},
doi = {10.1016/J.BIOSYSTEMS.2009.11.004},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biosystems/AcunaMSS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/AdiBFFMSSTW10,
author = {Said Sadique Adi and
Mar{\'{\i}}lia D. V. Braga and
Cristina G. Fernandes and
Carlos Eduardo Ferreira and
F{\'{a}}bio Viduani Martinez and
Marie{-}France Sagot and
Marco Aurelio Stefanes and
Christian Tjandraatmadja and
Yoshiko Wakabayashi},
title = {Repetition-free longest common subsequence},
journal = {Discret. Appl. Math.},
volume = {158},
number = {12},
pages = {1315--1324},
year = {2010},
url = {https://doi.org/10.1016/j.dam.2009.04.023},
doi = {10.1016/J.DAM.2009.04.023},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/AdiBFFMSSTW10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CottretWVBCSJ10,
author = {Ludovic Cottret and
David Wildridge and
Florence Vinson and
Michael P. Barrett and
Hubert Charles and
Marie{-}France Sagot and
Fabien Jourdan},
title = {MetExplore: a web server to link metabolomic experiments and genome-scale
metabolic networks},
journal = {Nucleic Acids Res.},
volume = {38},
number = {Web-Server-Issue},
pages = {132--137},
year = {2010},
url = {https://doi.org/10.1093/nar/gkq312},
doi = {10.1093/NAR/GKQ312},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/CottretWVBCSJ10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/CottretMAMSCS10,
author = {Ludovic Cottret and
Paulo Vieira Milreu and
Vicente Acu{\~{n}}a and
Alberto Marchetti{-}Spaccamela and
Leen Stougie and
Hubert Charles and
Marie{-}France Sagot},
title = {Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident
Intracellular Symbionts, \emph{Baumannia cicadellinicola} and \emph{Sulcia
muelleri}, with Their Insect Host, \emph{Homalodisca coagulata}},
journal = {PLoS Comput. Biol.},
volume = {6},
number = {9},
year = {2010},
url = {https://doi.org/10.1371/journal.pcbi.1000904},
doi = {10.1371/JOURNAL.PCBI.1000904},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/CottretMAMSCS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/Sagot10,
author = {Marie{-}France Sagot},
title = {{EIC} Editorial},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {7},
number = {2},
pages = {193--194},
year = {2010},
url = {https://doi.org/10.1109/TCBB.2010.29},
doi = {10.1109/TCBB.2010.29},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/Sagot10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/NorHCERDS10,
author = {Igor Nor and
Danny Hermelin and
Sylvain Charlat and
Jan Engelstadter and
Max Reuter and
Olivier Duron and
Marie{-}France Sagot},
editor = {Amihood Amir and
Laxmi Parida},
title = {Mod/Resc Parsimony Inference},
booktitle = {Combinatorial Pattern Matching, 21st Annual Symposium, {CPM} 2010,
New York, NY, USA, June 21-23, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6129},
pages = {202--213},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-13509-5\_19},
doi = {10.1007/978-3-642-13509-5\_19},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cpm/NorHCERDS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/spire/PeterlongoSPSL10,
author = {Pierre Peterlongo and
Nicolas Schnel and
Nadia Pisanti and
Marie{-}France Sagot and
Vincent Lacroix},
editor = {Edgar Ch{\'{a}}vez and
Stefano Lonardi},
title = {Identifying SNPs without a Reference Genome by Comparing Raw Reads},
booktitle = {String Processing and Information Retrieval - 17th International Symposium,
{SPIRE} 2010, Los Cabos, Mexico, October 11-13, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6393},
pages = {147--158},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-16321-0\_14},
doi = {10.1007/978-3-642-16321-0\_14},
timestamp = {Sat, 05 Sep 2020 18:08:29 +0200},
biburl = {https://dblp.org/rec/conf/spire/PeterlongoSPSL10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/MilreuABCMSSL10,
author = {Paulo Vieira Milreu and
Vicente Acu{\~{n}}a and
Etienne Birmel{\'{e}} and
Pierluigi Crescenzi and
Alberto Marchetti{-}Spaccamela and
Marie{-}France Sagot and
Leen Stougie and
Vincent Lacroix},
editor = {Vincent Moulton and
Mona Singh},
title = {Enumerating Chemical Organisations in Consistent Metabolic Networks:
Complexity and Algorithms},
booktitle = {Algorithms in Bioinformatics, 10th International Workshop, {WABI}
2010, Liverpool, UK, September 6-8, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6293},
pages = {226--237},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-15294-8\_19},
doi = {10.1007/978-3-642-15294-8\_19},
timestamp = {Sun, 12 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wabi/MilreuABCMSSL10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1002-1292,
author = {Igor Nor and
Danny Hermelin and
Sylvain Charlat and
Jan Engelstadter and
Max Reuter and
Olivier Duron and
Marie{-}France Sagot},
title = {Mod/Resc Parsimony Inference},
journal = {CoRR},
volume = {abs/1002.1292},
year = {2010},
url = {http://arxiv.org/abs/1002.1292},
eprinttype = {arXiv},
eprint = {1002.1292},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1002-1292.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/BragaGS09,
author = {Mar{\'{\i}}lia D. V. Braga and
Christian Gautier and
Marie{-}France Sagot},
title = {An asymmetric approach to preserve common intervals while sorting
by reversals},
journal = {Algorithms Mol. Biol.},
volume = {4},
pages = {16},
year = {2009},
url = {https://doi.org/10.1186/1748-7188-4-16},
