Research Side Effects

Statistics, Life, Science and Data as come across by Boris Hejblum

Hi, I’m Boris

I am currently Research Faculty (Chargé de Recherche) at Inserm Bordeaux Population Health research center U1219, and I am co-director of the SISTM team from both INRIA and INSERM institutes, which foster my research activities.

Broadly speaking, my main research focus is on the longitudinal analysis of high-dimensional biomedical data. My latest projects include gene set analysis of longitudinal gene expression, statistical processing of (longitudinal) flow-cytometry data through Bayesian nonparametric modeling and Optimal Transport, probabilistic analysis of high-dimensional data from Electronic Health Records, and methods development for multi-omics integrative analysis.

In 2024, I obtained my Accreditation to Supervize Research (Habilitation à Diriger des Recherches). Until 2021, I was tenured associate professor (Maître de Conférences) at the Bordeaux School of Public Health from the University of Bordeaux. Before that I was a postdoc with Tianxi Cai at the Harvard T.H. Chan School of Public Health in Boston. Before that I did my Ph.D. in Public Health - Biostatistics at ISPED in Bordeaux, France, under the supervision of François Caron and Rodolphe Thiébaut. I graduated from the ENSAI (National School for Statistics and Information Analysis — part of the very French Grandes Écoles system) in 2011, where I majored in Biostatistics. In case you would want to learn more about my curriculum, please go see my CV or check my LinkedIn profile.

Interests

Bayesian nonparametrics
High-dimensional biomedical data
Longitudinal analysis
RNAseq data analysis
Single-cell data analysis
Surrogate markers
Vaccine studies

Education

Accreditation to Supervize Research (H.D.R.), 2024

Université de Bordeaux
PhD in Biostatistics, 2015

Université de Bordeaux
Engineer in Statistics, 2011

ENSAI
MSc Statistics, 2011

Université de Rennes

Selected Publications

D Zhou, H Tong, L Wang, S Liu, X Xiong, Z Gan, R Griffier, B Hejblum, Y-C Liu, C Hong, C-L Bonzel, T Cai, K Pan, Y-L Ho, L Costa, VA Panickan, JM Gaziano, K Mandl, V Jouhet, R Thiebaut, Z Xia, K Cho, K Liao, T Cai (2025). Representation Learning to Advance Multi-institutional Studies with Electronic Health Record Data. arXiv 2502.08547.

Preprint PDF

A Hughes, L Parast, R Thiébaut, BP Hejblum (2025). Rank-Based Identification of High-dimensional Surrogate Markers: Application to Vaccinology. arXiv 2502.03030.

Preprint PDF R code

T Ferté, D Dutartre, BP Hejblum, R Griffier, V Jouhet, R Thiébaut, P Legrand, X Hinaut (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

B Hivert, D Agniel, R Thiébaut, BP Hejblum (2024). Running in circles: practical limitations for real-life application of data fission and data thinning in post-clustering differential analysis. arXiv 2405.13591.

Preprint PDF R code

B Hivert, D Agniel, R Thiébaut, BP Hejblum (2024). Post-clustering difference testing: valid inference and practical considerations. Computational Statistics & Data Analysis, 107916.

Preprint R package Article

A Collin, BP Hejblum, C Vignals, L Lehot, R Thiébaut, P Moireau, M Prague (2024). 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, 20(1):13-41.

Preprint PDF

Agniel D, Hejblum BP, Thiébaut R, Parast L (2023). Doubly-robust evaluation of high-dimensional surrogate markers. Biostatistics, 24(4):985-999.

Preprint Article R package

Freulon P, Bigot J, Hejblum BP (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

J Bigot, P Freulon, BP Hejblum, A Leclaire (2022). On the potential benefits of entropic regularization for smoothing Wasserstein estimators. arXiv 2210.06934.

Preprint PDF

HG Zhang*, BP Hejblum*, G Weber, N Palmer, S Churchill, P Szolovitz, S Murphy, K Liao, I Kohane, T Cai (2021). ATLAS: An automated association test using probabilistically linked health records with application to genetic studies. JAMIA, 28(12):2582-2592.

Preprint R package

L Lin, BP Hejblum (2021). Bayesian Mixture Models for Cytometry Data Analysis. WIREs Comp. Stat. 13(4):e1535.

PDF Article

T Ferté, S Cossin, T Schaeverbeke, T Barnetche, V Jouhet, BP Hejblum (2021). Automatic phenotyping of electronical health record: PheVis algorithm. Journal of Biomedical Informatics, 117:103746.

Preprint PDF Article R package

M Gauthier, D Agniel, R Thiébaut, BP Hejblum (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

BP Hejblum*, K Kunzmann*, E Lavagnini, A Hutchinson, DS Robertson, SC Jones, AH Eckes-Shephard (2020). Realistic and Robust Reproducible Research for Biostatistics. Preprints 2020060002.

Preprint PDF

E Lhomme, BP Hejblum, C Lacabaratz, A Wiedemann, JD Lelièvre, Y Lévy, R Thiébaut, L Richert (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

L Desquilbet, S Granger, BP Hejblum, A Legrand, P Pernot, NP Rougier (2019). Vers une recherche reproductible : Faire évoluer ses pratiques. Bordeaux : Urfist de Bordeaux. ISBN : 979-10-97595-05-0.

PDF Source Document Bookdown

BP Hejblum, C Alkhassim, R Gottardo, F Caron, R Thiébaut (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

D Commenges, C Alkhassim, R Gottardo, BP Hejblum, R Thiébaut (2018). cytometree: a binary tree algorithm for automatic gating in cytometry analysis. Cytom. A, 93(11):1132-1140.

Preprint Article R package

D Agniel, BP Hejblum (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

BP Hejblum, J Skinner, R Thiébaut (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

Hejblum BP, Ba K, Thiébaut R, Agniel D (2024). Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives. Genome Biol, 25:281.

Preprint PDF Article Zenodo sources

E White, L Papagno, A Samri, K Sugata, B Hejblum, AR Henry, DC Rogan, S Darko, P Recordon-Pinson, Y Dudoit, S Llewellyn-Lacey, LA Chakrabarti, F Buseyne, SA Migueles, DA Price, M-A Andreola, Y Satou, R Thiébaut, C Katlama, B Autran, DC Douek, V Appay (2024). Clonal succession after prolonged antiretroviral therapy rejuvenates CD8+ T cell responses against HIV-1. Nat Immunol, 25:1555–1564.

PDF Article

Blengio F, Hocini H, Richert L, Lefebvre C, Durand M, Hejblum B, Tisserand P, McLean C, Luhn K, Thiébaut R, Lévy Y (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