Bastien Cazaux

Présentation

Publications

Article dans une revue (11)

dipwmsearch: a python package for searching di-PWM motifs Marie Mille,Julie Ripoll,Bastien Cazaux,Eric Rivals Bioinformatics, 2023, 39 (4), pp.btad141. ⟨10.1093/bioinformatics/btad141⟩ Article dans une revue lirmm-03834008v1
Finding all maximal perfect haplotype blocks in linear time Jarno N Alanko,Hideo Bannai,Bastien Cazaux,Pierre Peterlongo,Jens Stoye Algorithms for Molecular Biology, 2020, pp.1-9. ⟨10.1186/s13015-020-0163-6⟩ Article dans une revue hal-02187246v1
Hierarchical Overlap Graph Bastien Cazaux,Eric Rivals Information Processing Letters, 2020, 155, pp.#105862. ⟨10.1016/j.ipl.2019.105862⟩ Article dans une revue lirmm-01674319v2
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⟩ Article dans une revue lirmm-01980994v1
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⟩ Article dans une revue lirmm-01617207v1
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⟩ Article dans une revue lirmm-01800340v1
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⟩ Article dans une revue lirmm-01525995v1
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⟩ Article dans une revue lirmm-01286943v1
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⟩ Article dans une revue hal-01349636v1
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 Rivalset al. GigaScience, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩ Article dans une revue hal-01280238v1
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⟩ Article dans une revue lirmm-01082098v1

Communication dans un congrès (11)

Toward Optimal Fingerprint Indexing for Large Scale Genomics Clément Agret,Bastien Cazaux,Antoine Limasset WABI 2022 - 22nd International Workshop on Algorithms in Bioinformatics, Sep 2022, Postdam, Germany. pp.25:1-25:15, ⟨10.4230/LIPIcs.WABI.2022.25⟩ Communication dans un congrès hal-04121819v1
A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs Sangsoo Park,Sung Gwan Park,Bastien Cazaux,Kunsoo Park,Eric Rivals 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⟩ Communication dans un congrès lirmm-03431830v1
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⟩ Communication dans un congrès lirmm-03014336v1
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⟩ Communication dans un congrès lirmm-02382066v1
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⟩ Communication dans un congrès lirmm-01929399v1
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⟩ Communication dans un congrès lirmm-01843225v1
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⟩ Communication dans un congrès lirmm-01314330v1
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⟩ Communication dans un congrès lirmm-01446428v1
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⟩ Communication dans un congrès hal-01955978v1
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⟩ Communication dans un congrès lirmm-01081429v1
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 Communication dans un congrès lirmm-01100683v1

Poster de conférence (3)

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 Poster de conférence lirmm-03442434v1
AquaPony: Visualization and interpretation of phylogeographic information on phylogenetic trees Bastien Cazaux,Guillaume G. Castel,Eric Rivals JOBIM 2018 - 19es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France. , 2018 Poster de conférence hal-02733925v1
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 Madrièreset al. 20èmes Journées Francophones de Virologie, Mar 2018, Paris, France. 2018 Poster de conférence hal-02789410v1

Pré-publication, Document de travail (2)

Greedy-reduction from Shortest Linear Superstring to Shortest Circular Superstring Bastien Cazaux,Eric Rivals 2021 Pré-publication, Document de travail lirmm-03442437v1
AQUAPONY: visualization and interpretation of phylogeographic information on phylogenetic trees Bastien Cazaux,Guillaume Castel,Eric Rivals 2018 Pré-publication, Document de travail lirmm-01702654v3

Rapport (4)

A linear time algorithm for Shortest Cyclic Cover of Strings Bastien Cazaux,Eric Rivals [Research Report] IBC; LIRMM. 2015 Rapport (rapport de recherche) lirmm-01240278v1
From Indexing Data Structures to de Bruijn Graphs Bastien Cazaux,Thierry Lecroq,Eric Rivals [Research Report] RR-14004, LIRMM. 2014 Rapport (rapport de recherche) lirmm-00950983v2
3-Shortest Superstring is 2-approximable by a greedy algorithm Bastien Cazaux,Eric Rivals [Research Report] RR-14009, LIRMM. 2014 Rapport (rapport de recherche) lirmm-01070596v1
Approximation of greedy algorithms for Max-ATSP, Maximal Compression, and Shortest Cyclic Cover of Strings Bastien Cazaux,Eric Rivals RR-14001, 2013, pp.12 Rapport lirmm-00932660v1

Thèse (1)

Approximation de superchaîne, indexation et assemblage de génome Bastien Cazaux Autre [cs.OH]. Université Montpellier, 2016. Français. ⟨NNT : 2016MONTT307⟩ Thèse tel-01816974v1