PHD Supervision and Mentoring
PHD
Anne-André Ruiz ,
co-supervision with
Véronique Godot (PUPH immunologist at Université Paris
Créteil).
Modeling of immune response to vaccination in mice.
expected 2028
Lisa Crépin ,
co-supervision with
Morgan Craig (Professeure agrégée at Université de
Montréal).
Modeling of immune response to vaccination in mice.
expected 2028
Théo Rene ,
co-supervision with
Moreno Ursino (Inria Paris HEKA team). Clinical trial
designs for assessment of medical devices based on digital twins.
expected 2028
Adrien Mitard ,
co-supervision with Jeremie Guedj (Inserm IAME, Paris).
Accelerating Vaccine Development Using Pre-Clinical Data.
expected 2026
Auriane Gabaut ,
co-supervision with
Cécile Proust-Lima (Inserm Bordeaux Population health).
Use of latent variable models to build mechanistic models
in high dimension: application in immunology for vaccine development.
2025
Iris Ganser ,
supervised by David Buckeridge (Mc Gills University) and
Rodolphe Thiébaut (Inserm Bordeaux Population health).
I am Co-Mentor.
Insights from mathematical models into COVID-19 :
analyzing public health interventions and immunity dynamics.
2024
Marie Alexandre,
co-supervision with
R. Thiébaut (Inserm Bordeaux Population health).
Mechanistic modeling and optimization of vaccine response
in infectious diseases: Application to HIV, Ebola,
SARS-CoV-2. Postdoctoral fellow in the inria SISTM team.
2022
Laura Villain,
supervised by Daniel Commenges and Rodolphe Thiébaut (Inserm Bordeaux Population health). I was Co-Mentor.
Analyse et modélisation de l’effet des injections
d’interleukine 7 sur les patients
infectés par le VIH.
Scientist consultant in industry (NovaDiscovery then
esqLABS GmbH).
2018
Patrick Staples,
Supervised by JP Onnela at Harvard T.H. Chan School of public health.
Collaboration 2nd and
partially 3rd paper. Networks and Statistical Approaches in Biological Contexts.
VP of Data Science at Alto Neuroscience USA.
2018
Postdoctoral fellows, research
scientist supervision, Research Engineer
Mircea Dimitru ,
recovering results from clinical trials for antiviral treatments by emulating in
silico patients using mechanistic models based on the HIV Aquitaine
cohort. postdoc within the PEPR SMATCH Project.
Jan.2026-now
Jad el Karchi,
co-supervision with R. Thiébaut and Inria
SED. Developpement of
plug-in for the labkey data warehouse to disseminate our statistical methods to
collaborarors. Engineer paid by VRI.
Apr.2025-now
Myriam Nafti,
co-supervision with R. Thiébaut and UMS MART. Datamanager in charge of integration of data into our
labkey data warehouse. Engineer paid by VRI.
Jan.2024-now
Francois Plessier,
co-supervision with C. Proust-Lima.
Developpement of an R package to fit mixed effect models in which the fixed effect part is based on a RNN or
reservoir computing. Engineer within the PHDS network Impulsion.
2025-now
Bastien Reyné,
co-supervision with L. Wittko. Developpement of a pipeline for in sillico mice experiment
based on a mechanistic model of Hepatitis B.
Postdoc within the IP-CURE-B Project. He is now a postdoc in Montpellier CEFE.
Aug.2024-Aug.2025
Nicolas Boesfplug ,
co-supervision with E. Lhomme Prediction of the
establishment
and maintenance of humoral response after Ebola
vaccination.
Engineer within the PREVAC-UP Project.
Apr.2023-Dec.2025
Quentin Clairon ,
New tool for estimation of parameters in non-linear
mixed-effects models based
on optimal control (EBOVAC 3 Project). postdoc within
the EBOVAC 3 Project
now researcher ISFP at inria within the SISTM team.
