peccoud lab

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 attention. Sequence validation is equally important for other kinds of curated clone collections. Ensuring that […]

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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. Design strategies include limited sets of user-defined parts and rules indicating how these parts are […]

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 suggests that CAD tools are lagging behind the front line of the field. Here, we […]

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 sample of cell-cycle proteins has not been made until now. Using time-lapse fluorescence microscopy, we […]

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 new standards proposing different avenues to overcome these shortcomings. The lack of compatibility between standards, […]

Writing DNA with GenoCAD

This paper is a little dated now but I still like to look at these screenshots. They are good memories of a time when GenoCAD was blazing a new trail in synthetic biology. Several years later, we are still living the vision. It just takes longer than expected to make it a reality.

What is Gene Synthesis?

This article explains what is gene synthesis, a combination of chemical and biological processes to produce synthetic DNA that does not exist in nature.  This technology transforming genetic engineering from a laborious art to an information-driven discipline. Although substantial advances have been made in the development of gene synthesis, the methods employed vary widely based on […]

Analyzing the Registry of Standard Biological Parts

The design and construction of novel biological systems by combining standard biological parts represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to streamline the fabrication of complex constructs. The Registry of Standard Biological Parts (Registry) is the most advanced implementation of this idea.By analyzing […]