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ORCIDBibTeX records: Cédric Chauve
@article{DBLP:journals/bioinformatics/ManeFVBC23,
author = {Aniket C. Mane and
Mahsa Faizrahnemoon and
Tom{\'{a}}s Vinar and
Brona Brejov{\'{a}} and
C{\'{e}}dric Chauve},
title = {PlasBin-flow: a flow-based {MILP} algorithm for plasmid contigs binning},
journal = {Bioinform.},
volume = {39},
number = {Supplement-1},
pages = {288--296},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad250},
doi = {10.1093/BIOINFORMATICS/BTAD250},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ManeFVBC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recombcg/ManeFC22,
author = {Aniket C. Mane and
Mahsa Faizrahnemoon and
C{\'{e}}dric Chauve},
editor = {Lingling Jin and
Dannie Durand},
title = {A Mixed Integer Linear Programming Algorithm for Plasmid Binning},
booktitle = {Comparative Genomics - 19th International Conference, {RECOMB-CG}
2022, La Jolla, CA, USA, May 20-21, 2022, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13234},
pages = {279--292},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-06220-9\_16},
doi = {10.1007/978-3-031-06220-9\_16},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/recombcg/ManeFC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbcb/DoerrC21,
author = {Daniel Doerr and
C{\'{e}}dric Chauve},
title = {Small parsimony for natural genomes in the DCJ-indel model},
journal = {J. Bioinform. Comput. Biol.},
volume = {19},
number = {6},
pages = {2140009:1--2140009:15},
year = {2021},
url = {https://doi.org/10.1142/S0219720021400096},
doi = {10.1142/S0219720021400096},
timestamp = {Thu, 05 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbcb/DoerrC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stringology/ChauveMP21,
author = {C{\'{e}}dric Chauve and
Marni Mishna and
France Paquet{-}Nadeau},
editor = {Jan Holub and
Jan Zd{\'{a}}rek},
title = {Refined Upper Bounds on the Size of the Condensed Neighbourhood of
Sequences},
booktitle = {Prague Stringology Conference 2021, Prague, Czech Republic, August
30-31, 2021},
pages = {30--40},
publisher = {Czech Technical University in Prague, Faculty of Information Technology,
Department of Theoretical Computer Science},
year = {2021},
url = {http://www.stringology.org/event/2021/p03.html},
timestamp = {Wed, 31 Jan 2024 17:00:02 +0100},
biburl = {https://dblp.org/rec/conf/stringology/ChauveMP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2108-04297,
author = {Daniel Doerr and
C{\'{e}}dric Chauve},
title = {Small Parsimony for Natural Genomes in the DCJ-Indel Model},
journal = {CoRR},
volume = {abs/2108.04297},
year = {2021},
url = {https://arxiv.org/abs/2108.04297},
eprinttype = {arXiv},
eprint = {2108.04297},
timestamp = {Wed, 11 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2108-04297.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/ManeLFC20,
author = {Aniket C. Mane and
Manuel Lafond and
Pedro Cipriano Feij{\~{a}}o and
C{\'{e}}dric Chauve},
title = {The distance and median problems in the single-cut-or-join model with
single-gene duplications},
journal = {Algorithms Mol. Biol.},
volume = {15},
number = {1},
pages = {8},
year = {2020},
url = {https://doi.org/10.1186/s13015-020-00169-y},
doi = {10.1186/S13015-020-00169-Y},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/almob/ManeLFC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/iandc/JiangLCZ20,
author = {Haitao Jiang and
Hong Liu and
C{\'{e}}dric Chauve and
Binhai Zhu},
title = {Breakpoint distance and PQ-trees},
journal = {Inf. Comput.},
volume = {275},
pages = {104584},
year = {2020},
url = {https://doi.org/10.1016/j.ic.2020.104584},
doi = {10.1016/J.IC.2020.104584},
timestamp = {Tue, 15 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/iandc/JiangLCZ20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alcob/KatebiFBMLSMNWH20,
author = {Mohsen Katebi and
Pedro Feij{\~{a}}o and
Julius Booth and
Mehrdad Mansouri and
Sean La and
Alex Sweeten and
Reza Miraskarshahi and
Matthew Nguyen and
Johnathan Wong and
William Hsiao and
C{\'{e}}dric Chauve and
Leonid Chindelevitch},
editor = {Carlos Mart{\'{\i}}n{-}Vide and
Miguel A. Vega{-}Rodr{\'{\i}}guez and
Travis J. Wheeler},
title = {PathOGiST: {A} Novel Method for Clustering Pathogen Isolates by Combining
Multiple Genotyping Signals},
booktitle = {Algorithms for Computational Biology - 7th International Conference,
AlCoB 2020, Missoula, MT, USA, April 13-15, 2020, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12099},
pages = {108--124},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-42266-0\_9},
doi = {10.1007/978-3-030-42266-0\_9},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/alcob/KatebiFBMLSMNWH20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/DufresneSMLCC20,
author = {Yoann Dufresne and
Chen Sun and
Pierre Marijon and
Dominique Lavenier and
C{\'{e}}dric Chauve and
Rayan Chikhi},
editor = {Carl Kingsford and
Nadia Pisanti},
title = {A Graph-Theoretic Barcode Ordering Model for Linked-Reads},
booktitle = {20th International Workshop on Algorithms in Bioinformatics, {WABI}
2020, September 7-9, 2020, Pisa, Italy (Virtual Conference)},
series = {LIPIcs},
volume = {172},
pages = {11:1--11:17},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2020},
url = {https://doi.org/10.4230/LIPIcs.WABI.2020.11},
doi = {10.4230/LIPICS.WABI.2020.11},
timestamp = {Sat, 06 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wabi/DufresneSMLCC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/OrabiEMVBBCCH19,
author = {Baraa Orabi and
Emre Erhan and
Brian McConeghy and
Stanislav V. Volik and
Stephane Le Bihan and
Robert Bell and
Colin C. Collins and
C{\'{e}}dric Chauve and
Faraz Hach},
title = {Alignment-free clustering of {UMI} tagged {DNA} molecules},
journal = {Bioinform.},
volume = {35},
number = {11},
pages = {1829--1836},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/bty888},
doi = {10.1093/BIOINFORMATICS/BTY888},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/OrabiEMVBBCCH19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MullerC19,
author = {Robert M{\"{u}}ller and
C{\'{e}}dric Chauve},
title = {HyAsP, a greedy tool for plasmids identification},
journal = {Bioinform.},
volume = {35},
number = {21},
pages = {4436--4439},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/btz413},
doi = {10.1093/BIOINFORMATICS/BTZ413},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/MullerC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/GanWCC19,
author = {Guo Liang Gan and
Elijah Willie and
C{\'{e}}dric Chauve and
Leonid Chindelevitch},
title = {Deconvoluting the diversity of within-host pathogen strains in a multi-locus
sequence typing framework},
journal = {{BMC} Bioinform.},
volume = {20-S},
number = {20},
pages = {637},
year = {2019},
url = {https://doi.org/10.1186/s12859-019-3204-8},
doi = {10.1186/S12859-019-3204-8},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/GanWCC19.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}
}
@inproceedings{DBLP:conf/bcb/YaoCRP19,
author = {Hua{-}Ting Yao and
C{\'{e}}dric Chauve and
Mireille R{\'{e}}gnier and
Yann Ponty},
editor = {Xinghua Mindy Shi and
Michael Buck and
Jian Ma and
Pierangelo Veltri},
title = {Exponentially Few {RNA} Structures are Designable},
booktitle = {Proceedings of the 10th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, {BCB} 2019, Niagara
