References analysis of the Wikipedia article "Directed evolution" in the English version

doi.org

Lutz S (December 2010). "Beyond directed evolution—semi-rational protein engineering and design". Current Opinion in Biotechnology. 21 (6): 734–43. doi:10.1016/j.copbio.2010.08.011. PMC 2982887. PMID 20869867.

Cobb RE, Chao R, Zhao H (May 2013). "Directed Evolution: Past, Present and Future". AIChE Journal. 59 (5): 1432–1440. doi:10.1002/aic.13995. PMC 4344831. PMID 25733775.

Mills DR, Peterson RL, Spiegelman S (July 1967). "An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule". Proceedings of the National Academy of Sciences of the United States of America. 58 (1): 217–24. Bibcode:1967PNAS...58..217M. doi:10.1073/pnas.58.1.217. PMC 335620. PMID 5231602.

Hall BG (July 1978). "Experimental evolution of a new enzymatic function. II. Evolution of multiple functions for ebg enzyme in E. coli". Genetics. 89 (3): 453–65. doi:10.1093/genetics/89.3.453. PMC 1213848. PMID 97169.

Smith GP (June 1985). "Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface". Science. 228 (4705): 1315–7. Bibcode:1985Sci...228.1315S. doi:10.1126/science.4001944. PMID 4001944.

Chen K, Arnold FH (1991). "Enzyme Engineering for Nonaqueous Solvents: Random Mutagenesis to Enhance Activity of Subtilisin E in Polar Organic Media". Bio/Technology. 9 (11): 1073–1077. doi:10.1038/nbt1191-1073. ISSN 0733-222X. PMID 1367624. S2CID 12380597.

Kim, Eun-Sung (2008-11-27). "Directed Evolution: A Historical Exploration into an Evolutionary Experimental System of Nanobiotechnology, 1965–2006". Minerva. 46 (4): 463–484. doi:10.1007/s11024-008-9108-9. ISSN 0026-4695. S2CID 55845851.

Packer MS, Liu DR (July 2015). "Methods for the directed evolution of proteins". Nature Reviews. Genetics. 16 (7): 379–94. doi:10.1038/nrg3927. PMID 26055155. S2CID 205486139.

Voigt CA, Kauffman S, Wang ZG (2000). "Rational evolutionary design: the theory of in vitro protein evolution". Evolutionary Protein Design. Vol. 55. pp. 79–160. doi:10.1016/s0065-3233(01)55003-2. ISBN 9780120342556. PMID 11050933. {{cite book}}: |journal= ignored (help)

Dalby PA (August 2011). "Strategy and success for the directed evolution of enzymes". Current Opinion in Structural Biology. 21 (4): 473–80. doi:10.1016/j.sbi.2011.05.003. PMID 21684150.

Lipovsek D, Plückthun A (July 2004). "In-vitro protein evolution by ribosome display and mRNA display". Journal of Immunological Methods. 290 (1–2): 51–67. doi:10.1016/j.jim.2004.04.008. PMID 15261571.

Dryden DT, Thomson AR, White JH (August 2008). "How much of protein sequence space has been explored by life on Earth?". Journal of the Royal Society, Interface. 5 (25): 953–6. doi:10.1098/rsif.2008.0085. PMC 2459213. PMID 18426772.

Kuchner O, Arnold FH (December 1997). "Directed evolution of enzyme catalysts". Trends in Biotechnology. 15 (12): 523–30. doi:10.1016/s0167-7799(97)01138-4. PMID 9418307.

Sen S, Venkata Dasu V, Mandal B (December 2007). "Developments in directed evolution for improving enzyme functions". Applied Biochemistry and Biotechnology. 143 (3): 212–23. doi:10.1007/s12010-007-8003-4. PMID 18057449. S2CID 32550018.

