Synthetic evolution
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Andrew D Ellington | Anna J Simon | Simon d'Oelsnitz | A. Ellington | Simon d’Oelsnitz | Anna J. Simon
[1] Hal S Alper,et al. In vivo continuous evolution of genes and pathways in yeast , 2016, Nature Communications.
[2] Jameson K. Rogers,et al. Evolution-guided optimization of biosynthetic pathways , 2014, Proceedings of the National Academy of Sciences.
[3] J. Keasling,et al. CasPER, a method for directed evolution in genomic contexts using mutagenesis and CRISPR/Cas9. , 2018, Metabolic engineering.
[4] David R. Liu,et al. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage , 2016, Nature.
[5] Cédric R. Weber,et al. High-throughput antibody engineering in mammalian cells by CRISPR/Cas9-mediated homology-directed mutagenesis , 2018, bioRxiv.
[6] Feng Zhang,et al. Engineered Cpf1 variants with altered PAM specificities increase genome targeting range , 2017, Nature Biotechnology.
[7] M Boutabout,et al. DNA synthesis fidelity by the reverse transcriptase of the yeast retrotransposon Ty1. , 2001, Nucleic acids research.
[8] Yan Zhang,et al. Metabolic engineering of Escherichia coli using CRISPR-Cas9 meditated genome editing. , 2015, Metabolic engineering.
[9] Stan Wang,et al. The Future of Multiplexed Eukaryotic Genome Engineering. , 2017, ACS chemical biology.
[10] David A. Scott,et al. Functionally diverse type V CRISPR-Cas systems , 2019, Science.
[11] David A. Scott,et al. Genome engineering using the CRISPR-Cas9 system , 2013, Nature Protocols.
[12] D. Botstein,et al. Identification of amino acid substitutions that alter the substrate specificity of TEM-1 beta-lactamase , 1992, Journal of bacteriology.
[13] P. Jennings,et al. Random mutagenesis of the substrate-binding site of a serine protease can generate enzymes with increased activities and altered primary specificities. , 1993, Biochemistry.
[14] Farren J. Isaacs,et al. Programming cells by multiplex genome engineering and accelerated evolution , 2009, Nature.
[15] Andrew D. Ellington,et al. Synthetic evolutionary origin of a proofreading reverse transcriptase , 2016, Science.
[16] Dan S. Tawfik,et al. Man-made cell-like compartments for molecular evolution , 1998, Nature Biotechnology.
[17] S. Benkovic,et al. Hybrid enzymes: manipulating enzyme design. , 1998, Trends in biotechnology.
[18] Merja Penttilä,et al. Yeast oligo-mediated genome engineering (YOGE). , 2013, ACS synthetic biology.
[19] K. Struhl,et al. An efficient method for generating proteins with altered enzymatic properties: application to beta-lactamase. , 1989, Proceedings of the National Academy of Sciences of the United States of America.
[20] G. Stephanopoulos,et al. Global transcription machinery engineering: a new approach for improving cellular phenotype. , 2007, Metabolic engineering.
[21] W. Stemmer,et al. DNA shuffling of a family of genes from diverse species accelerates directed evolution , 1998, Nature.
[22] Ping Wang,et al. Continuous evolution of Bacillus thuringiensis toxins overcomes insect resistance , 2016 .
[23] J. Boeke,et al. Replication infidelity during a single cycle of Ty1 retrotransposition. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[24] Jeff F. Miller,et al. Diversity-generating retroelements. , 2007, Current opinion in microbiology.
[25] Martin J. Aryee,et al. In vivo CRISPR editing with no detectable genome-wide off-target mutations , 2018, Nature.
[26] Andrew D Ellington,et al. Directed evolution of a synthetic phylogeny of programmable Trp repressors , 2018, Nature Chemical Biology.
[27] Yan Song,et al. Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells , 2016, Nature Methods.
[28] George M. Church,et al. Developmental barcoding of whole mouse via homing CRISPR , 2018, Science.
[29] C. Auerbach. CHEMICAL MUTAGENESIS , 1949, Biological Reviews of The Cambridge Philosophical Society.
[30] T. Lu,et al. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations , 2014, Science.
[31] G. F. Joyce,et al. Directed evolution of an RNA enzyme. , 1992, Science.
[32] J. Keasling,et al. High-throughput metabolic engineering: advances in small-molecule screening and selection. , 2010, Annual review of biochemistry.
[33] G. F. Joyce,et al. Randomization of genes by PCR mutagenesis. , 1992, PCR methods and applications.
[34] Joel S. Bader,et al. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design , 2011, Nature.
