peccoud lab

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 […]

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. […]

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 […]

Measurement and modeling of transcriptional noise in the cell cycle regulatory network

Fifty years of genetic and molecular experiments have revealed a wealth of molecular interactions involved in the control of cell division. In light of the complexity of this control system, mathematical modeling has proved useful in analyzing biochemical hypotheses that can be tested experimentally. Stochastic modeling has been especially useful in understanding the intrinsic variability […]