Journals

1. Roza Ghamari, Swapnil Bhatia, Alec Neilsen, Traci Haddock, Christopher Voigt, and Douglas Densmore, Cello: A Specify-Design-Assemble Workflow for Biological Circuits, ACS Synthetic Biology, 2012. (In preparation)
2. Fusun Yaman, Swapnil Bhatia, Aaron Adler, Douglas Densmore, Jake Beal, Automated Selection of Synthetic Biological Parts for Genetic Regulatory Networks, ACS Synthetic Biology, 2012. (In submission)
3. 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, An End-to-End Workflow for Engineering of Biological Circuits from High-Level Specifications, ACS Synthetic Biology, 2012. (In submission)
4. Bing Xia, Swapnil Bhatia, Ben Bubenheim, Maisam Dadgar, Douglas Densmore, and J. Christopher Anderson, Clotho: A Software Platform for the Creation of Synthetic Biological Systems, A Developer’s and User’s Guide for Clotho v2.0, Methods in Enzymology, Volume 498, 2011. PMID: 21601675

Conferences

1. Ernst Oberortner, Haiyao Huang, Swapnil Bhatia, Douglas Densmore, Allan Kuchinsky, Eugene: Language-based Design of Synthetic Biological Systems, SPLASH 2012. (In submission)
2. Boyan Yordanov, Evan Appleton, Rishi Ganguly, Ebru Aydin Gol, Swati Banerjee Carr, Swapnil Bhatia,Traci Haddock, Calin Belta, Douglas Densmore, Experimentally Driven Verification for Synthetic Biological Circuits, Design, Automation, and Test Europe (DATE) 2012, Dresden Germany, March 2012. pdf

Abstracts/Workshops

1. E. Appleton, S. Bhatia, T. Haddock, V. Vasilev, R. Ghamari, R. Ganguly, and D. Densmore. "Specify, Design, and Assemble: A Top-Down Design Flow Using Clotho," talk at Cold Springs Harbor Asia Series – 2011 Symposium: Design & Synthesis of Biological Systems, November, 2011.
2. J. Beal, R. Weiss, D. Densmore, A. Adler, J. Babb, S. Bhatia, N. Davidsohn, T. Haddock, E. Appleton, F. Yaman, R. Schantz, and J. Loyall. “TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering," poster at Cold Springs Harbor Asia Series – 2011 Symposium: Design & Synthesis of Biological Systems, November, 2011.
3. V. Vasilev, C. Liu, T. Haddock, S. Bhatia, A. Adler, F. Yaman, J. Beal, J. Babb, R. Weiss and D. Densmore, "A Software Stack for Specification and Robotic Execution of Protocols for Synthetic Biological Engineering," talk at the International Workshop on Bio-Design Automation, June 2011.
4. R. Ghamari, B. Stanton, T. Haddock, S. Bhatia, K. Clancy, T. Peterson, C. Voigt and D. Densmore, "Applying Hardware Description Languages to Genetic Circuit Design," poster at the International Workshop on Bio-Design Automation, June 2011.
   1. poster at Tapia 2011 Conference, San Francisco, April 2011.
5. J. Beal, R. Weiss, D. Densmore, A. Adler, J. Babb, S. Bhatia, N. Davidsohn, T. Haddock, F. Yaman, R. Schantz and J. Loyall, "TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering," talk at the International Workshop on Bio-Design Automation, June 2011.
6. A. Adler, J. Beal, S. Bhatia, N. Davidsohn, D. Densmore, T. Haddock, J. Loyall, R. Schantz, R. Weiss, and F. Yaman, "Towards automated selection of parts for genetic regulatory networks,"
   1. talk at the International Workshop on Bio-Design Automation, San Diego, CA, June 2011.
   2. poster at Synthetic Biology 5.0, BioBricks Foundation, Palo Alto CA, June 2011.
   3. talk at the Annual Conference of the Institute of Biological Engineering, Atlanta, GA, March 2011.

Thesis

1. Roza Ghamari, "Applying Hardware Description Languages to Genetic Circuit Design," MS Thesis, September 2011.