Memory and Combinatorial Logic Based on DNA Inversions: Dynamics and Evolutionary Stability.
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Thomas E Gorochowski | Christopher A. Voigt | Jesus Fernandez-Rodriguez | Christopher A Voigt | D Benjamin Gordon | C. Voigt | D. B. Gordon | T. Gorochowski | J. Fernandez-Rodriguez | Lei Yang | Lei Yang | Ben Gordon
[1] Christopher A. Voigt,et al. A Synthetic Genetic Edge Detection Program , 2009, Cell.
[2] J. Broach,et al. Identification of the crossover site during FLP-mediated recombination in the Saccharomyces cerevisiae plasmid 2 microns circle , 1986, Molecular and Cellular Biology.
[3] M. Masters,et al. The pcnB gene of Escherichia coli, which is required for ColE1 copy number maintenance, is dispensable , 1993, Journal of bacteriology.
[4] C. Dorman,et al. Interaction of the FimB Integrase with thefimS Invertible DNA Element in Escherichia coliIn Vivo and In Vitro , 2000, Journal of bacteriology.
[5] R. Welch,et al. Regulation of Type 1 Fimbriae by Unlinked FimB- and FimE-Like Recombinases in Uropathogenic Escherichia coli Strain CFT073 , 2006, Infection and Immunity.
[6] R. Segev,et al. GENERAL PROPERTIES OF THE TRANSCRIPTIONAL TIME-SERIES IN ESCHERICHIA COLI , 2011, Nature Genetics.
[7] Nicolas E. Buchler,et al. Protein sequestration generates a flexible ultrasensitive response in a genetic network , 2009, Molecular systems biology.
[8] A. G. Lenich,et al. Amino acid sequence homology between Piv, an essential protein in site-specific DNA inversion in Moraxella lacunata, and transposases of an unusual family of insertion elements , 1994, Journal of bacteriology.
[9] Herbert M Sauro,et al. Designing and engineering evolutionary robust genetic circuits , 2010, Journal of biological engineering.
[10] Christopher A. Voigt,et al. Ribozyme-based insulator parts buffer synthetic circuits from genetic context , 2012, Nature Biotechnology.
[11] Gürol M. Süel,et al. Engineered E. coli that detect and respond to gut inflammation through nitric oxide sensing. , 2012, ACS synthetic biology.
[12] I. Blomfield,et al. The leucine-responsive regulatory protein binds to the fim switch to control phase variation of type 1 fimbrial expression in Escherichia coli K-12 , 1994, Journal of bacteriology.
[13] Christopher A. Voigt,et al. Genomic Mining of Prokaryotic Repressors for Orthogonal Logic Gates , 2013, Nature chemical biology.
[14] Jaai Kim,et al. Absolute and relative QPCR quantification of plasmid copy number in Escherichia coli. , 2006, Journal of biotechnology.
[15] M. Simon,et al. Hin-mediated site-specific recombination requires two 26 by recombination sites and a 60 by recombinational enhancer , 1985, Cell.
[16] K. Dybvig,et al. Regulation of a restriction and modification system via DNA inversion in Mycoplasma pulmonis , 1994, Molecular microbiology.
[17] Margaret C. M. Smith,et al. Control of directionality in the site‐specific recombination system of the Streptomyces phage φC31 , 2000, Molecular microbiology.
[18] P. Klemm,et al. Two regulatory fim genes, fimB and fimE, control the phase variation of type 1 fimbriae in Escherichia coli. , 1986, The EMBO journal.
[19] D. Galas,et al. Specificity of insertion of IS1. , 1985, Journal of molecular biology.
[20] Tamás Fehér,et al. Low-mutation-rate, reduced-genome Escherichia coli: an improved host for faithful maintenance of engineered genetic constructs , 2012, Microbial Cell Factories.
[21] Timothy K Lu,et al. Synthetic circuits integrating logic and memory in living cells , 2013, Nature Biotechnology.
