Wednesday, October 01, 2014

Adventures in the high dimensional space of genomes

2000+ views in 4 months is not bad considering that this is a genomics paper but uses terms like phase transition, sparsity, L1-penalized regression, Gaussian random matrices, etc. I wish I knew how many views the arXiv and BioMed Central versions of the paper have received. Related posts.
Dear Dr Hsu,

We thought you might be interested to know how many people have read your article:

Applying compressed sensing to genome-wide association studies
Shashaank Vattikuti, James J Lee, Christopher C Chang, Stephen D H Hsu and Carson C Chow
GigaScience, 3:10 (16 Jun 2014)

Total accesses to this article since publication: 2266

This figure includes accesses to the full text, abstract and PDF of the article on the GigaScience website. It does not include accesses from PubMed Central or other archive sites (see The total access statistics for your article are therefore likely to be significantly higher. ...
My guess is still that it will take some time before these methods become widely understood in genomics.
Crossing boundaries: ... In a similar way Turing found a home in Cambridge mathematical culture, yet did not belong entirely to it. The division between 'pure' and 'applied' mathematics was at Cambridge then as now very strong, but Turing ignored it, and he never showed mathematical parochialism. If anything, it was the attitude of a Russell that he acquired, assuming that mastery of so difficult a subject granted the right to invade others.

PS I will be at the ASHG meeting in San Diego later this month along with (I think) all of the other authors of the paper. Vattikuti will be giving a poster session.


Cornelius said...

On the subject of crossing boundaries:

You might enjoy reading Shakhnovich's work:

He's not just doing traditional biophysics, he's finding the biophysical determinants of protein evolution.

efalken said...

I'm mystified by the way genes create many different proteins, and are transcribed via introns, one way vs. the other (ie, 3'-- 5' and vice versa), with genes regulating expression of other genes, and then how do they know where to go, when to start, how to edit and fold. It sure is more complicated that what I was taught about eyes being bb for blue and Bb for brown. Plus, the hapmap was potentially a goldmine, now seems quaint. I feel we only understand some basics, and the language of genes is still pretty much a mystery, so we are basically looking at keywords trying to figure out meaning.

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