Helene Touzet

Publications

Article dans une revue (35)

Simultaneous Taxonomic and Sex Identification of Bos and Bison Teeth Using Low-Invasive High-Resolution Mass Spectrometry Fabrice Bray,Marie-Anne Julien,Louis Delegue,Stéphanie Flament,Hélène Touzetet al. Journal of Proteome Research, 2025, 24 (7), pp.3625-3641. ⟨10.1021/acs.jproteome.5c00219⟩ Article dans une revue hal-05169280v1
Simultaneous taxonomic and sex identification of Bos and Bison teeth using low-invasive high-resolution mass spectrometry Fabrice Bray,Marie-Anne Julien,Louis Delegue,Stéphanie Flament,Hélène Touzetet al. Journal of Proteome Research, In press Article dans une revue hal-05107804v1
PAMPA: A Software for Peptide Markers and Taxonomic Identification for ZooMS Samples in Archaeology and Paleontology Fabrice Bray,Hélène Touzet Journal of Proteome Research, 2025, 24 (10), pp.5011-5025. ⟨10.1021/acs.jproteome.5c00389⟩ Article dans une revue hal-05476548v1
Automated evaluation of multiple sequence alignment methods to handle third generation sequencing errors Coralie Rohmer,Hélène Touzet,Antoine Limasset PeerJ, 2024, 12, pp.e17731. ⟨10.7717/peerj.17731⟩ Article dans une revue hal-04798144v1
Fascin-1 expression is associated with neuroendocrine prostate cancer and directly suppressed by androgen receptor Anthony Turpin,Carine Delliaux,Pauline Parent,Hortense Chevalier,Carmen Escudero-Iriarteet al. British Journal of Cancer, 2023, 129 (12), pp.1903-1914. ⟨10.1038/s41416-023-02449-x⟩ Article dans une revue hal-04774153v1
Décoder le génome : vers la compréhension du fonctionnement du SARS-CoV-2 Hélène Touzet,Mikaël Salson,Claire Lemaitre Interstices, 2022 Article dans une revue hal-03750389v1
Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming Quentin Bonenfant,Laurent Noé,Hélène Touzet Bioinformatics Advances, 2022, 3 (1), pp.vbac085. ⟨10.1093/bioadv/vbac085⟩ Article dans une revue hal-03932719v1
TgAP2IX-5 is a key transcriptional regulator of the asexual cell cycle division in Toxoplasma gondii Asma S. Khelifa,Cecilia Guillen Sanchez,Kevin M. Lesage,Ludovic Huot,Thomas Mouveauxet al. Nature Communications, 2021, 12, pp.116. ⟨10.1038/s41467-020-20216-x⟩ Article dans une revue hal-03107529v2
Conservation of the glycogen metabolism pathway underlines a pivotal function of storage polysaccharides in Chlamydiae Matthieu Colpaert,Derifa Kadouche,Mathieu Ducatez,Trestan Pillonel,Carole Kebbi-Beghdadiet al. Communications Biology, 2021, 4 (1), ⟨10.1038/s42003-021-01794-y⟩ Article dans une revue hal-03174571v1
Use of whole-genome sequencing in the molecular investigation of care-associated HCoV-OC43 infections in a hematopoietic stem cell transplant unit Delphine Beury,Léa Fléchon,Florence Maurier,Ségolène Caboche,Jean-Stéphane Varréet al. Journal of Clinical Virology, 2020, 122, pp.104206. ⟨10.1016/j.jcv.2019.104206⟩ Article dans une revue hal-02403094v1
Genetic basis for virulence differences of various Cryptosporidium parvum carcinogenic isolates Christophe Audebert,Franck Bonardi,Ségolène Caboche,Karine Guyot,Hélène Touzetet al. Scientific Reports, 2020, 10 (1), pp.7316. ⟨10.1038/s41598-020-64370-0⟩ Article dans une revue inserm-02873228v1
