Claire Toffano-Nioche

33
Documents
Identifiants chercheurs

Publications

Publications

Image document

A Unix competency framework for learning bioinformatics

Hélène Chiapello , Thomas Denecker , Lucie Khamvongsa Charbonnier , Pierre Poulain , Denis Puthier et al.
JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques 2024, Jun 2024, Toulouse, France.
Poster de conférence hal-04619317 v1
Image document

Search for ncRNA targets in Clostridioides difficile by crossreferencing MAPS data and RNA-RNA interaction predictions

Claire Toffano-Nioche , Joe Ueda , Adeline Humbert , Johann Peltier , Daniel Gautheret et al.
JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques 2024, Jun 2024, Toulouse, France.
Poster de conférence hal-04823442 v1
Image document

The IFB e-Learning Working Group

Hélène Chiapello , Thomas Denecker , Gildas Le Corguillé , Pierre Poulain , Denis Puthier et al.
JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques) 2021, Jul 2021, Paris, France.
Poster de conférence hal-03296617 v1
Image document

FAIR_bioinfo : a software perspective of reproducibility of bioinformatics analyses

Thomas Denecker , Céline Hernandez , Claire Toffano-Nioche
Journées Ouvertes de Biologie Informatique et Mathématiques - JOBIM 2020, Jun 2020, Montpellier, France
Poster de conférence hal-03071717 v1
Image document

Staphylococcal aconitase expression during iron deficiency is controlled by an sRNA-driven feedforward loop and moonlighting activity

Maxime Barrault , Svetlana Chabelskaya , Rodrigo H Coronel-Tellez , Claire Toffano-Nioche , Eric Jacquet et al.
Nucleic Acids Research, 2024, 13, pp.gkae506. ⟨10.1093/nar/gkae506⟩
Article dans une revue hal-04614896 v1
Image document

Dual RNA-seq study of the dynamics of coding and non-coding RNA expression during Clostridioides difficile infection in a mouse model

Victor Kreis , Claire Toffano-Nioche , Cécile Denève-Larrazet , Jean-Christophe Marvaud , Julian R Garneau et al.
mSystems, In press, Host-Microbial Interactions, pp.e0086324. ⟨10.1128/msystems.00863-24⟩
Article dans une revue hal-04823328 v1
Image document

Transinteractome analysis reveals distinct niche requirements for isotype‐based plasma cell subsets in the bone marrow

Amélie Bonaud , Pierre Larraufie , Mélanie Khamyath , Ugo Szachnowski , Shaun M Flint et al.
European Journal of Immunology, 2023, ⟨10.1002/eji.202250334⟩
Article dans une revue hal-04145276 v1
Image document

Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogen Clostridioides difficile

Pierre Boudry , Emma Piattelli , Emilie Drouineau , Johann Peltier , Anaïs Boutserin et al.
RNA Biology, 2021, 18 (11), pp.1931-1952. ⟨10.1080/15476286.2021.1882180⟩
Article dans une revue hal-03215481 v1
Image document

FAIR_Bioinfo: a turnkey training course and protocol for reproducible computational biology

Thomas Denecker , Claire Toffano-Nioche
JOSE - Journal of Open Source Education, 2021, ⟨10.21105/jose.00068⟩
Article dans une revue hal-02880655 v2
Image document

CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers

Christine Pourcel , Marie Touchon , Nicolas Villeriot , Jean-Philippe Vernadet , David Couvin et al.
Nucleic Acids Research, 2020, 48 (D1), pp.D535-D544. ⟨10.1093/nar/gkz915⟩
Article dans une revue hal-02990278 v1
Image document

Accurate characterization of Escherichia coli tRNA modifications with a simple method of deep sequencing library preparation

Ji Wang , Claire Toffano-Nioche , Florence Lorieux , Daniel Gautheret , Jean Lehmann
RNA Biology, 2020, pp.1-14. ⟨10.1080/15476286.2020.1790871⟩
Article dans une revue hal-02898094 v1
Image document

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

Ioanna Kalvari , Eric P. Nawrocki , Nancy Ontiveros-Palacios , Joanna Argasinska , Kevin Lamkiewicz et al.
Nucleic Acids Research, 2020, ⟨10.1093/nar/gkaa1047⟩
Article dans une revue hal-03031715 v1
Image document

The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus

Tatiana Rochat , Chantal Bohn , Claire Morvan , Thao Nguyen Le Lam , Fareha Razvi et al.
Nucleic Acids Research, 2018, 46 (17), pp.8803--8816. ⟨10.1093/nar/gky584⟩
Article dans une revue hal-02183490 v1
Image document

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

David Couvin , Aude Bernheim , Claire Toffano-Nioche , Marie Touchon , Juraj Michalik et al.
Nucleic Acids Research, 2018, 46 (W1), pp.W246-W251. ⟨10.1093/nar/gky425⟩
Article dans une revue pasteur-02098389 v1
Image document

Assessment of Bona Fide sRNAs in Staphylococcus aureus

Wenfeng Liu , Tatiana Rochat , Claire Toffano-Nioche , Thao Nguyen Le Lam , Philippe Bouloc et al.
Frontiers in Microbiology, 2018, 9, pp.228. ⟨10.3389/fmicb.2018.00228⟩
Article dans une revue hal-02180788 v1

Another example of enzymatic promiscuity: the polyphosphate kinase of Streptomyces lividans is endowed with phospholipase D activity

Catherine Esnault , Denis Leiber , Claire Toffano-Nioche , Zahra Tanfin , Marie-Joelle Virolle
Applied Microbiology and Biotechnology, 2016, 101 (1), pp.139-145. ⟨10.1007/s00253-016-7743-x⟩
Article dans une revue hal-01412320 v1
Image document

