Hiding in the Trees – Positive Selection in Humans – My public talk on evolution

At the beginning of Oct I gave a public talk on Human selection and I have finally gotten the video edited together. Let me know what you think!!

Research Proposal – what am I doing for the next three years?

I am working on writing my research proposal at the moment. It is surprisingly difficult to produce 6 pages of high level speculative information about what I want to do for the next 3 years. I know that I want to study human evolution and that I am going to be looking at different types of selection but the guessing what I will be doing when is a little tenuous.

So as a broad stroke: I will be developing a method to detect positive selection in Homo sapiens and then using that method to data mine several publicly available genome repositories (HapoMap, 1000G, etc) to see what I can find.  What I will be interested in initially are “selective sweeps”, this is the classic form of selection where a beneficial mutation appears in the population and spreads like wildfire through the population over the next 10s of thousands of years.  I will also be looking at other types of selection and the two that I am most excited about are standing variation and epistasis. Standing variation is a mutation that is neutral when introduced to the population and only becomes beneficial through a change in the environment. Epistasis is where a gene is mutated and that affects the function of another gene.  I think epistasis will be difficult to find given the vast amounts of data that I will have to crunch to find it. But I suppose these computationally difficult problems are why computer scientists are needed in genetics.

After I finish with my analysis of our species I will use the methods developed on other species such as mice and chimpanzees.

Trouble switching tracks

Over the summer I have been involved in two projects, one on human evolution and the other on building phylogenetic trees.  I have chosen the human evolution project to continue as my PhD project because that is what I am more interested in but I am having trouble switching gears between the two projects.  I am so used to thinking about building trees but thinking about analysing them for biological significance is escaping me.  I am very interested in the project and I want to pursue it for the next 3 years but switching gears is proving hard.


So those of you out in blog-reading-land: how do you switch mental tracks?

Teaching programming

I have spent the last week or so teaching the new set of PhD students how to program in C and Perl and it has been a lot of fun doing it.  Though I am lucky that I am dealing with post-grads that want to learn. I did get a bit of an ego boost this morning when the lecturer asked to use my report from last year as an example of what a good report is.

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