Billerbeck group Publications

Maciá Valero, A., Prins, R. C., de Vroet, T., & Billerbeck, S. (2025). Erratum: Correction to: Combining Oligo Pools and Golden Gate Cloning to Create Protein Variant Libraries or Guide RNA Libraries for CRISPR Applications (Methods in molecular biology (Clifton, N.J.) (2025) 2850 DOI: 10.1007/978-1-0716-4220-7_15). Methods in molecular biology (Clifton, N.J.), 2850, C1. Advance online publication. https://doi.org/10.1007/978-1-0716-4220-7_28

Prins, R. C., & Billerbeck, S. (2025). Protocol to study toxic, immune, and suicidal phenotypes of killer yeast. STAR protocols, 6(1), Article 103611. https://doi.org/10.1016/j.xpro.2025.103611

Maciá Valero, A., Tabatabaeifar, F., & Billerbeck, S. (2025). Screening a 681-membered yeast collection for the secretion of proteins with antifungal activity. New Biotechnology, 86, 55-72. https://doi.org/10.1016/j.nbt.2025.01.008

Prins, R. C., & Billerbeck, S. (2025). Small proteins and peptides conferring protection against antimicrobial compounds. Trends in Microbiology. Advance online publication. https://doi.org/10.1016/j.tim.2025.01.011

Billerbeck, S. (2024). A new Editor-in-chief for Synthetic Biology. Synthetic biology (Oxford, England), 9(1), Article ysae006. https://doi.org/10.1093/synbio/ysae006

Maciá Valero , A., Prins, R. C., de Vroet, T., & Billerbeck, S. (2024). Combining oligo pools and Golden Gate cloning to create protein variant libraries or guide RNA libraries for CRISPR applications. Methods in Molecular Biology, 2850, 297-306. https://doi.org/10.1007/978-1-0716-4220-7_15

Lu, M., & Billerbeck, S. (2024). Improving homology-directed repair by small molecule agents for genetic engineering in unconventional yeast?-Learning from the engineering of mammalian systems. Microbial Biotechnology, 17(2), Article e14398. https://doi.org/10.1111/1751-7915.14398

Billerbeck, S., Walker, R. S. K., & Pretorius, I. S. (2024). Killer yeasts: expanding frontiers in the age of synthetic biology. Trends in Biotechnology, 42(9), 1081-1096. https://doi.org/10.1016/j.tibtech.2024.03.003

Prins, R. C., & Billerbeck, S. (2024). The signal peptide of yeast killer toxin K2 confers producer self-protection and allows conversion into a modular toxin-immunity system. Cell reports, 43(7), Article 114449. https://doi.org/10.1016/j.celrep.2024.114449

Billerbeck, S., Prins, R. C., & Marquardt, M. (2023). A Modular Cloning Toolkit Including CRISPRi for the Engineering of the Human Fungal Pathogen and Biotechnology Host Candida glabrata. ACS Synthetic Biology, 12, 1358-1363. Article 00560. https://doi.org/10.1021/acssynbio.2c00560

Matragrano, J., Cornish, V. W., & Billerbeck, S. (2023). A Multiplex GPCR-Mediated Peptide Tagging System for a Growing Yeast Synthetic Biology Toolbox. Helvetica Chimica Acta, 106(2), Article e202300094. https://doi.org/10.1002/hlca.202300094

Aldulijan, I., Beal, J., Billerbeck, S., Bouffard, J., Chambonnier, G., Ntelkis, N., Guerreiro, I., Holub, M., Ross, P., Selvarajah, V., Sprent, N., Vidal, G., & Vignoni, A. (2023). Functional Synthetic Biology. Synthetic biology (Oxford, England), 8(1), Article ysad006. https://doi.org/10.1093/synbio/ysad006

Widodo, W. S., & Billerbeck, S. (2023). Natural and engineered cyclodipeptides: Biosynthesis, chemical diversity, and engineering strategies for diversification and high-yield bioproduction. Engineering Microbiology, 3(1), Article 100067. https://doi.org/10.1016/j.engmic.2022.100067

Berezin, C.-T., Aguilera, L. U., Billerbeck, S., Bourne, P. E., Densmore, D., Freemont, P., Gorochowski, T. E., Hernandez, S. I., Hillson, N. J., King, C. R., Köpke, M., Ma, S., Miller, K. M., Moon, T. S., Moore, J. H., Munsky, B., Myers, C. J., Nicholas, D. A., Peccoud, S. J., ... Peccoud, J. (2023). Ten simple rules for managing laboratory information. PLoS Computational Biology, 19(12), Article e1011652. https://doi.org/10.1371/journal.pcbi.1011652

Bhatt, D., Crooijmans, M. E., Coenradij, J., Macia Valero, A., Lubbers, M. J., Asin-Garcia, E., Amy Yewdall, N., D'Adamo, S., Claassens, N. J., & Billerbeck, S. (2022). A SynBio community comes of age: Political, academical, industrial, and societal developments in the Netherlands. Biotechnology notes, 3, 62-69. https://doi.org/10.1016/j.biotno.2022.07.004

Billerbeck, S., Oliveira, A. G., & Gonçalves, A. P. (2022). Editorial: Fungi as cell factories: Genetic engineering and applications. Frontiers in Bioengineering and Biotechnology, 10, Article 1109992. https://doi.org/10.3389/fbioe.2022.1109992

