René Goscinny would probably have done a better job of naming the new trend of personal genomics (genomix?) companies to sequence celebrities genomes. Heck, we might have even done Obelix’s and Asterix’s genomes to find out if Obelix can drink the magic potion without Getafix’s (Panoramix’s) admonishments that it might do him harm, or to [...]
A bit of background information: this is a meeting I am really happy to be part of, and even more so honored to be a co-organizer. One of my main scientific interests is the prediction of the function of genes and proteins of unknown function. Some background information: we have sequenced more than 1000 genomes [...]
Would you have your genome sequenced for free? Conditions: you must license it for all use; a liberal CC-no attribution-like license which allows for commercial use as well. Also, your genome will be made public with many personal data such as age, height, sex, weight, ethnicity, personal status (we want to find the “money making [...]
Seriously, this is what I first thought when I saw the cover of this week’s Nature, and the associated drawings in the press. The dude’s haircut seems like it was even bad in the ’80s… 2080 BCE that is, which is when his body is dated. Approximately. A large group of researchers were involved in [...]
After hearing Jonathan Eisen and Nikos Kyripdes talk about GEBA in various meetings, it is great to see the paper finally come out, and under a CC license too. Good move for everyone. GEBA is the Genomic Encyclopedia of Bacteria and Archaea. The idea is simple: we have >1000 prokaryotic genomes in GenBank as of [...]
Glimmer is a program that predicts ORFs in bacterial and archeal genomes. The input is the assembled genome FASTA file, the output are several files of the predictions in different stages. The terminal output file is the .predict file. which looks something like this: >NODE_1_length_38001_cov_935.551880 orf00001 481 362 -2 1.45 orf00002 451 567 +1 0.59 [...]
Mass Extinctions and Genomics The geological signs for mass extinctions are very distinct: the photo shows the boundary of the Cretaceous-Tertiary KT extinction that happened ~65 million years ago (Mya), and killed some 70% of the species on Earth, most famously the dinosaurs. This was the last mass extinction, and its effects on Earth’s life [...]
Apparently sequencing two white males of European extraction does not make for a very good sample of mankind, and that if we really want to get a good view of what we are really like, we need to sequence a couple more. Maybe even, you know, a woman, or someone from India or China or [...]
Most of the Earth’s surface is colder than the inside of your refrigerator. Deep sea temperatures are almost universally 2-4C. That’s already 73% of the Earth’s surface. Then add to that the polar regions, mountain ranges and permafrost and you have about 85% of the Earth’s surface constantly at refrigerator or freezer temperatures. While there [...]
Maybe I am slow on the uptake, but I never quite liked the term “post genomic”, and I used it very sparingly. (Yes, I do have that term in one of my better cited papers, smack in the first sentence of the abstract, but I never liked that). Perhaps because of all the associated abuse [...]
(Continued from “On Microbial Sequencing“). Well, it’s really been a great meeting. The biology of pathogens, parasites and symbionts is amazing. Historically, the microbes that chiefly interested us were one of those three: those that causes disease in humans, animals (focus on domesticated animals), plants (again, mostly domesticated). However, as we are (alas, too slowly) [...]
A friend of mine who is also a scientist once told me: “the only time I read, is when I write”. What he meant was, that the only time he reads scientific literature, is when he writes his own papers, and needs to do the proper research to place his research in the context of [...]