[22] F. Bontems,et al. Expression of highly toxic genes in E. coli: special strategies and genetic tools. , 2006, Current protein & peptide science.
[23] N. W. Davis,et al. The complete genome sequence of Escherichia coli K-12. , 1997, Science.
[24] Christopher A. Voigt,et al. Principles of genetic circuit design , 2014, Nature Methods.
[25] D. Endy. Foundations for engineering biology , 2005, Nature.
[26] D. Endy,et al. Rewritable digital data storage in live cells via engineered control of recombination directionality , 2012, Proceedings of the National Academy of Sciences.
[27] Karsten Hokamp,et al. Compensatory Evolution of Gene Regulation in Response to Stress by Escherichia coli Lacking RpoS , 2009, PLoS genetics.
[28] F. Blattner,et al. Reduced evolvability of Escherichia coli MDS42, an IS-less cellular chassis for molecular and synthetic biology applications , 2010, Microbial cell factories.
[29] Christopher A. Voigt,et al. Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters , 2013, Molecular Systems Biology.
[30] J. Collins,et al. Toehold Switches: De-Novo-Designed Regulators of Gene Expression , 2014, Cell.
[31] Timothy S. Ham,et al. A tightly regulated inducible expression system utilizing the fim inversion recombination switch. , 2006, Biotechnology and bioengineering.
[32] J. S. Parkinson,et al. Genetics and sequence analysis of the pcnB locus, an Escherichia coli gene involved in plasmid copy number control , 1989, Journal of bacteriology.
[33] Narendra Maheshri,et al. A regulatory role for repeated decoy transcription factor binding sites in target gene expression , 2012, Molecular systems biology.
[34] D. Leach,et al. Bacterial Genome Instability , 2014, Microbiology and Molecular Reviews.
[35] Yufeng Yao,et al. HbiF Regulates Type 1 Fimbriation Independently of FimB and FimE , 2006, Infection and Immunity.
[36] M. Blaser,et al. Generation of Campylobacter fetus S‐layer protein diversity utilizes a single promoter on an invertible DNA segment , 1996, Molecular microbiology.
[37] Tanja Kortemme,et al. Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli. , 2011, Journal of molecular biology.
[38] Complete Nucleotide Sequence of Tn10 , 2000, Journal of bacteriology.
[39] I. Blomfield,et al. Comparative analysis of FimB and FimE recombinase activity. , 2007, Microbiology.
[40] Laurie J. Heyer,et al. Engineering bacteria to solve the Burnt Pancake Problem , 2008, Journal of biological engineering.
[41] Takashi Matsuyama,et al. A modified Cre-lox genetic switch to dynamically control metabolic flow in Saccharomyces cerevisiae. , 2012, ACS synthetic biology.
[42] Lei Yang,et al. Permanent genetic memory with >1 byte capacity , 2014, Nature Methods.
[43] Allan Kuchinsky,et al. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology , 2014, Nature Biotechnology.
[44] J. Beckwith,et al. Mutations in a new chromosomal gene of Escherichia coli K-12, pcnB, reduce plasmid copy number of pBR322 and its derivatives , 1986, Molecular and General Genetics MGG.
[45] T. Hwa,et al. Interdependence of Cell Growth and Gene Expression: Origins and Consequences , 2010, Science.
[46] Luke A. Gilbert,et al. Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression , 2013, Cell.
[47] N. Sternberg,et al. Bacteriophage P1 site-specific recombination. I. Recombination between loxP sites. , 1981, Journal of molecular biology.
[48] A Malcolm Campbell,et al. Solving a Hamiltonian Path Problem with a bacterial computer , 2009, Journal of biological engineering.
[49] H. Sommer,et al. Nucleotide sequence of the transposable DNA-element IS2. , 1979, Nucleic acids research.
