Publications, Software and Other Outputs

Publications, Software and Other Outputs

Here you will find a list of the project outputs, including publications, links to software, etc.


  1. RevNano: a computational tool that reverse engineers a schematic diagram for a nucleic acid origami nanostructure, given just the the raw scaffold and staple sequences for that nanostructure.
  2. CellRepo: a specialised version control system for engineering biology. Technical details in (Tellechea-Luzardo et al., 2020; Tellechea-Luzardo et al., 2021; Tellechea-Luzardo et al., 2022)
  3. DNAStack: a stochastic model of the the DNA stack chemistry described in (Lopiccolo et al., 2021). Full documentation can be found here.
  4. InfoBiotics Workbench: a full-stack software suit to specify, model, verify and bio-compile (multi)cellular systems based on the paper (Konur et al., 2021)


  1. Todd, D., & Krasnogor, N. (2023). Homebrew Photolithography for the Rapid and Low-Cost, “Do It Yourself” Prototyping of Microfluidic Devices. ACS Omega, 8(38), 35393–35409.
  2. Shirt-Ediss, B., Connolly, J., Elezgaray, J., Torelli, E., Navarro, S. A., Bacardit, J., & Krasnogor, N. (2023). Reverse engineering DNA origami nanostructure designs from raw scaffold and staple sequence lists. Computational and Structural Biotechnology Journal, 21, 3615–3626.
  3. Pelechova, L. (2022). Public Awareness of Novel Technologies: DNA Data Storage as a study case (Version 1). Zenodo.
  4. Vizzini, P., Beltrame, E., Coppede, N., Vurro, F., Andreatta, F., Torelli, E., & Manzado, M. (2023). Detection of Listeria monocytogenes in foods with a textile organic electrochemical transistor biosensor . Applied Microbiology and Biotechnology, 107, 3789–3800.
  5. Torelli, E., Shirt-Ediss, B., Navarro, S. A., Manzano, M., Vizzini, P., & Krasnogor, N. (2023). Light-Up Split Broccoli Aptamer as a Versatile Tool for RNA Assembly Monitoring in Cell-Free TX-TL Systems, Hybrid RNA/DNA Origami Tagging and DNA Biosensing. . International Journal of Molecular Sciences, 24(8483).
  6. Konur, S., Gheorghe, M., & Krasnogor, N. (2023). Verifiable Biology. Journal of the Royal Society Interface, 20(20230019).
  7. Jiang, S., Otero-Muras, I., Banga, J. R., Wang, Y., Kaiser, M., & Krasnogor, N. (2022). OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production. ACS Synthetic Biology, 11(4), 1531–1541.
  8. Li, B., Mackenzie, N., Shirt-Ediss, B., Krasnogor, N., & Zuliani, P. (2022). Modelling and Optimisation of a DNA Stack Nano-Device Using Probabilistic Model Checking. In T. E. Ouldridge & S. F. J. Wickham (Eds.), 28th International Conference on DNA Computing and Molecular Programming (DNA 28) (Vol. 238, pp. 5:1–5:22). Schloss Dagstuhl – Leibniz-Zentrum für Informatik.
  9. Tellechea-Luzardo, J., Hobbs, L., Velazques, E., Pelechova, L., Woods, S., de Lorenzo, V., & Krasnogor, N. (2022). Versioning Biological Cells for Trustworthy Cell Engineering. Nature Communications, 13(765).
  10. Lopiccolo, A., Shirt-Ediss, B., Torelli, E., Olulana, A. F. A., Castronovo, M., Fellermann, H., & Krasnogor, N. (2021). A last-in first-out stack data structure implemented in DNA. Nature Communications, 12(1).
  11. Velázquez, E., Al-Ramahi, Y., Tellechea-Luzardo, J., Krasnogor, N., & de Lorenzo, V. (2021). Targetron-Assisted Delivery of Exogenous DNA Sequences into Pseudomonas putida through CRISPR-Aided Counterselection. ACS Synthetic Biology, 10(10), 2552–2565.
  12. Konur, S., Mierla, L., Fellermann, H., Ladroue, C., Brown, B., Wipat, A., Twycross, J., Dun, B. P., Kalvala, S., Gheorghe, M., & Krasnogor, N. (2021). Toward Full-Stack In Silico Synthetic Biology: Integrating Model Specification, Simulation, Verification, and Biological Compilation. ACS Synthetic Biology, 10(8), 1931–1945.
  13. Callaghan, M. M., Koch, B., Hackett, K. T., Klimowicz, A. K., Schaub, R. E., Krasnogor, N., & Dillard, J. P. (2021). Expression, Localization, and Protein Interactions of the Partitioning Proteins in the Gonococcal Type IV Secretion System. Frontiers in Microbiology, 12.
  14. Partridge, N. (2021). Towards greater transparency: Digital opportunities to promote traceability in genetic engineering. Zenodo.
  15. Tellechea-Luzardo, J., Hobbs, L., Velazques, E., Pelechova, L., Woods, S., de Lorenzo, V., & Krasnogor, N. (2021). Versioning Biological Cells for Trustworthy Cell Engineering. BioRxiv.
  16. de Lorenzo, V., Krasnogor, N., & Schmidt, M. (2021). For the sake of the Bioeconomy: define what a Synthetic Biology Chassis is! New Biotechnology, 60(C), 44–51.
  17. Tellechea-Luzardo, J., Winterhalter, C., Widera, P., Kozyra, J., de Lorenzo, V., & Krasnogor, N. (2020). Linking Engineered Cells to Their Digital Twins: A Version Control System for Strain Engineering. ACS Synthetic Biology, 9(3), 536–545.
  18. Jiang, S., Wang, Y., Kaiser, M., & Krasnogor, N. (2020). NIHBA: a network interdiction approach for metabolic engineering design. Bioinformatics, 36(11), 3482–3492.
  19. Torelli, E., Kozyra, J., Shirt-Ediss, B., Piantanida, L., Voïtchovsky, K., & Krasnogor, N. (2020). Cotranscriptional Folding of a Bio-orthogonal Fluorescent Scaffolded RNA Origami. ACS Synthetic Biology, 9(7), 1682–1692.
  20. Koch, B., Callaghan, M. M., Tellechea‐Luzardo, J., Seeger, A. Y., Dillard, J. P., & Krasnogor, N. (2020). Protein interactions within and between two F‐type type IV secretion systems. Molecular Microbiology, 114(5), 823–838.
  21. Torelli, E., Kozyra, J., Shirt-Ediss, B., Voitchovsky, K., & Krasnogor, N. (2020). Towards in vivo origami: bio-orthogonal scaffolded RNA nanoribbons self-assembled via co-transcriptional folding. Proc. of the The 1st International Biodesign Research Conference.
  22. Shirt-Ediss, B., Connolly, J., Torelli, E., & Krasnogor, N. (2020). REVNANO: An Algorithm to Reverse Engineer Scaffolded DNA/RNA Origami Designs from Sequence Information Only. Proc. of the 26th International Conference on DNA Computing and Molecular Programming.