Transmission dynamics

This group is about understanding infectious diseases transmission from the analysis of incidence and/or surveillance data from surveillance systems. We will explore a number of techniques of data visualization and time series analysis in order to characterize meaningful signals in the data. We will also develop mathematical and computational models of disease transmission, fit them to real data and compare different modeling techniques as a function of the type of data and the kind of question under investigation. Models will be used to test different hypotheses regarding transmission mechanism, to estimate key epidemiological parameters such as R0 and to explore optimal interventions to reduce disease incidence.

    • Compartmental models
    • Stochastic simulations
    • Differential equations
    • Agent-based models
    • Time series analysis
    • Spatial dynamics
    • Infectious diseases control
    • Models parameters estimation

  • Alexis Drogoul

    Alexis Drogoul graduated in artificial intelligence in 1990 and received his PhD degree from the University of Paris 6 in 1993. Recruited in 1995 as associate professor, he became full professor in 2000 and joined the Institute of Research for Development as a senior researcher in 2004, within the UMMISCO international research unit. He works on agent-based simulation of complex systems, mainly by developing the GAMA simulation platform. Since 2007, he has been working in Vietnam to enhance the research capacity of Vietnamese teams (MSI-IFI, DREAM-CTU, ICTLab-USTH) on the design of models for environmental decision-support and epidemiology, in the framework of several international research projects. He has the director of the ICTLab of the University of Science and Technology of Hanoi since 2015.

    Cécile Viboud

    Cécile Viboud is a Senior Research Scientist in the Division of International Epidemiology and Population Studies of the Fogarty International Center, NIH, where she has worked over the past 13 years. She received an engineer degree in biomedical technologies from Lyon University (1998), a Master of Public Health (1999) and PhD in Biomathematics (2003) from the University of Paris. Her research focuses on modeling the transmission dynamics and epidemiology of influenza and other acute viral infections, at the interface of public health, epidemiology and evolution. Recently she has become interested in the transmission dynamics of Ebola and MERS-CoV, and the potential use of disease forecasts in government.

    Wladimir Alonso

    Wladimir J. Alonso is a Research Fellow at the Fogarty International Center (US National Institutes of Health). He has pioneered the analyses of latitudinal gradients of seasonal parameters of diseases, as well as the analytical approach that enabled revealing that the annual influenza vaccine is administered at the wrong timing in several tropical regions. Wladimir also has a number of studies on historical epidemiology and on how epidemiological knowledge can be translated into better public health decisions. He teaches workshops on time-series analysis and data visualization, using Epipoi , a software of his authorship, which has been made freely available and is currently used by epidemiologists, public health researchers and students around the globe. He also works (pro-bono) on evolutionary theory, environmental science and animal welfare.

    Nicolas Marilleau

    Nicolas Marilleau has been a researcher engineer at the UMMISCO international research unit of IRD (Institut de recherche pour le développement) and UPMC (Pierre et Marie Curie University) since 2006. In addition, he has been an associate researcher at the DISC team of FEMTO-ST institut since 2012. Nicolas focuses on distributed systems, collaborative systems and the modeling and simulation of complex systems. From real case studies of various domains such as soil sciences or social science, he designs and develops technics for a domain expert oriented modeling/simulating process that takes into account collaboration to share knowledge and data and high performance computing to speed up large scale simulations. He applies his researches to various domains such as urban dynamics, sol sciences and epidemiology.

    Alex Becker

    Alex Becker is a PhD student with Prof. Bryan Grenfell in the Department of Ecology and Evolutionary Biology at Princeton University. His current research is focused on dissecting the cross-scale dynamics of measles transmission, with the most recent work being on transmission within primary schools. Generally, he is interested in developing and expanding the methods used to analyse and fit infectious disease time series data.

  • R, RStudio, Epipoi, GAMA

    R packages: gamar, deSolve, bbmle, knitr, rmarkdown