Featured Publications

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Synthetic Biology

Nielsen, A.A., Der, B.S., Shin, J., Vaidyanathan, P., Paralanov, V., Strychalski, E.A., Ross, D., Densmore, D. and Voigt, C.A., Science. "Genetic circuit design automation." 2016

10.1126/science.aac7341

Publications

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2021

Hamer, Davidson H., Laura White, Helen E. Jenkins, Hannah N. Landsberg, Catherine Klapperich, Katia Bulekova, Judy Platt et al. "Control of COVID-19 transmission on an urban university campus during a second wave of the pandemic." medRxiv (2021).

Vaidyanathan, Prashant, Evan Appleton, David Tran, Alexander Vahid, George Church, and Douglas Densmore. "Algorithms for the selection of fluorescent reporters." Communications biology 4, no. 1 (2021): 1-8.

Lashkaripour, Ali, Christopher Rodriguez, Noushin Mehdipour, Rizki Mardian, David McIntyre, Luis Ortiz, Joshua Campbell, and Douglas Densmore. "Machine learning enables design automation of microfluidic flow-focusing droplet generation." Nature communications 12, no. 1 (2021): 1-14.

2020

L Ortiz. "High-throughput functional screening of oxidase enzymes. " PhD Thesis. 2020

McIntyre, David, Ali Lashkaripour, and Douglas Densmore. "Rapid and inexpensive microfluidic electrode integration with conductive ink." Lab on a Chip 20, no. 20 (2020): 3690-3695.

Lashkaripour, Ali, David McIntyre, and Douglas Densmore. "Efficient large-scale microfluidic design-space exploration: from data to model to data." International Workshop on Bio-Design Automation. (2020).

McIntyre, David, Ali Lashkaripour, and Douglas Densmore. "Active learning for efficient microfluidic design automation." International Workshop on Bio-Design Automation. (2020).

Chen, Ye, Shuyi Zhang, Eric M. Young, Timothy S. Jones, Douglas Densmore, and Christopher A. Voigt. "Genetic circuit design automation for yeast." Nature Microbiology 5, no. 11 (2020): 1349-1360.

Timmons, Joshua J., and Doug Densmore. "Repository-based plasmid design." PloS one 15, no. 1 (2020): e0223935.

2019

Walsh III, David I., Marilene Pavan, Luis Ortiz, Scott Wick, Johanna Bobrow, Nicholas J. Guido, Sarah Leinicke et al. "Standardizing automated DNA assembly: best practices, metrics, and protocols using robots." SLAS TECHNOLOGY: Translating Life Sciences Innovation 24, no. 3 (2019): 282-290.

P. Vaidyanathan. "Functional synthesis of genetic systems." PhD Thesis. (2019).

Sanka, Radhakrishna, and Douglas Densmore. "Integration of performance metrics into microfluidic design automation." International Workshop on Bio-Design Automation. (2019).

McIntyre, David, and Douglas Densmore. "Design automation of microfluidic droplet sorting platforms." International Workshop on Bio-Design Automation (2019).

Lashkaripour, Ali, Christopher Rodriguez, Noushin Mehdipour, David McIntyre, and Douglas Densmore. "Modular microfluidic design automation using machine learning." International Workshop on Bio-Design Automation, (2019).

Lashkaripour, Ali, Christopher Rodriguez, Luis Ortiz, and Douglas Densmore. "Performance tuning of microfluidic flow-focusing droplet generators." Lab on a Chip 19, no. 6 (2019): 1041-1053.

Madsen, Curtis, Prashant Vaidyanathan, Sadra Sadraddini, Cristian-Ioan Vasile, Nicholas A. DeLateur, Ron Weiss, Douglas Densmore, and Calin Belta. “Metrics for Signal Temporal Logic Formulae.” In 2018 IEEE Conference on Decision and Control (CDC), 1542–47, 2018.

Nguyen, Tramy, Timothy S. Jones, Pedro Fontanarrosa, Jeanet V. Mante, Zach Zundel, Douglas Densmore, and Chris J. Myers. "Design of asynchronous genetic circuits." Proceedings of the IEEE 107, no. 7 (2019): 1356-1368.

Walsh, David I., Marilene Pavan, Luis Ortiz, Scott Wick, Johanna Bobrow, Nicholas J. Guido, Sarah Leinicke, et al. “Standardizing Automated DNA Assembly: Best Practices, Metrics, and Protocols Using Robots.” SLAS TECHNOLOGY: Translating Life Sciences Innovation 24, no. 3 (June 1, 2019): 282–90.

