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Quantitative Viral Dynamics

Master in Life Science, ENS
UNBIO1-088 (E35) | Quantitative Viral Dynamics
Level | Semester : M2 | S1
Where : Biology department, ENS
Duration : 1 week, 30 hours
Date : November 12-15, 2024. Note that due to the holiday on Monday 11, the afternoon of Thursday 14 will not be freed of courses.
This course is open to external students : please read the paragraph “Registrer” below and then, consult this link .

—2024-2025 program—

Coordination

François Blanquart

Credits

3 ECTS

Keywords

Viral life cycle | Viral life-history traits. Viral ecology (e.g., phage-bacteria) | Within-host dynamics (e.g., HIV) | Epidemic dynamics (e.g., SARS-CoV-2).

Course Prerequisites

The course is targeted to interdisciplinary audiences, including students with background in ecology, evolutionary biology, life sciences, physics, mathematics, engineering, and/or computing, with experience and interest in mathematical modeling. Participants are welcome given the following prerequisites :
• Introductory ecology : population dynamics, population regulation (density-dependence), exponential growth, logistic model, Lotka-Volterra model.
• Basic systems modeling : non-linear differential equations, equilibrium, stability analysis.
• Some experience in programming (Python, MATLAB or R).

Course objectives and description

Aims & Themes : The course presents a theoretical foundation from which to model and predict the ecological and evolutionary dynamics that result from the interaction between viruses and their hosts, both microbial and human.
The course will present foundational principles and applications of viral ecology and evolution in bacteria populations, epidemiological dynamics of endemic and emerging viruses in human populations, and the models used to understand and control viral dynamics.
Finally, the course will present how genomic data can give insights into the origins, epidemiological dynamics and spatial spread of pathogens. In doing so, students will learn more about how to link mechanisms of virus-host interactions across scales from cells to populations.
Organisation : This is a one-week intensive course. Lecture-style presentations will be complemented by computer-based tutorials. In the tutorial sessions, students will work to implement the theory and numerically study model examples. This will involve the guided writing of simple code in Python.
This is a one-week intensive course. Lecture-style presentations will be complemented by computer-based tutorials. In the tutorial sessions, students will work to implement the theory via the numerically study of model examples. Tutorials will involve the guided development of simulations and analysis in Python and/or R. The course is targeted to interdisciplinary audiences, including students with background in the life sciences, physics, mathematics, engineering, and/or computing.

Assessment

Evaluation is based on the students presenting the work they carried out in the tutorial sessions. The presentations will take place at the end of the week.

Register

The course is open to selected non-IMaLis Master’s and PhD students. To apply, please send a short CV and explain your motivation in an email to François Blanquart no later than 18th October.

Course material

Readings, slides, computer simulation tutorial and video-recorded presentations will be made available to enrolled students.

Suggested readings

Weitz JS (2016) Quantitative Viral Ecology : Dynamics of Viruses and their Microbial Hosts. Monographs in Population Biology, Princeton University Press.