Publications

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. SSRN, 4071506.

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, in press.

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 (2021). 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.

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 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.

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.

A Collin, BP Hejblum, C Vignals, L Lehot, R Thiébaut, P Moireau, M Prague (2021). 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.

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

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.

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.

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.

Preprint PDF Article R package

T Ferte, 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.

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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D Agniel, L Parast, BP Hejblum (2020). Doubly-robust evaluation of high-dimensional surrogate markers. arXiv 2012.01236.

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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.

V Philipps, BP Hejblum, M Prague, D Commenges, C Proust-Lima (2020). Robust and Efficient Optimization Using a Marquardt-Levenberg Algorithm with R Package `marqLevAlg`. R journal in press.

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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.

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.

Preprint PDF Python notebooks

P Freulon, J Bigot, BP Hejblum (2020). CytOpT: Optimal Transport with Domain Adaptation for Interpreting Flow Cytometry data. arXiv 2006.09003.

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.

PDF R package Shiny web app Article

M Prague, L Wittkop, Q Clairon, D Dutartre, R Thiébaut, BP Hejblum (2020). 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.

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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.

Article R code

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.

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.

PDF Article R code

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.

PDF Source Document Bookdown

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.

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

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.

Preprint Article R package

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.

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.

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.

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.

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.

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.

Article R package

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.

Preprint PDF 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.

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.

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.

PDF Code Article R package

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

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.

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