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Bibliography

Publications of the year

Doctoral Dissertations and Habilitation Theses

  • 1M. Avalos Fernandez.

    Contribution to model selection via Lasso penalization in Epidemiology, Université de Bordeaux, December 2018, Habilitation à diriger des recherches.

    https://hal.archives-ouvertes.fr/tel-01964508
  • 2C. Pasin.

    Modeling and optimizing the response to vaccines and immunotherapeutic interventions. Application to Ebola virus and HIV, Université de Bordeaux, October 2018.

    https://hal.inria.fr/tel-01973077
  • 3L. Villain.

    Analysing and modeling the effect of interleukin 7 in HIV-infected patients, Université de bordeaux, December 2018.

    https://hal.inria.fr/tel-01973123

Articles in International Peer-Reviewed Journals

  • 4A. Ammassari, W. Stöhr, A. Antinori, J.-M. Molina, C. Schwimmer, P. Domingo, A. Thalme, M. Di Pietro, C. Wallet, A. Pozniak, L. Richert, F. Raffi.

    Patient Self-Reported Adherence to Ritonavir-Boosted Darunavir Combined with Either Raltegravir or Tenofovir Disoproxil Fumarate /Emtricitabine in the Neat 001/Anrs 143 Trial, in: Journal of Acquired Immune Deficiency Syndromes, 2018. [ DOI : 10.1097/QAI.0000000000001834 ]

    https://hal.inria.fr/hal-01888899
  • 5I. Balelli, V. Milisic, G. Wainrib.

    Multi-type Galton-Watson processes with affinity-dependent selection applied to antibody affinity maturation, in: Bulletin of Mathematical Biology, 2018, https://arxiv.org/abs/1609.00823v2. [ DOI : 10.1007/s11538-018-00548-y ]

    https://hal.inria.fr/hal-01937856
  • 6D. 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, bioRxiv 335554. [ DOI : 10.1002/cyto.a.23601 ]

    https://hal.inria.fr/hal-01887966
  • 7E. George, R. Bucciardini, L. Richert, N. Dedes, V. Fragola, P. Nieuwkerk, B. Spire, A. Volny-Anne, B. West, J.-M. Molina, A. Horban, J. Fox, A. Pozniak, S. Vella, M. Termote, F. Raffi.

    Patient-Reported Outcomes in First-Line Antiretroviral Therapy: Results from NEAT001/ANRS143 Trial Comparing Darunavir/Ritonavir in Combination with Tenofovir/Emtricitabine or Raltegravir, in: Journal of Acquired Immune Deficiency Syndromes, 2018. [ DOI : 10.1097/QAI.0000000000001844 ]

    https://hal.inria.fr/hal-01888891
  • 8L. Gross, É. Lhomme, C. Pasin, L. Richert, R. Thiébaut.

    Ebola vaccine development: Systematic review of pre-clinical and clinical studies, and meta-analysis of determinants of antibody response variability after vaccination, in: International Journal of Infectious Diseases, September 2018, vol. 74, pp. 83 - 96. [ DOI : 10.1016/j.ijid.2018.06.022 ]

    https://hal.inria.fr/hal-01888913
  • 9B. 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, 2018, https://arxiv.org/abs/1702.04407 - 39 pages, 11 figures.

    https://hal.inria.fr/hal-01579063
  • 10B. P. Hejblum, J. Cui, L. J. Lahey, A. Cagan, J. A. Sparks, J. Sokolove, T. Cai, K. P. Liao.

    Association between anti-citrullinated fibrinogen antibodies and coronary artery disease in rheumatoid arthritis, in: Arthritis Care and Research, June 2018, vol. 70, no 7, pp. 1113-1117. [ DOI : 10.1002/acr.23444 ]

    https://hal.inria.fr/hal-01654403
  • 11B. 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 , 2018.

    https://hal.inria.fr/hal-01942279
  • 12S. Lefèvre-Arbogast, D. Gaudout, J. Bensalem, L. Letenneur, J.-F. Dartigues, B. P. Hejblum, C. Feart, C. Delcourt, C. Samieri.