doi = {10.1186/1748-7188-4-16},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/BragaGS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/PeterlongoSLPS09,
author = {Pierre Peterlongo and
Gustavo Akio Tominaga Sacomoto and
Alair Pereira do Lago and
Nadia Pisanti and
Marie{-}France Sagot},
title = {Lossless filter for multiple repeats with bounded edit distance},
journal = {Algorithms Mol. Biol.},
volume = {4},
year = {2009},
url = {https://doi.org/10.1186/1748-7188-4-3},
doi = {10.1186/1748-7188-4-3},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/PeterlongoSLPS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SagotMM09,
author = {Marie{-}France Sagot and
B. J. Morrison McKay and
Gene Myers},
title = {{ISMB/ECCB} 2009 Stockholm},
journal = {Bioinform.},
volume = {25},
number = {12},
pages = {1570--1573},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp280},
doi = {10.1093/BIOINFORMATICS/BTP280},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/SagotMM09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biosystems/AcunaCLMSS09,
author = {Vicente Acu{\~{n}}a and
Flavio Chierichetti and
Vincent Lacroix and
Alberto Marchetti{-}Spaccamela and
Marie{-}France Sagot and
Leen Stougie},
title = {Modes and cuts in metabolic networks: Complexity and algorithms},
journal = {Biosyst.},
volume = {95},
number = {1},
pages = {51--60},
year = {2009},
url = {https://doi.org/10.1016/j.biosystems.2008.06.015},
doi = {10.1016/J.BIOSYSTEMS.2008.06.015},
timestamp = {Thu, 20 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biosystems/AcunaCLMSS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ejbsb/SchbathLS09,
author = {Sophie Schbath and
Vincent Lacroix and
Marie{-}France Sagot},
title = {Assessing the Exceptionality of Coloured Motifs in Networks},
journal = {{EURASIP} J. Bioinform. Syst. Biol.},
volume = {2009},
year = {2009},
url = {https://doi.org/10.1155/2009/616234},
doi = {10.1155/2009/616234},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ejbsb/SchbathLS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/Sagot09,
author = {Marie{-}France Sagot},
title = {New {EIC} Editorial},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {6},
number = {1},
pages = {3},
year = {2009},
url = {https://doi.org/10.1109/TCBB.2009.19},
doi = {10.1109/TCBB.2009.19},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/Sagot09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/Sagot09a,
author = {Marie{-}France Sagot},
title = {{EIC} Editorial},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {6},
number = {2},
pages = {177},
year = {2009},
url = {https://doi.org/10.1109/TCBB.2009.44},
doi = {10.1109/TCBB.2009.44},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/Sagot09a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/Sagot09b,
author = {Marie{-}France Sagot},
title = {{EIC} Editorial: Introducing New Associate Editors},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {6},
number = {3},
pages = {369},
year = {2009},
url = {https://doi.org/10.1109/TCBB.2009.66},
doi = {10.1109/TCBB.2009.66},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/Sagot09b.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/DenielouBVS09,
author = {Yves{-}Pol Deni{\'{e}}lou and
Fr{\'{e}}d{\'{e}}ric Boyer and
Alain Viari and
Marie{-}France Sagot},
editor = {Gregory Kucherov and
Esko Ukkonen},
title = {Multiple Alignment of Biological Networks: {A} Flexible Approach},
booktitle = {Combinatorial Pattern Matching, 20th Annual Symposium, {CPM} 2009,
Lille, France, June 22-24, 2009, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5577},
pages = {263--273},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-02441-2\_23},
doi = {10.1007/978-3-642-02441-2\_23},
timestamp = {Tue, 14 May 2019 10:00:38 +0200},
biburl = {https://dblp.org/rec/conf/cpm/DenielouBVS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LemaitreTGS08,
author = {Claire Lemaitre and
Eric Tannier and
Christian Gautier and
Marie{-}France Sagot},
title = {Precise detection of rearrangement breakpoints in mammalian chromosomes},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-286},
doi = {10.1186/1471-2105-9-286},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LemaitreTGS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/endm/AdiBFFMSSTW08,
author = {Said Sadique Adi and
Mar{\'{\i}}lia D. V. Braga and
Cristina G. Fernandes and
Carlos Eduardo Ferreira and
F{\'{a}}bio Viduani Martinez and
Marie{-}France Sagot and
Marco Aurelio Stefanes and
Christian Tjandraatmadja and
Yoshiko Wakabayashi},
title = {Repetition-free longest common subsequence},
journal = {Electron. Notes Discret. Math.},
volume = {30},
pages = {243--248},
year = {2008},
url = {https://doi.org/10.1016/j.endm.2008.01.042},
doi = {10.1016/J.ENDM.2008.01.042},
timestamp = {Mon, 13 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/endm/AdiBFFMSSTW08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijfcs/PeterlongoAS08,
author = {Pierre Peterlongo and
Julien Allali and
Marie{-}France Sagot},
title = {Indexing Gapped-Factors Using a Tree},
journal = {Int. J. Found. Comput. Sci.},
volume = {19},
number = {1},
pages = {71--87},
year = {2008},
url = {https://doi.org/10.1142/S0129054108005541},
doi = {10.1142/S0129054108005541},
timestamp = {Sat, 27 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijfcs/PeterlongoAS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jda/GuimaraesS08,
