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Bibliography

Major publications by the team in recent years
  • 1M. Avalos, N. D. Adroher, E. Lagarde, F. Thiessard, Y. Grandvalet, B. Contrand, L. Orriols.

    Prescription-Drug-Related Risk in Driving: Comparing Conventional and Lasso Shrinkage Logistic Regressions, in: Epidemiology, 2012, vol. 23, no 5, pp. 706–712.
  • 2D. Furman, P. Hejblum, N. Simon, V. Jojic, L. Dekker, R. Thiébaut, J. Tibshirani, M. Davis.

    Systems analysis of sex differences reveals an immunosuppressive role for testosterone in the response to influenza vaccination, in: Proceedings of the National Academy of Sciences, January 2014, vol. 111, no 2, pp. 869-74.

    http://dx.doi.org/10.1073/pnas.1321060111
  • 3B. Liquet, K.-A. Le Cao, H. Hocini, R. Thiébaut.

    A novel approach for biomarker selection and the integration of repeated measures experiments from two assays, in: BMC bioinformatics, 2012, vol. 13, no 1, 14 p.

    http://dx.doi.org/10.1186/1471-2105-13-325
  • 4M. Prague, D. Commenges, J. Drylewicz, R. Thiébaut.

    Treatment monitoring of HIV infected patients based on mechanistic models, in: Biometrics, 2012, vol. 68, no 3, pp. 902–911.
  • 5R. Thiébaut, J. Drylewicz, M. Prague, C. Lacabaratz, S. Beq, A. Jarne, T. Croughs, R.-P. Sekaly, M. M. Lederman, I. Sereti.

    Quantifying and Predicting the Effect of Exogenous Interleukin-7 on CD4+ T Cells in HIV-1 Infection, in: PLoS computational biology, 2014, vol. 10, no 5, e1003630.
Publications of the year

Articles in International Peer-Reviewed Journals

  • 6M. Avalos, L. Orriols, H. Pouyes, Y. Grandvalet, F. Thiessard, E. Lagarde.

    Variable selection on large case-crossover data: application to a registry-based study of prescription drugs and road traffic crashes, in: Pharmacoepidemiology and Drug Safety, 2014, pp. 140-51. [ DOI : 10.1002/pds.3539 ]

    https://hal.archives-ouvertes.fr/hal-01099301
  • 7D. Furman, B. P. Hejblum, N. Simon, V. Jojic, C. L. Dekker, R. Thiebaut, R. J. Tibshirani, M. M. Davis.

    Systems analysis of sex differences reveals an immunosuppressive role for testosterone in the response to influenza vaccination, in: Proceedings of the National Academy of Sciences U S A, January 2014, vol. 111, no 2, pp. 869-74. [ DOI : 10.1073/pnas.1321060111 ]

    https://hal.inria.fr/hal-01108208
  • 8D. Furman, B. P. Hejblum, N. Simon, V. Jojic, L. Dekker, R. Thiébaut, J. Tibshirani, M. Davis.

    Systems analysis of sex differences reveals an immunosuppressive role for testosterone in the response to influenza vaccination, in: Proceedings of the National Academy of Sciences U S A, January 2014, vol. 111, no 2, pp. 869-74. [ DOI : 10.1073/pnas.1321060111 ]

    http://www.hal.inserm.fr/inserm-00933693
  • 9J. Gaudart, L. Huiart, P. J. Milligan, R. Thiebaut, R. Giorgi.

    Reproducibility issues in science, is P value really the only answer?, in: Proceedings of the National Academy of Sciences U S A, May 2014, vol. 111, no 19, E1934. [ DOI : 10.1073/pnas.1323051111 ]

    https://hal.inria.fr/hal-01108195
  • 10N. Hellard, M. Avalos, F. Guimaraes, J. F. Toussaint, P. David.

    Training-Related Risk of Common Illnesses in Elite Swimmers over a Four-Year Period, in: Medicine and Science in Sports and Exercise, 2014, 1 p. [ DOI : 10.1249/MSS.0000000000000461 ]

    https://hal.archives-ouvertes.fr/hal-01099379
  • 11Y. Lévy, R. Thiébaut, M. Montes, C. Lacabaratz, L. Sloan, B. King, S. Pérusat, C. Harrod, A. Cobb, L. K. Roberts, M. Surenaud, C. Boucherie, S. Zurawski, C. Delaugerre, L. Richert, G. Chêne, J. Banchereau, K. Palucka.

