A Framework for Genetic Logic Synthesis In this paper, the authors introduce af ramework to address the challenges of applying logic synthesis techniques to genetic logic devices.
暂无分享,去创建一个
Prashant Vaidyanathan | Swapnil Bhatia | Douglas Densmore | Nicholas Roehner | Christopher A. Voigt | Swapnil P Bhatia | Bryan S. Der | Ryan Silva | C. Voigt | D. Densmore | Nicholas Roehner | P. Vaidyanathan | Ryan Silva
[1] Timothy K Lu,et al. Synthetic circuits integrating logic and memory in living cells , 2013, Nature Biotechnology.
[2] P. Silver,et al. A tunable zinc finger-based framework for Boolean logic computation in mammalian cells , 2012, Nucleic acids research.
[3] G. Church,et al. Synthetic Gene Networks That Count , 2009, Science.
[4] A. Arkin,et al. Contextualizing context for synthetic biology – identifying causes of failure of synthetic biological systems , 2012, Biotechnology journal.
[5] J. Collins,et al. Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.
[6] Takafumi Miyamoto,et al. Synthesizing biomolecule-based Boolean logic gates. , 2013, ACS synthetic biology.
[7] Christopher A. Voigt,et al. Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks , 2014, Molecular systems biology.
[8] Mario Andrea Marchisio,et al. Parts & Pools: A Framework for Modular Design of Synthetic Gene Circuits , 2014, Front. Bioeng. Biotechnol..
[9] Madhukar S. Dasika,et al. OptCircuit: An optimization based method for computational design of genetic circuits , 2008, BMC Systems Biology.
[10] Andrew Phillips,et al. Towards programming languages for genetic engineering of living cells , 2009, Journal of The Royal Society Interface.
[11] Rahul Sarpeshkar,et al. Synthetic analog computation in living cells , 2013, Nature.
[12] R. Weiss,et al. Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks , 2011, PloS one.
[13] Chueh Loo Poh,et al. Characterization of a quorum sensing device for synthetic biology design: Experimental and modeling validation , 2013 .
[14] Matthias Köppe,et al. Automatic Design of Synthetic Gene Circuits through Mixed Integer Non-linear Programming , 2012, PloS one.
[15] Christopher A. Voigt,et al. Genomic Mining of Prokaryotic Repressors for Orthogonal Logic Gates , 2013, Nature chemical biology.
[16] Christopher A. Voigt,et al. Ribozyme-based insulator parts buffer synthetic circuits from genetic context , 2012, Nature Biotechnology.
[17] James Chappell,et al. Creating small transcription activating RNAs. , 2015, Nature chemical biology.
[18] Ryan R. Richardson,et al. Two- and three-input TALE-based AND logic computation in embryonic stem cells , 2013, Nucleic acids research.
[19] R. Sarpeshkar. Analog synthetic biology , 2014, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.
[20] Feng Zhang,et al. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system , 2013, Nucleic acids research.
[21] Hiroaki Kitano,et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..
[22] J. Collins,et al. Toehold Switches: De-Novo-Designed Regulators of Gene Expression , 2014, Cell.
[23] Robert K. Brayton,et al. ABC: An Academic Industrial-Strength Verification Tool , 2010, CAV.
[24] Jonathan A. Goler. BioJADE: A Design and Simulation Tool for Synthetic Biological Systems , 2004 .
[25] Jacob Beal,et al. Proposed data model for the next version of the synthetic biology open language. , 2015, ACS synthetic biology.
[26] Jacob Beal,et al. A Method for Fast, High-Precision Characterization of Synthetic Biology Devices , 2012 .
[27] Randal E. Bryant,et al. Graph-Based Algorithms for Boolean Function Manipulation , 1986, IEEE Transactions on Computers.
[28] Matthew R Bennett,et al. Library of synthetic transcriptional AND gates built with split T7 RNA polymerase mutants , 2013, Proceedings of the National Academy of Sciences.
[29] Christopher A. Voigt,et al. Principles of genetic circuit design , 2014, Nature Methods.
[30] Allan Kuchinsky,et al. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology , 2014, Nature Biotechnology.
[31] Priscilla E. M. Purnick,et al. The second wave of synthetic biology: from modules to systems , 2009, Nature Reviews Molecular Cell Biology.
[32] Matthias Köppe,et al. SBROME: a scalable optimization and module matching framework for automated biosystems design. , 2013, ACS synthetic biology.
[33] Alfonso Jaramillo,et al. AutoBioCAD: full biodesign automation of genetic circuits. , 2013, ACS synthetic biology.
[34] James J. Collins,et al. Next-Generation Synthetic Gene Networks , 2009, Nature Biotechnology.
[35] Ilias Tagkopoulos,et al. Optimal part and module selection for synthetic gene circuit design automation. , 2014, ACS synthetic biology.
[36] Jacques Haiech,et al. Modeling Biology With HDL Languages: A First Step Toward a Genetic Design Automation Tool Inspired From Microelectronics , 2014, IEEE Transactions on Biomedical Engineering.
[37] Chris J Myers,et al. Directed acyclic graph-based technology mapping of genetic circuit models. , 2014, ACS synthetic biology.
[38] Andreas Kremling,et al. Modular Modeling of Cellular Systems with ProMoT/Diva , 2003, Bioinform..
[39] Christopher A. Voigt,et al. Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’ , 2011, Nature.
[40] Ilias Tagkopoulos,et al. Promoter element arising from the fusion of standard BioBrick parts. , 2013, ACS synthetic biology.
[41] Gordon D. Plotkin,et al. A Language for Biochemical Systems: Design and Formal Specification , 2010, Trans. Comp. Sys. Biology.
[42] Stefano Cardinale,et al. Effects of genetic variation on the E. coli host-circuit interface. , 2013, Cell reports.
[43] Adam Paul Arkin,et al. A wise consistency: engineering biology for conformity, reliability, predictability. , 2013, Current opinion in chemical biology.
[44] Luke A. Gilbert,et al. Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression , 2013, Cell.
[45] Eduardo Sontag,et al. Modular cell biology: retroactivity and insulation , 2008, Molecular systems biology.
[46] Christopher A. Voigt,et al. Genetic programs constructed from layered logic gates in single cells , 2012, Nature.
[47] Drew Endy,et al. Measuring the activity of BioBrick promoters using an in vivo reference standard , 2009, Journal of biological engineering.
[48] Kenneth H. Rosen,et al. Discrete Mathematics and its applications , 2000 .
[49] Jeffrey C. Lagarias,et al. Solving low density subset sum problems , 1983, 24th Annual Symposium on Foundations of Computer Science (sfcs 1983).
[50] Jacob Beal,et al. Automated selection of synthetic biology parts for genetic regulatory networks. , 2012, ACS synthetic biology.
[51] Jacob Beal,et al. An end-to-end workflow for engineering of biological networks from high-level specifications. , 2012, ACS synthetic biology.
[52] Drew Endy,et al. Precise and reliable gene expression via standard transcription and translation initiation elements , 2013, Nature Methods.
[53] Vincent Danos,et al. Rule-Based Modelling, Symmetries, Refinements , 2008, FMSB.
[54] 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.