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It’s a small (RNA) world after all

The central dogma of molecular biology edit: the sequence hypothesis (thanks for setting me straight, Kamel!) as formulated 57 years ago was simple: DNA is transcribed to mRNA,and  mRNA is translated to proteins. Proteins are the business end of this process. mRNA is only the messenger: its sole function is to deliver information from the […]


Celebromics? HeavyMetalomics? Advertomics? Anniversomics!

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 […]

Bioinformatics Open Source Conference 2010 (and a poll)

The 11th Annual Bioinformatics Open Source Conference (BOSC) 2010 is coming up in Boston, July 9-10 2010. The BOSC meetings are a great get-together of a community of programmers who are like-minded in their advocacy of open source code for science, and specifically for bioinformatics. The whole thing is run by volunteers who take a […]

Protein function, promiscuity, moonlighting and philosophy

I recently received an email from a graduate student in Philosophy regarding protein function. Not sure if that person wants his name advertised, so I will keep it to myself. “I am a fan of your blog, and interested in the philosophy of biology. One particularly interesting question is what makes something have a function; […]

Computational Bridge to Experiments

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 […]

Closing gaps

Geek alert: this post for coders. So you sequenced your genome, reached an optimally small number of contigs, they look sane, and now you would like to see what you need for the finishing stage. Namely, how many gaps you have and what are their sizes. UPDATE: “might just be worth clarifying this is for […]

A cure for Ebola?

There are few infectious diseases as violent and as lethal as the Ebola Haemorragic Fever.  This terrible disease was first described in 1976 at a mission hospital at the Ebola river in Zaire (now the Democratic Republic of Congo).  The disease is 80% fatal, the victims die painfully from a literal meltdown of their organs. […]

A non-post about Craig Venter’s new bug

In case you have been vacationing in a parallel universe in the past two days, you should have heard about the new synthetic bacterium created at the J Craig Venter Institute. In a nutshell, the scientific team synthesized an artificial chromosome of the bacterium Mycoplasma mycoides and transferred it to another bacterium, Mycoplasma capricolum. The […]

There is a little bit of Neanderthal in many of us

Big party at Science journal today, with the publication of a comprehensive draft Neanderthal genome. (Free access, nice going Science). Actually, it is a partially assembled draft of 60% of the total genome, but 60% of the genome from a human that was last seen on Earth 28,000 years ago is quite an achievement. The […]

Comparative Functional Genomics: Penguin vs. Bacterium

No, not the flesh-blood-and-feathers penguin, but rather Tux, the beloved mascot of the Linux operating system. Compared with Escherichia coli, the model organism of choice for microbiologists. We refer to DNA as “the book of life”; some geeks refer to it as the “operating system of life”. Just like in a computer’s operating system, DNA […]

Combrex: Computational Bridge to Experiments

Combrex is an exciting new project at Boston University to bridge computational and experimental techniques to functionally annotate proteins. They are hiring, see below: JOB POST We are seeking to hire a creative computational scientist for a transformative project: COMBREX: A Computational Bridge to Experiments. The work will involve building a novel resource that combines […]

Well, color me surprised

Nature is colorful. And the family of pigments that is mostly responsible for these colors are carotenoids. Carotenoids  make the apples and tomatoes red, the lemons and grapefruit yellow, the pumpkins oranges and, yes carrots, (from which their name is derived), orange. Carotenoids also make flamingos and salmon pink, and color the puffin’s bill orange. […]

New poll: would you make your genome public?

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 […]

Obesity: the role of the immune system

Obesity is one symptom of several, which together constitute what is now termed metabolic syndrome. Morbid obesity is also associated with a host of other symptoms including high blood sugar, high blood lipids, insulin resistance  and liver disorders. The root causes of which are traced back to excessive food consumption, reduced physical activity and in […]