Falls, NY, USA, September 7-10, 2019},
pages = {289--298},
publisher = {{ACM}},
year = {2019},
url = {https://doi.org/10.1145/3307339.3342163},
doi = {10.1145/3307339.3342163},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/YaoCRP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1905-04971,
author = {C{\'{e}}dric Chauve and
Yann Ponty and
Michael Wallner},
title = {Counting and sampling gene family evolutionary histories in the duplication-loss
and duplication-loss-transfer models},
journal = {CoRR},
volume = {abs/1905.04971},
year = {2019},
url = {http://arxiv.org/abs/1905.04971},
eprinttype = {arXiv},
eprint = {1905.04971},
timestamp = {Fri, 01 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1905-04971.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuxBCLLAH18,
author = {Markus Lux and
Ryan Remy Brinkman and
C{\'{e}}dric Chauve and
Adam Laing and
Anna Lorenc and
Lucie Abeler{-}D{\"{o}}rner and
Barbara Hammer},
title = {flowLearn: fast and precise identification and quality checking of
cell populations in flow cytometry},
journal = {Bioinform.},
volume = {34},
number = {13},
pages = {2245--2253},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty082},
doi = {10.1093/BIOINFORMATICS/BTY082},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuxBCLLAH18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcgenomics/AnselmettiDTCB18,
author = {Yoann Anselmetti and
Wandrille Duchemin and
Eric Tannier and
C{\'{e}}dric Chauve and
S{\`{e}}verine B{\'{e}}rard},
title = {Phylogenetic signal from rearrangements in 18 Anopheles species by
joint scaffolding extant and ancestral genomes},
journal = {{BMC} Genom.},
volume = {19},
number = {{S2}},
year = {2018},
url = {https://doi.org/10.1186/s12864-018-4466-7},
doi = {10.1186/S12864-018-4466-7},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcgenomics/AnselmettiDTCB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijfcs/ChauveCP18,
author = {C{\'{e}}dric Chauve and
Julien Courtiel and
Yann Ponty},
title = {Counting, Generating, Analyzing and Sampling Tree Alignments},
journal = {Int. J. Found. Comput. Sci.},
volume = {29},
number = {5},
pages = {741--767},
year = {2018},
url = {https://doi.org/10.1142/S0129054118420030},
doi = {10.1142/S0129054118420030},
timestamp = {Tue, 12 Mar 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ijfcs/ChauveCP18.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}
}
@article{DBLP:journals/tcbb/LuhmannCSW18,
author = {Nina Luhmann and
C{\'{e}}dric Chauve and
Jens Stoye and
Roland Wittler},
title = {Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic
Framework},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {15},
number = {6},
pages = {2094--2100},
year = {2018},
url = {https://doi.org/10.1109/TCBB.2018.2816034},
doi = {10.1109/TCBB.2018.2816034},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/LuhmannCSW18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ManeLFC18,
author = {Aniket C. Mane and
Manuel Lafond and
Pedro Feij{\~{a}}o and
C{\'{e}}dric Chauve},
editor = {Mathieu Blanchette and
A{\"{\i}}da Ouangraoua},
title = {The Rooted {SCJ} Median with Single Gene Duplications},
booktitle = {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},
pages = {28--48},
publisher = {Springer},
year = {2018},
url = {https://doi.org/10.1007/978-3-030-00834-5\_2},
doi = {10.1007/978-3-030-00834-5\_2},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ManeLFC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ChauveFW18,
author = {C{\'{e}}dric Chauve and
Jingxue Feng and
Liangliang Wang},
editor = {Mathieu Blanchette and
A{\"{\i}}da Ouangraoua},
title = {Detecting Introgression in Anopheles Mosquito Genomes Using a Reconciliation-Based
Approach},
booktitle = {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},
pages = {163--178},
publisher = {Springer},
year = {2018},
url = {https://doi.org/10.1007/978-3-030-00834-5\_9},
doi = {10.1007/978-3-030-00834-5\_9},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ChauveFW18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/MansouriBVCC18,
author = {Mehrdad Mansouri and
Julian Booth and
Margaryta Vityaz and
C{\'{e}}dric Chauve and
Leonid Chindelevitch},
editor = {Laxmi Parida and
Esko Ukkonen},
title = {{PRINCE:} Accurate Approximation of the Copy Number of Tandem Repeats},
booktitle = {18th International Workshop on Algorithms in Bioinformatics, {WABI}
2018, August 20-22, 2018, Helsinki, Finland},
series = {LIPIcs},
volume = {113},
pages = {20:1--20:13},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2018},
url = {https://doi.org/10.4230/LIPIcs.WABI.2018.20},
doi = {10.4230/LIPICS.WABI.2018.20},
timestamp = {Tue, 29 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wabi/MansouriBVCC18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/almob/DoerrBFC17,
author = {Daniel Doerr and
Metin Balaban and
Pedro Feij{\~{a}}o and
C{\'{e}}dric Chauve},
title = {The gene family-free median of three},
journal = {Algorithms Mol. Biol.},
volume = {12},
number = {1},
pages = {14:1--14:14},
year = {2017},
url = {https://doi.org/10.1186/s13015-017-0106-z},
doi = {10.1186/S13015-017-0106-Z},
timestamp = {Fri, 13 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/almob/DoerrBFC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LowesCPG17,
author = {Benedikt L{\"{o}}wes and
C{\'{e}}dric Chauve and
Yann Ponty and
Robert Giegerich},
title = {The BRaliBase dent - a tale of benchmark design and interpretation},
journal = {Briefings Bioinform.},
volume = {18},
number = {2},
pages = {306--311},
year = {2017},
url = {https://doi.org/10.1093/bib/bbw022},
doi = {10.1093/BIB/BBW022},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/LowesCPG17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LaHC17,
author = {Sean La and
Ehsan Haghshenas and
C{\'{e}}dric Chauve},
title = {LRCstats, a tool for evaluating long reads correction methods},
journal = {Bioinform.},
volume = {33},
number = {22},
pages = {3652--3654},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx489},
doi = {10.1093/BIOINFORMATICS/BTX489},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LaHC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/RajaramanZMC17,
author = {Ashok Rajaraman and
Jo{\~{a}}o Paulo Pereira Zanetti and
J{\'{a}}n Manuch and
C{\'{e}}dric Chauve},
title = {Algorithms and Complexity Results for Genome Mapping Problems},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {14},
number = {2},
pages = {418--430},
year = {2017},
url = {https://doi.org/10.1109/TCBB.2016.2528239},
doi = {10.1109/TCBB.2016.2528239},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/RajaramanZMC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/analco/ChauveFL17,
author = {C{\'{e}}dric Chauve and
{\'{E}}ric Fusy and
J{\'{e}}r{\'{e}}mie O. Lumbroso},
editor = {Conrado Mart{\'{\i}}nez and
Mark Daniel Ward},
title = {An Exact Enumeration of Distance-Hereditary Graphs},
booktitle = {Proceedings of the Fourteenth Workshop on Analytic Algorithmics and
Combinatorics, {ANALCO} 2017, Barcelona, Spain, Hotel Porta Fira,
January 16-17, 2017},
pages = {31--45},
publisher = {{SIAM}},
year = {2017},
url = {https://doi.org/10.1137/1.9781611974775.3},
doi = {10.1137/1.9781611974775.3},
timestamp = {Mon, 02 Jul 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/analco/ChauveFL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/FeijaoMC17,
