Bacterial Cells as Engineered Chassis.

[1]  H M Sauro,et al.  Mathematical modeling and synthetic biology. , 2008, Drug Discovery Today : Disease Models.

[2]  Bor-Sen Chen,et al.  Robust synchronization control scheme of a population of nonlinear stochastic synthetic genetic oscillators under intrinsic and extrinsic molecular noise via quorum sensing , 2012, BMC Systems Biology.

[3]  Doheon Lee,et al.  Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes , 2010, BMC Systems Biology.

[4]  E. Greenberg,et al.  Quorum-Sensing Signals and Quorum-Sensing Genes in Burkholderia vietnamiensis , 2002, Journal of bacteriology.

[5]  M. Inouye,et al.  The ompA signal peptide directed secretion of Staphylococcal nuclease A by Escherichia coli. , 1985, The Journal of biological chemistry.

[6]  Hidde de Jong,et al.  Modeling and Simulation of Genetic Regulatory Systems: A Literature Review , 2002, J. Comput. Biol..

[7]  D. Nesbeth,et al.  Growth and productivity impacts of periplasmic nuclease expression in an Escherichia coli Fab' fragment production strain , 2012, Biotechnology and bioengineering.

[8]  E. Pennisi,et al.  The Allure of Synthetic Biology , 2011 .

[9]  Elizabeth Van Itallie,et al.  Modeling synthetic gene oscillators. , 2012, Mathematical biosciences.

[10]  Moritz Lang,et al.  Autonomous Synchronization of Chemically Coupled Synthetic Oscillators , 2011, Bulletin of mathematical biology.

[11]  M. Record,et al.  Protein diffusion in the periplasm of E. coli under osmotic stress. , 2011, Biophysical journal.

[12]  Rafael Silva-Rocha,et al.  Mining logic gates in prokaryotic transcriptional regulation networks , 2008, FEBS letters.

[13]  Farren J. Isaacs,et al.  Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement , 2011, Science.

[14]  Fedbatch design for periplasmic product retention in Escherichia coli. , 2008, Journal of biotechnology.

[15]  E. Andrianantoandro,et al.  Synthetic biology: new engineering rules for an emerging discipline , 2006, Molecular systems biology.

[16]  C. Mason,et al.  Cell therapy worldwide: an incipient revolution. , 2015, Regenerative medicine.

[17]  I. Wang,et al.  Phages will out: strategies of host cell lysis. , 2000, Trends in microbiology.

[18]  Peter G Schultz,et al.  An enhanced system for unnatural amino acid mutagenesis in E. coli. , 2010, Journal of molecular biology.

[19]  Sergio G Peisajovich,et al.  Evolutionary synthetic biology. , 2012, ACS synthetic biology.

[20]  B. Wallace,et al.  Chaperone-mediated native folding of a β-scorpion toxin in the periplasm of Escherichia coli , 2014, Biochimica et biophysica acta.

[21]  D. Gillespie.  A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions , 1976 .

[22]  D. A. Baxter,et al.  Mathematical Modeling of Gene Networks , 2000, Neuron.

[23]  D. Nesbeth,et al.  Step change in the efficiency of centrifugation through cell engineering: co‐expression of Staphylococcal nuclease to reduce the viscosity of the bioprocess feedstock , 2009, Biotechnology and bioengineering.

[24]  R. Roos,et al.  Sleep and circadian rhythm alterations correlate with depression and cognitive impairment in Huntington's disease. , 2010, Parkinsonism & related disorders.

[25]  A. Grossman.  Genetic networks controlling the initiation of sporulation and the development of genetic competence in Bacillus subtilis. , 1995, Annual review of genetics.

[26]  M. Mackey,et al.  Feedback regulation in the lactose operon: a mathematical modeling study and comparison with experimental data. , 2003, Biophysical journal.

[27]  Michael B. Elowitz,et al.  Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits , 2009, Cell.

[28]  Christopher A. Voigt,et al.  Advances in genetic circuit design: novel biochemistries, deep part mining, and precision gene expression. , 2013, Current opinion in chemical biology.

[29]  Colin Kleanthous,et al.  Molecular mimicry enables competitive recruitment by a natively disordered protein. , 2007, Journal of the American Chemical Society.

[30]  A. J. Link,et al.  Bcl-2 family interactome analysis using bacterial surface display. , 2011, Integrative biology : quantitative biosciences from nano to macro.

