Publications | Boris Hejblum

T Ferté, K Ba, D Dutartre, P Legrand, V Jouhet, R Thiébaut, X Hinaut, B Hejblum (2025). Reservoir Computing in R: a Tutorial for Using reservoirnet to Predict Complex Time-Series. Computo, in press.

Chouleur T, Etchegaray C, Villain L, Lesur, A, Ferté, T, Rossi, M, Andrique, L, Simoncini C, Giacobbi, A-S, Gambaretti M, Lopci E, Fernades B, Dittmar G, Bjerkvig R, Hejblum B, Thiébaut R, Saut O, Bello L, Bikfalvi A (2025). A strategy for multimodal integration of transcriptomics, proteomics, and radiomics data for the prediction of recurrence in patients with IDH-mutant gliomas. Int. J. Cancer, 157(3):573-587.

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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.

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

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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.

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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.

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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.

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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.

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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.

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

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

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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.

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Thiébaut R, Hejblum BP, Mougin F, Tzourio C, Richert L (2023). ChatGPT and beyond with artificial intelligence (AI) in health: Lessons to be learned. Joint Bone Spine, 90(5):105607.

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C Vignals, BP Hejblum, M Prague (2023). Modéliser la COVID-19: de la population à l'individu. Interstices.

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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.

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Rinchai D, Deola S, Zoppoli G, Kabeer BS, Taleb SA, Pavlovski I, Maacha S, Gentilcore G, Toufiq M, Matthew L, Liu L, Vempalli FR, Mubarak G, Lorenz S, Sivieri I, Cirmena G, Dentone G, Cuccarolo P, Giacobbe D, Baldi F, Garbarino A, Cigolini B, Cremonesi P, Bedognetti M, Ballestrero A, Bassetti A, Hejblum BP, Augustine T, Van Panhuys N, Thiébaut R, Branco R, Chew T, Shojaei M, Short K, Feng C, PREDICT-19 consortium, Zughaier SM, De Maria A, Tang B, Ait Hssain A, Bedognetti D, Grivel J-C, Chaussabel D (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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Ferté T, Jouhet V, Greffier R, Hejblum BP, Thiébaut R (2022). The Benefit of Augmenting Open Data with Clinical Data-Warehouse EHR for Forecasting SARS-CoV-2 Hospitalizations in Bordeaux Area, France. JAMIA Open, ooac086.

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

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L Richert, JD Lelièvre, C Lacabaratz, L Hardel, H Hocini, A Wiedemann, F Lucht, I Poizot-Martin, C Bauduin, A Diallo, V Rieux, M Durand, BP Hejblum, O Launay, R Thiébaut, Y Lévy, on behalf of the ANRS VRI01 Study group (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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V Philipps, BP Hejblum, M Prague, D Commenges, C Proust-Lima (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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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.

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L Villain, T Ferté, R Thiébaut, BP Hejblum (2021). Gene Set Analysis for time-to-event outcome with the Generalized Berk–Jones statistic. bioRxiv 2021.09.07.459329.

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C Colas, B Hejblum, S Rouillon, R Thiébaut, P-Y Oudeyer, C Moulin-Frier*, M Prague* (2021). EpidemiOptim: A Toolbox for the Optimization of Control Policies in Epidemiological Models. JAIR, 71:479–519.

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Y Lévy, A Wiedemann, BP Hejblum, M Durand, C Lefebvre, M Surenaud, C Lacabaratz, MPerreau, E Foucat, M Décheneaud, P Tisserand, F Blengio, B Hivert, M Gauthier, M Cervantes-Gonzalez, D Bachelet, C Laouénan, L Bouadma, J-F Timsit, Y Yazdanpanah, G Pantaléo, H Hocini, R Thiébaut, for the French COVID cohort study group (2021). CD177, a specific marker of neutrophil activation, is a hallmark of COVID-19 severity and death. iScience, 24(7):102711.

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

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N Acar, BMJ Merle, S Ajana, Z He, S Grégoire, BP Hejblum, L Martine, B Buaud, AM Bron, CP Creuzot-Garcher, J-F Korobelnik, O Berdeaux, H Jacqmin-Gadda, L Bretillon, C Delcourt, for the Biomarkers of Lipid Status And metabolism in Retinal ageing (BLISAR) Study Group (2021). Predicting the retinal content in omega-3 fatty acids for age-related macular-degeneration. Clin. Transl. Med., 11:e404.

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M Gauthier, D Agniel, R Thiébaut, BP Hejblum (2021). Distribution-free complex hypothesis testing for single-cell RNA-seq differential expression analysis. bioRxiv 2021.05.21.445165.

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S Ajana, A Cougnard-Grégoire, JM Colijn, BMJ Merle, T Verzijden, PTVM de Jong, A Hofman, EYE-RISK Consortium, JR Vingerling, BP Hejblum, J-F Korobelnik, MA Meester-Smoor, H Jacqmin-Gadda, CCW Klaver, C Delcourt (2021). Predicting progression to advanced age-related macular degeneration from clinical, genetic and lifestyle factors using machine learning. Ophthalmology 128(4):587-597.

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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.