[35] George M. Church,et al. Rapidly evolving homing CRISPR barcodes , 2016, Nature Methods.
[36] Feng Zhang,et al. Engineered Cpf1 variants with altered PAM specificities increase genome targeting range , 2017, Nature Biotechnology.
[37] J. H. Shim,et al. Combinatorial protein engineering by incremental truncation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[38] A. Rasheed,et al. Combinatorial Chemistry: A Review , 2014 .
[39] George M. Church,et al. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems , 2013, Nucleic acids research.
[40] A. Ellington,et al. Compartmentalized partnered replication for the directed evolution of genetic parts and circuits , 2017, Nature Protocols.
[41] D. Gordenin,et al. Chromosomal site-specific double-strand breaks are efficiently targeted for repair by oligonucleotides in yeast , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[42] David R. Liu,et al. Continuous evolution of B. thuringiensis toxins overcomes insect resistance , 2016, Nature.
[43] Gaelen T. Hess,et al. Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions , 2017, Nature Biotechnology.
[44] A. Camilli,et al. Tn-seq; high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms , 2009, Nature Methods.
[45] R. Simons,et al. Tropism switching in Bordetella bacteriophage defines a family of diversity-generating retroelements , 2004, Nature.
[46] S. Kosuri,et al. Highly parallel genome variant engineering with CRISPR/Cas9 , 2018, Nature Genetics.
[47] Andrew D Ellington,et al. Generalized bacterial genome editing using mobile group II introns and Cre-lox , 2013, Molecular systems biology.
[48] Jennifer A. Doudna,et al. Biology and Applications of CRISPR Systems: Harnessing Nature’s Toolbox for Genome Engineering , 2016, Cell.
[49] O. Gamborg,et al. Plant protoplast fusion and growth of intergeneric hybrid cells , 2004, Planta.
[50] J. Toscano-Garibay,et al. RNA Aptamer Evolution: Two Decades of SELEction , 2011, International journal of molecular sciences.
[51] Gaelen T. Hess,et al. Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells , 2016, Nature Methods.
[52] Ryan T Gill,et al. Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides , 2010, Nature Biotechnology.
[53] Dan S. Tawfik,et al. Evolution of new protein topologies through multistep gene rearrangements , 2006, Nature Genetics.
[54] Marc Ostermeier,et al. A combinatorial approach to hybrid enzymes independent of DNA homology , 1999, Nature Biotechnology.
[55] Jennifer A. Doudna,et al. CRISPR-Cas guides the future of genetic engineering , 2018, Science.
[56] K. Lam,et al. Combinatorial chemistry in drug discovery. , 2017, Current opinion in chemical biology.
[57] M. Maluszynski,et al. Global impact of mutation-derived varieties , 2004, Euphytica.
[58] Feng Zhang,et al. CRISPR-assisted editing of bacterial genomes , 2013, Nature Biotechnology.
[59] David R. Liu,et al. Phage-assisted continuous evolution of proteases with altered substrate specificity , 2017, Nature Communications.
[60] Arjun Ravikumar,et al. Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds , 2018, Cell.
[61] K. Struhl,et al. Saturation mutagenesis of a yeast his3 "TATA element": genetic evidence for a specific TATA-binding protein. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[62] S. Harayama,et al. Novel family shuffling methods for the in vitro evolution of enzymes. , 1999, Gene.
[63] Dieter Söll,et al. Continuous directed evolution of aminoacyl-tRNA synthetases , 2017, Nature chemical biology.
[64] L. Loeb,et al. On the fidelity of DNA replication: manganese mutagenesis in vitro. , 1985, Biochemistry.
[65] Ki-Hyun Kim,et al. Advanced Selection Methodologies for DNAzymes in Sensing and Healthcare Applications. , 2019, Trends in biochemical sciences.
[66] D. M. Brown,et al. An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues. , 1996, Journal of molecular biology.
[67] Barrett R. Morrow,et al. Retroelement-Based Genome Editing and Evolution. , 2018, ACS synthetic biology.
[68] D. Court,et al. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[69] Michael J. Shen,et al. Precise control of SCRaMbLE in synthetic haploid and diploid yeast , 2018, Nature Communications.
[70] Bryan C Dickinson,et al. Evolution of a split RNA polymerase as a versatile biosensor platform. , 2017, Nature chemical biology.
[71] W. Stemmer. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[72] John E. Dueber,et al. CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window , 2018, Nature.
[73] Joseph C. Hogan,et al. Combinatorial chemistry in drug discovery , 1997, Nature Biotechnology.
