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Bibliography

Major publications by the team in recent years
  • 1R. Bouteloup, R. Sabin, R. Mocroft, M. Gras, M. Pantazis, M. Le Moing, M. d'Arminio Monforte, R. Mary-Krause, R. Roca, C. Miro, R. Battegay, R. Brockmeyer, M. Berenguer, R. Morlat, C. Obel, L. De Wit, R. Fätkenheuer, R. Zangerle, C. Ghosn, R. Pérez-Hoyos, R. Campbell, C. Prins, R. Chêne, R. Meyer, R. Dorrucci, C. Torti, R. Thiébaut.

    Reference curves for CD4 T-cell count response to combination antiretroviral therapy in HIV-1-infected treatment-naïve patients, in: HIV Medicine, September 2016.

    https://hal.inria.fr/hal-01406622
  • 2C. C. Iwuji, J. Orne-Gliemann, J. Larmarange, N. Okesola, F. Tanser, R. Thiebaut, C. Rekacewicz, M.-L. Newell, F. Dabis, N. Low.

    Uptake of Home-Based HIV Testing, Linkage to Care, and Community Attitudes about ART in Rural KwaZulu-Natal, South Africa: Descriptive Results from the First Phase of the ANRS 12249 TasP Cluster-Randomised Trial, in: PLoS Medicine, August 2016, vol. 13, no 8.

    https://hal.inria.fr/hal-01406616
  • 3A. Jarne, D. Commenges, L. Villain, M. Prague, Y. Lévy, R. Thiébaut.

    Modeling CD4+ T cells dynamics in HIV-infected patients receiving repeated cycles of exogenous Interleukin 7, in: Submitted in Annals of Applied statistics, Sept 2016, vol. X, no X.
  • 4R. Le Grand, N. Dereuddre-Bosquet, S. Dispinseri, L. Gosse, D. Desjardins, X. Shen, M. Tolazzi, C. Ochsenbauer, H. Saidi, G. Tomaras, M. Prague, S. W. Barnett, R. Thiebaut, A. Cope, G. Scarlatti, R. J. Shattock, G. Silvestri.

    Superior Efficacy of a Human Immunodeficiency Virus Vaccine Combined with Antiretroviral Prevention in Simian-Human Immunodeficiency Virus-Challenged Nonhuman Primates, in: Journal of Virology, May 2016, vol. 90, no 11, pp. 5315 - 5328.

    https://hal.inria.fr/hal-01406364
  • 5P. Schommers, G. Martrus, U. Matschl, M. Sirignano, M. Lütgehetmann, L. Richert, T. J. Hope, G. Fätkenheuer, M. Altfeld, F. Kirchhoff.

    Changes in HIV-1 Capsid Stability Induced by Common Cytotoxic-T-Lymphocyte-Driven Viral Sequence Mutations, in: Journal of Virology, July 2016, vol. 90, no 16, pp. 7579 - 7586. [ DOI : 10.1128/JVI.00867-16 ]

    https://hal.archives-ouvertes.fr/hal-01404506
  • 6M. Surenaud, C. Manier, L. Richert, R. Thiébaut, Y. Levy, S. Hue, C. Lacabaratz.

    Optimization and evaluation of Luminex performance with supernatants of antigen-stimulated peripheral blood mononuclear cells, in: BMC Immunology, December 2015, vol. 17, no 1, 44 p. [ DOI : 10.1186/s12865-016-0182-8 ]

    http://www.hal.inserm.fr/inserm-01395760
  • 7R. 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

  • 8S. Arlot, R. Genuer.

    Comments on: "A Random Forest Guided Tour" by G. Biau and E. Scornet, in: Test, 2016, vol. 25, no 2, pp. 228–238, The final publication is available at Springer: http://dx.doi.org/10.1007/s11749-016-0484-4. [ DOI : 10.1007/s11749-016-0484-4 ]

    https://hal.archives-ouvertes.fr/hal-01297557
  • 9E. Balestre, D. K. Ekouevi, B. Tchounga, S. P. Eholie, E. Messou, A. Sawadogo, R. Thiébaut, M. T. May, J. Ac Sterne, F. Dabis.