Sanka, Radhakrishna, Brian Crites, Jeffrey McDaniel, Philip Brisk, and Douglas Densmore. "Specification, Integration, and Benchmarking of Continuous Flow Microfluidic Devices." In 2019 IEEE/ACM International Conference on Computer-Aided Design (ICCAD), pp. 1-8. IEEE, 2019.

Sanka, Radhakrishna, Joshua Lippai, Dinithi Samarasekera, Sarah Nemsick, and Douglas Densmore. "3d μ f-interactive design environment for continuous flow microfluidic devices." Scientific reports 9, no. 1 (2019): 1-10.

2018

Sanka, Radhakrishna, Brian Crites, Joshua Lippai, Jeffery McDaniel, Philip Brisk, and Douglas Densmore. "Standardizing design performance comparison in microfluidic manufacturing." International Workshop in Bio-Deign Automation. (2018).

Cox, Robert Sidney, Curtis Madsen, James Alastair McLaughlin, Tramy Nguyen, Nicholas Roehner, Bryan Bartley, Jacob Beal et al. "Synthetic biology open language (SBOL) version 2.2. 0." Journal of integrative bioinformatics 15, no. 1 (2018).

Crites, Brian, Radhakrishna Sanka, Joshua Lippai, Jeffrey McDaniel, Philip Brisk, and Douglas Densmore. "Parchmint: A microfluidics benchmark suite." In 2018 IEEE International Symposium on Workload Characterization (IISWC), pp. 78-79. IEEE, 2018.

Madsen, Curtis, Prashant Vaidyanathan, Sadra Sadraddini, Cristian-Ioan Vasile, Nicholas A. DeLateur, Ron Weiss, Douglas Densmore, and Calin Belta. "Metrics for signal temporal logic formulae." In 2018 IEEE Conference on Decision and Control (CDC), pp. 1542-1547. IEEE, 2018.

Lashkaripour, Ali, Masoud Goharimanesh, Ali Abouei Mehrizi, and Douglas Densmore. "An adaptive neural-fuzzy approach for microfluidic droplet size prediction." Microelectronics Journal 78 (2018): 73-80.

A. Lashkaripour, C. Rodriguez, and D. Douglas, “A reverse predictive model towards design automation of microfluidic droplet generators.” 2018.

Misirli, Göksel, Tramy Nguyen, James Alastair McLaughlin, Prashant Vaidyanathan, Timothy S. Jones, Douglas Densmore, Chris Myers, and Anil Wipat. "A computational workflow for the automated generation of models of genetic designs." ACS synthetic biology 8, no. 7 (2018): 1548-1559.

Ortiz, Luis, Ali Lashkaripour, and Douglas Densmore. "Automating functional enzyme screening & characterization." International Workshop on Bio-Design Automation (IWBDA), (2018).

Lashkaripour, Ali, Ryan Silva, and Douglas Densmore. "Desktop micromilled microfluidics." Microfluidics and Nanofluidics 22, no. 3 (2018): 1-13.

Wagner, Tyler E., Jacob R. Becraft, Katie Bodner, Brian Teague, Xin Zhang, Amanda Woo, Ely Porter et al. "Small-molecule-based regulation of RNA-delivered circuits in mammalian cells." Nature chemical biology 14, no. 11 (2018): 1043-1050.

2017

Sanka, Radhakrishna, Joshua Lippai, and Douglas Densmore. “mLSI Design with MINT.” International Workshop on Bio-Design Automation. (2017)

Lashkaripour, Ali, Radhakrishna Sanka, Joshua Lippai and Douglas Densmore. “Design Automation Based On Fluid Dynamics” International Workshop on Bio-Design Automation. (2017)

Lippai, Joshua, Radhakrishna Sanka, Ali Lashkaripour and Douglas Densmore. “Function-driven, graphical design tool for microfluidic chips: 3duf.” International Workshop on Bio-Design Automation (IWBDA). (2017)

Wagner, Tyler. "Engineering a regulatory framework for synthetic self-amplifying RNA circuits." PhD Thesis. (2017)

Silva, Ryan. "MakerFluidics: low cost microfluidics for synthetic biology." PhD Thesis. (2017)

Woodruff, Lauren, Thomas E. Gorochowski, Nicholas Roehner, Tarjei S. Mikkelsen, Douglas Densmore, D. Benjamin Gordon, Rob Nicol, and Christopher A. Voigt. “Registry in a Tube: Multiplexed Pools of Retrievable Parts for Genetic Design Space Exploration.” Nucleic Acids Research 45. no. 3 (2017): 1553-1565

Appleton, Evan, Douglas Densmore, Curtis Madsen, and Nicholas Roehner. “Needs and opportunities in bio-design automation: four areas for focus.” Current Opinion in Chemical Biology 40. (2017): 111-118.

