# Selected Publications

(2022). CytOpT: Optimal Transport with Domain Adaptation for Interpreting Flow Cytometry data. Annals of Applied Statistics, in press, 2022.

(2022). On the potential benefits of entropic regularization for smoothing Wasserstein estimators. arXiv 2210.06934.

(2022). Post-clustering difference testing: valid inference and practical considerations. arXiv 2210.13172.

(2022). Doubly-robust evaluation of high-dimensional surrogate markers. Biostatistics kxac020, in press.

(2021). ATLAS: An automated association test using probabilistically linked health records with application to genetic studies. JAMIA, 28(12):2582-2592.

(2021). Bayesian Mixture Models for Cytometry Data Analysis. WIREs Comp. Stat. 13(4):e1535.

(2021). Automatic phenotyping of electronical health record: PheVis algorithm. Journal of Biomedical Informatics, 117:103746.

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

(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

(2023). Using population based Kalman estimator to model COVID-19 epidemics in France: estimating the burden of SARS-CoV-2 and the effects of NPI. International of Biostatistics, in press.

(2022). High–temporal resolution profiling reveals distinct immune trajectories following the first and second doses of COVID-19 mRNA vaccines. Science Advances, 8(45): eabp9961.

(2022). T-cell immunogenicity, gene expression profile and safety of four heterologous prime-boost combinations of HIV vaccine candidates in healthy volunteers - results of the randomized multi-arm phase I/II ANRS VRI01 trial. Journal of Immunology, 208 (12): 2663–2674.

(2021). Robust and Efficient Optimization Using a Marquardt-Levenberg Algorithm with R Package marqLevAlg. The R journal, 13(2):365-379, 2021.

# 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.