[50] Christopher A. Voigt,et al. Characterization of 582 natural and synthetic terminators and quantification of their design constraints , 2013, Nature Methods.
[51] D. Endy,et al. Refinement and standardization of synthetic biological parts and devices , 2008, Nature Biotechnology.
[52] G. Węgrzyn,et al. Transcription start sites in the promoter region of the Escherichia coli pcnB (plasmid copy number) gene coding for poly(A) polymerase I. , 2006, Plasmid.
[53] Olaf Piepenburg,et al. DNA Detection Using Recombination Proteins , 2006, PLoS biology.
[54] Norma P. Tavakoli,et al. Transposition is modulated by a diverse set of host factors in Escherichia coli and is stimulated by nutritional stress , 2005, Molecular microbiology.
[55] Farren J. Isaacs,et al. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement , 2011, Science.
[56] I. Mäger,et al. Sensitive and rapid detection of Chlamydia trachomatis by recombinase polymerase amplification directly from urine samples. , 2014, The Journal of molecular diagnostics : JMD.
[57] I. Blomfield,et al. The molecular basis for the specificity of fimE in the phase variation of type 1 fimbriae of Escherichia coli K‐12 , 1999, Molecular microbiology.
[58] Christopher A. Voigt,et al. Programming cells: towards an automated 'Genetic Compiler'. , 2010, Current opinion in biotechnology.
[59] Adam P Arkin,et al. Versatile RNA-sensing transcriptional regulators for engineering genetic networks , 2011, Proceedings of the National Academy of Sciences.
[60] T. Baker,et al. ClpS modulates but is not essential for bacterial N-end rule degradation. , 2007, Genes & development.
[61] Z. Livneh,et al. UV light induces IS10 transposition in Escherichia coli. , 1998, Genetics.
[62] Christopher A. Voigt,et al. Targeted DNA degradation using a CRISPR device stably carried in the host genome , 2015, Nature Communications.
[63] Richard E. Lenski,et al. Genetic Basis of Evolutionary Adaptation by Escherichia coli to Stressful Cycles of Freezing, Thawing and Growth , 2008, Genetics.
[64] K. Prather,et al. Proton exchange membrane and electrode surface areas as factors that affect power generation in microbial fuel cells , 2006, Applied Microbiology and Biotechnology.
[65] H. Bergmans,et al. The fim genes responsible for synthesis of type 1 fimbriae in Escherichia coli, cloning and genetic organization , 2004, Molecular and General Genetics MGG.
[66] R. Losick,et al. The Bacillus subtilis gene for the development transcription factor sigma K is generated by excision of a dispensable DNA element containing a sporulation recombinase gene. , 1990, Genes & development.
[67] Feng Zhang,et al. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system , 2013, Nucleic acids research.
[68] K. Takeshita,et al. Genetic organization of transposon Tn10 , 1981, Cell.
[69] Christopher A. Voigt,et al. Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’ , 2011, Nature.
[70] I. Blomfield,et al. Interaction of FimB and FimE with the fim switch that controls the phase variation of type 1 fimbriae in Escherichia coli K‐12 , 1996, Molecular microbiology.
[71] Michael S. Samoilov,et al. Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction , 2010, PLoS Comput. Biol..
[72] Christopher A. Voigt,et al. Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks , 2014, Molecular systems biology.
[73] Le Cong,et al. Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.
[74] J. Abraham,et al. An invertible element of DNA controls phase variation of type 1 fimbriae of Escherichia coli. , 1985, Proceedings of the National Academy of Sciences of the United States of America.
[75] Peter G. Schultz,et al. Genomically Recoded Organisms Expand Biological Functions , 2013, Science.
[76] G. Niu,et al. Genome engineering and direct cloning of antibiotic gene clusters via phage ϕBT1 integrase-mediated site-specific recombination in Streptomyces , 2015, Scientific Reports.
