© 2017 Living Computing Project.

Sponsored by National Science Foundation’s Expeditions in Computing Program

(Awards #1522074 / 1521925 / 1521759).

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Related Publications

  • 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. 
     

  • A. J. Keung and A. S. Khalil, "A Unifying Model of Epigenetic Regulation (Perspective)," Science, vol. 351, iss. 661-662, 2016.
     

  • A. J. Keung, J. K. Joung, A. S. Khalil and J. J. Collins, "Chromatin Regulation at the Frontier of Synthetic Biology," Nature Reviews Genetics, vol. 16, iss. 159-171, 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. 

  • J. R. Rubens, G. Selvaggio, T. K. Lu, “Synthetic Mixed-signal Computation in Living Cells,” Nature Communications, vol. 7, article 11658, June 3, 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. 

  • N. Roehner and D. Densmore, "How to Remember and Revisit Genetic Designs Automatically," 2016. 
     

  • A. J. Keung, C. J. Bashor, S. Kiriakov, J. J. Collins and A. S. Khalil, "Using Targeted Chromatin Regulators to Engineer Combinatorial and Spatial Transcriptional Regulation," Cell, vol. 158, iss. 110-120, 2014.

Funded Publications

__2018______________________________________________________________________

  • A. Lashkaripour, R. Silva, and D. Densmore, "Desktop Micromilled Microfluidics," Microfluidics and Nanofluidics, vol 22, iss. 31, 2018.

  • P. Chen, Y. Qian, and D. Del Vecchio, "A Model of Resource Competition in CRISPR-mediated Gene Repression," Proc. IEEE Conf. Decision and Control, 2018 (to appear)

 

  • C. McBride and D. Del Vecchio, "Resource Sensor Design for Quantifying Resource Competition in Genetic Circuits," Proc. IEEE Conf. Decision and Control, 2018 (to appear)

 

  • McBride and D. Del Vecchio, "The Steady State Landscape of Resource Constrained Nonlinear Positive Dynamical Systems," Under Review (Automatica) 2018

__2017______________________________________________________________________

  • B. H. Weinberg, H. N. T. Pham, L. D. Caraballo, T. Lozanoski, A. Engel, S. Bhatia, W. W. Wong, "Large-scale Design of Robust Genetic Circuits with Multiple Inputs and Outputs for Mammalian Cells," Nature Biotechnology, 2017.
        

  • C. McBride and D. Del Vecchio, "Analyzing and Exploiting the Effects of Protease Sharing in Genetic Circuits," Proc. of International Federation of Automatic Control World Congress, 2017.​
     

  • C. Myers, J. Beal, T. E. Gorochowski, H. Kuwahara, C. Madsen, J. A. McLaughlin, G. Misirli, T. Nguyen, E. Oberortner, M. Samineni, A. Wipat, M. Zhang, and Z. Zundel, "A Standard-enabled Workflow for Synthetic Biology," Biochemical Society Transactions, vol. 45, iss. 3, 2017.

  • D. I. Walsh, D. S. Kong, S. K. Murthy,  P. A. Carr, "Enabling Microfluidics: from Clean Rooms to Makerspaces," Trends in Biotechnology, 2017.

  • D. S. Kong, T. A. Thorsen, J. Babb, S. T. Wick, J. J. Gam, R. Weiss, and P. A. Carr, "Open-source, Community-driven Microfluidics with Metafluidics," Nature Biotechnology, 2017.

  • G. A. Newby, S. Kiriakov, E. Hallacli, C. Kayatekin, P. Tsvetkov, C. P. Mancuso, J. Maeve Bonner, W. R. Hesse, S. Chakrabortee, A. L. Manogaran, S. W. Liebman, S. Lindquist, and A. S. Khalil, "A Genetic Tool to Track Protein Aggregates and Control Prion Inheritance," Cell, vol. 171, iss. 4, 2017. 

  • L. Ortiz, M. Pavan, L. McCarthy, J. Timmons,  D. M. Densmore, "Automated Robotic Liquid Handling Assembly of Modular DNA Devices," Journal of Visualized Experiments, 2017.

