Thursday, November 15, 2012

New paper: 3rd in the “in silico series”

Hello People!

I am excited to announce the paper “Escherichia coli adapts to tetracycline resistance plasmid (pBR322) by mutating endogenous potassium transport: in silico hypothesis testing” to be published in FEMS Microbiology Ecology.

This is the third paper in my “in silico series”. The other two papers in the series are:

Carrying photosynthesis genes increases ecological fitness of cyanophage in silico


Resonating circadian clocks enhance fitness in cyanobacteria in silico

Take a quick look at the model schematic in each paper (below). I think they nicely capture the spirit of the series. Specifically, all show cells with intracellular mechanisms (resolved down to the level of individual genes) [systems biology] and populations made up of individual cells [systems ecology]. This approach [systems bioecology] explicitly investigates the role of genes in the fitness of microbes.

Prochlorococcus model:

Synechococcus model: 

E. coli model: 

For this paper, you may also like ...

… the source code:

… the movie:

… the poster:

The fourth paper planned for the series is the yeast bet hedging one I am presently developing.

Do you have any interesting problems that can be investigated with this approach? I am always interested in talking and collaborating. Drop me a line!

Best regards,