COPASI's Use In Synthetic Biology

2017
Baumgart L, Mather W, Hasty J (2017) Synchronized DNA cycling across a bacterial population. Nature Genetics, 49:1282–128 Synthetic Biology Microbiology Link

1 publication
2016
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
2015
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. J Biomol. Struct. Dyn. 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
2014
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. J. Royal Soc. 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
2013

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

1 publication
2011
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 Comput. Biol. 7:e1001083 Synthetic Biology Link
Qian L, Winfree E (2011) A simple DNA gate motif for synthesizing large-scale circuits. J. Royal Soc. 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
2010
Hallinan JS, Misirli G, Wipat A (2010) Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits. IEEE, 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
2009
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
2008
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
2007

0 publication
2006

0 publication