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ORCIDBibTeX records: Aïda Ouangraoua
@inproceedings{DBLP:conf/recombcg/OuedraogoO24,
author = {Wend Yam Donald Davy Ouedraogo and
A{\"{\i}}da Ouangraoua},
editor = {C{\'{e}}line Scornavacca and
Maribel Hern{\'{a}}ndez{-}Rosales},
title = {Inferring Transcript Phylogenies from Transcript Ortholog Clusters},
booktitle = {Comparative Genomics - 21st International Conference, {RECOMB-CG}
2024, Boston, MA, USA, April 27-28, 2024, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {14616},
pages = {47--68},
publisher = {Springer},
year = {2024},
url = {https://doi.org/10.1007/978-3-031-58072-7\_3},
doi = {10.1007/978-3-031-58072-7\_3},
timestamp = {Wed, 24 Apr 2024 16:58:28 +0200},
biburl = {https://dblp.org/rec/conf/recombcg/OuedraogoO24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2402-03455,
author = {Bertrand Marchand and
Yoann Anselmetti and
Manuel Lafond and
A{\"{\i}}da Ouangraoua},
title = {Median and Small Parsimony Problems on {RNA} trees},
journal = {CoRR},
volume = {abs/2402.03455},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2402.03455},
doi = {10.48550/ARXIV.2402.03455},
eprinttype = {arXiv},
eprint = {2402.03455},
timestamp = {Mon, 12 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2402-03455.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/VannutelliSPO23,
author = {Ana{\"{\i}}s Vannutelli and
Lauriane lucienne noele Schell and
Jean{-}Pierre Perreault and
A{\"{\i}}da Ouangraoua},
title = {{GAIA:} G-quadruplexes in alive creature database},
journal = {Nucleic Acids Res.},
volume = {51},
number = {{D1}},
pages = {135--140},
year = {2023},
url = {https://doi.org/10.1093/nar/gkac657},
doi = {10.1093/NAR/GKAC657},
timestamp = {Wed, 16 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/VannutelliSPO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recombcg/OuedraogoO23,
author = {Wend Yam Donald Davy Ouedraogo and
A{\"{\i}}da Ouangraoua},
editor = {Katharina Jahn and
Tom{\'{a}}s Vinar},
title = {Inferring Clusters of Orthologous and Paralogous Transcripts},
booktitle = {Comparative Genomics - 20th International Conference, {RECOMB-CG}
2023, Istanbul, Turkey, April 14-15, 2023, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13883},
pages = {19--34},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-3-031-36911-7\_2},
doi = {10.1007/978-3-031-36911-7\_2},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recombcg/OuedraogoO23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/wabi/2023,
editor = {Djamal Belazzougui and
A{\"{\i}}da Ouangraoua},
title = {23rd International Workshop on Algorithms in Bioinformatics, {WABI}
2023, September 4-6, 2023, Houston, TX, {USA}},
series = {LIPIcs},
volume = {273},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2023},
url = {https://www.dagstuhl.de/dagpub/978-3-95977-294-5},
isbn = {978-3-95977-294-5},
timestamp = {Tue, 29 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/2023.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KuitcheQTPO21,
author = {Esaie Kuitche and
Yanchun Qi and
Nadia Tahiri and
Jack Parmer and
A{\"{\i}}da Ouangraoua},
title = {DoubleRecViz: a web-based tool for visualizing transcript-gene-species
tree reconciliation},
journal = {Bioinform.},
volume = {37},
number = {13},
pages = {1920--1922},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btaa882},
doi = {10.1093/BIOINFORMATICS/BTAA882},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KuitcheQTPO21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/AnselmettiELO21,
author = {Yoann Anselmetti and
Nadia El{-}Mabrouk and
Manuel Lafond and
A{\"{\i}}da Ouangraoua},
title = {Gene tree and species tree reconciliation with endosymbiotic gene
transfer},
journal = {Bioinform.},
volume = {37},
number = {Supplement},
pages = {120--132},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab328},
doi = {10.1093/BIOINFORMATICS/BTAB328},
timestamp = {Tue, 21 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/AnselmettiELO21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BrunetLLLJAGGAF21,
