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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.