Christine GASPIN

Permanent researcher (DR1) in the MathNum dpt of INRAE in Toulouse (MIA-T lab).

Contact informations

INRAE Toulouse - MIA-T lab & Genotoul Bioinfo Platform
Chemin de Borde-Rouge BP 52627
31326 Castanet-Tolosan Cedex France

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

Qualifications

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

Responsabilities at INRAE

• 2003- : Scientific head for the "Plate-forme GenoToul Bioinfo"
• 2009-2015 : Co-animation of the "Cellule Bioinformatique de l'INRAE"
• 2019- : Deputy head of the INRAE MathNum division

Expertise (since 2015)

• 2016-2019 : member of of the INRIA Evaluation Committee
• 2017- : member of the Scientific board of IBiSA (Infrastructure en Biologie Santé et Agronomie)
• 2016- : member of the direction board of IFB (Institut National de Bioinformatique) national infrastructure
• 2019- : member of the IRD CSS (commissions scientifiques sectorielles)
• 2019- : member of the executive committee of the France Genomique national infrastructure

Research interests

• Optimization, Constraint networks, Graph theory
  

• Bioinformatics, Sequence analysis, (nc)RNA bioinformatics
  

Publications in Journals 2015-2020

1: Zytnicki M, Gaspin C. mmannot: How to improve small-RNA annotation? PLoS One. 2020 May 28;15(5):e0231738. doi: 10.1371/journal.pone.0231738. PMID: 32463818; PMCID: PMC7255610.

2: Ipoutcha T, Tsarmpopoulos I, Talenton V, Gaspin C, Moisan A, Walker CA, Brownlie J, Blanchard A, Thebault P, Sirand-Pugnet P. Multiple Origins and Specific Evolution of CRISPR/Cas9 Systems in Minimal Bacteria (Mollicutes). Front Microbiol. 2019 Nov 21;10:2701. doi: 10.3389/fmicb.2019.02701. PMID: 31824468; PMCID: PMC6882279.

3: Polonais V, Niehus S, Wawrzyniak I, Franchet A, Gaspin C, Belkorchia A, Reichstadt M, Belser C, Labadie K, Couloux A, Delbac F, Peyretaillade E, Ferrandon D. Draft Genome Sequence of Tubulinosema ratisbonensis, a Microsporidian Species Infecting the Model Organism Drosophila melanogaster. Microbiol Resour Announc. 2019 Aug 1;8(31):e00077-19. doi: 10.1128/MRA.00077-19. PMID: 31371528; PMCID: PMC6675976.

4: Plomion C, Aury JM, Amselem J, Leroy T, Murat F, Duplessis S, Faye S, Francillonne N, Labadie K, Le Provost G, Lesur I, Bartholomé J, Faivre-Rampant P, Kohler A, Leplé JC, Chantret N, Chen J, Diévart A, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Bogeat-Triboulot MB, Bouffaud ML, Brachi B, Chancerel E, Cohen D, Couloux A, Da Silva C, Dossat C, Ehrenmann F, Gaspin C, Grima-Pettenati J, Guichoux E, Hecker A, Herrmann S, Hugueney P, Hummel I, Klopp C, Lalanne C, Lascoux M, Lasserre E, Lemainque A, Desprez-Loustau ML, Luyten I, Madoui MA, Mangenot S, Marchal C, Maumus F, Mercier J, Michotey C, Panaud O, Picault N, Rouhier N, Rué O, Rustenholz C, Salin F, Soler M, Tarkka M, Velt A, Zanne AE, Martin F, Wincker P, Quesneville H, Kremer A, Salse J. Oak genome reveals facets of long lifespan. Nat Plants. 2018 Jul;4(7):440-452. doi: 10.1038/s41477-018-0172-3. Epub 2018 Jun 18. PMID: 29915331; PMCID: PMC6086335.

