genomics

Kevin White (aka, Mr. Drosophila microarray data) has a paper coming out in tomorrow's issue of Nature. The paper (which is not available on the Nature website yet) compares the expression of over 1,000 genes from humans, chimpanzees, orangutans and rhesus monkeys. From a news write up of the findings: When they also looked for human genes with significantly higher or lower expression levels, they found 14 genes with increased expression and five with decreased expression. While only ten percent of the genes in the total array were transcription factors, 42 percent of those with increased…

This paper is rather timely considering I just finished reviewing methods for detecting natural selection. Jonathan Pritchard's group has scanned SNP data from three populations (Europeans, East Asians, and Nigerians) for signatures of positive natural selection. The authors used measures of polymorphism to detect natural selection. In their approach, they polarized polymorphic SNPs as ancestral and derived (kind of like a Fay and Wu test) using the other populations as outgroups. In this type of test, high frequency derived SNPs are a hallmark of recent positive selection; the authors…

I have a little bit of an infatuation with copy number polymorphism (CNP), which describes the fact that individuals within a population can differ from each other in gene content. Some genes, such as olfactory receptors (ORs), have many different related variants in any animal genome. New copies spring up via duplication events (a type of mutation), so one could imagine that individuals from a single population differ in the number of copies of these genes. In fact, this is the case with any gene or gene family (a group of related genes) in the genome -- there may be duplications…

The Scientist has a good review of genome sequencing (coming from a more biomedical perspective). I tend to present genomics from an evolutionary angle (rather than functional). This is a good read if you're not too familiar with the field, and all you know about genomics is what I've told you.

There are quite a few articles sitting around on my desktop waiting for me to write about them. It's gotten to the point where I just need to unload them on the blogosphere. Click through below the fold for some cool stuff from the scientific literature. More on Neutrality from Laurence Hurst and Colleagues -- I just wrote about the nearly neutral theory, and here is an analysis of selection on silent sites in the human genome. Is this a coincidence or was this article subconsciously on my mind? From the abstract: "At least in species with large populations, even synonymous mutations in…

This blog doesn't seem to want to write itself. I've got a few posts in the pipeline (including the next on detecting natural selection), but I can't seem to finish them. I'm in this writing funk where I start to lay some words onto paper (well, text editor, actually), and then I can't organize all my thoughts or just can't finish writing the post (do I have an undiagnosed case of ADD?). Luckily for me, I have Chad at Uncertain Principles to inspire me, as he's already done once before. This time he's asking people about their least favorite misconception in their field. One commentor…