Chercheur (Chargé de Recherche à l’Inserm)

Parcours

  • 2021 – en cours Chargé de Recherche en Biostatistique à l’Inserm Bordeaux-Population-Health — équipe SISTM
  • 2016 – 2021 Maître de Conférences section 26 en Biostatistique à l’ISPED
  • 2015 – 2016 Post-doctorant à la Harvard T.H. Chan School of Public Health avec Tianxi Cai
  • 2015 Docteur en Santé Publique – option Biostatistique de l’université de Bordeaux
    Thèse « Analyse intégrative de données de grande dimension appliquée à la recherche vaccinale » effectuée sous la direction de Rodolphe Thiébaut et de François Caron à l’ISPED (Institut de Santé Publique, d’Epidémiologie et de Developpement) ; Inserm U897, au sein l’équipe Biostatistiques
  • 2011 Ingénieur en Statistique de l’ENSAI (École Nationale de la Statistique et de l’Analyse de l’Information) –  spécialité Statistique pour les Sciences de la Vie
  • 2011 Master en Statistique, Économétrie de l’Université de Rennes 1

Logiciels

  • dearseq an R package to perform Differential Expression Analysis for RNA-seq data through a robust variance component test. Available on Bioconductor, development version available on GitHub.
  • cytometree an R package to perform Automatic gating and annotation of cytometry data. Available on CRAN, development version available on GitHub.
  • kernSCR an R package to perform KERNel machine score test for pathway analysis in the presence of Semi-Competing Risks. Available on CRAN, development version available on GitHub.
  • ludic an R package to perform probabilistic record Linkage Using only DIagnosis Codes without direct identifiers, using C++ code to speed up computations. Available on CRAN, development version on github.
  • foodingraph an R package to perform Food Network Inference and Visualization developped with Victor Gasque. Available on CRAN, development version on GitHub.
  • kernscr an R package to perform kernel machine score test for pathway analysis in the presence of semi-competing risks. Available on CRAN, development version available on github.
  • NPflow an R package to perform Dirichlet process mixture of multivariate normal, skew-normal or skew t-distributions modeling oriented towards flow-cytometry data preprocessing applications, using C++ code to speed up computations. Available on CRAN, development version on github.
  • PheVis an R package to perform automatic instant phenotype prediction at the visit level from EHR data that can be used for either chronic or acute conditions, developped with Thomas Ferte. Development version available on gitlab.
  • TcGSA an R package to analyze longitudinal gene-expression data at the gene set level. Available on CRAN, development version on github.
  • tcgsaseq an R package to perform gene set analysis of longitudinal RNA-seq data with variance component score test, accounting for data heteroscedasticity through precision weights. Available on CRAN, development version on github.
  • vici an R package to perform accurate estimation of vaccine induced cellular immunogenicity with bivariate linear modeling. Available on CRAN, development version on GitHub. Try te interactive web app here.

Publications

*: equal contribution

preprints

  • 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
  • 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
  • Collin A, Hejblum BP, Vignals C, Lehot L, Thiébaut R, Moireau P, Prague M. Using population based Kalman estimator to model COVID-19 epidemics in France: estimating the burden of SARS-CoV-2 and the effects of NPI. medRxiv 2021.07.09.21260259, 2021.
    DOI: 10.1101/2021.07.09.21260259
  • Freulon P, Bigot J, Hejblum BP. CytOpT: Optimal Transport with Domain Adaptation for Interpreting Flow Cytometry data. arXiv:2006.09003, 2020.
    arXiv:2006.09003
  • Prague M, Wittkop L, Clairon Q, Dutartre D, Thiébaut R, Hejblum BP. Population modeling of early COVID-19 epidemic dynamics in French regions and estimation of the lockdown impact on infection rate. medRxiv 2020.04.21.20073536, 2020.
    DOI: 10.1101/2020.04.21.20073536
  • 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

2021

  • 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. High temporal resolution transcriptomic profiling delineates distinct patterns of interferon response following Covid-19 mRNA vaccination and SARS-CoV2 infection. bioRxiv 2021.12.12.472257, 2021.
    DOI: 10.1101/2021.12.12.472257
  • 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
  • Lin L, Hejblum BP. Bayesian Mixture Models for Cytometry Data Analysis. Wiley Interdisciplinary Reviews: Computational Statistics 13(4):e1535, 2021.
    DOI: 10.1002/wics.1535
  • Zhang HG*, Hejblum BP*, Weber G, Palmer N, Churchill S, Szolovitz 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
  • Philipps V, Hejblum BP, M Prague, D Commenges, C Proust-Lima. Robust and Efficient Optimization Using a Marquardt-Levenberg Algorithm with R Package marqLevAlg. R journal, in press, 2021.
    arXiv:2009.03840
  • Colas C, Hejblum B, Rouillon S, Thiébaut R, Oudeyer PY, 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
  • 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 JF, Yazdanpanah Y, Pantaleo G, Hocini H, Thiébaut R, for the French COVID cohort study group. CD177, a specific marker of neutrophil activation, is a hallmark of COVID-19 severity and death. iScience, 24(7):102711, 2021.
    DOI: 10.1016/j.isci.2021.102711
  • Acar N, Merle BMJ, Ajana S, He Z, Grégoire S, Hejblum BP, Martine L, Buaud B, Bron AM, Creuzot-Garcher CP, Korobelnik J-F, 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. Clin. Transl. Med., 11:e404, 2021.
    DOI: 10.1002/ctm2.404
  • Ajana S, Cougnard-Grégoire A, Colijn JM, Merle BMJ, Verzijden T, de Jong PTVM, Hofman A, EYE-RISK Consortium, Vingerling JR, Hejblum BP, Korobelnik J-F, Meester-Smoor MA, Jacqmin-Gadda H, Klaver CCW, 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
  • 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

