Freulon P, Bigot J & Hejblum BP. CytOpT: Optimal Transport with Domain Adaptation for Interpreting Flow Cytometry data. Annals of Applied Statistics 17(2):1086-1104, 2023.
DOI: 10.1214/22-AOAS1660

Agniel D, Hejblum BP, Thiébaut R & Parast L. Doubly-robust evaluation of high-dimensional surrogate markers. Biostatistics 24(4):985-999, 2023.
DOI: 10.1093/biostatistics/kxac020

Blengio F, Hocini H, Richert L, Lefebvre C, Durand M, Hejblum B, Tisserand P, McLean C, Luhn K, Thiebaut R & Lévy Y. 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, 2023.
DOI: 10.1016/j.celrep.2023.113101

Collin A, Hejblum BP, Vignals C, Lehot L, Thiébaut R, Moireau P & Prague M. Using population based kalman estimator to model COVID-19 epidemic in france: Estimating the effects of non-pharmaceutical interventions on the dynamics of epidemic. International Journal of Biostatistics in press, 2023.
DOI: 10.1515/ijb-2022-0087

Vignals C, Hejblum BP & Prague M. Modéliser la COVID-19: De la population à l’individu. Interstices, 2023.

Thiébaut R, Hejblum B, Mougin F, Tzourio C & Richert L. ChatGPT and beyond with artificial intelligence (AI) in health: Lessons to be learned. Joint Bone Spine 90(5):105607, 2023.
DOI: 10.1016/j.jbspin.2023.105607

Bigot J, Freulon P, Hejblum BP & Leclaire A. On the potential benefits of entropic regularization for smoothing wasserstein estimators. arXiv 2210.06934, 2022.
DOI: 10.48550/arXiv.2210.06934

Hejblum BP, Ba K, Thiébaut R & Agniel D. Neglecting normalization impact in semi-synthetic RNA-Seq data simulation generates artificial false positives. bioRxiv 2022.05.10.490529, 2022.
DOI: 10.1101/2022.05.10.490529

Ferté T, Jouhet V, Greffier R, Hejblum BP & Thiébaut R. The benefit of augmenting open data with clinical data-warehouse EHR for forecasting SARS-CoV-2 hospitalizations in Bordeaux area, France. JAMIA open ooac086, 2022.
DOI: 10.1093/jamiaopen/ooac086

Richert L, Lelièvre J, Lacabaratz C, Hardel L, Hocini H, Wiedemann A, Lucht F, Poizot-Martin I, Bauduin C, Diallo A, Rieux V, Durand M, Hejblum BP, Launay O, Thiébaut R, Lévy Y, on behalf of the ANRS VRI01 Study group. 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, 2022.
DOI: 10.4049/jimmunol.2101076

Rinchai D, Deola S, Zoppoli G, Ahamed Kabeer BS, Taleb S, Pavlovski I, Maacha S, Gentilcore G, Toufiq M, Mathew L, Liu L, Vempalli FR, Mubarak G, Lorenz S, Sivieri I, Cirmena G, Dentone C, Cuccarolo P, Giacobbe D, Baldi F, Garbarino A, Cigolini B, Cremonesi P, Bedognetti M, Ballestrero A, Bassetti M, 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, Chaussabel D. High–temporal resolution profiling reveals distinct immune trajectories following the first and second doses of COVID-19 mRNA vaccines. Science Advances 8(45):eabp9961, 2022.
DOI: 10.1126/sciadv.abp9961

Gauthier M, Agniel D, Thiébaut R & Hejblum BP. Distribution-free complex hypothesis testing for single-cell RNA-seq differential expression analysis. bioRxiv 2021.05.21.445165, 2021.
DOI: 10.1101/2021.05.21.445165

Acar N, Merle BMJ, Ajana S, He Z, Grégoire S, Hejblum BP, Martine L, Buaud B, Bron AM, Creuzot-Garcher CP, Korobelnik J, Berdeaux O, Jacqmin-Gadda H, Bretillon L, Delcourt C, for the Biomarkers of Lipid Status And metabolism in Retinal ageing (BLISAR) Study Group. Predicting the retinal content in omega-3 fatty acids for age-related macular-degeneration. Clinical and Translational Medicine 11(7):e404, 2021.
DOI: 10.1002/ctm2.404

Lefèvre-Arbogast S, Hejblum BP, Helmer C, Klose C, Manach C, Low DY, Urpi-Sarda M, Andres-Lacueva C, González-Domínguez R, Aigner L, Altendorfer B, Lucassen PJ, Ruigrok SR, De Lucia C, Du Preez A, Proust-Lima C, Thuret S, Korosi A & Samieri C. 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, 2021.
DOI: 10.1016/j.ebiom.2021.103216

