Synthetic Biology Informatics

Bioinformatics Conceptual
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Overview

I lead the Synthetic Biology Informatics Group at the Virginia Bioinformatics Institute (VBI). VBI is a research institute of Virginia Tech.   My group combines experimental and computational approaches to understand how complex phenotypes are encoded natural and synthetic genomes. We develop software to design DNA molecules and analyze the phenotype of individual cells. Recently, we have started analyzing the security of the synthetic biology supply chain.

Synthetic Biology Informatics = computers + pipettes

Over the last 20 years, progress in biology has been driven by new ways of generating large amounts of data. Big data sets can be used to test biological  requires hypotheses.  Their analysis requires a deep understanding of the potential and limitations of experimental methods used to generate them. It also requires adapting existing modeling techniques to the analysis of these new datasets. The Synthetic Biology Informatics Group is a place where experimental biologists and computational biologists work together and can have productive conversations by the water cooler. We develop new models of the regulatory network controlling the cell cycle. This project is a collaboration with bioinformaticians and computational biologists. We focus on the the experimental validation of biological hypotheses generated by their computational effort. We work in collaboration with people having expertise designing expression vectors for different hosts. We help them formalize design rules using  GenoCAD. GenoCAD is a software tool inspired by methods from computational linguistics. We are collaborating with people having expertise in biosecurity, cyber-security and bio-manufacturing. We are working toward improving the security of synthetic biology informatics. We identify and mitigate the vulnerabilities of synthetic biology workflows.

More information

Cell Cycle: In collaboration with John Tyson and T.M. Murali, we participate in two NIH-funded projects to develop mathematical models of the regulatory network controlling cell division in yeast.

DNA Design: We are exploring how to streamline the design of synthetic DNA sequences by using methods from computational linguistics. GenoCAD (www.genocad.com) is a product of our early work in this field.

Gene Synthesis: It is now possible to use chemical processes to produce custom synthetic DNA molecules. Our group has been developing methods to streamline DNA synthesis workflows.

Imaging cytometry: Many cellular processes like cell division are noisy. It is necessary to collect data in individual cells to better understand their dynamics. We are developing closed-loop control algorithms to make smarter miscroscopes better capable of handling this challenging application.

Biosecurity: Through research projects and education programs, we help government agencies understand the security implications of synthetic biology.