Hélène Touzet - Publications

Asma Khelifa, Cecilia Guillen Sanchez, Kevin Lesage, Ludovic Huot, Thomas Mouveaux, et al.. TgAP2IX-5 is a key transcriptional regulator of the asexual cell cycle division in Toxoplasma gondii. Nature Communications, Nature Publishing Group, 2021, 12, pp.116. ⟨10.1038/s41467-020-20216-x⟩. ⟨hal-03107529⟩

Delphine Beury, Léa Fléchon, Florence Maurier, Ségolène Caboche, Jean-Stéphane Varré, et al.. Use of whole-genome sequencing in the molecular investigation of care-associated HCoV-OC43 infections in a hematopoietic stem cell transplant unit. Journal of Clinical Virology, Elsevier, 2020, 122, pp.104206. ⟨10.1016/j.jcv.2019.104206⟩. ⟨hal-02403094⟩

Christophe Audebert, Franck Bonardi, Ségolène Caboche, Karine Guyot, Hélène Touzet, et al.. Genetic basis for virulence differences of various Cryptosporidium parvum carcinogenic isolates. Scientific Reports, Nature Publishing Group, 2020, 10 (1), pp.7316. ⟨10.1038/s41598-020-64370-0⟩. ⟨inserm-02873228⟩

Isabelle Guigon, Sylvain Legrand, Jean-Frédéric Berthelot, Sébastien Bini, Delphine Lanselle, et al.. miRkwood: a tool for the reliable identification of microRNAs in plant genomes. BMC Genomics, BioMed Central, 2019, 20 (1), ⟨10.1186/s12864-019-5913-9⟩. ⟨hal-02265367⟩

Florence Maurier, Delphine Beury, Léa Fléchon, Jean-Stéphane Varré, Hélène Touzet, et al.. A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43. Virology, Elsevier, 2019, 531, pp.141-148. ⟨10.1016/j.virol.2019.03.006⟩. ⟨hal-02167880⟩

Leandro Lima, Camille Marchet, Ségolène Caboche, Corinne da Silva, Benjamin Istace, et al.. Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data. Briefings in Bioinformatics, Oxford University Press (OUP), 2019, pp.1-18. ⟨10.1093/bib/bbz058⟩. ⟨hal-02394395⟩

Chadi Saad, Laurent Noé, Hugues Richard, Julie Leclerc, Marie-Pierre Buisine, et al.. DiNAMO: highly sensitive DNA motif discovery in high-throughput sequencing data. BMC Bioinformatics, BioMed Central, 2018, 19 (1), ⟨10.1186/s12859-018-2215-1⟩. ⟨hal-01881466⟩

Pierre Pericard, Yoann Dufresne, Loïc Couderc, Samuel Blanquart, Hélène Touzet. MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes. Bioinformatics, Oxford University Press (OUP), 2017, 34 (4), pp.585-591. ⟨10.1093/bioinformatics/btx644⟩. ⟨hal-01646297v2⟩

Léa Siegwald, Hélène Touzet, Yves Lemoine, David Hot, Christophe Audebert, et al.. Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics. PLoS ONE, Public Library of Science, 2017, 12 (1), pp.e0169563. ⟨10.1371/journal.pone.0169563⟩. ⟨hal-01575755⟩

Christophe Vroland, Mikael Salson, Sébastien Bini, Hélène Touzet. Approximate search of short patterns with high error rates using the 01⁎0 lossless seeds. Journal of Discrete Algorithms, Elsevier, 2016, 37, pp.3-16. ⟨10.1016/j.jda.2016.03.002⟩. ⟨hal-01360485⟩

Azadeh Saffarian, Mathieu Giraud, Hélène Touzet. Modeling alternate RNA structures in genomic sequences.. Journal of Computational Biology, Mary Ann Liebert, 2015, 22 (3), pp.190-204. ⟨hal-01228130⟩

Robert Giegerich, Hélène Touzet. Modeling Dynamic Programming Problems over Sequences and Trees with Inverse Coupled Rewrite Systems. Algorithms, MDPI, 2014, 7, pp.62 - 144. ⟨10.3390/a7010062⟩. ⟨hal-01084318⟩

Azadeh Saffarian, Mathieu Giraud, Antoine de Monte, Hélène Touzet. RNA Locally Optimal Secondary Structures. Journal of Computational Biology, Mary Ann Liebert, 2012, 19 (10), pp.1120-1133. ⟨10.1089/cmb.2010.0178⟩. ⟨hal-00756249⟩

Julien Allali, Cédric Saule, Cedric Chauve, Yves d'Aubenton-Carafa, Alain Denise, et al.. BRASERO: A resource for benchmarking RNA secondary structure comparison algorithms. Advances in Bioinformatics, Hindawi Publishing Corporation, 2012, 2012, pp.1-5. ⟨10.1155/2012/893048⟩. ⟨hal-00647725⟩

Evguenia Kopylova, Laurent Noé, Héléne Touzet. SortMeRNA: Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.. Bioinformatics, Oxford University Press (OUP), 2012, 28 (24), pp.3211-3217. ⟨10.1093/bioinformatics/bts611⟩. ⟨hal-00748990⟩

