Selected Publications

(2024). Reservoir Computing for Short High-Dimensional Time Series: an Application to SARS-CoV-2 Hospitalization Forecast. 41st ICML, PMLR 235:13570-13591.

PDF Article

(2024). Running in circles: is practical application feasible for data fission and data thinning in post-clustering differential analysis?. arXiv 2405.13591.

Preprint PDF R code

(2024). Post-clustering difference testing: valid inference and practical considerations. Computational Statistics & Data Analysis, 107916.

Preprint R package Article

(2023). Doubly-robust evaluation of high-dimensional surrogate markers. Biostatistics, 24(4):985-999.

Preprint Article R package

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

Preprint PDF Python library R package Article

(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.

Preprint PDF

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

Preprint PDF

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

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). 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.

Preprint PDF Article R package

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

Preprint PDF

(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.

PDF R package Shiny web app Article

(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

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

Preprint PDF 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

Other recent publications

More Publications

(2024). Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives. Genome Biol, 25:281.

Preprint PDF Article Zenodo sources

(2024). Clonal succession after prolonged antiretroviral therapy rejuvenates CD8+ T cell responses against HIV-1. Nat Immunol, 25:1555–1564.

PDF Article

(2023). Identification of early gene expression profiles associated with long-lasting antibody responses to the Ebola vaccine Ad26. ZEBOV/MVA-BN-Filo. Cell Reports, 42(9):113101.

PDF Article

Useful tips

Blogroll

Podcasts:

Contact