    Immunologic response in treatment-naïve HIV-2-infected patients: the IeDEA West Africa cohort, in: Journal of the International AIDS Society, February 2016, vol. 19, no 1. [ DOI : 10.7448/IAS.19.1.20044 ]

    https://hal.inria.fr/hal-01288896
  • 10C. Hotz, M. Boniotto, A. Guguin, M. Surenaud, F. Jean-Louis, P. Tisserand, N. Ortonne, B. Hersant, R. Bosc, F. Poli, H. Bonnabau, R. Thiébaut, V. Godot, P. Wolkenstein, H. Hocini, Y. Lévy, S. Hüe.

    Intrinsic Defect in Keratinocyte Function Leads to Inflammation in Hidradenitis Suppurativa, in: Journal of Investigative Dermatology, September 2016, vol. 136, no 9, pp. 1768 - 1780.

    https://hal.inria.fr/hal-01406612
  • 11H. Kaminski, I. Garrigue, L. Couzi, B. Taton, T. Bachelet, J.-F. Moreau, J. Dechanet-Merville, R. Thiebaut, P. Merville.

    Surveillance of T Cells Predicts Cytomegalovirus Infection Resolution in Kidney Transplants, in: Journal of the American Society of Nephrology, 2016, vol. 27, no 2, pp. 637-645. [ DOI : 10.1681/ASN.2014100985 ]

    https://hal.inria.fr/hal-01288893
  • 12E. Lhomme, L. Richert, Z. Moodie, C. Pasin, S. A. Kalams, C. Morgan, S. Self, S. C. De Rosa, R. Thiébaut.

    Early CD4+ T Cell Responses Are Associated with Subsequent CD8+ T Cell Responses to an rAd5-Based Prophylactic Prime-Boost HIV Vaccine Strategy, in: PLoS ONE, April 2016, vol. 11, no 4.

    https://hal.inria.fr/hal-01406611
  • 13B. Liquet, P. Lafaye De Micheaux, B. P. Hejblum, R. Thiébaut.

    Group and sparse group partial least square approaches applied in genomics context, in: Bioinformatics, 2016, vol. 32, no 1, pp. 35-42. [ DOI : 10.1093/bioinformatics/btv535 ]

    https://hal.inria.fr/hal-01288891
  • 14F. Nakagawa, A. Van Sighem, R. Thiebaut, C. Smith, O. Ratmann, V. Cambiano, J. Albert, A. Amato-Gauci, D. Bezemer, C. Campbell, D. Commenges, M. Donoghoe, D. Ford, R. Kouyos, R. Lodwick, J. Lundgren, N. Pantazis, A. Pharris, C. Quinten, C. Thorne, G. Touloumi, V. Delpech, A. Phillips.

    A method to estimate the size and characteristics of HIV-positive populations using an individual-based stochastic simulation model, in: Epidemiology, 2016, vol. 27, no 2, pp. 247-256. [ DOI : 10.1097/EDE.0000000000000423 ]

    https://hal.inria.fr/hal-01288889
  • 15M. 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, July 2016.

    https://hal.inria.fr/hal-01406614
  • 16M. Prague.

    Use of dynamical models for treatment optimization in HIV infected patients : a sequential Bayesian analysis approach. , in: Journal de la Société Française de Statistiques, September 2016, vol. 157, no 2, 20 p.

    https://hal.inria.fr/hal-01416102
  • 17R. Thiébaut, A. Jarne, J.-P. Routy, I. Sereti, M. Fischl, P. Ive, R. F. Speck, G. D'Offizi, S. Casari, D. Commenges, S. Foulkes, V. Natarajan, T. Croughs, J.-F. Delfraissy, G. Tambussi, Y. Levy, M. M. Lederman.

