Team, Visitors, External Collaborators
Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
Dissemination
Bibliography
XML PDF e-pub
PDF e-Pub


Bibliography

Major publications by the team in recent years
[1]
D. Agniel, B. P. Hejblum.
Variance component score test for time-course gene set analysis of longitudinal RNA-seq data, in: Biostatistics, 2017, vol. 18, no 4, pp. 589-604.
https://hal.inria.fr/hal-01579077
[2]
D. Commenges, C. Alkhassim, R. Gottardo, B. P. Hejblum, R. Thiébaut.
cytometree: A binary tree algorithm for automatic gating in cytometry analysis, in: Cytometry Part A, 2018, vol. 93, no 11, pp. 1132-1140.
https://hal.inria.fr/hal-01887966
[3]
D. Commenges, H. Jacqmin-Gadda.
Dynamical Biostatistical Models, Chapman and Hall/CRC, 2015.
https://hal.inria.fr/hal-01580149
[4]
A. Jarne, D. Commenges, M. Prague, Y. Levy, R. Thiébaut.
Modeling CD4 + T cells dynamics in HIV-infected patients receiving repeated cycles of exogenous Interleukin 7, in: Annals of Applied Statistics, 2017.
https://hal.inria.fr/hal-01579008
[5]
C. Pasin, F. Dufour, L. Villain, H. Zhang, R. Thiébaut.
Controlling IL-7 injections in HIV-infected patients, in: Bulletin of Mathematical Biology, 2018.
[6]
M. Prague, D. Commenges, J. M. Gran, B. Ledergerber, J. Young, H. Furrer, R. Thiébaut.
Dynamic models for estimating the effect of HAART on CD4 in observational studies: Application to the Aquitaine Cohort and the Swiss HIV Cohort Study, in: Biometrics, 2017.
https://hal.inria.fr/hal-01406614
[7]
A. Rechtien, L. Richert, H. Lorenzo, G. Martrus, B. P. Hejblum, C. Dahlke, R. Kasonta, M. Zinser, H. Stubbe, U. Matschl, A. Lohse, V. Krähling, M. Eickmann, S. Becker, R. Thiébaut, M. Altfeld, M. Addo.
Systems Vaccinology Identifies an Early Innate Immune Signature as a Correlate of Antibody Responses to the Ebola Vaccine rVSV-ZEBOV, in: Cell Reports , 2017, vol. 20, no 9, pp. 2251 - 2261.
https://hal.inria.fr/hal-01579246
[8]
L. Villain, D. Commenges, C. Pasin, M. Prague, R. Thiébaut.
Adaptive protocols based on predictions from a mechanistic model of the effect of IL7 on CD4 counts, in: Statistics in Medicine, 2018, vol. 38, no 2, pp. 221-235.
Publications of the year

Doctoral Dissertations and Habilitation Theses

[9]
E. Lhomme.
Analysis of the determinants and modelisation of the post- vaccination immune response in experimental vaccine strategies, Université de bordeaux, November 2019.
https://hal.inria.fr/tel-02430642
[10]
H. Lorenzo.
Supervised analysis of high dimensional multiblock data, Université de bordeaux, November 2019.
https://hal.inria.fr/tel-02433612
[11]
L. Richert.
Statistical approaches and methodological developments to optimize clinical vaccine research, Université de Bordeaux, December 2019, Habilitation à diriger des recherches.
https://hal.inria.fr/tel-02426909
[12]
P. Soret.
Penalized Lasso regression for the analysis of high-dimensional biological data: application to HIV viral load censored by a limit of quantification and to microbiota compositional data, Université de bordeaux, November 2019.
https://hal.inria.fr/tel-02425113