2020

  • Wiedemann A, Foucat E, Hocini H, Lefebvre C, Hejblum BP, Durand M, Krüger M, Keita AK, Ayouba A, Mély S, Fernandez J-C, Touré A, Fourati S, Lévy-Marchal C, Raoul H, Delaporte E, Koivogui L, Thiébaut R, Lacabaratz C, Lévy Y, PostEboGui Study Group (2020). Long-lasting severe immune dysfunction in Ebola virus disease survivors. Nat Commun 11, 3730.
    DOI: 10.1038/s41467-020-17489-7
  • Bouadma L, Wiedemann A, Patrier J, Surenaud M, Wicky PH, Foucat E, Diehl JL, Hejblum BP, Sinnah F, de Montmollin E, Lacabaratz C, Thiébaut R, Timsit J-F, Lévy Y. Immune alterations during SARS-CoV-2-related acute respiratory distress syndrome. Journal of Clinical Investigations in press, 2020.
    DOI: 10.1007/s10875-020-00839-x
  • Lhomme E, Hejblum BP, Lacabaratz C, Wiedemann A, Lelièvre JD, 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
  • 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(2):455-465, 2020.
    DOI: 10.1177/ 0962280219837676
  • Ajana S, Cougnard-Grégoire A, Colijn JM, Merle BMJ, Verzijden T, de Jong PTVM, Hofman A, EYE-RISK Consortium, Vingerling JR, Hejblum BP, Korobelnik J-F, Meester-Smoor MA, Jacqmin-Gadda H, Klaver CCW, Delcourt C, Predicting progression to advanced age-related macular degeneration from clinical, genetic and lifestyle factors using machine learning, Ophthalmology, in press, 2020.

2019

  • Ajana S, Niyazi A, Bretillon L, Hejblum BP, Jacqmin-Gadda H, Delcourt C, 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, 2019.
    DOI: 10.1093/bioinformatics/btz135
  • Desquilbet L, Granger S, Hejblum BP, Legrand A, Pernot P, Rougier NP, Vers une recherche reproductible : Faire évoluer ses pratiques, Bordeaux : Urfist de Bordeaux, 2019.
    ISBN: 979-10-97595-05-0
  • 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
  • Hejblum BP, Weber GM, Liao KP, Palmer NP, Churchill S, Shadick NA, Szolovits P, Murphy S, Kohane IS, Cai T, Probabilistic record linkage of de-identified research datasets with discrepancies using diagnosis codes, Scientific Data, 6:180298, 2019.
    DOI: 10.1038/sdata.2018.298
  • 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 S*, González‐Domínguez R, Urpi‐Sarda M, Micheau P, Petera M, Centeno D, Durand S, Pujos‐Guillot E, 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(18):1900177, 2019.
    DOI: 10.1002/mnfr.201900177

2018

  • 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, Huong 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
  • 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(7):1113-1117, 2018.
    DOI: 10.1002/acr.23444
  • Lefèvre-Arbogast S, Gaudout D, Bensalem J, Letenneur L, Dartigues JF, Hejblum BP, Féart C, Delcourt C, Samieri C, Pattern of polyphenol intake and the long-term risk of dementia in older persons, Neurology, 90(22):e1979-e1988, 2018.
    DOI: 10.1212/WNL.0000000000005607
  • Neykov M, Hejblum BP, Sinnott JA, Kernel Machine Score Test for Pathway Analysis in the Presence of Semi-Competing Risks, Stat Methods in Med Res, 27(4):1099-1114, 2018.
    DOI: 10.1177/ 0962280216653427

2017

  • Agniel D and 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 BP, Dahlke C, Kasonta R, Zinser M, Stubbe H, Matschl U, Lohse A, Krähling V, Eickmann M, Becker S, VEBCON Consortium, Thiébaut R, Altfeld M, and 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 IH, 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 non-citrullinated epitopes in rheumatoid arthritis, Arthritis & Rheumatology, 69: 742–749, 2017. DOI: 10.1002/art.39974

2016

  • Liquet B, Lafaye de Micheaux P, Hejblum BP, Thiébaut R, Group and Sparse Group Partial Least Square Approaches Applied in Genomics Context, Bioinformatics 32(1): 35-42, 2016. DOI:10.1093/bioinformatics/btv535

2015

  • Hejblum BP, Skinner J, Thiébaut R, Time-Course Gene Set Analysis for Longitudinal Gene Expression Data, PLoS Comput Biol 11(6): e1004310, 2015. DOI: 10.1371/journal.pcbi.1004310.
  • Furman D*, Hejblum BP*, Simon N, Jojic V, Dekker CL, Thiébaut R, Tibshirani RJ, Davis MM, A systems analysis of sex differences reveals an immunosuppressive role for testosterone in the response to influenza vaccination, PNAS, 111(2):869–874, 2014. DOI: 10.1073/pnas.1321060111.

2014

  • Thiébaut R, Hejblum B, Richert L, L’analyse des «Big Data» en recherche clinique, Revue d’Épidémiologie et de Santé Publique, 62(1):1–4, 2014. DOI: 10.1016/j.respe.2013.12.021

2013

  • Commenges D and Hejblum BP,  Evidence synthesis through a degradation model applied to myocardial infarction, Lifetime Data Analysis 19(1): 1–18, 2013. DOI: 10.1007/s10985-012-9227-3.
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