Publications
An
End-to-End
Workflow for Engineering of Biological Networks from High-Level
Specifications,
Jacob Beal, Ron Weiss, Douglas Densmore, Aaron Adler, Evan Appleton,
Jonathan Babb, Swapnil Bhatia, Noah Davidsohn, Traci Haddock, Joseph
Loyall, Richard Schantz, Viktor Vasilev, and Fusun Yaman, ACS Synthetic
Biology, online publication July 2012.
Automated
Selection of Synthetic Biology Parts for Genetic Regulatory Networks,
Fusun
Yaman,
Swapnil Bhatia, Aaron Adler, Douglas Densmore, and Jacob
Beal, ACS Synthetic Biology, online publication July 2012.
- Results
from TASBE, Jacob Beal, Ron Weiss, Douglas Densmore, Aaron Adler,
Evan Appleton, Jonathan Babb, Swapnil Bhatia, Noah Davidsohn, Traci
Haddock, Joseph Loyall, Richard Schantz, Viktor Vasilev, and Fusun
Yaman, peer-reviewed abstract in 4th International Workshop on
Bio-Design Automation, June 2012.
- Toward
Automated Design of Cell State Detectors, Jacob Beal and Fusun
Yaman, peer-reviewed abstract in 4th International Workshop on
Bio-Design Automation, June 2012.
A Method
for Fast,
High-Precision Characterization of Synthetic Biology Devices, Jacob
Beal, Ron Weiss, Fusun Yaman, Noah Davidsohn, and Aaron Adler, MIT
CSAIL Tech Report 2012-008, April, 2012.
Automatic
Compilation
from High-Level Biologically-Oriented Programming Language
to Genetic Regulatory Networks, Jacob Beal, Ting Lu, Ron Weiss,
PLoS ONE 6(8): e22490. doi:10.1371/journal.pone.0022490, August 2011.
- TASBE: A Tool-Chain to Accelerate
Synthetic Biological Engineering. Jacob Beal, Ron Weiss, Douglas
Densmore, Aaron Adler, Jonathan Babb, Swapnil Bhatia, Noah Davidsohn,
Traci Haddock, Fusun Yaman, Richard Schantz, and Joseph Loyall.
Peer-reviewed abstract in 3rd International Workshop
on Bio-Design Automation, June 2011. [pdf] [talk pdf]
- Toward Automated Selection of
Parts for Genetic Regulatory Networks. Fusun Yaman, Swapnil
Bhatia, Aaron Adler, Douglas Densmore, Jacob Beal, Ron Weiss, and Noah
Davidsohn. Peer-reviewed abstract in 3rd
International Workshop on Bio-Design Automation, June 2011. [pdf] [talk pdf]
- A Software Stack for
Specification and Robotic Execution of Protocols for Synthetic
Biological Engineering. Viktor Vasilev, Chenkai Liu, Traci
Haddock, Swapnil Bhatia, Aaron Adler, Fusun Yaman, Jacob Beal, Jonathan
Babb, Ron Weiss, and Douglas Densmore. peer-reviewed abstract in 3rd International Workshop on Bio-Design Automation,
June
2011. [pdf]
- High-Level Programming Languages
for Bio-Molecular Systems. Jacob Beal, Andrew Phillips, Douglas
Densmore, and Yizhi Cai. Chapter in Design and
Analysis of Bio-Molecular Circuits, edited by Heinz Koeppl,
Douglas Densmore, Mario di Bernardo, and Gianluca Setti, Springer, 2011.
Cells Are Plausible Targets for
High-Level Spatial Languages. Jacob Beal and Jonathan Bachrach. Spatial Computing Workshop, October 2008. [pdf]
Other Conference Talks
- A Tool-Chain to Accelerate
Synthetic Biological Engineering. Jacob Beal, Ron Weiss, Douglas
Densmore, Aaron Adler, Jonathan Babb, Swapnil Bhatia, Noah Davidsohn,
Traci Haddock, Fusun Yaman, Richard Schantz, and Joseph Loyall.
Abstract in SB5.0: the Fifth International Meeting
on Synthetic Biology, June 2011. [pdf] [poster pdf]
- Toward Automated Selection of
Parts for Genetic Regulatory Networks. Fusun Yaman, Swapnil
Bhatia, Aaron Adler, Jonathan Babb, Jacob Beal, Noah Davidson, Douglas
Densmore, Traci Haddock, Joseph Loyall, Richard Schantz, and Ron Weiss.
Abstract in SB5.0: the Fifth International Meeting
on Synthetic Biology, June 2011. [pdf] [talk pdf]
- Toward Automated Selection of
Parts for Genetic Regulatory Networks. Fusun Yaman, Swapnil
Bhatia, Aaron Adler, Douglas Densmore, Jacob Beal, Jonathan Babb, Noah
Davidson, Traci Haddock, Joseph Loyall, Richard Schantz, and Ron Weiss.
Abstract in IBE 2011, March 2011. [pdf] [talk
pdf]
Other Related Publications
- Synthetic
Biology Open Language (SBOL) Version 1.0.0,
Anil Wipat, Alan
Villalobos, Guy-Bart Stan, Trevor Smith, Herbert Sauro, Nicholas
Roehner, Matthew Pocock, Hector Plahar,
Jean Peccoud, Chris Myers, Goksel Misirli, Curtis Madsen, Matthex Lux,
Allan Kuchinsky, Timothy Ham, Raik Grunberg, John Gennari, Drew
Endy, Omri Drory, Douglas Densmore, Deepak Chandran, Jacob Beal, J.
Christopher Anderson, Aaron Adler, Laura Adam, Cesar
Rodriguez, Mandy Wilson, and Michal Galdzicki, BioBricks Foundation
Request for Comments (BBF RFC) #84, October 2011.
- Bringing
Biology
and
Engineering Together with Spatial Computing, Jacob Beal,
extended abstract for 12th International Conference on Membrane
Computing, August 2011.
Last Updated: 9/5/2012