Selected Publications

(2021). ATLAS: An automated association test using probabilistically linked health records with application to genetic studies. JAMIA, in press.

Preprint R package

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

PDF Article

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

Preprint PDF Article R package

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

Preprint PDF

(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.

Preprint PDF R code

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

PDF Source Document Bookdown

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

Preprint PDF R package Article

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

Preprint Article R package

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

PDF Code Article R package

Recent Publications

More Publications

(2021). Gene Set Analysis for time-to-event outcome with the Generalized Berk–Jones statistic. bioRxiv 2021.09.07.459329.

Preprint PDF

(2021). CD177, a specific marker of neutrophil activation, is a hallmark of COVID-19 severity and death. iScience, 24(7):102711.

Preprint PDF Article

(2021). EpidemiOptim: A Toolbox for the Optimization of Control Policies in Epidemiological Models. JAIR, 71:479–519.

Preprint PDF Code

(2021). Using population based Kalman estimator to model COVID-19 epidemics in France: estimating the burden of SARS-CoV-2 and the effects of NPI. medRxiv 2021.07.09.21260259.

Preprint PDF

(2021). Predicting the retinal content in omega-3 fatty acids for age-related macular-degeneration. Clin. Transl. Med., 11:e404.


Recent Posts

More Posts

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…


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:


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.


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