2019-2022
Marie Alexandre ,
Statistical analysis and design of pre-clinical (NHP and
rodents) and clinical trials promoted by the Vaccine
Research institute. Post-doc Vaccine Research Institute,
now a postdoc at John Hopkins.
2022-jan.2025
Maria Prieto,
She worked on the modeling of the COVID19 epidemics in
France and particularly helped in estimating the effect of
non-pharmaceutical
interventions of the epidemics dynamics. She is now a
"Head of projects" at Octopia.
sept.2020-Sept.2021
Irene Balleli Modeling
response to Ebola vaccines. Researcher ISFP at inria Sophia Antipolis.
2017-2020
Laura Villain Joint
modeling of
dynamical biomarkers and high-dimensional data.
Biomodeler at esqLabs GmbH.
2018-2019
Myrtille Richard ,
Engineer within the NIPAH Project. To propose a pipeline for in
silico trials. She is now continuing her curriculum of Public Health Medical Doctor.
Mar.2022-Dec.2022
Dan Dutartre ,
Detached by Inria to work within SISTM team. He designed a connector
between R and Monolix that
was particularly useful to share our codes during the
pandemics.
He is now on a long-term contract as research engineer at Inria.
May2020-Nov.2020
Internships
Lisa CREPIN(Agrotech Paris),
Jade Lety (High School - 2 weeks, created a game
for public outreach)
2025
Anne-André Ruiz (M2 Biostat ISPED),
Tristan Candido Da Silva (M2 Biostat ISPED),
Jay Awale (L3 Indian Inst. Tech.),
Arthur Leroudier(Ensae).
2024
Marie Colin (ENSAI 2ième année),
Junior Jumbong (ENSAI 2ième année),
Fanny Moreau (L3 MIASCHG Bordeaux),
Auriane Gabaut(M2 MSV Polytechnique).
2023
Marie Poupelin (M1 Biostat ISPED),
Florian Robert (M2 Paris Sorbonne),
2022
Marie-Laure Charpignon (PhD Candidate MIT),
2021
Carole Vignals (M2 EPI ISPED),
Abdelghani Nehaus (M2 Bioinfo Labri, Université Bordeaux),
2020
Clément Lemoigne (Mathmeca 2nd year),
Guillaume Sotton (Master 2 Bioinformatique, Université Bordeaux),
2019
Marie Alexandre (Master 2 Centrale Marseille),
2018
Marie Alexandre (Master 1 Centrale Marseille),
Paul Tauzia ( Master 2 MSS Université de Bordeaux),
Augusta Alphonse (Master 2 Vaccinology Creteil),
2017
Damien Fossat-Cercle (Master 2 in Statistics and ENSAI 3rd
year),
2013
Ana Jarne (Master 2 in Biostatistics,
Université de Pau),
Paul Tauzia ( Master 2 MSS Université de Bordeaux),
Augusta Alphonse (Master 2 Vaccinology Creteil),
2012
Sybille Masse(ENSAI 2nd year).
2011
Publications
HAL
DBLP
Google Scholar
Three major publications
- Modelling the response to vaccine in non-human primates to define SARS-CoV-2 mechanistic correlates of protection
Marie Alexandre, Romain Marlin, Mélanie Prague,
Severin Coleon, Nidhal Kahlaoui, Sylvain Cardinaud, Thibaut
Naninck,
Benoit Delache, Mathieu Surenaud, Mathilde Galhaut,
Nathalie Dereuddre-Bosquet, Mariangela Cavarelli,
Pauline Maisonnasse, Mireille Centlivre, Christine
Lacabaratz, Aurelie Wiedemann,
Sandra Zurawski, Gerard Zurawski, Olivier Schwartz, Rogier
W Sanders, Roger Le Grand,Rodolhe Thiébaut, eLife, 2022, 11, ⟨10.7554/elife.75427⟩, pdf
- Comparative evaluation of methodologies for estimating
the effectiveness of nonpharmaceutical interventions in the context of COVID-19: a simulation study
Iris Ganser, Juliette Paireau, David L. Buckeridge, Simon Cauchemez, Rodolphe Thiébaut, Mélanie Prague
pdf
- SAMBA: A novel method for fast automatic model building in nonlinear mixed-effects models
Mélanie Prague, Marc Lavielle
pdf
Softwares
- R package "REMixed"
is a library that provides an iterative
algorithm to estimate parameters of a model whose latent dynamics are
inferred through latent processes, jointly regularized.
