Publications

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My DBLP entry

 

Synthetic Biology

Books:

  1. Heinz Koeppl, Douglas Densmore, Mario di Bernardo, Gianluca Setti (editors), Design and Analysis of Biomolecular Circuits, Springer Books, ISBN: 978-1-4419-6765-7, 2011.

Journal Papers:

  1. Swapnil Bhatia, Douglas Densmore, Pigeon: A Design Visualizer for Synthetic Biology, ACS Synthetic Biology, 2013. PMID: 23654259

  2. Mariana Leguia, Jennifer Brophy, Douglas Densmore, Angel Asante and J. Christopher Anderson, 2ab Assembly: A Methodology for Automatable, High-throughput Assembly of Standard Biological Parts, Journal of Biological Engineering, 7:2, 2013. PMID: 23305072. Highly Accessed

  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 (8), 317-331. PMID: 23651286

  4. Fusun Yaman, Swapnil Bhatia, Aaron Adler, Douglas Densmore, Jake Beal, Automated Selection of Synthetic Biological Parts for Genetic Regulatory Networks, ACS Synthetic Biology, 2012 1 (8), 332-344. PMID: 23651287

  5. Joanna Chen, Douglas Densmore, Timothy S. Ham, Jay D. Keasling, and Nathan J. Hillson, DeviceEditor Biological CAD Canvas, Journal of Biological Engineering, 6:1, February 28th, 2012. PMID: 22373390

  6. Douglas Densmore, Soha Hassoun, Design Automation for Synthetic Biological Systems, IEEE Design and Test of Computers, vol.29, no.3, pp.7-20, June 2012.

  7. Lesia Bilitchenko, Adam Liu, Sherine Cheung, Emma Weeding, Bing Xia, Mariana Leguia, J. Christopher Anderson, Douglas Densmore, Eugene - A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems, PLoS ONE, Volume 6, Issue 4, April 2011. PMID: 21559524


  8. Mariana Leguia, Jennifer Brophy, Douglas Densmore and J. Christopher Anderson, Automated Assembly of Standard Biological Parts, Methods in Enzymology, Volume 498, 2011. PMID: 21601686

  9. Lesia Bilitchenko, Adam Liu, and Douglas Densmore, The Eugene Language for Synthetic Biology, Methods in Enzymology, Volume 498, 2011. PMID: 21601677


  10. 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

  11. Douglas Densmore, Timothy H.-C. Hsiau, Joshua T. Kittleson, Will DeLoache, Christopher Batten, J.Christopher Anderson, Algorithms for Automated DNA Assembly, Nucleic Acids Research (2010) 38 (8): 2607-2616. PMID: 20335162

Conference Papers:

  1. Ebru Gol, Douglas Densmore, Calin Belta, Data-driven Verification of Synthetic Gene Networks, 52nd IEEE Conference on Decision and Control (CDC), 2013. (accepted)

  2. Ernst Oberortner, Swapnil Bhatia, Douglas Densmore, J. Christopher Anderson, A New Architecture for the Clotho Software Platform: A Pattern-based Architecture Review, Pattern Languages of Programs Conference (PLoP), 2012.

  3. 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. 21% acceptance rate.

  4. Douglas Densmore, Joshua T. Kittleson, Lesia Bilitchenko, Adam Liu, J. Christopher Anderson, Rule Based Constraints for the Construction of Genetic Devices, IEEE International Symposium on Circuits and Systems (ISCAS) 2010, Paris France, May 2010.

  5. Douglas Densmore, J. Christopher Anderson, Combinational Logic Design in Synthetic Biology, IEEE International Symposium on Circuits and Systems (ISCAS) 2009, Taipei Taiwan, May 2009.

  6. Douglas Densmore, Anne Van Devender, Matthew Johnson, Nade Sritanyaratana, A Platform-Based Design Environment for Synthetic Biological Systems, TAPIA 09: Proceedings of the 2009 Conference on Diversity in Computing, ACM, Portland Oregon, April 2009.

Misc:

  1. Douglas Densmore, Bio-Design Automation: Nobody Said It Would Be Easy, ACS Synthetic Biology 2012 1 (8), 296-296. PMID: 23651283

  2. Douglas Densmore, Soha Hassoun: Guest Editors' Introduction: Synthetic Biology. IEEE Design & Test of Computers 29(3): 5-6 (2012).

  3. Jean Peccoud, J Christopher Anderson, Deepak Chandran, Douglas Densmore, Michal Galdzicki, Matthew W Lux, Cesar A Rodriguez, Guy-Bart Stan, and Herbert M Sauro, Essential Information for Synthetic DNA Sequences, Nature Biotechnology Correspondence, Nature Biotechnology, Volume: 29, Page: 22 Year published: (2011). PMID: 21221092

 

Electronic Design Automation

Books:

  1. Douglas Densmore, Abhijit Davare, A Platform-Based Design Methodology for the Electronic System Level: Frameworks, Design Flows, and Case Studies, VDM Verlag Dr. Mueller, ISBN 3836473143, 2008.