author = {Katia S. Guimar{\~{a}}es and
Marie{-}France Sagot},
title = {Editorial},
journal = {J. Discrete Algorithms},
volume = {6},
number = {2},
pages = {163},
year = {2008},
url = {https://doi.org/10.1016/j.jda.2007.06.004},
doi = {10.1016/J.JDA.2007.06.004},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jda/GuimaraesS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jda/PeterlongoPBLS08,
author = {Pierre Peterlongo and
Nadia Pisanti and
Fr{\'{e}}d{\'{e}}ric Boyer and
Alair Pereira do Lago and
Marie{-}France Sagot},
title = {Lossless filter for multiple repetitions with Hamming distance},
journal = {J. Discrete Algorithms},
volume = {6},
number = {3},
pages = {497--509},
year = {2008},
url = {https://doi.org/10.1016/j.jda.2007.03.003},
doi = {10.1016/J.JDA.2007.03.003},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jda/PeterlongoPBLS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/spe/AllaliS08,
author = {Julien Allali and
Marie{-}France Sagot},
title = {A multiple layer model to compare {RNA} secondary structures},
journal = {Softw. Pract. Exp.},
volume = {38},
number = {8},
pages = {775--792},
year = {2008},
url = {https://doi.org/10.1002/spe.846},
doi = {10.1002/SPE.846},
timestamp = {Thu, 09 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/spe/AllaliS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/BragaSST08,
author = {Mar{\'{\i}}lia D. V. Braga and
Marie{-}France Sagot and
C{\'{e}}line Scornavacca and
Eric Tannier},
title = {Exploring the Solution Space of Sorting by Reversals, with Experiments
and an Application to Evolution},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {5},
number = {3},
pages = {348--356},
year = {2008},
url = {https://doi.org/10.1109/TCBB.2008.16},
doi = {10.1109/TCBB.2008.16},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/BragaSST08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/LacroixCTS08,
author = {Vincent Lacroix and
Ludovic Cottret and
Patricia Th{\'{e}}bault and
Marie{-}France Sagot},
title = {An Introduction to Metabolic Networks and Their Structural Analysis},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {5},
number = {4},
pages = {594--617},
year = {2008},
url = {https://doi.org/10.1109/TCBB.2008.79},
doi = {10.1109/TCBB.2008.79},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/LacroixCTS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/LemaitreS08,
author = {Claire Lemaitre and
Marie{-}France Sagot},
title = {A small trip in the untranquil world of genomes: {A} survey on the
detection and analysis of genome rearrangement breakpoints},
journal = {Theor. Comput. Sci.},
volume = {395},
number = {2-3},
pages = {171--192},
year = {2008},
url = {https://doi.org/10.1016/j.tcs.2008.01.014},
doi = {10.1016/J.TCS.2008.01.014},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/LemaitreS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/FonsecaGS08,
author = {Paulo G. S. da Fonseca and
Katia S. Guimar{\~{a}}es and
Marie{-}France Sagot},
title = {Efficient representation and \emph{P}-value computation for high-order
Markov motifs},
booktitle = {ECCB'08 Proceedings, Seventh European Conference on Computational
Biology, 22-26 September 2008, Cagliari, Italy},
pages = {160--166},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn282},
doi = {10.1093/BIOINFORMATICS/BTN282},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/eccb/FonsecaGS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/CottretMAMMSS08,
author = {Ludovic Cottret and
Paulo Vieira Milreu and
Vicente Acu{\~{n}}a and
Alberto Marchetti{-}Spaccamela and
F{\'{a}}bio Viduani Martinez and
Marie{-}France Sagot and
Leen Stougie},
editor = {Keith A. Crandall and
Jens Lagergren},
title = {Enumerating Precursor Sets of Target Metabolites in a Metabolic Network},
booktitle = {Algorithms in Bioinformatics, 8th International Workshop, {WABI} 2008,
Karlsruhe, Germany, September 15-19, 2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5251},
pages = {233--244},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-87361-7\_20},
doi = {10.1007/978-3-540-87361-7\_20},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wabi/CottretMAMMSS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-0810-4002,
author = {Julien Allali and
Marie{-}France Sagot},
title = {A new distance for high level {RNA} secondary structure comparison},
journal = {CoRR},
volume = {abs/0810.4002},
year = {2008},
url = {http://arxiv.org/abs/0810.4002},
eprinttype = {arXiv},
eprint = {0810.4002},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-0810-4002.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/BourquiCLAMSJ07,
author = {Romain Bourqui and
Ludovic Cottret and
Vincent Lacroix and
David Auber and
Patrick Mary and
Marie{-}France Sagot and
Fabien Jourdan},
title = {Metabolic network visualization eliminating node redundance and preserving
metabolic pathways},
journal = {{BMC} Syst. Biol.},
volume = {1},
pages = {29},
year = {2007},
url = {https://doi.org/10.1186/1752-0509-1-29},
doi = {10.1186/1752-0509-1-29},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/BourquiCLAMSJ07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/TannierBS07,
author = {Eric Tannier and
Anne Bergeron and
Marie{-}France Sagot},
title = {Advances on sorting by reversals},
journal = {Discret. Appl. Math.},
volume = {155},
number = {6-7},
pages = {881--888},
