select research projects
The human gut microbiota is one of the most densely populated ecosystems of microorganisms on earth. With an estimated 100 trillion micro-organisms, the gut is an extraordinarily complex system of microbe-microbe and microbe-host interactions. In collaboration with Professor Eric Alm, co-director of the MIT Microbiome Center, we are building a three-dimensional, artificial gut using the latest digital fabrication technologies for the systematic construction and study of synthetic microbial communities, including exploring the influence of engineered microorganisms on population dynamics.
miRNA-based Genetic Circuits for Cancer Detection
synbio | High-throughput library generation
miRNAs are a recently discovered class of nucleic acids involved in almost every aspect of human development. By querying only a small number of miRNAs in a cell, cell-type, and even disease state, can be discerned. In collaboration with MIT Professor Ron Weiss, we are developing tools for the high-throughput generation of libraries of genetic circuits to identify and destroy cancer cells via miRNA signatures. Additionally, with these circuit libraries we are cataloging expression profiles for every known human miRNA.
3D Printed Fluidic Hardware for DNA Assembly
synbio | digital fabrication
The ability to rapidly and cheaply produce hardware for biological engineering would enable new communities of users to explore biology as a medium for creative expression. Utilizing commodity 3D printing, we fabricated multiple functional fluidic devices for miniaturizing DNA assembly, the foundational technology for synthetic biology, along with support hardware, like syringe pumps, for fluid handling. 3D print your own DNA assembler today!
open repository for bio-hardware
Fluidics are promising foundational tools for synthetic biology. Unfortunately, fluidics are not broadly used, because they are difficult to manufacture and operate, and designs are currently not shared. I am building an open repository of both device and hardware designs to enable communities of users from around the world to share and remix bio-hardware. This repository will also serve as the home for student-generated hardware projects as a part of the 2015 International Genetically Engineered Machines competition (iGEM).
Rapid Protein Engineering for Bioremediation and Personalized Therapeutics
synbio | designer enzymes
A major bottleneck in protein engineering is the rate at which protein designs can be tested. We are developing fluidic platforms for the high-throughput synthesis and assay of hundreds of enzyme variants, in parallel, enabling protein engineers to rapidly test their designs to find the best candidates. We have utilized these platforms to prototype enzymes for the bioremediation of toxic chemicals and anti-viral therapeutics for personalized medicine.
synbio | Rapid prototyping
Plants have evolved sophisticated mechanisms to continuously sense and respond to their environment, suggesting that these properties can be capitalized upon to make biological monitors for detecting toxins and other human threats. We are developing a set of tools to accelerate the design cycle for manufacturing and screening "plant sentinels" by automating and miniaturizing processes for harvesting, culturing, and screening plant protoplasts, a promising organism for testing genetic variants for sentinel development.
In my post-doctoral work, I served as a team leader for the $10 million DARPA-funded “RealNose” Project. In collaboration with Principal Research Scientist Shuguang Zhang, I demonstrated the first synthesis
of olfactory receptors in a microfluidic device for use with an odorant-detecting biosensor.
Microfluidic Gene Synthesis
synbio |automated DNA assembly
DNA synthesis is the foundational technology of synthetic biology. In my doctoral work, I demonstrated the first assembly of genes in a microfluidic, "lab-on-a-chip" system. I also developed platforms integrating gene synthesis with protein synthesis. Such miniaturized fluidic platforms are promising tools for the high-throughput automation of not only DNA assembly, but also the integration of protein and cellular engineering.
Ion- and Electron-beam Mediated Nanostructure Fabrication
In my masters work I developed technologies for creating nanostructures utilizing energetic beams. I used a focused ion beam (FIB) to directly pattern nanoparticles composed of a variety of materials, and a technique for electrostatically attracting ionized inorganic nanoparticles to surfaces, termed nanoxerography.