    Pattern of polyphenol intake and the long-term risk of dementia in older persons, in: Neurology, May 2018, vol. 90, no 22, pp. e1979 - e1988. [ DOI : 10.1212/WNL.0000000000005607 ]

    https://hal.inria.fr/hal-01887895
  • 13S. Lunemann, A. Schöbel, J. Kah, P. Fittje, A. Hölzemer, A. Langeneckert, L. Heß, T. Poch, G. Martrus, W. Garcia-Beltran, C. Körner, A.-R. Ziegler, L. Richert, K. Oldhafer, J. Schulze Zur Wiesch, C. Schramm, M. Dandri, E. Herker, M. Altfeld.

    Interactions Between KIR3DS1 and HLA-F Activate Natural Killer Cells to Control HCV Replication in Cell Culture, in: Gastroenterology, July 2018. [ DOI : 10.1053/j.gastro.2018.07.019 ]

    https://hal.inria.fr/hal-01888904
  • 14C. Pasin, F. Dufour, L. Villain, H. Zhang, R. Thiébaut.

    Controlling IL-7 injections in HIV-infected patients, in: Bulletin of Mathematical Biology, August 2018.

    https://hal.inria.fr/hal-01933170
  • 15W. Salzberger, G. Martrus, K. Bachmann, H. Goebels, L. Heß, M. Koch, A. Langeneckert, S. Lunemann, K. Oldhafer, C. Pfeifer, T. Poch, L. Richert, C. Schramm, R. Wahib, M. Bunders, M. Altfeld.

    Tissue-resident NK cells differ in their expression profile of the nutrient transporters Glut1, CD98 and CD71, in: PLoS ONE, July 2018, vol. 13, no 7, e0201170 p. [ DOI : 10.1371/journal.pone.0201170 ]

    https://hal.inria.fr/hal-01888905
  • 16J. A. Sinnott, F. Cai, S. Yu, B. P. Hejblum, C. Hong, I. Kohane, K. P. Liao.

    PheProb: probabilistic phenotyping using diagnosis codes to improve power for genetic association studies, in: Journal of the American Medical Informatics Association, May 2018. [ DOI : 10.1093/jamia/ocy056 ]

    https://hal.inria.fr/hal-01887930
  • 17P. Soret, M. Avalos Fernandez, L. Wittkop, D. Commenges, R. Thiébaut.

    Lasso regularization for left-censored Gaussian outcome and high-dimensional predictors, in: BMC Medical Research Methodology, 2018. [ DOI : 10.1186/s12874-018-0609-4 ]

    https://hal.archives-ouvertes.fr/hal-01945367
  • 18M. Tabue-Teguo, L. Grasset, J. A. Avila-Funes, R. Genuer, C. Proust-Lima, K. Pérès, C. Feart, H. Amieva, M. G.-C. Harmand, C. Helmer, N. Salles, M. Rainfray, J.-F. Dartigues.

    Prevalence and Co-Occurrence of Geriatric Syndromes in People Aged 75 Years and Older in France: Results From the Bordeaux Three-city Study, in: Journals of Gerontology, Series A, January 2018. [ DOI : 10.1093/gerona/glx068 ]

    https://hal.inria.fr/hal-01652204
  • 19L. 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, September 2018, vol. 38, no 2, pp. 221-235. [ DOI : 10.1002/sim.7957 ]

    https://hal.inria.fr/hal-01973045
  • 20S. M. Ziegler, C. N. Feldmann, S. H. Hagen, L. Richert, T. Barkhausen, J. Goletzke, V. Jazbutyte, G. Martrus, W. Salzberger, T. Renné, K. Hecher, A. Diemert, P. C. Arck, M. Altfeld.

