Featured Publications

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

arrow&v

2020

Lashkaripour, A., McIntyre, D. and Densmore, D., 2020. Efficient large-scale microfluidic design-space exploration: from data to model to data.

McIntyre, D., Lashkaripour, A. and Densmore, D., 2020. Active learning for efficient microfluidic design automation.

Chen, Y., Zhang, S., Young, E. M., Jones, T. S., Densmore, D., & Voigt, C. A. (2020). Genetic circuit design automation for yeast. Nature Microbiology, 1-12.

Timmons, Joshua J., and Doug Densmore. “Repository-Based Plasmid Design.” PLOS ONE 15, no. 1 (January 9, 2020): e0223935.

2019

Lashkaripour, Ali, Christopher Rodriguez, Noushin Mehdipour, David McIntyre, and Douglas Densmore. “Modular Microfluidic Design Automation Using Machine Learning,” July 10, 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 (March 13, 2019): 1041–53

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 (July 2019): 1356–68.

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: Invited Paper.” In 2019 IEEE/ACM International Conference on Computer-Aided Design (ICCAD), 1–8, 2019. https://doi.org/10.1109/ICCAD45719.2019.8942171.

Sanka, Radhakrishna, Joshua Lippai, Dinithi Samarasekera, Sarah Nemsick, and Douglas Densmore. “3DμF - Interactive Design Environment for Continuous Flow Microfluidic Devices.” Scientific Reports 9, no. 1 (December 2019). https://doi.org/10.1038/s41598-019-45623-z.

2018

A. Lashkaripour, M. Goharimanesh, A. A. Mehrizi, and D. Densmore, “An adaptive neural-fuzzy approach for microfluidic droplet size prediction,” Microelectronics Journal, vol. 78, pp. 73-80, 2018.

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

G. Misirli, T. Nguyen, J. A. McLaughlin, P. Vaidyanathan, T. Jones, D. Densmore, C. J. Myers, and A. Wipat, “A computational workflow for the automated generation of models of genetic designs,” ACS synthetic biology, 2018.

L. Ortiz, A. Lashkaripour, and D. Densmore, Automating Functional Enzyme Screening & Characterization, Poster presented at the International Workshop on Bio-Design Automation (IWBDA) , August, 2018.

A. Lashkaripour, R. Silva, and D. Densmore, “Desktop micromilled microfluidics,” Microfluidics and Nanofluidics, vol. 22, iss. 3, p. 31, 2018.

T. E. Wagner, J. R. Becraft, K. Bodner, B. Teague, X. Zhang, A. Woo, E. Porter, B. Alburquerque, B. Dobosh, O. Andries, N. N. Sanders, J. Beal, D. Densmore, T. Kitada, and R. Weiss, “Small-molecule-based regulation of RNA-delivered circuits in mammalian cells,” Nature Chemical Biology, vol. 14, iss. 11, pp. 1043-1050, 2018.

2017

L. Woodruff, T. E. Gorochowski, N. Roehner, T. S. Mikkelsen, D. Densmore, D. Gordon, R. Nicol, and C. A. Voigt, “Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration,” Nucleic Acids Research, vol. 45, iss. 3, p. 1553, 2017.

E. Appleton, D. Densmore, C. Madsen, and N. Roehner, “Needs and opportunities in bio-design automation: four areas for focus,” Current Opinion in Chemical Biology, vol. 40, pp. 111-118, 2017.

E. Appleton, C. Madsen, N. Roehner, and D. Densmore, “Design Automation in Synthetic Biology,” Cold Spring Harbor Perspectives in Biology, 2017.

S. B. Carr, J. Beal, and D. M. Densmore, “Reducing DNA context dependence in bacterial promoters,” PLOS ONE, vol. 12, iss. 4, p. e0176013, 2017.

S. Bhatia, M. Smanski, C. A. Voigt, and D. Densmore, “Genetic design via combinatorial constraint specification,” ACS Synthetic Biology, iss. ja, p. null, 2017.

R. Silva, P. Dow, R. Dubay, C. Lissandrello, J. Holder, D. Densmore, and J. Fiering, “Rapid prototyping and parametric optimization of plastic acoustofluidic devices for blood–bacteria separation,” Biomedical Microdevices, vol. 19, iss. 3, p. 70, 2017.

