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We are investigating strategies for the engineering of biological systems
next meeting: Friday, February 5, 2010 - 9:00am at Steele Library
Promoter architecture and the evolvability of gene expression. Tirosh Itay (2009) J Biol.
Here's the paper for tomorrow!
What about this paper? If you have better ideas, let me know.
Hey everyone-would it be okay if we shifted our meetings to 9am on Fridays? Let me know.
There will be bagels for breakfast!
Paper about noise...
Molecular Systems Biology 5 Article number: 318 doi:10.1038/msb.2009.75
Published online: 13 October 2009
Citation: Molecular Systems Biology 5:318
Listening to the noise: random fluctuations reveal gene network parameters
Brian Munsky1, Brooke Trinh2 & Mustafa Khammash3
Potential date for starting our meetings again! I picked a random paper...
Phosphorelays
signaling network
integration of multiple signals
EGF, Insulin MAPK cascades
* Leibler
* evolution of cooperation
Ultrasensitivity and molecular titration
Negative feedback and linearization
Stress transient transcriptional responses
Modeling and experiments to understand mechanisms of gene regulation by sRNA in bacteria
Control of Stem Cell Proliferation and Lineages
Synthetic Controller to tune fitness tradeoffs.
Or, following up on our "Endy" topic with "Smolke" :P -F
Drew Endy
* Is Drew the author or the topic?
robust gene networks
complex regulation of genes in yeast due to nucleosome positioning
synthetic promoters
Quantitative models of gene expression in Yeast
* Activity motifs
* principles of timing
* transcriptional control
* yeast
* metabolic networks
Comments:
Promising, but ultimately disappointing. The curve fitting to the mRNA data was not convincing (the shape of the data did not match the fit). Measurements (mRNA and ChIP-chip in particular) should probably have large error bars, bringing fine distinctions in timing or affinity into question. Time resolution was also questionable - the first measurement was taken at 15 minutes, but differences in activation time of 3 minutes vs. 4 minutes were treated as significant. No data was presented to support the claim on correlation between binding affinity motifs and transcriptional activation motifs, and the conclusions were presented in a confusing fashion (why claim that 20/48 data sets showed correlation, rather than breaking things out by individual motifs?).
A better repressilator
Biophysics of gene regulation
