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
  http://www.ee.surrey.ac.uk/Teaching/Unix
  http://swcarpentry.github.io/shell-novice/.
• 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.