    Dendritic cell-based therapeutic vaccine elicits polyfunctional HIV-specific T-cell immunity associated with control of viral load, in: European Journal of Immunology, August 2014, vol. 44, no 9, pp. 2802-10.

    https://hal.inria.fr/hal-01108024
  • 12K. Moreau, A. Desseix, C. Germain, N. Barthe, T. Bachelet, D. Morel, P. Merville, L. Couzi, R. Thiebaut, P. Chauveau.

    Body composition in 98 patients awaiting kidney transplantation, in: Nutrition, January 2014, vol. 30, no 2, pp. 186-91.

    https://hal.inria.fr/hal-01108163
  • 13A. D. Olson, L. Meyer, M. Prins, R. Thiebaut, D. Gurdasani, M. Guiguet, M.-L. Chaix, P. Amornkul, A. Babiker, M. S. Sandhu, K. Porter, J. F. Okulicz.

    An Evaluation of HIV Elite Controller Definitions within a Large Seroconverter Cohort Collaboration, in: PLoS ONE, January 2014, vol. 9, no 1, e86719. [ DOI : 10.1371/journal.pone.0086719 ]

    https://hal.inria.fr/hal-01108192
  • 14L. Orriols, M. Avalos, N. Moore, P. Philip, B. Delorme, B. Laumon, B. Gadegbeku, L. R. Salmi, E. Lagarde.

    Long-term chronic diseases and crash responsibility: a record linkage study, in: Accident Analysis and Prevention, 2014, 1 p. [ DOI : 10.1016/j.aap.2014.05.001 ]

    https://hal.archives-ouvertes.fr/hal-01099306
  • 15M.-Q. Picat, R. Thiébaut, F. Lifermann, X. Delbrel, D. Adoue, L. Wittkop, A.-L. Fauchais, P. Rispal, J.-F. Moreau, J.-F. Viallard.

    T-cell activation discriminates subclasses of symptomatic primary humoral immunodeficiency diseases in adults, in: BMC Immunology, 2014, vol. 15, no 1, 13 p. [ DOI : 10.1186/1471-2172-15-13 ]

    http://www.hal.inserm.fr/inserm-00981320
  • 16L. Richert, A. Doussau, J.-D. Lelièvre, V. Arnold, V. Rieux, A. Bouakane, Y. Lévy, G. Chêne, R. Thiébaut.

    Accelerating clinical development of HIV vaccine strategies: methodological challenges and considerations in constructing an optimised multi-arm phase I/II trial design, in: Trials, February 2014, vol. 15, no 1, 68 p. [ DOI : 10.1186/1745-6215-15-68 ]

    http://www.hal.inserm.fr/inserm-00955157
  • 17E. Ross, F. Tanser, P. Pei, M.-L. Newell, E. Losina, R. Thiebaut, M. Weinstein, K. Freedberg, X. Anglaret, C. Scott, F. Dabis, R. Walensky.

    The Impact of the 2013 WHO Antiretroviral Therapy Guidelines on the Feasibility of HIV Population Prevention Trials, in: HIV Clinical Trials, January 2014, vol. 15, no 5, pp. 185-98. [ DOI : 10.1310/hct1505-185 ]

    https://hal.inria.fr/hal-01108183
  • 18R. Thiébaut, J. Drylewicz, M. Prague, C. Lacabaratz, S. Beq, A. Jarne, T. Croughs, R.-P. Sekaly, M. M. Lederman, I. Sereti, D. Commenges, Y. Lévy, B. Asquith.

    Quantifying and Predicting the Effect of Exogenous Interleukin-7 on CD4+T Cells in HIV-1 Infection, in: PLoS Computational Biology, May 2014, vol. 10, no 5, e1003630. [ DOI : 10.1371/journal.pcbi.1003630 ]

    https://hal.inria.fr/hal-01108204
  • 19R. Thiébaut, 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, epub ahead of print. [ DOI : 10.1016/j.respe.2013.12.021 ]

    http://www.hal.inserm.fr/inserm-00933691
  • 20R. Thiébaut, M. Prague, D. Commenges.

    Mathematical dynamical models for personalized medicine, in: médecine/sciences, October 2014, vol. 30 Spec No 2, pp. 23-6.

    https://hal.inria.fr/hal-01108013

International Conferences with Proceedings

  • 21N. Fouret, M. Avalos, L. Wittkop, T. Rodolphe, D. Commenges.