K. Subacius, P. Kapadia, S. McCormack, A. Asthana, R. Sanka, and D. Densmore, Fluigi Cloud – A Cloud CAD Platform for Microfluidics, Poster presented at the 9th International Workshop on Bio-Design Automation (IWBDA) , Aug, 2017.

C. Madsen, E. Appleton, P. Vaidyanathan, R. Mardian, C. Vasile, K. Elkind, A. Bennett, F. Cao, M. Nagata, C. Belta, and D. Densmore, Phoenix: A Systems Engineering Approach to Genetic Circuit Synthesis, Poster presented at the 9th International Workshop on Bio-Design Automation (IWBDA) , August, 2017.

P. Vaidyanathan, R. Ivison, G. Bombara, N. A. DeLateur, R. Weiss, D. Densmore, and C. Belta, “Grid-based temporal logic inference,” in 2017 IEEE 56th Annual Conference on Decision and Control (CDC), 2017, pp. 5354-5359.

L. Ortiz, M. Pavan, L. McCarthy, J. Timmons, and D. Densmore, Automated Robotic Liquid Handling Assembly of Modular DNA Devices, Journal of Visual Experiments , December, 2017.

C. Rodriguez, A. Lashkaripour, and D. Densmore, u-DROP and DAFD: Tools for Microfluidic Droplet Generator Design, Poster presented at Annual Biomedical Research Conference for Minority Students (ABRCMS) , Nov, 2017.

2016

A. Lashkaripour, L. Ortiz, M. Pavan, R. Sanka, and D. Densmore, Cell-Free Transcription and Translation Reactions with Droplet Microfluidics, talk presented at the Engineering Biology Research Consortium (EBRC) , 2016.

A. A. K. Nielsen, B. S. Der, J. Shin, P. Vaidyanathan, V. Paralanov, E. A. Strychalski, D. Ross, D. Densmore, and C. A. Voigt, “Genetic circuit design automation,” Science, vol. 352, iss. 6281, 2016.

E. M. Appleton, “A design-build-test-learn tool for synthetic biology,” PhD Thesis, 2016.

R. Sanka, H. Huang, R. Silva, and D. Densmore, MINT – Microfluidic Netlist, poster presented at IWBDA 2016 , 2016.

S. V. Iverson, “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.

S. Bhatia, C. LaBoda, V. Yanez, T. Haddock-Angelli, and D. Densmore, “Permutation Machines,” ACS Synthetic Biology, p. null, 2016.

M. J. Quintin, N. J. Ma, S. Ahmed, S. Bhatia, A. Lewis, F. J. Isaacs, and D. Densmore, “Merlin: Computer-Aided Oligonucleotide Design for Large Scale Genome Engineering with MAGE,” ACS Synthetic Biology, iss. ja, p. null, 2016

R. Silva, S. Bhatia, and D. Densmore, “A reconfigurable continuous-flow fluidic routing fabric using a modular, scalable primitive,” Lab Chip, vol. 16, pp. 2730-2741, 2016.

S. B. Carr, “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.

N. Roehner, E. M. Young, C. A. Voigt, B. D. Gordon, and D. Densmore, “Double Dutch: A Tool for Designing Combinatorial Libraries of Biological Systems,” ACS Synthetic Biology, 2016.

N. Roehner, J. Beal, K. Clancy, B. Bartley, G. Misirli, R. Gruenberg, E. Oberortner, M. Pocock, M. Bissell, C. Madsen, T. Nguyen, M. Zhang, Z. Zhang, Z. Zundel, D. Densmore, J. Gennari, A. Wipat, H. Sauro, and C. J. Myers, “Sharing Structure and Function in Biological Design with SBOL 2.0,” ACS Synthetic Biology, 2016.

C. Madsen, P. Vaidyanathan, C. Vasile, R. Ivison, J. Wang, C. Belta, and D. Densmore, Utilizing Signal Temporal Logic to Characterize and Compose Modules in Synthetic Biology, talk presented at the International Workshop on Bio-Design Automation (IWBDA) , August, 2016.

2015

S. Iverson, T. L. Haddock, J. Beal, and D. Densmore, “CIDAR MoClo: Improved MoClo Assembly Standard and New E. coli Part Library Enables Rapid Combinatorial Design for Synthetic and Traditional Biology,” ACS Synthetic Biology, iss. ja, p. null, 2015.