Articles in International Peer-Reviewed Journals

[13]
S. Ajana, N. N. Acar, L. Bretillon, B. P. Hejblum, H. Jacqmin-Gadda, C. Delcourt.
Benefits of dimension reduction in penalized regression methods for high dimensional grouped data: a case study in low sample size, in: Bioinformatics, 2019. [ DOI : 10.1093/bioinformatics/btz135 ]
https://hal.inria.fr/hal-02425449
[14]
M. Chavent, R. Genuer, J. Saracco.
Combining clustering of variables and feature selection using random forests, in: Communications in Statistics - Simulation and Computation, February 2019, pp. 1-20. [ DOI : 10.1080/03610918.2018.1563145 ]
https://hal.archives-ouvertes.fr/hal-02013631
[15]
M. Coppry, C. Leroyer, M. Saly, A. G. Venier, B. Megarbane, C. Slekovec, X. Bertrand, S. Parer, S. Alfandari, E. Cambau, C. Lawrence, B. Clair, A. Lepape, P. Cassier, D. Trivier, A. Boyer, J. Asselineau, V. Dubois, R. Thiébaut, A. M. Rogues.
Exogenous acquisition of Pseudomonas aeruginosa in intensive care units: a prospective multi-centre study (DYNAPYO study), in: Journal of Hospital Infection, August 2019. [ DOI : 10.1016/j.jhin.2019.08.008 ]
https://hal.archives-ouvertes.fr/hal-02315665
[16]
S. Doerken, M. F. Avalos, E. Lagarde, M. Schumacher.
Penalized logistic regression with low prevalence exposures beyond high dimensional settings, in: PLoS ONE, May 2019, vol. 14, no 5, e0217057 p. [ DOI : 10.1371/journal.pone.0217057 ]
https://hal.inria.fr/hal-02140472
[17]
L. Gras, M. May, L. P. Ryder, A. Trickey, M. Helleberg, N. Obel, R. Thiébaut, J. Guest, J. Gill, H. Crane, V. Dias Lima, A. dʼArminio Monforte, T. Sterling, J. Miró, S. Moreno, C. Stephan, C. Smith, J. Tate, L. Shepherd, M. Saag, A. Rieger, D. Gillor, M. Cavassini, M. Montero, S. Ingle, P. Reiss, D. Costagliola, F. W. Wit, J. A. C. Sterne, F. De Wolf, R. B. Geskus.
Determinants of Restoration of CD4 and CD8 Cell Counts and Their Ratio in HIV-1-Positive Individuals With Sustained Virological Suppression on Antiretroviral Therapy, in: Journal of Acquired Immune Deficiency Syndromes, 2019, vol. 80, no 3, pp. 292-300. [ DOI : 10.1097/QAI.0000000000001913 ]
https://hal.sorbonne-universite.fr/hal-02279469
[18]
B. P. Hejblum, C. Alkhassim, R. Gottardo, F. Caron, R. Thiébaut.
Sequential Dirichlet Process Mixtures of Multivariate Skew t-distributions for Model-based Clustering of Flow Cytometry Data, in: Annals of Applied Statistics, 2019, vol. 13, no 1, pp. 638-660, https://arxiv.org/abs/1702.04407 - 39 pages, 11 figures. [ DOI : 10.1214/18-AOAS1209 ]
https://hal.inria.fr/hal-01579063
[19]
B. P. Hejblum, G. M. Weber, K. P. Liao, N. P. Palmer, S. Churchill, N. Shadick, P. Szolovits, S. N. Murphy, I. Kohane, T. Cai.
Probabilistic record linkage of de-identified research datasets with discrepancies using diagnosis codes, in: Scientific Data , 2019, vol. 6, 180298 p. [ DOI : 10.1038/sdata.2018.298 ]
https://hal.inria.fr/hal-01942279
[20]
P. Hellard, M. F. Avalos, G. Lefort, R. Pla, I. Mujika, J.-F. Toussaint, D. B. Pyne.
Elite Swimmers’ Training Patterns in the 25 Weeks Prior to Their Season’s Best Performance: Insights Into Periodization From a 20-Years Cohort, in: Frontiers in Physiology, April 2019, vol. 10. [ DOI : 10.3389/fphys.2019.00363 ]
https://hal.inria.fr/hal-02095063
[21]
É. Lhomme, B. P. Hejblum, C. Lacabaratz, A. Wiedemann, J.-D. Lelièvre, Y. Levy, R. Thiébaut, L. Richert.
Analyzing cellular immunogenicity in vaccine clinical trials: a new statistical method including non-specific responses for accurate estimation of vaccine effect, in: Journal of Immunological Methods, December 2019, 112711 p. [ DOI : 10.1016/j.jim.2019.112711 ]
https://hal.inria.fr/hal-02425379
[22]
É. Lhomme, C. Modet, A. Augier, S. Faye, T. S. Dabakuyo-Yonli, C. Lévy-Marchal, E. D'Ortenzio, Y. Yazdanpanah, G. Chene, A. H. Beavogui, L. Richert.