[31]  S. Elena,et al.  Computational design of genomic transcriptional networks with adaptation to varying environments , 2012, Proceedings of the National Academy of Sciences.

[32]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..

[33]  Matthias Heinemann,et al.  Synthetic biology - putting engineering into biology , 2006, Bioinform..

[34]  Christopher A. Voigt,et al.  Automated Design of Synthetic Ribosome Binding Sites to Precisely Control Protein Expression , 2009, Nature Biotechnology.

[35]  S. Andersson,et al.  Research on small genomes: implications for synthetic biology , 2010, BioEssays : news and reviews in molecular, cellular and developmental biology.

[36]  Michael B Elowitz,et al.  Synthetic biology of multicellular systems: new platforms and applications for animal cells and organisms. , 2014, ACS synthetic biology.

[37]  Alexey Zaikin,et al.  Stochastic resonance in an intracellular genetic perceptron. , 2014, Physical review. E, Statistical, nonlinear, and soft matter physics.

[38]  V. Mauro,et al.  A critical analysis of codon optimization in human therapeutics. , 2014, Trends in molecular medicine.

[39]  G. Georgiou,et al.  Development of an optimized expression system for the screening of antibody libraries displayed on the Escherichia coli surface. , 1999, Protein engineering.

[40]  P. Ruoff,et al.  The Goodwin model: simulating the effect of light pulses on the circadian sporulation rhythm of Neurospora crassa. , 2001, Journal of theoretical biology.

[41]  Hao Song,et al.  A synthetic biology challenge: making cells compute. , 2007, Molecular bioSystems.

[42]  Christopher A. Voigt,et al.  Prokaryotic gene clusters: A rich toolbox for synthetic biology , 2010, Biotechnology journal.

[43]  Farren J. Isaacs,et al.  Programming cells by multiplex genome engineering and accelerated evolution , 2009, Nature.

[44]  William I. Bacchus,et al.  A novel vector platform for vitamin H-inducible transgene expression in mammalian cells. , 2007, Journal of biotechnology.

[45]  Martin Fussenegger,et al.  A synthetic low-frequency mammalian oscillator , 2010, Nucleic acids research.

[46]  Adam C. Fisher,et al.  Glycans‐by‐design: Engineering bacteria for the biosynthesis of complex glycans and glycoconjugates , 2013, Biotechnology and bioengineering.

[47]  Gregory Stephanopoulos,et al.  Synthetic biology and metabolic engineering. , 2012, ACS synthetic biology.

[48]  Huimin Zhao,et al.  Directed evolution: an evolving and enabling synthetic biology tool. , 2012, Current opinion in chemical biology.

[49]  R. F. Good,et al.  A bidirectional rho-independent transcription terminator between the E. coli tonB gene and an opposing gene , 1985, Cell.

[50]  Martin Fussenegger,et al.  Recent advances in mammalian synthetic biology-design of synthetic transgene control networks. , 2009, Current opinion in biotechnology.

[51]  Farren J. Isaacs,et al.  Precise manipulation of bacterial chromosomes by conjugative assembly genome engineering , 2014, Nature Protocols.

[52]  R. Weiss,et al.  Directed evolution of a genetic circuit , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[53]  Mads Kaern,et al.  The engineering of gene regulatory networks. , 2003, Annual review of biomedical engineering.

[54]  D. Volfson,et al.  Delay-induced stochastic oscillations in gene regulation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[55]  Ryo Takeuchi,et al.  Biocontainment of genetically modified organisms by synthetic protein design , 2015, Nature.

[56]  J. Mandelstam,et al.  Commitment to sporulation in Bacillus subtilis and its relationship to development of actinomycin resistance. , 1969, The Biochemical journal.

[57]  A. Plückthun,et al.  Secretion and in vivo folding of the Fab fragment of the antibody McPC603 in Escherichia coli: influence of disulphides and cis-prolines. , 1991, Protein engineering.

[58]  Chung-Jr Huang,et al.  Industrial production of recombinant therapeutics in Escherichia coli and its recent advancements , 2012, Journal of Industrial Microbiology & Biotechnology.

[59]  C. Robertson McClung,et al.  Plant Circadian Rhythms , 2006, The Plant Cell Online.

[60]  Ahmad S. Khalil,et al.  Synthetic biology: applications come of age , 2010, Nature Reviews Genetics.

