Blogging the biotechnology revolution

Systems Biology is changing the way biology is done. Is it a fad or is it effective? This blog tracks current happenings and helps you stay on top of the field. You can find a list of relevant papers at systems biology paper watch Have you heard a talk or read a paper in bioinformatics / systems biology you would like to tell other people about? Email: and get the word out!

Saturday, December 03, 2005

David Gifford, MIT
"Embryonic Stem Cell Regulatory Networks"

This is prety much an explanation of their cell paper earlier this year. However hey shows how they use the approach of joint binding deconvolution (JBD) to discern binding to 50bp Resolution outperforms other methods. Using this they can get a positional prior for motif searching and use that as a seed for motif searching. find that it works remakably well.
Binding of PolII in stem cells. They find that those transcripts down regulated and bound by PolII are more likely to be bound by miRNAs. They use Agilent arrays and havent yet published their JBD algorithm.
Studies three transcription factors : NANOG, OCT4, SOX2. these are supposed master regulators of stem cells (control differentiation)
moving toward studying groups of similiarly differentiated sets of cells using genomic technologies.
Mentions that joint learning of motif and binding data would be a good idea
also that a binding algorithms that account for steric hinderance might be of use since the DNA is sonicated and looses structure.


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