Enrolling study personnel in Ebola vaccine trials: from guidelines to practice in a non-epidemic context, in: Trials, December 2019, vol. 20, no 1, 422 p. [ DOI : 10.1186/s13063-019-3487-0 ]
https://hal.inria.fr/hal-02426902
[23]
D. Low, S. Lefèvre-Arbogast, R. Dominguez-Gonzalez, M. Urpi Sarda, P. Micheau, M. Pétéra, D. Centeno, S. Durand, E. Pujos-Guillot, A. Korosi, P. J. Lucassen, L. Aigner, C. Proust-Lima, C. Manach, B. P. Hejblum, C. Helmer, C. Andres-Lacueva, S. Thuret, C. Samieri.
Diet-Related Metabolites Associated with Cognitive Decline Revealed by Untargeted Metabolomics in a Prospective Cohort, in: Molecular Nutrition and Food Research, 2019, e1900177 p, Epub ahead of print. [ DOI : 10.1002/mnfr.201900177 ]
https://hal.archives-ouvertes.fr/hal-02167524
[24]
O. Lucar, M. Sadjo Diallo, C. Bayard, A. Samri, N. Tarantino, P. Debré, R. Thiébaut, F. Brun-Vézinet, S. Matheron, R. Cheynier, V. Vieillard.
B7-H6-mediated downregulation of NKp30 in natural killer cells contributes to HIV-2 immune escape, in: AIDS, 2019, vol. 33, no 1, pp. 23-32. [ DOI : 10.1097/QAD.0000000000002061 ]
https://hal.archives-ouvertes.fr/hal-02307134
[25]
C. Moore, W. Stöhr, A. Crook, L. Richert, J.-D. Lelièvre, G. Pantaleo, F. García, S. Vella, Y. Lévy, R. Thiébaut, S. McCormack.
Multi-arm, multi-stage randomised controlled trials for evaluating therapeutic HIV cure interventions, in: Lancet HIV, May 2019, vol. 6, no 5, pp. e334-e340. [ DOI : 10.1016/S2352-3018(19)30082-7 ]
https://hal.inria.fr/hal-02426904
[26]
A. Niehrs, W. Garcia-Beltran, P. Norman, G. Watson, A. Hölzemer, A. Chapel, L. Richert, A. Pommerening-Röser, C. Körner, M. Ozawa, G. Martrus, J. Rossjohn, J.-H. Lee, R. Berry, M. Carrington, M. Altfeld.
A subset of HLA-DP molecules serve as ligands for the natural cytotoxicity receptor NKp44, in: Nature Immunology, September 2019, vol. 20, no 9, pp. 1129-1137. [ DOI : 10.1038/s41590-019-0448-4 ]
https://hal.inria.fr/hal-02426901
[27]
C. Pasin, I. Balelli, T. Van Effelterre, V. Bockstal, L. Solforosi, M. Prague, M. Douoguih, R. Thiébaut.
Dynamics of the Humoral Immune Response to a Prime-Boost Ebola Vaccine: Quantification and Sources of Variation, in: Journal of Virology, September 2019, vol. 93, no 18. [ DOI : 10.1128/JVI.00579-19 ]
https://hal.inria.fr/hal-02280792
[28]
A. Samri, C. Charpentier, M. S. Diallo, M. Bertine, S. Even, V. Morin, A. Oudin, C. Parizot, G. Collin, A. Hosmalin, R. Cheynier, R. Thiébaut, S. Matheron, F. Collin, R. Zoorob, F. Brun-Vézinet, B. Autran.
Limited HIV-2 reservoirs in central-memory CD4 T-cells associated to CXCR6 co-receptor expression in attenuated HIV-2 infection, in: PLoS Pathogens, 2019, vol. 15, no 5, e1007758 p. [ DOI : 10.1371/journal.ppat.1007758 ]
https://hal.sorbonne-universite.fr/hal-02165899
[29]
B. Silenou, M. F. Avalos, C. Helmer, C. Berr, a. Pariente, H. Jacqmin-Gadda.
Health administrative data enrichment using cohort information: Comparative evaluation of methods by simulation and application to real data, in: PLoS ONE, January 2019, vol. 14, no 1, e0211118 p. [ DOI : 10.1371/journal.pone.0211118 ]
https://hal.inria.fr/hal-02008499
[30]
R. Thiébaut, B. P. Hejblum, H. Hocini, H. Bonnabau, J. Skinner, M. Montes, C. Lacabaratz, L. Richert, K. Palucka, J. Banchereau, Y. Lévy.
Gene Expression Signatures Associated With Immune and Virological Responses to Therapeutic Vaccination With Dendritic Cells in HIV-Infected Individuals, in: Frontiers in Immunology, April 2019, vol. 10, 874 p. [ DOI : 10.3389/fimmu.2019.00874 ]
https://hal.archives-ouvertes.fr/hal-02267014
[31]
T. van Stigt Thans, J. Akko, A. Niehrs, W. Garcia-Beltran, L. Richert, C. M. Stürzel, C. Ford, H. Li, C. Ochsenbauer, J. Kappes, B. H. Hahn, F. Kirchhoff, G. Martrus, D. Sauter, M. Altfeld, A. Hölzemer.
Primary HIV-1 Strains Use Nef To Downmodulate HLA-E Surface Expression, in: Journal of Virology, October 2019, vol. 93, no 20. [ DOI : 10.1128/JVI.00719-19 ]
https://hal.inria.fr/hal-02426899