author = {Pedro Feij{\~{a}}o and
Aniket C. Mane and
C{\'{e}}dric Chauve},
editor = {Joao Meidanis and
Luay Nakhleh},
title = {A Tractable Variant of the Single Cut or Join Distance with Duplicated
Genes},
booktitle = {Comparative Genomics - 15th International Workshop, {RECOMB} {CG}
2017, Barcelona, Spain, October 4-6, 2017, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10562},
pages = {14--30},
publisher = {Springer},
year = {2017},
url = {https://doi.org/10.1007/978-3-319-67979-2\_2},
doi = {10.1007/978-3-319-67979-2\_2},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/FeijaoMC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/spire/ChauveJLSW17,
author = {C{\'{e}}dric Chauve and
Mark Jones and
Manuel Lafond and
C{\'{e}}line Scornavacca and
Mathias Weller},
editor = {Gabriele Fici and
Marinella Sciortino and
Rossano Venturini},
title = {Constructing a Consensus Phylogeny from a Leaf-Removal Distance (Extended
Abstract)},
booktitle = {String Processing and Information Retrieval - 24th International Symposium,
{SPIRE} 2017, Palermo, Italy, September 26-29, 2017, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10508},
pages = {129--143},
publisher = {Springer},
year = {2017},
url = {https://doi.org/10.1007/978-3-319-67428-5\_12},
doi = {10.1007/978-3-319-67428-5\_12},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/spire/ChauveJLSW17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/ChauveJLSW17,
author = {C{\'{e}}dric Chauve and
Mark Jones and
Manuel Lafond and
C{\'{e}}line Scornavacca and
Mathias Weller},
title = {Constructing a Consensus Phylogeny from a Leaf-Removal Distance},
journal = {CoRR},
volume = {abs/1705.05295},
year = {2017},
url = {http://arxiv.org/abs/1705.05295},
eprinttype = {arXiv},
eprint = {1705.05295},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/ChauveJLSW17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JacoxCSPS16,
author = {Edwin Jacox and
C{\'{e}}dric Chauve and
Gergely J. Sz{\"{o}}llosi and
Yann Ponty and
C{\'{e}}line Scornavacca},
title = {ecceTERA: comprehensive gene tree-species tree reconciliation using
parsimony},
journal = {Bioinform.},
volume = {32},
number = {13},
pages = {2056--2058},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw105},
doi = {10.1093/BIOINFORMATICS/BTW105},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JacoxCSPS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HaghshenasHSC16,
author = {Ehsan Haghshenas and
Faraz Hach and
S{\"{u}}leyman Cenk Sahinalp and
C{\'{e}}dric Chauve},
title = {CoLoRMap: Correcting Long Reads by Mapping short reads},
journal = {Bioinform.},
volume = {32},
number = {17},
pages = {545--551},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw463},
doi = {10.1093/BIOINFORMATICS/BTW463},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HaghshenasHSC16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alcob/ChauveCP16,
author = {C{\'{e}}dric Chauve and
Julien Courtiel and
Yann Ponty},
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 = {Counting, Generating and Sampling Tree Alignments},
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 = {53--64},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-38827-4\_5},
doi = {10.1007/978-3-319-38827-4\_5},
timestamp = {Tue, 14 May 2019 10:00:49 +0200},
biburl = {https://dblp.org/rec/conf/alcob/ChauveCP16.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}
}
@inproceedings{DBLP:conf/wabi/DoerrFBC16,
author = {Daniel Doerr and
Pedro Feij{\~{a}}o and
Metin Balaban and
C{\'{e}}dric Chauve},
editor = {Martin C. Frith and
Christian N{\o}rgaard Storm Pedersen},
title = {The Gene Family-Free Median of Three},
booktitle = {Algorithms in Bioinformatics - 16th International Workshop, {WABI}
2016, Aarhus, Denmark, August 22-24, 2016. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9838},
pages = {102--120},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-43681-4\_9},
doi = {10.1007/978-3-319-43681-4\_9},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/DoerrFBC16.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/DoerrFBC16,
author = {Daniel Doerr and
Pedro Feij{\~{a}}o and
Metin Balaban and
C{\'{e}}dric Chauve},
title = {The gene family-free median of three},
journal = {CoRR},
volume = {abs/1606.05910},
year = {2016},
url = {http://arxiv.org/abs/1606.05910},
eprinttype = {arXiv},
eprint = {1606.05910},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/DoerrFBC16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/ChauveFL16,
author = {C{\'{e}}dric Chauve and
{\'{E}}ric Fusy and
J{\'{e}}r{\'{e}}mie O. Lumbroso},
title = {An Exact Enumeration of Distance-Hereditary Graphs},
journal = {CoRR},
volume = {abs/1608.01464},
year = {2016},
url = {http://arxiv.org/abs/1608.01464},
eprinttype = {arXiv},
eprint = {1608.01464},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/ChauveFL16.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/bmcbi/ChauvePZ15,
author = {C{\'{e}}dric Chauve and
Yann Ponty and
Jo{\~{a}}o Paulo Pereira Zanetti},
title = {Evolution of genes neighborhood within reconciled phylogenies: an
ensemble approach},
journal = {{BMC} Bioinform.},
volume = {16},
number = {{S19}},
pages = {S6},
year = {2015},
url = {https://doi.org/10.1186/1471-2105-16-s19-s6},
doi = {10.1186/1471-2105-16-S19-S6},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ChauvePZ15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BourgeadeCA15,
author = {Laetitia Bourgeade and
C{\'{e}}dric Chauve and
Julien Allali},
title = {Chaining Sequence/Structure Seeds for Computing {RNA} Similarity},
journal = {J. Comput. Biol.},
volume = {22},
number = {3},
pages = {205--217},
year = {2015},
url = {https://doi.org/10.1089/cmb.2014.0283},
doi = {10.1089/CMB.2014.0283},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/BourgeadeCA15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/RajaramanCP15,
author = {Ashok Rajaraman and
C{\'{e}}dric Chauve and
Yann Ponty},
editor = {Robert W. Harrison and
Yaohang Li and
Ion I. Mandoiu},
title = {Assessing the Robustness of Parsimonious Predictions for Gene Neighborhoods
from Reconciled Phylogenies: Supplementary Material},
booktitle = {Bioinformatics Research and Applications - 11th International Symposium,
{ISBRA} 2015, Norfolk, VA, USA, June 7-10, 2015 Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9096},
pages = {260--271},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-19048-8\_22},
doi = {10.1007/978-3-319-19048-8\_22},
timestamp = {Tue, 14 May 2019 10:00:51 +0200},
biburl = {https://dblp.org/rec/conf/isbra/RajaramanCP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/McPhersonRCS15,
author = {Andrew W. McPherson and
Andrew Roth and
C{\'{e}}dric Chauve and
S{\"{u}}leyman Cenk Sahinalp},
editor = {Teresa M. Przytycka},
title = {Joint Inference of Genome Structure and Content in Heterogeneous Tumor
Samples},
booktitle = {Research in Computational Molecular Biology - 19th Annual International
Conference, {RECOMB} 2015, Warsaw, Poland, April 12-15, 2015, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9029},
pages = {256--258},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-16706-0\_25},
doi = {10.1007/978-3-319-16706-0\_25},
