Journal Papers

Gebhardt, C.M., and Niopek, D. (2024). Anti-CRISPR Proteins and Their Application to Control CRISPR Effectors in Mammalian Systems. Methods Mol Biol 2774, 205-231. https://doi.org/10.1007/978-1-0716-3718-0_14.

Muench, P., Fiumara, M., Southern, N., Coda, D., Aschenbrenner, S., Correia, B., Graeff, J., Niopek, D., and Mathony, J. (2023). A modular toolbox for the optogenetic deactivation of transcription. bioRxiv. https://doi.org/10.1101/2023.11.06.565805.

Mathony, J., and Niopek, D. (2023). Domäneninsertion: Untersuchung zur Konstruktion schaltbarer Hybridproteine. BIOspektrum 29, 595–598. https://doi.org/10.1007/s12268-023-2032-6.

Mathony, J., Aschenbrenner, S., Becker, P., and Niopek, D. (2023). Dissecting the Determinants of Domain Insertion Tolerance and Allostery in Proteins. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 10, e2303496. https://doi.org/10.1002/advs.202303496.

Adam, L., Stanifer, M., Springer, F., Mathony, J., Brune, M., Di Ponzio, C., Eils, R., Boulant, S., Niopek, D., and Kallenberger, S.M. (2023). Transcriptomics-inferred dynamics of SARS-CoV-2 interactions with host epithelial cells. Science signaling 16. https://doi.org/10.1126/scisignal.abl8266.

Stadelmann, T., Heid, D., Jendrusch, M., Mathony, J., Rosset, S., Correia, B.E., and Niopek, D. (2021). A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins. bioRxiv, 2021‐2008. https://doi.org/10.1101/2021.08.21.457204.

Mathony, J., and Niopek, D. (2021). Enlightening allostery: designing switchable proteins by photoreceptor fusion. Advanced Biology 5, 2000181. https://doi.org/10.1002/adbi.202000181.

Hoffmann, M.D., Mathony, J., Upmeier zu Belzen, J., Harteveld, Z., Aschenbrenner, S., Stengl, C., Grimm, D., Correia, B.E., Eils, R., and Niopek, D. (2021). Optogenetic control of Neisseria meningitidis Cas9 genome editing using an engineered, light-switchable anti-CRISPR protein. Nucleic acids research 49, e29. https://doi.org/10.1093/nar/gkaa1198.

Adam, L., Stanifer, M., Springer, F., Mathony, J., Di Ponzio, C., Eils, R., Boulant, S., Niopek, D., and Kallenberger, S.M. (2021). Dynamics of SARS-CoV-2 host cell interactions inferred from transcriptome analyses. https://doi.org/10.1101/2021.07.04.450986.

Mathony, J., Hoffmann, M.D., and Niopek, D. (2020). Optogenetics and CRISPR: a new relationship built to last. Photoswitching Proteins: Methods and Protocols, 261–281. https://doi.org/10.1007/978-1-0716-0755-8_18.

Mathony, J., Harteveld, Z., Schmelas, C., Upmeier zu Belzen, J., Aschenbrenner, S., Sun, W., Hoffmann, M.D., Stengl, C., Scheck, A., Georgeon, S., et al. (2020). Computational design of anti-CRISPR proteins with improved inhibition potency. Nature chemical biology 16, 725–730. https://doi.org/10.1038/s41589-020-0518-9.

Hoffmann, M.D., Bubeck, F., and Niopek, D. (2020). Light-Inducible CRISPR Labeling. Methods in molecular biology (Clifton, N.J.) 2173, 137–150. https://doi.org/10.1007/978-1-0716-0755-8_9.

Aschenbrenner, S., Kallenberger, S.M., Hoffmann, M.D., Huck, A., Eils, R., and Niopek, D. (2020). Coupling Cas9 to artificial inhibitory domains enhances CRISPR-Cas9 target specificity. Science advances 6. https://doi.org/10.1126/sciadv.aay0187.

Upmeier zu Belzen, J., Bürgel, T., Holderbach, S., Bubeck, F., Adam, L., Gandor, C., Klein, M., Mathony, J., Pfuderer, P., Platz, L., et al. (2019). Leveraging implicit knowledge in neural networks for functional dissection and engineering of proteins. Nature Machine Intelligence 1, 225–235. https://doi.org/10.1038/s42256-019-0049-9.

Hoffmann, M.D., Aschenbrenner, S., Grosse, S., Rapti, K., Domenger, C., Fakhiri, J., Mastel, M., Börner, K., Eils, R., Grimm, D., and Niopek, D. (2019). Cell-specific CRISPR-Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins. Nucleic acids research 47, e75. https://doi.org/10.1093/nar/gkz271.

Herrmann, A.-K., Bender, C., Kienle, E., Grosse, S., El Andari, J., Botta, J., Schürmann, N., Wiedtke, E., Niopek, D., and Grimm, D. (2019). A Robust and All-Inclusive Pipeline for Shuffling of Adeno-Associated Viruses. ACS synthetic biology 8, 194–206. https://doi.org/10.1021/acssynbio.8b00373.