Substitution of nucleotide-sugar by trehalose-dependent glycogen synthesis pathways in Chlamydiales underlines an unusual requirement for storage polysaccharides within obligate intracellular bacteria Matthieu Colpaert,Derifa Kadouche,Mathieu Ducatez,Trestan Pillonel,Carole Kebbi-Beghdadiet al. BioRxiv, 2020, BioRxiv, ⟨10.1101/2020.06.02.131169⟩ Article dans une revue hal-03382208v1
Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data Leandro Lima,Camille Marchet,Ségolène Caboche,Corinne da Silva,Benjamin Istaceet al. Briefings in Bioinformatics, 2019, 21 (4), pp.1-18. ⟨10.1093/bib/bbz058⟩ Article dans une revue hal-02394395v1
A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43 Florence Maurier,Delphine Beury,Léa Fléchon,Jean-Stéphane Varré,Hélène Touzetet al. Virology, 2019, 531, pp.141-148. ⟨10.1016/j.virol.2019.03.006⟩ Article dans une revue hal-02167880v1
Proteomic characterisation of leech microglia extracellular vesicles (EVs): comparison between differential ultracentrifugation and Optiprep™ density gradient isolation T Arab,A Raffo-Romero,C van Camp,Q Lemaire,F Le Marrec-Croqet al. Journal of Extracellular Vesicles, 2019, 8 (1), pp.1603048. ⟨10.1080/20013078.2019.1603048⟩ Article dans une revue inserm-02941660v1
miRkwood: a tool for the reliable identification of microRNAs in plant genomes Isabelle Guigon,Sylvain Legrand,Jean-Frédéric Berthelot,Sébastien Bini,Delphine Lanselleet al. BMC Genomics, 2019, 20 (1), ⟨10.1186/s12864-019-5913-9⟩ Article dans une revue hal-02265367v1
DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data Chadi Saad,Laurent Noé,Hugues Richard,Julie Leclerc,Marie-Pierre Buisineet al. BMC Bioinformatics, 2018, 19 (1), pp.223. ⟨10.1186/s12859-018-2215-1⟩ Article dans une revue hal-01881466v1
MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes Pierre Pericard,Yoann Dufresne,Loïc Couderc,Samuel Blanquart,Hélène Touzet Bioinformatics, 2018, 34 (4), pp.585-591. ⟨10.1093/bioinformatics/btx644⟩ Article dans une revue pasteur-03263400v1
Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics Léa Siegwald,Hélène Touzet,Yves Lemoine,David Hot,Christophe Audebertet al. PLoS ONE, 2017, 12 (1), pp.e0169563. ⟨10.1371/journal.pone.0169563⟩ Article dans une revue hal-01575755v1
MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes Pierre Pericard,Yoann Dufresne,Loïc Couderc,Samuel Blanquart,Hélène Touzet Bioinformatics, 2017, 34 (4), pp.585-591. ⟨10.1093/bioinformatics/btx644⟩ Article dans une revue hal-01646297v2
Approximate search of short patterns with high error rates using the 01⁎0 lossless seeds Christophe Vroland,Mikael Salson,Sébastien Bini,Hélène Touzet Journal of Discrete Algorithms, 2016, 37, pp.3-16. ⟨10.1016/j.jda.2016.03.002⟩ Article dans une revue hal-01360485v1
Modeling alternate RNA structures in genomic sequences. Azadeh Saffarian,Mathieu Giraud,Hélène Touzet Journal of Computational Biology, 2015, 22 (3), pp.190-204 Article dans une revue hal-01228130v1