year = {2007},
url = {https://doi.org/10.1016/j.dam.2005.02.033},
doi = {10.1016/J.DAM.2005.02.033},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/TannierBS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/isci/CambouropoulosCIMS07,
author = {Emilios Cambouropoulos and
Maxime Crochemore and
Costas S. Iliopoulos and
Manal Mohamed and
Marie{-}France Sagot},
title = {All maximal-pairs in step-leap representation of melodic sequence},
journal = {Inf. Sci.},
volume = {177},
number = {9},
pages = {1954--1962},
year = {2007},
url = {https://doi.org/10.1016/j.ins.2006.11.012},
doi = {10.1016/J.INS.2006.11.012},
timestamp = {Tue, 29 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/isci/CambouropoulosCIMS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/DiekmannST07,
author = {Yoan Diekmann and
Marie{-}France Sagot and
Eric Tannier},
title = {Evolution under Reversals: Parsimony and Conservation of Common Intervals},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {4},
number = {2},
pages = {301--309},
year = {2007},
url = {https://doi.org/10.1109/TCBB.2007.1042},
doi = {10.1109/TCBB.2007.1042},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/DiekmannST07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/RodriguesSW07,
author = {Estela Maris Rodrigues and
Marie{-}France Sagot and
Yoshiko Wakabayashi},
title = {The maximum agreement forest problem: Approximation algorithms and
computational experiments},
journal = {Theor. Comput. Sci.},
volume = {374},
number = {1-3},
pages = {91--110},
year = {2007},
url = {https://doi.org/10.1016/j.tcs.2006.12.011},
doi = {10.1016/J.TCS.2006.12.011},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/RodriguesSW07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ausai/CarvalhoOS07,
author = {Alexandra M. Carvalho and
Arlindo L. Oliveira and
Marie{-}France Sagot},
editor = {Mehmet A. Orgun and
John Thornton},
title = {Efficient Learning of Bayesian Network Classifiers},
booktitle = {{AI} 2007: Advances in Artificial Intelligence, 20th Australian Joint
Conference on Artificial Intelligence, Gold Coast, Australia, December
2-6, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4830},
pages = {16--25},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-76928-6\_4},
doi = {10.1007/978-3-540-76928-6\_4},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ausai/CarvalhoOS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/BragaSST07,
author = {Mar{\'{\i}}lia D. V. Braga and
Marie{-}France Sagot and
C{\'{e}}line Scornavacca and
Eric Tannier},
editor = {Ion I. Mandoiu and
Alexander Zelikovsky},
title = {The Solution Space of Sorting by Reversals},
booktitle = {Bioinformatics Research and Applications, Third International Symposium,
{ISBRA} 2007, Atlanta, GA, USA, May 7-10, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4463},
pages = {293--304},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-72031-7\_27},
doi = {10.1007/978-3-540-72031-7\_27},
timestamp = {Tue, 14 May 2019 10:00:51 +0200},
biburl = {https://dblp.org/rec/conf/isbra/BragaSST07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/wob/2007,
editor = {Marie{-}France Sagot and
Maria Em{\'{\i}}lia Telles Walter},
title = {Advances in Bioinformatics and Computational Biology, Second Brazilian
Symposium on Bioinformatics, {BSB} 2007, Angra dos Reis, Brazil, August
29-31, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4643},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-73731-5},
doi = {10.1007/978-3-540-73731-5},
isbn = {978-3-540-73730-8},
timestamp = {Tue, 02 Mar 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wob/2007.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/CarvalhoFOS06,
author = {Alexandra M. Carvalho and
Ana T. Freitas and
Arlindo L. Oliveira and
Marie{-}France Sagot},
title = {An Efficient Algorithm for the Identification of Structured Motifs
in {DNA} Promoter Sequences},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {3},
number = {2},
pages = {126--140},
year = {2006},
url = {https://doi.org/10.1109/TCBB.2006.16},
doi = {10.1109/TCBB.2006.16},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/CarvalhoFOS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/LacroixFS06,
author = {Vincent Lacroix and
Cristina G. Fernandes and
Marie{-}France Sagot},
title = {Motif Search in Graphs: Application to Metabolic Networks},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {3},
number = {4},
pages = {360--368},
year = {2006},
url = {https://doi.org/10.1109/TCBB.2006.55},
doi = {10.1109/TCBB.2006.55},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/LacroixFS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/CrochemoreIMS06,
author = {Maxime Crochemore and
Costas S. Iliopoulos and
Manal Mohamed and
Marie{-}France Sagot},
title = {Longest repeats with a block of \emph{k} don't cares},
journal = {Theor. Comput. Sci.},
volume = {362},
number = {1-3},
pages = {248--254},
year = {2006},
url = {https://doi.org/10.1016/j.tcs.2006.06.029},
doi = {10.1016/J.TCS.2006.06.029},
timestamp = {Tue, 29 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/CrochemoreIMS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/latin/PisantiCMS06,
author = {Nadia Pisanti and
Alexandra M. Carvalho and
Laurent Marsan and
Marie{-}France Sagot},
editor = {Jos{\'{e}} R. Correa and
Alejandro Hevia and
Marcos A. Kiwi},
title = {{RISOTTO:} Fast Extraction of Motifs with Mismatches},