5: Laguerre S, González I, Nouaille S, Moisan A, Villa-Vialaneix N, Gaspin C, Bouvier M, Carpousis AJ, Cocaign-Bousquet M, Girbal L. Large-Scale Measurement of mRNA Degradation in Escherichia coli: To Delay or Not to Delay. Methods Enzymol. 2018;612:47-66. doi: 10.1016/bs.mie.2018.07.003. Epub 2018 Aug 29. PMID: 30502954.

6: Cerutti F, Mallet L, Painset A, Hoede C, Moisan A, Bécavin C, Duval M, Dussurget O, Cossart P, Gaspin C, Chiapello H. Unraveling the evolution and coevolution of small regulatory RNAs and coding genes in Listeria. BMC Genomics. 2017 Nov 16;18(1):882. doi: 10.1186/s12864-017-4242-0. PMID: 29145803; PMCID: PMC5689173.

7: Caldelari I, Chane-Woon-Ming B, Noirot C, Moreau K, Romby P, Gaspin C, Marzi S. Complete Genome Sequence and Annotation of the Staphylococcus aureus Strain HG001. Genome Announc. 2017 Aug 10;5(32):e00783-17. doi: 10.1128/genomeA.00783-17. PMID: 28798184; PMCID: PMC5552993.

8: Belkorchia A, Pombert JF, Polonais V, Parisot N, Delbac F, Brugère JF, Peyret P, Gaspin C, Peyretaillade E. Comparative genomics of microsporidian genomes reveals a minimal non-coding RNA set and new insights for transcription in minimal eukaryotic genomes. DNA Res. 2017 Jun 1;24(3):251-260. doi: 10.1093/dnares/dsx002. PMID: 28338834; PMCID: PMC5499648.

9: Bécavin C, Koutero M, Tchitchek N, Cerutti F, Lechat P, Maillet N, Hoede C, Chiapello H, Gaspin C, Cossart P. Listeriomics: an Interactive Web Platform for Systems Biology of Listeria. mSystems. 2017 Mar 14;2(2):e00186-16. doi: 10.1128/mSystems.00186-16. PMID: 28317029; PMCID: PMC5350546.

10: 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;17:164. doi: 10.1186/s12864-016-2505-9. PMID: 26931235; PMCID: PMC4774146.

11: 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;32(3):456-8. doi: 10.1093/bioinformatics/btv589. Epub 2015 Oct 10. PMID: 26454273; PMCID: PMC5859998.

12: Belkorchia A, Gasc C, Polonais V, Parisot N, Gallois N, Ribière C, Lerat E, Gaspin C, Pombert JF, Peyret P, Peyretaillade E. 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. doi: 10.1371/journal.pone.0139075. PMID: 26421846; PMCID: PMC4589312.

13: Higashi S, Fournier C, Gautier C, Gaspin C, Sagot MF. Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data. BMC Bioinformatics. 2015 May 29;16:179. doi: 10.1186/s12859-015-0594-0. PMID: 26022464; PMCID: PMC4448272.

14: 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 J, Quesneville H, Kremer A. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol Ecol Resour. 2016 Jan;16(1):254-65. doi: 10.1111/1755-0998.12425. Epub 2015 May 29. PMID: 25944057.

15: Esquerré T, Moisan A, Chiapello H, Arike L, Vilu R, Gaspin C, Cocaign- Bousquet M, Girbal L. Genome-wide investigation of mRNA lifetime determinants in Escherichia coli cells cultured at different growth rates. BMC Genomics. 2015 Apr 9;16(1):275. doi: 10.1186/s12864-015-1482-8. PMID: 25887031; PMCID: PMC4421995.

16: Thébault P, Bourqui R, Benchimol W, Gaspin C, Sirand-Pugnet P, Uricaru R, Dutour I. Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks. Brief Bioinform. 2015 Sep;16(5):795-805. doi: 10.1093/bib/bbu045. Epub 2014 Dec 3. PMID: 25477348; PMCID: PMC4570199.

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.