COPASI's Use In Synthetic Biology


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Appleton E, Madsen C, Roehner N, Densmore D (2017) Design Automation in Synthetic Biology. Cold Spring Harbor Perspectives in Biology 9:a023978 Synthetic Biology Computational Methods Link
Baumgart L, Mather W, Hasty J (2017) Synchronized DNA cycling across a bacterial population. Nature Genetics 49:1282–128 Synthetic Biology Microbiology Link
Chizzolini F, Forlin M, Yeh Martín N, Berloffa G, Cecchi D, Mansy SS (2017) Cell-free translation is more variable than transcription. ACS Synthetic Biology 6:638–647 Macromolecular Biochemistry Synthetic Biology Link
Korman TP, Opgenorth PH, Bowie JU (2017) A synthetic biochemistry platform for cell free production of monoterpenes from glucose. Nature Communications 8:15526 Synthetic Biology Metabolism Link
Zhao W, Pferdehirt L, Segatori L (2017) Quantitatively predictable control of cellular protein levels through proteasomal degradation. ACS Synthetic Biology 7:540–552 Synthetic Biology Macromolecular Biochemistry Link

5 publications
Rantasalo A, Czeizler E, Virtanen R, Rousu J, Lähdesmäki H, Penttilä M, Jäntti J, Mojzita D (2016) Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae. PLOS One 11:e0148320 Genetics Microbiology Synthetic Biology Link

1 publication
D'Aguanno E, Altamura E, Mavelli F, Fahr A, Stano P, Luisi PL (2015) Physical Routes to Primitive Cells: An Experimental Model Based on the Spontaneous Entrapment of Enzymes inside Micrometer-Sized Liposomes. Life 5:969-96 Synthetic Biology Link
Mandlik V, Gurav M, Singh S (2015) Regulatory dynamics of network architecture and function in tristable genetic circuit of Leishmania: a mathematical biology approach. Journal of Biomolecular Structure and Dynamics 33:2554-62 Synthetic Biology Genetics Metabolism Link
Talawar B (2015) A Crossbar Interconnection Network in DNA. Proceedings of 2015 IEEE International Parallel and Distributed Processing Symposium Workshop, pp. 342-5 Synthetic Biology Link

3 publications
Gautam VK, Czeizler E, Haddow PC, Kuiper M (2014) Design of a Minimal System for Self-replication of Rectangular Patterns of DNA Tiles. In: Dediu AH, Lozano M, Martín-Vide C (eds) Theory and Practice of Natural Computing. TPNC 2014. Lecture Notes in Computer Science 8890:119-133 Synthetic Biology Link
Hallinan JS, Gilfellon O, Misirli G, Wipat A (2014) Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts. Proceedings of the 2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 1-8 Synthetic Biology Link
Ivan ANY (2014) Assisted Design of DNA Computing Systems: the DNA Toolbox and Beyond. PhD Thesis, University of Tokyo. Synthetic Biology Computational Method Link
Lakin MR, Minnich A, Lane T, Stefanovic D (2014) Design of a biochemical circuit motif for learning linear functions. Journal of the Royal Society Interface 11:20140902 Synthetic Biology Link
Liao C, Cai Y (2014) Towards Modeling Automation for Synthetic Biology. In: Kulkarni V., Stan GB., Raman K. (eds.) A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems. Springer, Dordrecht, 201–217 Synthetic Biology Computational Method Link
Machado D, Rodrigues LR, Rocha I (2014) A kinetic model for curcumin production in Escherichia coli. Biosystems 125:16-21 Synthetic Biology Metabolism Link

6 publications

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Hoffman-Sommer M (2012) Cell-to-cell communication circuits: quantitative analysis of synthetic logic gates. Frontiers in Physiology 3:287 Synthetic Biology Link

1 publication
Chandran D (2011) TinkerCell: Computer-Aided Design for Synthetic Biology. PhD Thesis, University of Washington, Seattle. Software Synthetic Biology Link
Checkley S (2011) Engineering Tuneable Gene Circuits in Yeast. PhD Thesis, University of Manchester. Synthetic Biology Link
Hoffman-Sommer M, Supady A, Klipp E (2011) Cell-to-Cell Communication Circuits: Quantitative Analysis of Synthetic Logic Gates. Frontiers in Physiology 3:287–287 Synthetic Biology Link
Marchisio MA, Stelling J (2011) Automatic Design of Digital Synthetic Gene Circuits. PLOS Computational Biology 7:e1001083 Synthetic Biology Link
Qian L, Winfree E (2011) A simple DNA gate motif for synthesizing large-scale circuits. Journal of the Royal Society Interface 8:1281-97 Synthetic Biology Link
Qian L, Winfree E (2011) Scaling up digital circuit computation with DNA strand displacement cascades. Science 332:1196–1201 Synthetic Biology Link

6 publications
Hallinan JS, Misirli G, Wipat A (2010) Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits. Proceedings of the 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology 768–774 Synthetic Biology Link
Yao G, Tan C, West M, Nevins JR, You L (2010) A Minimal Gene Circuit Underlying the Bistable Cell Cycle Entry. Synthetic Biology Link

2 publications
Cai Y, Lux MW, Adam L, Peccoud J (2009) Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars. PLOS Computational Biology 5:e1000529 Synthetic Biology Computational Method Laboratory Method Link

1 publication
Jungmann R, Renner S, Simmel FC (2008) From DNA nanotechnology to synthetic biology. HFSP Journal 2:99-109 Synthetic Biology Link
Marchisio MA (2008) How to design synthetic gene circuits with composable parts and pools in the ProMoT framework. Synthetic Biology Link
Marchisio MA, Stelling J (2008) Computational design of synthetic gene circuits with composable parts. Bioinformatics 24:1903-10. Synthetic Biology Link

3 publications

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