Jones DD (May 2005). "Triplet nucleotide removal at random positions in a target gene: the tolerance of TEM-1 beta-lactamase to an amino acid deletion". Nucleic Acids Research. 33 (9): e80. doi:10.1093/nar/gni077. PMC 1129029. PMID 15897323.

Stemmer WP (August 1994). "Rapid evolution of a protein in vitro by DNA shuffling". Nature. 370 (6488): 389–91. Bibcode:1994Natur.370..389S. doi:10.1038/370389a0. PMID 8047147. S2CID 4363498.

Crameri A, Raillard SA, Bermudez E, Stemmer WP (January 1998). "DNA shuffling of a family of genes from diverse species accelerates directed evolution". Nature. 391 (6664): 288–91. Bibcode:1998Natur.391..288C. doi:10.1038/34663. PMID 9440693. S2CID 4352696.

Reetz MT, Carballeira JD (2007). "Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes". Nature Protocols. 2 (4): 891–903. doi:10.1038/nprot.2007.72. PMID 17446890. S2CID 37361631.

Hartl DL (October 2014). "What can we learn from fitness landscapes?". Current Opinion in Microbiology. 21: 51–7. doi:10.1016/j.mib.2014.08.001. PMC 4254422. PMID 25444121.

Badran AH, Liu DR (February 2015). "In vivo continuous directed evolution". Current Opinion in Chemical Biology. 24: 1–10. doi:10.1016/j.cbpa.2014.09.040. PMC 4308500. PMID 25461718.

Kumar A, Singh S (December 2013). "Directed evolution: tailoring biocatalysts for industrial applications". Critical Reviews in Biotechnology. 33 (4): 365–78. doi:10.3109/07388551.2012.716810. PMID 22985113. S2CID 42821437.

Willats WG (December 2002). "Phage display: practicalities and prospects". Plant Molecular Biology. 50 (6): 837–54. doi:10.1023/A:1021215516430. PMID 12516857. S2CID 4960676.

Leemhuis H, Stein V, Griffiths AD, Hollfelder F (August 2005). "New genotype–phenotype linkages for directed evolution of functional proteins". Current Opinion in Structural Biology. 15 (4): 472–8. doi:10.1016/j.sbi.2005.07.006. PMID 16043338.

Verhoeven KD, Altstadt OC, Savinov SN (March 2012). "Intracellular detection and evolution of site-specific proteases using a genetic selection system". Applied Biochemistry and Biotechnology. 166 (5): 1340–54. doi:10.1007/s12010-011-9522-6. PMID 22270548. S2CID 36583382.

Nguyen AW, Daugherty PS (March 2005). "Evolutionary optimization of fluorescent proteins for intracellular FRET". Nature Biotechnology. 23 (3): 355–60. doi:10.1038/nbt1066. PMID 15696158. S2CID 24202205.

Schaerli Y, Hollfelder F (December 2009). "The potential of microfluidic water-in-oil droplets in experimental biology". Molecular BioSystems. 5 (12): 1392–404. doi:10.1039/b907578j. PMID 20023716.

Marshall SA, Lazar GA, Chirino AJ, Desjarlais JR (March 2003). "Rational design and engineering of therapeutic proteins". Drug Discovery Today. 8 (5): 212–21. doi:10.1016/s1359-6446(03)02610-2. PMID 12634013.

Wilson CJ (27 October 2014). "Rational protein design: developing next-generation biological therapeutics and nanobiotechnological tools". Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology. 7 (3): 330–41. doi:10.1002/wnan.1310. PMID 25348497.

Giger L, Caner S, Obexer R, Kast P, Baker D, Ban N, Hilvert D (August 2013). "Evolution of a designed retro-aldolase leads to complete active site remodeling". Nature Chemical Biology. 9 (8): 494–8. doi:10.1038/nchembio.1276. PMC 3720730. PMID 23748672.

Bornscheuer UT, Pohl M (April 2001). "Improved biocatalysts by directed evolution and rational protein design". Current Opinion in Chemical Biology. 5 (2): 137–43. doi:10.1016/s1367-5931(00)00182-4. PMID 11282339.

