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.

Software

  1. DNA Origami Scaffold Selector: a computational tool for DNA origami nanostructure sequence design, in particular, the tool can be used to select the most appropriate origami scaffold sequence from any pool of DNA sequences desired including pools of synthetic random sequence, De Bruijn sequences or natural biological ones. Full technical details are described in details here (Shirt-Ediss et al., 2025)
  2. 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. Scientific details are described in (Shirt-Ediss et al., 2023)
  3. 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)
  4. DNAStack: a stochastic model of the the DNA stack chemistry described in (Lopiccolo et al., 2021). Full documentation can be found here.
  5. 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)

Publications

  1. Shirt-Ediss, B., Torelli, E., Navarro, S. A., Khamis, H., Kaplan, A., Trewby, W., Elezgaray, J., Moradzadeh-Esmaeili, N., Haydell, M., Keppner, D., Famulok, M., & Krasnogor, N. (2025). Optimizing DNA origami assembly through selection of scaffold sequences that minimise off-target interactions. BioRxiv. https://doi.org/10.1101/2025.01.29.635450
  2. 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. https://doi.org/10.1021/acsomega.3c05544
  3. 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. https://doi.org/https://doi.org/10.1016/j.csbj.2023.07.011
  4. Pelechova, L. (2022). Public Awareness of Novel Technologies: DNA Data Storage as a study case (Version 1). Zenodo. https://doi.org/10.5281/zenodo.7926530
  5. 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. https://doi.org/10.1007/s00253-023-12543-y
  6. 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). https://doi.org/10.3390/ijms24108483
  7. Konur, S., Gheorghe, M., & Krasnogor, N. (2023). Verifiable Biology. Journal of the Royal Society Interface, 20(20230019). https://doi.org/10.1098/rsif.2023.0019
  8. 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. https://doi.org/10.1021/acssynbio.1c00610
  9. 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. https://doi.org/10.4230/LIPIcs.DNA.28.5
  10. 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). https://doi.org/10.1038/s41467-022-28350-4
  11. 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). https://doi.org/10.1038/s41467-021-25023-6
  12. 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. https://doi.org/10.1021/acssynbio.1c00199
  13. 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. https://doi.org/10.1021/acssynbio.1c00143
  14. 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. https://doi.org/10.3389/fmicb.2021.784483
  15. Partridge, N. (2021). Towards greater transparency: Digital opportunities to promote traceability in genetic engineering. Zenodo. https://doi.org/10.5281/zenodo.5343358
  16. 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. https://doi.org/10.1101/2021.04.23.441106
  17. 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. https://doi.org/10.1016/j.nbt.2020.08.004
  18. 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. https://doi.org/10.1021/acssynbio.9b00400
  19. Jiang, S., Wang, Y., Kaiser, M., & Krasnogor, N. (2020). NIHBA: a network interdiction approach for metabolic engineering design. Bioinformatics, 36(11), 3482–3492. https://doi.org/10.1093/bioinformatics/btaa163
  20. 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. https://doi.org/10.1021/acssynbio.0c00009
  21. 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. https://doi.org/10.1111/mmi.14582
  22. 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. https://www.biodesign-conference.com/2020/abstract2.php?id=80
  23. 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. https://eprints.ncl.ac.uk/272723