Senior Researcher in Statistical Genetics and Pathogen Dynamics
After a PhD and 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 (jointly with Matthew Hall) for analysing within- and between-host pathogen genetic diversity. Here is a webinar I gave on these tools. A few other bits of my code for working with sequence data are here.
My publications 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 give talks.
- Read this if you're a scientist using a computer.
- These resources were recommended for learning to use the command line aka the terminal aka the shell: 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 for remembering obscure latex symbols.
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
Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.
Blanquart F. et al, (2017), Plos biology, 15