documentation and download
- R package"LSamba" is a
library based on Rsmlx for covariates model building in
high-dimension using regularization.
documentation and download
- R package "Rsmlx" is a library that allows to interface optimization
algorithms with models of epidemic propagation. Epidemiological models are wrapped
in OpenAI Gym interfaces, making them readily compatible with state-of-the-art
optimization algorithms.Modest contribution.
documentation and download
- Python Toolboox "EpidemiOptim" is a library that allows
to interface optimization algorithms with models of epidemic propagation.
Epidemiological models are wrapped in OpenAI Gym interfaces,
making them readily compatible with state-of-the-art optimization algorithms.
documentation and download
Dissemination paper
- R package "SEIRcovid19FR" is an R package for multi-level
inference of epidemic dynamics applied to COVID-19 in France..
documentation and download
- R package CRTgeeDR is an R package for Doubly Robust
Generalized Estimating Equations Estimations in Cluster
Randomized Trials with missing data.
Link to the documentation
Download CRTgeeDR sources
Dissemination paper
- N.I.M.R.O.D. Normal approximation
Inference in Models with Random
effects based on Ordinary Differential equations
Models based on ordinary differential equations (ODE) are
a widespread tool to describe dynamical system. In
biomedical sciences, data within each subject
can be sparse but information is often gained from
between-subjects variability. This makes natural the use
of mixed effect models to estimate population
parameters. Although maximum likelihood based approaches
are a valuable option, both numerical and identifiability
issues favor a Bayesian approach which
can incorporate prior knowledge in a flexible way. However
the combination of difficulties coming from the ODE system
and from the presence of random effects raises a major
numerical challenge.
A normal approximation of the posterior can be obtained by computing
the maximum of the posterior distribution (MAP).
Link to the documentation and sources
Dissemination paper
- marqLevAlg : R package for Marquardt-Levenberg minimization.
This algorithm provides a numerical solution to the
problem of minimizing a function.
This is more efficient than the Gauss-Newton-like algorithm when
starting from points very far from the final minimum. A
new convergence test is implemented (RDM) in addition to
the usual stopping criterion :
stopping rule is when the gradients are small enough in the parameters metric (GH-1G).
Link to the documentation
Download marqLevAlg sources
Dissemination paper
Positions
Chaire Ecole Polytechnique, Sanofi,
Paris , Secondary appointment of research and
teaching. "Numerical Innovation and Data
Science for Health", work in collaboration with Marc
Lavialle and the Inria Team XPOP.
2021 - 2023
Post-doctoral fellow
, Harvard School of Public Health Boston USA,
Semi-parametric estimation of treatment effect in
clustered randomized trials in presence of missing data:
application to HIV prevention in South Africa (Victor de Gruttola).
2014 - 2016
32 months
Invited researcher,
University of Oslo, Norway, Comparison of propensity score
based methods and dynamical methods for estimation of
treatment effect in observational studies (Odd Aalen).
2013-2014
1 month
Postdoctoral fellow,
INSERM U121, France, Dynamical mechanistic modeling of HIV’ (Rodolphe Thiébaut).
Oct-Dec 2013
PHD and teaching assistant position,
INSERM U121 and Université de Bordeaux, France
(Daniel Commenges).
Oct 2010-sep 2013
Master 2 Internship ,
INSERM U121 and Université de Bordeaux, France,
Analysis of Phase II/III HIV Clinical trials (Daniel Commenges).
Apr-Sep 2010
SAS programmer,
Averion International, Basel Switzerland,Analysis of a Phase III Clinical Trial in oncology.