timestamp = {Thu, 10 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/McPhersonRCS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/spire/AllaliCB15,
author = {Julien Allali and
C{\'{e}}dric Chauve and
Laetitia Bourgeade},
editor = {Costas S. Iliopoulos and
Simon J. Puglisi and
Emine Yilmaz},
title = {Chaining Fragments in Sequences: to Sweep or Not (Extended Abstract)},
booktitle = {String Processing and Information Retrieval - 22nd International Symposium,
{SPIRE} 2015, London, UK, September 1-4, 2015, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9309},
pages = {116--123},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-23826-5\_12},
doi = {10.1007/978-3-319-23826-5\_12},
timestamp = {Tue, 14 May 2019 10:00:55 +0200},
biburl = {https://dblp.org/rec/conf/spire/AllaliCB15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/McPhersonRHSCS15,
author = {Andrew W. McPherson and
Andrew Roth and
Gavin Ha and
Sohrab P. Shah and
C{\'{e}}dric Chauve and
S{\"{u}}leyman Cenk Sahinalp},
title = {Joint Inference of Genome Structure and Content in Heterogeneous Tumour
Samples},
journal = {CoRR},
volume = {abs/1504.03080},
year = {2015},
url = {http://arxiv.org/abs/1504.03080},
eprinttype = {arXiv},
eprint = {1504.03080},
timestamp = {Thu, 10 Oct 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/McPhersonRHSCS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/ChauveCP15,
author = {C{\'{e}}dric Chauve and
Julien Courtiel and
Yann Ponty},
title = {An Unambiguous And Complete Dynamic Programming Algorithm For Tree
Alignment},
journal = {CoRR},
volume = {abs/1505.05983},
year = {2015},
url = {http://arxiv.org/abs/1505.05983},
eprinttype = {arXiv},
eprint = {1505.05983},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/ChauveCP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/AllaliBC15,
author = {Julien Allali and
Laetitia Bourgeade and
C{\'{e}}dric Chauve},
title = {Chaining fragments in sequences: to sweep or not},
journal = {CoRR},
volume = {abs/1506.07458},
year = {2015},
url = {http://arxiv.org/abs/1506.07458},
eprinttype = {arXiv},
eprint = {1506.07458},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/AllaliBC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LafondCDE14,
author = {Manuel Lafond and
C{\'{e}}dric Chauve and
Riccardo Dondi and
Nadia El{-}Mabrouk},
title = {Polytomy refinement for the correction of dubious duplications in
gene trees},
journal = {Bioinform.},
volume = {30},
number = {17},
pages = {519--526},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu463},
doi = {10.1093/BIOINFORMATICS/BTU463},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LafondCDE14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/eccb/BourgeadeAC14,
author = {Laetitia Bourgeade and
Julien Allali and
C{\'{e}}dric Chauve},
editor = {Fabrice Jossinet and
Yann Ponty and
J{\'{e}}r{\^{o}}me Waldisp{\"{u}}hl},
title = {Chaining Sequence/Structure Seeds for Computing {RNA} Similarity},
booktitle = {Proceedings of the 1st Workshop on Computational Methods for Structural
RNAs {(CMSR} 2014), Strasbourg, France, September 7, 2014},
pages = {1--12},
publisher = {McGill University},
year = {2014},
url = {https://doi.org/10.15455/CMSR.2014.0001},
doi = {10.15455/CMSR.2014.0001},
timestamp = {Mon, 08 Feb 2021 13:26:46 +0100},
biburl = {https://dblp.org/rec/conf/eccb/BourgeadeAC14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/ChauvePZ14,
author = {C{\'{e}}dric Chauve and
Yann Ponty and
Jo{\~{a}}o Paulo Pereira Zanetti},
editor = {S{\'{e}}rgio Vale Aguiar Campos},
title = {Evolution of Genes Neighborhood within Reconciled Phylogenies: An
Ensemble Approach},
booktitle = {Advances in Bioinformatics and Computational Biology - 9th Brazilian
Symposium on Bioinformatics, {BSB} 2014, Belo Horizonte, Brazil, October
28-30, 2014, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8826},
pages = {49--56},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-12418-6\_7},
doi = {10.1007/978-3-319-12418-6\_7},
timestamp = {Sun, 23 Jan 2022 21:20:49 +0100},
biburl = {https://dblp.org/rec/conf/wob/ChauvePZ14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wob/LuhmannCSW14,
author = {Nina Luhmann and
C{\'{e}}dric Chauve and
Jens Stoye and
Roland Wittler},
editor = {S{\'{e}}rgio Vale Aguiar Campos},
title = {Scaffolding of Ancient Contigs and Ancestral Reconstruction in a Phylogenetic
Framework},
booktitle = {Advances in Bioinformatics and Computational Biology - 9th Brazilian
Symposium on Bioinformatics, {BSB} 2014, Belo Horizonte, Brazil, October
28-30, 2014, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8826},
pages = {135--143},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-12418-6\_17},
doi = {10.1007/978-3-319-12418-6\_17},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/wob/LuhmannCSW14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RajaramanTC13,
author = {Ashok Rajaraman and
Eric Tannier and
C{\'{e}}dric Chauve},
title = {{FPSAC:} fast phylogenetic scaffolding of ancient contigs},
journal = {Bioinform.},
volume = {29},
number = {23},
pages = {2987--2994},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt527},
doi = {10.1093/BIOINFORMATICS/BTT527},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RajaramanTC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwoca/ChauvePR13,
author = {C{\'{e}}dric Chauve and
Murray Patterson and
Ashok Rajaraman},
editor = {Thierry Lecroq and
Laurent Mouchard},
title = {Hypergraph Covering Problems Motivated by Genome Assembly Questions},
booktitle = {Combinatorial Algorithms - 24th International Workshop, {IWOCA} 2013,
Rouen, France, July 10-12, 2013, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {8288},
pages = {428--432},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-45278-9\_37},
doi = {10.1007/978-3-642-45278-9\_37},
timestamp = {Wed, 25 Sep 2019 18:08:04 +0200},
biburl = {https://dblp.org/rec/conf/iwoca/ChauvePR13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/daglib/p/ChauveEGST13,
author = {C{\'{e}}dric Chauve and
Nadia El{-}Mabrouk and
Laurent Gu{\'{e}}guen and
Magali Semeria and
Eric Tannier},
editor = {C{\'{e}}dric Chauve and
Nadia El{-}Mabrouk and
Eric Tannier},
title = {Duplication, Rearrangement and Reconciliation: {A} Follow-Up 13 Years
Later},
booktitle = {Models and Algorithms for Genome Evolution},
pages = {47--62},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-1-4471-5298-9\_4},
doi = {10.1007/978-1-4471-5298-9\_4},
timestamp = {Thu, 03 Dec 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/books/daglib/p/ChauveEGST13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/daglib/p/BragaCDJSTW13,
author = {Mar{\'{\i}}lia D. V. Braga and
C{\'{e}}dric Chauve and
Daniel Doerr and
Katharina Jahn and
Jens Stoye and
Annelyse Th{\'{e}}venin and
Roland Wittler},
editor = {C{\'{e}}dric Chauve and
Nadia El{-}Mabrouk and
Eric Tannier},
title = {The Potential of Family-Free Genome Comparison},
booktitle = {Models and Algorithms for Genome Evolution},
pages = {287--307},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-1-4471-5298-9\_13},
doi = {10.1007/978-1-4471-5298-9\_13},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/books/daglib/p/BragaCDJSTW13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@book{DBLP:books/daglib/0032286,
editor = {C{\'{e}}dric Chauve and
Nadia El{-}Mabrouk and
Eric Tannier},
title = {Models and Algorithms for Genome Evolution},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-1-4471-5298-9},
