An integrative circuit–host modelling framework for predicting synthetic gene network behaviours

[1]  Christopher J Petzold,et al.  Programming mRNA decay to modulate synthetic circuit resource allocation , 2016, Nature Communications.

[2]  Lingchong You,et al.  Addressing biological uncertainties in engineering gene circuits. , 2016, Integrative biology : quantitative biosciences from nano to macro.

[3]  Ting Lu,et al.  Bacterial social interactions drive the emergence of differential spatial colony structures , 2015, BMC Systems Biology.

[4]  P. Swain,et al.  Mechanistic links between cellular trade-offs, gene expression, and growth , 2015, Proceedings of the National Academy of Sciences.

[5]  K. Dill,et al.  Bacterial growth laws reflect the evolutionary importance of energy efficiency , 2014, Proceedings of the National Academy of Sciences.

[6]  David H Burkhardt,et al.  Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources , 2014, Cell.

[7]  Christopher A. Voigt,et al.  Principles of genetic circuit design , 2014, Nature Methods.

[8]  Adam Paul Arkin,et al.  A wise consistency: engineering biology for conformity, reliability, predictability. , 2013, Current opinion in chemical biology.

[9]  Terence Hwa,et al.  The Innate Growth Bistability and Fitness Landscapes of Antibiotic-Resistant Bacteria , 2013, Science.

[10]  U. Sauer,et al.  Dissecting specific and global transcriptional regulation of bacterial gene expression , 2013, Molecular systems biology.

[11]  J. Keasling,et al.  Microbial engineering for the production of advanced biofuels , 2012, Nature.

[12]  Jonathan R. Karr,et al.  A Whole-Cell Computational Model Predicts Phenotype from Genotype , 2012, Cell.

[13]  A. Arkin,et al.  Contextualizing context for synthetic biology – identifying causes of failure of synthetic biological systems , 2012, Biotechnology journal.

[14]  J. Collins,et al.  Synthetic Biology Moving into the Clinic , 2011, Science.

[15]  Andreas Bracher,et al.  Molecular chaperones in protein folding and proteostasis , 2011, Nature.

[16]  N. Philippe,et al.  ppGpp is the major source of growth rate control in E. coli. , 2011, Environmental microbiology.

[17]  M. Elowitz,et al.  Build life to understand it , 2010, Nature.

[18]  T. Hwa,et al.  Interdependence of Cell Growth and Gene Expression: Origins and Consequences , 2010, Science.

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

[20]  R. Kwok.  Five hard truths for synthetic biology , 2010, Nature.

[21]  T. Hwa,et al.  Growth Rate-Dependent Global Effects on Gene Expression in Bacteria , 2009, Cell.

[22]  James J. Collins,et al.  Next-Generation Synthetic Gene Networks , 2009, Nature Biotechnology.

[23]  R. Kishony,et al.  Nonoptimal Microbial Response to Antibiotics Underlies Suppressive Drug Interactions , 2009, Cell.

[24]  L. You,et al.  Emergent bistability by a growth-modulating positive feedback circuit. , 2009, Nature chemical biology.

[25]  Christopher A. Voigt,et al.  A Synthetic Genetic Edge Detection Program , 2009, Cell.

[26]  T. Hwa,et al.  Growth-rate-dependent partitioning of RNA polymerases in bacteria , 2008, Proceedings of the National Academy of Sciences.

[27]  P. Dennis,et al.  Modulation of Chemical Composition and Other Parameters of the Cell at Different Exponential Growth Rates , 2008, EcoSal Plus.

[28]  K. Potrykus,et al.  (p)ppGpp: still magical? , 2008, Annual review of microbiology.

[29]  Joel T. Smith,et al.  The global, ppGpp‐mediated stringent response to amino acid starvation in Escherichia coli , 2008, Molecular microbiology.

[30]  Tetsuya J. Kobayashi,et al.  Reconstructing the single‐cell‐level behavior of a toggle switch from population‐level measurements , 2008, FEBS letters.

[31]  Jeff Hasty,et al.  Phenotypic variability of growing cellular populations , 2007, Proceedings of the National Academy of Sciences.

[32]  Christopher A. Voigt,et al.  Environmental signal integration by a modular AND gate , 2007, Molecular systems biology.

[33]  D. J. Greenwood,et al.  RNA:protein ratio of the unicellular organism as a characteristic of phosphorous and nitrogen stoichiometry and of the cellular requirement of ribosomes for protein synthesis , 2006, BMC Biology.

[34]  S. Basu,et al.  A synthetic multicellular system for programmed pattern formation , 2005, Nature.

[35]  John W. Foster,et al.  DksA A Critical Component of the Transcription Initiation Machinery that Potentiates the Regulation of rRNA Promoters by ppGpp and the Initiating NTP , 2004, Cell.

[36]  R. Cox,et al.  Quantitative relationships for specific growth rates and macromolecular compositions of Mycobacterium tuberculosis, Streptomyces coelicolor A3(2) and Escherichia coli B/r: an integrative theoretical approach. , 2004, Microbiology.

[37]  R. Gourse,et al.  Control of rRNA expression by small molecules is dynamic and nonredundant. , 2003, Molecular cell.

[38]  R. Gourse,et al.  Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. , 2001, Journal of molecular biology.

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

[40]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[41]  David Vanderbilt,et al.  Origins and Consequences of Surface Stress , 1996 .

[42]  C. Kurland,et al.  Gratuitous overexpression of genes in Escherichia coli leads to growth inhibition and ribosome destruction , 1995, Journal of bacteriology.

[43]  B. Glick.  Metabolic load and heterologous gene expression. , 1995, Biotechnology advances.

[44]  A. G. Marr,et al.  Growth rate of Escherichia coli. , 1991, Microbiological reviews.

[45]  I. Chopra,et al.  Sensitive biological detection method for tetracyclines using a tetA-lacZ fusion system , 1990, Antimicrobial Agents and Chemotherapy.

[46]  R. Gourse,et al.  Control of Ribosome Synthesis in Escherichia coli , 1986 .

[47]  D. Gillespie.  Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[48]  S. Molin,et al.  Control of Protein Synthesis in Escherichia coli: Analysis of an Energy Source Shift-Down , 1977, Journal of bacteriology.

[49]  K. von Meyenburg,et al.  Synthesis and turnover of basal level guanosine tetraphosphate in Escherichia coli. , 1975, The Journal of biological chemistry.

[50]  A. L. Koch,et al.  In vivo assay of protein synthesizing capacity of Escherichia coli from slowly growing chemostat cultures. , 1971, Journal of molecular biology.

[51]  O. Maaløe,et al.  Dependency on medium and temperature of cell size and chemical composition during balanced grown of Salmonella typhimurium. , 1958, Journal of general microbiology.