Conferences without Proceedings

[32]
H. Lorenzo, R. Misbah, J. Odeber, P.-E. Morange, J. Saracco, D.-A. Trégouët, R. Thiébaut.
High-Dimensional Multi-Block Analysis of Factors Associated with Thrombin Generation Potential, in: CBMS 2019 - 32nd IEEE International Symposium on Computer-Based Medical Systems (CBMS), Cordoba, Spain, IEEE, June 2019, pp. 453-458. [ DOI : 10.1109/CBMS.2019.00094 ]
https://hal.archives-ouvertes.fr/hal-02429302

Scientific Books (or Scientific Book chapters)

[33]
L. Desquilbet, S. Granger, B. P. Hejblum, A. Legrand, P. Pernot, N. P. Rougier, E. de Castro Guerra, M. Courbin-Coulaud, L. Duvaux, P. Gravier, G. Le Campion, S. Roux, F. Santos.
U. régionale de formation à l'information scientifique et technique de Bordeaux (editor), Towards reproducible research : Evolve your practices, Unité régionale de formation à l'information scientifique et technique de Bordeaux, May 2019, pp. 1-161.
https://hal.archives-ouvertes.fr/hal-02144142
[34]
R. Genuer, J.-M. Poggi.
Les forêts aléatoires avec R, Presses Universitaires de Rennes, 2019.
https://hal.archives-ouvertes.fr/hal-02409535

