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Douglas M. Densmore, Ph.D. - Publications

Affiliations: 
2007 University of California, Berkeley, Berkeley, CA, United States 
Area:
Design, Modeling and Analysis (DMA), Embedded System Design; Design methodologies and tools; Control, Intelligent Systems, and Robotics (CIR), Hybrid systems; Design methodologies and tools; Communications & Networking (COMNET), Wireless sensor network de
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52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Roehner N, Roberts J, Lapets A, Gould D, Akavoor V, Qin L, Gordon DB, Voigt C, Densmore D. GOLDBAR: A Framework for Combinatorial Biological Design. Acs Synthetic Biology. PMID 39162314 DOI: 10.1021/acssynbio.4c00296  0.48
2022 Oliveira SMD, Densmore D. Hardware, Software, and Wetware Codesign Environment for Synthetic Biology. Biodesign Research. 2022: 9794510. PMID 37850136 DOI: 10.34133/2022/9794510  0.412
2022 Jones TS, Oliveira SMD, Myers CJ, Voigt CA, Densmore D. Genetic circuit design automation with Cello 2.0. Nature Protocols. PMID 35197606 DOI: 10.1038/s41596-021-00675-2  0.458
2021 Lashkaripour A, Rodriguez C, Mehdipour N, Mardian R, McIntyre D, Ortiz L, Campbell J, Densmore D. Machine learning enables design automation of microfluidic flow-focusing droplet generation. Nature Communications. 12: 25. PMID 33397940 DOI: 10.1038/s41467-020-20284-z  0.306
2020 McIntyre DP, Lashkaripour A, Densmore D. Rapid and inexpensive microfluidic electrode integration with conductive ink. Lab On a Chip. PMID 32895672 DOI: 10.1039/D0Lc00763C  0.309
2020 Chen Y, Zhang S, Young EM, Jones TS, Densmore D, Voigt CA. Genetic circuit design automation for yeast. Nature Microbiology. PMID 32747797 DOI: 10.1038/S41564-020-0757-2  0.434
2020 Timmons JJ, Densmore D. Correction: Repository-based plasmid design. Plos One. 15. PMID 32108829 DOI: 10.1371/Journal.Pone.0229981  0.494
2019 Sanka R, Lippai J, Samarasekera D, Nemsick S, Densmore D. 3DμF - Interactive Design Environment for Continuous Flow Microfluidic Devices. Scientific Reports. 9: 9166. PMID 31235804 DOI: 10.1038/S41598-019-45623-Z  0.518
2019 Walsh DI, Pavan M, Ortiz L, Wick S, Bobrow J, Guido NJ, Leinicke S, Fu D, Pandit S, Qin L, Carr PA, Densmore D. Standardizing Automated DNA Assembly: Best Practices, Metrics, and Protocols Using Robots. Slas Technology. 2472630318825335. PMID 30768372 DOI: 10.1177/2472630318825335  0.344
2019 Lashkaripour A, Rodriguez C, Ortiz L, Densmore D. Performance tuning of microfluidic flow-focusing droplet generators. Lab On a Chip. PMID 30762047 DOI: 10.1039/C8Lc01253A  0.312
2018 Wagner TE, Becraft JR, Bodner K, Teague B, Zhang X, Woo A, Porter E, Alburquerque B, Dobosh B, Andries O, Sanders NN, Beal J, Densmore D, Kitada T, Weiss R. Small-molecule-based regulation of RNA-delivered circuits in mammalian cells. Nature Chemical Biology. 14: 1043-1050. PMID 30327560 DOI: 10.1038/S41589-018-0146-9  0.316
2018 Mısırlı G, Nguyen T, McLaughlin JA, Vaidyanathan P, Jones T, Densmore D, Myers CJ, Wipat A. A computational workflow for the automated generation of models of genetic designs. Acs Synthetic Biology. PMID 29782151 DOI: 10.1021/Acssynbio.7B00459  0.469
2018 Lashkaripour A, Goharimanesh M, Mehrizi AA, Densmore D. An adaptive neural-fuzzy approach for microfluidic droplet size prediction Microelectronics Journal. 78: 73-80. DOI: 10.1016/J.Mejo.2018.05.018  0.325
2018 Lashkaripour A, Silva R, Densmore D. Desktop micromilled microfluidics Microfluidics and Nanofluidics. 22: 31. DOI: 10.1007/S10404-018-2048-2  0.336
2017 Ortiz L, Pavan M, McCarthy L, Timmons J, Densmore DM. Automated Robotic Liquid Handling Assembly of Modular DNA Devices. Journal of Visualized Experiments : Jove. PMID 29286379 DOI: 10.3791/54703  0.425