Appleton, Evan, Curtis Madsen, Nicholas Roehner, and Douglas Densmore. “Design Automation in Synthetic Biology.” Cold Spring Harbor Perspectives in Biology 9. no. 4 (2017)

Carr, Swati, Jacob Beal, and Douglas Densmore. “Reducing DNA Context Dependence in Bacterial Promoters.” PLoS One 12. no. 4 (2017)

Bhatia, Swapnil, Michael J. Smanski, Christopher A. Voigt, and Douglas Densmore. “Genetic Design Via Combinatorial Constraint Specification.” ACS Synthetic Biology 6. no. 11 (2017): 2130–2135.

Silva, Ryan, P. Dow, Ryan Dubay, C. Lissandrello, Jason Holder, Douglas Densmore, and Jason Fiering. “Rapid prototyping and parametric optimization of plastic acoustofluidic devices for blood bacteria separation.” Biomedical Microdevices 19. no. 3 (2017).

Subacius, Kestutis, Priya Kapadia, Shane McCormack, Anish Asthana, Radhakrishna Sanka, and Douglas Densmore. “Fluigi Cloud – A Cloud CAD Platform for Microfluidics.” International Workshop on Bio-Design Automation. (2017)

2016

Iverson, Sonya V., Traci L. Haddock, Jacob Beal, and Douglas M. Densmore. "CIDAR MoClo: improved MoClo assembly standard and new E. coli part library enable rapid combinatorial design for synthetic and traditional biology." ACS synthetic biology 5, no. 1 (2016): 99-103.

Lashkaripour, Ali, Luis Ortiz, Marilene Pavan, Radhakrishna Sanka, and Douglas Densmore. “Cell-Free Transcription and Translation Reactions with Droplet Microfluidics.” Engineering Biology Research Consortium (EBRC). (2016).

Nielsen, Alec AK, Bryan S. Der, Jonghyeon Shin, Prashant Vaidyanathan, Vanya Paralanov, Elizabeth A. Strychalski, David Ross, Douglas Densmore, and Christopher A. Voigt. "Genetic circuit design automation." Science 352, no. 6281 (2016).

Appleton, Evan M. A Design-Build-Test-Learn Tool for Synthetic Biology. PhD Thesis, Boston University. (2016).

Sanka, Radhakrishna, Haiyao Huang, Ryan Silva, and Douglas Densmore. “MINT – Microfluidic Netlist.”International Workshop on Bio-Design Automation (IWBDA). (2016).

Iverson, Sonya V. Improved Modular Multipart DNA Assembly, Development of a DNA Part Toolkit for E. Coli, and Applications in Traditional Biology and Bioelectronic Systems. PhD Thesis, Boston University. (2016).

Bhatia, Swapnil, Craig LaBoda, Vanessa Yanez, Traci Haddock-Angelli, and Douglas Densmore. "Permutation machines." ACS synthetic biology 5, no. 8 (2016): 827-834.

Quintin, Michael, Natalie J. Ma, Samir Ahmed, Swapnil Bhatia, Aaron Lewis, Farren J. Isaacs, and Douglas Densmore. "Merlin: computer-aided oligonucleotide design for large scale genome engineering with MAGE." ACS synthetic biology 5, no. 6 (2016): 452-458.

Silva, Ryan, Swapnil Bhatia, and Douglas Densmore. "A reconfigurable continuous-flow fluidic routing fabric using a modular, scalable primitive." Lab on a Chip 16, no. 14 (2016): 2730-2741.

Carr, Swati B. Reliable Gene Expression and Assembly for Synthetic Biological Devices in E. Coli through Customized Promoter Insulator Elements and Automated DNA Assembly. PhD Thesis, Boston University. (2016).

Roehner, Nicholas, Eric M. Young, Christopher A. Voigt, D. Benjamin Gordon, and Douglas Densmore. "Double dutch: a tool for designing combinatorial libraries of biological systems." ACS synthetic biology 5, no. 6 (2016): 507-517.

Roehner, Nicholas, Jacob Beal, Kevin Clancy, Bryan Bartley, Goksel Misirli, Raik Grunberg, Ernst Oberortner et al. "Sharing structure and function in biological design with SBOL 2.0." ACS synthetic biology 5, no. 6 (2016): 498-506.

2015

Haiyao Huang, “Fluigi: An end-to-end Software Workflow for Microfluidic Design,” PhD Thesis, Boston University, 2015.

