Senior Researcher in Statistical Genetics and Pathogen Dynamics
In more normal times:
After a PhD and some postdoctoral research in theoretical particle physics, I decided to join Christophe Fraser's group, initially at Imperial College London and now here in the Big Data Institute. I work on HIV genomics and epidemiology 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.
Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing.
Ferretti L. et al, (2020), Science (New York, N.Y.)
Quantifying SARS-CoV-2 transmission suggests epidemic control with digital contact tracing
Ferretti L. et al, (2020)
Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda.
Ratmann O. et al, (2020), The lancet. HIV, 7, e173 - e183
Evaluation of phylogenetic methods for inferring the direction of HIV transmission: HPTN 052.
Zhang Y. et al, (2020), Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis.
Ratmann O. et al, (2019), Nature communications, 10