Kaznatcheev, Artem (2019-05-01). "Computational Complexity as an Ultimate Constraint on Evolution". Genetics. 212 (1): 245–265. doi:10.1534/genetics.119.302000. ISSN 0016-6731. PMC 6499524. PMID 30833289.

Iram, Shamreen; Dolson, Emily; Chiel, Joshua; Pelesko, Julia; Krishnan, Nikhil; Güngör, Özenç; Kuznets-Speck, Benjamin; Deffner, Sebastian; Ilker, Efe; Scott, Jacob G.; Hinczewski, Michael (2020-08-24). "Controlling the speed and trajectory of evolution with counterdiabatic driving". Nature Physics. 17: 135–142. arXiv:1912.03764. doi:10.1038/s41567-020-0989-3. ISSN 1745-2481. S2CID 224474363.

Goldsmith M, Tawfik DS (August 2012). "Directed enzyme evolution: beyond the low-hanging fruit". Current Opinion in Structural Biology. 22 (4): 406–12. doi:10.1016/j.sbi.2012.03.010. PMID 22579412.

Chen MM, Snow CD, Vizcarra CL, Mayo SL, Arnold FH (April 2012). "Comparison of random mutagenesis and semi-rational designed libraries for improved cytochrome P450 BM3-catalyzed hydroxylation of small alkanes". Protein Engineering, Design & Selection. 25 (4): 171–8. doi:10.1093/protein/gzs004. PMID 22334757.

Acevedo-Rocha CG, Hoebenreich S, Reetz MT (2014). "Iterative Saturation Mutagenesis: A Powerful Approach to Engineer Proteins by Systematically Simulating Darwinian Evolution". Directed Evolution Library Creation. Methods in Molecular Biology. Vol. 1179. pp. 103–28. doi:10.1007/978-1-4939-1053-3_7. ISBN 978-1-4939-1052-6. PMID 25055773.

Jochens H, Bornscheuer UT (September 2010). "Natural diversity to guide focused directed evolution". ChemBioChem. 11 (13): 1861–6. doi:10.1002/cbic.201000284. PMID 20680978. S2CID 28333030.

Jochens H, Aerts D, Bornscheuer UT (December 2010). "Thermostabilization of an esterase by alignment-guided focussed directed evolution". Protein Engineering, Design & Selection. 23 (12): 903–9. doi:10.1093/protein/gzq071. PMID 20947674.

Turner NJ (August 2009). "Directed evolution drives the next generation of biocatalysts". Nature Chemical Biology. 5 (8): 567–73. doi:10.1038/nchembio.203. PMID 19620998.

Romero PA, Arnold FH (December 2009). "Exploring protein fitness landscapes by directed evolution". Nature Reviews. Molecular Cell Biology. 10 (12): 866–76. doi:10.1038/nrm2805. PMC 2997618. PMID 19935669.

Gatti-Lafranconi P, Natalello A, Rehm S, Doglia SM, Pleiss J, Lotti M (January 2010). "Evolution of stability in a cold-active enzyme elicits specificity relaxation and highlights substrate-related effects on temperature adaptation". Journal of Molecular Biology. 395 (1): 155–66. doi:10.1016/j.jmb.2009.10.026. PMID 19850050.

Zhao H, Arnold FH (January 1999). "Directed evolution converts subtilisin E into a functional equivalent of thermitase". Protein Engineering. 12 (1): 47–53. doi:10.1093/protein/12.1.47. PMID 10065710.

Favor AH, Llanos CD, Youngblut MD, Bardales JA (2020). "Optimizing bacteriophage engineering through an accelerated evolution platform". Scientific Reports. 10 (1): 13981. doi:10.1038/s41598-020-70841-1. PMC 7438504. PMID 32814789.

