Beyond directed evolution: Darwinian selection as a tool for synthetic biology

On the origin of species by means of natural selection, or, The preservation of favoured races in the struggle for life /

Darwin, C. R., Darwin, C. R., & Edmonds & Remnants (1859) · J. Murray eBooks · doi:10.5962/bhl.title.59991 · Cited by 7,019 · see citing works

On the origin of species by means of natural selection, or, The preservation of favoured races in the struggle for life

Darwin, C. R., Murray, J. J., Sons, W. C. A., & Evans., B. &. (1859) · doi:10.5962/bhl.title.82303 · Cited by 5,610 · see citing works

The Blind Watchmaker

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Drug Discovery and Natural Products: End of an Era or an Endless Frontier?

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The variation of animals and plants under domestication /

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In vitro selection and evolution of functional proteins by using ribosome display

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The variation of animals and plants under domestication /

Darwin, C. R. (1883) · D. Appleton and company eBooks · doi:10.5962/bhl.title.87899 · Cited by 998 · see citing works

Man-made cell-like compartments for molecular evolution

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Tuning genetic control through promoter engineering

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On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life

Darwin, C. R. (1888) · Springer eBooks · doi:10.1007/978-3-319-19650-3_303511 · Cited by 869 · see citing works

Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth

Ibarra, R. U., Edwards, J. S., & Palsson, B. O. (2002) · Nature · doi:10.1038/nature01149 · Cited by 857 · see citing works

Engineering Yeast Transcription Machinery for Improved Ethanol Tolerance and Production

Alper, H., Moxley, J., Nevoigt, E., Fink, G. R., & Stephanopoulos, G. (2006) · Science · doi:10.1126/science.1131969 · Cited by 823 · cited 1× · see citing works

Genome shuffling leads to rapid phenotypic improvement in bacteria

Zhang, Y., Perry, K., Vinci, V. A., Powell, K. A., Stemmer, W. P. C., & del Cardayré, S. B. (2002) · Nature · doi:10.1038/415644a · Cited by 562 · see citing works

Combinatorial Synthesis of Genetic Networks

Guet, C. C., Elowitz, M. B., Hsing, W., & Leibler, S. (2002) · Science · doi:10.1126/science.1067407 · Cited by 527 · see citing works

Directed evolution of a genetic circuit

Yokobayashi, Y., Weiss, R., & Arnold, F. H. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.252535999 · Cited by 457 · see citing works

In silico design and adaptive evolution of Escherichia coli for production of lactic acid

Fong, S. S., Burgard, A. P., Herring, C. D., Knight, E. M., Blattner, F. R., Maranas, C. D., & Palsson, B. Ø. (2005) · Biotechnology and Bioengineering · doi:10.1002/bit.20542 · Cited by 363 · see citing works

Refactoring bacteriophage T7

Chan, L. Y., Kosuri, S., & Endy, D. (2005) · Molecular Systems Biology · doi:10.1038/msb4100025 · Cited by 359 · see citing works

Parallel adaptive evolution cultures of<i>Escherichia coli</i>lead to convergent growth phenotypes with different gene expression states

Fong, S. S., Joyce, A. R., & Palsson, B. Ø. (2005) · Genome Research · doi:10.1101/gr.3832305 · Cited by 265 · see citing works

Synthetic biology: discovering new worlds and new words

de Lorenzo, V., & Danchin, A. (2008) · EMBO Reports · doi:10.1038/embor.2008.159 · Cited by 193 · see citing works

Directed Evolution of AraC for Improved Compatibility of Arabinose- and Lactose-Inducible Promoters

Lee, S. K., Chou, H. H., Pfleger, B. F., Newman, J. D., Yoshikuni, Y., & Keasling, J. D. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00791-07 · Cited by 102 · see citing works

Novel folded protein domains generated by combinatorial shuffling of polypeptide segments

Riechmann, L., & Winter, G. P. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.170145497 · Cited by 92 · see citing works

Construction and Enhancement of a Minimal Genetic AND Logic Gate

Sayut, D. J., Niu, Y. D., & Sun, L. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.01684-08 · Cited by 45 · see citing works

Functional Screening Yields a New β-1,4-Endoglucanase Gene from Heterodera glycines that May be the Product of Recent Gene Duplication

Yan, Y., Smant, G., & Davis, E. (2001) · Molecular Plant-Microbe Interactions · doi:10.1094/mpmi.2001.14.1.63 · Cited by 42 · see citing works

Engineering Escherichia coli heat-resistance by synthetic gene amplification

Christ, D., & Chin, J. W. (2008) · Protein Engineering Design and Selection · doi:10.1093/protein/gzm085 · Cited by 30 · see citing works

A Dual Selection Module for Directed Evolution of Genetic Circuits

Yokobayashi, Y., & Arnold, F. H. (2005) · Natural Computing · doi:10.1007/s11047-004-7442-x · Cited by 29 · see citing works

In vitro evolution of an antibody fragment population to find high-affinity hapten binders

Persson, H., Wallmark, H., Ljungars, A., Hallborn, J., & Ohlin, M. (2008) · Protein Engineering Design and Selection · doi:10.1093/protein/gzn024 · Cited by 24 · see citing works

Can we build synthetic, multicellular systems by controlling developmental signaling in space and time?

Ismagilov, R. F., & Maharbiz, M. M. (2007) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2007.10.003 · Cited by 14 · see citing works

Selective gene amplification

Kelly, B. T., & Griffiths, A. D. (2007) · Protein Engineering Design and Selection · doi:10.1093/protein/gzm060 · Cited by 12 · see citing works

Random screening of promoters from Escherichia coli and classification based on the promoter strength.