    Repeated Cycles of Recombinant Human Interleukin 7 in HIV-Infected Patients With Low CD4 T-Cell Reconstitution on Antiretroviral Therapy: Results of 2 Phase II Multicenter Studies, in: Clinical Infectious Diseases, May 2016, vol. 62, no 9, pp. 1178 - 1185.

    https://hal.inria.fr/hal-01406362
  • 18G. Zurawski, S. Zurawski, A.-L. Flamar, L. Richert, R. Wagner, G. D. Tomaras, D. C. Montefiori, M. Roederer, G. Ferrari, C. Lacabaratz, H. Bonnabau, P. Klucar, Z. Wang, K. E. Foulds, S.-F. Kao, N. L. Yates, C. LaBranche, B. L. Jacobs, K. Kibler, B. Asbach, A. Kliche, A. Salazar, S. Reed, S. Self, R. Gottardo, L. Galmin, D. Weiss, A. Cristillo, R. Thiebaut, G. Pantaleo, Y. Levy.

    Targeting HIV-1 Env gp140 to LOX-1 Elicits Immune Responses in Rhesus Macaques, in: PLoS ONE, April 2016, vol. 11, no 4. [ DOI : 10.1371/journal.pone.0153484 ]

    https://hal.inria.fr/hal-01389087

International Conferences with Proceedings

  • 19M. F. Avalos, M. Le Goff, P. Joly, M.-A. Jutand, A. Alioum.

    Evolution of Teaching Strategies in a French ODL University Course, in: 9th Australian Conference on Teaching Statistics (OZCOTS), Canberra, Australia, H. MacGillivray, M. Martin, B. Phillips (editors), Proceedings of the Ninth Australian Conference on Teaching Statistics, The International Association for Statistical Education (IASE), December 2016, 183 p, ISBN: 978-0-9805950-2-4.

    https://hal.inria.fr/hal-01396772
  • 20M. F. Avalos, P. Soret, C. Meza, K. Bertin, H. Ren, P. Hellard.

    Exploring variable selection in additive mixed effects models using group lasso, in: 23rd Australian Statistical Conference, Canberra, Australia, Statistical Society of Australia (SSA), December 2016.

    https://hal.inria.fr/hal-01396767
  • 21G. Lefort, M. F. Avalos, P. Soret, P. David, J. F. Toussaint, P. Hellard.

    A comparison of unsupervised curve classification methods for sport training data, in: 3rd conference of the International Society for Non-Parametric Statistics (ISNPS), Avignon, France, The International Society for NonParametric Statistics (ISNPS), June 2016.

    https://hal.inria.fr/hal-01396366
  • 22G. Lefort, M. F. Avalos, P. Soret, P. David, J. F. Toussaint, P. N. Hellard.

    Clustering of temporal sport training curves: a comparison of FDA and LDA approaches, in: 23rd Australian Statistical Conference, Canberra, Australia, December 2016.

    https://hal.inria.fr/hal-01396372
  • 23B. Silenou Chawo, M. F. Avalos, A. Pariente, H. Jacqmin-Gadda.

    Adjustment for Unobserved Confounders in Health Administrative Databases, in: 32nd International Conference on Pharmacoepidemiology & Therapeutic Risk Management, Dublin, Ireland, INTERNATIONAL SOCIETY FOR PHARMACOEPIDEMIOLOGY (ISPE), August 2016.

    https://hal.inria.fr/hal-01396349
  • 24P. Soret, C. Meza, M. F. Avalos, K. Bertin, R. Thiébaut.

    Lasso-type estimators for non-parametric mixed-effects models: application to high-dimensional data from a vaccine clinical trial for HIV, in: 3rd conference of the International Society for Non-Parametric Statistics (ISNPS), Avignon, France, June 2016.

    https://hal.inria.fr/hal-01396378

National Conferences with Proceedings

  • 25P. Soret, C. Meza, M. Avalos, K. Bertin.

    Estimateur de type Lasso pour modèle mixte non-paramétrique, in: 48èmes Journées de Statistique, Montpellier, France, Société Française de Statistique (SFdS), May 2016.

    https://hal.inria.fr/hal-01396802

Other Publications

References in notes
  • 28O. 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.
  • 29R. Bouteloup, R. Sabin, R. Mocroft, M. Gras, M. Pantazis, M. Le Moing, M. d'Arminio Monforte, R. Mary-Krause, R. Roca, C. Miro, R. Battegay, R. Brockmeyer, M. Berenguer, R. Morlat, C. Obel, L. De Wit, R. Fätkenheuer, R. Zangerle, C. Ghosn, R. Pérez-Hoyos, R. Campbell, C. Prins, R. Chêne, R. Meyer, R. Dorrucci, C. Torti, R. Thiébaut.