author = {Marie A. Brunet and
Jean{-}Fran{\c{c}}ois Lucier and
Maxime Levesque and
S{\'{e}}bastien Leblanc and
Jean{-}Francois Jacques and
Hassan R. H. Al{-}Saedi and
No{\'{e}} Guilloy and
Fr{\'{e}}d{\'{e}}ric Grenier and
Mariano Avino and
Isabelle Fournier and
Michel Salzet and
A{\"{\i}}da Ouangraoua and
Michelle S. Scott and
Fran{\c{c}}ois{-}Michel Boisvert and
Xavier Roucou},
title = {OpenProt 2021: deeper functional annotation of the coding potential
of eukaryotic genomes},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D380--D388},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa1036},
doi = {10.1093/NAR/GKAA1036},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BrunetLLLJAGGAF21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JammaliAKO19,
author = {Safa Jammali and
Jean{-}David Aguilar and
Esaie Kuitche and
A{\"{\i}}da Ouangraoua},
title = {SplicedFamAlign: CDS-to-gene spliced alignment and identification
of transcript orthology groups},
journal = {{BMC} Bioinform.},
volume = {20-S},
number = {3},
pages = {37--52},
year = {2019},
url = {https://doi.org/10.1186/s12859-019-2647-2},
doi = {10.1186/S12859-019-2647-2},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/JammaliAKO19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KuitcheJO19,
author = {Esaie Kuitche and
Safa Jammali and
A{\"{\i}}da Ouangraoua},
title = {SimSpliceEvol: alternative splicing-aware simulation of biological
sequence evolution},
journal = {{BMC} Bioinform.},
volume = {20-S},
number = {20},
pages = {640},
year = {2019},
url = {https://doi.org/10.1186/s12859-019-3207-5},
doi = {10.1186/S12859-019-3207-5},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KuitcheJO19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BrunetBLDLGSLAD19,
author = {Marie A. Brunet and
Myl{\`{e}}ne Brunelle and
Jean{-}Fran{\c{c}}ois Lucier and
Vivian Delcourt and
Maxime Levesque and
Fr{\'{e}}d{\'{e}}ric Grenier and
Sondos Samandi and
S{\'{e}}bastien Leblanc and
Jean{-}David Aguilar and
Pascal Dufour and
Jean{-}Francois Jacques and
Isabelle Fournier and
A{\"{\i}}da Ouangraoua and
Michelle S. Scott and
Fran{\c{c}}ois{-}Michel Boisvert and
Xavier Roucou},
title = {OpenProt: a more comprehensive guide to explore eukaryotic coding
potential and proteomes},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Database-Issue},
pages = {D403--D410},
year = {2019},
url = {https://doi.org/10.1093/nar/gky936},
doi = {10.1093/NAR/GKY936},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/BrunetBLDLGSLAD19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/LuhmannLTOWC19,
author = {Nina Luhmann and
Manuel Lafond and
Annelyse Th{\'{e}}venin and
A{\"{\i}}da Ouangraoua and
Roland Wittler and
C{\'{e}}dric Chauve},
title = {The {SCJ} Small Parsimony Problem for Weighted Gene Adjacencies},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {16},
number = {4},
pages = {1364--1373},
year = {2019},
url = {https://doi.org/10.1109/TCBB.2017.2661761},
doi = {10.1109/TCBB.2017.2661761},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/LuhmannLTOWC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GlouzonO18,
author = {Jean{-}Pierre S{\'{e}}hi Glouzon and
A{\"{\i}}da Ouangraoua},
title = {aliFreeFold: an alignment-free approach to predict secondary structure
from homologous {RNA} sequences},
journal = {Bioinform.},
volume = {34},
number = {13},
pages = {i70--i78},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty234},
doi = {10.1093/BIOINFORMATICS/BTY234},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GlouzonO18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/LafondCEO18,
author = {Manuel Lafond and
C{\'{e}}dric Chauve and
Nadia El{-}Mabrouk and
A{\"{\i}}da Ouangraoua},
title = {Gene Tree Construction and Correction Using SuperTree and Reconciliation},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {15},
number = {5},
pages = {1560--1570},
year = {2018},
