

Computational feat speeds finding of genes to milliseconds instead of years - dailo10
http://med.stanford.edu/ism/2010/march/boolean.html

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randomwalker
Here is the paper: <http://www.pnas.org/content/107/13/5732.long>

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Tycho
So in terms of curing cancer... where does this get us? (i'm not being
sarcastic. it sounds very promising but I don't know enough on the topic to
judge how significant it is)

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thisisnotmyname
First of all, don't ever trust a popular science writeup from the school of
the corresponding author. It is almost certainly meaningless hype.

Secondly, PNAS is a good journal, but not a great one. He was almost certainly
rejected from the top tier. (Nature, Science)

As someone who works in this field, finding genes that are similar in some way
to two disease related genes is not at all novel. This is the goal of
literally hundreds of computational methods. It sounds like what he did was to
build a decision tree from a set of training data - hardly an earth-shattering
application.

Edit: Wow, after fully reading the paper I am stunned how commonplace this
analysis is. This exact approach has been taken for analyzing microarray data
for the last decade. This does not warrant in any way the breathless writeup
it receives in the original post.

Under what hypothesis would one expect nature to follow boolean rules? This
approach ignores any subtle relationships or multifactorial causes of gene
expression changes. The more I read the more I am convinced that this is utter
garbage.

What really makes me mad about this is that increasingly the way to get ahead
in science is to overstate your results and then have friends of the
corresponding author "review" the manuscript. If you'll notice, this was
submitted by Irving L Weissman who, according to his website is "Director,
Institute of Stem Cell Biology and Regenerative Medicine, Stanford University
School of Medicine". It is very odd that it wasn't submitted by either the
corresponding, nor the lead author. It is very clear that this article did not
receive the scientific scrutiny that it should have.

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aposteriori
Regarding who submitted it, PNAS works differently from other journals.
Weissman is a member of the National Academy of Sciences, and as such he gets
to contribute a paper X times a year. It still gets peer reviewed. The
question of how well things are reviewed applies to other journals as well.

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rflrob
There's also the process of "communicating" papers. In those, a NAS member can
essentially vouch for other authors twice a year, and provide outside
reviewers of their choice. This track is ending as an option this July,
however.

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Estragon
With this kind of thing, the devil is always in the details. He's looking for
genes whose expression levels correlate with those of genes known to be
involved in the process of interest. This is not a new idea. The trouble is
that spurious correlations can arise in all kinds of surprising ways, and
swamp the interesting ones.

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loboman
What's the computational technique used for this?

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itjitj
Call the oracle function.

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seshagiric
I started off thinking it was another gpgpu application but the theory of
boolean implications is something new to learn. thanks for the article.

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rmorrison
Before clicking on this, I jokingly thought to myself "let me guess, this is
yet another NoSQL is better than ___ article"