Vaidyanathan, Prashant, Bryan S. Der, Swapnil Bhatia, Nicholas Roehner, Ryan Silva, Christopher A. Voigt, and Douglas Densmore. "A framework for genetic logic synthesis." Proceedings of the IEEE 103, no. 11 (2015): 2196-2207.

Haddock, Traci, Douglas Densmore, Evan Appleton, Swati Carr, Sonya Iverson, Monique De Freitas, Shawn Jin et al. BBF RFC 94: Type IIS Assembly for Bacterial Transcriptional Units: A Standardized Assembly Method for Building Bacterial Transcriptional Units Using the Type IIS Restriction Enzymes BsaI and BbsI. 2015. BioBricks Foundation Request for Comments , August, 2015.

Appleton, Evan, Oberortner, Ernst, Vaidyanathan, Prashant, Chapasko, Zachary, Pacheco, Alan, Agarwal, Yash Roehner, Nicholas, Haddock, Traci, and Densmore, Douglas. Phoenix: An automated design-build. International Workshop on Bio-Design Automation (IWBDA). (2015).

Kathleen Lewis, Allison Durkan, Inna Turshudzhyan, Kara Le Fort, Nicholas Roehner, Prashant Vaidyanathan, and Douglas Densmore, Phagebook, poster presented at the International Workshop on Bio-Design Automation (IWBDA) , August, 2015.

Nicholas Roehner and Douglas Densmore, Double Dutch: A Tool for Designing Libraries of Variant Metabolic Pathways, talk presented at the International Workshop on Bio-Design Automation (IWBDA) , August, 2015.

Sonya Iverson, Jacob Beal, Traci Haddock, and Douglas Densmore, E. coli MoClo assembly & part library: Applications in traditional biological research, poster presented at the Systems and Synthetic Biology Summer School in Italy , July, 2015.

Aaron Heuckroth, Haiyao Huang, Ryan Silva, Sonya Iverson, Traci Haddock, Alan Pacheco, and Douglas Densmore, Accessible Microfluidic Mold Fabrication Using 3D Printing, poster presented at the Synberc 2015 Spring Retreat, Berkeley CA , March, 2015.

Nicholas Roehner and Douglas Densmore, Double Dutch: A Tool for Designing Libraries of Variant Metabolic Pathways, poster presented at the SynBERC 2014 Spring Retreat , March, 2015.

2014

Shaer, Orit, Consuelo Valdes, Sirui Liu, Kara Lu, Kimberly Chang, Wendy Xu, Traci L. Haddock, Swapnil Bhatia, Douglas Densmore, and Robert Kincaid. "Designing reality-based interfaces for experiential bio-design." Personal and Ubiquitous Computing 18, no. 6 (2014): 1515-1532.

Beal, Jacob, Tyler E. Wagner, Tasuku Kitada, Odisse Azizgolshani, Jordan Moberg Parker, Douglas Densmore, and Ron Weiss. "Model-driven engineering of gene expression from RNA replicons." ACS synthetic biology 4, no. 1 (2015): 48-56.

Beal, Jacob, Tyler E. Wagner, and Tasuku Kitada. "Precision Design of Expression from RNA Replicons." (2014)

Gol, Ebru Aydin, Douglas Densmore, and Calin Belta. "Data-driven verification of synthetic gene networks." In 52nd IEEE Conference on Decision and Control, pp. 4074-4079. IEEE, (2013).

Appleton, Evan, Jenhan Tao, Traci Haddock, and Douglas Densmore. "Interactive assembly algorithms for molecular cloning." Nature methods 11, no. 6 (2014): 657-662.

Galdzicki, Michal, Kevin P. Clancy, Ernst Oberortner, Matthew Pocock, Jacqueline Y. Quinn, Cesar A. Rodriguez, Nicholas Roehner et al. "The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology." Nature biotechnology 32, no. 6 (2014): 545-550.

Huang, Haiyao, and Douglas Densmore. "Fluigi: Microfluidic device synthesis for synthetic biology." ACM Journal on Emerging Technologies in Computing Systems (JETC) 11, no. 3 (2014): 1-19.

Oberortner, Ernst, and Douglas Densmore. "Web-based software tool for constraint-based design specification of synthetic biological systems." ACS synthetic biology 4, no. 6 (2015): 757-760.

Densmore, Douglas M., and Swapnil Bhatia. "Bio-design automation: software+ biology+ robots." Trends in biotechnology 32, no. 3 (2014): 111-113.