url = {https://doi.org/10.1109/TCBB.2017.2720581},
doi = {10.1109/TCBB.2017.2720581},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/LafondCEO18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/recomb/2018cg,
editor = {Mathieu Blanchette and
A{\"{\i}}da Ouangraoua},
title = {Comparative Genomics - 16th International Conference, {RECOMB-CG}
2018, Magog-Orford, QC, Canada, October 9-12, 2018, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {11183},
publisher = {Springer},
year = {2018},
url = {https://doi.org/10.1007/978-3-030-00834-5},
doi = {10.1007/978-3-030-00834-5},
isbn = {978-3-030-00833-8},
timestamp = {Mon, 13 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/2018cg.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/JammaliKRBSO17,
author = {Safa Jammali and
Esaie Kuitche and
Ayoub Rachati and
Fran{\c{c}}ois B{\'{e}}langer and
Michelle S. Scott and
A{\"{\i}}da Ouangraoua},
title = {Aligning coding sequences with frameshift extension penalties},
journal = {Algorithms Mol. Biol.},
volume = {12},
number = {1},
pages = {10:1--10:18},
year = {2017},
url = {https://doi.org/10.1186/s13015-017-0101-4},
doi = {10.1186/S13015-017-0101-4},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/JammaliKRBSO17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/KuitcheLO17,
author = {Esaie Kuitche and
Manuel Lafond and
A{\"{\i}}da Ouangraoua},
title = {Reconstructing protein and gene phylogenies using reconciliation and
soft-clustering},
journal = {J. Bioinform. Comput. Biol.},
volume = {15},
number = {6},
pages = {1740007:1--1740007:25},
year = {2017},
url = {https://doi.org/10.1142/S0219720017400078},
doi = {10.1142/S0219720017400078},
timestamp = {Wed, 24 Mar 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbcb/KuitcheLO17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/El-MabroukO17,
author = {Nadia El{-}Mabrouk and
A{\"{\i}}da Ouangraoua},
editor = {Russell Schwartz and
Knut Reinert},
title = {A General Framework for Gene Tree Correction Based on Duplication-Loss
Reconciliation},
booktitle = {17th International Workshop on Algorithms in Bioinformatics, {WABI}
2017, August 21-23, 2017, Boston, MA, {USA}},
series = {LIPIcs},
volume = {88},
pages = {8:1--8:14},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2017},
url = {https://doi.org/10.4230/LIPIcs.WABI.2017.8},
doi = {10.4230/LIPICS.WABI.2017.8},
timestamp = {Tue, 11 Feb 2020 15:52:14 +0100},
biburl = {https://dblp.org/rec/conf/wabi/El-MabroukO17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1709-06169,
author = {Jean{-}David Aguilar and
Safa Jammali and
Esaie Kuitche and
A{\"{\i}}da Ouangraoua},
title = {Improving spliced alignment for identification of ortholog groups
and multiple {CDS} alignment},
journal = {CoRR},
volume = {abs/1709.06169},
year = {2017},
url = {http://arxiv.org/abs/1709.06169},
eprinttype = {arXiv},
eprint = {1709.06169},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1709-06169.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/LuhmannTOWC16,
author = {Nina Luhmann and
Annelyse Th{\'{e}}venin and
A{\"{\i}}da Ouangraoua and
Roland Wittler and
C{\'{e}}dric Chauve},
editor = {Anu G. Bourgeois and
Pavel Skums and
Xiang Wan and
Alex Zelikovsky},
title = {The {SCJ} Small Parsimony Problem for Weighted Gene Adjacencies},
booktitle = {Bioinformatics Research and Applications - 12th International Symposium,
{ISBRA} 2016, Minsk, Belarus, June 5-8, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9683},
pages = {200--210},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-38782-6\_17},
doi = {10.1007/978-3-319-38782-6\_17},
timestamp = {Tue, 14 May 2019 10:00:51 +0200},
biburl = {https://dblp.org/rec/conf/isbra/LuhmannTOWC16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/LuhmannTOWC16,
author = {Nina Luhmann and
Annelyse Th{\'{e}}venin and
A{\"{\i}}da Ouangraoua and
Roland Wittler and
C{\'{e}}dric Chauve},
title = {The {SCJ} small parsimony problem for weighted gene adjacencies (Extended
version)},
journal = {CoRR},
volume = {abs/1603.08819},
