Genetic circuit design automation with Cello 2.0

Christopher A. Voigt, Timothy S. Jones, Samuel M. D. Oliveira, Chris J. Myers, Douglas Densmore

Published: 2022-02-22 DOI: 10.1038/s41596-021-00675-2

Synthetic biology

Cello 2.0

Genetic circuit design

Computer-aided design

DNA sequence automation

AI 解读

Supplementary information

Supplementary Information

Supplementary Manual, Supplementary Listings 1–35 and Supplementary Figs. 1–6.

The maternal serum metabolome by multisegment injection-capillary electrophoresis-mass spectrometry: a high-throughput platform and standardized data workflow for large-scale epidemiological studies

High-yield production of mono- or few-layer transition metal dichalcogenide nanosheets by an electrochemical lithium ion intercalation-based exfoliation method

Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages

Generation of proximal tubule-enhanced kidney organoids from human pluripotent stem cells

ProBac-seq, a bacterial single-cell RNA sequencing methodology using droplet microfluidics and large oligonucleotide probe sets

Implementation of a 4Pi-SMS super-resolution microscope

Responsive and activable nanomedicines for remodeling the tumor microenvironment

Rapid ordering of barcoded transposon insertion libraries of anaerobic bacteria

GLORI for absolute quantification of transcriptome-wide m6A at single-base resolution

Human fetal whole-body postmortem microfocus computed tomographic imaging

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References

Supplementary information

Wolf, C. Yosys Open Synthesis Suite (2016).
Cheng, A. A. & Lu, T. K. Synthetic biology: an emerging engineering discipline. Annu. Rev. Biomed. Eng. 14, 155–178 (2012).
Khalil, A. S. & Collins, J. J. Synthetic biology: applications come of age. Nat. Rev. Genet. 11, 367–379 (2010).
Endy, D. Foundations for engineering biology. Nature 438, 449–453 (2005).
Bueso, Y. F. & Tangney, M. Synthetic biology in the driving seat of the bioeconomy. Trends Biotechnol. 35, 373–378 (2017).
Purnick, P. E. & Weiss, R. The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 10, 410–422 (2009).
Mano, M. M. R. & Ciletti, M. D. Digital Design: With an Introduction to the Verilog HDL, VHDL, and SystemVerilog (Pearson, 2018).
Rabaey, J. M., Chandrakasan, A. P. & Nikolić, B. Digital Integrated Circuits: A Design Perspective (Prentice Hall, 2008).
Oliveira, S. M. D. et al. Temperature-dependent model of multi-step transcription initiation in Escherichia coli based on live single-cell measurements. PLoS Comput. Biol. https://doi.org/10.1371/journal.pcbi.1005174 (2016).
Tabor, J. J. et al. A synthetic genetic edge detection program. Cell 137, 1272–1281 (2009).
Stephens, K. & Bentley, W. E. Synthetic biology for manipulating quorum sensing in microbial consortia. Trends Microbiol. 28, 633–643 (2020).
Brophy, J. A. N. & Voigt, C. A. Principles of genetic circuit design. Nat. Methods 11, 508–520 (2014).
Nielsen, A. A. K. et al. Genetic circuit design automation. Science 352, aac7341 (2016).
Hasty, J., McMillen, D. & Collins, J. J. Engineered gene circuits. Nature 420, 224–230 (2002).
Andrews, L. B., Nielsen, A. A. K. & Voigt, C. A. Cellular checkpoint control using programmable sequential logic. Science 361, eaap8987 (2018).
Bilitchenko, L. et al. Eugene—a domain specific language for specifying and constraining synthetic biological parts, devices, and systems. PLoS ONE 6, e18882 (2011).
Woodruff, L. B. et al. Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration. Nucleic Acids Res. 45, 1553–1565 (2017).
Hossain, A. et al. Automated design of thousands of nonrepetitive parts for engineering stable genetic systems. Nat. Biotechnol. 38, 1466–1475 (2020).
Huynh, L., Tsoukalas, A., Köppe, M. & Tagkopoulos, I. SBROME: a scalable optimization and module matching framework for automated biosystems design. ACS Synth. Biol. 2, 263–273 (2013).
Yaman, F., Bhatia, S., Adler, A., Densmore, D. & Beal, J. Automated selection of synthetic biology parts for genetic regulatory networks. ACS Synth. Biol. 1, 332–344 (2012).
Beal, J., Lu, T. & Weiss, R. Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks. PLoS ONE 6, e22490 (2011).
Czar, M. J., Cai, Y. & Peccoud, J. Writing DNA with GenoCADTM. Nucleic Acids Res. 37, W40–W47 (2009).
Chen, J., Densmore, D., Ham, T. S., Keasling, J. D. & Hillson, N. J. DeviceEditor visual biological CAD canvas. J. Biol. Eng. 6, 1–12 (2012).
Roehner, N. & Myers, C. J. Directed acyclic graph-based technology mapping of genetic circuit models. ACS Synth. Biol. 3, 543–555 (2014).
Salis, H. M. The ribosome binding site calculator. Methods Enzymol. 498, 19–42 (2011).
Rodrigo, G., Carrera, J. & Jaramillo, A. Genetdes: automatic design of transcriptional networks. Bioinformatics 23, 1857–1858 (2007).
Wilson, E. H., Macklin, C., & Platt, D. Engineering genomes with genotype specification language. in Synthetic Biology 373–398 (Humana Press, 2018).
Pedersen, M. & Phillips, A. Towards programming languages for genetic engineering of living cells. J. R. Soc. Interface 6, S437–S450 (2009).
Vaidyanathan, P. et al. A framework for genetic logic synthesis. Proc. IEEE 103, 2196–2207 (2015).
Roehner, N. et al. Sharing structure and function in biological design with SBOL 2.0. ACS Synth. Biol. 5, 498–506 (2016).
McLaughlin, J. A. et al. SynBioHub: a standards-enabled design repository for synthetic biology. ACS Synth. Biol. 7, 682–688 (2018).
Shin, J., Zhang, S., Der, B. S., Nielsen, A. A. & Voigt, C. A. Programming Escherichia coli to function as a digital display. Mol. Syst. Biol. 16, e9401 (2020).
Der, B. S. et al. DNAplotlib: programmable visualization of genetic designs and associated data. ACS Synth. Biol. 6, 1115–1119 (2017).
Häkkinen, A., Oliveira, S. M. D., Neeli-Venkata, R. & Ribeiro, A. S. Transcription closed and open complex formation coordinate expression of genes with a shared promoter region. J. R. Soc. Interface 16, 20190507 (2019).
Park, Y., Espah Borujeni, A., Gorochowski, T. E., Shin, J. & Voigt, C. A. Precision design of stable genetic circuits carried in highly-insulated E. coli genomic landing pads. Mol. Syst. Biol. 16, e9584 (2020).
Taketani, M. et al. Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron. Nat. Biotechnol. 38, 962–969 (2020).
Chen, Y. et al. Genetic circuit design automation for yeast. Nat. Microbiol. 5, 1349–1360 (2020).

Genetic circuit design automation with Cello 2.0

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