Hawkins RE, Russell SJ, Winter G (August 1992). "Selection of phage antibodies by binding affinity. Mimicking affinity maturation". Journal of Molecular Biology. 226 (3): 889–96. doi:10.1016/0022-2836(92)90639-2. PMID 1507232.

Shaikh FA, Withers SG (April 2008). "Teaching old enzymes new tricks: engineering and evolution of glycosidases and glycosyl transferases for improved glycoside synthesis". Biochemistry and Cell Biology. 86 (2): 169–77. doi:10.1139/o07-149. PMID 18443630.

Cheriyan M, Walters MJ, Kang BD, Anzaldi LL, Toone EJ, Fierke CA (November 2011). "Directed evolution of a pyruvate aldolase to recognize a long chain acyl substrate". Bioorganic & Medicinal Chemistry. 19 (21): 6447–53. doi:10.1016/j.bmc.2011.08.056. PMC 3209416. PMID 21944547.

MacBeath G, Kast P, Hilvert D (March 1998). "Redesigning enzyme topology by directed evolution". Science. 279 (5358): 1958–61. Bibcode:1998Sci...279.1958M. doi:10.1126/science.279.5358.1958. PMID 9506949.

Toscano MD, Woycechowsky KJ, Hilvert D (2007). "Minimalist active-site redesign: teaching old enzymes new tricks". Angewandte Chemie. 46 (18): 3212–36. doi:10.1002/anie.200604205. PMID 17450624.

Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M (2004). "Genetic analyses from ancient DNA". Annual Review of Genetics. 38 (1): 645–79. doi:10.1146/annurev.genet.37.110801.143214. PMID 15568989.

Höss M, Jaruga P, Zastawny TH, Dizdaroglu M, Pääbo S (April 1996). "DNA damage and DNA sequence retrieval from ancient tissues". Nucleic Acids Research. 24 (7): 1304–7. doi:10.1093/nar/24.7.1304. PMC 145783. PMID 8614634.

Bloom JD, Arnold FH (June 2009). "In the light of directed evolution: pathways of adaptive protein evolution". Proceedings of the National Academy of Sciences of the United States of America. 106 Suppl 1 (Supplement_1): 9995–10000. doi:10.1073/pnas.0901522106. PMC 2702793. PMID 19528653.

Moses AM, Davidson AR (May 2011). "In vitro evolution goes deep". Proceedings of the National Academy of Sciences of the United States of America. 108 (20): 8071–2. Bibcode:2011PNAS..108.8071M. doi:10.1073/pnas.1104843108. PMC 3100951. PMID 21551096.

Salehi-Ashtiani K, Szostak JW (November 2001). "In vitro evolution suggests multiple origins for the hammerhead ribozyme". Nature. 414 (6859): 82–4. Bibcode:2001Natur.414...82S. doi:10.1038/35102081. PMID 11689947. S2CID 4401483.

Sumper M, Luce R (January 1975). "Evidence for de novo production of self-replicating and environmentally adapted RNA structures by bacteriophage Qbeta replicase". Proceedings of the National Academy of Sciences of the United States of America. 72 (1): 162–6. Bibcode:1975PNAS...72..162S. doi:10.1073/pnas.72.1.162. PMC 432262. PMID 1054493.

Marden JH, Wolf MR, Weber KE (November 1997). "Aerial performance of Drosophila melanogaster from populations selected for upwind flight ability". The Journal of Experimental Biology. 200 (Pt 21): 2747–55. doi:10.1242/jeb.200.21.2747. PMID 9418031.

Ratcliff WC, Denison RF, Borrello M, Travisano M (January 2012). "Experimental evolution of multicellularity". Proceedings of the National Academy of Sciences of the United States of America. 109 (5): 1595–600. Bibcode:2012PNAS..109.1595R. doi:10.1073/pnas.1115323109. PMC 3277146. PMID 22307617.

Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF (October 2009). "Genome evolution and adaptation in a long-term experiment with Escherichia coli". Nature. 461 (7268): 1243–7. Bibcode:2009Natur.461.1243B. doi:10.1038/nature08480. PMID 19838166. S2CID 4330305.

