Christine GASPIN

De MIAT INRA
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Permanent researcher in the MIA dpt of the INRA in Toulouse (BIA Unit).

Portrait Christine.png

Contact informations

INRA Toulouse - BIA unit
Chemin de Borde-Rouge BP 52627
31326 Castanet-Tolosan Cedex France

Tel: +33(0)5.61.28.52.82.
Mail: Christine.Gaspin[at]toulouse.inra.fr.


Research interests

  • Optimization, Constraint networks, Graph theory
  • Bioinformatics, Sequence analysis, ncRNA gene prediction and analysis

External collaborations (2005-2011)

  • Institut Pasteur (P. Cossart) et IBMC Strabourg (E. Westhof) - BACNET project (ANR, IA, Bioinformatique, 2012-2016).
  • Laboratoire des Interactions Plantes Microorganismes, INRA, Toulouse, France (C. Boucher & S. Génin) - Pathoregulom project (ANR, Programme Blanc, 2005-2008): Pathogenicity and Regulation in the plant pathogen Ralstonia solanacearum.In this project. Prediction and analysis of ncRNA involved in the process of pathogenicity in the plant pathogen R. solanacearum.
  • IBMC Strabourg (P. Romby) and INSERM E0230, Faculté Laennec Lyon (F. Vandenesch) - SaRNA project (ANR, Microbiologie-Immunologie, 2005-2008): Characterization of the RNA-dependent regulatory networks that affect virulence gene expression or adaptation of the bacteria to different environments. Specific aims studied inS. aureus: identification of novel RNAIII targets and the regulatory mechanisms, and the action of several RNAIII-binding proteins in virulence; identification of mRNA riboswitches, and of novel ncRNAs, characterization of their targets and the regulatory mechanisms, and their involvement in establishing S. aureus pathogenicity. Different experimental approaches (biochemistry, structure analysis, gene expression in S. aureus, animal model for S. aureus pathogenesis, bioinformatics) commonly used by the three teams.
  • SIGENAE-LGC team, Toulouse (P. Bardou), Plate-forme GenoToul Bioinfo (C. Gaspin & J. Mariette), LIFL Lille (H. Touzet) and IGM Orsay (D. Gautheret) - RNAspace project (IBiSA, 2007-2011) : Development of a web application dedicated to ncRNA prediction and annotation.
  • IBCG Toulouse (B. Clouet d'Orval) - ncRNA prediction and analysis in the archea P. abyssi (2007-2010).