[61]  B. G. Davis,et al.  Rewriting the bacterial glycocalyx via Suzuki-Miyaura cross-coupling. , 2013, Chemical communications.

[62]  S S Tambe,et al.  Application of artificial neural networks for prokaryotic transcription terminator prediction , 1994, FEBS letters.

[63]  S. Leibler,et al.  Biological rhythms: Circadian clocks limited by noise , 2000, Nature.

[64]  T. Fujii,et al.  Determination of the termination efficiency of the transcription terminator using different fluorescent profiles in green fluorescent protein mutants. , 2005, Analytical sciences : the international journal of the Japan Society for Analytical Chemistry.

[65]  Jeffrey C Way,et al.  Designing biological systems. , 2007, Genes & development.

[66]  Jeff Hasty,et al.  Distributed Classifier Based on Genetically Engineered Bacterial Cell Cultures , 2014, ACS synthetic biology.

[67]  U. Alon,et al.  A comprehensive library of fluorescent transcriptional reporters for Escherichia coli , 2006, Nature Methods.

[68]  Y. Ni,et al.  lpp deletion as a permeabilization method , 2007, Biotechnology and bioengineering.

[69]  L. Tsimring,et al.  A synchronized quorum of genetic clocks , 2009, Nature.

[70]  P. Kambam,et al.  Engineering and applications of genetic circuits. , 2007, Molecular bioSystems.

[71]  Jürgen Kurths,et al.  Synthetic multicellular oscillatory systems: controlling protein dynamics with genetic circuits , 2011 .

[72]  Gerald R. Smith.  Conjugational recombination in E. coli: Myths and mechanisms , 1991, Cell.

[73]  G. Church,et al.  Synthetic Gene Networks That Count , 2009, Science.

[74]  E. Winfree,et al.  Synthetic in vitro transcriptional oscillators , 2011, Molecular systems biology.

[75]  D. Gonze.  Modeling the effect of cell division on genetic oscillators. , 2013, Journal of theoretical biology.

[76]  T. F. O’Brien,et al.  Regulation of T‐cell survival and mitochondrial homeostasis by TSC1 , 2011, European journal of immunology.

[77]  S. Xiang,et al.  Escherichia coli surface display of single-chain antibody VRC01 against HIV-1 infection. , 2015, Virology.

[78]  Christina D Smolke,et al.  Synthetic biology: advancing biological frontiers by building synthetic systems , 2012, Genome Biology.

[79]  Joseph H. Davis,et al.  Design, construction and characterization of a set of insulated bacterial promoters , 2010, Nucleic acids research.

[80]  J. Ward,et al.  A modified Escherichia coli protein production strain expressing staphylococcal nuclease, capable of auto-hydrolysing host nucleic acid. , 2003, Journal of biotechnology.

[81]  Santiago Comba,et al.  Emerging engineering principles for yield improvement in microbial cell design , 2012, Computational and structural biotechnology journal.

[82]  Y. Zhuo,et al.  Engineering of a genome-reduced host: practical application of synthetic biology in the overproduction of desired secondary metabolites , 2010, Protein & Cell.

[83]  J. Collins,et al.  A brief history of synthetic biology , 2014, Nature Reviews Microbiology.

[84]  Quan Liu,et al.  Bacterial surface display of endoglin by antigen 43 induces antitumor effectiveness via bypassing immunotolerance and inhibition of angiogenesis , 2014, International journal of cancer.

[85]  M. Sasai,et al.  Roles of noise in single and coupled multiple genetic oscillators. , 2007, The Journal of chemical physics.

[86]  Vijai Singh,et al.  Recent advancements in synthetic biology: current status and challenges. , 2014, Gene.

[87]  D. Dubnau,et al.  DNA uptake in bacteria. , 1999, Annual review of microbiology.

[88]  J. Craig Venter,et al.  Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast , 2009, Science.

[89]  C. V. Rao,et al.  Expanding the synthetic biology toolbox: engineering orthogonal regulators of gene expression. , 2012, Current opinion in biotechnology.

[90]  M. Bennett,et al.  A fast, robust, and tunable synthetic gene oscillator , 2008, Nature.

[91]  Chen Li,et al.  Designing and encoding models for synthetic biology , 2009, Journal of The Royal Society Interface.

[92]  Mauricio Barahona,et al.  Switchable genetic oscillator operating in quasi-stable mode , 2009, Journal of The Royal Society Interface.