Kubota, M., Yamazaki, Y., & Ishihama, A. (1991) · The Japanese Journal of Genetics · doi:10.1266/jjg.66.399 · Cited by 7 · see citing works

Adaptive laboratory evolution—Principles and applications for biotechnology

Dragosits, M., & Mattanovich, D. (2013) · Microbial Cell Factories · doi:10.1186/1475-2859-12-64 · Cited by 827 · see citing works

Directed evolution: an evolving and enabling synthetic biology tool

Cobb, R. E., Si, T., & Zhao, H. (2012) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2012.05.186 · Cited by 98 · see citing works

The ten grand challenges of synthetic life

Porcar, M., Danchin, A., de Lorenzo, V., dos Santos, V. A. P. M., Krasnogor, N., Rasmussen, S., & Moyá, A. (2011) · Systems and Synthetic Biology · doi:10.1007/s11693-011-9084-5 · Cited by 67 · see citing works

Design and testing of a synthetic biology framework for genetic engineering of Corynebacterium glutamicum

Ravasi, P., Peirú, S., Gramajo, H. C., & Menzella, H. G. (2012) · Microbial Cell Factories · doi:10.1186/1475-2859-11-147 · Cited by 52 · see citing works

Bacterial Microcolonies in Gel Beads for High-Throughput Screening of Libraries in Synthetic Biology

Duarte, J. M., Barbier, I., & Schaerli, Y. (2017) · ACS Synthetic Biology · doi:10.1021/acssynbio.7b00111 · Cited by 47 · see citing works

Cognizance of Molecular Methods for the Generation of Mutagenic Phage Display Antibody Libraries for Affinity Maturation

Lim, C. C., Choong, Y. S., & Lim, T. S. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20081861 · Cited by 44 · see citing works

Building synthetic gene circuits from combinatorial libraries: screening and selection strategies

Schaerli, Y., & Isalan, M. (2013) · Molecular BioSystems · doi:10.1039/c2mb25483b · Cited by 37 · see citing works

From bricolage to BioBricks™: Synthetic biology and rational design

Lewens, T. (2013) · Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences · doi:10.1016/j.shpsc.2013.05.011 · Cited by 20 · see citing works

Designing de novo: interdisciplinary debates in synthetic biology

Delgado, A. M., & Porcar, M. (2013) · Systems and Synthetic Biology · doi:10.1007/s11693-013-9106-6 · Cited by 18 · see citing works

Are we doing synthetic biology?

Porcar, M., & Peretó, J. G. (2012) · Systems and Synthetic Biology · doi:10.1007/s11693-012-9101-3 · Cited by 15 · see citing works

Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation

Mozhayskiy, V., & Tagkopoulos, I. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-s10-s10 · Cited by 13 · see citing works

Implementing conventional logic unconventionally: Photochromic molecular populations as registers and logic gates

Chaplin, J. C., Russell, N. A., & Krasnogor, N. (2012) · Biosystems · doi:10.1016/j.biosystems.2011.12.005 · Cited by 9 · see citing works

Is synthetic biology mechanical biology?

Holm, S. (2015) · History & Philosophy of the Life Sciences · doi:10.1007/s40656-015-0081-y · Cited by 9 · see citing works

De novo design of synthetic microbial genomes

Koster, C. C., Oliveira, H. D. C., van Beveren, F., Houkes, J., van Hooff, J. J. E., Ettema, T. J. G., John van der, O. O. S. T., & Claassens, N. J. (2026) · Nature Reviews Bioengineering · doi:10.1038/s44222-026-00410-0 · Cited by 8 · see citing works

Detection of pks Island mRNAs Using Toehold Sensors in Escherichia coli

Heo, T., Kang, H., Choi, S., & Kim, J. (2021) · Life · doi:10.3390/life11111280 · Cited by 8 · see citing works

The Hidden Charm of Life

Porcar, M. (2019) · Life · doi:10.3390/life9010005 · Cited by 4 · see citing works

Integrating ethical analysis “Into the DNA” of synthetic biology

Heavey, P. (2014) · Medicine Health Care and Philosophy · doi:10.1007/s11019-014-9588-3 · Cited by 4 · see citing works

Design Methodologies and the Limits of the Engineering-Dominated Conception of Synthetic Biology

Ijäs, T. (2018) · Acta Biotheoretica · doi:10.1007/s10441-018-9338-7 · Cited by 3 · see citing works

Genomic analysis of regulatory mechanisms involved in secondary metabolite production

Castro-Melchor, M. (2010) · University of Minnesota Digital Conservancy (University of Minnesota)

Directed evolution as a powerful synthetic biology tool

Cobb, R. E., Sun, N., & Zhao, H. (2012) · Methods · doi:10.1016/j.ymeth.2012.03.009 · Cited by 124 · see citing works

A powerful toolkit for synthetic biology: Over 3.8 billion years of evolution

Rothschild, L. J. (2010) · BioEssays · doi:10.1002/bies.200900180 · Cited by 18 · see citing works

Building synthetic gene circuits from combinatorial libraries: screening and selection strategies

Schaerli, Y., & Isalan, M. (2013) · Molecular BioSystems · doi:10.1039/c2mb25483b · Cited by 37 · see citing works

Directed evolution: an evolving and enabling synthetic biology tool

Cobb, R. E., Si, T., & Zhao, H. (2012) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2012.05.186 · Cited by 98 · see citing works

Performing selections under dynamic conditions for synthetic biology applications

Lindle, J. M., & Dunlop, M. J. (2016) · Integrative Biology · doi:10.1039/c5ib00286a · Cited by 1 · see citing works