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

P. Vaidyanathan, B. S. Der, S. Bhatia, N. Roehner, R. Silva, C. A. Voigt, and D. Densmore, “A Framework for Genetic Logic Synthesis,” Proceedings of the IEEE, vol. 103, iss. 11, pp. 2196-2207, 2015.

T. Haddock, D. Densmore, E. Appleton, S. Carr, S. Iverson, and M. De Freitas, 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, BioBricks Foundation Request for Comments , August, 2015.

E. Appleton, E. Oberortner, P. Vaidyanathan, Z. Chapasko, Y. Pacheco Alan andAgarwal, N. Roehner, T. Haddock, and D. Densmore, Phoenix: An automated design-build, poster presented at the International Workshop on Bio-Design Automation (IWBDA) , August, 2015.

K. Lewis, A. Durkan, Turshudzhyan, K. Le Fort, N. Roehner, P. Vaidyanathan, and D. Densmore, Phagebook, poster presented at the International Workshop on Bio-Design Automation (IWBDA) , August, 2015.

N. Roehner and D. 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.

S. Iverson, J. Beal, T. Haddock, and D. 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.

A. Heuckroth, C. Huang, R. Silva, S. Iverson, T. Haddock, A. Pacheco, and D. Densmore, Accessible Microfluidic Mold Fabrication Using 3D Printing, poster presented at the Synberc 2015 Spring Retreat, Berkeley CA , March, 2015.

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

C. Belta, D. Densmore, V. Kumar, and R. Weiss, CPS: Frontier: Collaborative Research: bioCPS for Engineering Living Cells, poster presented at the NSF CPS PI Meeting 2015 , November, 2015.

E. Appleton, P. Vaidyanathan, A. Pacheco, I. Haghighi, C. Vasile, C. Madsen, N. Roehner, Y. Agarwal, Z. Chapasko, C. Belta, and D. Densmore, Phoenix: A Design-Build-Test-Learn Tool, talk presented at the Synberc 2015 Fall Retreat , September, 2015.

2014

E. Appleton, J. Tao, T. Haddock, and D. Densmore, “Interactive assembly algorithms for molecular cloning,” Nature Methods, 2014.

M. Galdzicki, K. P. Clancy, E. Oberortner, M. Pocock, J. Y. Quinn, C. A. Rodriguez, N. Roehner, M. L. Wilson, L. Adam, C. J. Anderson, B. A. Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. Grunberg, J. Hallinan, N. J. Hillson, J. D. Johnson, A. Kuchinsky, M. Lux, G. Misirli, J. Peccoud, H. A. Plahar, E. Sirin, G. Stan, A. Villalobos, A. Wipat, J. H. Gennari, C. J. Myers, and H. M. Sauro, “The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology,” Nature Biotechnology, vol. 32, iss. 6, pp. 545-550, 2014.

H. Huang and D. Densmore, “Fluigi: Microfluidic Device Synthesis for Synthetic Biology,” J. Emerg. Technol. Comput. Syst. Special Issue on Synthetic Biology, vol. 11, iss. 3, p. 26:1–26:19, 2014.

E. Oberortner and D. Densmore, “Web-Based Software Tool for Constraint-Based Design Specification of Synthetic Biological Systems,” ACS Synthetic Biology, p. null, 2014.

D. M. Densmore and S. Bhatia, “Bio-design automation: software + biology + robots,” Trends in Biotechnology, vol. 32, iss. 3, pp. 111-113, 2014.

E. Appleton, J. Tao, C. F. Wheatley, D. H. Desai, T. M. Lozanoski, P. D. Shah, J. A. Awtry, S. S. Jin, T. L. Haddock, and D. M. Densmore, “Owl: Electronic Datasheet Generator,” ACS Synthetic Biology, vol. 3, iss. 12, pp. 966-968, 2014.

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.

H. Huang and D. Densmore, “Integration of microfluidics into the synthetic biology design flow,” Lab on a Chip, vol. 14, iss. 18, pp. 3459-3474, 2014.

K. A. Oye, K. Esvelt, E. Appleton, F. Catteruccia, G. Church, T. Kuiken, S. B. Lightfoot, J. McNamara, A. Smidler, and J. P. Collins, “Regulating gene drives,” Science, vol. 345, iss. 6197, pp. 626-628, 2014.