[93]  S. Bernard,et al.  Spontaneous synchronization of coupled circadian oscillators. , 2005, Biophysical journal.

[94]  Hal S Alper,et al.  Frontiers of yeast metabolic engineering: diversifying beyond ethanol and Saccharomyces. , 2013, Current opinion in biotechnology.

[95]  Kathleen Marchal,et al.  A network-based approach to identify substrate classes of bacterial glycosyltransferases , 2014, BMC Genomics.

[96]  Byung-gee Kim,et al.  Bacterial Surface Display of a Co-Factor Containing Enzyme, ω-Transaminase from Vibrio fluvialis Using the Bacillus subtilis Spore Display System , 2011, Bioscience, biotechnology, and biochemistry.

[97]  K. Cline.  Mechanistic Aspects of Folded Protein Transport by the Twin Arginine Translocase (Tat)* , 2015, The Journal of Biological Chemistry.

[98]  Peter G. Schultz,et al.  Genomically Recoded Organisms Expand Biological Functions , 2013, Science.

[99]  Anirban Mitra,et al.  WebGeSTer DB—a transcription terminator database , 2010, Nucleic Acids Res..

[100]  Y. Ni,et al.  Extracellular recombinant protein production from Escherichia coli , 2009, Biotechnology Letters.

[101]  Adam Arkin,et al.  Setting the standard in synthetic biology , 2008, Nature Biotechnology.

[102]  M. Kumar,et al.  Bacterial glycoproteins: Functions, biosynthesis and applications , 2003, Proteomics.

[103]  Leo Eberl,et al.  Essential genes as antimicrobial targets and cornerstones of synthetic biology. , 2012, Trends in biotechnology.

[104]  J. Tyson,et al.  Design principles of biochemical oscillators , 2008, Nature Reviews Molecular Cell Biology.

[105]  Oliver Purcell,et al.  A Multi-Functional Synthetic Gene Network: A Frequency Multiplier, Oscillator and Switch , 2011, PloS one.

[106]  L. Álvarez-Vallina,et al.  Programming Controlled Adhesion of E. coli to Target Surfaces, Cells, and Tumors with Synthetic Adhesins , 2014, ACS synthetic biology.

[107]  Wolfgang Wintermeyer,et al.  Signal sequence–independent membrane targeting of ribosomes containing short nascent peptides within the exit tunnel , 2008, Nature Structural &Molecular Biology.

[108]  Jacek Blazewicz,et al.  Automated 3D structure composition for large RNAs , 2012, Nucleic acids research.

[109]  M. Elowitz,et al.  A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[110]  T. Elston,et al.  Stochasticity in gene expression: from theories to phenotypes , 2005, Nature Reviews Genetics.

[111]  P. Dunnill,et al.  Factors determining more efficient large-scale release of a periplasmic enzyme from E. coli using lysozyme. , 1997, Journal of biotechnology.

[112]  D. Endy,et al.  Refinement and standardization of synthetic biological parts and devices , 2008, Nature Biotechnology.

[113]  Ahmed Alsaedi,et al.  Complex and unexpected dynamics in simple genetic regulatory networks , 2014 .

[114]  W. Ma,et al.  Modified Recombinant Proteins Can Be Exported via the Sec Pathway in Escherichia coli , 2012, PloS one.

[115]  Gregory M. Goldgof,et al.  Direct transfer of whole genomes from bacteria to yeast , 2013, Nature Methods.

[116]  H. Salis.  The ribosome binding site calculator. , 2011, Methods in enzymology.

[117]  D. Endy,et al.  Refactoring bacteriophage T7 , 2005, Molecular systems biology.

[118]  J E Bailey,et al.  Mathematical Modeling and Analysis in Biochemical Engineering: Past Accomplishments and Future Opportunities , 1998, Biotechnology progress.

[119]  María-Eugenia Guazzaroni,et al.  Expanding the logic of bacterial promoters using engineered overlapping operators for global regulators. , 2014, ACS synthetic biology.

[120]  J. Liao,et al.  A synthetic gene–metabolic oscillator , 2005, Nature.

[121]  N. Pérez,et al.  Production of recombinant proteins in E. coli by the heat inducible expression system based on the phage lambda pL and/or pR promoters , 2010, Microbial cell factories.