[74] A. Ellington,et al. Directed Evolution of a Panel of Orthogonal T7 RNA Polymerase Variants for in Vivo or in Vitro Synthetic Circuitry. , 2015, ACS synthetic biology.
[75] Prashant Mali,et al. Rapidly evolving homing CRISPR barcodes , 2017, Nature Methods.
[76] S. Epstein,et al. Chemical Mutagenesis , 1971, Nature.
[77] David R. Liu,et al. Negative selection and stringency modulation in phage-assisted constinuous evolution , 2014, Nature chemical biology.
[78] Jennifer L. Ong,et al. Directed evolution of polymerase function by compartmentalized self-replication , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[79] Mario Hupfeld,et al. A functional type II-A CRISPR–Cas system from Listeria enables efficient genome editing of large non-integrating bacteriophage , 2018, Nucleic acids research.
[80] Frank Buchholz,et al. A new logic for DNA engineering using recombination in Escherichia coli , 1998, Nature Genetics.
[81] Farren J. Isaacs,et al. Precise Editing at DNA Replication Forks Enables Multiplex Genome Engineering in Eukaryotes , 2017, Cell.
[82] F. Sherman,et al. Transformation of yeast with synthetic oligonucleotides. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[83] Christopher A. Voigt,et al. Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors , 2018, Nature Chemical Biology.
[84] D. Valentine,et al. Targeted diversity generation by intraterrestrial archaea and archaeal viruses , 2015, Nature Communications.
[85] H J Muller,et al. ARTIFICIAL TRANSMUTATION OF THE GENE. , 1927, Science.
[86] Farren J. Isaacs,et al. Rapid editing and evolution of bacterial genomes using libraries of synthetic DNA , 2014, Nature Protocols.
[87] S. Inouye,et al. Retrons, msDNA, and the bacterial genome , 2005, Cytogenetic and Genome Research.
[88] N. Costantino,et al. Recombineering: Genetic Engineering in Bacteria Using Homologous Recombination , 2003 .
[89] Vitor B. Pinheiro,et al. Evolving a polymerase for hydrophobic base analogues. , 2009, Journal of the American Chemical Society.
[90] W. Stemmer,et al. Genome shuffling leads to rapid phenotypic improvement in bacteria , 2002, Nature.
[91] David R. Liu,et al. A System for the Continuous Directed Evolution of Biomolecules , 2011, Nature.
[92] W. Stemmer. Rapid evolution of a protein in vitro by DNA shuffling , 1994, Nature.
[93] Feng Zhang,et al. Genome engineering using CRISPR-Cas9 system. , 2015, Methods in molecular biology.
[94] J. Peberdy. Developments in protoplast fusion in fungi. , 1987, Microbiological sciences.
[95] R. Simons,et al. Reverse Transcriptase-Mediated Tropism Switching in Bordetella Bacteriophage , 2002, Science.
[96] Alex Toftgaard Nielsen,et al. CRMAGE: CRISPR Optimized MAGE Recombineering , 2016, Scientific Reports.
[97] E. M. DeGennaro,et al. Multiplex gene editing by CRISPR-Cpf1 through autonomous processing of a single crRNA array , 2016, Nature Biotechnology.
[98] D. Court,et al. Recombineering: a homologous recombination-based method of genetic engineering , 2009, Nature Protocols.
[99] S. Pääbo,et al. Molecular breeding of polymerases for amplification of ancient DNA , 2007, Nature Biotechnology.
[100] R. Tsien,et al. Evolution of new nonantibody proteins via iterative somatic hypermutation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[101] Vincent L. Butty,et al. An Adaptable Platform for Directed Evolution in Human Cells. , 2018, Journal of the American Chemical Society.
[102] Tony P. Huang,et al. Continuous directed evolution of proteins with improved soluble expression , 2018, Nature Chemical Biology.
[103] Daniel E. Deatherage,et al. Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli , 2013, Proceedings of the National Academy of Sciences.
[104] Xintian Li,et al. Recombineering: Genetic Engineering in Bacteria Using Homologous Recombination , 2003, Current protocols in molecular biology.
[105] B. González,et al. Positive selection of DNA-protein interactions in mammalian cells through phenotypic coupling with retrovirus production , 2009, Nature Structural &Molecular Biology.
[106] S. Zimmerly,et al. An Unexplored Diversity of Reverse Transcriptases in Bacteria , 2015, Microbiology spectrum.
[107] David R. Liu,et al. Evolved Cas9 variants with broad PAM compatibility and high DNA specificity , 2018, Nature.
[108] David R. Liu,et al. Development of potent in vivo mutagenesis plasmids with broad mutational spectra , 2015, Nature Communications.
