Journal Club

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 can be used for plant synthetic biology. It includes a library of plant biological parts […]

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 MIT. A couple of years ago, we wrote a GenoCAD grammar to represent the structure of these […]

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 derived from features of previously described plasmids using ad hoc, error-prone and time-consuming curation processes. […]

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 the development of new parameter estimation algorithms and for innovative software implementations. This paper describes […]

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. Of course, there is a long way to go before substantial amounts of illicit substances […]

Rule-based design of synthetic transcription factors

To design and build living systems, synthetic biologists have at their disposal an increasingly large library of naturally derived and synthetic parts. These parts must be combined together in particular orders, orientations, and spacings to achieve desired functionalities. These structural constraints can be viewed as grammatical rules describing how to assemble parts together into larger […]

Adaptive Imaging Cytometry

The use of microfluidics in live cell imaging allows the acquisition of dense time-series from individual cells that can be perturbed through computer-controlled changes of growth medium. Systems and synthetic biologists frequently perform gene expression studies that require changes in growth conditions to characterize the stability of switches, the transfer function of a genetic device, […]

The Synthetic Biology Open Language – SBOL

The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange […]

Article-level metrics and the evolution of scientific impact

This is one of the first and best papers about the use of article-level metrics. It provides a detailed overview of the different options and their possible adoption challenges, Interestingly, the paper also discuss how to use them to help identify what papers to read. The Altmetric section of our web site is an implementation of […]