Journal Papers

Wolf B., Shehu P., Brenker L., von Bachmann A., Kroell A., Southern N., Holderbach S., Eigenmann J., Aschenbrenner S., Mathony J.# and Niopek D.# (2024). Rational engineering of allosteric protein switches by in silico prediction of domain insertion sites. bioRxiv. https://doi.org/10.1101/2024.12.04.626757.

Muench P., Fiumara M., Southern N., Coda D., Aschenbrenner S., Correia B., Graeff J., Niopek D.#, and Mathony J.# (2024). A modular toolbox for the optogenetic deactivation of transcription. Nucleic Acids Research, gkae1237. https://doi.org/10.1093/nar/gkae1237. (BioRxiv: https://doi.org/10.1101/2023.11.06.565805.)

Brenker L.*, Aschenbrenner S.*, Bubeck F.*, Staykov K., Gebhardt C., Wolf B., Jendrusch M., Kröll A., Mathony J. and Niopek D. (2024). A Versatile Anti-CRISPR Platform for Opto- and Chemogenetic Control of CRISPR-Cas9 and Cas12 across a Wide Range of Orthologs. bioRxiv. https://doi.org/10.1101/2024.11.25.625186.

Stadelmann T.*, Heid D.*, Jendrusch M.*, Mathony J., Rosset S., Correia B.E., and Niopek D. (2024). A deep mutational scanning platform to characterize the fitness landscape of anti-CRISPR proteins. Nucleic Acids Research, gkae1052. https://doi.org/10.1093/nar/gkae1052 (BioRxiv: https://doi.org/10.1101/2021.08.21.457204.)

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. (BioRxiv: https://doi.org/10.1101/2023.04.11.536407)

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. (BioRxiv: https://doi.org/10.1101/2021.07.04.450986)

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. (BioRxiv: https://doi.org/10.1101/858589)

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. (BioRxiv: https://doi.org/10.1101/685032)

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.