Other Publications

[35]
L. Capitaine, R. Genuer, R. Thiébaut.
Fréchet random forests, December 2019, https://arxiv.org/abs/1906.01741 - working paper or preprint.
https://hal.archives-ouvertes.fr/hal-02409430
[36]
L. Capitaine, R. Genuer, R. Thiébaut.
Random forests for high-dimensional longitudinal data, February 2019, https://arxiv.org/abs/1901.11279 - working paper or preprint.
https://hal.archives-ouvertes.fr/hal-02002979
[37]
M. Gauthier, D. Agniel, R. Thiébaut, B. P. Hejblum.
dearseq: a variance component score test for RNA-Seq differential analysis that effectively controls the false discovery rate, May 2019, working paper or preprint. [ DOI : 10.1101/635714 ]
https://hal.inria.fr/hal-02138664
[38]
B. Xu, C. Gil-Jardiné, F. Thiessard, É. Tellier, M. F. Avalos, E. Lagarde.
Neural Language Model for Automated Classification of Electronic Medical Records at the Emergency Room. The Significant Benefit of Unsupervised Generative Pre-training, December 2019, https://arxiv.org/abs/1909.01136 - working paper or preprint.
https://hal.inria.fr/hal-02425097
References in notes
[39]
O. Aalen, K. Kjetil Roysland, J. Gran, B. Ledergerber.
Causality, mediation and time: a dynamic viewpoint, in: Journal of the Royal Statistical Society: Series A (Statistics in Society), 2007, vol. 175, no 4, pp. 831–861.
[40]
F. Castiglione, B. Piccoli.
Cancer immunotherapy, mathematical modeling and optimal control, in: Biometrical Journal, 2007, vol. 247, no 4, pp. 723-32.
[41]
R. M. Granich, C. F. Gilks, C. Dye, K. M. De Cock, B. G. Williams.
Universal voluntary HIV testing with immediate antiretroviral therapy as a strategy for elimination of HIV transmission: a mathematical model, in: Lancet, 2009, vol. 373, no 9657, pp. 48-57, 0140 6736 English.
[42]
L. Hood, Q. Tian.
Systems approaches to biology and disease enable translational systems medicine, in: Genomics Proteomics Bioinformatics, 2012, vol. 10, no 4, pp. 181–5.
[43]
Y. Huang, D. Liu, H. Wu.
Hierarchical Bayesian methods for estimation of parameters in a longitudinal HIV dynamic system, in: Biometrics, 2006, vol. 62, no 2, pp. 413–423.
[44]
E. Kuhn, M. Lavielle.
Maximum likelihood estimation in nonlinear mixed effects models, in: Computational Statistics & Data Analysis, 2005, vol. 49, no 4, pp. 1020–1038.
[45]
K.-A. Le Cao, P. Martin, C. Robert-Granié, P. Besse.
Sparse canonical methods for biological data integration: application to a cross-platform study, in: BMC bioinformatics, 2009, vol. 10, 34 p.
[46]
C. Lewden, D. Salmon, P. Morlat, S. Bevilacqua, E. Jougla, F. Bonnet, L. Heripret, D. Costagliola, T. May, G. Chêne.
Causes of death among human immunodeficiency virus (HIV)-infected adults in the era of potent antiretroviral therapy: emerging role of hepatitis and cancers, persistent role of AIDS, in: International Journal of Epidemiology, 2005, vol. 34, no 1, pp. 121-130, 0300 5771 English.
[47]
A. S. Perelson, A. U. Neumann, M. Markowitz, J. M. Leonard, D. D. Ho.
HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time, in: Science, 1996, vol. 271, no 5255, pp. 1582-6.
[48]
A. S. Perelson.
Modelling viral and immune system dynamics, in: Nature Reviews Immunology, 2002, vol. 2, no 1, pp. 28-36.
[49]
J. Pinheiro, D. Bates.
Approximations to the log-likelihood function in the nonlinear mixed-effects model, in: Journal of Computational and Graphical Statistics, 1995, vol. 4, no 1, pp. 12–35.
[50]
B. Pulendran.
Learning immunology from the yellow fever vaccine: innate immunity to systems vaccinology, in: Nature Reviews Immunology, 2009, vol. 9, no 10, pp. 741-7.
[51]
H. Putter, S. Heisterkamp, J. Lange, F. De Wolf.
A Bayesian approach to parameter estimation in HIV dynamical models, in: Statistics in Medicine, 2002, vol. 21, no 15, pp. 2199–2214.
[52]
A. Reiner, D. Yekutieli, Y. Benjamini.
Identifying differentially expressed genes using false discovery rate controlling procedures, in: Bioinformatics, 2003, vol. 19, no 3, pp. 368–375.
[53]
C. Schubert.
Systems immunology: complexity captured, in: Nature, 2011, vol. 473, no 7345, pp. 113-4.
[54]
R. Sun, S. Hui, G. D. Bader, X. Lin, P. Kraft.
Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic, in: PLoS genetics, 2019, vol. 15, no 3, e1007530 p.
[55]
R. Thiébaut, B. P. Hejblum, L. Richert.
[The analysis of "Big Data" in clinical research.], in: Epidemiology and Public Health / Revue d'Epidémiologie et de Santé Publique, January 2014, vol. 62, no 1, pp. 1–4. [ DOI : 10.1016/j.respe.2013.12.021 ]
http://www.hal.inserm.fr/inserm-00933691
[56]
R. Thiébaut, H. Jacqmin-Gadda, A. Babiker, D. Commenges.
Joint modelling of bivariate longitudinal data with informative dropout and left-censoring, with application to the evolution of CD4+cell count and HIV RNA viral load in response to treatment of HIV infection, in: Statistics in Medicine, 2005, vol. 24, no 1, pp. 65-82.
[57]
R. Tibshirani.
Regression shrinkage and selection via the lasso, in: Journal of the Royal Statistical Society: Series B (Statistical Methodology), 1996, vol. 58, pp. 267–288.
[58]
Y. Wang.
Derivation of various NONMEM estimation methods, in: Journal of Pharmacokinetics and pharmacodynamics, 2007, vol. 34, no 5, pp. 575–593.
[59]
H. Wu.
Statistical methods for HIV dynamic studies in AIDS clinical trials, in: Statistical Methods in Medical Research, 2005, vol. 14, no 2, pp. 171–192.