Heineman RH, Molineux IJ, Bull JJ (August 2005). "Evolutionary robustness of an optimal phenotype: re-evolution of lysis in a bacteriophage deleted for its lysin gene". Journal of Molecular Evolution. 61 (2): 181–91. Bibcode:2005JMolE..61..181H. doi:10.1007/s00239-004-0304-4. PMID 16096681. S2CID 31230414.

Steinberg B, Ostermeier M (January 2016). "Environmental changes bridge evolutionary valleys". Science Advances. 2 (1): e1500921. Bibcode:2016SciA....2E0921S. doi:10.1126/sciadv.1500921. PMC 4737206. PMID 26844293.

Arnold FH, Wintrode PL, Miyazaki K, Gershenson A (February 2001). "How enzymes adapt: lessons from directed evolution". Trends in Biochemical Sciences. 26 (2): 100–6. doi:10.1016/s0968-0004(00)01755-2. PMID 11166567. S2CID 13331137.

Aita T, Hamamatsu N, Nomiya Y, Uchiyama H, Shibanaka Y, Husimi Y (July 2002). "Surveying a local fitness landscape of a protein with epistatic sites for the study of directed evolution". Biopolymers. 64 (2): 95–105. doi:10.1002/bip.10126. PMID 11979520.

Bloom JD, Raval A, Wilke CO (January 2007). "Thermodynamics of neutral protein evolution". Genetics. 175 (1): 255–66. arXiv:q-bio/0605041. doi:10.1534/genetics.106.061754. PMC 1775007. PMID 17110496.

Bacher, J. M.; Ellington, A. D. (2001). "Selection and characterization of Escherichia coli variants capable of growth on an otherwise toxic tryptophan analogue". Journal of Bacteriology. 183 (18): 5414–5425. doi:10.1128/jb.183.18.5414-5425.2001. PMC 95426. PMID 11514527.

Wong, J. T. (1983). "Membership mutation of the genetic code: Loss of fitness by tryptophan". Proc. Natl. Acad. Sci. USA. 80 (20): 6303–6306. Bibcode:1983PNAS...80.6303W. doi:10.1073/pnas.80.20.6303. PMC 394285. PMID 6413975.

Hoesl, M. G.; Oehm, S.; Durkin, P.; Darmon, E.; Peil, L.; Aerni, H.-R.; Rappsilber, J.; Rinehart, J.; Leach, D.; Söll, D.; Budisa, N. (2015). "Chemical evolution of a bacterial proteome". Angewandte Chemie International Edition. 54 (34): 10030–10034. doi:10.1002/anie.201502868. PMC 4782924. PMID 26136259. NIHMSID: NIHMS711205

Agostini, F.; Völler, J-S.; Koksch, B.; Acevedo-Rocha, C. G.; Kubyshkin, V.; Budisa, N. (2017). "Biocatalysis with Unnatural Amino Acids: Enzymology Meets Xenobiology". Angewandte Chemie International Edition. 56 (33): 9680–9703. doi:10.1002/anie.201610129. PMID 28085996.

Sandberg, T. E.; Salazar, M. J.; Weng, L. L.; Palsson, B. O.; Kubyshkin, V.; Feist, A. M. (2019). "The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology". Metab Eng. 56: 1–16. doi:10.1016/j.ymben.2019.08.004. PMC 6944292. PMID 31401242.

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Stemmer WP (August 1994). "Rapid evolution of a protein in vitro by DNA shuffling". Nature. 370 (6488): 389–91. Bibcode:1994Natur.370..389S. doi:10.1038/370389a0. PMID 8047147. S2CID 4363498.

nature.com

nih.gov

pubmed.ncbi.nlm.nih.gov

Cobb RE, Chao R, Zhao H (May 2013). "Directed Evolution: Past, Present and Future". AIChE Journal. 59 (5): 1432–1440. doi:10.1002/aic.13995. PMC 4344831. PMID 25733775.