2017 Appleton E, Densmore D, Madsen C, Roehner N. Needs and opportunities in bio-design automation: four areas for focus. Current Opinion in Chemical Biology. 40: 111-118. PMID 28923279 DOI: 10.1016/J.Cbpa.2017.08.005  0.544
2017 Bhatia S, Smanski M, Voigt CA, Densmore D. Genetic design via combinatorial constraint specification. Acs Synthetic Biology. PMID 28874044 DOI: 10.1021/Acssynbio.7B00154  0.649
2017 Carr SB, Beal J, Densmore DM. Reducing DNA context dependence in bacterial promoters. Plos One. 12: e0176013. PMID 28422998 DOI: 10.1371/Journal.Pone.0176013  0.363
2017 Appleton E, Madsen C, Roehner N, Densmore D. Design Automation in Synthetic Biology. Cold Spring Harbor Perspectives in Biology. 9. PMID 28246188 DOI: 10.1101/Cshperspect.A023978  0.55
2016 Woodruff LB, Gorochowski TE, Roehner N, Mikkelsen TS, Densmore D, Gordon DB, Nicol R, Voigt CA. Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration. Nucleic Acids Research. PMID 28007941 DOI: 10.1093/Nar/Gkw1226  0.503
2016 Bhatia S, LaBoda C, Yanez VF, Haddock TL, Densmore D. Permutation Machines. Acs Synthetic Biology. PMID 27383067 DOI: 10.1021/acssynbio.5b00226  0.574
2016 Silva R, Bhatia S, Densmore D. A reconfigurable continuous-flow fluidic routing fabric using a modular, scalable primitive. Lab On a Chip. PMID 27345339 DOI: 10.1039/C6Lc00477F  0.647
2016 Roehner N, Beal J, Clancy K, Bartley B, Misirli G, Gruenberg R, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang M, Zhang Z, Zundel Z, Densmore D, et al. Sharing Structure and Function in Biological Design with SBOL 2.0. Acs Synthetic Biology. PMID 27111421 DOI: 10.1021/Acssynbio.5B00215  0.55
2016 Roehner N, Young E, Voigt CA, Gordon DB, Densmore D. Double Dutch: A Tool for Designing Combinatorial Libraries of Biological Systems. Acs Synthetic Biology. PMID 27110633 DOI: 10.1021/Acssynbio.5B00232  0.552
2016 Quintin MJ, Ma NJ, Ahmed S, Bhatia S, Lewis A, Isaacs FJ, Densmore D. Merlin: Computer-Aided Oligonucleotide Design for Large Scale Genome Engineering with MAGE. Acs Synthetic Biology. PMID 27054880 DOI: 10.1021/Acssynbio.5B00219  0.661
2016 Nielsen AA, Der BS, Shin J, Vaidyanathan P, Paralanov V, Strychalski EA, Ross D, Densmore D, Voigt CA. Genetic circuit design automation. Science (New York, N.Y.). 352: aac7341. PMID 27034378 DOI: 10.1126/Science.Aac7341  0.466
2015 Iverson SV, Haddock TL, Beal J, Densmore DM. CIDAR MoClo: Improved MoClo Assembly Standard and New E. coli Part Library Enable Rapid Combinatorial Design for Synthetic and Traditional Biology. Acs Synthetic Biology. PMID 26479688 DOI: 10.1021/Acssynbio.5B00124  0.718
2015 Beal J, Wagner TE, Kitada T, Azizgolshani O, Parker JM, Densmore D, Weiss R. Model-driven engineering of gene expression from RNA replicons. Acs Synthetic Biology. 4: 48-56. PMID 24877739 DOI: 10.1021/Sb500173F  0.327
2014 Appleton E, Tao J, Wheatley FC, Desai DH, Lozanoski TM, Shah PD, Awtry JA, Jin SS, Haddock TL, Densmore DM. Owl: electronic datasheet generator. Acs Synthetic Biology. 3: 966-8. PMID 25524100 DOI: 10.1021/Sb500053J  0.351
2014 Oberortner E, Densmore D. Web-based software tool for constraint-based design specification of synthetic biological systems. Acs Synthetic Biology. 4: 757-60. PMID 25426642 DOI: 10.1021/Sb500352B  0.555
2014 Smanski MJ, Bhatia S, Zhao D, Park Y, B A Woodruff L, Giannoukos G, Ciulla D, Busby M, Calderon J, Nicol R, Gordon DB, Densmore D, Voigt CA. Functional optimization of gene clusters by combinatorial design and assembly. Nature Biotechnology. 32: 1241-9. PMID 25419741 DOI: 10.1038/Nbt.3063  0.613
2014 Huang H, Densmore D. Integration of microfluidics into the synthetic biology design flow. Lab On a Chip. 14: 3459-3474. PMID 25012162 DOI: 10.1039/C4Lc00509K  0.463
2014 Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, et al. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nature Biotechnology. 32: 545-50. PMID 24911500 DOI: 10.1038/Nbt.2891  0.468