doi = {10.1007/978-1-4471-5298-9},
isbn = {978-1-4471-5297-2},
timestamp = {Tue, 16 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/books/daglib/0032286.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/colognetwente/ManuchPWCT13,
author = {J{\'{a}}n Manuch and
Murray Patterson and
Roland Wittler and
C{\'{e}}dric Chauve and
Eric Tannier},
editor = {Kamiel Cornelissen and
Ruben Hoeksma and
Johann L. Hurink and
Bodo Manthey},
title = {Linearization of ancestral multichromosomal genomes},
booktitle = {12th Cologne-Twente Workshop on Graphs and Combinatorial Optimization,
Enschede, Netherlands, May 21-23, 2013},
series = {{CTIT} Workshop Proceedings},
volume = {{WP} 13-01},
pages = {169--173},
year = {2013},
timestamp = {Mon, 06 Apr 2020 17:04:26 +0200},
biburl = {https://dblp.org/rec/conf/colognetwente/ManuchPWCT13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/ChauvePR13,
author = {C{\'{e}}dric Chauve and
Murray Patterson and
Ashok Rajaraman},
title = {Hypergraph covering problems motivated by genome assembly questions},
journal = {CoRR},
volume = {abs/1306.4353},
year = {2013},
url = {http://arxiv.org/abs/1306.4353},
eprinttype = {arXiv},
eprint = {1306.4353},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/ChauvePR13.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/bioinformatics/JonesRTC12,
author = {Bradley R. Jones and
Ashok Rajaraman and
Eric Tannier and
C{\'{e}}dric Chauve},
title = {{ANGES:} reconstructing ANcestral GEnomeS maps},
journal = {Bioinform.},
volume = {28},
number = {18},
pages = {2388--2390},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts457},
doi = {10.1093/BIOINFORMATICS/BTS457},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JonesRTC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ManuchPWCT12,
author = {J{\'{a}}n Manuch and
Murray Patterson and
Roland Wittler and
C{\'{e}}dric Chauve and
Eric Tannier},
title = {Linearization of ancestral multichromosomal genomes},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-19}},
pages = {S11},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-S19-S11},
doi = {10.1186/1471-2105-13-S19-S11},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ManuchPWCT12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/ManuchPC12,
author = {J{\'{a}}n Manuch and
Murray Patterson and
C{\'{e}}dric Chauve},
title = {Hardness results on the gapped consecutive-ones property problem},
journal = {Discret. Appl. Math.},
volume = {160},
number = {18},
pages = {2760--2768},
year = {2012},
url = {https://doi.org/10.1016/j.dam.2012.03.019},
doi = {10.1016/J.DAM.2012.03.019},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/ManuchPC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/MalekesmaeiliCS12,
author = {Mehrnoush Malekesmaeili and
C{\'{e}}dric Chauve and
Tamon Stephen},
title = {A tight bound on the length of odd cycles in the incompatibility graph
of a non-C1P matrix},
journal = {Inf. Process. Lett.},
volume = {112},
number = {20},
pages = {799--803},
year = {2012},
url = {https://doi.org/10.1016/j.ipl.2012.07.004},
doi = {10.1016/J.IPL.2012.07.004},
timestamp = {Fri, 26 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/MalekesmaeiliCS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jda/AllaliCFG12,
author = {Julien Allali and
C{\'{e}}dric Chauve and
Pascal Ferraro and
Anne{-}Laure Gaillard},
title = {Efficient chaining of seeds in ordered trees},
journal = {J. Discrete Algorithms},
volume = {14},
pages = {107--118},
year = {2012},
url = {https://doi.org/10.1016/j.jda.2011.12.013},
doi = {10.1016/J.JDA.2011.12.013},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jda/AllaliCFG12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/DoyonHC12,
author = {Jean{-}Philippe Doyon and
Sylvie Hamel and
C{\'{e}}dric Chauve},
title = {An Efficient Method for Exploring the Space of Gene Tree/Species Tree
Reconciliations in a Probabilistic Framework},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {9},
number = {1},
pages = {26--39},
year = {2012},
url = {https://doi.org/10.1109/TCBB.2011.64},
doi = {10.1109/TCBB.2011.64},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/DoyonHC12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1201-0940,
author = {Mathilde Bouvel and
C{\'{e}}dric Chauve and
Marni Mishna and
Dominique Rossin},
title = {Average-case analysis of perfect sorting by reversals (Journal Version)},
journal = {CoRR},
volume = {abs/1201.0940},
year = {2012},
url = {http://arxiv.org/abs/1201.0940},
eprinttype = {arXiv},
eprint = {1201.0940},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1201-0940.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GavranovicCST11,
author = {Haris Gavranovic and
C{\'{e}}dric Chauve and
J{\'{e}}r{\^{o}}me Salse and
Eric Tannier},
title = {Mapping ancestral genomes with massive gene loss: {A} matrix sandwich
problem},
journal = {Bioinform.},
volume = {27},
number = {13},
pages = {257--265},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr224},
doi = {10.1093/BIOINFORMATICS/BTR224},
timestamp = {Tue, 08 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GavranovicCST11.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/WittlerC11,
author = {Roland Wittler and
C{\'{e}}dric Chauve},
title = {Consistency-based detection of potential tumor-specific deletions
in matched normal/tumor genomes},
journal = {{BMC} Bioinform.},
volume = {12},
number = {{S-9}},
pages = {S21},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-S9-S21},
doi = {10.1186/1471-2105-12-S9-S21},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/WittlerC11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dmaa/BouvelCMR11,
author = {Mathilde Bouvel and
C{\'{e}}dric Chauve and
Marni Mishna and
Dominique Rossin},
title = {Average-Case Analysis of Perfect Sorting by Reversals},
journal = {Discret. Math. Algorithms Appl.},
volume = {3},
number = {3},
pages = {369--392},
year = {2011},
url = {https://doi.org/10.1142/S1793830911001280},
doi = {10.1142/S1793830911001280},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/dmaa/BouvelCMR11.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/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}
}
@inproceedings{DBLP:conf/cpm/ChauveMPW11,
author = {C{\'{e}}dric Chauve and
J{\'{a}}n Manuch and
Murray Patterson and
Roland Wittler},
editor = {Raffaele Giancarlo and
Giovanni Manzini},
title = {Tractability Results for the Consecutive-Ones Property with Multiplicity},
booktitle = {Combinatorial Pattern Matching - 22nd Annual Symposium, {CPM} 2011,
Palermo, Italy, June 27-29, 2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6661},
pages = {90--103},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-21458-5\_10},
doi = {10.1007/978-3-642-21458-5\_10},
timestamp = {Tue, 14 May 2019 10:00:38 +0200},
biburl = {https://dblp.org/rec/conf/cpm/ChauveMPW11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1109-0562,
author = {Mehrnoush Malekesmaeili and
C{\'{e}}dric Chauve and
Tamon Stephen},
title = {A tight bound on the length of odd cycles in the incompatibility graph
of a non-C1P matrix},
journal = {CoRR},
volume = {abs/1109.0562},
year = {2011},
url = {http://arxiv.org/abs/1109.0562},
eprinttype = {arXiv},
eprint = {1109.0562},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1109-0562.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1111-5872,
