The somewhat underpopulated website of Luke Jostins
It's Jostins with a soft J, think Yos-tins. I'm a grad student at Kings College, Cambridge and the Sanger Institute.
I split my time between research, teaching, blogging and a few other things
I am aware of the hilarious old-school appearance of this website. I wrote it a long time ago, and now feel sort of attached to it.
This comes first, not because it is the most important, but because it is the stuff you are most likely to be interested in
I write the blog Genetic Inference, a largely popular-level blog about genetics. There is a good chance that that blog is what you are looking for when you typed in the URL that got you here; for future reference, the URL is www.genetic-inference.co.uk/blog.
I also edit and write for Genomes Unzipped, and for the Medical Genomics team blog at the Sanger Institute.
I also, obviously, run this website, where you can find some of my writings and code (most of which is looking pretty old now). You will also find the game Biology or Physics, which I wrote with Olaf Davis of The Cosmic Web. The game involves indentifying whether images come from Biological or Physical Science; over 60,000 people have played it, it featured on the front page of Digg, and also on German Internet TV. In addition, you will find WineInference, a wiki dedicated to discovering drinkable wine.
I also tweet with relatively frequency. Personal stuff is @Lowk, and science-related stuff is @lukejostins.
My research interests are focused towards the usage of new sequencing and genotyping technologies in understanding human disease, particularly the contribution of rare variants to complex disease. Powerful technology available both now (high density genotype chips, second-generation sequencing) and in the mid-future (third generation sequencing) allows us to look at classes of variation far outside the standard common SNPs that we have looked at previously.
I look at using large-scale datasets such as produced by the 1000 Genomes Project and HapMap3 to perform imputation on existing reference data; studying how these new datasets can improve our inferences on disease genetics, and how to best design our imputation algorithms to use this new data. I am also interested in new tests for rare variant association to allow us to overcome the power barrier inherent in rare-variant association.
I also have interests more generally in the selective and population genetic impacts on the genetic variants that lead to disease in human populations, and discovering what forces shape the allele frequency of common complex disease.
I mostly focus on autoimmune diseases, such as Crohn's Disease, Ulcerative Colitis and Type I Diabetes.
My research involves trying to find out how differences in each person's DNA influences how likely they are to get different diseases, such as inflammatory bowel disease and diabetes. I want to track down which regions of DNA are associated with disease, so that we can explore what is in this region and find out what things are causing the disease (for more information on what this can tell us, see this essay that I wrote on the subject)
In recent years, a number of studies, called Genome-Wide Association Studies (GWAS), have looked at exactly this, and a number of very important genes and DNA regions have been discovered, leading to new ways of understanding and treating these diseases. For instance, GWAS studies have shown that the Autophagy pathway, a mechanism that our body uses to break down parts of our cells that are damaged or not needed, is disrupted in a type of Inflammatory Bowel Disease called Crohn's disease.
However, while we have found a lot of disease genes, we know that there are a lot more out there. We suspect that this has something to do with the way we have been looking: because the technologies we use have only let us look at variations in the DNA that are relatively common (more than 5% of people have them), we haven't been able to look at how rare variations influence disease. However, new technologies, such as machines that let us sequence a lot of DNA, or silincon chips that let us look at a large number of variants in a large number of people, are allowing us to look at the rare variants.
I am interested in using these technologies to find regions of the genome that contain rare variants that influence disease; this requires new ways of thinking about how we look for these variants, since the old ways weren't created with rare variants in mind. One thing I am working on is called Imputation: this involves using new technologies to look at which variants tend to occur together in one sample of people, and using this information to work out what variants are present in other people from the some population: this allows us to go back and get new information on rare variants from old information we collected before, potentially giving us new-techology style information from old-technology data. I also want to try and combine this information in new ways, to get better at tracking down which regions of the genome contribute to disease. I hope that, taken together, these methods will let me find new insight into autoimmune diseases.
I am also interested in generally what sort of forces act on the human genome; these include random changes in the DNA, people migrating around, and natural selection. I want to know how the frequency and positioning of disease-influencing variants is influenced by these forces, and whether this can tell us something about the way disease has occured in populations, both recently and in the distant past.
I supervise Mathematical Biology, the bio-maths course in first year Natural Sciences at Cambridge. I also teach occasional courses in mathematics for the MPhil in Computational Biology at the Cambridge Computational Biology Institute in the Centre for Mathematical Sciences.
I maintain the glfTools package, a subpackage of SAMTools, for manipulating, calling and analyzing Genotype Likelihood Files.
I am a strong supporter of Open Source software, and release all code I write under open source licencses. I am also a huge supporter of Open Access journals, such as the Public Library of Science.
I also a strong believer in equality; I am a member of the gender equality charity The Fawcett Society, and generally believe that the technologies and knowledge that come from science should be used to help create a fairer society, in terms of gender, race and class equality.
If you care (and you must, given that you have got this far), I spend my free playing music, storytelling and roleplaying, listening to podcasts, and drinking (and photographing) coffee and reading the Guardian in the King's College Coffee Shop (drop in if you are ever in the area and I'll get you a coffee - you've earned it)
Things that are here:
Genetic Inference, my blog
Biology or Physics A game of image recognition on a very coarse scale
WineInference A wiki for wines
Writing Poems, short stories and other things I've written
Bits of Code
Things for QB students
Information on my MPhil Thesis
Information I always forget (for my use)
Save the cheerleader, save the world.
Luke Jostins lj237 @ etcetc