Endy:Research

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(Synthetic Biology)
(PhD Students)
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==PhD Students==
==PhD Students==
*'''Francois St-Pierre''' (MIT class of 200?)
*'''Francois St-Pierre''' (MIT class of 200?)
-
** ''Deterministic cell-fate selection during phage lambda infection'', or equivalent (in prep., Research Paper)
+
**''Deterministic cell-fate selection during phage lambda infection'', or equivalent (in prep., Research Paper)
*'''Barry Canton''' (MIT class of 2008, TBA)
*'''Barry Canton''' (MIT class of 2008, TBA)
-
** ''Engineering the interface between cellular chassis and synthetic biological systems'' ([URL pending, Dissertation])
+
**''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)
+
**''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)
+
**''A virtual machine for synthetic biology'', or equivalent (in prep., Research Paper)
*'''Jason Kelly''' (MIT class of 2008, TBA)
*'''Jason Kelly''' (MIT class of 2008, TBA)
-
** ''Tools and reference standards for evolving engineered biological systems'' ([URL pending, Dissertation])
+
**''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)  
+
**''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)
+
**''Programmed selection and preferential promotion of disadvantaged bacteria'', or equivalent (in prep., Research Paper)
*'''Reshma Shetty''' (MIT 2008 PhD, w/ Tom Knight, TBA)
*'''Reshma Shetty''' (MIT 2008 PhD, w/ Tom Knight, TBA)
**''Applying engineering principles to the design and construction of transcriptional devices'' ([http://dspace.mit.edu/handle/1721.1/41843 Dissertation])
**''Applying engineering principles to the design and construction of transcriptional devices'' ([http://dspace.mit.edu/handle/1721.1/41843 Dissertation])
Line 23: Line 23:
**''Signal levels, load, and error rates in engineered transcriptional devices'', or equivalent (in prep., 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)
*'''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'' ([URL pending, Dissertation])
-
** ''Engineering phosphorylation-dependent post-translational protein devices'' (submitted, Research Paper)
+
**''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)
+
**''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)
*'''Ty Thomson''' (MIT class of 2008 PhD, moving to Epitome Biosystems)
-
**a
+
**''Models and analysis of yeast mating response: Tools for model building, from documentation to time-dependent stimulation'' ([URL pending, Dissertation])
-
**b
+
**''Tools for making systems biology models more scientific'' (in prep., Research Paper)
-
**c
+
**''Mechanics, controls, and models of yeast mating response'' (in prep., Research Paper)
-
**d
+
**''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)
*'''Sri Kosuri''' (MIT class of 2007 PhD, now at a very low-profile biotechnology startup)
**''Simulation, models, and refactoring of bacteriophage T7 gene expression'' ([http://dspace.mit.edu/handle/1721.1/39912 Dissertation])
**''Simulation, models, and refactoring of bacteriophage T7 gene expression'' ([http://dspace.mit.edu/handle/1721.1/39912 Dissertation])

Revision as of 20:33, 27 May 2008

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Contents

Synthetic Biology

The lab's goal is to make biology easy to engineer. Our research is largely student-initiated and driven. Students have joined the lab from a wide-range of backgrounds including biology, chemistry, english, mathematics, physics, and all fields of engineering. Reading our dissertations and research papers (below) is a great way to learn about the sort of work that the lab has been able to support, and provides good background and introductory materials as well as glimpses of future ideas and directions. You'll find that the lab has a strong interest in foundational technology development, that we pursue both experimental and theoretical work, and that we are interested in the applications of biological technologies too. If you are searching for a passionate place to work on a new (or old) research idea that's relevant to synthetic biology then we would very much like to hear from you.

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, 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

  • iGEM 2008
  • iGEM 2007
  • iGEM 2006
  • Synthetic Biology Competition 2005
  • IAP 2004
  • IAP 2003
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