year = {2016},
url = {http://arxiv.org/abs/1603.08819},
eprinttype = {arXiv},
eprint = {1603.08819},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/LuhmannTOWC16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/LafondCEO16,
author = {Manuel Lafond and
C{\'{e}}dric Chauve and
Nadia El{-}Mabrouk and
A{\"{\i}}da Ouangraoua},
title = {Gene Tree Construction and Correction using SuperTree and Reconciliation},
journal = {CoRR},
volume = {abs/1610.05068},
year = {2016},
url = {http://arxiv.org/abs/1610.05068},
eprinttype = {arXiv},
eprint = {1610.05068},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/LafondCEO16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/JammaliKRBSO16,
author = {Safa Jammali and
Esaie Kuitche and
Ayoub Rachati and
Fran{\c{c}}ois B{\'{e}}langer and
Michelle S. Scott and
A{\"{\i}}da Ouangraoua},
title = {Aligning coding sequences with frameshift extension penalties},
journal = {CoRR},
volume = {abs/1610.08809},
year = {2016},
url = {http://arxiv.org/abs/1610.08809},
eprinttype = {arXiv},
eprint = {1610.08809},
timestamp = {Thu, 21 Feb 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/JammaliKRBSO16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/KuitcheO16,
author = {Esaie Kuitche and
A{\"{\i}}da Ouangraoua},
title = {Reconstructing protein and gene phylogenies by extending the framework
of reconciliation},
journal = {CoRR},
volume = {abs/1610.09732},
year = {2016},
url = {http://arxiv.org/abs/1610.09732},
eprinttype = {arXiv},
eprint = {1610.09732},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/KuitcheO16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LafondOE15,
author = {Manuel Lafond and
A{\"{\i}}da Ouangraoua and
Nadia El{-}Mabrouk},
title = {Reconstructing a SuperGeneTree minimizing reconciliation},
journal = {{BMC} Bioinform.},
volume = {16},
number = {{S14}},
pages = {S4},
year = {2015},
url = {https://doi.org/10.1186/1471-2105-16-s14-s4},
doi = {10.1186/1471-2105-16-S14-S4},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LafondOE15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/peerj-cs/Lavoie-Mongrain15,
author = {Philippe Lavoie{-}Mongrain and
Mahdi Belcaid and
A{\"{\i}}da Ouangraoua and
Anne Bergeron and
Guylaine Poisson},
title = {Reconstructing the history of a {WD40} beta-propeller tandem repeat
using a phylogenetically informed algorithm},
journal = {PeerJ Comput. Sci.},
volume = {1},
pages = {e6},
year = {2015},
url = {https://doi.org/10.7717/peerj-cs.6},
doi = {10.7717/PEERJ-CS.6},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/peerj-cs/Lavoie-Mongrain15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/BelangerO15,
author = {Fran{\c{c}}ois B{\'{e}}langer and
A{\"{\i}}da Ouangraoua},
title = {Alignment of protein-coding sequences with frameshift extension penalties},
journal = {CoRR},
volume = {abs/1508.04783},
year = {2015},
url = {http://arxiv.org/abs/1508.04783},
eprinttype = {arXiv},
eprint = {1508.04783},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/BelangerO15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/OuangraouaR14,
author = {A{\"{\i}}da Ouangraoua and
Mathieu Raffinot},
title = {On the Identification of Conflicting Contiguities in Ancestral Genome
Reconstruction},
journal = {J. Comput. Biol.},
volume = {21},
number = {1},
pages = {64--79},
year = {2014},
url = {https://doi.org/10.1089/cmb.2013.0086},
doi = {10.1089/CMB.2013.0086},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/OuangraouaR14.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}
}
@inproceedings{DBLP:conf/biostec/ThomasOV12,
author = {Antoine Thomas and
A{\"{\i}}da Ouangraoua and
Jean{-}St{\'{e}}phane Varr{\'{e}}},
editor = {Jan Schier and
Carlos Manuel B. A. Correia and
Ana L. N. Fred and
Hugo Gamboa},
title = {Genome Halving by Block Interchange},
booktitle = {{BIOINFORMATICS} 2012 - Proceedings of the International Conference
on Bioinformatics Models, Methods and Algorithms, Vilamoura, Algarve,
Portugal, 1 - 4 February, 2012},