Publications in Journals 2005-2016

  • Juanchich A., Bardou P., Rué O., Gabillard JC., Gaspin C., Bobe J., Guiguen Y. Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing. BMC Genomics. 2016 Mar 1;17(1):164. doi:10.1186/s12864-016-2505-9.
  • Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leplé JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse S, Quesneville H, Kremer A (2014) Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol Ecol Resour. 2016 Jan;16(1):254-265.
  • Mariette J, Escudié F, Bardou P, Nabihoudine I, Noirot C, Trotard MS, Gaspin C, Klopp C. Jflow: a workflow management system for web applications. Bioinformatics. 2016 Feb 1.
  • Belkorchia, A., Gasc C., Polonais V., Parisot N., Gallois N., Ribière C., Lerat E., Gaspin C., Pombert JF., Peyret P. and Peyretaillade P. The prediction and validation of small CDSs expand the gene repertoire of the smallest known eukaryotic genomes. PLoS One, 2015, Sep 30;10(9):e0139075.
  • Higashi S., Fournier C., Gautier C., Gaspin C. and Sagot MF. Mirinho: An effcient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data, BMC Bioinformatics, 2015 May 29;16:179.
  • Esquerré T., Moisan A., Chiapello H., Arike L., Vilu R., Gaspin C., Cocaign-Bousquet M. and Girbal L. Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates, BMC Genomics 2015 Apr 9;16:275.
  • Thébault P., Bourqui R., Benchimol W., Gaspin C., Sirand-Pugnet P., Uricaru R. and Dutour I. Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks. Briefings in Bioinformatics, December 3, 2014, 1-11.
  • Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Pingault L, Sourdille P, Couloux A, Paux E, Leroy P, Mangenot S, Guilhot N, Le Gouis J, Balfourier F, Alaux M, Jamilloux V, Poulain J, Durand C, Bellec A, Gaspin C, Safar J, Dolezel J, Rogers J, Vandepoele K, Aury JM, Mayer K, Berges H, Quesneville H, Wincker P, Feuillet C. Structural and functional partitioning of bread wheat chromosome 3B. Science. 2014 Jul 18;345(6194):1249721.
  • Berthelot C, Brunet F, Chalopin D, Juanchich A, Bernard M, Noël B, Bento P, DaSilva C, Labadie K, Alberti A, Aury JM, Louis A, Dehais P, Bardou P, Montfort J, Klopp C, Cabau C, Gaspin C, Thorgaard GH, Boussaha M, Quillet E, Guyomard R, Galiana D, Bobe J, Volff JN, Genêt C, Wincker P, Jaillon O, Roest Crollius H, Guiguen Y. The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun. 2014 Apr 22;5:3657.
  • Norais C, Moisan A, Gaspin C, Clouet-d'Orval B. Diversity of CRISPR systems in the euryarchaeal Pyrococcales. RNA Biol. 2013 May;10(5):659-70.
  • Caldelari I, Fechter P, Lioliou E, Romilly C, Chevalier C, Gaspin C, and Romby P. A current overview of regulatory RNAs in Staphylococcus aureus, In Regulatory RNAs in prokaryotes (Hess W.R. and Marchfelder A., eds) pp. 51-75. SpringerWienNewYork, 2012.
  • Cros MJ, de Monte A, Mariette J, Bardou P, Grenier-Boley B, Gautheret D, Touzet H, and Gaspin C. RNAspace.org: an integrated environment for the prediction, annotation and analysis of ncRNA. RNA 2011 17 (11).
  • Phok K, Moisan A, Rinaldi D, Brucato N, Carpousis AJ, Gaspin C, Clouet-d'Orval B. Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi. BMC Genomics. 2011 Jun 13;12:312.
  • Gaspin C, Rami JF, Lescure B. Distribution of short interstitial telomere motifs in two plant genomes: putative origin and function. BMC Plant Biol. 2010 Dec 20;10:283.
  • Beaume M, Hernandez D, Farinelli L, Deluen C, Linder P, Gaspin C, Romby P, Schrenzel J, Francois P. Cartography of methicillin-resistant S. aureus transcripts: detection, orientation and temporal expression during growth phase and stress conditions. PLoS One. 2010 May 20;5(5):e10725.
  • Geissmann T, Chevalier C, Cros MJ, Boisset S, Fechter P, Noirot C, Schrenzel J, François P, Vandenesch F, Gaspin C, Romby P (2009). A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation. Nucleic Acids Res. 2009 Sep 28.
  • M. Zytnicki, C. Gaspin, S. de Givry and T. Schiex (2009). Bounds Arc Consistency for Weighted CSPs, JAIR, Vol; 35, pages 593-621
  • Grosjean H, Gaspin C, Marck C, Decatur WA, de Crécy-Lagard V. RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes. BMC Genomics. 2008 Oct 9;9:470.
  • M. Zytnicki, C. Gaspin, T. Schiex (2008). DARN! A soft constraint solver for RNA motif localization, Constraints, 13(1), 2008.
  • Noirot C, Gaspin C, Schiex T, Gouzy J (2008). LeARN: a platform for detecting, clustering and annotating non-coding RNAs. BMC Bioinformatics. 2008 Jan 14;9:21.
  • Boisset S, Geissmann T, Huntzinger E, Fechter P, Bendridi N, Possedko M, Chevalier C, Helfer AC, Benito Y, Jacquier A, Gaspin C, Vandenesch F, Romby P (2007). Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism. Genes Dev. 2007 Jun 1;21(11):1353-66.
  • Thébault P, de Givry S, Schiex T, Gaspin C (2006). Searching RNA motifs and their intermolecular contacts with constraint networks. Bioinformatics. 2006 Sep 1;22(17):2074-80. Epub 2006 Jul 4.
  • Clouet-d'Orval B, Gaspin C, Mougin A (2005). Two different mechanisms for tRNA ribose methylation in Archaea: a short survey. Biochimie. 2005 Sep-Oct;87(9-10):889-95.
  • Renalier MH, Joseph N, Gaspin C, Thebault P, Mougin A (2005). The Cm56 tRNA modification in archaea is catalyzed either by a specific 2'-O-methylase, or a C/D sRNP. RNA. 2005 Jul;11(7):1051-63.
  • Aubourg S, Brunaud V, Bruyère C, Cock M, Cooke R, Cottet A, Couloux A, Déhais P, Deléage G, Duclert A, Echeverria M, Eschbach A, Falconet D, Filippi G, Gaspin C, Geourjon C, Grienenberger JM, Houlné G, Jamet E, Lechauve F, Leleu O, Leroy P, Mache R, Meyer C, Nedjari H, Negrutiu I, Orsini V, Peyretaillade E, Pommier C, Raes J, Risler JL, Rivière S, Rombauts S, Rouzé P, Schneider M, Schwob P, Small I, Soumayet-Kampetenga G, Stankovski D, Toffano C, Tognolli M, Caboche M, Lecharny A (2005). GeneFarm, structural and functional annotation of Arabidopsis gene and protein families by a network of experts. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D641-6.
  • Gaspin, C. & Thébault P. (2005), Identification d’ARN non codants, Biofutur, pp. 33-36, Janvier 2005.

Softwares (2005-2011)

  • ApolloRNA: ApolloRNA is a  a genome annotation viewer and editor dedicated to support ncRNA identification. It has been built as an extension of the annotation environment Apollo.
  • RNAspace: RNAspace is an environment dedicated to ncRNA prediction and annotation. It is developed in collaboration with the teams of Hélène Touzet (Lille) and Daniel Gautheret (Orsay).
  • MilPat: MilPat a constraint based efficient and powerful structured motif search engine for genomic DNA. It allows to look for new members of known RNA gene families, taking into account possible interactions with other nucleotidic sequences. Developped by P. Thébault during her PhD-thesis.
  • DARN!: Darn! is a weighted constraint based efficient and powerful structured motif search engine for genomic DNA. It allows to look for new members of known RNA gene families, taking into account possible interactions with other nucleotidic sequences. Developped by Matthias Zytnicki during his PhD-thesis. DARN! can also find RNA genes from an alignment.
  • Publications in Journals 2005-2011

Training support

Training support

Qualifications and other responsabilities

Qualifications

  • 1990 : PhD in Computer Science of "The École Nationale Supérieure de l'Aéronautique et de l'Espace" (ENSAE), Toulouse
  • 2001 : Director of Research at INRA

Other responsabilities at INRA

Génotoul BioInfo
Équipe RECORD
IMABS
Outils personnels