author = {Ahmad Mahmoody{-}Ghaidary and
C{\'{e}}dric Chauve and
Ladislav Stacho},
title = {Tractability results for the Double-Cut-and-Join circular median problem},
journal = {CoRR},
volume = {abs/1111.5872},
year = {2011},
url = {http://arxiv.org/abs/1111.5872},
eprinttype = {arXiv},
eprint = {1111.5872},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1111-5872.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/ChauveHSY10,
author = {C{\'{e}}dric Chauve and
Utz{-}Uwe Haus and
Tamon Stephen and
Vivija P. You},
title = {Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral
Genome Reconstruction},
journal = {J. Comput. Biol.},
volume = {17},
number = {9},
pages = {1167--1181},
year = {2010},
url = {https://doi.org/10.1089/cmb.2010.0113},
doi = {10.1089/CMB.2010.0113},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/ChauveHSY10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/JiangCZ10,
author = {Haitao Jiang and
C{\'{e}}dric Chauve and
Binhai Zhu},
editor = {Amihood Amir and
Laxmi Parida},
title = {Breakpoint Distance and PQ-Trees},
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 = {112--124},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-13509-5\_11},
doi = {10.1007/978-3-642-13509-5\_11},
timestamp = {Tue, 14 May 2019 10:00:38 +0200},
biburl = {https://dblp.org/rec/conf/cpm/JiangCZ10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iwoca/AllaliCFG10,
author = {Julien Allali and
C{\'{e}}dric Chauve and
Pascal Ferraro and
Anne{-}Laure Gaillard},
editor = {Costas S. Iliopoulos and
William F. Smyth},
title = {Efficient Chaining of Seeds in Ordered Trees},
booktitle = {Combinatorial Algorithms - 21st International Workshop, {IWOCA} 2010,
London, UK, July 26-28, 2010, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {6460},
pages = {260--273},
publisher = {Springer},
year = {2010},
url = {https://doi.org/10.1007/978-3-642-19222-7\_27},
doi = {10.1007/978-3-642-19222-7\_27},
timestamp = {Tue, 14 May 2019 10:00:53 +0200},
biburl = {https://dblp.org/rec/conf/iwoca/AllaliCFG10.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 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/OuangraouaSC10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/endm/ChauveMP09,
author = {C{\'{e}}dric Chauve and
J{\'{a}}n Manuch and
Murray Patterson},
title = {On the Gapped Consecutive-Ones Property},
journal = {Electron. Notes Discret. Math.},
volume = {34},
pages = {121--125},
year = {2009},
url = {https://doi.org/10.1016/j.endm.2009.07.020},
doi = {10.1016/J.ENDM.2009.07.020},
timestamp = {Thu, 20 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/endm/ChauveMP09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/BerardCCPT09,
author = {S{\`{e}}verine B{\'{e}}rard and
Annie Chateau and
C{\'{e}}dric Chauve and
Christophe Paul and
Eric Tannier},
title = {Computation of Perfect {DCJ} Rearrangement Scenarios with Linear and
Circular Chromosomes},
journal = {J. Comput. Biol.},
volume = {16},
number = {10},
pages = {1287--1309},
year = {2009},
url = {https://doi.org/10.1089/cmb.2009.0088},
doi = {10.1089/CMB.2009.0088},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/BerardCCPT09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/DoyonCH09,
author = {Jean{-}Philippe Doyon and
C{\'{e}}dric Chauve and
Sylvie Hamel},
title = {Space of Gene/Species Trees Reconciliations and Parsimonious Models},
journal = {J. Comput. Biol.},
volume = {16},
number = {10},
pages = {1399--1418},
year = {2009},
url = {https://doi.org/10.1089/cmb.2009.0095},
doi = {10.1089/CMB.2009.0095},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/DoyonCH09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cpm/BouvelCMR09,
author = {Mathilde Bouvel and
C{\'{e}}dric Chauve and
Marni Mishna and
Dominique Rossin},
editor = {Gregory Kucherov and
Esko Ukkonen},
title = {Average-Case Analysis of Perfect Sorting by Reversals},
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 = {314--325},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-02441-2\_28},
doi = {10.1007/978-3-642-02441-2\_28},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cpm/BouvelCMR09.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/ChauveE09,
author = {C{\'{e}}dric Chauve and
Nadia El{-}Mabrouk},
editor = {Serafim Batzoglou},
title = {New Perspectives on Gene Family Evolution: Losses in Reconciliation
and a Link with Supertrees},
booktitle = {Research in Computational Molecular Biology, 13th Annual International
Conference, {RECOMB} 2009, Tucson, AZ, USA, May 18-21, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5541},
pages = {46--58},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-02008-7\_4},
doi = {10.1007/978-3-642-02008-7\_4},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ChauveE09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ChauveHSY09,
author = {C{\'{e}}dric Chauve and
Utz{-}Uwe Haus and
Tamon Stephen and
Vivija P. You},
editor = {Francesca D. Ciccarelli and
Istv{\'{a}}n Mikl{\'{o}}s},
title = {Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral
Genome Reconstruction},
booktitle = {Comparative Genomics, International Workshop, {RECOMB-CG} 2009, Budapest,
Hungary, September 27-29, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5817},
pages = {48--58},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-04744-2\_5},
doi = {10.1007/978-3-642-04744-2\_5},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ChauveHSY09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-0901-2847,
author = {Mathilde Bouvel and
C{\'{e}}dric Chauve and
Marni Mishna and
Dominique Rossin},
title = {Average-case analysis of perfect sorting by reversals},
journal = {CoRR},
volume = {abs/0901.2847},
year = {2009},
url = {http://arxiv.org/abs/0901.2847},
eprinttype = {arXiv},
eprint = {0901.2847},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-0901-2847.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/corr/abs-0912-0309,
author = {C{\'{e}}dric Chauve and
J{\'{a}}n Manuch and
Murray Patterson},
title = {Hardness Results for the Gapped Consecutive-Ones Property},
journal = {CoRR},
volume = {abs/0912.0309},
year = {2009},
url = {http://arxiv.org/abs/0912.0309},
eprinttype = {arXiv},
eprint = {0912.0309},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-0912-0309.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/ChauveHSY09,
author = {C{\'{e}}dric Chauve and
Utz{-}Uwe Haus and
Tamon Stephen and
Vivija P. You},
title = {Minimal Conflicting Sets for the Consecutive Ones Property in ancestral
genome reconstruction},
journal = {CoRR},
volume = {abs/0912.4196},
year = {2009},
url = {http://arxiv.org/abs/0912.4196},
eprinttype = {arXiv},
eprint = {0912.4196},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/ChauveHSY09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/BerardCP08,
author = {S{\`{e}}verine B{\'{e}}rard and
C{\'{e}}dric Chauve and
Christophe Paul},
title = {A more efficient algorithm for perfect sorting by reversals},
journal = {Inf. Process. Lett.},
volume = {106},
number = {3},
pages = {90--95},
year = {2008},
url = {https://doi.org/10.1016/j.ipl.2007.10.012},
doi = {10.1016/J.IPL.2007.10.012},
timestamp = {Mon, 06 Nov 2017 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ipl/BerardCP08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ChauveDE08,
