Endy:Research

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(Synthetic Biology)
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(Genetic Data Storage)
 
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==Synthetic Biology==
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===Genetic Data Storage===
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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.
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We are focused on the development of engineered DNA systems that are capable of data storage inside living cells.  Our [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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==Postdocs==
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===Engineering Biology===
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*'''Jerome Bonnet''' (Stanford, October 2008 start)
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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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**''[[Endy:Notebook/Genetic_Memory | Genetically Encoded Memory]],'' in progress
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==PhD Students==
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===Research Background & Context, Additional Materials===
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*'''Francois St-Pierre''' (MIT class of 200?)
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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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**''Deterministic cell-fate selection during phage lambda infection'', or equivalent (in prep., Research Paper)
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*'''Barry Canton''' (MIT class of 2008, TBA)
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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''' (MIT class of 2008, TBA)
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**''Tools and reference standards for evolving engineered biological systems'' ([URL pending, Dissertation])
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**''Measurement kits and reference standards for characterizing BioBrick promoters and ribosome binding sites'', (submitted, Research Paper)
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**''Programmed selection and preferential promotion of disadvantaged bacteria'', or equivalent (in prep., Research Paper)
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*'''Reshma Shetty''' (MIT 2008 PhD, w/ Tom Knight as lead advisor, 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''' (MIT class of 2008 PhD, TBA)
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**''Engineering phosphorylation-dependent post-translational protein devices'' ([URL pending, Dissertation])
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**''Engineering phosphorylation-dependent post-translational protein devices'' (submitted, Research Paper)
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**''Signals and specifications for a family of phosphorylation-dependent devices'', or equivalent (in prep., Research Paper)
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*'''Ty Thomson''' (MIT class of 2008 PhD, moving to Epitome Biosystems)
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**''Models and analysis of yeast mating response: Tools for model building, from documentation to time-dependent stimulation'' ([URL pending, Dissertation])
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**''Tools for making systems biology models more scientific'' (in prep., Research Paper)
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**''Mechanics, controls, and models of yeast mating response'' (in prep., Research Paper)
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**''Measurement and analysis of protein abundances suggests tradeoff between signaling system output and dynamic range'' (in prep., Research Paper)
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*'''Sri Kosuri''' (MIT 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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*'''Alex Mallet''' (MIT class of 2007, now at Microsoft, Inc.)
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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''' (MIT class of 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''' [http://openwetware.org/wiki/IGEM:MIT/2008 Project TBD] (MIT team's wiki)
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*'''iGEM 2007''' [http://openwetware.org/wiki/IGEM:MIT/2007 Bioremediation] (MIT team's wiki)
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*'''iGEM 2006''' [http://openwetware.org/wiki/IGEM:MIT/2006 Eau d'E. coli] (MIT team's wiki)
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*'''iGEM 2005''' [http://openwetware.org/wiki/IGEM:MIT/2005 Biosensing] (MIT team's wiki)
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*'''2004 Synthetic Biology Competition''', [http://images.google.com/images?hl=en&q=2004%20synthetic%20biology%20competition&um=1&ie=UTF-8&sa=N&tab=wi see Google] (web search)
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*'''IAP 2004''' [http://parts.mit.edu/wiki/index.php/IAP2004:Polkadorks Polkadorks] (an "typical" project)
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*'''IAP 2003''' [http://web.mit.edu/newsoffice/2003/blinkers-0226.html MIT News Report]
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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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