Publications

Filter by type:

(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). 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

(2023). ChatGPT and beyond with artificial intelligence (AI) in health: Lessons to be learned. Joint Bone Spine, 90(5):105607.

Article

(2023). Modéliser la COVID-19: de la population à l'individu. Interstices.

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

Preprint PDF Article

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

Preprint PDF

(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.

Article

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

Preprint PDF R code Article

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

Preprint PDF

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

Preprint PDF Code

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

PDF Article

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

Article

(2021). Distribution-free complex hypothesis testing for single-cell RNA-seq differential expression analysis. bioRxiv 2021.05.21.445165.

Preprint PDF

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

Article

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

Preprint PDF Article R package

(2021). Early signature in the blood lipidome associated with subsequent cognitive decline in the elderly: A case-control analysis nested within the Three-City cohort study. EBioMedicine, 64:103216.

Article

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

Preprint PDF Article

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

PDF Article

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

Preprint PDF

(2019). Benefits of dimension reduction in penalized regression methods for high dimensional grouped data: a case study in low sample size. Bioinformatics, 35(19):3628-3634.

PDF Article R code

(2019). Diet‐Related Metabolites Associated with Cognitive Decline Revealed by Untargeted Metabolomics in a Prospective Cohort. Mol. Nutr. Food Res., 63(18):1900177.

PDF 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

(2019). Gene expression signatures associated with immune and virological responses to therapeutic vaccination with Dendritic Cells in HIV-infected individuals. Front. Immunol., 10:874.

PDF Article

(2019). Probabilistic record linkage of de-identified research datasets with discrepancies using diagnosis codes. Sci. Data, 6:180298.

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

(2018). Association between anti-citrullinated fibrinogen antibodies and coronary artery disease in rheumatoid arthritis. Arthritis Care Res, 70(7):1113-1117.

Article

(2018). PheProb: probabilistic phenotyping using diagnosis codes to improve power for genetic association studies. JAMIA, 25(10):1359-1365.

Article

(2018). Pattern of polyphenol intake and the long-term risk of dementia in older persons. Neurology, 90(22):e1979-e1988.

Article

(2018). Kernel Machine Score Test for Pathway Analysis in the Presence of Semi-Competing Risks. Stat Methods in Med Res, 27(4):1099-1114.

Article R package

(2017). Phenome-wide association study of autoantibodies to citrullinated and non-citrullinated epitopes in rheumatoid arthritis. Arthritis & Rheumatology, 69(4):742-749.

Article

(2017). Systems Vaccinology Identifies an Early Innate Immune Signature as a Correlate of Antibody Responses to the Ebola Vaccine rVSV-ZEBOV. Cell Reports, 20(9):2251-2261.

PDF Article

(2016). Group and Sparse Group Partial Least Square Approaches Applied in Genomics Context. Bioinformatics, 32(1):35-42.

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

(2014). The analysis of 'Big Data' in clinical research. Rev Epidemiol Sante Publique, 62(1):1-4.

Article

(2014). A systems analysis of sex differences reveals an immunosuppressive role for testosterone in the response to influenza vaccination. Proc Natl Acad Sci USA, 111(2):869-874.

PDF Article