Topic outline
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This course page is not finalized: more information will appear later
Course Instructors
Erik Volz, Imperial College London
Nicola de Maio, EMBL-EBI
Course contents:# Summary
This course provides and in-depth introduction to pathogen genomics and evolution with a focus on applications of genomics to understanding epidemiological dynamics. At the end of this course, students will have a practical understanding of how to analyse pathogen genetic data to address a variety of public health questions, such as investigations of epidemic origins, identifying emerging variants, evolution of antimicrobial resistance, epidemic growth rates, and transmission patterns.
We will review- Population genetics of evolving pathogens, including how epidemiological and immunological dynamics influence pathogen genetic diversity.- Evolution of antimicrobial resistance, including mechanisms of resistance, how natural selection leads to development of resistance and how to detect and quantify natural selection in genomic data.- Phylogenetic methods and approaches to understanding how pathogen genetic diversity changes over time. This will include tutorials on software used to estimate pathogen phylogenies, including BEAST.- Epidemiological modelling and phylodynamics. This will include applications of phylogenomics to epidemiological surveillance, such as monitoring for emerging variants and estimating transmission patterns over space and time.
# Software
IMPORTANT: All participants are expected to bring a laptop.Students should install R:- Optionally use R Studio: https://posit.co/products/open-source/rstudio/- Students should be able to install the `ape` R package.Students should install BEAST >1.10: https://beast.community/
Time and PlaceAll lectures take place at Stockholm University in Campus Albano, house 1, level 2, room 2. See Registration and Venue for further details.
Lecture times (includes also problem solving, tutorials, computer sessions, ...):
Wednesday June 26: 14.00-15.30, 16.00-17.30
Thursday June 27: 9.00-10.30, 11.00-12.30, 14.00-15.30, 16.00-17.30
Friday June 28: 9.00-10.30, 11.00-12.30, 14.00-15.30, 16.00-17.30
General prerequisites
It is expected that course participants have basic knowledge of statistics and mathematics and rudimentary knowledge of infectious disease epidemiology. It is also expected that participants have basic computer software knowledge and preferably are familiar with the software R.
IMPORTANT: All participants are expected to bring a laptop with R installed on it.
Additional prerequisites for this course
Basic educational experience in genetics and evolutionary biology is helpful but not required.
Relevant literature
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Instructions for installing R, introduction to R?
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Upload lecture slides and other relevant materials...