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Bastien Cazaux

31
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Finding all maximal perfect haplotype blocks in linear time

Jarno N Alanko , Hideo Bannai , Bastien Cazaux , Pierre Peterlongo , Jens Stoye et al.
Algorithms for Molecular Biology, 2020, pp.1-9. ⟨10.1186/s13015-020-0163-6⟩
Journal articles hal-02187246v1
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Hierarchical Overlap Graph

Bastien Cazaux , Eric Rivals
Information Processing Letters, 2020, 155, pp.#105862. ⟨10.1016/j.ipl.2019.105862⟩
Journal articles lirmm-01674319v2
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Linking indexing data structures to de Bruijn graphs: Construction and update

Bastien Cazaux , Thierry Lecroq , Eric Rivals
Journal of Computer and System Sciences, 2019, 104, pp.165-183. ⟨10.1016/j.jcss.2016.06.008⟩
Journal articles lirmm-01617207v1
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AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees

Bastien Cazaux , Guillaume Castel , Eric Rivals
Bioinformatics, 2019, 35 (17), pp.3163-3165. ⟨10.1093/bioinformatics/btz011⟩
Journal articles lirmm-01980994v1
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Relationship between superstring and compression measures: New insights on the greedy conjecture

Bastien Cazaux , Eric Rivals
Discrete Applied Mathematics, 2018, 245, pp.59-64. ⟨10.1016/j.dam.2017.04.017⟩
Journal articles lirmm-01800340v1

The power of greedy algorithms for approximating Max-ATSP, Cyclic Cover, and superstrings

Bastien Cazaux , Eric Rivals
Discrete Applied Mathematics, 2016, 212, pp.48-60. ⟨10.1016/j.dam.2015.06.003⟩
Journal articles lirmm-01286943v1
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Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Yvan Le Bras , Olivier Collin , Cyril Monjeaud , Vincent Lacroix , Eric Rivals et al.
GigaScience, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩
Journal articles hal-01280238v1
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Read mapping on de Bruijn graphs

Antoine Limasset , Bastien Cazaux , Eric Rivals , Pierre Peterlongo
BMC Bioinformatics, 2016, 17 (1), ⟨10.1186/s12859-016-1103-9⟩
Journal articles hal-01349636v1
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A linear time algorithm for Shortest Cyclic Cover of Strings

Bastien Cazaux , Eric Rivals
Journal of Discrete Algorithms, 2016, 37, pp.56-67. ⟨10.1016/j.jda.2016.05.001⟩
Journal articles lirmm-01525995v1
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Reverse engineering of compact suffix trees and links: A novel algorithm

Bastien Cazaux , Eric Rivals
Journal of Discrete Algorithms, 2014, StringMasters 2012 & 2013 Special Issue (Volume 1), 28, pp.9-22. ⟨10.1016/j.jda.2014.07.002⟩
Journal articles lirmm-01082098v1
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A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs

Sangsoo Park , Sung Gwan Park , Bastien Cazaux , Kunsoo Park , Eric Rivals et al.
CPM 2021 - 32nd Annual Symposium on Combinatorial Pattern Matching, Institute of Computer Science of University of Wrocław, Poland., Jul 2021, Wrocław, Poland. pp.22:1--22:9, ⟨10.4230/LIPIcs.CPM.2021.22⟩
Conference papers lirmm-03431830v1
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Efficient Construction of Hierarchical Overlap Graphs

Sung Gwan Park , Bastien Cazaux , Kunsoo Park , Eric Rivals
SPIRE 2020 - 27th International Symposium on String Processing and Information Retrieval, Oct 2020, Orlando, FL, United States. pp.277-290, ⟨10.1007/978-3-030-59212-7_20⟩
Conference papers lirmm-03014336v1
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Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding

Bastien Cazaux , Eric Rivals
CPM 2019 - 30th Annual Symposium on Combinatorial Pattern Matching, University of Pisa, Jun 2019, Pise, Italy. pp.24:1--24:20, ⟨10.4230/LIPIcs.CPM.2019.24⟩
Conference papers lirmm-02382066v1
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Superstrings with multiplicities

Eric Rivals , Bastien Cazaux
29th Annual Symposium on Combinatorial Pattern Matching (CPM), Qingdao University, Jul 2018, Qingdao, China. pp.21:1-21:16, ⟨10.4230/LIPIcs.CPM.2018.21⟩
Conference papers lirmm-01843225v1
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Practical lower and upper bounds for the Shortest Linear Superstring

Bastien Cazaux , Samuel Juhel , Eric Rivals
SEA: Symposium on Experimental Algorithms, Jun 2018, L'Aquilla, Italy. pp.18:1--18:14, ⟨10.4230/LIPIcs.SEA.2018.18⟩
Conference papers lirmm-01929399v1
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Shortest DNA cyclic cover in compressed space

Bastien Cazaux , Rodrigo Cánovas , Eric Rivals
DCC: Data Compression Conference, Mar 2016, Snowbird, UT, United States. pp.536-545, ⟨10.1109/DCC.2016.79⟩
Conference papers lirmm-01314330v1
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Superstring Graph: A New Approach for Genome Assembly

Bastien Cazaux , Gustavo Sacomoto , Eric Rivals
AAIM: Algorithmic Aspects in Information and Management, Università degli Studi di Bergamo, Jul 2016, Bergamo, Italy. pp.39-52, ⟨10.1007/978-3-319-41168-2_4⟩
Conference papers lirmm-01446428v1
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Construction of a de Bruijn Graph for Assembly from a Truncated Suffix Tree

Bastien Cazaux , Thierry Lecroq , Eric Rivals
LATA: Language and Automata Theory and Applications, Mar 2015, Nice, France. pp.109-120, ⟨10.1007/978-3-319-15579-1_8⟩
Conference papers hal-01955978v1
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Approximation of Greedy Algorithms for Max-ATSP, Maximal Compression, Maximal Cycle Cover, and Shortest Cyclic Cover of Strings

Bastien Cazaux , Eric Rivals
PSC: Prague Stringology Conference, Czech Technical University in Prague, Sep 2014, Prague, Czech Republic. pp.148-161
Conference papers lirmm-01100683v1
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From Indexing Data Structures to de Bruijn Graphs

Bastien Cazaux , Thierry Lecroq , Eric Rivals
CPM: Combinatorial Pattern Matching, Moscow State University, Jun 2014, Moscow, Russia. pp.89-99, ⟨10.1007/978-3-319-07566-2_10⟩
Conference papers lirmm-01081429v1
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Search algorithms for dinucleotide Position Weight Matrices

Marie Mille , Julie Ripoll , Bastien Cazaux , Eric Rivals
Société Française de Bioinformatique (S.F.B.I.). Journées Ouvertes en Biologie, Informatique et Mathématiques 2021, Jul 2021, Paris, France. , pp.100, 2021, Actes des Journées Ouvertes en Biologie, Informatique et Mathématiques 2021
Conference poster lirmm-03442434v1
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AquaPony: Visualization and interpretation of phylogeographic information on phylogenetic trees

Bastien Cazaux , Guillaume G. Castel , Eric Rivals
Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2018, Marseilles, France. 2018, Journées Ouvertes en Biologie, Informatique et Mathématiques : JOBIM 2018 Abstracts
Conference poster hal-02733925v1
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Etude de l’évolution de la diversité génétique intrahôte du virus Puumala lors d’infections expérimentales

Caroline Tatard , Maxime Galan , Bastien Cazaux , Adelaïde Dubois , Sarah Madrières et al.
20èmes Journées Francophones de Virologie, Mar 2018, Paris, France. 2018
Conference poster hal-02789410v1