Literature DB >> 22596318

Foundations for the design and implementation of synthetic genetic circuits.

Adrian L Slusarczyk1, Allen Lin, Ron Weiss.   

Abstract

Synthetic gene circuits are designed to program new biological behaviour, dynamics and logic control. For all but the simplest synthetic phenotypes, this requires a structured approach to map the desired functionality to available molecular and cellular parts and processes. In other engineering disciplines, a formalized design process has greatly enhanced the scope and rate of success of projects. When engineering biological systems, a desired function must be achieved in a context that is incompletely known, is influenced by stochastic fluctuations and is capable of rich nonlinear interactions with the engineered circuitry. Here, we review progress in the provision and engineering of libraries of parts and devices, their composition into large systems and the emergence of a formal design process for synthetic biology.

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Year:  2012        PMID: 22596318     DOI: 10.1038/nrg3227

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  134 in total

1.  Design of genetic networks with specified functions by evolution in silico.

Authors:  Paul François; Vincent Hakim
Journal:  Proc Natl Acad Sci U S A       Date:  2004-01-02       Impact factor: 11.205

2.  Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms.

Authors:  Sang-Hyun Park; Ali Zarrinpar; Wendell A Lim
Journal:  Science       Date:  2003-01-02       Impact factor: 47.728

3.  Synthetic ecosystems based on airborne inter- and intrakingdom communication.

Authors:  Wilfried Weber; Marie Daoud-El Baba; Martin Fussenegger
Journal:  Proc Natl Acad Sci U S A       Date:  2007-06-05       Impact factor: 11.205

Review 4.  Forty years of in vitro evolution.

Authors:  Gerald F Joyce
Journal:  Angew Chem Int Ed Engl       Date:  2007       Impact factor: 15.336

5.  Developer's and user's guide to Clotho v2.0 A software platform for the creation of synthetic biological systems.

Authors:  Bing Xia; Swapnil Bhatia; Ben Bubenheim; Maisam Dadgar; Douglas Densmore; J Christopher Anderson
Journal:  Methods Enzymol       Date:  2011       Impact factor: 1.600

6.  Genomic cis-regulatory logic: experimental and computational analysis of a sea urchin gene.

Authors:  C H Yuh; H Bolouri; E H Davidson
Journal:  Science       Date:  1998-03-20       Impact factor: 47.728

7.  Rapid diversification of cell signaling phenotypes by modular domain recombination.

Authors:  Sergio G Peisajovich; Joan E Garbarino; Ping Wei; Wendell A Lim
Journal:  Science       Date:  2010-04-16       Impact factor: 47.728

8.  Writing DNA with GenoCAD.

Authors:  Michael J Czar; Yizhi Cai; Jean Peccoud
Journal:  Nucleic Acids Res       Date:  2009-05-08       Impact factor: 16.971

9.  A synthetic Escherichia coli predator-prey ecosystem.

Authors:  Frederick K Balagaddé; Hao Song; Jun Ozaki; Cynthia H Collins; Matthew Barnet; Frances H Arnold; Stephen R Quake; Lingchong You
Journal:  Mol Syst Biol       Date:  2008-04-15       Impact factor: 11.429

10.  A fast, robust and tunable synthetic gene oscillator.

Authors:  Jesse Stricker; Scott Cookson; Matthew R Bennett; William H Mather; Lev S Tsimring; Jeff Hasty
Journal:  Nature       Date:  2008-10-29       Impact factor: 49.962

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  83 in total

1.  Translational cross talk in gene networks.

Authors:  William H Mather; Jeff Hasty; Lev S Tsimring; Ruth J Williams
Journal:  Biophys J       Date:  2013-06-04       Impact factor: 4.033

2.  Blue light-mediated transcriptional activation and repression of gene expression in bacteria.

Authors:  Premkumar Jayaraman; Kavya Devarajan; Tze Kwang Chua; Hanzhong Zhang; Erry Gunawan; Chueh Loo Poh
Journal:  Nucleic Acids Res       Date:  2016-06-28       Impact factor: 16.971

3.  Collective Space-Sensing Coordinates Pattern Scaling in Engineered Bacteria.

Authors:  Yangxiaolu Cao; Marc D Ryser; Stephen Payne; Bochong Li; Christopher V Rao; Lingchong You
Journal:  Cell       Date:  2016-04-21       Impact factor: 41.582

4.  Protease-based synthetic sensing and signal amplification.

Authors:  Viktor Stein; Kirill Alexandrov
Journal:  Proc Natl Acad Sci U S A       Date:  2014-10-29       Impact factor: 11.205

5.  A Practical Step-by-Step Guide for Quantifying Retroactivity in Gene Networks.

Authors:  Andras Gyorgy
Journal:  Methods Mol Biol       Date:  2021

6.  Recursively constructing analytic expressions for equilibrium distributions of stochastic biochemical reaction networks.

Authors:  X Flora Meng; Ania-Ariadna Baetica; Vipul Singhal; Richard M Murray
Journal:  J R Soc Interface       Date:  2017-05       Impact factor: 4.118

7.  Modular gene-circuit design takes two steps forward.

Authors:  Jeffrey J Tabor
Journal:  Nat Methods       Date:  2012-11       Impact factor: 28.547

8.  Bottom-up approaches in synthetic biology and biomaterials for tissue engineering applications.

Authors:  Mitchell S Weisenberger; Tara L Deans
Journal:  J Ind Microbiol Biotechnol       Date:  2018-03-19       Impact factor: 3.346

Review 9.  Synthetic nanoelectronic probes for biological cells and tissues.

Authors:  Bozhi Tian; Charles M Lieber
Journal:  Annu Rev Anal Chem (Palo Alto Calif)       Date:  2013-02-28       Impact factor: 10.745

10.  Bacteriophage-based synthetic biology for the study of infectious diseases.

Authors:  Robert J Citorik; Mark Mimee; Timothy K Lu
Journal:  Curr Opin Microbiol       Date:  2014-07-03       Impact factor: 7.934

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