2014 Appleton E, Tao J, Haddock T, Densmore D. Interactive assembly algorithms for molecular cloning. Nature Methods. 11: 657-62. PMID 24776633 DOI: 10.1038/Nmeth.2939  0.338
2014 Densmore DM, Bhatia S. Bio-design automation: software + biology + robots. Trends in Biotechnology. 32: 111-3. PMID 24269087 DOI: 10.1016/J.Tibtech.2013.10.005  0.6
2014 Huang H, Densmore D. Fluigi: Microfluidic Device Synthesis for Synthetic Biology Acm Journal On Emerging Technologies in Computing Systems. 11: 26. DOI: 10.1145/2660773  0.445
2014 Oberortner E, Bhatia S, Lindgren E, Densmore D. A Rule-Based Design Specification Language for Synthetic Biology Acm Journal On Emerging Technologies in Computing Systems. 11: 1-19. DOI: 10.1145/2641571  0.682
2013 Bhatia S, Densmore D. Pigeon: a design visualizer for synthetic biology. Acs Synthetic Biology. 2: 348-50. PMID 23654259 DOI: 10.1021/Sb400024S  0.638
2013 Leguia M, Brophy JA, Densmore D, Asante A, Anderson JC. 2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts. Journal of Biological Engineering. 7: 2. PMID 23305072 DOI: 10.1186/1754-1611-7-2  0.438
2013 Davare A, Densmore D, Guo L, Passerone R, Sangiovanni-Vincentelli AL, Simalatsar A, Zhu Q. METROII: A design environment for cyber-physical systems Transactions On Embedded Computing Systems. 12. DOI: 10.1145/2435227.2435245  0.729
2012 Yaman F, Bhatia S, Adler A, Densmore D, Beal J. Automated selection of synthetic biology parts for genetic regulatory networks. Acs Synthetic Biology. 1: 332-44. PMID 23651287 DOI: 10.1021/Sb300032Y  0.67
2012 Beal J, Weiss R, Densmore D, Adler A, Appleton E, Babb J, Bhatia S, Davidsohn N, Haddock T, Loyall J, Schantz R, Vasilev V, Yaman F. An end-to-end workflow for engineering of biological networks from high-level specifications. Acs Synthetic Biology. 1: 317-31. PMID 23651286 DOI: 10.1021/Sb300030D  0.631
2012 Densmore D. Bio-design automation: nobody said it would be easy. Acs Synthetic Biology. 1: 296-296. PMID 23651283 DOI: 10.1021/Sb300062C  0.52
2012 Chen J, Densmore D, Ham TS, Keasling JD, Hillson NJ. DeviceEditor visual biological CAD canvas. Journal of Biological Engineering. 6: 1. PMID 22373390 DOI: 10.1186/1754-1611-6-1  0.587
2012 Densmore D, Hassoun S. Guest editors' introduction: Synthetic biology Ieee Design and Test of Computers. 29: 5-6. DOI: 10.1109/Mdt.2012.2194609  0.472
2012 Densmore D, Hassoun S. Design automation for synthetic biological systems Ieee Design and Test of Computers. 29: 7-20. DOI: 10.1109/Mdt.2012.2193370  0.483
2011 Leguia M, Brophy J, Densmore D, Anderson JC. Automated assembly of standard biological parts. Methods in Enzymology. 498: 363-97. PMID 21601686 DOI: 10.1016/B978-0-12-385120-8.00016-4  0.457
2011 Bilitchenko L, Liu A, Densmore D. The Eugene language for synthetic biology. Methods in Enzymology. 498: 153-172. PMID 21601677 DOI: 10.1016/B978-0-12-385120-8.00007-3  0.477
2011 Xia B, Bhatia S, Bubenheim B, Dadgar M, Densmore D, Anderson JC. Developer's and user's guide to Clotho v2.0 A software platform for the creation of synthetic biological systems. Methods in Enzymology. 498: 97-135. PMID 21601675 DOI: 10.1016/B978-0-12-385120-8.00005-X  0.636
2011 Bilitchenko L, Liu A, Cheung S, Weeding E, Xia B, Leguia M, Anderson JC, Densmore D. Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems. Plos One. 6: e18882. PMID 21559524 DOI: 10.1371/Journal.Pone.0018882  0.479
2010 Densmore D, Hsiau TH, Kittleson JT, DeLoache W, Batten C, Anderson JC. Algorithms for automated DNA assembly Nucleic Acids Research. 38: 2607-2616. PMID 20335162 DOI: 10.1093/Nar/Gkq165  0.403
2006 Densmore D, Passerone R, Sangiovanni-Vincentelli A. A platform-based taxonomy for ESL design Ieee Design and Test of Computers. 23: 359-373. DOI: 10.1109/Mdt.2006.112  0.702
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