
Reprogramming cells by computer - jonbaer
http://www.kurzweilai.net/cells-reprogrammed-on-the-computer
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ghkbrew
So, basically what the paper linked from this article describes is a method of
taking a set of interacting regulator genes and determining the minimum set of
genes which have to be perturbed (activated or repressed) to move the overall
expression pattern from one stable state to another.

Their method involved grouping the genes into small sub-sets which have a
small number of stable states. Their example is two genes which repress each
other acting as a toggle switch. They then connect those "switches" which
influence each other, forming a larger graph. The final step is to find the
minimal set of genes (one from each strongly connected sub-graph of the DAG
they just created) which will influence the entire network.

So once you know the major regulatory genes involved in different cell types
this method allows you to pick a small groups of genes whose expression has to
be modified to convert between the two.

Of course this entirely ignores the problem of coming with these regulatory
networks in the first place. Many genes and networks of genes have already
been characterized in scientific literature, but I think it's safe to say that
there are many more that haven't. The issue being that there is no good way
for determining gene interaction without lengthy in vivo analysis of each
individual gene.

There are other difficulties as well. As the authors mention, some effects of
differentiation aren't reversible with this technique, e.g. epigenetic
modification.

This method, seems like it will gradually become more useful as our base of
knowledge increases. Just don't expect it to do anything magical at the
moment. And contrary to what TFT implies it is far from computer-controlled
cell reprogramming.