[122]  R. Rahim,et al.  Optimization of an induction strategy for improving interferon‐α2b production in the periplasm of Escherichia coli using response surface methodology , 2010, Biotechnology and applied biochemistry.

[123]  Sophia Hober,et al.  Effect of substrate feed rate on recombinant protein secretion, degradation and inclusion body formation in Escherichia coli , 2005, Applied Microbiology and Biotechnology.

[124]  G. Huisman,et al.  Reduction of Cell Lysate Viscosity during Processing of Poly(3-Hydroxyalkanoates) by Chromosomal Integration of the Staphylococcal Nuclease Gene in Pseudomonas putida , 1999, Applied and Environmental Microbiology.

[125]  Linda R. Petzold,et al.  Stochastic modelling of gene regulatory networks , 2005 .

[126]  Pamela A Silver,et al.  Parts plus pipes: synthetic biology approaches to metabolic engineering. , 2012, Metabolic engineering.

[127]  Peter Ruhdal Jensen,et al.  A synthetic promoter library for constitutive gene expression in Lactobacillus plantarum. , 2006, Microbiology.

[128]  Timothy K Lu,et al.  Synthetic circuits integrating logic and memory in living cells , 2013, Nature Biotechnology.

[129]  R. Freedman,et al.  Investigation of the impact of Tat export pathway enhancement on E. coli culture, protein production and early stage recovery , 2012, Biotechnology and bioengineering.

[130]  Thomas H Segall-Shapiro,et al.  Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome , 2010, Science.

[131]  Ganesh Sriram,et al.  Mathematical Modeling: Bridging the Gap between Concept and Realization in Synthetic Biology , 2010, Journal of biomedicine & biotechnology.

[132]  B. Yakhchali,et al.  Development of a Bacterial Surface Display of Hexahistidine Peptide Using CS3 Pili for Bioaccumulation of Heavy Metals , 2007, Current Microbiology.

[133]  G. Stan,et al.  Quantifying cellular capacity identifies gene expression designs with reduced burden , 2015, Nature Methods.

[134]  Sang Woo Seo,et al.  Synthetic biology: tools to design microbes for the production of chemicals and fuels. , 2013, Biotechnology advances.

[135]  Xiaobo Zhang,et al.  Characterization of a novel non-specific nuclease from thermophilic bacteriophage GBSV1 , 2008, BMC biotechnology.

[136]  M. Fussenegger,et al.  Inducible product gene expression technology tailored to bioprocess engineering. , 2007, Current opinion in biotechnology.

[137]  L. Serrano,et al.  Engineering stability in gene networks by autoregulation , 2000, Nature.

[138]  Harris H. Wang,et al.  Genome-scale engineering for systems and synthetic biology , 2013, Molecular systems biology.

[139]  Hyun‐dong Shin,et al.  Extracellular recombinant protein production from an Escherichia coli lpp deletion mutant , 2008, Biotechnology and bioengineering.

[140]  S. Alexeeva,et al.  Differential Bacterial Surface Display of Peptides by the Transmembrane Domain of OmpA , 2009, PloS one.

[141]  Joachim Jose,et al.  Autodisplay: efficient bacterial surface display of recombinant proteins , 2006, Applied Microbiology and Biotechnology.

[142]  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.

[143]  A. Ninfa,et al.  Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli , 2003, Cell.

[144]  Jennifer A. Getz,et al.  A Novel Quantitative Kinase Assay Using Bacterial Surface Display and Flow Cytometry , 2013, PloS one.

[145]  Juan F. Poyatos,et al.  Dynamical Principles of Two-Component Genetic Oscillators , 2006, PLoS Comput. Biol..

[146]  C. Gatz,et al.  Control of expression of the Tn10-encoded tetracycline resistance genes. Equilibrium and kinetic investigation of the regulatory reactions. , 1983, Journal of molecular biology.

[147]  J. Stelling,et al.  A tunable synthetic mammalian oscillator , 2009, Nature.

[148]  Mark A. Schembri,et al.  Fimbriae assisted bacterial surface display of heterologous peptides , 2000, International Journal of Medical Microbiology.

[149]  J. Raser,et al.  Control of Stochasticity in Eukaryotic Gene Expression , 2004, Science.

[150]  G. Mufti,et al.  Human CD80/IL2 lentivirus‐transduced acute myeloid leukaemia (AML) cells promote natural killer (NK) cell activation and cytolytic activity: implications for a phase I clinical study , 2009, British journal of haematology.