Book Chapters:

  1. Felice Balarin, Massimiliano DAngelo, Abhijit Davare, Douglas Densmore, Trevor Meyerowitz, Roberto Passerone, Alessandro Pinto, Alberto Sangiovanni-Vincentelli, Alena Simalatsar, Yosinori Watanabe, Guang Yang, Qi Zhu, Platform-Based Design and Frameworks: Metropolis and Metro II, Model-Based Design of Heterogeneous Embedded Systems; Gabriela Nicolescu, Pieter Mosterman (Eds.), CRC Press, ISBN 1420067842, 2009.

  2. Douglas Densmore, Adam Donlin, Alberto Sangiovanni-Vincentelli, Programmable Platform Characterization for System Level Performance Analysis, Platform Based Design at the Electronic System Level: Industry Perspectives and Experiences; Mark Burton, Adam Morawiec (Eds.), Springer Books, ISBN 1402051379, pg 13-30, 2006.

Journal Papers:

  1. Abhijit Davare, Douglas Densmore, Lianpeng Guo, Roberto Passerone, Alberto L. Sangiovanni-Vincentelli, Alena Simalatsar, Qi Zhu, MetroII: A Design
    Environment for Cyber-Physical Systems    , ACM Transactions on Embedded Computing Systems, Volume 12, Issue 1, March 2013.

  2. Douglas Densmore, Roberto Passerone, Alberto Sangiovanni-Vincentelli, A Platform-Based Taxonomy for ESL Design, IEEE Design and Test of Computers, vol. 23, no. 5, pp. 359-374, Sept/Oct, 2006.

  3. Douglas Densmore, Alberto Sangiovanni-Vincentelli, Adam Donlin, Leveraging Programmability in Electronic System Level Designs, Xcell Journal, Q1-2006, Issue 56, pg 29-31.

Conference Papers:

  1. Douglas Densmore, Alena Simalatsar, Abhijit Davare, Roberto Passerone, Alberto Sangiovanni-Vincentelli, UMTS MPSoC Design Evaluation Using a System Level Design Framework, Design, Automation, and Test Europe (DATE) 2009, Nice France, April 2009. 27% acceptance rate

  2. Alena Simalatsar, Douglas Densmore, Roberto Passerone, A Methodology for Architecture Exploration and Performance Analysis Using System Level Design Languages and Rapid Architecture Profiling, Third International IEEE Symposium on Industrial Embedded Systems (SIES) 2008, La Grande Motte France, June 2008.

  3. Abhijit Davare, Douglas Densmore, Trevor Meyerowitz, Alessandro Pinto, Alberto Sangiovanni-Vincentelli, Guang Yang, Haibo Zeng, Qi Zhu, A Next-Generation Design Framework for Platform-Based Design, Conference on Using Hardware Design and Verification Languages (DVCon) 2007, San Jose California, February 2007.

  4. Shinjiro Kakita, Yosinori Watanabe, Douglas Densmore, Abhijit Davare, Alberto Sangiovanni-Vincentelli, Functional Model Exploration for Multimedia Applications via Algebraic Operators, Sixth International Conference on Application of Concurrency to System Design (ACSD) 2006, Turku Finland, June 2006.

  5. Douglas Densmore, Adam Donlin, Alberto Sangiovanni-Vincentelli, FPGA Architecture Characterization for System Level Performance Analysis, Design, Automation, and Test Europe (DATE) 2006, Munich Germany, March 2006. 16% acceptance rate.

  6. Douglas Densmore, Sanjay Rekhi, Alberto Sangiovanni-Vincentelli, Microarchitecture Development via Metropolis Successive Platform Refinement, Design Automation and Test Europe (DATE) 2004, Paris France, February 2004. 17% acceptance rate.

Technical Reports:

  1. Douglas Densmore, Trevor Meyerowitz, Abhijit Davare, Qi Zhu, Guang Yang, Metro II Execution Semantics for Mapping, Technical Report No. UCB/EECS-2008-16, EECS Department, University of California, Berkeley, February 18, 2008.

  2. Abhijit Davare, Jike Chong, Qi Zhu, Douglas Densmore and Alberto L. Sangiovanni-Vincentelli, Classification, Customization, and Characterization: Using MILP for Task Allocation and Scheduling, Technical Report No. UCB/EECS-2006-166, EECS Department, University of California, Berkeley, December 11, 2006.

  3. Abhijit Davare, Douglas Densmore, Vishal Shah, Haibo Zeng, Simple Case Study in Metropolis, University of California, Berkeley, UCB/ERL M04/37, September 2004.

  4. Douglas Densmore, Metropolis Architecture Refinement Styles and Methodology, University of California, Berkeley, UCB/ERL M04/36, 14 September 2004.

  5. Douglas Densmore, Formal Refinement Verification in Metropolis, University of California, Berkeley, UCB/ERL M04/10, 22 May 2004.

PhD Thesis:

  1. Douglas Densmore, A Design Flow for the Development, Characterization, and Refinement of System Level Architectural Services, Spring 2007.

Masters Report:

  1. Douglas Densmore, Platform Based Reconfigurable Architecture Exploration via Boolean Constraints, Spring 2004.

Patents:

  1. Adam Donlin and Douglas Densmore, Method and Apparatus for Precharacterizing Systems for Use in System Level Design of Integrated Circuits, Issued August 31, 2010. Patent Number 7,788,625