Bubeck, F., Hoffmann, M.D., Harteveld, Z., Aschenbrenner, S., Bietz, A., Notbohm, J., Stengl, C., Mathony, J., Waldhauer, M.C., Dietz, L., et al. (2019). Engineered Anti-CRISPR Proteins for Precision Control of CRISPR-Cas9. Molecular Therapy 27, 297.

Senís, E., Mosteiro, L., Wilkening, S., Wiedtke, E., Nowrouzi, A., Afzal, S., Fronza, R., Landerer, H., Abad, M., Niopek, D., et al. (2018). AAVvector-mediated in vivo reprogramming into pluripotency. Nature Communications 9, 2651. https://doi.org/10.1038/s41467-018-05059-x. 

Hoffmann, M.D., Bubeck, F., Eils, R., and Niopek, D. (2018). Controlling Cells with Light and LOV. Advanced Biosystems 2. https://doi.org/10.1002/adbi.201800098.

Domenger, C., Kachel, B., Niopek, D., and Grimm, D. (2018). Post-transcriptional fine-tuning of AAV vector gene expression for hemophilia A gene therapy. In HUMAN GENE THERAPY, pp. A156‐A156.

Bubeck, F., Hoffmann, M.D., Harteveld, Z., Aschenbrenner, S., Bietz, A., Waldhauer, M.C., Börner, K., Fakhiri, J., Schmelas, C., Dietz, L., et al. (2018). Engineered anti-CRISPR proteins for optogenetic control of CRISPR-Cas9. Nature methods 15, 924–927. https://doi.org/10.1038/s41592-018-0178-9.

Wehler, P., Niopek, D., Eils, R., and Di Ventura, B. (2016). Optogenetic Control of Nuclear Protein Import in Living Cells Using Light-Inducible Nuclear Localization Signals (LINuS). Current protocols in chemical biology 8, 131–145. https://doi.org/10.1002/cpch.4.

Niopek, D., Wehler, P., Roensch, J., Eils, R., and Di Ventura, B. (2016). Optogenetic control of nuclear protein export. Nature Communications 7, 10624. https://doi.org/10.1038/ncomms10624.

Senís, E., Fatouros, C., Große, S., Wiedtke, E., Niopek, D., Mueller, A.-K., Börner, K., and Grimm, D. (2014). CRISPR/Cas9-mediated genome engineering: an adeno-associated viral (AAV) vector toolbox. Biotechnology journal 9, 1402–1412. https://doi.org/10.1002/biot.201400046.

Niopek, D., Benzinger, D., Roensch, J., Draebing, T., Wehler, P., Eils, R., and Di Ventura, B. (2014). Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells. Nature Communications 5, 4404. https://doi.org/10.1038/ncomms5404.

Beer, R., Herbst, K., Ignatiadis, N., Kats, I., Adlung, L., Meyer, H., Niopek, D., Christiansen, T., Georgi, F., Kurzawa, N., et al. (2014). Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange. Molecular BioSystems 10, 1709–1718. https://doi.org/10.1039/c3mb70594c.

Damm, U., Hopfengärtner, B., Niopek, D., and Bayer, P. (2013). Are artists and engineers inventing the culture of tomorrow? Futures 48, 55–64. https://doi.org/10.1016/j.futures.2013.02.007.

Börner, K., Niopek, D., Cotugno, G., Kaldenbach, M., Pankert, T., Willemsen, J., Zhang, X., Schürmann, N., Mockenhaupt, S., Serva, A., et al. (2013). Robust RNAi enhancement via human Argonaute-2 overexpression from plasmids, viral vectors and cell lines. Nucleic acids research 41, e199. https://doi.org/10.1093/nar/gkt836.

Kienle, E., Senís, E., Börner, K., Niopek, D., Wiedtke, E., Grosse, S., and Grimm, D. (2012). Engineering and evolution of synthetic adeno-associated virus (AAV) gene therapy vectors via DNA family shuffling. Journal of visualized experiments : JoVE. https://doi.org/10.3791/3819.

Niopek, D., Berrens, R., Mockenhaupt, S., Lewis, M.D., Mueller, A.-K., and Grimm, D. (2011). To go, or not to go, that is the question – six personal reflections on how geographic mobility may affect your career and life. Bioessays 33, 728–731. https://doi.org/10.1002/bies.201100083.

Books

Niopek, Dominik (2020): Photoswitching Proteins. New York, NY: Springer US (2173).

Patents

Aschenbrenner, S., Hoffmann, M., Kallenberger, S., Eils, R., Huck, A., and Niopek, D. (2022) Improving cas nuclease target specificity.

Niopek, D., Eils, R., Bubeck, F., Grimm, D., Hoffmann, M.D., Waldhauer, M.C., Dietz, L., Fakhiri, J., Bietz, A., and others (2021). Modulated cas-inhibitors.  Google Patents.

Eils, R., Di Ventura, B., Adlung, L., Genreith, K., Heinemann, T., Meyer, H., Niopek, D., Georgi, F., Beer, R., Christiansen, T.C., et al. (2016) Non-ribosomal protein synthesis pigment fusion peptides.

Other

Niopek, D. (2019). Harvard oder Heidelberg? Wissenschaftsstandort Deutschland gewinnt an Bedeutung.  Heidelberg University Library.