Packer MS, Liu DR (July 2015). "Methods for the directed evolution of proteins". Nature Reviews. Genetics. 16 (7): 379–94. doi:10.1038/nrg3927. PMID 26055155. S2CID 205486139.

Dalby PA (August 2011). "Strategy and success for the directed evolution of enzymes". Current Opinion in Structural Biology. 21 (4): 473–80. doi:10.1016/j.sbi.2011.05.003. PMID 21684150.

Kuchner O, Arnold FH (December 1997). "Directed evolution of enzyme catalysts". Trends in Biotechnology. 15 (12): 523–30. doi:10.1016/s0167-7799(97)01138-4. PMID 9418307.

Stemmer WP (August 1994). "Rapid evolution of a protein in vitro by DNA shuffling". Nature. 370 (6488): 389–91. Bibcode:1994Natur.370..389S. doi:10.1038/370389a0. PMID 8047147. S2CID 4363498.

Hartl DL (October 2014). "What can we learn from fitness landscapes?". Current Opinion in Microbiology. 21: 51–7. doi:10.1016/j.mib.2014.08.001. PMC 4254422. PMID 25444121.

Badran AH, Liu DR (February 2015). "In vivo continuous directed evolution". Current Opinion in Chemical Biology. 24: 1–10. doi:10.1016/j.cbpa.2014.09.040. PMC 4308500. PMID 25461718.

Willats WG (December 2002). "Phage display: practicalities and prospects". Plant Molecular Biology. 50 (6): 837–54. doi:10.1023/A:1021215516430. PMID 12516857. S2CID 4960676.

Goldsmith M, Tawfik DS (August 2012). "Directed enzyme evolution: beyond the low-hanging fruit". Current Opinion in Structural Biology. 22 (4): 406–12. doi:10.1016/j.sbi.2012.03.010. PMID 22579412.

Jochens H, Bornscheuer UT (September 2010). "Natural diversity to guide focused directed evolution". ChemBioChem. 11 (13): 1861–6. doi:10.1002/cbic.201000284. PMID 20680978. S2CID 28333030.

Turner NJ (August 2009). "Directed evolution drives the next generation of biocatalysts". Nature Chemical Biology. 5 (8): 567–73. doi:10.1038/nchembio.203. PMID 19620998.

Toscano MD, Woycechowsky KJ, Hilvert D (2007). "Minimalist active-site redesign: teaching old enzymes new tricks". Angewandte Chemie. 46 (18): 3212–36. doi:10.1002/anie.200604205. PMID 17450624.

ncbi.nlm.nih.gov

semanticscholar.org

api.semanticscholar.org

Packer MS, Liu DR (July 2015). "Methods for the directed evolution of proteins". Nature Reviews. Genetics. 16 (7): 379–94. doi:10.1038/nrg3927. PMID 26055155. S2CID 205486139.

Stemmer WP (August 1994). "Rapid evolution of a protein in vitro by DNA shuffling". Nature. 370 (6488): 389–91. Bibcode:1994Natur.370..389S. doi:10.1038/370389a0. PMID 8047147. S2CID 4363498.

Willats WG (December 2002). "Phage display: practicalities and prospects". Plant Molecular Biology. 50 (6): 837–54. doi:10.1023/A:1021215516430. PMID 12516857. S2CID 4960676.

Jochens H, Bornscheuer UT (September 2010). "Natural diversity to guide focused directed evolution". ChemBioChem. 11 (13): 1861–6. doi:10.1002/cbic.201000284. PMID 20680978. S2CID 28333030.

worldcat.org

Arnold, Frances; Georgiou, George (2003). Directed enzyme evolution: screening and selection methods. Totowa, N.J.: Humana Press. ISBN 9781588292865. OCLC 52400248.

Directed evolution (English Wikipedia)

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api.semanticscholar.org

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