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INRA GABI Unit

GABI : Génétique Animale et Biologie IntégrativeUnité Mixte de Recherche INRA - AgroParisTech

Florence JAFFREZIC, Senior Research Scientist

JAFFREZIC florence
Fields of research : Methodological development for high-throughput genomic data, mainly transcriptomic (microarray and RNA-seq): differential analysis and gene network inference. Mixed models (linear, non linear and generalized linear models), stochastic EM algorithm, heterogeneous variance modelling, longitudinal data analysis (covariance structure modelling).
  • INRA, UMR 1313 Génétique Animale et Biologie Intégrative
  • Domaine de Vilvert, Bat 211, 78352 Jouy en Josas
  • Phone: +33 (0) 1 34 65 21 94   Fax  : +33 (0) 1 34 65 22 10
  • Email : florence.jaffrezic(at)jouy.inra.fr

 CV 

2011 : HDR (Habilitation à Diriger les Recherches), University of Rennes I : "Mixed Model Methodology for Genomic Data Analysis".

2001 : PhD at Edinburgh University (UK) : "Statistical Models for the Genetic Analysis of Longitudinal Data", with WG Hill and R. Thompson.

1998 : Master of Science in Mathematical Statistics, with distinction, University of Rennes I.

1998 : Engineer School of Statistics ENSAI (Ecole Nationale de la Statistique et de l’Analyse de l’Information).

Team 

Populations, Statistics and Genome (PSGen)

 

Fields of research

Methodological development for high-throughput genomic data, mainly transcriptomic (microarray and RNA-seq): differential analysis and gene network inference. Mixed models (linear, non linear and generalized linear models), stochastic EM algorithm, heterogeneous variance modelling, longitudinal data analysis (covariance structure modelling).

 

Other activities 

Supervision

Since Sept. 2014: Co-supervision with Grégory Nuel (UPMC) of Gilles Monneret PhD "Estimation d'effets causaux dans les réseaux de régulation génique à partir d'observations et d'interventions".

Since Sept. 2013: Co-supervision with Gilles Celeux (INRIA, Orsay) of Mélina Gallopin (ISUP) PhD « Gene network inference from high-throughput RNA-seq data ».

2006-2009: Co-supervision with Jean-Louis Foulley of Guillemette Marot (ENSAI) PhD : « Statistical analysis of gene expression data (detection of differentially expressed genes, meta-analysis) ».

2007-2010: Co-supervision with Rebecca Doerge and Jean-Louis Foulley of Andrea Rau (Purdue University, USA) PhD : « Dynamic gene network inference from transcriptomic data ».

Teaching 

Mixed model course at ENSAI (20h)

Software (R packages) 

HTSFilter (2013): Filter replicated high-throughput transcriptome sequencing data
http://bioconductor.org/packages/release/bioc/html/HTSFilter.html
metaRNASeq (2013): Meta-analysis of RNA-seq data
http://r-forge.r-project.org/R/?group_id=1504

Most relevant publications and other productions

Marot G, Foulley JL, Mayer CD,Jaffrézic F, 2009. Moderated effect size combination for microarray meta-analyses and comparison study.Bioinformatics,25(20): 2692-2699.

Rau A,Jaffrézic F, Foulley JL, Doerge RW, 2010. An empirical bayesian method for estimating biological networks from temporal microarray data,Statistical Applications in Genetics and Molecular Biology, 9(1):9.

Rau A,Jaffrézic F, Foulley JL, Doerge RW, 2012. Reverse engineering gene regulatory networks using approximate bayesian computation,Statistics and Computing,22:1257–1271, DOI 10.1007/s11222-011-9309-1.

Mary-Huard T, Jaffrézic F, Robin S, 2012 ExactDAS: An exact test procedure for the detection of differential alternative splicing in microarray experiments, 11(5).

Dillies MA, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, Keime C, Marot G, Castel D, Estelle J, Guernec G, Jagla B, Jouneau L, Laloë D, Le Gall C, Schaëffer B, Le Crom S, Guedj M, andJaffrézic Fon behalf of The French StatOmique Consortium, 2012. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis,Briefings in Bioinformatics,doi:10.1093/bib/bbs046.

Rau A, Gallopin M, Celeux G, Jaffrézic F, 2013. Data-based filtering for replicated high-throughput transcriptome sequencing experiments, Bioinformatics, 29:2146-2152.