Lévy Y, Wiedemann A*, Hejblum BP*, Durand M, Lefebvre C, Surénaud M, Lacabaratz C, Perreau M, Foucat E, Déchenaud M, Tisserand P, Blengio F, Hivert B, Gauthier M, Cervantes-Gonzalez M, Bachelet D, Laouénan C, Bouadma L, Timsit J, Yazdanpanah Y, Pantaleo G, Hocini H & Thiébaut R. CD177, a specific marker of neutrophil activation, is associated with coronavirus disease 2019 severity and death. iScience 24(7):102711, 2021.
DOI: 10.1016/j.isci.2021.102711

Colas C, Hejblum B, Rouillon S, Thiébaut R, Oudeyer P, Moulin-Frier C & Prague M. EpidemiOptim: A toolbox for the optimization of control policies in epidemiological models. Journal of Artificial Intelligence Research 71:479-519, 2021.
DOI: 10.1613/jair.1.12588

Zhang HG*, Hejblum BP*, Weber G, Palmer N, Churchill S, Szolovits P, Murphy S, Liao K, Kohane I & Cai T. ATLAS: An automated association test using probabilistically linked health records with application to genetic studies. Journal of the American Medical Informatics Association 28(12):2582-2592, 2021.
DOI: 10.1093/jamia/ocab187

Ferte T, Cossin S, Schaeverbeke T, Barnetche T, Jouhet V & Hejblum BP. Automatic phenotyping of electronical health record: PheVis algorithm. Journal of Biomedical Informatics 117:103746, 2021.
DOI: 10.1016/j.jbi.2021.103746

Ajana S, Cougnard-Grégoire A, Colijn J, Merle BM, Verzijden T, Jong P, Hofman A, EYE-RISK Consortium, Vingerling J, Hejblum BP, Korobelnik J, Meester-Smoor M, Jacqmin-Gadda H, Klaver C, Delcourt C. Predicting progression to advanced age-related macular degeneration from clinical, genetic and lifestyle factors using machine learning. Ophthalmology 128(4):587-597, 2021.
DOI: 10.1016/j.ophtha.2020.08.031

Philipps V, Hejblum BP, Prague M, Commenges D & Proust-Lima C. Robust and efficient optimization using a marquardt- levenberg algorithm with r package marqLevAlg. The R Journal 13(2):365-379, 2021.
DOI: 10.32614/RJ-2021-089

Villain L, Ferté T, Thiébaut R & Hejblum BP. Gene set analysis for time-to-event outcome with the generalized berk-jones statistic. bioRxiv 2021.09.07.459329, 2021.
DOI: 10.1101/2021.09.07.459329

Lin L & Hejblum BP. Bayesian mixture models for cytometry data analysis. Wiley Interdisciplinary Reviews: Computational Statistics 13:e1535, 2021.
DOI: 10.1002/wics.1535

Hejblum BP, Kunzmann K, Lavagnini E, Hutchinson A, Robertson DS, Jones SC & Eckes-Shephard AH. Realistic and robust reproducible research for biostatistics. Preprints 2020060002, 2020.
DOI: 10.20944/preprints202006.0002.v1

Bouadma L, Wiedemann A, Patrier J, Surenaud M, Wicky P, Foucat E, Diehl J, Hejblum BP, Sinnah F, Montmollin E, Lacabaratz C, Thiébaut R, Timsit J & Lévy Y. Immune alterations during SARS-CoV-2-related acute respiratory distress syndrome. Journal of Clinical Immunology 40:1082-1092, 2020.
DOI: 10.1007/s10875-020-00839-x

Lhomme E, Hejblum BP, Lacabaratz C, Wiedemann A, Lelièvre J, Lévy Y, Thiébaut R & Richert L. Analyzing cellular immunogenicity in vaccine clinical trials: A new statistical method including non-specific responses for accurate estimation of vaccine effect. Journal of Immunological Methods 477:112711, 2020.
DOI: 10.1016/j.jim.2019.112711

Gauthier M, Agniel D, Thiébaut R & Hejblum BP. 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, 2020.
DOI: 10.1093/nargab/lqaa093

Wiedemann A, Foucat E, Hocini H, Lefebvre C, Hejblum BP, Durand M, Krüger M, Keita AK, Ayouba A, Mély S, Fernandez J, Touré A, Fourati S, Lévy-Marchal C, Raoul H, Delaporte E, Koivogui L, Thiébaut R, Lacabaratz C, Lévy Y, PostEboGui Study Group. Long-lasting severe immune dysfunction in ebola virus disease survivors. Nature Communications 11:3730, 2020.
DOI: 10.1038/s41467-020-17489-7

Chan SF, Hejblum BP, Chakrabortty A & Cai T. Semi-supervised estimation of covariance with application to phenome-wide association studies with electronic medical records data. Statistical Methods in Medical Research 29:455-465, 2020.
DOI: 10.1177/0962280219837676

Hejblum BP, Alkhassim C, Gottardo R, Caron F & Thiébaut R. Sequential dirichlet process mixture of skew t-distributions for model-based clustering of flow cytometry data. Annals of Applied Statistics 13(1):638-660, 2019.
DOI: 10.1214/18-AOAS1209

