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For: Rodrigo G, Jaramillo A. AutoBioCAD: full biodesign automation of genetic circuits. ACS Synth Biol 2013;2:230-6. [PMID: 23654253 DOI: 10.1021/sb300084h] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Number Cited by Other Article(s)
1
Sinzger-D'Angelo M, Hanst M, Reinhardt F, Koeppl H. Effects of mRNA conformational switching on translational noise in gene circuits. J Chem Phys 2024;160:134108. [PMID: 38573847 DOI: 10.1063/5.0186927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/08/2024] [Indexed: 04/06/2024]  Open
2
Mousavi R, Lobo D. Automatic design of gene regulatory mechanisms for spatial pattern formation. NPJ Syst Biol Appl 2024;10:35. [PMID: 38565850 PMCID: PMC10987498 DOI: 10.1038/s41540-024-00361-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/19/2024] [Indexed: 04/04/2024]  Open
3
Mousavi R, Lobo D. Automatic design of gene regulatory mechanisms for spatial pattern formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.26.550573. [PMID: 37546866 PMCID: PMC10402059 DOI: 10.1101/2023.07.26.550573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
4
Obayashi N, Junge K, Ilić S, Hughes J. Robotic automation and unsupervised cluster assisted modeling for solving the forward and reverse design problem of paper airplanes. Sci Rep 2023;13:4212. [PMID: 36918733 PMCID: PMC10015042 DOI: 10.1038/s41598-023-31395-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/10/2023] [Indexed: 03/16/2023]  Open
5
Gupta D, Sharma G, Saraswat P, Ranjan R. Synthetic Biology in Plants, a Boon for Coming Decades. Mol Biotechnol 2021;63:1138-1154. [PMID: 34420149 DOI: 10.1007/s12033-021-00386-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/16/2021] [Indexed: 02/01/2023]
6
David F, Davis AM, Gossing M, Hayes MA, Romero E, Scott LH, Wigglesworth MJ. A Perspective on Synthetic Biology in Drug Discovery and Development-Current Impact and Future Opportunities. SLAS DISCOVERY 2021;26:581-603. [PMID: 33834873 DOI: 10.1177/24725552211000669] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
7
Karkaria BD, Fedorec AJH, Barnes CP. Automated design of synthetic microbial communities. Nat Commun 2021;12:672. [PMID: 33510148 PMCID: PMC7844305 DOI: 10.1038/s41467-020-20756-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022]  Open
8
Van Brempt M, Clauwaert J, Mey F, Stock M, Maertens J, Waegeman W, De Mey M. Predictive design of sigma factor-specific promoters. Nat Commun 2020;11:5822. [PMID: 33199691 PMCID: PMC7670410 DOI: 10.1038/s41467-020-19446-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/13/2020] [Indexed: 02/07/2023]  Open
9
Gene networks that compensate for crosstalk with crosstalk. Nat Commun 2019;10:4028. [PMID: 31492904 PMCID: PMC6731275 DOI: 10.1038/s41467-019-12021-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 08/12/2019] [Indexed: 12/18/2022]  Open
10
Gomez‐Marquez J, Hamad‐Schifferli K. Distributed Biological Foundries for Global Health. Adv Healthc Mater 2019;8:e1900184. [PMID: 31420954 DOI: 10.1002/adhm.201900184] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/24/2019] [Indexed: 01/25/2023]
11
Jeong D, Klocke M, Agarwal S, Kim J, Choi S, Franco E, Kim J. Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems. Methods Protoc 2019;2:E39. [PMID: 31164618 PMCID: PMC6632179 DOI: 10.3390/mps2020039] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/12/2019] [Accepted: 05/08/2019] [Indexed: 01/07/2023]  Open
12
Component Characterization in a Growth-Dependent Physiological Context: Optimal Experimental Design. Processes (Basel) 2019. [DOI: 10.3390/pr7010052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
13
Yehl K, Lu T. Scaling Computation and Memory in Living Cells. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2017;4:143-151. [PMID: 29915814 PMCID: PMC6003718 DOI: 10.1016/j.cobme.2017.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
14
Decoene T, De Paepe B, Maertens J, Coussement P, Peters G, De Maeseneire SL, De Mey M. Standardization in synthetic biology: an engineering discipline coming of age. Crit Rev Biotechnol 2017;38:647-656. [PMID: 28954542 DOI: 10.1080/07388551.2017.1380600] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
15
Otero-Muras I, Banga JR. Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality. ACS Synth Biol 2017;6:1180-1193. [PMID: 28350462 DOI: 10.1021/acssynbio.6b00306] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
16
Appleton E, Madsen C, Roehner N, Densmore D. Design Automation in Synthetic Biology. Cold Spring Harb Perspect Biol 2017;9:a023978. [PMID: 28246188 PMCID: PMC5378053 DOI: 10.1101/cshperspect.a023978] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
17
Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells. Nat Biotechnol 2017;35:453-462. [PMID: 28346402 PMCID: PMC5423837 DOI: 10.1038/nbt.3805] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 01/27/2017] [Indexed: 01/03/2023]
18