[77] Luke A. Gilbert,et al. CRISPR interference (CRISPRi) for sequence-specific control of gene expression , 2013, Nature Protocols.
[78] A. Camilli,et al. Multiplex genome editing by natural transformation , 2014, Proceedings of the National Academy of Sciences.
[79] G. Church,et al. Synthetic Gene Networks That Count , 2009, Science.
[80] J. Guest,et al. Identification and Characterization of a Two-Component Sensor-Kinase and Response-Regulator System (DcuS-DcuR) Controlling Gene Expression in Response to C4-Dicarboxylates in Escherichia coli , 1999, Journal of bacteriology.
[81] Adam P Arkin,et al. An adaptor from translational to transcriptional control enables predictable assembly of complex regulation , 2012, Nature Methods.
[82] Drew Endy,et al. Amplifying Genetic Logic Gates , 2013, Science.
[83] Timothy K Lu,et al. Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota. , 2016, Cell systems.
[84] Farren J. Isaacs,et al. Rational optimization of tolC as a powerful dual selectable marker for genome engineering , 2014, Nucleic acids research.
[85] H. Araki,et al. Molecular and functional organization of yeast plasmid pSR1. , 1985, Journal of molecular biology.
[86] James J Collins,et al. Programmable bacteria detect and record an environmental signal in the mammalian gut , 2014, Proceedings of the National Academy of Sciences.
[87] Arkady B. Khodursky,et al. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[88] Christopher A. Voigt,et al. Environmental signal integration by a modular AND gate , 2007, Molecular systems biology.
[89] R. Britton,et al. Precision genome engineering in lactic acid bacteria , 2014, Microbial Cell Factories.
[90] Farren J. Isaacs,et al. Programming cells by multiplex genome engineering and accelerated evolution , 2009, Nature.
[91] J. Collins,et al. Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.
[92] K. Shearwin,et al. Transcriptional interference--a crash course. , 2005, Trends in genetics : TIG.
[93] Herbert M Sauro,et al. Visualization of evolutionary stability dynamics and competitive fitness of Escherichia coli engineered with randomized multigene circuits. , 2013, ACS synthetic biology.
[94] P. Foster. Stress-Induced Mutagenesis in Bacteria , 2007, Critical reviews in biochemistry and molecular biology.
[95] M. Elowitz,et al. A synthetic oscillatory network of transcriptional regulators , 2000, Nature.
[96] B. Glick. Metabolic load and heterologous gene expression. , 1995, Biotechnology advances.
[97] Drew Endy,et al. Precise and reliable gene expression via standard transcription and translation initiation elements , 2013, Nature Methods.
[98] J. Parkhill,et al. Tyrosine site‐specific recombinases mediate DNA inversions affecting the expression of outer surface proteins of Bacteroides fragilis , 2004, Molecular microbiology.
[99] I. Blomfield,et al. In vivo phase variation of MR/P fimbrial gene expression in Proteus mirabilis infecting the urinary tract , 1997, Molecular microbiology.
[100] Jeffrey E. Barrick,et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli , 2009, Nature.
[101] R. Lenski,et al. Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population , 2011, Science.
[102] N. Grindley,et al. Mechanisms of site-specific recombination. , 2003, Annual review of biochemistry.
[103] W. Brown,et al. Serine recombinases as tools for genome engineering. , 2011, Methods.
[104] J. W. Golden,et al. Two heterocyst-specific DNA rearrangements of nif operons in Anabaena cylindrica and Nostoc sp. strain Mac. , 1995, Microbiology.
[105] Justin R Klesmith,et al. The Interrelationship between Promoter Strength, Gene Expression, and Growth Rate , 2014, PloS one.
[106] Vivek K. Mutalik,et al. Measurement and modeling of intrinsic transcription terminators , 2013, Nucleic acids research.
[107] R. Weiss,et al. Directed evolution of a genetic circuit , 2002, Proceedings of the National Academy of Sciences of the United States of America.