Revisiting the structure/function relationships of H/ACA(-like) RNAs: A unified model for Euryarchaea and Crenarchaea

Claire Toffano-Nioche , Daniel Gautheret , Fabrice Leclerc
Nucleic Acids Research, 2015, 43 (16), pp.7744-7761. ⟨10.1093/nar/gkv756⟩
Article dans une revue hal-01464539 v1
Image document

Comparative genomics reveals conserved positioning of essential genomic clusters in highly rearranged Thermococcales chromosomes

Matteo Cossu , Violette Da Cunha , Claire Toffano-Nioche , Patrick Forterre , Jacques Oberto
Article dans une revue hal-01234160 v1
Image document

RNA at 92 °C: The non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi.

Claire Toffano-Nioche , Alban Ott , Estelle Crozat , an N Nguyen , Matthias Zytnicki et al.
RNA Biology, 2013, 10 (7), pp.1211-20. ⟨10.4161/rna.25567⟩
Article dans une revue hal-00863721 v1

Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline

Claire Toffano-Nioche , Yufei Luo , Claire Kuchly , Claire Wallon , Delphine D. Steinbach et al.
Methods, 2013, 63 (1), pp.60 - 65. ⟨10.1016/j.ymeth.2013.06.003⟩
Article dans une revue hal-02648776 v1

Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus.

Claire Toffano-Nioche , an N Nguyen , Claire Kuchly , Alban Ott , Daniel Gautheret et al.
RNA, 2012, 18 (12), pp.2201-19. ⟨10.1261/rna.033324.112⟩
Article dans une revue hal-00757205 v1
Image document

Genes of the most conserved WOX clade in plants affect root and flower development in Arabidopsis

Yves Deveaux , Claire Toffano-Nioche , Gaëlle Claisse , Vincent Thareau , Halima Morin et al.
BMC Evolutionary Biology, 2008, 8, pp.1-19. ⟨10.1186/1471-2148-8-291⟩
Article dans une revue hal-02663715 v1

Formation of the Arabidopsis Pentatricopeptide Repeat Family

Eric Rivals , Clémence Bruyère , Claire Toffano-Nioche , Alain Lecharny
Plant Physiology, 2006, 141, pp.825-839. ⟨10.1104/pp.106.077826⟩
Article dans une revue lirmm-00109042 v1
Image document

GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts

Sebastien Aubourg , Veronique Brunaud , Clémence Bruyère , J. Mark Cock , Richard Cooke et al.
Nucleic Acids Research, 2005, 33, pp.D641-D646. ⟨10.1093/nar/gki115⟩
Article dans une revue hal-01189162 v1

DEAD-box RNA helicases in Arabidopsis thaliana: establishing a link between quantitative expression, gene structure and evolution of a family of genes

A. Mingam , Claire Toffano-Nioche , Véronique Brunaud , Nathalie Boudet , M. Kreis et al.
Plant Biotechnology Journal, 2004, 2 (5), pp.401-405. ⟨10.1111/j.1467-7652.2004.00084.x⟩
Article dans une revue istex hal-02682507 v1

Evolution of intron/exon structure of DEAD helicase family genes in Arabidopsis, Caenorhabdtitis, and Drosophila

Nathalie Boudet , Sebastien Aubourg , Claire Toffano-Nioche , M. Kreis
Genome Research, 2001, 11, pp.2101-2114
Article dans une revue hal-02672398 v1

Genomic exploration of the hemiascomycetous yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae

B. Llorente , P. Durrens , A. Malpertuy , M. Aigle , Francois Artiguenave et al.
FEBS Letters, 2000, 487, pp.122-133
Article dans une revue hal-02696721 v1

Genomic Exploration of the Hemiascomycetous Yeasts: 4. The genome of Saccharomyces cerevisiae revisited

Pascal Durrens , Elisabeth Bon , Cécile Neuvéglise , Gaëlle Blandin , Fredj Tekaia et al.
FEBS Letters, 2000, 487, pp.31--36. ⟨10.1016/S0014-5793(00)02275-4⟩
Article dans une revue hal-00306551 v1

Genomic exploration of the hemiascomycetous yeasts: 3. Methods and strategies used for sequence analysis and annotation

F. Tekaia , Gallien Blandin , A. Malpertuy , B. Llorente , P. Durrens et al.
FEBS Letters, 2000, 487, pp.17-30
Article dans une revue hal-02696093 v1
Image document

REVIVOS: REalité VIrtuelle pour la construction de VOcabulaires Spécialisés

Nicolas Férey , Nioche Claire Toffano , Taillez Oriane Matte , Rachid Gherbi , W. Turner
18es Journées Francophones d'Ingénierie des Connaissances, Jul 2007, Grenoble, France. not specified
Communication dans un congrès hal-00509922 v1
Image document

Towards a semi-automatic functional annotation tool based on decision tree techniques

Jérôme Azé , L. Gentils , Claire Toffano-Nioche , Valentin Loux , Jean-François Gibrat et al.
Machine Learning in Systems Biology: MLSB 2007, Sep 2007, Evry, France
Communication dans un congrès hal-02754400 v1

Formation of the Arabidopsis Pentatricopeptide Repeat (PPR) Protein Family

Eric Rivals , Clémence Bruyère , Claire Toffano-Nioche , Alain Lecharny
JOBIM 2005 - 6es Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2005, Lyon, France. pp.291-298
Communication dans un congrès lirmm-00106048 v1