Monday, February 16, 2015

GenomeWeb profiles Jonathan Karr

Note the allusion to industrial applications involving Cyanobacteria:

Many modelers had been focusing on metabolism, Karr said, and this paper showed that other physiological processes could also be included, "and that once you put it all together, you can generate much more quantitative predictions that you can if you just focus on one physiological process at a time," he said.
The paper also, he said, laid out a new scheme for developing a dynamic model that didn't rely solely on flux balance analysis, but could also include other mathematical representations like differential equations.
"So now, we're coming back and trying to use that same framework, but apply it to a much larger system, and much more data," Karr said.
Looking ahead
In the next few years, Karr said that more people would likely adopt methods like theirs to model more bacteria, especially ones with industrial applications like Escherichia coli or cyanobacteria.
Then in the years after that he said that's when people would start to use models to engineer bacteria — as long as the cost of genome synthesis comes down.


The paper in Cell is

A Whole-Cell Computational Model Predicts Phenotype from Genotype


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