    Innate immune responses to toll-like receptor stimulation are altered during the course of pregnancy, in: Journal of Reproductive Immunology, August 2018, vol. 128, pp. 30 - 37. [ DOI : 10.1016/j.jri.2018.05.009 ]

    https://hal.inria.fr/hal-01888920

International Conferences with Proceedings

  • 21M. Avalos Fernandez, R. Nock, C. S. Ong, J. Rouar, K. Sun.

    Representation Learning of Compositional Data, in: NIPS 2018 - Thirty-second Conference on Neural Information Processing Systems, Montréal, Canada, S. Bengio, H. Wallach, H. Larochelle, K. Grauma, N. Cesa-Bianchi, R. Garnett (editors), Advances in Neural Information Processing Systems 31 (NIPS 2018) pre-proceedings, December 2018, vol. 31.

    https://hal.archives-ouvertes.fr/hal-01945508
  • 22M. Rojas Castro, M. Travanca, M. Avalos Fernandez, D. V. Conesa, L. Orriols, E. Lagarde.

    MAVIE-Lab Sports: a mHealth for Injury Prevention and Risk Management in Sport, in: DIGITAL HEALTH 2018 - 8th International Digital Health Conference, Lyon, France, April 2018.

    https://hal.inria.fr/hal-01782964

Conferences without Proceedings

  • 23H. Lorenzo, J. Saracco, R. Thiébaut.

    Une PLS multivoie parcimonieuse avec observations manquantes pour données hétérogènes, in: Journées de Statistique 2018 - Société Française de Statistique, EDF Lab Paris Saclay, France, May 2018.

    https://hal.archives-ouvertes.fr/hal-01963431
  • 24H. Lorenzo, R. Thiébaut, J. Saracco.

    Multi-block high-dimensional lasso-penalized analysis with imputation of missing data applied to postgenomic data in an Ebola vaccine trial, in: Annual workshop on Statistical Methods for Post Genomic Data - SMPGD 2018, Montpellier, France, January 2018.

    https://hal.archives-ouvertes.fr/hal-01664610
  • 25C. Pasin, L. Villain, F. Dufour, D. Commenges, M. Prague, R. Thiébaut.

    Use of mathematical modeling for optimizing and adapting immunotherapy protocols in HIV-infected patients, in: Population Approach Group Europe, Montreux, Switzerland, May 2018.

    https://hal.inria.fr/hal-01934340
  • 26M. Rojas Castro, M. Travanca, M. Avalos Fernandez, D. V. Conesa, E. Lagarde.

    Usefulness of Bayesian modeling in risk analysis and prevention of Home Leisure and Sport Injuries (HLIs), in: III Jornadas Científicas de Estudiantes de la Sociedad Española de Biometría, Bilbao, Spain, January 2018.

    https://hal.archives-ouvertes.fr/hal-01964484
  • 27M. Rojas Castro, M. Travanca, M. Avalos Fernandez, L. Orriols, D. V. Conesa, E. Lagarde.

    Mavie-lab sports: a mhealth for injury prevention and risk management in sport, in: The 13th World Conference on Injury Prevention and Safety Promotion (Safety 2018), Bangkok, Thailand, November 2018.

    https://hal.archives-ouvertes.fr/hal-01945586
  • 28L. Villain, D. Commenges, M. Prague, C. Pasin, R. Thiébaut.

    Adaptive protocols based on predictions from a mechanistic model of the effect of IL7 on CD4 counts, in: International Biometric Conference, Bacelone, Spain, July 2018.

    https://hal.inria.fr/hal-01973877

Other Publications

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

    Cancer immunotherapy, mathematical modeling and optimal control, in: Biometrical Journal, 2007, vol. 247, no 4, pp. 723-32.
  • 33R. 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.
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    Systems approaches to biology and disease enable translational systems medicine, in: Genomics Proteomics Bioinformatics, 2012, vol. 10, no 4, pp. 181–5.
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    Modelling viral and immune system dynamics, in: Nature Reviews Immunology, 2002, vol. 2, no 1, pp. 28-36.
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    http://www.hal.inserm.fr/inserm-00933691
  • 47R. 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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