Christine CIERCO-AYROLLES

Permanent researcher

INRA

Research Center of Toulouse Midi-Pyrénées 

Toulouse Applied Mathematics and Computer Science Unit  

Division of Applied Mathematics and Informatics

Research interests

• Statistics : asymptotic distribution of test statistitics
• Stochastic processes : Gaussian processes, crossings and Rice formulae for one-dimensional parameter processes, approximation for the tails of the distribution of the Supremum
• Genetical statistics : Quantitative Trait Loci detection and location, use of linkage disequilibrium, combining linkage and linkage disequilibrium
• Prediction of non-protein-coding RNA sequences
• Genetical genomics

External collaborations (2005-2014)

• Sébastien Gadat (Toulouse School of Economics) : Magali Champion's PhD Thesis: Contribution à la modélisation et l'inférence de réseaux de régulation de gènes.
  
• UMR Diversité et Adaptation des Plantes Cultivées, INRA Montpellier, France ; UMR Santé de la Vigne et Qualité du Vin, INRA Colmar, France; Jukius Kuehn-Institute Federal Research Centre for Cultivated Plants, Institute for Grapevine Breeding, Quedlinburg, Germany. DLVitis Project (ANR, Programme de Génomique, 2009-2011): Genetic structure and linkage disequilibrium in 3 species of the Vitis genus.It is a fundamental research project aiming at optimizing, through association genetics at the whole genome scale, the discovery of molecular markers and genes directly usable for breeding new grapevine cultivars. In this project, new statistical methods for linkage disequilibrium assesment willhave been developed and evaluated. 
  
• Station de Génétique Quantitative et Appliquée, INRA, Jouy-en-Josas, France; Station d'Amélioration Génétique des Animaux, INRA, Toulouse, France. LDLmapQTL Project (ANR, GENANIMAL, 2006-2007): Combining linkage analysis and linkage disequilibrium for QTL fine mapping in animal pedigrees.
  
• Laboratoire des Interactions Plantes Microorganismes, INRA, Toulouse, France. Pathoregulom Project(ANR, Programme Blanc, 2005-2008): Pathogenicity and Regulation in the plant pathogen Ralstonia solanacearum.In this project, we deloped a new prediction algorithm, suited to high GC% bacteria such as R. solanacearum, to identify small non coding RNA involved in the process of pathogenicity.
  

Selected publications and softwares

Publications

- Champion, M., Cierco-Ayrolles, C., Gadat, S., and Vignes, M. (2014) Sparse regression and support recovery with L2-Boosting algorithms. J. Statist. Plann. Inference, http://dx.doi.org/10.1016/j.jspi.2014.07.006

- Mangin, B, Siberchicot, A, Nicolas, S, Doligez, A, This, P and Cierco-Ayrolles, C. (2012). Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness. Heredity, 108, 285-291.

- Vignes, M, Vandel, J, Allouche, D, Ramadan-Alban, N, Cierco-Ayrolles, C, Schiex, T, Mangin, B and de Givry, S. (2011). Gene Regulatory Network Reconstruction Using Bayesian Networks, the Dantzig Selector, the Lasso and Their Meta-Analysis. PLoS ONE, 6, e29165.

- Cierco-Ayrolles, C, Dejean, S, Legarra, A, Gilbert, H, Druet, T, Ytournel, F, Estivals, D and Oumouhou, N. and Mangin, B. (2010). Does probabilistic modelling of linkage disequilibrium evolution improve the accuracy of QTL location in animal pedigree? Genetics Selection Evolution, 42:38.

- Mangin, B., Garnier-Géré, P. and Cierco-Ayrolles, C. (2008). The estimator of the optimal measure of allelic association : mean, variance and probability distribution when the sample size tends to infinity. Statistical Applications in Genetics and Molecular Biology, Vol. 7: Issue 1, Article 20.

- Cros, M.-J., Sallet, E., Moisan, A., Cierco-Ayrolles, C. and Gaspin, C. (2007). Visualizing and exploring genomic information for non-protein-coding RNA identification using ApolloRNA. Nature Protocol, 10.2038/nprot. 2007.285.

- Boitard S., Abdallah J.M., De Rochambeau H., Cierco-Ayrolles C. and Mangin B. (2006). Linkage disequilibrium interval mapping of quantitative trait loci. BMC Genomics, 7:54.

- Abdallah J.M., Mangin B., Goffinet B., Cierco-Ayrolles C. and Pérez-Enciso M. (2004). A comparison between methods for linkage disequilibrium fine mapping of quantitative trait loci. Genetical Research, 83 (1), 41-47.

- Cierco-Ayrolles, C., Croquette, A. and Delmas, C. (2003). Computing the distribution of the Maximum of Gaussian random processes. Methodology and Computing in Applied Probability, 5 (4), 427-438.

- Abdallah J.M., Goffinet B., Cierco-Ayrolles C. and Pérez-Enciso M. (2003). Linkage disequilibrium fine mapping of quantitative trait loci: a simulation study. Genetics Selection Evolution, 35, 513-532.

