Bioinformatics

Bacteria can cause other epidemics, why not obesity? Is there a relationship between our body weight and our bacterial inhabitants? Two reports in Nature (1, 2) suggest that bacterial populations differ between people who are obese and people who not, and that the bacterial inhabitants of their guts, may be partly to blame. In one study, the authors studied the bacterial populations of their volunteers' intestines by compiling a data set of 18,348 DNA sequences for bacterial 16S ribosomal RNA by sampling feces. Wow! That's a lot of ... well, I won't say it, but you know what ... Read more
Five Bulgarian nurses and a Palestinian doctor (dubbed the Tripoli six) may be executed soon by the Libyan government for the crime of deliberately infecting over 400 children with HIV. If they did infect the children, this would be a horrendous crime. If they did not infect the children, it's the Libyan government that will be killing innocent people. The clock is ticking. Some of you might be wondering (I know I was): How exactly is molecular sequence data being used to solve the crime? Why are scientists and science bloggers claiming that the ... Read more
In which I present a quick guide for the omically challenged and a defense of 'arth and "ome." Other SciBloggers have shared their thoughts on the use of ome here and here. Sometimes I get frustrated too, with the way language is abused and tweaked by those around me. So many word pairs that once made phrases—;log in, data set, file name, set up, and pick up—;have been condensed into single words, that I've had to ... Read more
The EMBL graduate students have organized an ingenious conference titled: Life Sciences - Shaping the Future. Learn about Omics and Systems Biology from speakers like Leroy Hood, Stuart Kim, and Ronald Krause (and more). Explore options for career development, and learn how you can join the Web 2.0 science revolution in the session on scientific communication. The conference will take place Dec. 4th-8th, 2006. Don't worry if you don't have a plane ticket or a place to stay, you're virtually there. How? It's all on-line. Some of you might be ... Read more
In last week's episode, your assignment was to think of an interesting plant trait and find a description about a gene, related to that trait, by searching PubMed. Since coming up with an interesting trait might be a challenge for some people, let's think about how to approach this step. Picking your trait. ... Read more
Why is an eye, an eye and a nose, a nose? Why do different cells create different kinds of tissues when all the cells in a single organism start out with the same set of instructions (aka DNA)? Head, Shoulders, Knees, and Toes is a learning activity that helps students discover, for themselves, that certain genes are expressed in some tissues but not in others. My goal here, as part of our NSF-funded project, is to show how students can learn biology by doing science with bioinformatics tools. If ... Read more
Many of you might take this for granted, and I know it seems amazing today, but I when first started teaching, our access to scientific literature was pretty limited. I could go to the UW and use Grateful Med to search Medline, but we didn't have anything like it at my college and web browsers, like Mosaic, had yet to be invented. So, when I first started giving workshops for teachers on biotechnology and the world of the web, many were quite surprised to find out about the PubMed database. Since PubMed is (to me) one of the best resources to ever come along, I think we ... Read more
Welcome to the fourth edition of Bio::Blogs! This is the carnival where we explore topics at the intersection of computing, biology, and sometimes a bit human behavior. In this edition, we consider issues with annotation, agonize over standards, explore the question of whether or not it's possible to tame those wild and wooly computational biologists and make them laugh their way into writing programs that other people can use, give the Perl fans something to do while waiting for that program to run, and much, much, more. Today, we'll begin on the biology side of spectrum and ... Read more
i-466b1890141827e0782cfe1538fdb374-dino.jpgWe went on an excursion last weekend to see the Dead Sea Scrolls at the Pacific Science Center. None of us could resist going downtown to look at written texts over 2000 years old. Uncovered in 1946, by a Bedouin shepherd, the scrolls have had an interesting history over the past 50 years, most of it out of the public eye. Only recently, have a large number of scholars and members of the public ... Read more

Razib inspired me to share some of the story behind why white people are considered derivatives.

No red herrings, here! Lamason et. al. found a single gene that controls human skin color while studying pigmentation in zebra fish (1). These zebra fish had an unusual golden color that turned out to be an important clue. Lamason and collaborators found that the golden zebra fish lost their normal color because of a mutation in the slc24a5 gene. When the zebra fish have the mutant form, they produce fewer melanosomes.

A short language lesson Fewer ... Read more

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