Appleton, Evan, Jenhan Tao, F. Carter Wheatley, Devina H. Desai, Thomas M. Lozanoski, Pooja D. Shah, Jake A. Awtry, Shawn S. Jin, Traci L. Haddock, and Douglas M. Densmore. "Owl: Electronic datasheet generator." (2014): 966-968.

J. Beal, T. E. Wagner, T. Kitada, O. Azizgolshani, J. M. Parker, D. Densmore, and R. Weiss, “Model-Driven Engineering of Gene Expression from RNA Replicons,” ACS Synthetic Biology, 2014.

Huang, Haiyao, and Douglas Densmore. "Integration of microfluidics into the synthetic biology design flow." Lab on a Chip 14, no. 18 (2014): 3459-3474.

2013

Traci Haddock, Sonya Iverson, Monique De Freitas, Shawn Jin, and Douglas Densmore. “The Design, Assembly, and Characterization of a New Library of Standardized Modular DNA Parts” 6th International Meeting on Synthetic Biology (SB6.0) (2013).

Pocock, Michal Galdzicki Ernst Oberortner Matthew, Jacqueline Quinn Mandy Wilson, Evan Appleton Bryan Bartley Jacob Beal, Swapnil Bhatia Robert Cox Raik Grünberg, Goksel Misirli Hector Plahar Nicholas Roehner, Larisa Soldotova Guy-Bart Stan, Doug Densmore Chris J. Myers Herbert, and Sauro Anil Wipat. "Recent Advances in the Synthetic Biology Open Language." International Workshop on Bio-Design Automation (IWBDA) (2013).

Huang, Haiyao, Ernst Oberortner, Douglas Densmore, Allan Kuchinsky. “Eugene’s enriched set of features to design synthetic biological devices.” International Workshop on Bio-Design Automation. (2013).

Gol, Ebru Aydin, Douglas Densmore, Calin Belta. “Data-driven verification of synthetic gene networks.” 52nd IEEE Conference on Decision and Control (2013): 4074-4079.

Davare, Abhijit, Douglas Densmore, Liangpeng Guo, Roberto Passerone, Alberto L. Sangiovanni-Vincentelli, Alena Simalatsar, and Qi Zhu. "METROII: A design environment for cyber-physical systems." ACM Transactions on Embedded Computing Systems (TECS) 12, no. 1s (2013): 1-31.

Leguia, Mariana, Jennifer AN 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, no. 1 (2013): 1-16.

Shaer, Orit, Consuelo Valdes, Sirui Liu, Kara Lu, Traci L. Haddock, Swapnil Bhatia, Douglas Densmore, and Robert Kincaid. "Moclo planner: Interactive visualization for modular cloning bio-design." In 2013 IEEE Symposium on Biological Data Visualization (BioVis), pp. 57-64. IEEE, 2013.

O. Shaer, C. Valdes, S. Liu, K. Lu, K. Chang, W. Xu, T. Haddock, S. Bhatia, D. Densmore, and R. Kincaid, “Designing reality-based interfaces for experiential bio-design,” Personal and Ubiquitous Computing, pp. 1-18, 2013.

Bhatia, Swapnil, Douglas Densmore. “Pigeon: a design visualizer for synthetic biology.” ACS Synthetic Biology Vol. 2, no. 6 (2013): 348-350.

M. Galdzicki, E. Oberortner, M. Pocock, J. Quinn, M. Wilson, E. Appleton, B. Bartley, J. Beal, S. Bhatia, R. Cox, R. Grunberg, G. Misirli, H. Plahar, N. Roehner, L. Soldotova, G. Stan, D. Densmore, C. Myers, H. Sauro, and A. Wipat, Recent Advances in the Synthetic Biology Open Language, talk presented at the International Workshop on Bio-Design Automation (IWBDA), London, England , July, 2013.

Carr, Swati, Douglas Densmore. “Compositional Genetic Inverter Circuits for Complex Logic Functions." 6th International Meeting on Synthetic Biology (SB6.0) (2013).

T. Haddock, M. D. Freitas, S. Jin, and D. Densmore, The Design, Assembly, and Characterization of a New Library of Standardized Modular DNA Parts, poster presented at the 6th International Meeting on Synthetic Biology (SB6.0) , July, 2013.

Appleton, Evan, Jenhan Tao, and Douglas Densmore. “Interactive Experimentally Driven Algorithms for Optimized DNA Assembly.” International Workshop on Bio-Design Automation (IWBDA) (2013).

J. Quinn, S. Bhatia, R. S. Cox, C. Rodriguez, L. Soldatova, J. Beal, K. Clancy, and D. Endy, Synthetic Biology Open Language Visual: An Open-Source Graphical Notation for Synthetic Biology, talk presented at the International Workshop on Bio-Design Automation (IWBDA), London, England , July, 2013.