M. J. Smanski, S. Bhatia, D. Zhao, Y. Park, L. B A Woodruff, G. Giannoukos, D. Ciulla, M. Busby, J. Calderon, R. Nicol, B. D. Gordon, D. Densmore, and C. A. Voigt, “Functional optimization of gene clusters by combinatorial design and assembly,” Nat Biotech, vol. advance online publication, 2014.

J. McNamara, S. Lightfoot, K. Drinkwater, E. Appleton, and K. Oye, “Designing safety policies to meet evolving needs: iGEM as a testbed for proactive and adaptive risk management.,” ACS Synthetic Biology, in press., 2014.

S. Paige, S. Iverson, A. Heuckroth, S. Carr, T. Haddock, and D. Densmore, The Boston University Center of Synthetic Biology (CoSBi) ICE Repository, poster presented at the Internaional Workshop on Bio-Design Automation (IWBDA) , June, 2014.

2013

E. A. Gol, D. Densmore, and C. Belta, “Data-driven Verification of Synthetic Gene Networks,” in 52nd IEEE Conference on Decision and Control (CDC), Firenze, Italy, 2013.

A. Davare, D. Densmore, L. Guo, R. Passerone, A. L. Sangiovanni-Vincentelli, A. Simalatsar, and Q. Zhu, “MetroII: A design environment for cyber-physical systems,” ACM Trans. Embed. Comput. Syst., vol. 12, iss. 1, p. 49:1–49:31, 2013.

M. Leguia, J. A. Brophy, D. Densmore, A. Asante, and J. C. Anderson, “2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts,” J Biol Eng, vol. 7, iss. 1, p. 2, 2013.

O. Shaer, C. Valdes, S. Liu, K. Lu, T. Haddock, S. Bhatia, D. Densmore, and R. Kincaid, “MoClo Planner: Interactive Visualization for Modular Cloning Bio-Design,” in IEEE Symposium on Biological Data Visualization (BioVis), 2013, pp. 57-64.

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.

S. Bhatia and D. Densmore, “Pigeon: A Design Visualizer for Synthetic Biology,” ACS Synth Biol, vol. 2, iss. 6, pp. 348-350, 2013.

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.

S. B. Carr and D. Densmore, Compositional Genetic Inverter Circuits for Complex Logic Functions" Abstract for SB 6.0 (accepted), poster presented at the 6th International Meeting on Synthetic Biology (SB6.0), London, England , July, 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.

E. Appleton, J. Tao, and D. Densmore, Interactive Experimentally Driven Algorithms for Optimized DNA Assembly, talk presented at the International Workshop on Bio-Design Automation (IWBDA), London, England London, England: , July, 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.

S. Iverson, T. Haddock, and D. Densmore, Development of a Multiplex Modular Cloning Assembly System, poster presented at the 6th International Meeting on Synthetic Biology (SB6.0) , July, 2013.

H. Huang, S. Bhatia, A. Khalil, and D. Densmore, Fluigi: a computer aided design framework for combining microfluidics and synthetic biology, poster presented at the 6th International Meeting on Synthetic Biology (SB6.0) , July, 2013.

S. Iverson, T. Haddock, and D. Densmore, Multiplex Modular Assembly and Protein Engineering, poster presented at the SynBERC Spring Retreat, University of California-Berkeley , March, 2013.

S. B. Carr and D. Densmore, Compositional Genetic Inverter Circuits for Complex Logic Functions, poster presented at the UK-US Partnerships in Synthetic Biology Poster Session, Boston University , September, 2013.

S. B. Carr, E. Appleton, E. A. Gol, C. Belta, and D. M. Densmore, Transcriptional Inverters as Tools for Engineering Principle Formulation, poster presented at SynBERC 2013 Fall Retreat, Massachusetts Institute of Technology, Cambridge MA , September, 2013.

2012

D. Densmore and S. Hassoun, “Design Automation for Synthetic Biological Systems,” IEEE Design & Test of Computers, vol. 29, iss. 3, pp. 7-20, 2012.

J. Chen, D. Densmore, T. S. Ham, J. D. Keasling, and N. J. Hillson, “DeviceEditor visual biological CAD canvas,” J Biol Eng, vol. 6, iss. 1, p. 1, 2012.

