Claire Toffano-Nioche

Identifiants chercheurs

IdHAL :

claire-toffano-nioche

ORCID :

0000-0003-4134-6844

Publications

Article dans une revue (29)

Iron Sulfides Produced by Thermococcales: An Iron Detoxification Mechanism T. Mariotte,R. Coudray,C Toffano‐nioche,F. Guyot,A. Gorlas Environmental Microbiology, 2026, 28 (1), pp.e70242. ⟨10.1111/1462-2920.70242⟩ Article dans une revue hal-05491370v1
Training biologists in Unix command-line skills: From curriculum to interactive online tutorials Lucie Khamvongsa-Charbonnier,Robert Aboukhalil,Hélène Chiapello,Thomas Denecker,Pierre Poulainet al. PLoS Computational Biology, 2026, 22 (4), pp.e1014133. ⟨10.1371/journal.pcbi.1014133⟩ Article dans une revue hal-05583485v1
Deciphering the RNA-based regulation mechanism of the phage-encoded AbiF system in Clostridioides difficile Marion Saunier,Adeline Humbert,Victor Kreis,Johann Peltier,Arianna Tisbaet al. PLoS Genetics, 2025, 21 (8), pp.e1011831. ⟨10.1371/journal.pgen.1011831⟩ Article dans une revue hal-05493468v1
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 Jacquetet al. Nucleic Acids Research, 2024, 13, pp.gkae506. ⟨10.1093/nar/gkae506⟩ Article dans une revue hal-04614896v1
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 Garneauet al. mSystems, 2024, Host-Microbial Interactions, 9 (12), pp.e0086324. ⟨10.1128/msystems.00863-24⟩ Article dans une revue hal-04823328v1
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 Flintet al. European Journal of Immunology, 2023, ⟨10.1002/eji.202250334⟩ Article dans une revue hal-04145276v1
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 Boutserinet al. RNA Biology, 2021, 18 (11), pp.1931-1952. ⟨10.1080/15476286.2021.1882180⟩ Article dans une revue hal-03215481v1
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-02880655v2
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 Couvinet al. Nucleic Acids Research, 2020, 48 (D1), pp.D535-D544. ⟨10.1093/nar/gkz915⟩ Article dans une revue hal-02990278v1
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-02898094v1
Rfam 14: expanded coverage of metagenomic, viral and microRNA families Ioanna Kalvari,Eric P. Nawrocki,Nancy Ontiveros-Palacios,Joanna Argasinska,Kevin Lamkiewiczet al. Nucleic Acids Research, 2020, ⟨10.1093/nar/gkaa1047⟩ Article dans une revue hal-03031715v1
Assessment of Bona Fide sRNAs in Staphylococcus aureus Wenfeng Liu,Tatiana Rochat,Claire Toffano-Nioche,Thao Nguyen Le Lam,Philippe Boulocet al. Frontiers in Microbiology, 2018, 9, pp.228. ⟨10.3389/fmicb.2018.00228⟩ Article dans une revue hal-02180788v1
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 Razviet al. Nucleic Acids Research, 2018, 46 (17), pp.8803--8816. ⟨10.1093/nar/gky584⟩ Article dans une revue hal-02183490v1
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 Michaliket al. Nucleic Acids Research, 2018, 46 (W1), pp.W246-W251. ⟨10.1093/nar/gky425⟩ Article dans une revue pasteur-02098389v1
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-01412320v1
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 Biochimie, 2015, 118, ⟨10.1016/j.biochi.2015.07.008⟩ Article dans une revue hal-01234160v1
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-01464539v1
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. Steinbachet al. Methods, 2013, 63 (1), pp.60 - 65. ⟨10.1016/j.ymeth.2013.06.003⟩ Article dans une revue hal-02648776v1
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 Zytnickiet al. RNA Biology, 2013, 10 (7), pp.1211-20. ⟨10.4161/rna.25567⟩ Article dans une revue hal-00863721v1
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 Gautheretet al. RNA, 2012, 18 (12), pp.2201-19. ⟨10.1261/rna.033324.112⟩ Article dans une revue hal-00757205v1
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 Morinet al. BMC Evolutionary Biology, 2008, 8, pp.1-19. ⟨10.1186/1471-2148-8-291⟩ Article dans une revue hal-02663715v1
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-00109042v1
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 Cookeet al. Nucleic Acids Research, 2005, 33, pp.D641-D646. ⟨10.1093/nar/gki115⟩ Article dans une revue hal-01189162v1
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. Kreiset al. Plant Biotechnology Journal, 2004, 2 (5), pp.401-405. ⟨10.1111/j.1467-7652.2004.00084.x⟩ Article dans une revue istex hal-02682507v1
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-02672398v1
Genomic exploration of the hemiascomycetous yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae Bertrand Llorente,Pascal Durrens,Alain Malpertuy,Michel Aigle,François Artiguenaveet al. FEBS Letters, 2000, 487 (1), pp.122-133. ⟨10.1016/s0014-5793(00)02291-2⟩ Article dans une revue hal-02696721v1
Genomic Exploration of the Hemiascomycetous Yeasts: 4. The genome of Saccharomyces cerevisiae revisited Gaëlle Blandin,Pascal Durrens,Fredj Tekaia,Michel Aigle,Monique Bolotin-Fukuharaet al. FEBS Letters, 2000, 487, pp.31--36. ⟨10.1016/S0014-5793(00)02275-4⟩ Article dans une revue hal-00306551v1
Genomic exploration of the hemiascomycetous yeasts: I. A set of yeast species for molecular evolution studies Jean-Luc Souciet,Michel Aigle,François Artiguenave,Gaëlle Blandin,Monique Bolotin-Fukuharaet al. FEBS Letters, 2000, 487 (1), pp.3-12. ⟨10.1016/S0014-5793(00)02272-9⟩ Article dans une revue hal-02694630v1
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. Durrenset al. FEBS Letters, 2000, 487, pp.17-30 Article dans une revue hal-02696093v1