Iverson, Sonia, Traci Haddock, and Douglas Densmore. “Multiplex Modular Assembly and Protein Engineering.” SynBERC Spring Retreat (2013).

Huang, Haiyao, Swapnil Bhatia, Ahmad Khalil, and Douglas Densmore. “Fluigi: a computer aided design framework for combining microfluidics and synthetic biology.” 6th International Meeting on Synthetic Biology (SB6.0) (2013).

2012

Oberortner, Ernst, Douglas Densmore, and J. Christopher Anderson. "An interactive pattern story on designing the architecture of clotho." In Proc. of the 19th Conf. Pattern Languages of Programs, p. 21. 2012.

Chen, Joanna, Douglas Densmore, Timothy S. Ham, Jay D. Keasling, and Nathan J. Hillson. "DeviceEditor visual biological CAD canvas." Journal of biological engineering 6, no. 1 (2012): 1-12.

Oberortner, Ernst, Douglas Densmore, and J. Christopher Anderson. "An interactive pattern story on designing the architecture of clotho." In Proc. of the 19th Conf. Pattern Languages of Programs, p. 21. 2012.

Densmore, Douglas. "Bio-design automation: Nobody said it would be easy." ACS Synthetic Biology. (2012): 296-296.

Yaman, Fusun, Swapnil Bhatia, Aaron Adler, Douglas Densmore, and Jacob Beal. "Automated selection of synthetic biology parts for genetic regulatory networks." ACS synthetic biology 1, no. 8 (2012): 332-344.

Yordanov, Boyan, Evan Appleton, Rishi Ganguly, Ebru Aydin Gol, Swati Banerjee Carr, Swapnil Bhatia, Traci Haddock, Calin Belta, and Douglas Densmore. "Experimentally driven verification of synthetic biological circuits." In 2012 Design, Automation & Test in Europe Conference & Exhibition (DATE), pp. 236-241. IEEE, 2012.

Beal, Jacob, Ron Weiss, Douglas Densmore, Aaron Adler, Evan Appleton, Jonathan Babb, Swapnil Bhatia et al. "An end-to-end workflow for engineering of biological networks from high-level specifications." ACS Synthetic Biology 1, no. 8 (2012): 317-331.

Yaman, Fusun, Swapnil Bhatia, Aaron Adler, Douglas Densmore, and Jacob Beal. "Automated selection of synthetic biology parts for genetic regulatory networks." ACS synthetic biology 1, no. 8 (2012): 332-344.

Huang, Haiyao, Ernst Oberortner, Douglas Densmore, and Allan Kuchinsky. "Eugene’s enriched set of features to design synthetic biological devices." Proc. IWBDA (2013).

Bhatia, Swapnil, Alex Nielsen, Michael Smanski, Douglas Densmore, and Christopher Voigt, “How to build an n-input circuit library.” SynBERC Spring Retreat. (2012).

Bhatia, Evan Appleton, Viktor Vasilev, Swapnil Bhatia, and Traci Haddock, Douglas Densmore. "Testing-Optimized DNA Assembly Algorithms." International Workshop on Bio-Design Automation (IWBDA). 2012.

Bhatia, Swapnil, Alex Nielsen, Michael Smanski, Douglas Densmore, and Christopher Voigt, “How to build an n-input circuit library.” SynBERC Spring Retreat. (2012).

2011

Chandran, Deepak, Frank T. Bergmann, Herbert M. Sauro, and Douglas Densmore. "Computer-aided design for synthetic biology." In Design and analysis of biomolecular circuits, pp. 203-224. Springer, New York, NY, 2011.

Beal, Jacob, Andrew Phillips, Douglas Densmore, and Yizhi Cai. "High-level programming languages for biomolecular systems." In Design and analysis of biomolecular circuits, pp. 225-252. Springer, New York, NY, 2011.

Yaman, Fusun, Swapnil Bhatia, Aaron Adler, Douglas Densmore, Jacob Beal, Ron Weiss, and Noah Davidsohn. "Toward automated selection of parts for genetic regulatory networks." In 3rd International Workshop on Bio-Design Automation. 2011.

Densmore, Douglas, Mark Horowitz, Smita Krishnaswamy, Xiling Shen, Adam Arkin, Erik Winfree, and Chris Voigt. "Joint DAC/IWBDA special session design and synthesis of biological circuits." In Proceedings of the 48th Design Automation Conference, pp. 114-115. 2011.