Marie-Josée Cros, Antoine de Monte, Mariette Jerome, Philippe Bardou, Benjamin Grenier-Boley, et al.. RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA. RNA, Cold Spring Harbor Laboratory Press, 2011, 17, pp.1947-1956. ⟨10.1261/rna.2844911⟩. ⟨hal-00642716⟩

Marie-Josée Cros, Antoine de Monte, Jérôme Mariette, Philippe Bardou, Benjamin Grenier-Boley, et al.. RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA.. RNA, Cold Spring Harbor Laboratory Press, 2011, 17 (11), pp.1947-56. ⟨10.1261/rna.2844911⟩. ⟨hal-00639174⟩

Tonon Laurie, Hélène Touzet, Jean-Stéphane Varré. TFM-Explorer: mining cis-regulatory regions in genomes. Nucleic Acids Research, Oxford University Press, 2010, 38 (S2), pp.W286-W292. ⟨10.1093/nar/gkq473⟩. ⟨hal-00823465⟩

Guillaume Blin, Alain Denise, Serge Dulucq, Claire Herrbach, Helene Touzet. Alignments of RNA structures.. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2010, 7 (2), pp.309-322. ⟨10.1109/TCBB.2008.28⟩. ⟨hal-00506348⟩

Arnaud Fontaine, Hélène Touzet. Computational identification of protein-coding sequences by comparative analysis.. International Journal of Data Mining and Bioinformatics, Inderscience, 2009, 3 (2), pp.160-76. ⟨hal-00823601⟩

Arnaud Fontaine, Antoine de Monte, Hélène Touzet. MAGNOLIA: multiple alignment of protein-coding and structural RNA sequences.. Nucleic Acids Research, Oxford University Press, 2008, 36 (Web Server issue), pp.W14-8. ⟨10.1093/nar/gkn321⟩. ⟨hal-00823594⟩

Anne Chenuil, Emilie Egea, Caroline Rocher, Hélène Touzet, Jean-Pierre Féral. Does hybridization increase evolutionary rate? Data from the 28S-rDNA D8 domain in echinoderms.. Journal of Molecular Evolution, Springer Verlag, 2008, 67 (5), pp.539-50. ⟨10.1007/s00239-008-9171-8⟩. ⟨hal-00824034⟩

Helene Touzet, Jean-Stéphane Varré. Efficient and accurate P-value computation for Position Weight Matrices. Algorithms for Molecular Biology, BioMed Central, 2007, 2 (15), pp.1-12. ⟨inria-00270263⟩

Serge Dulucq, Hélène Touzet. Decomposition algorithms for the tree edit distance problem. Journal of Discrete Algorithms, Elsevier, 2005, pp.448-471. ⟨hal-00307523⟩

Guillaume Bonfante, Adam Cichon, Jean-Yves Marion, Helene Touzet. Algorithms with Polynomial Interpretation Termination Proof. Journal of Functional Programming, Cambridge University Press (CUP), 2001, 11 (1), pp.33-53. ⟨inria-00100819⟩

Chadi Saad, Laurent Noé, Hugues Richard, Julie Leclerc, Marie-Pierre Buisine, et al.. DiNAMO: Exact method for degenerate IUPAC motifs discovery, characterization of sequence-specific errors. JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France. ⟨hal-01574630⟩

Pierre Pericard, Yoann Dufresne, Samuel Blanquart, Hélène Touzet. Reconstruction of full-length 16S rRNA sequences for taxonomic assignment in metagenomics. JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France. ⟨hal-01574629⟩

Juraj Michálik, Hélène Touzet, Yann Ponty. Efficient approximations of RNA kinetics landscape using non-redundant sampling. 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⟩. ⟨hal-01500115⟩

Hélène Touzet. On the Levenshtein Automaton and the Size of the Neighborhood of a Word. 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⟩. ⟨hal-01360482⟩

Isabelle Guigon, Sylvain Legrand, Jean-Frédéric Berthelot, Mohcen Benmounah, Helene Touzet. Finding and analysing microRNAs in plant genomes with miRkwood. JOBIM 2015, Jul 2015, Clermont-Ferrand, France. ⟨hal-01247604⟩

Azadeh Saffarian, Mathieu Giraud, Hélène Touzet. Searching for alternate RNA structures in genomic sequences. Computational Methods for Structural RNAs, CMSR'14, Sep 2014, Strasbourg, France. pp.13-24, ⟨10.15455/CMSR.2014.0002⟩. ⟨hal-01084319⟩

Evguenia Kopylova, Laurent Noé, Pierre Pericard, Mikaël Salson, Hélène Touzet. SortMeRNA 2: ribosomal RNA classification for taxonomic assignation. Workshop on Recent Computational Advances in Metagenomics, ECCB 2014, Sep 2014, Strasbourg, France. ⟨hal-01094011⟩

Christophe Vroland, Mikaël Salson, Hélène Touzet. Lossless seeds for searching short patterns with high error rates. International Workshop On Combinatorial Algorithms, Oct 2014, Duluth, United States. ⟨hal-01079840⟩