    Reference curves for CD4 T-cell count response to combination antiretroviral therapy in HIV-1-infected treatment-naïve patients, in: HIV Medicine, September 2016.

    https://hal.inria.fr/hal-01406622
  • 30F. Castiglione, B. Piccoli.

    Cancer immunotherapy, mathematical modeling and optimal control, in: Biometrical Journal, 2007, vol. 247, no 4, pp. 723-32.
  • 31R. 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.
  • 32L. 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.
  • 33Y. 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.
  • 34C. C. Iwuji, J. Orne-Gliemann, J. Larmarange, N. Okesola, F. Tanser, R. Thiebaut, C. Rekacewicz, M.-L. Newell, F. Dabis, N. Low.

    Uptake of Home-Based HIV Testing, Linkage to Care, and Community Attitudes about ART in Rural KwaZulu-Natal, South Africa: Descriptive Results from the First Phase of the ANRS 12249 TasP Cluster-Randomised Trial, in: PLoS Medicine, August 2016, vol. 13, no 8.

    https://hal.inria.fr/hal-01406616
  • 35A. Jarne, D. Commenges, L. Villain, M. Prague, Y. Lévy, R. Thiébaut.

    Modeling CD4+ T cells dynamics in HIV-infected patients receiving repeated cycles of exogenous Interleukin 7, in: Submitted in Annals of Applied statistics, Sept 2016, vol. X, no X.
  • 36E. Kuhn, M. Lavielle.

    Maximum likelihood estimation in nonlinear mixed effects models, in: Computational Statistics & Data Analysis, 2005, vol. 49, no 4, pp. 1020–1038.
  • 37K.-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.
  • 38R. Le Grand, N. Dereuddre-Bosquet, S. Dispinseri, L. Gosse, D. Desjardins, X. Shen, M. Tolazzi, C. Ochsenbauer, H. Saidi, G. Tomaras, M. Prague, S. W. Barnett, R. Thiebaut, A. Cope, G. Scarlatti, R. J. Shattock, G. Silvestri.

    Superior Efficacy of a Human Immunodeficiency Virus Vaccine Combined with Antiretroviral Prevention in Simian-Human Immunodeficiency Virus-Challenged Nonhuman Primates, in: Journal of Virology, May 2016, vol. 90, no 11, pp. 5315 - 5328.

    https://hal.inria.fr/hal-01406364
  • 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.
  • 43B. 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.
  • 44H. 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.
  • 45A. 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.
  • 46P. Schommers, G. Martrus, U. Matschl, M. Sirignano, M. Lütgehetmann, L. Richert, T. J. Hope, G. Fätkenheuer, M. Altfeld, F. Kirchhoff.

    Changes in HIV-1 Capsid Stability Induced by Common Cytotoxic-T-Lymphocyte-Driven Viral Sequence Mutations, in: Journal of Virology, July 2016, vol. 90, no 16, pp. 7579 - 7586. [ DOI : 10.1128/JVI.00867-16 ]

    https://hal.archives-ouvertes.fr/hal-01404506
  • 47C. Schubert.

    Systems immunology: complexity captured, in: Nature, 2011, vol. 473, no 7345, pp. 113-4.
  • 48M. Surenaud, C. Manier, L. Richert, R. Thiébaut, Y. Levy, S. Hue, C. Lacabaratz.

    Optimization and evaluation of Luminex performance with supernatants of antigen-stimulated peripheral blood mononuclear cells, in: BMC Immunology, December 2015, vol. 17, no 1, 44 p. [ DOI : 10.1186/s12865-016-0182-8 ]

    http://www.hal.inserm.fr/inserm-01395760
  • 49R. 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.
  • 50R. Thiébaut, B. 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
  • 51R. 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.
  • 52R. 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.
  • 53Y. Wang.

    Derivation of various NONMEM estimation methods, in: Journal of Pharmacokinetics and pharmacodynamics, 2007, vol. 34, no 5, pp. 575–593.
  • 54H. 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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