Modeling Dynamic Programming Problems over Sequences and Trees with Inverse Coupled Rewrite Systems Robert Giegerich,Hélène Touzet Algorithms, 2014, 7, pp.62 - 144. ⟨10.3390/a7010062⟩ Article dans une revue hal-01084318v1
RNA Locally Optimal Secondary Structures Azadeh Saffarian,Mathieu Giraud,Antoine de Monte,Hélène Touzet Journal of Computational Biology, 2012, 19 (10), pp.1120-1133. ⟨10.1089/cmb.2010.0178⟩ Article dans une revue hal-00756249v1
SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data. Evguenia Kopylova,Laurent Noé,Héléne Touzet Bioinformatics, 2012, 28 (24), pp.3211-3217. ⟨10.1093/bioinformatics/bts611⟩ Article dans une revue hal-00748990v1
BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms Julien Allali,Cédric Saule,Cedric Chauve,Yves d'Aubenton-Carafa,Alain Deniseet al. Advances in Bioinformatics, 2012, 2012, pp.1-5. ⟨10.1155/2012/893048⟩ Article dans une revue hal-00647725v1
RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA. Marie-Josée Cros,Antoine de Monte,Jérôme J. Mariette,Philippe Bardou,Benjamin Grenier-Boleyet al. RNA, 2011, 17 (11), pp.1947-56. ⟨10.1261/rna.2844911⟩ Article dans une revue hal-00639174v1
TFM-Explorer: mining cis-regulatory regions in genomes Tonon Laurie,Hélène Touzet,Jean-Stéphane Varré Nucleic Acids Research, 2010, 38 (S2), pp.W286-W292. ⟨10.1093/nar/gkq473⟩ Article dans une revue hal-00823465v1
Alignments of RNA structures. Guillaume Blin,Alain Denise,Serge Dulucq,Claire Herrbach,Helene Touzet IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2010, 7 (2), pp.309-322. ⟨10.1109/TCBB.2008.28⟩ Article dans une revue hal-00506348v1
Computational identification of protein-coding sequences by comparative analysis Arnaud Fontaine,Hélène Touzet International Journal of Data Mining and Bioinformatics, 2009, 3 (2), pp.160-76. ⟨10.1504/ijdmb.2009.024849⟩ Article dans une revue hal-00823601v1
MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences. Arnaud Fontaine,Antoine de Monte,Hélène Touzet Nucleic Acids Research, 2008, 36 (Web Server issue), pp.W14-8. ⟨10.1093/nar/gkn321⟩ Article dans une revue hal-00823594v1
Does hybridization increase evolutionary rate? Data from the 28S-rDNA D8 domain in echinoderms. Anne Chenuil,Emilie Egea,Caroline Rocher,Hélène Touzet,Jean-Pierre Féral Journal of Molecular Evolution, 2008, 67 (5), pp.539-50. ⟨10.1007/s00239-008-9171-8⟩ Article dans une revue istex hal-00824034v1
Efficient and accurate P-value computation for Position Weight Matrices Helene Touzet,Jean-Stéphane Varré Algorithms for Molecular Biology, 2007, 2 (15), pp.1-12. ⟨10.1186/1748-7188-2-15⟩ Article dans une revue inria-00270263v1
Decomposition algorithms for the tree edit distance problem Serge Dulucq,Hélène Touzet Journal of Discrete Algorithms, 2005, pp.448-471 Article dans une revue hal-00307523v1
Algorithms with Polynomial Interpretation Termination Proof Guillaume Bonfante,Adam Cichon,Jean-Yves Marion,Helene Touzet Journal of Functional Programming, 2001, 11 (1), pp.33-53 Article dans une revue inria-00100819v1