Robert Giegerich, Hélène Touzet. Algebraic Dynamic Programming 2.0. Workshop Haskell-Treffen an der Universität Leipzig, Jun 2013, Leipzig, Germany. ⟨hal-00857801⟩

Evguenia Kopylova, Laurent Noé, Helene Touzet. SortMeRNA: a new software to filter total RNA for metatranscriptomic or RNA analysis. JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques - 2012, Jul 2012, Rennes, France. ⟨hal-00763792⟩

Jean-Frédéric Berthelot, Charles Deltel, Mathieu Giraud, Stéphane Janot, Laetitia Jourdan, et al.. biomanycores.org: a repository of interoperable open-source code for many-core bioinformatics. JOBIM 2011, Jul 2011, Paris, France. ⟨hal-00637847⟩

Mathieu Giraud, Stéphane Janot, Jean-Frédéric Berthelot, Charles Deltel, Laetitia Jourdan, et al.. Biomanycores, open-source parallel code for many-core bioinformatics. Bioinformatics Open Source Conference (BOSC 2011), 2011, Vienne, Austria. ⟨inria-00623390⟩

Aude Liefooghe, Helene Touzet, Jean-Stéphane Varré. Self-Overlapping Occurrences and Knuth-Morris-Pratt Algorithm for Weighted Matching. 3rd International Conference on Language and Automata Theory and Applications, Apr 2009, Tarragona, Spain. pp.481-492. ⟨inria-00365411⟩

Julien Allali, Yves d'Aubenton-Carafa, Cedric Chauve, Alain Denise, Christine Drevet, et al.. Benchmarking RNA secondary structure comparison algorithms. JOBIM'08, 2008, Lille, France. pp.67-68. ⟨hal-00375710⟩

Aude Liefooghe, Helene Touzet, Jean-Stéphane Varré. Large Scale Matching for Position Weight Matrices. Combinatorial Pattern Matching, Jul 2006, Barcelona, Spain. pp.401-412, ⟨10.1007/11780441_36⟩. ⟨inria-00270270⟩

Guillaume Blin, Helene Touzet. How to compare arc-annotated sequences: The alignment hierarchy. 13th String Processing and Information Retrieval, Oct 2006, Glasgow, United Kingdom. pp.291-303. ⟨inria-00178671⟩

Serge Dulucq, Hélène Touzet. Analysis of tree edit distance algorithms. Combinatorial pattern matching, 14th Annual Symposium, CPM 2003, 2003, Germany. pp.83--95. ⟨hal-00307516⟩

Hélène Touzet. A complex example of a simplifying rewrite system. International Colloquium on Automata, Languages, and Programming - ICALP'98, Jul 1998, Aalborg, Denmark, pp.507-517. ⟨inria-00098574⟩

Guillaume Bonfante, Adam Cichon, Jean-Yves Marion, Hélène Touzet. Complexity classes and rewrite systems with polynomial interpretation. CSl'98, 1998, Brno, République Tchèque, pp.372-384. ⟨inria-00098689⟩

Hélène Touzet. Encoding the Hydra battle as a rewrite system. International Symposium on the Mathematical Foundations of Computer Science - MFCS'98, Aug 1998, Brno, Czech Republic, pp.267-276. ⟨inria-00098575⟩

Iovka Boneva, Héléne Touzet. Traitement des données - introduction. Les Big Data à découvert, 2016. ⟨hal-01574692⟩

Evguenia Kopylova, Laurent Noé, Corinne da Silva, Jean-Frédéric Berthelot, Adriana Alberti, et al.. Deciphering metatranscriptomic data. 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⟩. ⟨hal-01104015⟩

Helene Touzet. Comparative analysis of RNA genes: the caRNAc software. Nicholas Bergman. Comparative Genomics, Volume 1, Humana Press, 2007, Methods in Molecular Biology, 978-1-58829-693-1. ⟨inria-00178557⟩

Hélène Touzet. Algorithms for bioinformatics: Proceedings of WABI 2015. Mihai Pop; Hélène Touzet. WABI, Sep 2015, Atlanta, United States. Springer Verlag, 2015, 15th International Workshop, WABI 2015, Atlanta, GA, USA, September 10-12, 2015, Proceedings, ⟨10.1007/978-3-662-48221-6⟩. ⟨hal-01228138⟩

Christian Barillot, Inbar Fijalkow, Isabelle Queinnec, Fabrice Theoleyre, Hélène Touzet, et al.. Rapport de Prospective du Conseil Scientifique de l’Institut des Sciences de l’Information et leurs Interactions (INS2I). [Autre] CNRS. 2018, pp.1-87. ⟨hal-01956087⟩

Benjamin Grenier-Boley, Antoine de Monte, Helene Touzet. CG-seq: a toolbox for automatic annotation of genomes by comparative analysis. [Research Report] RR-7428, INRIA. 2010, pp.12. ⟨inria-00530507⟩

Marie-Josee Cros, Antoine de Monte, Jérôme Mariette, Philippe Bardou, Benjamin Grenier-Boley, et al.. RNAspace. 2010. ⟨hal-02819286⟩