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Synthetic Biology

The immediate goal of our research is to enable the engineering of genetically encoded memory systems. Modest amounts of programmable memory, if implemented within living cells, would have a profound impact on the study and treatment of many diseases, and would broadly enable many non-medical applications of biotechnology. We are interested in both the basic and applied aspects of the problem, from considering how to best store information inside cells, to practical applications. Our overall long term goal is to help make biology easy to engineer, an area of research known as synthetic biology.


PhD Students

  • Francois St-Pierre (MIT class of 200?)
    • Deterministic cell-fate selection during phage lambda infection, or equivalent (in prep., Research Paper)
  • Barry Canton (MIT class of 2008, TBA)
    • Engineering the interface between cellular chassis and synthetic biological systems ([URL pending, Dissertation])
    • BBa_F2620, an engineered cell-cell communication receiver device (in press, Research Paper)
    • A virtual machine for synthetic biology, or equivalent (in prep., Research Paper)
  • Jason Kelly (MIT class of 2008, TBA)
    • Tools and reference standards for evolving engineered biological systems ([URL pending, Dissertation])
    • Measurement kits and reference standards for characterizing BioBrick promoters and ribosome binding sites, (submitted, Research Paper)
    • Programmed selection and preferential promotion of disadvantaged bacteria, or equivalent (in prep., Research Paper)
  • Reshma Shetty (MIT 2008 PhD, w/ Tom Knight as lead advisor, TBA)
    • Applying engineering principles to the design and construction of transcriptional devices (Dissertation)
    • Engineering BioBrick vectors from BioBrick parts (Research Paper)
    • A synthetic biology approach to reprogramming bacterial odor (submitted, Research Paper)
    • Signal levels, load, and error rates in engineered transcriptional devices, or equivalent (in prep., Research Paper)
  • Samantha Sutton (MIT class of 2008 PhD, TBA)
    • Engineering phosphorylation-dependent post-translational protein devices ([URL pending, Dissertation])
    • Engineering phosphorylation-dependent post-translational protein devices (submitted, Research Paper)
    • Signals and specifications for a family of phosphorylation-dependent devices, or equivalent (in prep., Research Paper)
  • Ty Thomson (MIT class of 2008 PhD, moving to Epitome Biosystems)
    • Models and analysis of yeast mating response: Tools for model building, from documentation to time-dependent stimulation ([URL pending, Dissertation])
    • Tools for making systems biology models more scientific (in prep., Research Paper)
    • Mechanics, controls, and models of yeast mating response (in prep., Research Paper)
    • Measurement and analysis of protein abundances suggests tradeoff between signaling system output and dynamic range (in prep., Research Paper)
  • Sri Kosuri (MIT class of 2007 PhD, now at a very low-profile biotechnology startup)
    • Simulation, models, and refactoring of bacteriophage T7 gene expression (Dissertation)
    • Refactoring bacteriophage T7 (Research Paper)
    • TABASCO: A single molecule, base-pair resolved gene expression simulator (Research Paper)
    • Measures and models of bacteriophage T7 gene expression (in prep., Research Paper)

MS Students

  • Alex Mallet (MIT class of 2007, now at Microsoft, Inc.)
    • Analysis of Targeted and Combinatorial Approaches to Phage T7 Genome Generation (Thesis)
  • Jeff Gritton (MIT class of 2006, now at Harvard Law School)
    • Architecture and evolutionary stability of yeast signaling pathways (Thesis)

Undergraduate Students