author = {C{\'{e}}dric Chauve and
Jean{-}Philippe Doyon and
Nadia El{-}Mabrouk},
title = {Gene Family Evolution by Duplication, Speciation, and Loss},
journal = {J. Comput. Biol.},
volume = {15},
number = {8},
pages = {1043--1062},
year = {2008},
url = {https://doi.org/10.1089/cmb.2008.0054},
doi = {10.1089/CMB.2008.0054},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/ChauveDE08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ChauveT08,
author = {C{\'{e}}dric Chauve and
Eric Tannier},
title = {A Methodological Framework for the Reconstruction of Contiguous Regions
of Ancestral Genomes and Its Application to Mammalian Genomes},
journal = {PLoS Comput. Biol.},
volume = {4},
number = {11},
year = {2008},
url = {https://doi.org/10.1371/journal.pcbi.1000234},
doi = {10.1371/JOURNAL.PCBI.1000234},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/ChauveT08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/siamdm/BergeronCMR08,
author = {Anne Bergeron and
C{\'{e}}dric Chauve and
Fabien de Montgolfier and
Mathieu Raffinot},
title = {Computing Common Intervals of {K} Permutations, with Applications
to Modular Decomposition of Graphs},
journal = {{SIAM} J. Discret. Math.},
volume = {22},
number = {3},
pages = {1022--1039},
year = {2008},
url = {https://doi.org/10.1137/060651331},
doi = {10.1137/060651331},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/siamdm/BergeronCMR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/DoyonCH08,
author = {Jean{-}Philippe Doyon and
C{\'{e}}dric Chauve and
Sylvie Hamel},
editor = {Craig E. Nelson and
St{\'{e}}phane Vialette},
title = {Algorithms for Exploring the Space of Gene Tree/Species Tree Reconciliations},
booktitle = {Comparative Genomics, International Workshop, {RECOMB-CG} 2008, Paris,
France, October 13-15, 2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5267},
pages = {1--13},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-87989-3\_1},
doi = {10.1007/978-3-540-87989-3\_1},
timestamp = {Sun, 02 Jun 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/DoyonCH08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/BerardCCPT08,
author = {S{\`{e}}verine B{\'{e}}rard and
Annie Chateau and
C{\'{e}}dric Chauve and
Christophe Paul and
Eric Tannier},
editor = {Craig E. Nelson and
St{\'{e}}phane Vialette},
title = {Perfect {DCJ} Rearrangement},
booktitle = {Comparative Genomics, International Workshop, {RECOMB-CG} 2008, Paris,
France, October 13-15, 2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5267},
pages = {158--169},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-87989-3\_12},
doi = {10.1007/978-3-540-87989-3\_12},
timestamp = {Mon, 13 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/BerardCCPT08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/gpb/PoissonCCB07,
author = {Guylaine Poisson and
C{\'{e}}dric Chauve and
Xin Chen and
Anne Bergeron},
title = {FragAnchor: {A} Large-Scale Predictor of Glycosylphosphatidylinositol
Anchors in Eukaryote Protein Sequences by Qualitative Scoring},
journal = {Genom. Proteom. Bioinform.},
volume = {5},
number = {2},
pages = {121--130},
year = {2007},
url = {https://doi.org/10.1016/S1672-0229(07)60022-9},
doi = {10.1016/S1672-0229(07)60022-9},
timestamp = {Thu, 20 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/gpb/PoissonCCB07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/BerardBCP07,
author = {S{\`{e}}verine B{\'{e}}rard and
Anne Bergeron and
C{\'{e}}dric Chauve and
Christophe Paul},
title = {Perfect Sorting by Reversals Is Not Always Difficult},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {4},
number = {1},
pages = {4--16},
year = {2007},
url = {https://doi.org/10.1109/TCBB.2007.1011},
doi = {10.1109/TCBB.2007.1011},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/BerardBCP07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/BlinCFRV07,
author = {Guillaume Blin and
C{\'{e}}dric Chauve and
Guillaume Fertin and
Romeo Rizzi and
St{\'{e}}phane Vialette},
title = {Comparing Genomes with Duplications: {A} Computational Complexity
Point of View},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {4},
number = {4},
pages = {523--534},
year = {2007},
url = {https://doi.org/10.1109/TCBB.2007.1069},
doi = {10.1109/TCBB.2007.1069},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/BlinCFRV07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apbc/BelcaidBCCGPV07,
author = {Mahdi Belcaid and
Anne Bergeron and
Annie Chateau and
C{\'{e}}dric Chauve and
Yannick Gingras and
Guylaine Poisson and
M. Vendette},
editor = {David Sankoff and
Lusheng Wang and
Francis Y. L. Chin},
title = {Exploring Genome Rearrangements using Virtual Hybridization},
booktitle = {Proceedings of 5th Asia-Pacific Bioinformatics Conference, {APBC}
2007, 15-17 January 2007, Hong Kong, China},
series = {Advances in Bioinformatics and Computational Biology},
volume = {5},
pages = {205--214},
publisher = {Imperial College Press},
year = {2007},
url = {http://www.comp.nus.edu.sg/\%7Ewongls/psZ/apbc2007/apbc217a.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/apbc/BelcaidBCCGPV07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ChauveDE07,
author = {C{\'{e}}dric Chauve and
Jean{-}Philippe Doyon and
Nadia El{-}Mabrouk},
editor = {Glenn Tesler and
Dannie Durand},
title = {Inferring a Duplication, Speciation and Loss History from a Gene Tree
(Extended Abstract)},
booktitle = {Comparative Genomics, {RECOMB} 2007 International Workshop, {RECOMB-CG}
2007, San Diego, CA, USA, September 16-18, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4751},
pages = {45--57},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-74960-8\_4},
doi = {10.1007/978-3-540-74960-8\_4},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ChauveDE07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccS/ChauveFRV06,
author = {C{\'{e}}dric Chauve and
Guillaume Fertin and
Romeo Rizzi and
St{\'{e}}phane Vialette},
editor = {Vassil N. Alexandrov and
G. Dick van Albada and
Peter M. A. Sloot and
Jack J. Dongarra},
title = {Genomes Containing Duplicates Are Hard to Compare},
booktitle = {Computational Science - {ICCS} 2006, 6th International Conference,
Reading, UK, May 28-31, 2006, Proceedings, Part {II}},
series = {Lecture Notes in Computer Science},
volume = {3992},
pages = {783--790},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11758525\_105},
doi = {10.1007/11758525\_105},
timestamp = {Tue, 14 May 2019 10:00:48 +0200},
biburl = {https://dblp.org/rec/conf/iccS/ChauveFRV06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/BlinCCG06,
author = {Guillaume Blin and
Annie Chateau and
C{\'{e}}dric Chauve and
Yannick Gingras},
editor = {Guillaume Bourque and
Nadia El{-}Mabrouk},
title = {Inferring Positional Homologs with Common Intervals of Sequences},
booktitle = {Comparative Genomics, {RECOMB} 2006 International Workshop, {RCG}
2006, Montreal, Canada, September 24-26, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4205},
pages = {24--38},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11864127\_3},
doi = {10.1007/11864127\_3},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/BlinCCG06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/esa/BergeronCMR05,
author = {Anne Bergeron and
C{\'{e}}dric Chauve and
Fabien de Montgolfier and
Mathieu Raffinot},
editor = {Gerth St{\o}lting Brodal and