[109] C. Craik,et al. Substrate specificity of trypsin investigated by using a genetic selection. , 1990, Proceedings of the National Academy of Sciences of the United States of America.
[110] A. Ellington,et al. Library Generation by Gene Shuffling , 2014, Current protocols in molecular biology.
[111] Arjun Ravikumar,et al. An orthogonal DNA replication system in yeast. , 2014, Nature chemical biology.
[112] Andrew D Griffiths,et al. Amplification of complex gene libraries by emulsion PCR , 2006, Nature Methods.
[113] Frances H Arnold,et al. General method for sequence-independent site-directed chimeragenesis. , 2003, Journal of molecular biology.
[114] Harri Savilahti,et al. Critical evaluation of random mutagenesis by error-prone polymerase chain reaction protocols, Escherichia coli mutator strain, and hydroxylamine treatment. , 2009, Analytical biochemistry.
[115] M. Ditzler,et al. In vitro evolution of distinct self-cleaving ribozymes in diverse environments , 2015, Nucleic acids research.
[116] Michael R. Green,et al. CRISPR-Cas9–mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy , 2017, Proceedings of the National Academy of Sciences.
[117] Harleen Kaur,et al. Recent developments in cell-SELEX technology for aptamer selection. , 2018, Biochimica et biophysica acta. General subjects.
[118] Frances H. Arnold,et al. Enzyme Engineering for Nonaqueous Solvents: Random Mutagenesis to Enhance Activity of Subtilisin E in Polar Organic Media , 1991, Bio/Technology.
[119] G. Weiss,et al. Protein Engineering with Biosynthesized Libraries from Bordetella bronchiseptica Bacteriophage , 2013, PloS one.
[120] G. Church,et al. Genome-scale promoter engineering by Co-Selection MAGE , 2012, Nature Methods.
[121] István Nagy,et al. Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance , 2018, Proceedings of the National Academy of Sciences.
[122] Ryan T Gill,et al. Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering , 2016, Nature Biotechnology.
[123] Manel Camps,et al. Targeted gene evolution in Escherichia coli using a highly error-prone DNA polymerase I , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[124] J. Doudna,et al. A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.
[125] R. Sauer,et al. Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences. , 1988, Science.
[126] M. Neuberger,et al. Generation and iterative affinity maturation of antibodies in vitro using hypermutating B-cell lines , 2002, Nature Biotechnology.
[127] Kyung-Soon Park,et al. Phenotypic alteration of eukaryotic cells using randomized libraries of artificial transcription factors , 2003, Nature Biotechnology.
[128] Alaksh Choudhury,et al. Iterative genome editing of Escherichia coli for 3-hydroxypropionic acid production. , 2018, Metabolic engineering.
[129] A. Ellington,et al. Compartmentalized Self‐Replication for Evolution of a DNA Polymerase , 2018, Current protocols in chemical biology.
[130] F. Arnold,et al. Evolving strategies for enzyme engineering. , 2005, Current opinion in structural biology.
[131] D. Gokhale,et al. Protoplast fusion: a tool for intergeneric gene transfer in bacteria. , 1993, Biotechnology advances.
[132] S. Jinks-Robertson,et al. Oligonucleotide transformation of yeast reveals mismatch repair complexes to be differentially active on DNA replication strands , 2007, Proceedings of the National Academy of Sciences.
[133] Jeff F. Miller,et al. Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey , 2017, Nucleic acids research.
[134] Brian C. Thomas,et al. Retroelement guided protein diversification abounds in vast lineages of bacteria and archaea , 2017, Nature Microbiology.
[135] Andrew D. Ellington,et al. Directed evolution of genetic parts and circuits by compartmentalized partnered replication , 2013, Nature Biotechnology.
[136] G. Stephanopoulos,et al. Engineering Yeast Transcription Machinery for Improved Ethanol Tolerance and Production , 2006, Science.
[137] Joseph D. Janizek,et al. Accurate classification of BRCA1 variants with saturation genome editing , 2018, Nature.
[138] Le Cong,et al. Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.
[139] Robert P. St.Onge,et al. Multiplexed precision genome editing with trackable genomic barcodes in yeast , 2018, Nature Biotechnology.
[140] Qi-li Zhu,et al. Using global transcription machinery engineering (gTME) to improve ethanol tolerance of Zymomonas mobilis , 2016, Microbial Cell Factories.
[141] Farren J. Isaacs,et al. Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection , 2012, Nucleic acids research.
[142] J. Doudna,et al. The new frontier of genome engineering with CRISPR-Cas9 , 2014, Science.
[143] D. Goeddel,et al. A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction , 1989 .