E. Oberortner, D. Densmore, and J. C. Anderson, “An Interactive Pattern Story on Designing the Architecture of Clotho,” in 19th Conference on Pattern Languages of Programs (PLoP), 2012, cidarlab_conference_papers.

D. Densmore, “Bio-Design Automation: Nobody Said It Would Be Easy,” ACS Synthetic Biology, vol. 1, iss. 8, pp. 296-296, 2012.

D. Densmore and S. Hassoun, “Guest Editors’ Introduction: Synthetic Biology,” Design Test of Computers, IEEE, vol. 29, iss. 3, pp. 5-6, 2012.

B. Yordanov, E. Appleton, R. Ganguly, E. A. Gol, S. B. Carr, S. Bhatia, T. Haddock, C. Belta, and D. Densmore, “Experimentally driven verification of synthetic biological circuits,” in Proceedings of the Conference on Design, Automation and Test in Europe, Dresden, Germany, 2012, pp. 236-241.

J. Beal, R. Weiss, D. Densmore, A. Adler, E. Appleton, J. Babb, S. Bhatia, N. Davidsohn, T. Haddock, J. Loyall, R. Schantz, V. Vasilev, and F. Yaman, “An end-to-end workflow for engineering of biological networks from high-level specifications,” ACS Synth Biol, vol. 1, iss. 8, pp. 317-331, 2012.

F. Yaman, S. Bhatia, A. Adler, D. Densmore, and J. Beal, “Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks,” ACS Synth Biol, vol. 1, iss. 8, pp. 332-344, 2012.

H. Huang, E. Oberortner, D. Densmore, and A. Kuchinsky, Eugene’s Enriched Set of Features to Design Synthetic Biological Devices, talk presented at the International Workshop on Bio-Design Automation (IWBDA) , June, 2012.

J. Beal, R. Weiss, D. Densmore, A. Adler, E. Appleton, J. Babb, S. Bhatia, N. Davidsohn, T. Haddock, J. Loyall, R. Schantz, V. Vasilev, and F. Yaman, Results from TASBE, talk presented at the International Workshop on Bio-Design Automation (IWBDA) , June, 2012.

E. Appleton, V. Vasilev, S. Bhatia, T. Haddock, and D. Densmore, Testing-Optimized DNA Assembly Algorithms, poster presented at the International Workshop on Bio-Design Automation (IWBDA) , June, 2012.

S. Bhatia, A. Nielsen, M. Smanski, D. Densmore, and C. Voigt, How to build an n-input circuit library, poster presented at the SynBERC Spring Retreat, University of California-Berkeley , March, 2012.

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.

L. Bilitchenko, A. Liu, S. Cheung, E. Weeding, B. Xia, M. Leguia, J. C. Anderson, and D. Densmore, “Eugene–a domain specific language for specifying and constraining synthetic biological parts, devices, and systems,” PLoS ONE, vol. 6, iss. 4, p. e18882, 2011.

H. Koeppl, D. Densmore, M. di Bernardo, and G. Setti, Design and Analysis of Biomolecular Circuits, Springer Books, 2011.

B. Xia, S. Bhatia, B. Bubenheim, M. Dadgar, D. Densmore, and J. C. Anderson, “Developer’s and user’s guide to Clotho v2.0 A software platform for the creation of synthetic biological systems,” Meth. Enzymol., vol. 498, pp. 97-135, 2011.

L. Bilitchenko, A. Liu, and D. Densmore, “The Eugene language for synthetic biology,” Meth. Enzymol., vol. 498, pp. 153-172, 2011.

M. Leguia, J. Brophy, D. Densmore, and J. C. Anderson, “Automated assembly of standard biological parts,” Meth. Enzymol., vol. 498, pp. 363-397, 2011.

J. Peccoud, C. J. Anderson, D. Chandran, D. Densmore, M. Galdzicki, M. W. Lux, C. A. Rodriguez, G. Stan, and H. M. Sauro, “Essential information for synthetic DNA sequences,” Nature Biotechnology, vol. 29, iss. 1, pp. 22-22, 2011.

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.

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

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,” , 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

D. Densmore, J. T. Kittleson, L. Bilitchenko, A. Liu, and J. C. Anderson, “Rule based constraints for the construction of genetic devices,” in Circuits and Systems (ISCAS), Proceedings of 2010 IEEE International Symposium on, 2010, pp. 557-560.

