COPASI

COPASI's Use In Synthetic Biology

2025

0 publication
2024
Castaño-Cerezo S, Chamas A, Kulyk H, Treitz C, Bellvert F, Tholey A, Galéote V, Camarasa C, Heux S, Garcia-Alles LF, Millard P, Truan G (2024) Combining systems and synthetic biology for in vivo enzymology. EMBO Journal 43:5169–5185 Synthetic Biology Metabolism Laboratory Method Link
Durmaz MG, Tulluk N, Aksoy RD, Yilmaz HB, Yang B, Wipat A, Pusane AE, Mısırlı G, Tugcu T (2024) BioRxToolbox: a computational framework to streamline genetic circuit design in molecular data communications. Synthetic Biology 9:ysae015 Synthetic Biology Computational Method Software Link
Khanijou JK, Hee YT, Scipion CPM, Chen X, Selvarajoo K (2024) Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli. npj Systems Biology and Applications. 10:1–14 Biotechnology Synthetic Biology Metabolism Link
Poprawa SM, Stasi M, Kriebisch BAK, Wenisch M, Sastre J, Boekhoven J (2024) Active droplets through enzyme-free, dynamic phosphorylation. Nature Communications 15:4204 Chemistry Synthetic Biology Signaling Link

4 publications
2023
Abraha BW, Marchisio MA (2023) Design of Gene Boolean Gates and Circuits with Convergent Promoters. In: Selvarajoo K (ed) Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology. New York, NY: Springer US, 121–154. Synthetic Biology Link
Olavarria K, Becker MV, Sousa DZ, van Loosdrecht MCM, Wahl SA (2023) Design and thermodynamic analysis of a pathway enabling anaerobic production of poly-3-hydroxybutyrate in Escherichia coli. Synthetic and Systems Biotechnology 8:629–639 Synthetic Biology Microbiology Metabolism Link

2 publications
2022
Abraha BW, Marchisio MA (2022) NOT Gates Based on Protein Degradation as a Case Study for a New Modular Modeling via SBML Level 3—Comp Package. Frontiers in Bioengineering and Biotechnology 10:845240 Synthetic Biology Link
Borg Y, Alsford S, Pavlika V, Zaikin A, Nesbeth DN (2022) Synthetic biology tools for engineering Goodwin oscillation in Trypanosoma brucei brucei. Heliyon 8:e08891 Synthetic Biology Link
Cho D-J, Függer M, Hopper C, Kushwaha M, Nowak T, Soubeyran Q (2022) Distributed computation with continual population growth. Distributed Computing 35:547–569 Synthetic Biology Link
Liu Y, Wang W, Zeng A-P (2022) Biosynthesizing structurally diverse diols via a general route combining oxidative and reductive formations of OH-groups. Nature Communications 13:1595 Biotechnology Synthetic Biology Link
Wang M (2022) Bottom-up synthesis of Nicotinamide Adenine Dinucleotide (NAD) regeneration modules for artificial cells. Ph.D. Thesis, Otto von Guericke Universität Magdeburg, Germany Synthetic Biology Chemistry Link

5 publications
2021
Kleineberg C (2021) Bottom-up assembly of a light-driven ATP regeneration module in lipid, polymer and hybrid vesicles. Ph.D. Thesis, Otto-von-Guericke Universität Magdeburg, Germany. Synthetic Biology Biochemistry Link
Mısırlı G, Yang B, James K, Wipat A (2021) Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits. ACS Synthetic Biology 10:3304–3315 Computational Method Synthetic Biology Link

2 publications
2020
Bartoli V, Meaker GA, di Bernardo M, Gorochowski TE (2020) Tunable genetic devices through simultaneous control of transcription and translation. Nature Communications 11:2095 Synthetic Biology Link
Greiss F, Daube SS, Noireaux V, Bar-Ziv R (2020) From deterministic to fuzzy decision-making in artificial cells. Nature Communications 11:5648 Synthetic Biology Genetics Link

2 publications
2019
Bartoli V, di Bernardo M, Gorochowski TE (2019) Tunable genetic devices through simultaneous control of transcription and translation. bioRxiv Preprint bioRxiv:711275 Synthetic Biology Link
Carbonell P, Faulon J-L, Breitling R (2019) Efficient learning in metabolic pathway designs through optimal assembling. IFAC-PapersOnLine 52:7–12 Synthetic Biology Link
Jayanthi BEK, Zhao W, Segatori L (2019) Input-dependent post-translational control of the reporter output enhances dynamic resolution of mammalian signaling systems. Methods in Enzymology 622:1–27 Signaling Synthetic Biology Link
Kaushik AC, Mao X, Li C-D, Li Y, Wei D-Q, Sahi S (2019) G-protein-coupled receptors function as logic gates for nanoparticle binding using systems and synthetic biology approach. Journal of Materials Research 34:1854–1867 Signaling Synthetic Biology Link
Lebar T, Verbič A, Ljubetič A, Jerala R (2019) Polarized displacement by transcription activator-like effectors for regulatory circuits. Nature Chemical Biology 15:80–87 Synthetic Biology Genetics Link
Rampioni G, Leoni L, Stano P (2019) Molecular Communications in the Context of “Synthetic Cells” Research. IEEE Transactions on NanoBioscience 18:43–50 Synthetic Biology Link
Shaw WM, Yamauchi H, Mead J, Gowers G-OF, Bell DJ, Öling D, Larsson N, Wigglesworth M, Ladds G, Ellis T (2019) Engineering a Model Cell for Rational Tuning of GPCR Signaling. Cell 177:782-796.e27 Synthetic Biology Signaling Link
Yang X, Yuan Q, Luo H, Li F, Mao Y, Zhao X, Du J, Li P, Ju X, Zheng Y, Chen Y, Liu Y, Jiang H, Yao Y, Ma H, Ma Y (2019) Systematic design and in vitro validation of novel one-carbon assimilation pathways. Metabolic Engineering 56:142–153 Metabolism Synthetic Biology Link
Yeoh JW, Ng KBI, Teh AY, Zhang J, Chee WKD, Poh CL (2019) An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs. ACS Synthetic Biology 8:1484–1497 Synthetic Biology Computational Method Link

9 publications
2018

0 publication
2017
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 Method 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
Kosey D, Singh S (2017) Computational design of molecular motors as nanocircuits in Leishmaniasis. F1000Research 6:94 Synthetic Biology Link
Opgenorth PH, Korman TP, Iancu L, Bowie JU (2017) A molecular rheostat maintains ATP levels to drive a synthetic biochemistry system. Nature Chemical Biology 13:938–942 Synthetic Biology 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

7 publications
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. 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
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. Ph.D. Thesis, University of Tokyo, Japan. 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 L, Rocha I (2014) A kinetic model for curcumin production in Escherichia coli. BioSystems 125:16-21 Synthetic Biology Metabolism Link

6 publications
2013
Saeidi N, Arshath M, Chang MW, Poh CL (2013) Characterization of a quorum sensing device for synthetic biology design: Experimental and modeling validation. Chemical Engineering Science 103:91–99 Synthetic Biology Microbiology Link

1 publication
2012
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
2011
Chandran D (2011) TinkerCell: Computer-Aided Design for Synthetic Biology. Ph.D. Thesis, University of Washington, Seattle, USA. Software Synthetic Biology Link
Checkley S (2011) Engineering Tuneable Gene Circuits in Yeast. Ph.D. Thesis, University of Manchester, UK. 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
2010
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. Citeseer Preprint 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. CiteSeer Preprint 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
2005

0 publication