# Selected Publications

(2021). Automatic phenotyping of electronical health record: PheVis algorithm. Journal of Biomedical Informatics, 103746, in press 2021.

(2020). dearseq: a variance component score test for RNA-Seq differential analysis that effectively controls the false discovery rate. NAR Genomics and Bioinformatics, 2(4):lqaa093.

(2020). Bayesian Mixture Models for Cytometry Data Analysis. Wiley Interdisciplinary Reviews: Computational Statistics e1535, 2020.

(2020). CytOpT: Optimal Transport with Domain Adaptation for Interpreting Flow Cytometry data. arXiv 2006.09003.

(2020). Realistic and Robust Reproducible Research for Biostatistics. Preprints 2020060002.

(2020). Population modeling of early COVID-19 epidemic dynamics in French regions and estimation of the lockdown impact on infection rate. medRxiv 2020.04.21.20073536.

(2020). Analyzing cellular immunogenicity in vaccine clinical trials: a new statistical method including non-specific responses for accurate estimation of vaccine effect. JIM, 477:112711.

(2019). Vers une recherche reproductible : Faire évoluer ses pratiques. Bordeaux : Urfist de Bordeaux. ISBN : 979-10-97595-05-0.

(2019). Sequential Dirichlet process mixture of skew t-distributions for model-based clustering of flow cytometry data. Ann. Appl. Stat., 13(1):638-660.

(2018). cytometree: a binary tree algorithm for automatic gating in cytometry analysis. Cytom. A, 93(11):1132-1140.

(2017). Variance component score test for time-course gene set analysis of longitudinal RNA-seq data. Biostatistics, 18(4):589–604.

(2015). Time-Course Gene Set Analysis for Longitudinal Gene Expression Data. PLoS Comput Biol, 11(6):e1004310.

# Recent Publications

(2020). EpidemiOptim: A Toolbox for the Optimization of Control Policies in Epidemiological Models. arXiv 2010.04452.

(2020). Robust and Efficient Optimization Using a Marquardt-Levenberg Algorithm with R Package marqLevAlg. arxiv 2009.03840.

(2020). Immune alterations during SARS-CoV-2-related acute respiratory distress syndrome. Journal of Clinical Immunology, 40:1082-1092, 2020.

(2020). Long-lasting severe immune dysfunction in Ebola virus disease survivors. Nat Commun 11, 3730.

(2020). Semi-Supervised Estimation of Covariance with Application to Phenome-wide Association Studies with Electronic Medical Records Data. Stat Methods Med Res, 29(2):455-465.

# Recent Posts

### Installing Rmpi under MacOS Sierra

I recently updated my set-up, and because I use a High-Performance cluster from my University (kudos to avakas) to run various simulations and analyses, I have MPI and Rmpi installed on my laptop in order to test my scripts before submitting them to the big cluster. So I installed openmpi from homebrew very easily: brew update brew install open-mpi But then I had extensive trouble installing the Rmpi package…

### CRAN CHECK NOTE sub-directories of 1Mb or more: libs

I just released a new package on CRAN. It's called NPflow, it performs Dirichlet process mixture of multivariate normal, skew-normal or skew t-distributions modeling, you should check it out. I was a little worried because the check from Travis CI was returning a NOTE. And even though the NOTEs seem like mild problems, “you should strive to eliminate all NOTEs” before submitting to CRAN ! Preparing for an email exchange with a member of the R core team, I wrote the following in the submission comments:

### F*** Yeah, I'm published!

After a bumpy road, along which I kept in mind Jeff Leak's own worst (recent) experience, we finally got our article on Time-Course Gene Set Analysis for Longitudinal Gene Expression Data published in PLoS Computational Biology, a very nice journal ! I am really happy about it, don't hesitate to check it out ! And there is the TcGSA R package that goes with it.