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

D. Densmore, T. H. Hsiau, J. T. Kittleson, W. DeLoache, C. Batten, and J. C. Anderson, “Algorithms for automated DNA assembly,” Nucleic Acids Res., vol. 38, iss. 8, pp. 2607-2616, 2010.

2009

F. Balarin, M. DAngelo, A. Davare, D. Densmore, T. Meyerowitz, R. Passerone, A. Pinto, A. Sangiovanni-Vincentelli, A. Simalatsar, Y. Watanabe, G. Yang, and Q. Zhu, “Platform-Based Design and Frameworks: Metropolis and Metro II,” in Model-Based Design for Embedded Systems (Computational Analysis, Synthesis, and Design of Dynamic Systems), G. Nicolescu and P. J. Mosterman, Eds., CRC Press, 2009.

D. Densmore, A. Simalatsar, A. Davare, R. Passerone, and A. Sangiovanni-Vincentelli, “UMTS MPSoC design evaluation using a system level design framework,” in Design, Automation Test in Europe Conference Exhibition, 2009. DATE ’09., Nice, France, 2009, pp. 478-483.

D. Densmore, A. Van Devender, M. Johnson, and N. 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, New York, NY, USA, 2009, pp. 24-29.

D. Densmore and J. C. Anderson, “Combinational logic design in Synthetic Biology,” in Circuits and Systems, 2009. ISCAS 2009. IEEE International Symposium on, 2009, pp. 301-304.

2008

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

D. Densmore, T. Meyerowitz, A. Davare, Q. Zhu, and G. Yang, “Metro II Execution Semantics for Mapping,” University of California, Berkeley, UCB/EECS-2008-16, , 2008.

A. Simalatsar, R. Passerone, and D. Densmore, “A methodology for architecture exploration and performance analysis using system level design languages and rapid architecture profiling,” in Industrial Embedded Systems, 2008. SIES 2008. International Symposium on, La Grande Motte, France, 2008, pp. 95-102.

2007

D. Densmore, “A Design Flow for the Development, Characterization, and Refinement of System Level Architectural Services,” PhD Thesis, University of California, Berkeley, 2007.

A. Davare, D. Densmore, T. Meyerowitz, A. Pinto, A. Sangiovanni-Vincentelli, G. Yang, H. Zeng, and Q. Zhu, “A Next-Generation Design Framework for Platform-Based Design,” in Conference on Using Hardware Design and Verification Languages (DVCon), San Jose, CA, 2007.

2006

A. Davare, J. Chong, Q. Zhu, D. M. Densmore, and A. L. Sangiovanni-Vincentelli, “Classification, Customization, and Characterization: Using MILP for Task Allocation and Scheduling,” EECS Department, University of California, Berkeley, UCB/EECS-2006-166, , 2006.

D. Densmore, A. Donlin, and A. Sangiovanni-Vincentelli, “Programmable Platform Characterization for System Level Performance Analysis,” in Platform Based Design at the Electronic System Level: Industry Perspectives and Experiences, M. Burton and A. Morawiec, Eds., Springer, 2006, pp. 13-30.

D. Densmore and R. Passerone, “A Platform-Based Taxonomy for ESL Design,” Design Test of Computers, IEEE, vol. 23, iss. 5, pp. 359-374, 2006.

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

D. Densmore, A. Donlin, and A. Sangiovanni-Vincentelli, “FPGA architecture characterization for system level performance analysis,” in Proceedings of the conference on Design, automation and test in Europe: Proceedings, Munich, Germany, 2006, pp. 734-739.

S. Kakita, Y. Watanabe, D. Densmore, A. Davare, and A. Sangiovanni-Vincentelli, “Functional Model Exploration for Multimedia Applications via Algebraic Operators,” in Application of Concurrency to System Design, 2006. ACSD 2006. Sixth International Conference on, Turku Finland, 2006, pp. 229-238.

2004

H. Zeng, V. Shah, D. Densmore, and A. Davare, “Simple Case Study in Metropolis,” EECS Department, University of California, Berkeley, UCB/ERL M04/37, , 2004.

D. Densmore, “Platform Based Reconfigurable Architecture Exploration via Boolean Constraints,” , University of California, Berkeley, 2004.