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Senior Researcher in Statistical Genetics and Pathogen Dynamics

Chris Wymant

Chris Wymant

After a PhD and the beginning of a postdoc in theoretical particle physics, I joined Christophe Fraser's group, initially at Imperial College London and now here in the Big Data Institute. I work on HIV genomics as part of the BEEHIVE project: analysing viral genetic data, in conjunction with patient clinical data, to gain insight into the viral-molecular basis of infection severity.

I wrote the tools shiver for reconstructing HIV (and other viral) genomes from short read data, and phyloscanner (with Matthew Hall and Christophe) for analysing within- and between-host pathogen genetic diversity. Here are some slides about shiver and phyloscanner and related ideas; here's a webinar in which I go through some of those slides. A few other bits of my code for working with sequence data are here.

My publications are here. (Here is an open-access link to the only one of those that's paywalled, on academic institutional policy on flying: Jean and Wymant, Science 2019.)

While at Imperial I taught Core Mathematics for masters courses in public health and epidemiology. Here is some material I wrote for this: the quiz testing all of the material covered, and the answers; basic manipulation of numbers - the slides for 2015 and prose-style notes from 2014; inequalities, functions and units - slides for 2015, solutions to the problems, and prose-style notes from 2014; probability parts one and two; calculus in more detail; a bit of supplementary material about trigonometric, exponential and logarithmic functions, and matrices.

I wrote some illustrative code for an introductory course in python, showing basic syntax and file input/ouput. Here are some bash commands (i.e. working with the terminal / command line) that I find helpful.

Assorted useful links:

Recent publications

More publications