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, talks presented at the International Workshop on Bio-Design Automation (IWBDA), San Diego, CA and at the Annual Conference of the Institute of Biological Engineering, Atlanta, GA , 2011.

Bilitchenko, Lesia, Adam Liu, Sherine Cheung, Emma Weeding, Bing Xia, Mariana Leguia, J. Christopher Anderson, and Douglas Densmore. "Eugene–a domain specific language for specifying and constraining synthetic biological parts, devices, and systems." PloS one 6, no. 4 (2011): e18882.

Koeppl, Heinz, Douglas Densmore, Gianluca Setti, and Mario di Bernardo, eds. Design and analysis of biomolecular circuits: engineering approaches to systems and synthetic biology. Springer Science & Business Media, 2011.

Xia, Bing, Swapnil Bhatia, Ben Bubenheim, Maisam Dadgar, Douglas Densmore, and J. Christopher Anderson. "Developer's and User's Guide to Clotho v2. 0: A Software Platform for the Creation of Synthetic Biological Systems." Methods in enzymology 498 (2011): 97-135.

Bilitchenko, Lesia, Adam Liu, and Douglas Densmore. "The Eugene language for synthetic biology." Methods in enzymology 498 (2011): 153-172.

Leguia, Mariana, Jennifer Brophy, Douglas Densmore, and J. Christopher Anderson. "Automated assembly of standard biological parts." Methods in enzymology 498 (2011): 363-397.

Peccoud, Jean, 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 29, no. 1 (2011): 22-22.

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 presented at the International Workshop on Bio-Design Automation (IWBDA) , June, 2011.

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, poster presented at the 5th International Meeting on Synthetic Biology (SB5.0), Palo Alto, CA , June, 2011.

T. Haddock, S. Bhatia, V. Vasilev, C. Liu, A. Adler, J. Beal, J. Babb, R. Weiss, and D. Densmore, A Novel Automated Assembly Approach for Use in Synthetic Circuit Construction, poster presented at the 5th International Meeting on Synthetic Biology (SB5.0), Palo Alto, CA , June, 2011.

Vasilev, Viktor, Chenkai Liu, Traci Haddock, Swapnil Bhatia, Aaron Adler, Fusun Yaman, Jacob Beal, Jonathan Babb, Ron Weiss, and Douglas Densmore. "A software stack for specification and robotic execution of protocols for synthetic biological engineering." In 3rd international workshop on bio-design automation. 2011.

Ghamari, Roza, B. Stanton, T. Haddock, S. Bhatia, K. Clancy, T. Peterson, C. Voigt, and D. Densmore. "Applying hardware description languages to genetic circuit design." PhD diss., Boston University, 2011.

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 presented at Cold Springs Harbor Asia Series 2011 Symposium: Design & Synthesis of Biological Systems , November, 2011.

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 presented at the Cold Springs Harbor Asia Series 2011 Symposium: Design & Synthesis of Biological Systems , November, 2011.

V. Vasilev, C. Liu, J. Fernandes, E. Orozco, 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, poster presented at the SynBERC Fall Retreat, Harvard University , September, 2011.

R. Ganguly, R. Ghamari, E. Appleton, S. P. Bhatia, B. Yordanov, E. AydinGol, C. Belta, and D. Densmore, Computational Design and Verification of Genetic Regulatory Circuits, poster presented at the SynBERC Fall Retreat, Harvard University , September, 2011.

2010

Densmore, Douglas, Joshua T. Kittleson, Lesia Bilitchenko, Adam Liu, and J. Christopher Anderson. "Rule based constraints for the construction of genetic devices." In Proceedings of 2010 IEEE International Symposium on Circuits and Systems, pp. 557-560. IEEE, 2010.

Densmore, Douglas. “Method and apparatus for precharacterizing systems for use in system level design of integrated circuits,” , iss. 7788625, 2010.

Densmore, Douglas, Timothy H-C. Hsiau, Joshua T. Kittleson, Will DeLoache, Christopher Batten, and J. Christopher Anderson. "Algorithms for automated DNA assembly." Nucleic acids research 38, no. 8 (2010): 2607-2616.

2009

Balarin, Felice, Abhijit Davare, Massimiliano D’Angelo, Douglas Densmore, Trevor Meyerowitz, Roberto Passerone, Alessandro Pinto et al. "Platform-based design and frameworks: METROPOLIS and METRO II." Model-Based Design for Embedded Systems (2009): 259.

