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For: Castle SD, Grierson CS, Gorochowski TE. Towards an engineering theory of evolution. Nat Commun 2021;12:3326. [PMID: 34099656 PMCID: PMC8185075 DOI: 10.1038/s41467-021-23573-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/04/2021] [Indexed: 02/07/2023]  Open
Number Cited by Other Article(s)
1
Chen YC, Destouches L, Cook A, Fedorec AJH. Synthetic microbial ecology: engineering habitats for modular consortia. J Appl Microbiol 2024;135:lxae158. [PMID: 38936824 DOI: 10.1093/jambio/lxae158] [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: 04/27/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 06/29/2024]
2
Mao J, Zhang H, Chen Y, Wei L, Liu J, Nielsen J, Chen Y, Xu N. Relieving metabolic burden to improve robustness and bioproduction by industrial microorganisms. Biotechnol Adv 2024;74:108401. [PMID: 38944217 DOI: 10.1016/j.biotechadv.2024.108401] [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: 02/01/2024] [Revised: 05/04/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024]
3
Torrillo PA, Lieberman TD. Reversions mask the contribution of adaptive evolution in microbiomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557751. [PMID: 37745437 PMCID: PMC10515931 DOI: 10.1101/2023.09.14.557751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
4
Gilliot PA, Gorochowski TE. Transfer learning for cross-context prediction of protein expression from 5'UTR sequence. Nucleic Acids Res 2024:gkae491. [PMID: 38864396 DOI: 10.1093/nar/gkae491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 04/28/2024] [Accepted: 05/28/2024] [Indexed: 06/13/2024]  Open
5
Castle SD, Stock M, Gorochowski TE. Engineering is evolution: a perspective on design processes to engineer biology. Nat Commun 2024;15:3640. [PMID: 38684714 PMCID: PMC11059173 DOI: 10.1038/s41467-024-48000-1] [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: 09/11/2023] [Accepted: 04/18/2024] [Indexed: 05/02/2024]  Open
6
Wang Z, Pan H, Ni S, Li Z, Lian J. Establishing CRISPRi for Programmable Gene Repression and Genome Evolution in Cupriavidus necator. ACS Synth Biol 2024;13:851-861. [PMID: 38350870 DOI: 10.1021/acssynbio.3c00664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
7
Stock M, Gorochowski TE. Open-endedness in synthetic biology: A route to continual innovation for biological design. SCIENCE ADVANCES 2024;10:eadi3621. [PMID: 38241375 DOI: 10.1126/sciadv.adi3621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
8
Gyorgy A. Competition and evolutionary selection among core regulatory motifs in gene expression control. Nat Commun 2023;14:8266. [PMID: 38092759 PMCID: PMC10719253 DOI: 10.1038/s41467-023-43327-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023]  Open
9
Lässig M, Mustonen V, Nourmohammad A. Steering and controlling evolution - from bioengineering to fighting pathogens. Nat Rev Genet 2023;24:851-867. [PMID: 37400577 PMCID: PMC11137064 DOI: 10.1038/s41576-023-00623-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
10
Ju Y, Zhang H, Du X, Wei J, Liu J, Wei L, Liu Q, Xu N. DRAGON: Harnessing the power of DNA repair for accelerating genome evolution in Corynebacterium glutamicum. Metab Eng 2023;79:182-191. [PMID: 37579915 DOI: 10.1016/j.ymben.2023.08.002] [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: 03/30/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023]
11
Sloan WT, Gómez-Borraz TL. Engineering biology in the face of uncertainty. Interface Focus 2023;13:20230001. [PMID: 37303745 PMCID: PMC10251114 DOI: 10.1098/rsfs.2023.0001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 03/24/2023] [Indexed: 06/13/2023]  Open
12
Hanson AD, Lorenzo VD. Synthetic Biology─High Time to Deliver? ACS Synth Biol 2023;12:1579-1582. [PMID: 37322887 PMCID: PMC10278163 DOI: 10.1021/acssynbio.3c00238] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Indexed: 06/17/2023]
13
