Identify, Infer, Inflict
Russ Altman looked at the field of translational bioinformatics in the past year and chose three papers worth highlighting in a post at his Building Confidence blog. The three items include Homer's PLoS Genetics paper demonstrating that you can discern an individual's DNA from a pooled sample if you already have that individual's genotype; the Nyholt paper from the European Journal of Human Genetics that resolved Jim Watson's APOE status by using linkage disequilibrium correlations; and the Christley paper in Bioinformatics showing that a genome can be compressed to a file of just 4 MB. "So the full circle (?) is achieved: we identify genomes, we infer things about them, and then we email them to our friends," Altman writes.
Open Access No More
The Journal of Visualized Experiments, a peer-reviewed journal that publishes research in video format, got bloggers' attention when it moved this spring from its original open access model to a subscription model. Cold Spring Harbor's David Crotty noted it on his Bench Marks blog, saying that perhaps JoVE had been too ambitious by "trying to break ground with a new type of science publishing [and also] trying to do so with an unproven business model." The journal's Moshe Pritsker responded to the community at Noah Gray's Nothing's Shocking blog, writing, "As much as I would like to continue to provide our content for free, JoVE has to survive."
Daniel MacArthur blogs at Genetic Future about 23andMe's newest foray: the launch of a service aimed at pregnant women, for which the company recruited a group of "mommy bloggers" to talk about it. 23andMe co-founders Linda Avey and Anne Wojcicki write about it on the company's blog, the Spittoon: "We believe mothers like us, and soon-to-be-moms, would prefer to carry out their pregnancies armed with as much knowledge as possible, for the sake of themselves and their families." MacArthur calls it "sheer marketing genius." He adds, "Come for the enthralling conversations about cloth vs disposable … and hey, while you're here, why don't you get yourself a genome scan?"
Everything Is New Again
At her Discovering Biology in a Digital World blog, Sandra Porter blogs about how significant the past two years have been in changing how people look at the genome — in particular, how the genome is assembled and how that information is translated to become proteins. While major changes such as translocation were once thought to be a surefire mark of genetic disease, it's now understood that that's not the case. "Like inversions, deletions, and duplications, our new ability to scrutinize the genome is making it clear that individual genomes vary more than we ever knew," she writes. Separately, Porter notes that the sheer number of RNAs being found with unknown function has turned the conventional wisdom on translation upside down as well.