Endy:Research: Difference between revisions

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==Design of Integrated Biological Systems==
===Genetic Data Storage===
We are working to enable the design and construction of large scale integrated biological systems. Biology presents a new medium for engineering and contains many domain-specific challenges (e.g., evolution). Still, in getting started, we can make use of past successful experience in other disciplines. We are currently exploring the application of three past engineering lessons: (1) standardization of components, conditions, and characterization, (2) abstraction as a tool for hiding information and managing complexity, and (3) decoupling of overwhelming, complicated problems into many simpler problems (e.g., design and fabrication).
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===
[[Image:Banner3.jpg|right|500px|Magritte, Clairvoyance (1936)]]
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]


==Current Projects==
===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.
[[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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