Research

Synthetic Biology Informatics

Bioinformatics Conceptual

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 […]

DNA Design

genocad dna design software

DNA Design: CAD of Gene Expression Systems We are developing DNA design strategies relying on design rules that accelerate the development of expression vectors and reduce costly errors. Most bioinformatics software packages include sequence editors that facilitate the design and assembly of new DNA sequences. Automatic recognition of sequence features, identification of restriction sites, and […]

Synthetic Biology Software

synthetic biology software stack

Synthetic biology software for Genetic Design Automation Computer Assisted Design (CAD) tools are ubiquitous in nearly all fields of engineering. They provide two primary functions: simplifying common tasks and making designs convenient for communication and evaluation.  In electronics, the development of consistent suites of CAD tools is called Electronic Design Automation (EDA).  The spectacular success […]

Cell Cycle Model

cell cycle regulator mRNA

Cell cycle model: a noisy yet robust network A cell cycle model can help better understand the property of this complex regulatory network. The cell cycle is the process by which a growing cell replicates its genome and partitions the two copies of each chromosome to two daughter cells at division. It is of utmost […]

Imaging Cytometry

imaging cytometry system

Imaging cytometry to measure stochastic gene expression in individual cells Molecular and cell biologists have uncovered so many molecular interactions involved in the control of various aspects of the cell physiology that it is often no longer possible to comprehend these regulatory networks by relying on intuition and semi-quantitative reasoning. Mathematical modeling and software simulations are […]

Gene Synthesis Optimization

Gene synthesis optimization through modeling In this project, we test the hypothesis that methods from manufacturing and industrial engineering can be used for gene synthesis optimization. Gene synthesis is the process of combining natural and chemically synthesized DNA fragments together in order to make larger DNA molecules that conform to computer-designed sequences. DNA fabrication includes […]

Biosecurity of Synthetic Biology

biosecurity team at the fbi

Biosecurity Screens to Keep Synthetic Biology Safe We have developed software that implements the screening algorithm recommended by the Department of Health and Human Services in a document entitled “Screening Frameworks Guidance for Synthetic Double-Stranded DNA Providers.” We characterized the relationship between the computational cost of the sequence screening algorithm, the rate of false positives […]