Ajana S, Niyazi A, Bretillon L, Hejblum BP, Jacqmin-Gadda H & Cécile D. Benefits of dimension reduction in penalized regression methods for high dimensional grouped data: A case study in low sample size. Bioinformatics 35:3628-3634, 2019.
DOI: 10.1093/bioinformatics/btz135

Thiébaut R, Hejblum BP, Hocini H, Bonnabau H, Skinner J, Montes M, Lacabaratz C, Richert L, Palucka K, Banchereau J & Levy Y. Gene expression signatures associated with immune and virological responses to therapeutic vaccination with dendritic cells in HIV-infected individuals. Frontiers in Immunology 10:874, 2019.
DOI: 10.3389/fimmu.2019.00874

Low DY, Lefèvre‐Arbogast G, Urpi‐Sarda M, Micheau P, Petera M, Centeno D, Durand S, Estelle P, Korosi A, Lucassen PJ, Aigner L, Proust‐Lima C, Hejblum BP, Helmer C, Andres‐Lacueva C, Thuret S, Samieri C & Manach C. Diet‐related metabolites associated with cognitive decline revealed by untargeted metabolomics in a prospective cohort. Molecular Nutrition & Food Research 63:1900177, 2019.
DOI: 10.1002/mnfr.201900177

Desquilbet L, Granger S, Hejblum BP, Legrand A, Pernot P & Rougier N. Vers une recherche reproductible : Faire évoluer ses pratiques. NA, 2019.

Hejblum BP, Cui J, Lahey LJ, Cagan A, Sparks JA, Sokolove J, Cai T & Liao KP. Association between anti-citrullinated fibrinogen antibodies and coronary artery disease in rheumatoid arthritis. Arthritis Care & Research 70:1113-1117, 2018.
DOI: 10.1002/acr.23444

Commenges D, Alkhassim C, Gottardo R, Hejblum BP & Thiébaut R. Cytometree: A binary tree algorithm for automatic gating in cytometry analysis. Cytometry: Part A 93(11):1132-1140, 2018.
DOI: 10.1002/cyto.a.23601

Sinnott JA, Cai F, Yu S, Hejblum BP, Hong C, Kohane IS & Liao KP. PheProb: probabilistic phenotyping using diagnosis codes to improve power for genetic association studies. Journal of the American Medical Informatics Association 25(10):1359-1365, 2018.
DOI: 10.1093/jamia/ocy056

Lefèvre-Arbogast S, Gaudout D, Bensalem J, Letenneur L, Dartigues J, Hejblum BP, Féart C, Delcourt C & Samieri C. Pattern of polyphenol intake and the long-term risk of dementia in older persons. Neurology, 2018.
DOI: 10.1212/WNL.0000000000005607

Hejblum BP, Weber GM, Liao KP, Palmer NP, Churchill S, Shadick NA, Szolovits P, Murphy SN, Kohane IS & Cai T. Probabilistic record linkage of de-identified research datasets with discrepancies using diagnosis codes. Scientific Data 6:180298, 2018.
DOI: 10.1038/sdata.2018.298

Neykov M, Hejblum BP & Sinnott JA. Kernel machine score test for pathway analysis in the presence of semi-competing risks. Statistical Methods in Medical Research 27(4):1099-1114, 2018.
DOI: 10.1177/0962280216653427

Agniel D & Hejblum BP. Variance component score test for time-course gene set analysis of longitudinal RNA-seq data. Biostatistics 18(4):589-604, 2017.
DOI: 10.1093/biostatistics/kxx005

Rechtien A, Richert L, Lorenzo H, Martrus G, Hejblum B, Dahlke C, Kasonta R, Zinser M, Stubbe H, Matschl U, Lohse A, Krähling V, Eickmann M, Becker S, Agnandji ST, Krishna S, Kremsner PG, Brosnahan JS, Bejon P, Njuguna P, Addo MM, Becker S, Krähling V, Siegrist CA, Huttner A, Kieny MP, Moorthy V, Fast P, Savarese B, Lapujade O, Thiébaut R, Altfeld M & Addo M. 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, 2017.
DOI: 10.1016/j.celrep.2017.08.023

Liao KP*, Sparks JA*, Hejblum BP, Kuo I, Cui J, Lahey LJ, Cagan A, Gainer VS, Liu W, Cai TT, Sokolove J & Cai T. Phenome‐wide association study of autoantibodies to citrullinated and noncitrullinated epitopes in rheumatoid arthritis. Arthritis & Rheumatology 69(4):742-749, 2017.
DOI: 10.1002/art.39974

Furman D*, Hejblum BP*, Simon N, Jojic V, Dekker CL, Thiébaut R, Tibshirani RJ & Davis MM. Systems analysis of sex differences reveals an immunosuppressive role for testosterone in the response to influenza vaccination. Proceedings of the National Academy of Sciences 111(2):869-874, 2014.
DOI: 10.1073/pnas.1321060111

Thiébaut R, Hejblum BP & Richert L. The analysis of “Big Data” in clinical research. Revue d’Épidemiologie et de Santé Publique 62(1):1-4, 2014.
DOI: 10.1016/j.respe.2013.12.021