Claire Toffano-Nioche

Documents

Identifiants chercheurs

claire-toffano-nioche
0000-0003-4134-6844

Publications

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

	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 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 Boutserin 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
	Rfam 14: expanded coverage of metagenomic, viral and microRNA families Ioanna Kalvari , Eric P. Nawrocki , Nancy Ontiveros-Palacios , Joanna Argasinska , Kevin Lamkiewicz Nucleic Acids Research, 2020, ⟨10.1093/nar/gkaa1047⟩ Article dans une revue hal-03031715v1
	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 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
	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 Nucleic Acids Research, 2018, 46 (17), pp.8803--8816. ⟨10.1093/nar/gky584⟩ Article dans une revue hal-02183490v1
	Assessment ofBona FidesRNAs inStaphylococcus aureus Wenfeng Liu , Tatiana Rochat , Claire Toffano-Nioche , Thao Nguyen Le Lam , Philippe Bouloc Frontiers in Microbiology, 2018, 9, pp.228. ⟨10.3389/fmicb.2018.00228⟩ Article dans une revue hal-02180788v1
	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 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. Steinbach 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 Zytnicki 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 Gautheret 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 Morin 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 Cooke 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. Kreis Plant Biotechnology Journal, 2004, 2 (5), pp.401-405. ⟨10.1111/j.1467-7652.2004.00084.x⟩ Article dans une revue 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: 4. The genome of Saccharomyces cerevisiae revisited Pascal Durrens , Elisabeth Bon , Cécile Neuvéglise , Gaëlle Blandin , Fredj Tekaia 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: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae B. Llorente , P. Durrens , A. Malpertuy , M. Aigle , Francois Artiguenave FEBS Letters, 2000, 487, pp.122-133 Article dans une revue hal-02696721v1
	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 FEBS Letters, 2000, 487, pp.17-30 Article dans une revue hal-02696093v1

	The IFB e-Learning Working Group Hélène Chiapello , Thomas Denecker , Gildas Le Corguillé , Pierre Poulain , Denis Puthier 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

Claire Toffano-Nioche

Publications

REVIVOS: REalité VIrtuelle pour la construction de VOcabulaires Spécialisés

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

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

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

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

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

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

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

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

Assessment ofBona FidesRNAs inStaphylococcus aureus

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

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

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

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

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

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

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

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

Formation of the Arabidopsis Pentatricopeptide Repeat Family

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

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

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

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

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

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

The IFB e-Learning Working Group

FAIR_bioinfo : a software perspective of reproducibility of bioinformatics analyses