Senior Researcher in Statistical Genetics and Pathogen Dynamics
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.
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:
- Read this if you write in English. Read this if you write in order to make a point.
- Read this if you give talks.
- Read this if you're a scientist using a computer.
- These resources were recommended for learning to use the command line (a.k.a. the terminal a.k.a. the shell), which is an important step in being able to use other people's computational scientific methods: http://rik.smith-unna.com/command_line_bootcamp
- This was highly recommended for learning version control with Git (aimed at users of R but with more general applicability).
- This helps one remember obscure latex symbols.
Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission.
Thompson RN. et al, (2019), Virus evolution, 5
The evolution of subtype B HIV-1 tat in the Netherlands during 1985-2012.
van der Kuyl AC. et al, (2018), Virus research, 250, 51 - 64
Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver.
Wymant C. et al, (2018), Virus evolution, 4
Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes.
Cornelissen M. et al, (2018), 1746, 55 - 61
PHYLOSCANNER: Inferring Transmission from Within- and Between-Host Pathogen Genetic Diversity.
Wymant C. et al, (2017), Molecular biology and evolution