Endy:Research

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==Synthetic Biology==
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===Genetic Data Storage===
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'''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 engineeringReading our dissertations and research papers 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.
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We are focused on the development of engineered DNA systems that are capable of data storage inside living cellsOur [http://blogs.scientificamerican.com/observations/2012/05/21/scientists-engineer-rewriteable-digital-data-storage-in-the-dna-of-living-bacteria/ recent work] has focused on non-volatile recombinase addressable data (RAD) storage engineered from serine recombinases that target reversibly-invertible chromosomal data registers. We are interested in scaling genetically-encoded data systems from from a few bits to a few bytes.
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==PhD Students==
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===Engineering Biology===
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*'''Barry Canton''' (class of 2008, TBA)
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Our overall long term goal is to help make biology easy to engineer, an area of research sometimes known as synthetic biology. In particular, we adapt ideas from metrology that help enable the distributed measurement and representation of in vivo molecular activities. We also develop genetic layout architectures that help establish reliably reusable standard biological parts supporting abstraction of biological functions.
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** ''Engineering the interface between cellular chassis and synthetic biological systems'' ([URL pending, Dissertation])
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** ''BBa_F2620, an engineered cell-cell communication receiver device'' (in press, Research Paper)
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** ''A virtual machine for synthetic biology,'' or equivalent (in prep., Research Paper)
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*'''Jason Kelly''' (class of 2008, TBA)
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*'''Reshma Shetty''' (2008 PhD, w/ Tom Knight, TBA)
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**''Applying engineering principles to the design and construction of transcriptional devices'' ([http://dspace.mit.edu/handle/1721.1/41843 Dissertation])
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**''Engineering BioBrick vectors from BioBrick parts'' ([http://www.jbioleng.org/content/2/1/5 Research Paper])
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**''A synthetic biology approach to reprogramming bacterial odor'' (submitted, Research Paper)
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**''Signal levels, load, and error rates in engineered transcriptional devices'', or equivalent (in prep., Research Paper)
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*'''Samantha Sutton''' (class of 2008 PhD, TBA)
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*'''Ty Thomson''' (class of 2008 PhD, moving to Epitome Biosystems)
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*'''Sri Kosuri''' (class of 2007 PhD, now at a very low-profile biotechnology startup)
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**''Simulation, models, and refactoring of bacteriophage T7 gene expression'' ([http://dspace.mit.edu/handle/1721.1/39912 Dissertation])
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**''Refactoring bacteriophage T7'' ([http://www.nature.com/msb/journal/v1/n1/full/msb4100025.html Research Paper])
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**''TABASCO: A single molecule, base-pair resolved gene expression simulator'' ([http://www.biomedcentral.com/1471-2105/8/480 Research Paper])
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**''Measures and models of bacteriophage T7 gene expression'' (in prep., Research Paper)
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==MS Students==
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===Research Background & Context, Additional Materials===
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*'''Alex Mallet''' (2007, now at Microsoft, Inc.)
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The many and diverse dissertations from past students in the lab, their peer-reviewed published articles, and our written perspectives and other published projects are all [[Endy:Reprints | freely available online]]. We hope that students who are interested in exploring and taking forward their own research projects in the lab will be informed and inspired by the curiosity and independence of past student's work. We hope that others who are interested in understanding, contributing to, or constructively criticizing the lab's work make full use of our published record.
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**''Analysis of Targeted and Combinatorial Approaches to Phage T7 Genome Generation'' ([http://dspace.mit.edu/handle/1721.1/35880 Thesis])
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*'''Jeff Gritton''' (2006, now at Harvard Law School)
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**''Architecture and evolutionary stability of yeast signaling pathways'' ([http://dspace.mit.edu/handle/1721.1/37258 Thesis])
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==Undergraduate Students==
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*iGEM 2008
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*iGEM 2007
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*iGEM 2006
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*Synthetic Biology Competition 2005
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*IAP 2004
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*IAP 2003
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==Current Projects (partial listing)==
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[[Engineering the Host/System Interface|Engineering the Chassis/System Interface]] - [[Barry Canton]]
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[[Library-based Construction]] - [[Jason Kelly]] & [[Josh Michener]]
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[[Rebuilding T7]] - [[Sri Kosuri]]
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[[Receiver Definition]] - [[Ania Labno]] & [[Barry Canton]]
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[[SortoStat]] - [[Jason Kelly]] & [[Bryan Hernandez]]
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[[TABASCO]] - [[Sri Kosuri]]
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[[Time-Dependent Analysis of Signaling Pathways]] - [[Ty Thomson]]
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Current revision

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Genetic Data Storage

We are focused on the development of engineered DNA systems that are capable of data storage inside living cells. Our recent work has focused on non-volatile recombinase addressable data (RAD) storage engineered from serine recombinases that target reversibly-invertible chromosomal data registers. We are interested in scaling genetically-encoded data systems from from a few bits to a few bytes.

Engineering Biology

Our overall long term goal is to help make biology easy to engineer, an area of research sometimes known as synthetic biology. In particular, we adapt ideas from metrology that help enable the distributed measurement and representation of in vivo molecular activities. We also develop genetic layout architectures that help establish reliably reusable standard biological parts supporting abstraction of biological functions.

Research Background & Context, Additional Materials

The many and diverse dissertations from past students in the lab, their peer-reviewed published articles, and our written perspectives and other published projects are all freely available online. We hope that students who are interested in exploring and taking forward their own research projects in the lab will be informed and inspired by the curiosity and independence of past student's work. We hope that others who are interested in understanding, contributing to, or constructively criticizing the lab's work make full use of our published record.

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