Ingram D, Stan GB. Modelling genetic stability in engineered cell populations. Nat Commun 2023;14:3471. [PMID: 37308512 DOI: 10.1038/s41467-023-38850-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/19/2023] [Indexed: 06/14/2023]  Open
14
Bailoni E, Partipilo M, Coenradij J, Grundel DAJ, Slotboom DJ, Poolman B. Minimal Out-of-Equilibrium Metabolism for Synthetic Cells: A Membrane Perspective. ACS Synth Biol 2023;12:922-946. [PMID: 37027340 PMCID: PMC10127287 DOI: 10.1021/acssynbio.3c00062] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Indexed: 04/08/2023]
15
Gilliot PA, Gorochowski TE. Design and Analysis of Massively Parallel Reporter Assays Using FORECAST. Methods Mol Biol 2023;2553:41-56. [PMID: 36227538 DOI: 10.1007/978-1-0716-2617-7_3] [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] [Indexed: 06/16/2023]
16
Martin JF, D'Avino PP. A theory of rapid evolutionary change explaining the de novo appearance of megakaryocytes and platelets in mammals. J Cell Sci 2022;135:285954. [PMID: 36515566 PMCID: PMC10112974 DOI: 10.1242/jcs.260286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
17
Yu H, Li L, Huffman A, Beverley J, Hur J, Merrell E, Huang HH, Wang Y, Liu Y, Ong E, Cheng L, Zeng T, Zhang J, Li P, Liu Z, Wang Z, Zhang X, Ye X, Handelman SK, Sexton J, Eaton K, Higgins G, Omenn GS, Athey B, Smith B, Chen L, He Y. A new framework for host-pathogen interaction research. Front Immunol 2022;13:1066733. [PMID: 36591248 PMCID: PMC9797517 DOI: 10.3389/fimmu.2022.1066733] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/14/2022] [Indexed: 12/23/2022]  Open
18
Butt H, Ramirez JLM, Mahfouz M. Synthetic evolution of herbicide resistance using a T7 RNAP-based random DNA base editor. Life Sci Alliance 2022;5:5/12/e202201538. [PMID: 36171140 PMCID: PMC9526444 DOI: 10.26508/lsa.202201538] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/24/2022]  Open
19
Moschner C, Wedd  C, Bakshi  S. The context matrix: Navigating biological complexity for advanced biodesign. Front Bioeng Biotechnol 2022;10:954707. [PMID: 36082163 PMCID: PMC9445834 DOI: 10.3389/fbioe.2022.954707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/29/2022] [Indexed: 12/05/2022]  Open
20
Rotrattanadumrong R, Yokobayashi Y. Experimental exploration of a ribozyme neutral network using evolutionary algorithm and deep learning. Nat Commun 2022;13:4847. [PMID: 35977956 PMCID: PMC9385714 DOI: 10.1038/s41467-022-32538-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022]  Open
21
Zachar I, Boza G. The Evolution of Microbial Facilitation: Sociogenesis, Symbiogenesis, and Transition in Individuality. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.798045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
22
Tarnowski MJ, Gorochowski TE. Massively parallel characterization of engineered transcript isoforms using direct RNA sequencing. Nat Commun 2022;13:434. [PMID: 35064117 PMCID: PMC8783025 DOI: 10.1038/s41467-022-28074-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 01/07/2022] [Indexed: 12/23/2022]  Open
23
A light tunable differentiation system for the creation and control of consortia in yeast. Nat Commun 2021;12:5829. [PMID: 34611168 PMCID: PMC8492667 DOI: 10.1038/s41467-021-26129-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023]  Open
24
Clark CJ, Scott-Brown J, Gorochowski TE. paraSBOLv: a foundation for standard-compliant genetic design visualization tools. Synth Biol (Oxf) 2021;6:ysab022. [PMID: 34712845 PMCID: PMC8546602 DOI: 10.1093/synbio/ysab022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/30/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022]  Open
25
Pentz JT, Lind PA. Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens. PLoS Genet 2021;17:e1009722. [PMID: 34351900 PMCID: PMC8370652 DOI: 10.1371/journal.pgen.1009722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 08/17/2021] [Accepted: 07/16/2021] [Indexed: 11/18/2022]  Open
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