booktitle = {{LATIN} 2006: Theoretical Informatics, 7th Latin American Symposium,
Valdivia, Chile, March 20-24, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3887},
pages = {757--768},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11682462\_69},
doi = {10.1007/11682462\_69},
timestamp = {Tue, 14 May 2019 10:00:53 +0200},
biburl = {https://dblp.org/rec/conf/latin/PisantiCMS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stringology/PeterlongoAS06,
author = {Pierre Peterlongo and
Julien Allali and
Marie{-}France Sagot},
editor = {Jan Holub and
Jan Zd{\'{a}}rek},
title = {The gapped-factor tree},
booktitle = {Proceedings of the Prague Stringology Conference, Prague, Czech Republic,
August 28-30, 2006},
pages = {182--196},
publisher = {Department of Computer Science and Engineering, Faculty of Electrical
Engineering, Czech Technical University},
year = {2006},
url = {http://www.stringology.org/event/2006/p18.html},
timestamp = {Wed, 10 Feb 2021 08:42:24 +0100},
biburl = {https://dblp.org/rec/conf/stringology/PeterlongoAS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijfcs/IliopoulosMPPRS05,
author = {Costas S. Iliopoulos and
James A. M. McHugh and
Pierre Peterlongo and
Nadia Pisanti and
Wojciech Rytter and
Marie{-}France Sagot},
title = {A first approach to finding common motifs with gaps},
journal = {Int. J. Found. Comput. Sci.},
volume = {16},
number = {6},
pages = {1145--1154},
year = {2005},
url = {https://doi.org/10.1142/S0129054105003716},
doi = {10.1142/S0129054105003716},
timestamp = {Tue, 06 Jun 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijfcs/IliopoulosMPPRS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/AllaliS05,
author = {Julien Allali and
Marie{-}France Sagot},
title = {A New Distance for High Level {RNA} Secondary Structure Comparison},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {2},
number = {1},
pages = {3--14},
year = {2005},
url = {https://doi.org/10.1109/TCBB.2005.2},
doi = {10.1109/TCBB.2005.2},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/AllaliS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/PisantiCGS05,
author = {Nadia Pisanti and
Maxime Crochemore and
Roberto Grossi and
Marie{-}France Sagot},
title = {Bases of Motifs for Generating Repeated Patterns with Wild Cards},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {2},
number = {1},
pages = {40--50},
year = {2005},
url = {https://doi.org/10.1109/TCBB.2005.5},
doi = {10.1109/TCBB.2005.5},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/PisantiCGS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apbc/CarvalhoFOS05,
author = {Alexandra M. Carvalho and
Ana T. Freitas and
Arlindo L. Oliveira and
Marie{-}France Sagot},
editor = {Yi{-}Ping Phoebe Chen and
Limsoon Wong},
title = {A highly scalable algorithm for the extraction of CIS-regulatory regions},
booktitle = {Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January
2005, Singapore},
pages = {273--282},
publisher = {Imperial College Press, London},
year = {2005},
url = {http://www.comp.nus.edu.sg/\%7Ewongls/psZ/apbc2005/camera-ready/188.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/apbc/CarvalhoFOS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cocoon/SagotT05,
author = {Marie{-}France Sagot and
Eric Tannier},
editor = {Lusheng Wang},
title = {Perfect Sorting by Reversals},
booktitle = {Computing and Combinatorics, 11th Annual International Conference,
{COCOON} 2005, Kunming, China, August 16-29, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3595},
pages = {42--51},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11533719\_7},
doi = {10.1007/11533719\_7},
timestamp = {Tue, 14 May 2019 10:00:35 +0200},
biburl = {https://dblp.org/rec/conf/cocoon/SagotT05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismir/CambouropoulosCIMS05,
author = {Emilios Cambouropoulos and
Maxime Crochemore and
Costas S. Iliopoulos and
Manal Mohamed and
Marie{-}France Sagot},
title = {A Pattern Extraction Algorithm for Abstract Melodic Representations
that Allow Partial Overlapping of Intervallic Categories},
booktitle = {{ISMIR} 2005, 6th International Conference on Music Information Retrieval,
London, UK, 11-15 September 2005, Proceedings},
pages = {167--174},
year = {2005},
url = {http://ismir2005.ismir.net/proceedings/1022.pdf},
timestamp = {Tue, 29 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismir/CambouropoulosCIMS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/spire/PeterlongoPBS05,
author = {Pierre Peterlongo and
Nadia Pisanti and
Fr{\'{e}}d{\'{e}}ric Boyer and
Marie{-}France Sagot},
editor = {Mariano P. Consens and
Gonzalo Navarro},
title = {Lossless Filter for Finding Long Multiple Approximate Repetitions
Using a New Data Structure, the Bi-factor Array},
booktitle = {String Processing and Information Retrieval, 12th International Conference,
{SPIRE} 2005, Buenos Aires, Argentina, November 2-4, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3772},
pages = {179--190},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11575832\_20},
doi = {10.1007/11575832\_20},
timestamp = {Wed, 28 Feb 2024 00:16:41 +0100},
biburl = {https://dblp.org/rec/conf/spire/PeterlongoPBS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/spire/AllaliS05,
author = {Julien Allali and
Marie{-}France Sagot},
editor = {Mariano P. Consens and
Gonzalo Navarro},
