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Metagenomics Metadata and Metaanalysis

I am a co-organizer of this… see for yourself. Cutting edge metagenomics research, discussion of standards applications to genomics and metagenomics, all in beautiful Stockholm this summer. If you are coming to ISMB/ECCB 2009, consider coming to the M3 SIG. Link to announcement 1-page poster, because you really want to tack this to your departmental […]

Naturally Obsessed

A new documentary film follows life in a molecular biology lab in Columbia University over the course of three years. It looks very promising: the title is certainly something many of us identify with.

Now this looks a lot better!

In any data-rich science, data visualization is of prime importance.  Finding ways to visually depict data is challenging, as we have opposing demands: we would like to see the data in the whole, but also be able to zoom in and analyze the details; we would like to know how the many details add up […]

Music: Vic Ruggiero and Lisa Mueller

These two have great chemistry, and the video captures the raw and gritty quality of a small club appearance.

Enzyme Promiscuity

Gradualism is a cornerstone principle in evolution.  Things happen in small increments;  all the time that changes happen, overall organism fitness cannot be compromised.  So how then do full-featured complex functions appear? One way is by functional re-purposing of an existing organ: …an organ may become rudimentary for its proper purpose, and be used for […]

Are you stupid enough to work here?

Almost every time you read an interview with a scientist, the subject turns invariably to their sense of accomplishment and awe when they finally discover something new. Somehow, I never could quite identify with this sentiment entirely. Research is excruciatingly hard, laborious, frustrating and accomplishing anything always takes longer than I thought. I always keep […]

Music: Reg Kehoe and his Marimba Queens

Note the bass player. Hang around past 1:10 and you are in for a treat.

My own post genomic moment

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 […]

Peace on Earth

Here is a little trick I performed as a first year grad student a while ago and which I would like to share. My PhD adviser, Hanah Margalit was supposed to give a talk at a  joint Israeli-Palestinian meeting. (Hopefully, such days will be back soon and permanently!) The audience was rather broad, and included […]

I’ve been slashdotted!

Slashdot article: Every man is an island (of Bacteria)

Genetic Algorithms

XKCD appeals to my geeky humor side. Also, as a staunch Pythoneer, I cherish the occasional Python reference. To complete the trifecta, I just saw T2 for the umptieth time two days ago.

Every Man an Island, Pt. 2

(Continued from  part 1) Why we are islands In the previous post we have seen how  our bacterial population affects  our weight  and that by changing our dietary habits we can change the species composition in our guts. Also, we saw how a metagenomic analysis can lead to verifiable hypotheses: using a metagenomic analysis, Gordon’s […]

Every Man an Island, Pt. 1

No man is an island, entire of itself — John Donne, Meditation XVII Scanning electron microscope images of B. thetaiotaomicron, a prominent human gut bacterium, and the intestine. From: Human Gut Hosts a Dynamically Evolving Microbial Ecosystem Gross L PLoS Biology Vol. 5, No. 7, e199 doi:10.1371/journal.pbio.0050199 Only one out of ten cells in our […]

Blog for Darwin

I just went to Shirley Wu’s blog and found this. Apparently February 12-15, 2009 there will be a Blog for Darwin blogswarm, in honor of his 200th birthday and 150th anniversary of the publication of On the Origin of Species (First time I hear this term, blogswarm; not sure if I like it). I wrote […]


They are very, VERY large (for intracellular particles, that is), there are hundreds of them most animal’s cells, and we don’t know what they are doing. Meet the vaults. Vaults are mysterious large ribonucleoprotein (protein and RNA) structures in the cell. Although three times larger than ribosomes, and present in many copies in the cell, […]