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. 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)
  2. DNAStack: a stochastic model of the the DNA stack chemistry described in (Lopiccolo et al., 2021). Full documentation can be found here.
  3. 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. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. Partridge, N. (2021). Towards greater transparency: Digital opportunities to promote traceability in genetic engineering. Zenodo. https://doi.org/10.5281/zenodo.5343358
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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