title = {A Multiple Graph Layers Model with Application to {RNA} Secondary
Structures Comparison},
booktitle = {String Processing and Information Retrieval, 12th International Conference,
{SPIRE} 2005, Buenos Aires, Argentina, November 2-4, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3772},
pages = {348--359},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11575832\_39},
doi = {10.1007/11575832\_39},
timestamp = {Wed, 24 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/spire/AllaliS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/LacroixFS05,
author = {Vincent Lacroix and
Cristina G. Fernandes and
Marie{-}France Sagot},
editor = {Rita Casadio and
Gene Myers},
title = {Reaction Motifs in Metabolic Networks},
booktitle = {Algorithms in Bioinformatics, 5th International Workshop, {WABI} 2005,
Mallorca, Spain, October 3-6, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3692},
pages = {178--191},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11557067\_15},
doi = {10.1007/11557067\_15},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wabi/LacroixFS05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/TannierS04,
author = {Eric Tannier and
Marie{-}France Sagot},
editor = {S{\"{u}}leyman Cenk Sahinalp and
S. Muthukrishnan and
Ugur Dogrus{\"{o}}z},
title = {Sorting by Reversals in Subquadratic Time},
booktitle = {Combinatorial Pattern Matching, 15th Annual Symposium, {CPM} 2004,
Istanbul,Turkey, July 5-7, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3109},
pages = {1--13},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-27801-6\_1},
doi = {10.1007/978-3-540-27801-6\_1},
timestamp = {Fri, 07 May 2021 12:57:04 +0200},
biburl = {https://dblp.org/rec/conf/cpm/TannierS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/latin/CrochemoreIMS04,
author = {Maxime Crochemore and
Costas S. Iliopoulos and
Manal Mohamed and
Marie{-}France Sagot},
editor = {Martin Farach{-}Colton},
title = {Longest Repeats with a Block of Don't Cares},
booktitle = {{LATIN} 2004: Theoretical Informatics, 6th Latin American Symposium,
Buenos Aires, Argentina, April 5-8, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2976},
pages = {271--278},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-24698-5\_31},
doi = {10.1007/978-3-540-24698-5\_31},
timestamp = {Tue, 29 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/latin/CrochemoreIMS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sac/CarvalhoOFS04,
author = {Alexandra M. Carvalho and
Arlindo L. Oliveira and
Ana T. Freitas and
Marie{-}France Sagot},
editor = {Hisham Haddad and
Andrea Omicini and
Roger L. Wainwright and
Lorie M. Liebrock},
title = {A parallel algorithm for the extraction of structured motifs},
booktitle = {Proceedings of the 2004 {ACM} Symposium on Applied Computing (SAC),
Nicosia, Cyprus, March 14-17, 2004},
pages = {147--153},
publisher = {{ACM}},
year = {2004},
url = {https://doi.org/10.1145/967900.967932},
doi = {10.1145/967900.967932},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/sac/CarvalhoOFS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/spire/CarvalhoFOS04,
author = {Alexandra M. Carvalho and
Ana T. Freitas and
Arlindo L. Oliveira and
Marie{-}France Sagot},
editor = {Alberto Apostolico and
Massimo Melucci},
title = {Efficient Extraction of Structured Motifs Using Box-Links},
booktitle = {String Processing and Information Retrieval, 11th International Conference,
{SPIRE} 2004, Padova, Italy, October 5-8, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3246},
pages = {267--268},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-30213-1\_37},
doi = {10.1007/978-3-540-30213-1\_37},
timestamp = {Tue, 14 May 2019 10:00:55 +0200},
biburl = {https://dblp.org/rec/conf/spire/CarvalhoFOS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/spire/CrochemoreGS04,
author = {Maxime Crochemore and
Raffaele Giancarlo and
Marie{-}France Sagot},
editor = {Alberto Apostolico and
Massimo Melucci},
title = {Longest Motifs with a Functionally Equivalent Central Block},
booktitle = {String Processing and Information Retrieval, 11th International Conference,
{SPIRE} 2004, Padova, Italy, October 5-8, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3246},
pages = {298--209},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-30213-1\_42},
doi = {10.1007/978-3-540-30213-1\_42},
timestamp = {Wed, 24 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/spire/CrochemoreGS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stringology/IliopoulosMPPRS04,
author = {Costas S. Iliopoulos and
James A. M. McHugh and
Pierre Peterlongo and
Nadia Pisanti and
Wojciech Rytter and
Marie{-}France Sagot},
editor = {Milan Sim{\'{a}}nek and
Jan Holub},
title = {A First Approach to Finding Common Motifs With Gaps},
booktitle = {Proceedings of the Prague Stringology Conference 2004, Prague, Czech
Republic, August 30 - September 1, 2004},
pages = {88--97},
publisher = {Department of Computer Science and Engineering, Faculty of Electrical
Engineering, Czech Technical University},
year = {2004},
url = {http://www.stringology.org/event/2004/p8.html},
timestamp = {Wed, 10 Feb 2021 08:42:22 +0100},
biburl = {https://dblp.org/rec/conf/stringology/IliopoulosMPPRS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/AllaliS04,
author = {Julien Allali and
Marie{-}France Sagot},
editor = {Inge Jonassen and
Junhyong Kim},
