Publications

Patent applications

  1. Martinez V, Uribe RV, Takos A, van der Helm E, Clube J Single-vector Type I vectors (16th April 2020)

  2. Uribe RV, van der Helm E, Sommer MOA, Lee SW A high-throughput platform to select for regulators of CRISPR-Cas associated activity (29th November 2018)

  3. Uribe RV, van der Helm E, Sommer MOA, Misiakou MA, Lee SW Inhibitors of CRISPR-Cas associated activity (27th March 2018)

  4. Sommer MOA, Martinez V, van der Helm E, Krause Haaber J, De Santiago Torio A, Grøndahl C, Clube J Treating & preventing microbial infections (25th March 2018)

  5. van der Helm E, Redl SMA A laboratory device to automatically measure growth of cell culture non-invasively (27th November 2017)

  6. Clube J, Sommer MOA, Grøndahl C, Uribe RV, van der Helm E Selectively altering microbiota for immune modulation (5th June 2016)

  7. van der Helm E, Sommer MOA High throughput in vivo protease inhibitor selection platform  (28th April 2016 )

  8. Clube J, Grøndahl C, Sommer MOA, van der Helm E, Uribe RV Altering microbial populations & modifying microbiota (6th May 2015)

  9. Malla S, van der Helm E, Wieschalka S, Forster J, Sommer MOA A family of microbial lysine transporter polypeptides (19th November 2015)

    Papers

  10. Kristensen, C., Petersen, A., Kilstrup, M., van der Helm, E., Takos, A. (2024). Cell-free synthesis of infective phages from in vitro assembled phage genomes for efficient phage engineering and production of large phage libraries. Synthetic Biology, https://doi.org/10.1093/synbio/ysae012

  11. Gencay, Y. E., Jasinskytė, D., Robert, C., Semsey, S., Martínez, V. and Petersen, A. Ø., […], van der Helm, E., Zdravkovic, M. and Sommer, M. O. A. (2023). Engineered phage with antibacterial CRISPR–Cas selectively reduce E. coli burden in mice. Nature Biotechnology, https://doi.org/10.1038/s41587-023-01759-y

  12. Malla, S., van der Helm, E., Darbani, B., Wieschalka, S., Forster, J., Borodina, B., Sommer, M. O. A. (2022). A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics. Frontiers in Microbiology, https://doi.org/10.3389/fmicb.2022.855736

  13. van der Helm, E., Redl, S. M A. (2021). Quantifying live bacterial densities using non-invasive optical measurements of E. coli. bioRxiv, https://doi.org/10.1101/2021.06.12.448182

  14. Reddington, K., Eccles D., O’Grady J., Drown D., Hestbjerg Hansen, L., Kjærgaard Nielsen, T., Ducluzeau, A., Leggett, R.M., Heavens, D., Peel, N., Snutch, T.P., Bayega, A., Oikonomopoulos, S., Ragoussis, J., Barry, T., van der Helm, E., Jolic, D., Richardson, H., Jansen, H., Tyson, J.R., Jain, M., Brown, B.L. (2020) Metagenomic Analysis of Planktonic Riverine Microbial Consortia Using Nanopore Sequencing Reveals Insight into River Microbe Taxonomy and Function GigaScience 9, no. giaa053 https://doi.org/10.1093/gigascience/giaa053.

  15. Uribe, R. V, van der Helm, E., Misiakou, M., Lee, S., Kol, S., & Sommer, M. O. A. (2019). Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla Short Article Discovery. Cell Host and Microbe, 25, 1–9. https://doi.org/10.1016/j.chom.2019.01.003

  16. Li, J., Rettedal, E. A., van der Helm, E., Ellabaan, M., & Sommer, M. O. A. (2019). Antibiotic Treatment Drives the Diversification of the Human Gut Resistome. Genomics, Proteomics & Bioinformatics, (17) 1. http://dx.doi.org/10.1016/j.gpb.2018.12.003

  17. van der Helm, E., Genee, H. J., & Sommer, M. O. A. (2018). The evolving interface between synthetic biology and functional metagenomics. Nature Chemical Biology. https://doi.org/10.1038/s41589-018-0100-x

  18. Imamovic, L., Misiakou, M.-A., van der Helm, E., Panagiotou, G., Muniesa, M., & Sommer, M. O. A. (2018). Complete Genome Sequence of Escherichia coli Strain WG5. Genome Announcements, 6(2), e01403-17. https://doi.org/10.1128/genomeA.00134-15

  19. van der Helm, E., Imamovic, L., Hashim Ellabaan, M. M., van Schaik, W., Koza, A., & Sommer, M. O. A. (2017). Rapid resistome mapping using nanopore sequencing. Nucleic Acids Research. https://doi.org/10.1093/nar/gkw1328

  20. van der Helm, E., Geertz-Hansen, H. M., Genee, H. J., Malla, S., & Sommer, M. O. A. (2015). deFUME: Dynamic exploration of functional metagenomic sequencing data. BMC Research Notes, 8(1), 328. https://doi.org/10.1186/s13104-015-1281-y