Densmore, Douglas, Alena Simalatsar, Abhijit Davare, Roberto Passerone, and Alberto Sangiovanni-Vincentelli. "UMTS MPSoC design evaluation using a system level design framework." In 2009 Design, Automation & Test in Europe Conference & Exhibition, pp. 478-483. IEEE, 2009.

Densmore, Douglas, Anne Van Devender, Matthew Johnson, and Nade Sritanyaratana. "A platform-based design environment for synthetic biological systems." In The Fifth Richard Tapia Celebration of Diversity in Computing Conference: Intellect, Initiatives, Insight, and Innovations, pp. 24-29. 2009.

Densmore, Douglas, and J. Christopher Anderson. "Combinational logic design in synthetic biology." In 2009 IEEE International Symposium on Circuits and Systems, pp. 301-304. IEEE, 2009.

2008

Vincentelli, A. Sangiovanni, Douglas Densmore, Jason Cong, and Radu Marculescu. "System-Level Synthesis-Functions, Architectures, and Communications." In ASP DAC. 2008.

Densmore, Douglas, A Platform-Based Design Methodology for the Electronic System Level: Frameworks, Designs Flows, and Case Studies, VDM Verlag, 2008.

Densmore, Douglas, Trevor Meyerowitz, Abhijit Davare, Qi Zhu, and Guang Yang. "Metro II execution semantics for mapping." Technical Report UCB/EECS-2008-16, University of California (2008).

Simalatsar, Alena, Roberto Passerone, and Douglas Densmore. "A methodology for architecture exploration and performance analysis using system level design languages and rapid architecture profiling." In 2008 International Symposium on Industrial Embedded Systems, pp. 95-102. IEEE, 2008.

2007

Densmore, Douglas Michael. "A design flow for the development, characterization, and refinement of system level architectural services." PhD diss., Electrical Engineering and Computer Sciences)--University of California, Berkeley, 2007.

Davare, Abhijit, Douglas Densmore, Trevor Meyerowitz, Alessandro Pinto, Alberto Sangiovanni-Vincentelli, Guang Yang, Haibo Zeng, and Qi Zhu. "A next-generation design framework for platform-based design." In Conference on using hardware design and verification languages (DVCon), vol. 152. 2007.

2006

Davare, Abhijit, Jike Chong, Qi Zhu, Douglas Michael Densmore, and Alberto L. Sangiovanni-Vincentelli. "Classification, customization, and characterization: Using milp for task allocation and scheduling." Systems Research (2006).

Densmore, Douglas, Adam Donlin, and Alberto Sangiovanni-Vincentelli. "Programmable Platform Characterization for System Level Performance Analysis." In Platform Based Design at the Electronic System Level, pp. 13-30. Springer, Dordrecht, 2006.

Densmore, Douglas, and Roberto Passerone. "A platform-based taxonomy for ESL design." IEEE Design & Test of Computers 23, no. 5 (2006): 359-374.

Densmore, Douglas, Alberto Sangiovanni-Vincentelli, and Adam Donlin, “Leveraging Programmability in Electronic System Level Designs,” Xcell Journal, vol. 56, pp. 29-31, 2006.

Densmore, Douglas, Adam Donlin, and Alberto Sangiovanni-Vincentelli. "FPGA architecture characterization for system level performance analysis." In Proceedings of the Design Automation & Test in Europe Conference, vol. 1, pp. 1-6. IEEE, 2006.

Kakita, Shinjiro, Yosinori Watanabe, Douglas Densmore, Abhijit Davare, and Alberto Sangiovanni-Vincentelli. "Functional model exploration for multimedia applications via algebraic operators." In Sixth International Conference on Application of Concurrency to System Design (ACSD'06), pp. 229-238. IEEE, 2006.

2004

Zeng, Haibo, Vishal Shah, Douglas Densmore, and Abhijit Davare. Simple Case Study in Metropolis. Vol. 4. Technical Memorandum UCB/ERL.

Densmore, Douglas. "Platform Based Reconfigurable Architecture Exploration via Boolean Constraints." PhD diss., Department of Electrical Engineering and Computer Sciences, University of California at Berkeley, 2004.

Densmore, Douglas. Metropolis architecture refinement styles and methodology. Electronics Research Laboratory, College of Engineering, University of California, 2004.

Densmore, Douglas. Formal refinement verification in metropolis. Electronics Research Laboratory, College of Engineering, University of California, 2004.

Densmore, Douglas, Sanjay Rekhi, and Alberto Sangiovanni-Vincentelli. "Microarchitecture development via metropolis successive platform refinement." In Proceedings Design, Automation and Test in Europe Conference and Exhibition, vol. 1, pp. 346-351. IEEE, 2004.