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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. […]

Nature by numbers

Beautiful video showing the mathematical beauty of nature, or the natural beauty of math. Here’s what I managed to figure out: 0:08-0:44 – Fibonacci sequence 0:45-1:40 – The Golden Ratio 2:40 – Delauney triangulations leading to Voronoi diagrams (2:56 and to the end)

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 […]


For old-school geeks who spent the better time of their childhood prefecting their Space Invaders and Donkey Kong skills. A NYC disaster movie meets… well, something. Hat tip to Mickey.

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 […]

Colbert on Gene Patents

Recently, a judge in Federal District Court in Manhattan ruled that Myriad’s patents on BRCA1 and BRCA2 genes were invalid, being a “products of the law nature” and could be patented no more than, say, mount Everest. These two genes are associated with breast and ovarian cancer, and are used in testing for susceptibility to […]

AMOS on Ubuntu

AMOS is a suite of genome assembly and editing software. It includes assemblers, validation, visualization, and scaffolding tools.  I have been having some issues installing AMOS on Ubuntu  9.10.  Specifically, Ubuntu 9.10 has gcc 4.4, which breaks the compilation of the AMOS release version. However, the development version has been fixed to accommodate that. If […]

Peer review: the neverending story

It seems like there is no institution that is more criticized in science than that of the peer-review system — an no one that is less mutable. While published paper evaluation metrics are being  revised (such as the recently introduced PLoS article level metrics, or the Australian National Health and Medical Research Council abandonment of […]

I never metagenomics I didn’t like

“Let another man praise thee, and not thine own mouth; a stranger, and not thine own lips.” — Proverbs 27:2 “What-ever” —  Me In PLoS Computational Biology this week, a trio of researchers provides a review of the challenges that metagenomics might ― and already do ― pose for bioinformaticians. The authors refer to metagenomic […]

M3 / Biosharing Meeting

A promising meeting you may want to attend. Full disclosure: I’m in the program committee for this one. ISMB SIG CALL FOR ABSTRACTS AND POSTERS – Deadline April 30 Metagenomics, Metadata and Meta-analysis / Biosharing A Special Interest Group (SIG) organized by the Genomic Standards Consortium (http://gensc.org) at ISMB 2010 on July 9-10, 2010 in […]

Paweł Szczęsny in TEDx Warsaw

Pawel on Open Science. Full disclosure: I consider sharing an office with this guy for over a year to be one of the best experiences of my postdoc.