Selected Publications

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

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

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

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(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.

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

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

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

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

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Recent Publications

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(2021). Predicting progression to advanced age-related macular degeneration from clinical, genetic and lifestyle factors using machine learning. Ophthalmology 128(4):587-597, 2021.


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

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

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

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

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Recent Posts

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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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