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S Lefèvre-Arbogast, BP Hejblum, C Helmer, C Klose, C Manach, DY Low, M Urpi-Sarda, C Andres-Lacueva, R González-Domínguez, L Aigner, B Altendorfer, PJ Lucassen, SR Ruigrok, C De Lucia, A Du Preez, C Proust-Lima, S Thuret, A Korosi, C Samieri (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.

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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.

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L Bouadma, A Wiedemann, J Patrier, M Surénaud, PH Wicky, E Foucat, JL Diehl, BP Hejblum, F Sinnah, E de Montmollin, C Lacabaratz, R Thiébaut, J-F Timsit, Y Lévy (2020). Immune alterations during SARS-CoV-2-related acute respiratory distress syndrome. Journal of Clinical Immunology, 40:1082-1092.

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A Wiedemann, E Foucat, H Hocini, C Lefebvre, BP Hejblum, M Durand, M Krüger, AK Keita, A Ayouba, S Mély, J-C Fernandez, A Touré, S Fourati, C Lévy-Marchal, H Raoul, E Delaporte, L Koivogui, R Thiébaut, C Lacabaratz, Y Lévy, PostEboGui Study Group (2020). Long-lasting severe immune dysfunction in Ebola virus disease survivors. Nat Commun 11, 3730.

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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.

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SF Chan, BP Hejblum, A Chakrabortty, T Cai (2020). Semi-Supervised Estimation of Covariance with Application to Phenome-wide Association Studies with Electronic Medical Records Data. Stat Methods Med Res, 29(2):455-465.

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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.

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S Ajana, A Niyazi, L Bretillon, BP Hejblum, H Jacqmin-Gadda, C Delcourt (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.

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DY Low*, S Lefèvre‐Arbogast*, R González‐Domínguez, M Urpi‐Sarda, P Micheau, M Petera, D Centeno, S Durand, E Pujos‐Guillot, A Korosi, PJ Lucassen, L Aigner, C Proust‐Lima, BP Hejblum, C Helmer, C Andres‐Lacueva, S Thuret, C Samieri*, C Manach* (2019). Diet‐Related Metabolites Associated with Cognitive Decline Revealed by Untargeted Metabolomics in a Prospective Cohort. Mol. Nutr. Food Res., 63(18):1900177.

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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.

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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.

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R Thiébaut, BP Hejblum, H Hocini, H Bonnabau, J Skinner, M Montes, C Lacabaratz, L Richert, K Palucka, J Banchereau, Y Levy (2019). Gene expression signatures associated with immune and virological responses to therapeutic vaccination with Dendritic Cells in HIV-infected individuals. Front. Immunol., 10:874.

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BP Hejblum, GM Weber, KP Liao, NP Palmer, S Churchill, NA Shadick, P Szolovits, SM Murphy, IS Kohane, T Cai (2019). Probabilistic record linkage of de-identified research datasets with discrepancies using diagnosis codes. Sci. Data, 6:180298.

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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.

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BP Hejblum, J Cui, LJ Lahey, A Cagan, JA Sparks, J Sokolove, T Cai, KP Liao (2018). Association between anti-citrullinated fibrinogen antibodies and coronary artery disease in rheumatoid arthritis. Arthritis Care Res, 70(7):1113-1117.

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JA Sinnott, F Cai, S Yu, BP Hejblum, C Huong, IS Kohane, KP Liao (2018). PheProb: probabilistic phenotyping using diagnosis codes to improve power for genetic association studies. JAMIA, 25(10):1359-1365.

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S Lefèvre-Arbogast, D Gaudout, J Bensalem, L Letenneur, JF Dartigues, BP Hejblum, C Féart, C Delcourt, C Samieri (2018). Pattern of polyphenol intake and the long-term risk of dementia in older persons. Neurology, 90(22):e1979-e1988.

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

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KP Liao*, JA Sparks*, BP Hejblum, IH Kuo, J Cui, LJ Lahey, A Cagan, VS Gainer, W Liu, TT Cai, J Sokolove, T Cai (2017). Phenome-wide association study of autoantibodies to citrullinated and non-citrullinated epitopes in rheumatoid arthritis. Arthritis & Rheumatology, 69(4):742-749.

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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.

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A Rechtien, L Richert, H Lorenzo, G Martrus, BP Hejblum, C Dahlke, R Kasonta, M Zinser, H Stubbe, U Matschl, A Lohse, V Krähling, M Eickmann, S Becker, VEBCON Consortium, R Thiébaut, M Altfeld, M Addo (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.

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B Liquet, P Lafaye de Micheaux, BP Hejblum, R Thiébaut (2016). Group and Sparse Group Partial Least Square Approaches Applied in Genomics Context. Bioinformatics, 32(1):35-42.

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BP Hejblum, J Skinner, R Thiébaut (2015). Time-Course Gene Set Analysis for Longitudinal Gene Expression Data. PLoS Comput Biol, 11(6):e1004310.

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R Thiébaut, B Hejblum, L Richert (2014). The analysis of 'Big Data' in clinical research. Rev Epidemiol Sante Publique, 62(1):1-4.

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D Furman*, BP Hejblum*, N Simon, V Jojic, CL Dekker, R Thiébaut, RJ Tibshirani, MM Davis (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.

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D Commenges, BP Hejblum (2013). Evidence synthesis through a degradation model applied to myocardial infarction. LiDA, 19(1):1-18.

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