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Helene Touzet

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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⟩
Journal articles hal-03932719v1
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Décoder le génome : vers la compréhension du fonctionnement du SARS-CoV-2

Hélène Touzet , Mikaël Salson , Claire Lemaitre
Interstices, 2022
Journal articles hal-03750389v1
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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-Beghdadi
Communications Biology, 2021, 4 (1), ⟨10.1038/s42003-021-01794-y⟩
Journal articles hal-03174571v1
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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 Mouveaux
Nature Communications, 2021, 12, pp.116. ⟨10.1038/s41467-020-20216-x⟩
Journal articles hal-03107529v2
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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 Varré
Journal of Clinical Virology, 2020, 122, pp.104206. ⟨10.1016/j.jcv.2019.104206⟩
Journal articles hal-02403094v1
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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-Beghdadi
BioRxiv, 2020, BioRxiv, ⟨10.1101/2020.06.02.131169⟩
Journal articles hal-03382208v1
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Genetic basis for virulence differences of various Cryptosporidium parvum carcinogenic isolates

Christophe Audebert , Franck Bonardi , Ségolène Caboche , Karine Guyot , Hélène Touzet
Scientific Reports, 2020, 10 (1), pp.7316. ⟨10.1038/s41598-020-64370-0⟩
Journal articles inserm-02873228v1

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-Croq
Journal of Extracellular Vesicles, 2019, 8 (1), pp.1603048. ⟨10.1080/20013078.2019.1603048⟩
Journal articles inserm-02941660v1
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miRkwood: a tool for the reliable identification of microRNAs in plant genomes

Isabelle Guigon , Sylvain Legrand , Jean-Frédéric Berthelot , Sébastien Bini , Delphine Lanselle
BMC Genomics, 2019, 20 (1), ⟨10.1186/s12864-019-5913-9⟩
Journal articles hal-02265367v1
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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 Touzet
Virology, 2019, 531, pp.141-148. ⟨10.1016/j.virol.2019.03.006⟩
Journal articles hal-02167880v1
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Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data

Leandro Lima , Camille Marchet , Ségolène Caboche , Corinne da Silva , Benjamin Istace
Briefings in Bioinformatics, 2019, pp.1-18. ⟨10.1093/bib/bbz058⟩
Journal articles hal-02394395v1
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DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data

Chadi Saad , Laurent Noé , Hugues Richard , Julie Leclerc , Marie-Pierre Buisine
BMC Bioinformatics, 2018, 19 (1), ⟨10.1186/s12859-018-2215-1⟩
Journal articles 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⟩
Journal articles pasteur-03263400v1
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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⟩
Journal articles hal-01646297v2
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Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics

Léa Siegwald , Hélène Touzet , Yves Lemoine , David Hot , Christophe Audebert
PLoS ONE, 2017, 12 (1), pp.e0169563. ⟨10.1371/journal.pone.0169563⟩
Journal articles hal-01575755v1
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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⟩
Journal articles 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
Journal articles hal-01228130v1
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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⟩
Journal articles hal-01084318v1
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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⟩
Journal articles hal-00756249v1
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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⟩
Journal articles hal-00748990v1
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BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms

Julien Allali , Cédric Saule , Cedric Chauve , Yves d'Aubenton-Carafa , Alain Denise
Advances in Bioinformatics, 2012, 2012, pp.1-5. ⟨10.1155/2012/893048⟩
Journal articles hal-00647725v1
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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-Boley
RNA, 2011, 17 (11), pp.1947-56. ⟨10.1261/rna.2844911⟩
Journal articles hal-00639174v1
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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⟩
Journal articles hal-00506348v1

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⟩
Journal articles hal-00823465v1

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⟩
Journal articles hal-00823601v1

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⟩
Journal articles hal-00824034v1
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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⟩
Journal articles hal-00823594v1
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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⟩
Journal articles inria-00270263v1

Decomposition algorithms for the tree edit distance problem

Serge Dulucq , Hélène Touzet
Journal of Discrete Algorithms, 2005, pp.448-471
Journal articles 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
Journal articles inria-00100819v1
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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⟩
Conference papers hal-01500115v1
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DiNAMO: Exact method for degenerate IUPAC motifs discovery, characterization of sequence-specific errors

Chadi Saad , Laurent Noé , Hugues Richard , Julie Leclerc , Marie-Pierre Buisine
JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France
Conference papers hal-01574630v1
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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
Conference papers hal-01574629v1
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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⟩
Conference papers 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
Conference papers 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
Conference papers hal-01094011v1
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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
Conference papers hal-01079840v1
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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⟩
Conference papers hal-01084319v1
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Algebraic Dynamic Programming 2.0

Robert Giegerich , Hélène Touzet
Workshop Haskell-Treffen an der Universität Leipzig, Jun 2013, Leipzig, Germany
Conference papers 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
Conference papers hal-00763792v1

biomanycores.org: a repository of interoperable open-source code for many-core bioinformatics

Jean-Frédéric Berthelot , Charles Deltel , Mathieu Giraud , Stéphane Janot , Laetitia Jourdan
JOBIM 2011, Jul 2011, Paris, France
Conference papers hal-00637847v1
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Biomanycores, open-source parallel code for many-core bioinformatics

Mathieu Giraud , Stéphane Janot , Jean-Frédéric Berthelot , Charles Deltel , Laetitia Jourdan
Bioinformatics Open Source Conference (BOSC 2011), 2011, Vienne, Austria
Conference papers inria-00623390v1

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
Conference papers inria-00365411v1

Benchmarking RNA secondary structure comparison algorithms

Julien Allali , Yves d'Aubenton-Carafa , Cedric Chauve , Alain Denise , Christine Drevet
JOBIM'08, 2008, Lille, France. pp.67-68
Conference papers 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⟩
Conference papers inria-00270270v1
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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
Conference papers 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
Conference papers hal-00307516v1
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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
Conference papers inria-00098689v1

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
Conference papers inria-00098574v1

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
Conference papers inria-00098575v1

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⟩
Books hal-03368750v1

Detecting MicroRNAs in Plant Genomes with miRkwood

Sylvain Legrand , Isabelle Guigon , Hélène Touzet
Plant Comparative Genomics, 2512, Springer US, pp.103-120, 2022, Methods in Molecular Biology, ⟨10.1007/978-1-0716-2429-6_8⟩
Book sections hal-03829719v1

Traitement des données - introduction

Iovka Boneva , Héléne Touzet
Les Big Data à découvert, 2016
Book sections hal-01574692v1

Deciphering metatranscriptomic data

Evguenia Kopylova , Laurent Noé , Corinne da Silva , Jean-Frédéric Berthelot , Adriana A. Alberti
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⟩
Book sections hal-01104015v1
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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
Book sections inria-00178557v1