Journal Club

Experimental design to optimize multigene expression systems

Experimental design to optimize multigene expression systems

This is a very dense paper that describes an principled approach to design experiments minimizing the number of constructs to test to optimize the expression of expression systems that rely on the co-expression of multiple genes. My understanding is that...

Testing of a New Integrated Model of the Yeast START Transition

Testing of a New Integrated Model of the Yeast START Transition

We propose a new model of the yeast start transition. We tested the accuracy of the model by simulating various mutants not described in the literature. The cell cycle is composed of bistable molecular switches that govern the transitions between...

Plant Synthetic Biology

Plant Synthetic Biology

Plant synthetic biology requires software tools to assist on the design of complex multi-genic expression plasmids. Here a vector design strategy to express genes in plants is formalized and implemented as a grammar in GenoCAD, a Computer-Aided Design software that...

CRISPR Cas9 Synthetic Eukaryotic Transcription Factors

CRISPR Cas9 Synthetic Eukaryotic Transcription Factors

The CRISPR Cas9 technology is used to design synthetic transcription factors in eukaryotes. The approach is used to design activators and repressors. Data shows that this approach can work in yeast and mammalian cells. This paper comes from Tim Lu’s group at...

Database of standard biological parts derived from plasmid features

Database of standard biological parts derived from plasmid features

Synthetic biologists rely on databases of standard biological parts to design genetic devices and systems. The Registry of Standard Biological Parts and other community resources provide the sequences and descriptions of thousands of genetic parts. The content of these database  is often...

Parameter estimation at the whole cell level

Parameter estimation at the whole cell level

This paper raises a number of interesting issues relative to the estimation of parameters of whole-cell models. The challenge here is obviously the underdetermination of the problem when the number of parameters is very large. This challenge calls both for...

Opiate synthesis in yeast

Opiate synthesis in yeast

This article got a lot of attention because of its potential biosecurity implications. Even though the paper only describes the synthesis of an intermediate, media quickly extrapolated to envision this as an avenue to home-brewed morphine and other addictive drugs....

Decoupling assembly and submission standards

Decoupling assembly and submission standards

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