Selected Publications

(2023). CytOpT: Optimal Transport with Domain Adaptation for Interpreting Flow Cytometry data. Annals of Applied Statistics, 17(2):1086-1104, 2022.

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

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

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

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

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

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

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

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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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(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.

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(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.

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(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.

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

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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…

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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:

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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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