Endy:Research: Difference between revisions

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==Synthetic Biology==
===Genetic Data Storage===
''Our goal is to make biology easy to engineer.'' Undergraduate and PhD students in the lab pursue independent research projects of their own choosing that fall within this broad agenda.  Reading their published dissertations and research papers is one good way to learn about the sort of work that the lab has been able to support, including background and introductory materials as well as future ideas and directions. If you are looking for a place to work on a new (or old) research idea that's relevant to synthetic biology we would like to hear from you.
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.


==Biological Systems Modeling==
===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.


We are working to develop and improve general methods for representing cellular behavior. Consider, for example, Magritte’s painting [http://images.google.com/images?q=clairvoyance%2Bmagritte Clairvoyance] (1936); a man appears to look at an egg while painting a bird. At least three models could explain the scene. First, the man is clairvoyant – he is able to perceive the potential of the egg and paint the appropriate animal (i.e., bird in place of platypus). Second, the man has prior knowledge that eggs of a certain type turn into particular birds – he describes what he expects will occur based on past experience. Third, the man has the ability, hidden from the viewer, to determine the relevant physical state of the egg. Furthermore, the man has access to a “standard model” for cellular chemistry and physics. Taken together, he is able to observe any particular egg and predict the relevant properties of the resulting animal. We are working to make the third model happen. [modeling would be easier if eggs were designed to be easy to model in the first place – please see our interests re: Design of Integrated Biological Systems above]
===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 [[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.
==Current Projects (partial listing)==
 
[[Engineering the Host/System Interface|Engineering the Chassis/System Interface]] - [[Barry Canton]]
 
[[Library-based Construction]] - [[Jason Kelly]] & [[Josh Michener]]
 
[[Rebuilding T7]] - [[Sri Kosuri]]
 
[[Receiver Definition]] - [[Ania Labno]] & [[Barry Canton]]
 
[[SortoStat]] - [[Jason Kelly]] & [[Bryan Hernandez]]
 
[[TABASCO]] - [[Sri Kosuri]]
 
[[Time-Dependent Analysis of Signaling Pathways]] - [[Ty Thomson]]
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Revision as of 15:37, 21 May 2012

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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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