Mohammadi P, Beerenwinkel N, Benenson Y. Automated Design of Synthetic Cell Classifier Circuits Using a Two-Step Optimization Strategy. Cell Syst 2017;4:207-218.e14. [DOI: 10.1016/j.cels.2017.01.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 10/25/2016] [Accepted: 01/06/2017] [Indexed: 10/20/2022]
19
Otero-Muras I, Henriques D, Banga JR. SYNBADm: a tool for optimization-based automated design of synthetic gene circuits. Bioinformatics 2016;32:3360-3362. [PMID: 27402908 DOI: 10.1093/bioinformatics/btw415] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/23/2016] [Indexed: 11/12/2022]  Open
20
Nielsen AAK, Der BS, Shin J, Vaidyanathan P, Paralanov V, Strychalski EA, Ross D, Densmore D, Voigt CA. Genetic circuit design automation. Science 2016;352:aac7341. [PMID: 27034378 DOI: 10.1126/science.aac7341] [Citation(s) in RCA: 574] [Impact Index Per Article: 71.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 01/21/2016] [Indexed: 12/12/2022]
21
Van Hove B, Love AM, Ajikumar PK, De Mey M. Programming Biology: Expanding the Toolset for the Engineering of Transcription. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
22
Sadowski MI, Grant C, Fell TS. Harnessing QbD, Programming Languages, and Automation for Reproducible Biology. Trends Biotechnol 2015;34:214-227. [PMID: 26708960 DOI: 10.1016/j.tibtech.2015.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/16/2015] [Accepted: 11/19/2015] [Indexed: 12/18/2022]
23
Qi H, Li BZ, Zhang WQ, Liu D, Yuan YJ. Modularization of genetic elements promotes synthetic metabolic engineering. Biotechnol Adv 2015;33:1412-9. [DOI: 10.1016/j.biotechadv.2015.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 01/12/2015] [Accepted: 04/05/2015] [Indexed: 01/24/2023]
24
Peters G, Coussement P, Maertens J, Lammertyn J, De Mey M. Putting RNA to work: Translating RNA fundamentals into biotechnological engineering practice. Biotechnol Adv 2015;33:1829-44. [PMID: 26514597 DOI: 10.1016/j.biotechadv.2015.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/13/2015] [Accepted: 10/22/2015] [Indexed: 11/19/2022]
25
Huynh L, Tagkopoulos I. Fast and Accurate Circuit Design Automation through Hierarchical Model Switching. ACS Synth Biol 2015;4:890-7. [PMID: 25916918 DOI: 10.1021/sb500339k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
26
Ball P. Forging patterns and making waves from biology to geology: a commentary on Turing (1952) 'The chemical basis of morphogenesis'. Philos Trans R Soc Lond B Biol Sci 2015;373:rsta.2014.0218. [PMID: 25750229 DOI: 10.1098/rsta.2014.0218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2015] [Indexed: 05/21/2023]  Open
27
Eckdahl TT, Campbell AM, Heyer LJ, Poet JL, Blauch DN, Snyder NL, Atchley DT, Baker EJ, Brown M, Brunner EC, Callen SA, Campbell JS, Carr CJ, Carr DR, Chadinha SA, Chester GI, Chester J, Clarkson BR, Cochran KE, Doherty SE, Doyle C, Dwyer S, Edlin LM, Evans RA, Fluharty T, Frederick J, Galeota-Sprung J, Gammon BL, Grieshaber B, Gronniger J, Gutteridge K, Henningsen J, Isom B, Itell HL, Keffeler EC, Lantz AJ, Lim JN, McGuire EP, Moore AK, Morton J, Nakano M, Pearson SA, Perkins V, Parrish P, Pierson CE, Polpityaarachchige S, Quaney MJ, Slattery A, Smith KE, Spell J, Spencer M, Taye T, Trueblood K, Vrana CJ, Whitesides ET. Programmed evolution for optimization of orthogonal metabolic output in bacteria. PLoS One 2015;10:e0118322. [PMID: 25714374 PMCID: PMC4340930 DOI: 10.1371/journal.pone.0118322] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/13/2015] [Indexed: 11/18/2022]  Open
28
Ding Y, Wu F, Tan C. Synthetic Biology: A Bridge between Artificial and Natural Cells. Life (Basel) 2014;4:1092-116. [PMID: 25532531 PMCID: PMC4284483 DOI: 10.3390/life4041092] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/02/2014] [Accepted: 12/11/2014] [Indexed: 12/24/2022]  Open
29
Kelwick R, MacDonald JT, Webb AJ, Freemont P. Developments in the tools and methodologies of synthetic biology. Front Bioeng Biotechnol 2014;2:60. [PMID: 25505788 PMCID: PMC4244866 DOI: 10.3389/fbioe.2014.00060] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/12/2014] [Indexed: 11/27/2022]  Open
30
Marchisio MA. Parts & pools: a framework for modular design of synthetic gene circuits. Front Bioeng Biotechnol 2014;2:42. [PMID: 25340051 PMCID: PMC4186347 DOI: 10.3389/fbioe.2014.00042] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 09/16/2014] [Indexed: 01/27/2023]  Open
31
Brophy JAN, Voigt CA. Principles of genetic circuit design. Nat Methods 2014;11:508-20. [PMID: 24781324 DOI: 10.1038/nmeth.2926] [Citation(s) in RCA: 568] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/18/2014] [Indexed: 12/17/2022]
32
Moskon M, Mraz M. Systematic Approach to Computational Design of Gene Regulatory Networks with Information Processing Capabilities. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014;11:431-440. [PMID: 26355789 DOI: 10.1109/tcbb.2013.2295792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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