Communication dans un congrès (21)

BioacPepFinder: Novel Bioinformatics Tool for the Discovery of Bioactive Peptides from Protein Digestion. Carlos Bathich,Isabelle Guigon,Hélène Touzet,Barbara Deracinois,Laurence Guimaset al. 4th International Conference on Food Bioactives & Health, Sep 2023, Prague, Czech Republic Communication dans un congrès hal-04548237v1
DiNAMO: Exact method for degenerate IUPAC motifs discovery, characterization of sequence-specific errors Chadi Saad,Laurent Noé,Hugues Richard,Julie Leclerc,Marie-Pierre Buisineet al. JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France Communication dans un congrès hal-01574630v1
Efficient approximations of RNA kinetics landscape using non-redundant sampling Juraj Michálik,Hélène Touzet,Yann Ponty ISMB/ECCB - 25th Annual international conference on Intelligent Systems for Molecular Biology/16th European Conference on Computational Biology - 2017, Jul 2017, Prague, Czech Republic. pp.i283 - i292, ⟨10.1093/bioinformatics/btx269⟩ Communication dans un congrès hal-01500115v1
Reconstruction of full-length 16S rRNA sequences for taxonomic assignment in metagenomics Pierre Pericard,Yoann Dufresne,Samuel Blanquart,Hélène Touzet JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France Communication dans un congrès hal-01574629v1
On the Levenshtein Automaton and the Size of the Neighborhood of a Word Hélène Touzet LATA 2016 - 10th International Conference on Language and Automata Theory and Applications, Mar 2016, Prague, Czech Republic. pp.207-218, ⟨10.1007/978-3-319-30000-9_16⟩ Communication dans un congrès hal-01360482v1
Finding and analysing microRNAs in plant genomes with miRkwood Isabelle Guigon,Sylvain Legrand,Jean-Frédéric Berthelot,Mohcen Benmounah,Helene Touzet JOBIM 2015, Jul 2015, Clermont-Ferrand, France Communication dans un congrès hal-01247604v1
SortMeRNA 2: ribosomal RNA classification for taxonomic assignation Evguenia Kopylova,Laurent Noé,Pierre Pericard,Mikaël Salson,Hélène Touzet Workshop on Recent Computational Advances in Metagenomics, ECCB 2014, Sep 2014, Strasbourg, France Communication dans un congrès hal-01094011v1
Searching for alternate RNA structures in genomic sequences Azadeh Saffarian,Mathieu Giraud,Hélène Touzet Computational Methods for Structural RNAs, CMSR'14, Sep 2014, Strasbourg, France. pp.13-24, ⟨10.15455/CMSR.2014.0002⟩ Communication dans un congrès hal-01084319v1
Lossless seeds for searching short patterns with high error rates Christophe Vroland,Mikaël Salson,Hélène Touzet International Workshop On Combinatorial Algorithms, Oct 2014, Duluth, United States Communication dans un congrès hal-01079840v1
Algebraic Dynamic Programming 2.0 Robert Giegerich,Hélène Touzet Workshop Haskell-Treffen an der Universität Leipzig, Jun 2013, Leipzig, Germany Communication dans un congrès hal-00857801v1
SortMeRNA: a new software to filter total RNA for metatranscriptomic or RNA analysis Evguenia Kopylova,Laurent Noé,Helene Touzet JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2012, Jul 2012, Rennes, France Communication dans un congrès hal-00763792v1
Biomanycores, open-source parallel code for many-core bioinformatics Mathieu Giraud,Stéphane Janot,Jean-Frédéric Berthelot,Charles Deltel,Laetitia Jourdanet al. Bioinformatics Open Source Conference (BOSC 2011), 2011, Vienne, Austria Communication dans un congrès inria-00623390v1
biomanycores.org: a repository of interoperable open-source code for many-core bioinformatics Jean-Frédéric Berthelot,Charles Deltel,Mathieu Giraud,Stéphane Janot,Laetitia Jourdanet al. JOBIM 2011, Jul 2011, Paris, France Communication dans un congrès hal-00637847v1
Self-Overlapping Occurrences and Knuth-Morris-Pratt Algorithm for Weighted Matching Aude Liefooghe,Helene Touzet,Jean-Stéphane Varré 3rd International Conference on Language and Automata Theory and Applications, Apr 2009, Tarragona, Spain. pp.481-492 Communication dans un congrès inria-00365411v1
Benchmarking RNA secondary structure comparison algorithms Julien Allali,Yves d'Aubenton-Carafa,Cedric Chauve,Alain Denise,Christine Drevetet al. JOBIM'08, 2008, Lille, France. pp.67-68 Communication dans un congrès hal-00375710v1
Large Scale Matching for Position Weight Matrices Aude Liefooghe,Helene Touzet,Jean-Stéphane Varré Combinatorial Pattern Matching, Jul 2006, Barcelona, Spain. pp.401-412, ⟨10.1007/11780441_36⟩ Communication dans un congrès istex inria-00270270v1
How to compare arc-annotated sequences: The alignment hierarchy Guillaume Blin,Helene Touzet 13th String Processing and Information Retrieval, Oct 2006, Glasgow, United Kingdom. pp.291-303 Communication dans un congrès inria-00178671v1
Analysis of tree edit distance algorithms Serge Dulucq,Hélène Touzet Combinatorial pattern matching, 14th Annual Symposium, CPM 2003, 2003, Germany. pp.83--95 Communication dans un congrès hal-00307516v1
Encoding the Hydra battle as a rewrite system Hélène Touzet International Symposium on the Mathematical Foundations of Computer Science - MFCS'98, Aug 1998, Brno, Czech Republic, pp.267-276 Communication dans un congrès inria-00098575v1
A complex example of a simplifying rewrite system Hélène Touzet International Colloquium on Automata, Languages, and Programming - ICALP'98, Jul 1998, Aalborg, Denmark, pp.507-517 Communication dans un congrès inria-00098574v1
Complexity classes and rewrite systems with polynomial interpretation Guillaume Bonfante,Adam Cichon,Jean-Yves Marion,Hélène Touzet CSl'98, 1998, Brno, République Tchèque, pp.372-384 Communication dans un congrès inria-00098689v1

Ouvrages (1)

String Processing and Information Retrieval Thierry Lecroq,Hélène Touzet Springer International Publishing, 12944, 2021, Lecture Notes in Computer Science, ⟨10.1007/978-3-030-86692-1⟩ Ouvrages hal-03368750v1

