Genomics

Mike the Mad Biologist

Category archives for Genomics

I don’t see the need to redescribe the recent paper about the discovery of bacteria that can might replace, in extremis, phosphorus with arsenic, which was overhyped by NASA, was poorly covered by most journalists, and which has compromising methodological problems (for good coverage, read here, here, and here; and snark). But what the paper…

I guess. Over at the Motley Fool, Brian Orelli asks, “Which Is a Better Buy: Complete Genomics or Pacific Biosciences?” While I agree that PacBio is probably the better bet (and bet is the operative word), I don’t think the reasoning is right. Orelli: If you’re interested in trying to catch the boom and get…

Gabe Rudy, blogging at our 2 snps, has a really good introduction to sequencing technology and its history. It’s worth the read, but I don’t entirely agree with the reason given for why ABI SOLiD lost out to Illumina: Coming to market at the same time, but seeming to have just missed the wave, was…

Last week, the U.S. Department of Justice filed an amicus brief which argued that naturally-occurring DNA sequences can’t be patented: Reversing a longstanding policy, the federal government said on Friday that human and other genes should not be eligible for patents because they are part of nature…. “We acknowledge that this conclusion is contrary to…

A problem in genome-wide association studies (“GWAS”) is the”missing heritability” issue–identified genetic variation can only account for a small fraction of the estimated genetic contribution to variation in that trait. Razib has a good roundup of several explanations (and I added some speculation about nearly-neutral mutations). GWAS also have problems accurately characterizing the trait. For…

And by hot, I mean employable. I’ll get to that in a bit, but I first want to relate some history. Back when I was a wee lil’ Mad Biologist, and molecular population genetics was in its infancy, there was a brief period where people had to be convinced that this stuff was useful (it…

The exciting thing about the recent technological advances in genomics is that we have a massive amount of data. The terrifying thing about the recent technological advances in genomics is that we have a massive amount of data. A while ago, I brought this up in the context of bacterial genomics: Most of the time,…

Why Are We Duplicating Genome Efforts?

SEQUENCE GENOMES!!! Proflikesubstance has a very good post about PR announcements in science, which stems from the duplicated sequencing of the cacao and Tasmanian Devil genomes. What struck me is this bit: What also seems ridiculous to me is that there are TWO groups sequencing either of these genomes. I can understand the race for…

A couple of weeks ago I attended the Human Microbiome Research Conference. At that meeting, one talk by Bruce Birren (and covered by Jonathan Eisen) mentioned something that was completely overlooked by the attendees. Now, I don’t blame them, since what Birren mentioned was about bacterial genomics, not the human microbiome. But here’s what I…

“I Was Wrong”: Some Refreshing Candor

One of science’s saving graces is that a fair number of scientists will publicly admit that they are wrong (and then there’s Marc Hauser*…). Last week, at the Human Microbiome Project meeting, Jonathan Eisen gave a talk about the GEBA project which is an effort to sequence the genomes of a diverse group of bacteria…