pages = {58--65},
publisher = {SciTePress},
year = {2012},
timestamp = {Tue, 29 May 2012 10:31:06 +0200},
biburl = {https://dblp.org/rec/conf/biostec/ThomasOV12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/biostec/ThomasOV12a,
author = {Antoine Thomas and
A{\"{\i}}da Ouangraoua and
Jean{-}St{\'{e}}phane Varr{\'{e}}},
editor = {Joaquim Gabriel and
Jan Schier and
Sabine Van Huffel and
Emmanuel Conchon and
Carlos Manuel B. A. Correia and
Ana L. N. Fred and
Hugo Gamboa},
title = {Single Tandem Halving by Block Interchange},
booktitle = {Biomedical Engineering Systems and Technologies - 5th International
Joint Conference, {BIOSTEC} 2012, Vilamoura, Portugal, February 1-4,
2012, Revised Selected Papers},
series = {Communications in Computer and Information Science},
volume = {357},
pages = {162--174},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-38256-7\_11},
doi = {10.1007/978-3-642-38256-7\_11},
timestamp = {Sun, 02 Oct 2022 15:55:42 +0200},
biburl = {https://dblp.org/rec/conf/biostec/ThomasOV12a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/OuangraouaR12,
author = {A{\"{\i}}da Ouangraoua and
Mathieu Raffinot},
editor = {Juha K{\"{a}}rkk{\"{a}}inen and
Jens Stoye},
title = {Faster and Simpler Minimal Conflicting Set Identification - (Extended
Abstract)},
booktitle = {Combinatorial Pattern Matching - 23rd Annual Symposium, {CPM} 2012,
Helsinki, Finland, July 3-5, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7354},
pages = {41--55},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-31265-6\_4},
doi = {10.1007/978-3-642-31265-6\_4},
timestamp = {Tue, 21 Mar 2023 21:02:12 +0100},
biburl = {https://dblp.org/rec/conf/cpm/OuangraouaR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/OuangraouaSB12,
author = {A{\"{\i}}da Ouangraoua and
Krister M. Swenson and
Anne Bergeron},
editor = {Leonidas G. Bleris and
Ion I. Mandoiu and
Russell Schwartz and
Jianxin Wang},
title = {On the Comparison of Sets of Alternative Transcripts},
booktitle = {Bioinformatics Research and Applications - 8th International Symposium,
{ISBRA} 2012, Dallas, TX, USA, May 21-23, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7292},
pages = {201--212},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-30191-9\_19},
doi = {10.1007/978-3-642-30191-9\_19},
timestamp = {Tue, 14 May 2019 10:00:51 +0200},
biburl = {https://dblp.org/rec/conf/isbra/OuangraouaSB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/ThomasOV12,
author = {Antoine Thomas and
A{\"{\i}}da Ouangraoua and
Jean{-}St{\'{e}}phane Varr{\'{e}}},
editor = {Benjamin J. Raphael and
Jijun Tang},
title = {Tandem Halving Problems by {DCJ}},
booktitle = {Algorithms in Bioinformatics - 12th International Workshop, {WABI}
2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7534},
pages = {417--429},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-33122-0\_33},
doi = {10.1007/978-3-642-33122-0\_33},
timestamp = {Sat, 19 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/ThomasOV12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1201-5513,
author = {A{\"{\i}}da Ouangraoua and
Mathieu Raffinot},
title = {Faster and Simpler Minimal Conflicting Set Identification},
journal = {CoRR},
volume = {abs/1201.5513},
year = {2012},
url = {http://arxiv.org/abs/1201.5513},
eprinttype = {arXiv},
eprint = {1201.5513},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1201-5513.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OuangraouaTC11,
author = {A{\"{\i}}da Ouangraoua and
Eric Tannier and
C{\'{e}}dric Chauve},
title = {Reconstructing the architecture of the ancestral amniote genome},
journal = {Bioinform.},
volume = {27},
number = {19},
pages = {2664--2671},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr461},
doi = {10.1093/BIOINFORMATICS/BTR461},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/OuangraouaTC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ThomasVO11,
author = {Antoine Thomas and
Jean{-}St{\'{e}}phane Varr{\'{e}} and
A{\"{\i}}da Ouangraoua},