title = {Novel Tree Edit Operations for {RNA} Secondary Structure Comparison},
booktitle = {Algorithms in Bioinformatics, 4th International Workshop, {WABI} 2004,
Bergen, Norway, September 17-21, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3240},
pages = {412--425},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-30219-3\_35},
doi = {10.1007/978-3-540-30219-3\_35},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/AllaliS04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/BlayoRS03,
author = {Philippe Blayo and
Pierre Rouz{\'{e}} and
Marie{-}France Sagot},
title = {Orphan gene finding - an exon assembly approach},
journal = {Theor. Comput. Sci.},
volume = {290},
number = {3},
pages = {1407--1431},
year = {2003},
url = {https://doi.org/10.1016/S0304-3975(02)00043-9},
doi = {10.1016/S0304-3975(02)00043-9},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/BlayoRS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/mfcs/PisantiCGS03,
author = {Nadia Pisanti and
Maxime Crochemore and
Roberto Grossi and
Marie{-}France Sagot},
editor = {Branislav Rovan and
Peter Vojt{\'{a}}s},
title = {A Basis of Tiling Motifs for Generating Repeated Patterns and Its
Complexity for Higher Quorum},
booktitle = {Mathematical Foundations of Computer Science 2003, 28th International
Symposium, {MFCS} 2003, Bratislava, Slovakia, August 25-29, 2003,
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2747},
pages = {622--631},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/978-3-540-45138-9\_56},
doi = {10.1007/978-3-540-45138-9\_56},
timestamp = {Tue, 14 May 2019 10:00:37 +0200},
biburl = {https://dblp.org/rec/conf/mfcs/PisantiCGS03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithmica/PisantiS02,
author = {Nadia Pisanti and
Marie{-}France Sagot},
title = {Further Thoughts on the Syntenic Distance between Genomes},
journal = {Algorithmica},
volume = {34},
number = {2},
pages = {157--180},
year = {2002},
url = {https://doi.org/10.1007/s00453-002-0960-y},
doi = {10.1007/S00453-002-0960-Y},
timestamp = {Wed, 17 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/algorithmica/PisantiS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/RobinDRSS02,
author = {St{\'{e}}phane Robin and
Jean{-}Jacques Daudin and
Hugues Richard and
Marie{-}France Sagot and
Sophie Schbath},
title = {Occurrence Probability of Structured Motifs in Random Sequences},
journal = {J. Comput. Biol.},
volume = {9},
number = {6},
pages = {761--773},
year = {2002},
url = {https://doi.org/10.1089/10665270260518254},
doi = {10.1089/10665270260518254},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/RobinDRSS02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/random/RodriguesSW01,
author = {Estela Maris Rodrigues and
Marie{-}France Sagot and
Yoshiko Wakabayashi},
editor = {Michel X. Goemans and
Klaus Jansen and
Jos{\'{e}} D. P. Rolim and
Luca Trevisan},
title = {Some Approximation Results for the Maximum Agreement Forest Problem},
booktitle = {Approximation, Randomization and Combinatorial Optimization: Algorithms
and Techniques, 4th International Workshop on Approximation Algorithms
for Combinatorial Optimization Problems, {APPROX} 2001 and 5th International
Workshop on Randomization and Approximation Techniques in Computer
Science, {RANDOM} 2001 Berkeley, CA, USA, August 18-20, 2001, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2129},
pages = {159--169},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-44666-4\_19},
doi = {10.1007/3-540-44666-4\_19},
timestamp = {Tue, 14 May 2019 10:00:48 +0200},
biburl = {https://dblp.org/rec/conf/random/RodriguesSW01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/jobim/2000,
editor = {Olivier Gascuel and
Marie{-}France Sagot},
title = {Computational Biology, First International Conference on Biology,
Informatics, and Mathematics, {JOBIM} 2000, Montpellier, France, May
3-5, 2000, Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {2066},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-45727-5},
doi = {10.1007/3-540-45727-5},
isbn = {3-540-42242-0},
timestamp = {Tue, 14 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/jobim/2000.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/MarsanS00,
author = {Laurent Marsan and
Marie{-}France Sagot},
title = {Algorithms for Extracting Structured Motifs Using a Suffix Tree with
an Application to Promoter and Regulatory Site Consensus Identification},
journal = {J. Comput. Biol.},
volume = {7},
number = {3-4},
pages = {345--362},
year = {2000},
url = {https://doi.org/10.1089/106652700750050826},
doi = {10.1089/106652700750050826},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/MarsanS00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/MarsanS00,
author = {Laurent Marsan and
Marie{-}France Sagot},
editor = {Ron Shamir and
Satoru Miyano and
Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {Extracting structured motifs using a suffix tree - algorithms and
application to promoter consensus identification},
booktitle = {Proceedings of the Fourth Annual International Conference on Computational
Molecular Biology, {RECOMB} 2000, Tokyo, Japan, April 8-11, 2000},
pages = {210--219},
publisher = {{ACM}},
year = {2000},
url = {https://doi.org/10.1145/332306.332553},
doi = {10.1145/332306.332553},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/MarsanS00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/SagotM98,
author = {Marie{-}France Sagot and