- Azaïs, J.-M., Cierco-Ayrolles, C. (2002) An asymptotic test for quantitative gene detection. Annales de l’Institut Henri Poincaré Probabilités et Statistiques, Vol.38 (6), 1087-1092.

- Azaïs, J.-M., Cierco-Ayrolles, C. and Croquette, A. (1999) Bounds and asymptotic expansions for the distribution of the maximum of a smooth stationary Gaussian process. ESAIM : Probability and Statistics, 3, 107-129.

- Cierco, C. (1998) Asymptotic Distribution of the Maximum Likelihood Ratio Test for Gene Detection. Statistics, 31, 3, 261-285.

Book chapters

 - Allouche, D.,Cierco-Ayrolles, C., de Givry, S., Guillermin, G., B. Mangin, B., T. Schiex, T., J. Vandel, J., and Vignes, M. (2013) A panel of learning methods for the reconstruction of gene regulatory networks in a systems genetics context. In Verification of methods for gene network inference from Systems Genetics data, eds: A. de la Fuente, Springer

- Cierco-Ayrolles, C., Abdallah, J.M., Boitard, S., Chikhi, L., De Rochambeau, H., Tsitrone, A., Veyrieras, J.-B. and Mangin, B. (2004). On linkage disequilibrium measures: Methods and Applications. Recent Research Developments in Genetics and Breeding, chapter 10, pages 151-180, Research Signpost Editions, Kerala, India.
 - Abdallah, J.-M., Mangin, B., Cierco-Ayrolles, C., Goffinet, B., De Rochambeau, H. and Pérez-Enciso, M. (2005). Outils Statistiques et Informatiques pour l'Analyse du Déséquilibre de Liaison. Les Actes du BRG, 5, 309-320.

Softwares

- LDcorSV: LDcorSV is an R package providing a set of functions to measure linkage disequilibrium.
- 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.

- HAPim: HAPim is an R package allowing to jointly use linkage analysis and linkage disequilibrium for QTL fine mapping in animal half-sib families.

Training support

- Cierco-Ayrolles, C. et San Cristobal, M. (2012) Rappels et compléments d’algèbre linéaire. Formation aux Statistiques pour les données post-génomiques – Module 2 « Outils statistiques de base », Genotoul

- Cierco-Ayrolles, C. et San Cristobal, M. (2012) Classification non supervisée. Formation aux Statistiques pour les données post-génomiques – Module 2 « Outils statistiques de base », Genotoul

- Baccini, A., Badia, J., Besse, P., Cierco-Ayrolles, C., Déjean, S., Gaspin, C., Goulard, M., Klopp, C., Jasson, S., San Cristobal, M., Sokol, S. and Tosser-Klopp, G. (2005) Bio-Informatique – Analyse des données d’expression – Travaux pratiques. Formation Toulouse Génopole Midi-Pyrénées

- Baccini, A., Badia, J., Besse, P., Cierco-Ayrolles, C., Déjean, S., Gaspin, C., Goulard, M., Klopp, C., Jasson, S., San Cristobal, M., Sokol, S. and Tosser-Klopp, G. (2005) Bio-Informatique – Analyse des données d’expression – Le logiciel R. Formation Toulouse Génopole Midi-Pyrénées

- Baccini, A., Badia, J., Besse, P., Cierco-Ayrolles, C., Déjean, S., Gaspin, C., Goulard, M., Klopp, C., Jasson, S., San Cristobal, M., Sokol, S. and Tosser-Klopp, G. (2005) Bio-Informatique – Analyse des données d’expression – Etude de cas. Formation Toulouse Génopole Midi-Pyrénées

- Cierco-Ayrolles, C. (2000). Cours de Probabilités de première année du Magistère d'Economiste-Statisticien, Universités Toulouse I Capitole et Toulouse III Paul Sabatier.

Qualifications and other responsibilities

Qualifications

• PhD in Applied Mathematics (1996), Problèmes statistiques liés à la détection et à la localisation d’un gène à effet quantitatif. PhD Thesis, Paul Sabatier University (Toulouse III)
  
• B.Sc in Pure Mathematics (1990) and M.Sc in Applied Mathematics (1993), Paul Sabatier University (Toulouse III)
• Agrégation de Mathématiques (1991)

Other responsibilities

2013 - now : In charge of the Human Ressources of the MIA Department

2012 - now : Deputy Director of the MIAT Unit

2011 - now : Statistical Editor of Animal

2010 - now : In charge of the UE « Génomique et Génétique Statistique » (with Maxime Bonhomme),  Master of Bioinformatics and System Biology, Paul Sabatier University (Toulouse III)

2013 : Co-chair of the organizing committee of JOBIM 2013

2010 – 2013 : Head of the SaAB Team

2008 – 2012 : In charge of the PhD students of the MIA Department

Contact informations

• Unité MIAT - Centre INRA de Toulouse Midi-Pyrénées - 24 Chemin de Borde-Rouge - CS 52627 - 31326 CASTANET-TOLOSAN Cedex
• Tel: +33(0)5.61.28.54.29
• Email: Christine[dot]Cierco-Ayrolles[at]toulouse[dot]inra[dot]fr