May-Aug 2009
Consolidator of data basis,
INSERM, Unit 897, Bordeaux France, Data entry in nutrition studies.
Jun-Jul 2008
Education
Qualification for assistant professor
CNU 26
2014
Ph.D. in Public Health and Biostatistics with highest honnors
, Monitoring of HIV infected patients based on dynamic
models, Advisor Daniel Commenges, Biostatistics, École Doctorale SP2 (Political science and public health)
within the Université de Bordeaux, France
2010-2013
Master of Science (M.Sc.) in Statistics and Econometrics with high honors
(dual curriculum) Department of Mathematics, Université de Rennes 1, France.
2009-2010
Master’s Degree in Engineering in
Statistics, (equivalent M.Sc)
ENSAI, National School for Statistics and Information Analysis, Rennes France.
2007-2010
Bachelor of Science (B.Sc.) in Economics (dual curriculum)
, Department of Economics, Université de Rennes 2, France.
2008-2009
Post-Secondary Preparatory Classes, Lycée Montaigne, Bordeaux, France.
University-level courses required in preparation for competitive exams into top universities, engineering, and graduate schools (France’s “Grandes Écoles”). Major : Mathematics and Physics.
2005-2007
Grants
Active Grants
Vaccine research
institute (VRI)
Role :I am involved in the scientific committee as the
head of SISTM.
Conduct research to accelerate the development of
effective vaccines against HIV/AIDS, and (re)-emerging
infectious diseases
2025-2035
Previx
Role : head of the "within host" WP
Pandemic Preparedness to Respiratory Virus X.
2023-2028
SMATCH – Addressing new methodological challenges in public health
data science.
Role : contributor and mentor of one PhD student.
Frame : PEPR Santé Numérique
The project aims to develop and apply statistical methods and AI-based approaches to
accelerate the development of medical interventions in clinical trials, focusing on the early phases
and integrating multi-source data.
2023-2029
PHDS Impulsion Réseaux Public Health Data Science network.
Head: Cecil Proust-Lima
Role : Principal investigator workpackage "Incorporate complex measurement
models into theoretical mechanistic models".
Frame : Université de Bordeaux
The PHDS network aims to utilize Bordeaux’s expertise in statistics, applied mathematics,
and public health to develop analytical methods that: precisely predict disease onset
and progression at an individual level, elucidate the mechanisms that underlie diseases,
and create and assess innovative therapeutic strategies.
2022-2026
Previous Grants
Coverage-Immuno
Head : Rodolphe Thiébaut
Role : WP leader for "Data analysis".
Frame: EIT Health COVID-19 Rapid Response.
COVERAGE-Immune aimed at performing a deep, repeated
evaluation of immunological markers and transcriptomics data
in COVID-19 positive patients treated at home
.
ended 2020
Prevac-Up
Role : WP leader for "System Vaccinology approach".
Frame: European project RIA EDCTP
PREVAC-UP is built around the PREVAC consortium and its
main objective is to evaluate
the long-term safety, as well as the durability of humoral and cellular immune responses, of three different Ebola vaccine regimens.
ended 2024
amfAR
Role : Contractor.
Frame: American Fundation for AIDS research
Mechanistic and empirical modeling of viral rebound to identify predictors of post-treatment control.
ended 2020
Nipah Virus Study
Role : co-WP leader for "Biostatistics and evolutionary".
Frame: Sino-French Agreement Aviesan
Preparedness against Nipah virus.
ended 2023
EBOVAC3
Role : co-WP leader for "Modeling" aspects.
Frame: European IMI2
The EBOVAC3 project aims to support
an essential part of the remaining clinical and
manufacturing activities required for the licensure of the
two-dose vaccine regimen in the European Union and the
United States.
ended 2023
Revealing Reservoirs during Rebound
Head : Smith D.
Role: Contributor.
Frame: P01AI131385 NIH.
.