Eugene W. Myers},
title = {Identifying Satellites and Periodic Repetitions in Biological Sequences},
journal = {J. Comput. Biol.},
volume = {5},
number = {3},
pages = {539--553},
year = {1998},
url = {https://doi.org/10.1089/cmb.1998.5.539},
doi = {10.1089/CMB.1998.5.539},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/SagotM98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/latin/Sagot98,
author = {Marie{-}France Sagot},
editor = {Claudio L. Lucchesi and
Arnaldo V. Moura},
title = {Spelling Approximate Repeated or Common Motifs Using a Suffix Tree},
booktitle = {{LATIN} '98: Theoretical Informatics, Third Latin American Symposium,
Campinas, Brazil, April, 20-24, 1998, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1380},
pages = {374--390},
publisher = {Springer},
year = {1998},
url = {https://doi.org/10.1007/BFb0054337},
doi = {10.1007/BFB0054337},
timestamp = {Tue, 14 May 2019 10:00:53 +0200},
biburl = {https://dblp.org/rec/conf/latin/Sagot98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/SagotM98,
author = {Marie{-}France Sagot and
Eugene W. Myers},
editor = {Sorin Istrail and
Pavel A. Pevzner and
Michael S. Waterman},
title = {Identifying satellites in nucleic acid sequences},
booktitle = {Proceedings of the Second Annual International Conference on Research
in Computational Molecular Biology, {RECOMB} 1998, New York, NY, USA,
March 22-25, 1998},
pages = {234--242},
publisher = {{ACM}},
year = {1998},
url = {https://doi.org/10.1145/279069.279120},
doi = {10.1145/279069.279120},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/SagotM98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/SagotVS97,
author = {Marie{-}France Sagot and
Alain Viari and
Henry Soldano},
title = {Multiple Sequence Comparison - {A} Peptide Matching Approach},
journal = {Theor. Comput. Sci.},
volume = {180},
number = {1-2},
pages = {115--137},
year = {1997},
url = {https://doi.org/10.1016/S0304-3975(96)00137-5},
doi = {10.1016/S0304-3975(96)00137-5},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/SagotVS97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/SagotV97,
author = {Marie{-}France Sagot and
Alain Viari},
editor = {Alberto Apostolico and
Jotun Hein},
title = {Flexible Identification of Structural Objects in Nucleic Acid Sequences:
Palindromes, Mirror Repeats, Pseudoknots and Triple Helices},
booktitle = {Combinatorial Pattern Matching, 8th Annual Symposium, {CPM} 97, Aarhus,
Denmark, June 30 - July 2, 1997, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1264},
pages = {224--246},
publisher = {Springer},
year = {1997},
url = {https://doi.org/10.1007/3-540-63220-4\_62},
doi = {10.1007/3-540-63220-4\_62},
timestamp = {Tue, 14 May 2019 10:00:38 +0200},
biburl = {https://dblp.org/rec/conf/cpm/SagotV97.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/SagotV96,
author = {Marie{-}France Sagot and
Alain Viari},
editor = {Daniel S. Hirschberg and
Eugene W. Myers},
title = {A Double Combinatorial Approach to Discovering Patterns in Biological
Sequences},
booktitle = {Combinatorial Pattern Matching, 7th Annual Symposium, {CPM} 96, Laguna
Beach, California, USA, June 10-12, 1996, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1075},
pages = {186--208},
publisher = {Springer},
year = {1996},
url = {https://doi.org/10.1007/3-540-61258-0\_15},
doi = {10.1007/3-540-61258-0\_15},
timestamp = {Tue, 14 May 2019 10:00:38 +0200},
biburl = {https://dblp.org/rec/conf/cpm/SagotV96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SagotVPS95,
author = {Marie{-}France Sagot and
Alain Viari and
Jo{\"{e}}l Pothier and
Henry Soldano},
title = {Finding flexible patterns in a text: an application to three-dimensional
molecular matching},
journal = {Comput. Appl. Biosci.},
volume = {11},
number = {1},
pages = {59--70},
year = {1995},
url = {https://doi.org/10.1093/bioinformatics/11.1.59},
doi = {10.1093/BIOINFORMATICS/11.1.59},
timestamp = {Fri, 15 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SagotVPS95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/SagotVS95,
author = {Marie{-}France Sagot and
Alain Viari and
Henry Soldano},
editor = {Zvi Galil and
Esko Ukkonen},
title = {Multiple Sequence Comparison: {A} Peptide Matching Approach},
booktitle = {Combinatorial Pattern Matching, 6th Annual Symposium, {CPM} 95, Espoo,
Finland, July 5-7, 1995, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {937},
pages = {366--385},
publisher = {Springer},
year = {1995},
url = {https://doi.org/10.1007/3-540-60044-2\_55},
doi = {10.1007/3-540-60044-2\_55},
timestamp = {Thu, 29 Aug 2019 15:20:22 +0200},
biburl = {https://dblp.org/rec/conf/cpm/SagotVS95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/SagotVS95,
author = {Marie{-}France Sagot and
Alain Viari and
Henry Soldano},
editor = {Christopher J. Rawlings and
Dominic A. Clark and
Russ B. Altman and
Lawrence Hunter and
Thomas Lengauer and
Shoshana J. Wodak},
title = {A Distance-Based Block Searching Algorithm},
booktitle = {Proceedings of the Third International Conference on Intelligent Systems
for Molecular Biology, Cambridge, United Kingdom, July 16-19, 1995},
pages = {322--331},
publisher = {{AAAI}},
year = {1995},
url = {http://www.aaai.org/Library/ISMB/1995/ismb95-039.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/SagotVS95.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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