    Prise en compte de la censure à gauche dans la modélisation de données de grande dimension, in: 46e Journées de Statistique, Rennes, France, June 2014.

    https://hal.archives-ouvertes.fr/hal-01099341
  • 22R. Genuer, J.-M. Poggi, C. Tuleau-Malot.

    VSURF : un package R pour la sélection de variables à l'aide de forêts aléatoires, in: 46èmes Journées de Statistique, Rennes, France, 2014.

    https://hal.inria.fr/hal-01096233
  • 23P. Hellard, P.-M. Lepretre, M. Avalos, L. Seifert, J. F. Toussaint, C. Hausswirth, P. Saunders, P. David.

    Ventilatory, metabolic and kinematic responses in sprint versus distance swimmers, in: XIIth International Symposium on Biomechanics and Medicine in Swimming, Canberra, France, April 2014.

    https://hal.archives-ouvertes.fr/hal-01099378
  • 24C. Scordia, M. Avalos, P. Hellard.

    Comparing methods for summarizing a training load in prediction models of swimming performance, in: XIIth International Symposium on Biomechanics and Medicine in Swimming, Canberra, Australia, B. Mason (editor), Australian Institute of Sport, April 2014.

    https://hal.archives-ouvertes.fr/hal-01099344

National Conferences with Proceedings

  • 25N. Mélanie, M. Avalos, L. Orriols, E. Lagarde.

    Etude de l’association entre consommation médicamenteuse et risque d’accident de la route : exploration par simulation de schémas d’études épidémiologiques applicables à partir des données médico-administratives, in: Journée Nationale Biopharmacie et Santé 2014, Paris, France, November 2014.

    https://hal.archives-ouvertes.fr/hal-01099320

Conferences without Proceedings

  • 26R. Genuer, J.-M. Poggi, C. Tuleau-Malot.

    VSURF : un package R pour la sélection de variables à l'aide de forêts aléatoires, in: 3èmes Rencontres R, Montpellier, France, 2014.

    https://hal.inria.fr/hal-01096237
  • 27P. Soret, M. Avalos.

    Données longitudinales en grande dimension : état des lieux des packages R, in: Troisièmes rencontres R, Montpellier, France, June 2014.

    https://hal.archives-ouvertes.fr/hal-01099337
  • 28P. Soret, M. Avalos.

    Méthodes d’apprentissage statistique pour des données longitudinales : une revue systématique, in: GdR Statistique et Santé, Toulouse, France, October 2014.

    https://hal.archives-ouvertes.fr/hal-01099331

Scientific Books (or Scientific Book chapters)

  • 29M. Avalos, Y. Grandvalet, H. Pouyes, L. Orriols, E. Lagarde.

    High–Dimensional Sparse Matched Case–Control and Case–Crossover Data: A Review of Recent Works, Description of an R Tool and an Illustration of the Use in Epidemiological Studies , in: Computational Intelligence Methods for Bioinformatics and Biostatistics, E. W. Enrico Formenti (editor), Lecture Notes in Computer Science, Springer, 2014.

    https://hal.archives-ouvertes.fr/hal-01099313

Internal Reports

Other Publications

References in notes
  • 32O. 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.
  • 33F. Castiglione, B. Piccoli.

    Cancer immunotherapy, mathematical modeling and optimal control, in: Biometrical Journal, 2007, vol. 247, no 4, pp. 723-32.
  • 34R. 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.
  • 35L. 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.
  • 36Y. 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.
  • 37E. Kuhn, M. Lavielle.

    Maximum likelihood estimation in nonlinear mixed effects models, in: Computational Statistics & Data Analysis, 2005, vol. 49, no 4, pp. 1020–1038.
  • 38K.-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.
  • 39C. 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.
  • 40A. 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.
  • 41A. S. Perelson.

    Modelling viral and immune system dynamics, in: Nature Reviews Immunology, 2002, vol. 2, no 1, pp. 28-36.
  • 42J. 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.
  • 43M. Prague, D. Commenges, J. Guedj, J. Drylewicz, R. Thiébaut.

    NIMROD: A program for inference via a normal approximation of the posterior in models with random effects based on ordinary differential equations, in: Computer Methods and Programs in Biomedicine, 2013, vol. 111, no 2, pp. 447–458.
  • 44B. 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.
  • 45H. 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.
  • 46A. 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.
  • 47C. Schubert.

    Systems immunology: complexity captured, in: Nature, 2011, vol. 473, no 7345, pp. 113-4.
  • 48R. 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.
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  • 50Y. Wang.

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  • 51H. 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.


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