peccoud lab

Design of expression vectors for Chlamydomonas reinhardtii using domain-specific language

Design of expression vectors for Chlamydomonas reinhardtii using domain-specific language

The design of expression vectors often requires to follow specific rules dictated by the requirements of a project. In this paper, we introduced the GenoCAD grammar editor. We demonstrated how it could be used to capture set of design rules...

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

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...

Sequence verification of synthetic DNA by assembly of sequencing reads

Sequence verification of synthetic DNA by assembly of sequencing reads

Gene synthesis attempts to assemble user-defined DNA sequences with base-level precision. Verifying the sequences of construction intermediates and the final product of a gene synthesis project is a critical part of the workflow, yet one that has received the least...

A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD.

A step-by-step introduction to rule-based design of synthetic genetic constructs using GenoCAD.

GenoCAD is an open source web-based system that provides a streamlined, rule-driven process for designing genetic sequences. GenoCAD provides a graphical interface that allows users to design sequences consistent with formalized design strategies specific to a domain, organization, or project....

Genetic design automation: engineering fantasy or scientific renewal?

Genetic design automation: engineering fantasy or scientific renewal?

The aim of synthetic biology is to make genetic systems more amenable to engineering, which has naturally led to the development of computer-aided design (CAD) tools. Experimentalists still primarily rely on project-specific ad hoc workflows instead of domain-specific tools, which...

Stochastic exit from mitosis in budding yeast: model predictions and experimental observations

Stochastic exit from mitosis in budding yeast: model predictions and experimental observations

Unlike many mutants that are completely viable or inviable, the CLB2-dbΔ clb5Δ mutant of Saccharomyces cerevisiae is inviable in glucose but partially viable on slower growth media such as raffinose. On raffinose, the mutant cells can bud and divide but...

Oscillatory dynamics of cell cycle proteins in single yeast cells analyzed by imaging cytometry

Oscillatory dynamics of cell cycle proteins in single yeast cells analyzed by imaging cytometry

Progression through the cell division cycle is orchestrated by a complex network of interacting genes and proteins. Some of these proteins are known to fluctuate periodically during the cell cycle, but a systematic study of the fluctuations of a broad...

GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs

GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs

One of the foundations of synthetic biology is the project to develop libraries of standardized genetic parts that could be assembled quickly and cheaply into large systems. The limitations of the initial BioBrick standard have prompted the development of multiple...

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