Stefano Leonardi},
title = {Computing Common Intervals of \emph{K} Permutations, with Applications
to Modular Decomposition of Graphs},
booktitle = {Algorithms - {ESA} 2005, 13th Annual European Symposium, Palma de
Mallorca, Spain, October 3-6, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3669},
pages = {779--790},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11561071\_69},
doi = {10.1007/11561071\_69},
timestamp = {Tue, 27 Dec 2022 09:06:31 +0100},
biburl = {https://dblp.org/rec/conf/esa/BergeronCMR05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/BlinCF05,
author = {Guillaume Blin and
C{\'{e}}dric Chauve and
Guillaume Fertin},
editor = {Aoife McLysaght and
Daniel H. Huson},
title = {Genes Order and Phylogenetic Reconstruction: Application to \emph{gamma}-Proteobacteria},
booktitle = {Comparative Genomics, {RECOMB} 2005 International Workshop, {RCG}
2005, Dublin, Ireland, September 18-20, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3678},
pages = {11--20},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11554714\_2},
doi = {10.1007/11554714\_2},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/BlinCF05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/spire/GuignonCH05,
author = {Valentin Guignon and
C{\'{e}}dric Chauve and
Sylvie Hamel},
editor = {Mariano P. Consens and
Gonzalo Navarro},
title = {An Edit Distance Between {RNA} Stem-Loops},
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 = {335--347},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11575832\_38},
doi = {10.1007/11575832\_38},
timestamp = {Wed, 28 Feb 2024 00:16:41 +0100},
biburl = {https://dblp.org/rec/conf/spire/GuignonCH05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/BerardBCP05,
author = {S{\`{e}}verine B{\'{e}}rard and
Anne Bergeron and
C{\'{e}}dric Chauve and
Christophe Paul},
editor = {Rita Casadio and
Gene Myers},
title = {Perfect Sorting by Reversals Is Not Always Difficult},
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 = {228--238},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11557067\_19},
doi = {10.1007/11557067\_19},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/BerardBCP05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/ChauveF04,
author = {C{\'{e}}dric Chauve and
Guillaume Fertin},
title = {On maximal instances for the original syntenic distance},
journal = {Theor. Comput. Sci.},
volume = {326},
number = {1-3},
pages = {29--43},
year = {2004},
url = {https://doi.org/10.1016/j.tcs.2004.05.006},
doi = {10.1016/J.TCS.2004.05.006},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/ChauveF04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/BerardBC04,
author = {S{\`{e}}verine B{\'{e}}rard and
Anne Bergeron and
C{\'{e}}dric Chauve},
editor = {Jens Lagergren},
title = {Conservation of Combinatorial Structures in Evolution Scenarios},
booktitle = {Comparative Genomics, {RECOMB} 2004 International Workshop, {RCG}
2004, Bertinoro, Italy, October 16-19, 2004, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {3388},
pages = {1--14},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-32290-0\_1},
doi = {10.1007/978-3-540-32290-0\_1},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/BerardBC04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/BergeronBCC04,
author = {Anne Bergeron and
Mathieu Blanchette and
Annie Chateau and
C{\'{e}}dric Chauve},
editor = {Inge Jonassen and
Junhyong Kim},
title = {Reconstructing Ancestral Gene Orders Using Conserved Intervals},
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 = {14--25},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-30219-3\_2},
doi = {10.1007/978-3-540-30219-3\_2},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/BergeronBCC04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dmtcs/Chauve03,
author = {C{\'{e}}dric Chauve},
title = {A Bijection Between Planar Constellations and Some Colored Lagrangian
Trees},
journal = {Discret. Math. Theor. Comput. Sci.},
volume = {6},
number = {1},
pages = {13--40},
year = {2003},
url = {https://doi.org/10.46298/dmtcs.340},
doi = {10.46298/DMTCS.340},
timestamp = {Tue, 24 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dmtcs/Chauve03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/BousquetCLL03,
author = {Michel Bousquet and
C{\'{e}}dric Chauve and
Gilbert Labelle and
Pierre Leroux},
title = {Two bijective proofs for the arborescent form of the Good-Lagrange
formula and some applications to colored rooted trees and cacti},
journal = {Theor. Comput. Sci.},
volume = {307},
number = {2},
pages = {277--302},
year = {2003},
url = {https://doi.org/10.1016/S0304-3975(03)00220-2},
doi = {10.1016/S0304-3975(03)00220-2},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/BousquetCLL03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dm/ChauveD02,
author = {C{\'{e}}dric Chauve and
Serge Dulucq},
title = {A geometric version of the Robinson-Schensted correspondence for skew
oscillating tableaux},
journal = {Discret. Math.},
volume = {246},
number = {1-3},
pages = {67--81},
year = {2002},
url = {https://doi.org/10.1016/S0012-365X(01)00252-7},
doi = {10.1016/S0012-365X(01)00252-7},
timestamp = {Fri, 12 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dm/ChauveD02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/Chauve02,
author = {C{\'{e}}dric Chauve},
title = {Tree pattern matching with a more general notion of occurrence of
the pattern},
journal = {Inf. Process. Lett.},
volume = {82},
number = {4},
pages = {197--201},
year = {2002},
url = {https://doi.org/10.1016/S0020-0190(01)00270-8},
doi = {10.1016/S0020-0190(01)00270-8},
timestamp = {Fri, 26 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/Chauve02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/spire/Chauve02,
author = {C{\'{e}}dric Chauve},
editor = {Alberto H. F. Laender and
Arlindo L. Oliveira},
title = {Tree Pattern Matching for Linear Static Terms},
booktitle = {String Processing and Information Retrieval, 9th International Symposium,
{SPIRE} 2002, Lisbon, Portugal, September 11-13, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2476},
pages = {160--169},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45735-6\_15},
doi = {10.1007/3-540-45735-6\_15},
timestamp = {Mon, 26 Jun 2023 20:44:05 +0200},
biburl = {https://dblp.org/rec/conf/spire/Chauve02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jct/ChauveDR01,
author = {C{\'{e}}dric Chauve and
Serge Dulucq and
Andrew Rechnitzer},
title = {Enumerating Alternating Trees},
journal = {J. Comb. Theory, Ser. {A}},
volume = {94},
number = {1},
pages = {142--151},
year = {2001},
url = {https://doi.org/10.1006/jcta.2000.3121},
doi = {10.1006/JCTA.2000.3121},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jct/ChauveDR01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@phdthesis{DBLP:phd/hal/Chauve00,
author = {C{\'{e}}dric Chauve},
title = {Structures arborescentes : probl{\`{e}}mes algorithmiques et combinatoires.
(Tree-like structures: algorithmics and combinatorial problems)},
school = {University of Bordeaux, France},
year = {2000},
url = {https://tel.archives-ouvertes.fr/tel-00007388},
timestamp = {Tue, 21 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/phd/hal/Chauve00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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