title = {Genome dedoubling by {DCJ} and reversal},
journal = {{BMC} Bioinform.},
volume = {12},
number = {{S-9}},
pages = {S20},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-S9-S20},
doi = {10.1186/1471-2105-12-S9-S20},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ThomasVO11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/OuangraouaSC11,
author = {A{\"{\i}}da Ouangraoua and
Krister M. Swenson and
C{\'{e}}dric Chauve},
title = {A 2-Approximation for the Minimum Duplication Speciation Problem},
journal = {J. Comput. Biol.},
volume = {18},
number = {9},
pages = {1041--1053},
year = {2011},
url = {https://doi.org/10.1089/cmb.2011.0108},
doi = {10.1089/CMB.2011.0108},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/OuangraouaSC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/OuangraouaBS11,
author = {A{\"{\i}}da Ouangraoua and
Anne Bergeron and
Krister M. Swenson},
title = {Theory and Practice of Ultra-Perfection},
journal = {J. Comput. Biol.},
volume = {18},
number = {9},
pages = {1219--1230},
year = {2011},
url = {https://doi.org/10.1089/cmb.2011.0086},
doi = {10.1089/CMB.2011.0086},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/OuangraouaBS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/OuangraouaGHC11,
author = {A{\"{\i}}da Ouangraoua and
Valentin Guignon and
Sylvie Hamel and
C{\'{e}}dric Chauve},
title = {A new algorithm for aligning nested arc-annotated sequences under
arbitrary weight schemes},
journal = {Theor. Comput. Sci.},
volume = {412},
number = {8-10},
pages = {753--764},
year = {2011},
url = {https://doi.org/10.1016/j.tcs.2010.11.020},
doi = {10.1016/J.TCS.2010.11.020},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/OuangraouaGHC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1107-1076,
author = {Antoine Thomas and
A{\"{\i}}da Ouangraoua and
Jean{-}St{\'{e}}phane Varr{\'{e}}},
title = {Genome Halving by Block Interchange},
journal = {CoRR},
volume = {abs/1107.1076},
year = {2011},
url = {http://arxiv.org/abs/1107.1076},
eprinttype = {arXiv},
eprint = {1107.1076},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1107-1076.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ChauveGOT10,
author = {C{\'{e}}dric Chauve and
Haris Gavranovic and
A{\"{\i}}da Ouangraoua and
Eric Tannier},
title = {Yeast Ancestral Genome Reconstructions: The Possibilities of Computational
Methods {II}},
journal = {J. Comput. Biol.},
volume = {17},
number = {9},
pages = {1097--1112},
year = {2010},
url = {https://doi.org/10.1089/cmb.2010.0092},
doi = {10.1089/CMB.2010.0092},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/ChauveGOT10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/OuangraouaB10,
author = {A{\"{\i}}da Ouangraoua and
Anne Bergeron},
title = {Combinatorial Structure of Genome Rearrangements Scenarios},
journal = {J. Comput. Biol.},
volume = {17},
number = {9},
pages = {1129--1144},
year = {2010},
url = {https://doi.org/10.1089/cmb.2010.0126},
doi = {10.1089/CMB.2010.0126},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/OuangraouaB10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/OuangraouaBS10,
author = {A{\"{\i}}da Ouangraoua and
Anne Bergeron and
Krister M. Swenson},
editor = {Eric Tannier},
title = {Ultra-Perfect Sorting Scenarios},
booktitle = {Comparative Genomics - International Workshop, {RECOMB-CG} 2010, Ottawa,
Canada, October 9-11, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6398},
pages = {50--61},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-16181-0\_5},
doi = {10.1007/978-3-642-16181-0\_5},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/OuangraouaBS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/OuangraouaSC10,
author = {A{\"{\i}}da Ouangraoua and
Krister M. Swenson and
C{\'{e}}dric Chauve},
editor = {Eric Tannier},
title = {An Approximation Algorithm for Computing a Parsimonious First Speciation
in the Gene Duplication Model},
booktitle = {Comparative Genomics - International Workshop, {RECOMB-CG} 2010, Ottawa,