Cours (2)

Sandbox.bio tutorials – Linux basics training modules (IFB ELIXIR-FR) Lucie Khamvongsa-Charbonnier,Thomas Denecker,Claire Toffano-Nioche,Denis Puthier,Olivier Sandet al. École thématique. France. 2026 Cours hal-05506951v1
Bioinformatics in a tense geopolitical context Claire Toffano-Nioche,Laurent Jourdren,Thomas Denecker École thématique. ANF Workflow et reproductibilité en Bioinformatique, Campanile Paris-Sud - Porte d'Orléans - Arcueil, 73 av. Aristide Briand, 94110 - ARCUEIL, France. 2025 Cours hal-05527702v1

Poster de conférence (4)

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 Gautheretet al. JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques 2024, Jun 2024, Toulouse, France. Poster de conférence hal-04823442v1
A Unix competency framework for learning bioinformatics Hélène Chiapello,Thomas Denecker,Lucie Khamvongsa Charbonnier,Pierre Poulain,Denis Puthieret al. JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques 2024, Jun 2024, Toulouse, France. Poster de conférence hal-04619317v1
The IFB e-Learning Working Group Hélène Chiapello,Thomas Denecker,Gildas Le Corguillé,Pierre Poulain,Denis Puthieret al. JOBIM (Journées Ouvertes en Biologie, Informatique et Mathématiques) 2021, Jul 2021, Paris, France. Poster de conférence hal-03296617v1
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-03071717v1

Pré-publication, Document de travail (1)

Staphylococcal aconitase expression during iron deficiency is controlled by an sRNA-driven feedforward loop and moonlighting activity Maxime Barrault,Svetlana Chabelskaya,Rodrigo Coronel-Tellez,Claire Toffano-Nioche,Eric Jacquetet al. 2024 Pré-publication, Document de travail hal-04770232v1

Communication dans un congrès (3)

Towards a semi-automatic functional annotation tool based on decision tree techniques Jérôme Azé,L. Gentils,Claire Toffano-Nioche,Valentin Loux,Jean-François Gibratet al. Machine Learning in Systems Biology: MLSB 2007, Sep 2007, Evry, France Communication dans un congrès hal-02754400v1
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-00509922v1
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-00106048v1