The mission of this research focus will be to create and apply new methods to address
analytical challenges arising from HIV reservoir measures and cure issues in anatomic
compartments using data from a variety of technological platforms.It supports my travel
expenses for USA.
2017-2022
DYNAMHIC
Heads M. Prague and A. Hill
Frame: Inria associate team
.
This collaboration allows the analysis of unique pre-clinical data in non-human
primates of HIV cure interventions.
2018-2022
EMERGEN-Modvar
Head: Cauchemez S. and Collizza V., Pasteur Institute
Role: co-workpackage leader for the within-host aspects of the project.
SISTM will contribute to modeling the impact on epidemic dynamics of SARS-CoV-2 variants based
on the estimation of their within-host characteristics.
Frame: ANRS Infectious diseases.
Consortium for Surveillance and Research on EMERgent Pathogens via Microbial
GENomics. EMERGEN, coordinated by Sante publique France and ANRS-Emerging Infec16
tious Diseases, aims to deploy a genomic surveillance system for SARS-CoV-2 infections throughout
France. Its main objective is to follow the genetic evolution of the SARS-CoV-2 virus in order to
detect the emergence and the spatio-temporal distribution of variants, i.e. viruses with mutations
likely to have functional consequences, such as infectivity, contagiousness, virulence or immune
escape.
2021-2024
Mechanistic modeling
and optimization of the response to HIV & Ebola vaccines
Head : Prague M.
Frame: inria CORDIS-S.
We propose to combine
exploratory analysis, dimension reduction methods for
high dimensional data, mathematical dynamical modeling
and optimal control theory to propose optimal vaccination
strategies in term vector choices and timing of vaccine
boosts. This grant aims at funding a 3 years of PhD student.
2018-2021
GESTEPID
Head Prague M.
Frame: Action Inria stop COVID19
Modeling of the COVID-19 epidemics in France with a focus on the region Nouvelle-Aquitaine.
A first output of this grant is the article "Population modeling of early COVID-19 epidemic dynamics in French regions
and estimation of the lockdown impact", which was cited by the Conseil Scientifique
COVID-19 on his report June 2nd
03/2020-12/2020
EVALUATES
Role: Principal investigator workpackage mechanistic modelling.
Frame: INCA project (National Institute for Cancer).
Evaluation of the efficacy of treatments on the evolution of tumor size and other
criteria of survival. Development of joint models
involving dynamical mechanistic model of tumor growth.
08/2017-06/2021
Philippe foundation grant
(renewal)
. My project concerned: "Evaluating
and targeting of HIV prevention strategies".
2015
Philippe
foundation grant.
It's a non-profit organization for
Franco-American exchanges. My project concerned: "Methods
for analyzing HIV clustered randomized data and cohort
data with informative missingness".
2014
Awards & Honnors
Top download. Paper in
the 10% most downloaded among work published in an issue
between 1 January 2022 – 31 December 2022 in CPT:
Pharmacometrics & Systems pharmacology.
M. Prague and
M. Lavielle, SAMBA: A novel
method for fast automatic model building in nonlinear
mixed-effects models, 11(2) - 161-172 - Feb 2022 (11 pages).
2024
Prime d'Excellence. It is
a special mention delivered by inria at the national level.
2017-2025
SFDS Conference travel
award.
This 600€-grant allow young scientists whose application
get selected to attend a the French annual conference JdS
2016
Harvard Rose fellowship
Award. Four
prices a year to offer a cross-cultural experience of
research in developing country. My project concerned:
"Estimation of incidence and prevalence of HIV in
Botswana: pooling data from different registers to
evaluate the impact of personal characteristics such as citizenship".
2016
Marie-Jeanne et Laurent Duhamel
Award. The price is
given once every other year by the Statistical French Society and awards scientific
quality of PhD works in Applied Statistics.
2015
Selected for summer school Sidaction
Young researchers. One week intensive class
program to mix multidisciplinary early-stage researchers
in order to promote collaborations in the field of HIV.
2011