Helene Touzet

Documents

Publications

	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
	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⟩ Article dans une revue hal-03174571v1
	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⟩ Article dans une revue hal-03107529v2
	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⟩ 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-Beghdadi BioRxiv, 2020, BioRxiv, ⟨10.1101/2020.06.02.131169⟩ Article dans une revue hal-03382208v1
	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⟩ Article dans une revue hal-02403094v1
	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⟩ 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-Croq 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 Lanselle BMC Genomics, 2019, 20 (1), ⟨10.1186/s12864-019-5913-9⟩ Article dans une revue hal-02265367v1
	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⟩ Article dans une revue hal-02394395v1
	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
	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⟩ 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, 2017, 34 (4), pp.585-591. ⟨10.1093/bioinformatics/btx644⟩ Article dans une revue hal-01646297v2
	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⟩ Article dans une revue hal-01575755v1
	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
	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⟩ Article dans une revue hal-00647725v1
	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
	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
	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⟩ 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
	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 hal-00824034v1
	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
	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

	BioacPepFinder: Novel Bioinformatics Tool for the Discovery of Bioactive Peptides from Protein Digestion. Carlos Bathich , Isabelle Guigon , Hélène Touzet , Barbara Deracinois , Laurence Guimas 4th International Conference on Food Bioactives & Health, Sep 2023, Prague, Czech Republic Communication dans un congrès hal-04548237v1
	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
	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 Communication dans un congrès hal-01574630v1
	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
	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
	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
	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.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 Communication dans un congrès hal-00637847v1
	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 Communication dans un congrès 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 Communication dans un congrès 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 Communication dans un congrès hal-00375710v1
	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
	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 inria-00270270v1
	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
	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
	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

	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

	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. 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⟩ 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

	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-Huard [Research Report] CNRS. 2021, pp.1-35 Rapport 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 Touzet [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 inria-00530507v1

	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 Bini 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-Boley 2010 Logiciel hal-02819286v1

Helene Touzet

Publications

Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming

Conservation of the glycogen metabolism pathway underlines a pivotal function of storage polysaccharides in Chlamydiae

TgAP2IX-5 is a key transcriptional regulator of the asexual cell cycle division in Toxoplasma gondii

Genetic basis for virulence differences of various Cryptosporidium parvum carcinogenic isolates

Substitution of nucleotide-sugar by trehalose-dependent glycogen synthesis pathways in Chlamydiales underlines an unusual requirement for storage polysaccharides within obligate intracellular bacteria

Use of whole-genome sequencing in the molecular investigation of care-associated HCoV-OC43 infections in a hematopoietic stem cell transplant unit

A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43

Proteomic characterisation of leech microglia extracellular vesicles (EVs): comparison between differential ultracentrifugation and Optiprep™ density gradient isolation

miRkwood: a tool for the reliable identification of microRNAs in plant genomes

Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data

MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes

DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data

MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes

Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics

Approximate search of short patterns with high error rates using the 01⁎0 lossless seeds

Modeling alternate RNA structures in genomic sequences.

Modeling Dynamic Programming Problems over Sequences and Trees with Inverse Coupled Rewrite Systems

BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms

SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.

RNA Locally Optimal Secondary Structures

RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA.

TFM-Explorer: mining cis-regulatory regions in genomes

Alignments of RNA structures.

Computational identification of protein-coding sequences by comparative analysis

Does hybridization increase evolutionary rate? Data from the 28S-rDNA D8 domain in echinoderms.

MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences.

Efficient and accurate P-value computation for Position Weight Matrices

Decomposition algorithms for the tree edit distance problem

Algorithms with Polynomial Interpretation Termination Proof

BioacPepFinder: Novel Bioinformatics Tool for the Discovery of Bioactive Peptides from Protein Digestion.

Efficient approximations of RNA kinetics landscape using non-redundant sampling

Reconstruction of full-length 16S rRNA sequences for taxonomic assignment in metagenomics

DiNAMO: Exact method for degenerate IUPAC motifs discovery, characterization of sequence-specific errors

On the Levenshtein Automaton and the Size of the Neighborhood of a Word

Finding and analysing microRNAs in plant genomes with miRkwood

Searching for alternate RNA structures in genomic sequences

Lossless seeds for searching short patterns with high error rates

SortMeRNA 2: ribosomal RNA classification for taxonomic assignation

Algebraic Dynamic Programming 2.0

SortMeRNA: a new software to filter total RNA for metatranscriptomic or RNA analysis

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

Biomanycores, open-source parallel code for many-core bioinformatics

Self-Overlapping Occurrences and Knuth-Morris-Pratt Algorithm for Weighted Matching

Benchmarking RNA secondary structure comparison algorithms

How to compare arc-annotated sequences: The alignment hierarchy

Large Scale Matching for Position Weight Matrices

Analysis of tree edit distance algorithms

A complex example of a simplifying rewrite system

Complexity classes and rewrite systems with polynomial interpretation

Encoding the Hydra battle as a rewrite system

String Processing and Information Retrieval

Detecting MicroRNAs in Plant Genomes with miRkwood

Traitement des données - introduction

Deciphering metatranscriptomic data

Comparative analysis of RNA genes: the caRNAc software

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

Rapport de Prospective du Conseil Scientifique de l’Institut des Sciences de l’Information et leurs Interactions (INS2I)

CG-seq: a toolbox for automatic annotation of genomes by comparative analysis

TnSeek

Porechop_ABI

Mirkwood

MATAM

RNAspace