  • R. Shah and D. Del Vecchio, "Signaling Architectures that Transmit Unidirectional Signals Despite Retroactivity," Biophysical Journal, 113(3):728-742, 2017

 

  • C. McBride, "A Mathematical and Engineering Framework to Predict the Effects of Resource Sharing on Genetic Networks," MIT, Mechanical Engineering Department Master’s Thesis. May 2017

  •  

  •  Y. Qian, C. McBride and D. Del Vecchio, "Programming Cells to Work for Us," Annual Reviews in Control, Robotics and Automation systems, 1:411-440, 2017 

  • S. Bhatia, M. J. Smanski, C. A. Voigt, and D. Densmore, "Genetic Design via Combinatorial Constraint Specification," ACS Synthetic Biology, vol. 6, iss. 11, 2017.

  • J. Beal, N. DeLateur, B. Teague, R. Weiss, J. Sexton, S. Castillo-Hair, and J. J. Tabor, "Toward Quantitative Comparison of Fluorescent Protein Expression Levels via Fluorescent Beads," International Workshop on Bio-Design Automation, 2017.

  • S. B. Carr, J. Beal, and D. M. Densmore, “Reducing DNA Context Dependence in Bacterial Promoters,” PLOS ONE, vol. 12, iss. 4, 2017.

  • R. S. Cox, J. A. McLaughlin, R. Grunberg, J. Beal, A. Wipat, and H. M. Sauro, "A Visual Language for Protein Design,", ACS Synthetic Biology, 2017.

  • J. Beal, "Biochemical Complexity Drives Log-Normal Variation in Genetic Expression," IET Engineering Biology, iss. 1, 2017.

__2016______________________________________________________________________

  • C. McBride and D. Del Vecchio, "Analyzing and Exploiting the Effects of Protease Sharing in Genetic Circuits," Proc. of IFAC World Congress, July 2016 (Invited paper)

  • J. Beal, A. Adler, and F. Yaman, "Managing Bioengineering Complexity with AI Techniques," Elsevier Biosystems, vol. 148, 2016.

  • J. Beal, "Mathematical Foundations of Variation in Gene Expression," IET/SynbiCITE Engineering Biology Conference, 2016.

  • A. Gyorgy and D. Del Vecchio, "Price and Utility of Protein in Synthetic Gene Circuits," PLOS, 2016.

  • J. Beal, R. S. Cox, R. Grunberg, J. McLaughlin, T. Nguyen, C. Macklin, M. Bissell, C. Madsen, N. Roehner, E. Oberortner, G. Misirli, K. Clancy, M. Pocock, Z. Zhang, C. Myers, M. Zhang, M. Samineni, Z. Zundel, B. Bartley, K. Choi, J. H. Gennari, and H. Sauro, "Synthetic Biology Open Language (SBOL) Version 2.1.0," Journal of Integrative Bioinformatics, 2016.
     

  • J. Beal, T. Haddock-Angelli, M. Gershater, K. de Mora, M. Lizarazo, J. Hollenhorst, R. Rettberg, and iGEM Interlab Study Contributors, "Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli," PLoS One, 2016.

  • L. Woodruff, T. E. Gorochowski, N. Roehner, T. S. Mikkelsen, D. Densmore, D. B. 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, 2016.

  • M. Park, A. J. Keung and A. S. Khalil, "The Epigenome: The Next Substrate for Engineering," Genome Biology, vol. 17, iss. 183, 2016.
     

  • N. J. Hillson, H. A. Plahar, J. Beal, and R. Prithviraj, "Improving Synthetic Biology Communication: Recommended Practices for Visual Depiction and Digital Submission of Genetic Designs," ACS Synthetic Biology, 2016.
     

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

  • N. Roquet and A. P. Soleimany and A. C. Ferris and S. Aaronson and T. K. Lu, "Synthetic Recombinase-based State Machines in Living Cells," Science, vol. 353, iss. 6297, 2016.
     

  • R. Shah and D. Del Vecchio, "An n-stage Cascade of Phosphorylation Cycles as an Insulation Device for Synthetic Biological Circuits," Proc. of European Conf. on Control, 2016.
     

  • S. Bhatia, C. LaBoda, V. Yanez, T. Haddock-Angelli, and D. Densmore, "Permutation Machines," ACS Synthetic Biology, vol. 5, iss. 8, 2016.

  • S. Perli*, C. Cui*, T. K. Lu, “Continuous Genetic Recording with Self-Targeting CRISPR-Cas in Human Cells,” Science, 2016.
     

  • Z. Zhang, T. Nguyen, N. Roehner, G. Misirli, M. Pocock, E. Oberortner, M. Samineni, Z. Zundel, J. Beal, K. Clancy, A. Wipat, and Chris Myers, "libSBOLj 2.0: A Java Library to Support SBOL 2.0," IEEE Life Sciences Letters, 2016.