Genetic circuit design automation with Cello 2.0

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

doi:10.1038/s41596-021-00675-2

Genetic circuit design automation with Cello 2.0

Journal Article · 23 February 2022 · Nature Protocols

DOI:https://doi.org/10.1038/s41596-021-00675-2· OSTI ID:1978708

Jones, Timothy S.; Oliveira, Samuel M. D.; ; ;

Not provided.

Research Organization:: Univ. of Colorado, Boulder, CO (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

DOE Contract Number:: SC0018368

OSTI ID:: 1978708

Journal Information:: Nature Protocols, Vol. 17, Issue 4; ISSN 1754-2189

Publisher:: Nature Publishing Group

Country of Publication:: United States

Language:: English

References (31)

Synthetic Biology: An Emerging Engineering Discipline Cheng, Allen A.; Lu, Timothy K. Annual Review of Biomedical Engineering, Vol. 14, Issue 1 https://doi.org/10.1146/annurev-bioeng-071811-150118	journal	August 2012
Synthetic biology: applications come of age Khalil, Ahmad S.; Collins, James J. Nature Reviews Genetics, Vol. 11, Issue 5 https://doi.org/10.1038/nrg2775	journal	May 2010
Foundations for engineering biology Endy, Drew Nature, Vol. 438, Issue 7067 https://doi.org/10.1038/nature04342	journal	November 2005
Synthetic Biology in the Driving Seat of the Bioeconomy Flores Bueso, Yensi; Tangney, Mark Trends in Biotechnology, Vol. 35, Issue 5 https://doi.org/10.1016/j.tibtech.2017.02.002	journal	May 2017
The second wave of synthetic biology: from modules to systems Purnick, Priscilla E. M.; Weiss, Ron Nature Reviews Molecular Cell Biology, Vol. 10, Issue 6 https://doi.org/10.1038/nrm2698	journal	June 2009
Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements Oliveira, Samuel M. D.; Häkkinen, Antti; Lloyd-Price, Jason PLOS Computational Biology, Vol. 12, Issue 10 https://doi.org/10.1371/journal.pcbi.1005174	journal	October 2016
A Synthetic Genetic Edge Detection Program Tabor, Jeffrey J.; Salis, Howard M.; Simpson, Zachary Booth Cell, Vol. 137, Issue 7 https://doi.org/10.1016/j.cell.2009.04.048	journal	June 2009
Synthetic Biology for Manipulating Quorum Sensing in Microbial Consortia Stephens, Kristina; Bentley, William E. Trends in Microbiology, Vol. 28, Issue 8 https://doi.org/10.1016/j.tim.2020.03.009	journal	August 2020
Principles of genetic circuit design Brophy, Jennifer A. N.; Voigt, Christopher A. Nature Methods, Vol. 11, Issue 5 https://doi.org/10.1038/nmeth.2926	journal	April 2014
Genetic circuit design automation Nielsen, A. A. K.; Der, B. S.; Shin, J. Science, Vol. 352, Issue 6281 https://doi.org/10.1126/science.aac7341	journal	March 2016
Engineered gene circuits Hasty, Jeff; McMillen, David; Collins, J. J. Nature, Vol. 420, Issue 6912 https://doi.org/10.1038/nature01257	journal	November 2002
Cellular checkpoint control using programmable sequential logic Andrews, Lauren B.; Nielsen, Alec A. K.; Voigt, Christopher A. Science, Vol. 361, Issue 6408 https://doi.org/10.1126/science.aap8987	journal	September 2018
Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems Bilitchenko, Lesia; Liu, Adam; Cheung, Sherine PLoS ONE, Vol. 6, Issue 4 https://doi.org/10.1371/journal.pone.0018882	journal	April 2011
Automated design of thousands of nonrepetitive parts for engineering stable genetic systems Hossain, Ayaan; Lopez, Eriberto; Halper, Sean M. Nature Biotechnology, Vol. 38, Issue 12 https://doi.org/10.1038/s41587-020-0584-2	journal	July 2020
SBROME: A Scalable Optimization and Module Matching Framework for Automated Biosystems Design Huynh, Linh; Tsoukalas, Athanasios; Köppe, Matthias ACS Synthetic Biology, Vol. 2, Issue 5 https://doi.org/10.1021/sb300095m	journal	March 2013
Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks Yaman, Fusun; Bhatia, Swapnil; Adler, Aaron ACS Synthetic Biology, Vol. 1, Issue 8 https://doi.org/10.1021/sb300032y	journal	July 2012
Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks Beal, Jacob; Lu, Ting; Weiss, Ron PLoS ONE, Vol. 6, Issue 8 https://doi.org/10.1371/journal.pone.0022490	journal	August 2011
Writing DNA with GenoCADTM Czar, M. J.; Cai, Y.; Peccoud, J. Nucleic Acids Research, Vol. 37, Issue Web Server https://doi.org/10.1093/nar/gkp361	journal	May 2009
DeviceEditor visual biological CAD canvas Chen, Joanna; Densmore, Douglas; Ham, Timothy S. Journal of Biological Engineering, Vol. 6, Issue 1 https://doi.org/10.1186/1754-1611-6-1	journal	December 2012
Directed Acyclic Graph-Based Technology Mapping of Genetic Circuit Models Roehner, Nicholas; Myers, Chris J. ACS Synthetic Biology, Vol. 3, Issue 8 https://doi.org/10.1021/sb400135t	journal	April 2014
Genetdes: automatic design of transcriptional networks Rodrigo, Guillermo; Carrera, Javier; Jaramillo, Alfonso Bioinformatics, Vol. 23, Issue 14 https://doi.org/10.1093/bioinformatics/btm237	journal	May 2007
Towards programming languages for genetic engineering of living cells Pedersen, Michael; Phillips, Andrew Journal of The Royal Society Interface, Vol. 6, Issue suppl_4 https://doi.org/10.1098/rsif.2008.0516.focus	journal	April 2009
A Framework for Genetic Logic Synthesis Vaidyanathan, Prashant; Der, Bryan S.; Bhatia, Swapnil Proceedings of the IEEE, Vol. 103, Issue 11 https://doi.org/10.1109/JPROC.2015.2443832	journal	November 2015
Sharing Structure and Function in Biological Design with SBOL 2.0 Roehner, Nicholas; Beal, Jacob; Clancy, Kevin ACS Synthetic Biology, Vol. 5, Issue 6 https://doi.org/10.1021/acssynbio.5b00215	journal	May 2016
SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology McLaughlin, James Alastair; Myers, Chris J.; Zundel, Zach ACS Synthetic Biology, Vol. 7, Issue 2 https://doi.org/10.1021/acssynbio.7b00403	journal	January 2018
Programming Escherichia coli to function as a digital display Shin, Jonghyeon; Zhang, Shuyi; Der, Bryan S. Molecular Systems Biology, Vol. 16, Issue 3 https://doi.org/10.15252/msb.20199401	journal	March 2020
DNAplotlib: Programmable Visualization of Genetic Designs and Associated Data Der, Bryan S.; Glassey, Emerson; Bartley, Bryan A. ACS Synthetic Biology, Vol. 6, Issue 7 https://doi.org/10.1021/acssynbio.6b00252	journal	October 2016
Transcription closed and open complex formation coordinate expression of genes with a shared promoter region Häkkinen, Antti; Oliveira, Samuel M. D.; Neeli-Venkata, Ramakanth Journal of The Royal Society Interface, Vol. 16, Issue 161 https://doi.org/10.1098/rsif.2019.0507	journal	December 2019
P recision design of stable genetic circuits carried in highly‐insulated E. coli genomic landing pads Park, Yongjin; Espah Borujeni, Amin; Gorochowski, Thomas E. Molecular Systems Biology, Vol. 16, Issue 8 https://doi.org/10.15252/msb.20209584	journal	August 2020
Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron Taketani, Mao; Zhang, Jianbo; Zhang, Shuyi Nature Biotechnology, Vol. 38, Issue 8 https://doi.org/10.1038/s41587-020-0468-5	journal	March 2020
Genetic circuit design automation for yeast Chen, Ye; Zhang, Shuyi; Young, Eric M. Nature Microbiology, Vol. 5, Issue 11 https://doi.org/10.1038/s41564-020-0757-2	journal	August 2020

Similar Records

Genetic circuit design automation for yeast

Journal Article · 2020 · Nature Microbiology · OSTI ID:1797308

Chen, Ye; Zhang, Shuyi; Young, Eric M.; +3 more

P recision design of stable genetic circuits carried in highly-insulated E. coli genomic landing pads

Journal Article · 2020 · Molecular Systems Biology · OSTI ID:1803378

Park, Yongjin; Espah Borujeni, Amin; Gorochowski, Thomas E.; +2 more

Genetic circuit characterization by inferring RNA polymerase movement and ribosome usage

Journal Article · 2020 · Nature Communications · OSTI ID:1816829

Espah Borujeni, Amin; Zhang, Jing; Doosthosseini, Hamid; +2 more

Related Subjects

Biochemistry & Molecular Biology

Genetic circuit design automation with Cello 2.0

Citation Formats

References (31)

Similar Records

Related Subjects