Chapitre d'ouvrage (4)

Detecting MicroRNAs in Plant Genomes with miRkwood Sylvain Legrand,Isabelle Guigon,Hélène Touzet Alejandro Pereira-Santana; Samuel David Gamboa-Tuz; Luis Carlos Rodríguez-Zapata. Plant Comparative Genomics, 2512, Springer; Humana, pp.103-120, 2022, Methods in Molecular Biology, 978-1-0716-2428-9. ⟨10.1007/978-1-0716-2429-6_8⟩ Chapitre d'ouvrage hal-03952910v1
Traitement des données - introduction Iovka Boneva,Héléne Touzet Les Big Data à découvert, 2016 Chapitre d'ouvrage hal-01574692v1
Deciphering metatranscriptomic data Evguenia Kopylova,Laurent Noé,Corinne da Silva,Jean-Frédéric Berthelot,Adriana A. Albertiet al. Methods in Molecular Biology, 1269, Springer, pp.279-291, 2015, RNA Bioinformatics, 978-1-4939-2290-1. ⟨10.1007/978-1-4939-2291-8_17⟩ Chapitre d'ouvrage hal-01104015v1
Comparative analysis of RNA genes: the caRNAc software Helene Touzet Nicholas Bergman. Comparative Genomics, Volume 1, Humana Press, 2007, Methods in Molecular Biology, 978-1-58829-693-1 Chapitre d'ouvrage inria-00178557v1

Rapport (3)

SARS-CoV-2 Through the Lens of Computational Biology: How bioinformatics is playing a key role in the study of the virus and its origins Samuel Alizon,Frédéric Cazals,Stéphane Guindon,Claire Lemaitre,Tristan Mary-Huardet al. [Research Report] CNRS. 2021, pp.1-35 Rapport (rapport de recherche) hal-03170023v1
Rapport de Prospective du Conseil Scientifique de l’Institut des Sciences de l’Information et leurs Interactions (INS2I) Christian Barillot,Inbar Fijalkow,Isabelle Queinnec,Fabrice Theoleyre,Hélène Touzetet al. [0] CNRS. 2018, pp.1-87 Rapport hal-01956087v1
CG-seq: a toolbox for automatic annotation of genomes by comparative analysis Benjamin Grenier-Boley,Antoine de Monte,Helene Touzet [Research Report] RR-7428, INRIA. 2010, pp.12 Rapport (rapport de recherche) inria-00530507v1

Logiciel (5)

TnSeek Hélène Touzet,Areski Flissi,Loïc Couderc 2022, ⟨swh:1:dir:5a4d461bfa0edddb5f36eda76bbc1eb93b32f26e;origin=https://hal.archives-ouvertes.fr/hal-04441970;visit=swh:1:snp:dccee2e5c5a988bcc927a55dd922c7ba6eca4a46;anchor=swh:1:rel:a832b435ac7524297ea6f2105444ca86e82f22db;path=/⟩ Logiciel hal-04441970v1
Porechop_ABI Quentin Bonenfant,Laurent Noé,Hélène Touzet 2020, ⟨swh:1:dir:0f3941e6a5eff88655189dc1879650a85ecb22c0;origin=https://github.com/bonsai-team/Porechop_ABI;visit=swh:1:snp:5b8452d627bc6b045f99ba265dc36877edb019ea;anchor=swh:1:rev:0bc9f17f31d4ec1dcbab4796871cc09324cc143b⟩ Logiciel hal-04490240v1
Mirkwood Hélène Touzet,Sylvain Legrand,Isabelle Guigon,Mohcen Benmounah,Sébastien Biniet al. 2019 Logiciel hal-04454133v1
MATAM Hélène Touzet,Pierre Pericard,Samuel Blanquart 2018, ⟨swh:1:dir:ad4b9d5ee4ecd6c901731a7e4f79b5481e949f01;origin=https://hal.archives-ouvertes.fr/hal-04454135;visit=swh:1:snp:6f8708c1b9e9a23cdc168fb6d796ff3805d768de;anchor=swh:1:rel:29d4e0794204463094dedf0d0d7c08835360e787;path=/⟩ Logiciel hal-04454135v1
RNAspace Marie-Josée Cros,Antoine de Monte,Jérôme J. Mariette,Philippe Bardou,Benjamin Grenier-Boleyet al. 2010 Logiciel hal-02819286v1