Beal, J., Telmer, C. A., Vignoni, A., Boada, Y., Baldwin, G. S., Hallett, L., Lee, T., Selvarajah, V., Billerbeck, S., Brown, B., Cai, G. N., Cai, L., Eisenstein, E., Kiga, D., Ross, D., Alperovich, N., Sprent, N., Thompson, J., Young, E. M., ... Haddock-Angelli, T. (2022). Multicolor plate reader fluorescence calibration. Synthetic Biology, 7(1), 1-9. https://doi.org/10.1093/synbio/ysac010

Billerbeck, S. (2022). Self-growing environmentally responsive houses made from agricultural waste and fungal mycelia. Synthetic biology (Oxford, England), 7(1), Article ysac003. https://doi.org/10.1093/synbio/ysac003

Kuiper, B. P., Prins, R. C., & Billerbeck, S. (2022). Oligo pools as an affordable source of synthetic DNA for cost-effective library construction in protein- and metabolic pathway engineering. ChemBioChem, 23(7), Article 202100507. https://doi.org/10.1002/cbic.202100507

Billerbeck, S., & Cornish, V. W. (2022). Peptide-Dependent Growth in Yeast via Fine-Tuned Peptide/GPCR-Activated Essential Gene Expression. Biochemistry, 61(3), 150-159. Article 00661. https://doi.org/10.1021/acs.biochem.1c00661

Prins, R. C., & Billerbeck, S. (2021). A buffered media system for yeast batch culture growth. BMC Microbiology, 21(1), Article 127. https://doi.org/10.1186/s12866-021-02191-5

Billerbeck, S. (2021). A computational walk to the hidden peaks of protein performance. Synthetic biology (Oxford, England), 6(1), Article ysab011. https://doi.org/10.1093/synbio/ysab011

Billerbeck, S. (2021). Moving towards chemical-free agriculture, 37 kb at a time. Synthetic biology (Oxford, England), 6(1), Article ysab009. https://doi.org/10.1093/synbio/ysab009

Billerbeck, S. (2021). Synthetic biological toggle circuits that respond within seconds and teach us new biology. Synthetic biology (Oxford, England), 6(1). https://doi.org/10.1093/synbio/ysab027

Billerbeck, S. (2020). Directed evolution of synthetic coexistence: A new path towards ecosystem design? Synthetic biology (Oxford, England), 5(1), Article ysaa025. https://doi.org/10.1093/synbio/ysaa025

Billerbeck, S., Brisbois, J., Agmon, N., Jimenez, M., Temple, J., Shen, M., Boeke, J. D., & Cornish, V. W. (2019). Author correction: A scalable peptide-GPCR language for engineering multicellular communication (vol 9, 5057, 2018). Nature Communications, 10, Article 554. https://doi.org/10.1038/s41467-019-08545-y

Billerbeck, S., Brisbois, J., Agmon, N., Jimenez, M., Temple, J., Shen, M., Boeke, J. D., & Cornish, V. W. (2018). A scalable peptide-GPCR language for engineering multicellular communication. Nature Communications, 9, Article 5057. https://doi.org/10.1038/s41467-018-07610-2

Ostrov, N., Jimenez, M., Billerbeck, S., Brisbois, J., Matragrano, J., Ager, A., & Cornish, V. W. (2017). A modular yeast biosensor for low-cost point-of-care pathogen detection. Science Advances, 3(6), Article e1603221. https://doi.org/10.1126/sciadv.1603221

Oesterle, S., Roberts, T. M., Widmer, L. A., Mustafa, H., Panke, S., & Billerbeck, S. (2017). Sequence-based prediction of permissive stretches for internal protein tagging and knockdown. BMC Biology, 15, Article 100. https://doi.org/10.1186/s12915-017-0440-0

Hold, C., Billerbeck, S., & Panke, S. (2016). Forward design of a complex enzyme cascade reaction. Nature Communications, 7, Article 12971. https://doi.org/10.1038/ncomms12971

Billerbeck, S., Haerle, J., & Panke, S. (2013). The good of two worlds: increasing complexity in cell-free systems. Current Opinion in Biotechnology, 24(6), 1037-1043. https://doi.org/10.1016/j.copbio.2013.03.007

Billerbeck, S., Calles, B., Mueller, C. L., de Lorenzo, V., & Panke, S. (2013). Towards functional orthogonalisation of protein complexes: individualisation of GroEL monomers leads to distinct quasihomogeneous single rings. ChemBioChem, 25(14), 2310-2312. https://doi.org/10.1002/cbic.201300332

Billerbeck, S., & Panke, S. (2012). A genetic replacement system for selection-based engineering of essential proteins. Microbial Cell Factories, 11, Article 110. https://doi.org/10.1186/1475-2859-11-110

Bujara, M., Billerbeck, S., & Panke, S. (2011). Multienzymnetzwerke für die Feinchemie. BIOspektrum, 17(4), 399-401. https://doi.org/10.1007/s12268-011-0061-z

Bujara, M., Schümperli, M., Billerbeck, S., Heinemann, M., & Panke, S. (2010). Exploiting Cell-Free Systems: Implementation and Debugging of a System of Biotransformations. Biotechnology and Bioengineering, 106(3), 376-389. https://doi.org/10.1002/bit.22666