Canada, October 9-11, 2010. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6398},
pages = {290--301},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-16181-0\_24},
doi = {10.1007/978-3-642-16181-0\_24},
timestamp = {Mon, 13 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/OuangraouaSC10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jda/OuangraouaF09,
author = {A{\"{\i}}da Ouangraoua and
Pascal Ferraro},
title = {A new constrained edit distance between quotiented ordered trees},
journal = {J. Discrete Algorithms},
volume = {7},
number = {1},
pages = {78--89},
year = {2009},
url = {https://doi.org/10.1016/j.jda.2008.05.001},
doi = {10.1016/J.JDA.2008.05.001},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jda/OuangraouaF09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/OuangraouaF09,
author = {A{\"{\i}}da Ouangraoua and
Pascal Ferraro},
title = {A constrained edit distance algorithm between semi-ordered trees},
journal = {Theor. Comput. Sci.},
volume = {410},
number = {8-10},
pages = {837--846},
year = {2009},
url = {https://doi.org/10.1016/j.tcs.2008.11.022},
doi = {10.1016/J.TCS.2008.11.022},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/OuangraouaF09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/OuangraouaBMTC09,
author = {A{\"{\i}}da Ouangraoua and
Fr{\'{e}}d{\'{e}}ric Boyer and
Andrew W. McPherson and
Eric Tannier and
C{\'{e}}dric Chauve},
editor = {Ion I. Mandoiu and
Giri Narasimhan and
Yanqing Zhang},
title = {Prediction of Contiguous Regions in the Amniote Ancestral Genome},
booktitle = {Bioinformatics Research and Applications, 5th International Symposium,
{ISBRA} 2009, Fort Lauderdale, FL, USA, May 13-16, 2009, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5542},
pages = {173--185},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-01551-9\_18},
doi = {10.1007/978-3-642-01551-9\_18},
timestamp = {Fri, 24 Mar 2023 16:31:04 +0100},
biburl = {https://dblp.org/rec/conf/isbra/OuangraouaBMTC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/OuangraouaB09,
author = {A{\"{\i}}da Ouangraoua and
Anne Bergeron},
editor = {Francesca D. Ciccarelli and
Istv{\'{a}}n Mikl{\'{o}}s},
title = {Parking Functions, Labeled Trees and {DCJ} Sorting Scenarios},
booktitle = {Comparative Genomics, International Workshop, {RECOMB-CG} 2009, Budapest,
Hungary, September 27-29, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5817},
pages = {24--35},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-04744-2\_3},
doi = {10.1007/978-3-642-04744-2\_3},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/OuangraouaB09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-0903-2499,
author = {A{\"{\i}}da Ouangraoua and
Anne Bergeron},
title = {Parking functions, labeled trees and {DCJ} sorting scenarios},
journal = {CoRR},
volume = {abs/0903.2499},
year = {2009},
url = {http://arxiv.org/abs/0903.2499},
eprinttype = {arXiv},
eprint = {0903.2499},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-0903-2499.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-0904-1645,
author = {C{\'{e}}dric Chauve and
A{\"{\i}}da Ouangraoua},
title = {A 3-approximation algorithm for computing a parsimonious first speciation
in the gene duplication model},
journal = {CoRR},
volume = {abs/0904.1645},
year = {2009},
url = {http://arxiv.org/abs/0904.1645},
eprinttype = {arXiv},
eprint = {0904.1645},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-0904-1645.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jda/OuangraouaFTD07,
author = {A{\"{\i}}da Ouangraoua and
Pascal Ferraro and
Laurent Tichit and
Serge Dulucq},
title = {Local similarity between quotiented ordered trees},
journal = {J. Discrete Algorithms},
volume = {5},
number = {1},
pages = {23--35},
year = {2007},
url = {https://doi.org/10.1016/j.jda.2006.03.010},
doi = {10.1016/J.JDA.2006.03.010},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jda/OuangraouaFTD07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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