Publications

Kaiser, S.; Shahmohammadi, N.; Goel, T. S. M.; Buchanan, C. J.; Garg, S.; Vidaurre Barahona, D.; Qian, Z.; Lefevfre, C.; Schindler, D.; Kim, Y. et al.; Bode, H. B.; Hochberg, G. K. A.: Drift, selection and convergence in the evolution of a nonribosomal peptide. bioRxiv: the preprint server for biology, 2025.12.15.694437 (2025)

Podolski, A.; Lindeboom, T. A.; Präve, L.; Dehghan, M.; Minas, H. A.; Kranz, J.; Schindler, D.; Bode, H. B.: High-Throughput Engineering and Modification of Non-Ribosomal Peptide Synthetases Based on Golden Gate Assembly. Angewandte Chemie International Edition 64 (49), e202508967 (2025)

de Vries, J.; Lindeboom, T. A.; de Vries, S. T.; Schindler, D.; Hoffmann, S. A.: Standardized modular assembly of polycistronic operons with modular cloning (MoClo) using the in-cloning toolkit. Journal of Visualized Experiments (223), e68103 (2025)

Xu, W.; Jalomo-Khayrova, E.; Gumerov, V. M.; Ross, P. A.; Köbel, T. S.; Schindler, D.; Bange, G.; Zhulin, I. B.; Sourjik, V.: Specificities of chemosensory receptors in the human gut microbiota. Proceedings of the National Academy of Sciences of the United States of America 122 (35), e2508950122 (2025)

Georg, J.; Berghoff, B. A.; Schindler, D.: Harnessing small RNAs as synthetic post-transcriptional regulators in bacteria. ACS Synthetic Biology 14 (7), pp. 2405 - 2417 (2025)

de Vries, J.; Lindeboom, T. A.; de Vries, S. T.; Schindler, D.; Hoffmann, S. A.: Standardized modular assembly of polycistronic operons with modular cloning (MoClo) using the in-cloning toolkit. Journal of Visualized Experiments (223), e68103 (2025)

de Vries, S. T.; Kley, L.; Schindler, D.: Use of a Golden Gate plasmid set enabling scarless MoClo-compatible transcription unit assembly. In: Golden Gate Cloning. Methods in Molecular Biology, Vol. 2850, pp. 105 - 131 (Ed. Schindler, D.). Humana, New York, NY (2025)

Keune, E.: Title not yet available. Bachelor, Philipps-Universität Marburg, Marburg (2025)

Köbel, T. S.; Schindler, D.: Automation and miniaturization of Golden Gate DNA Assembly reactions using acoustic dispensers. In: Golden Gate Cloning. Methods in Molecular Biology, Vol. 2850, pp. 149 - 169 (Ed. Schindler, D.). Humana, New York, NY (2025)

Lindeboom, T. A.: Title not yet available. Dissertation, Philipps-Universität Marburg, Marburg (2025)

Ramírez Rojas, A. A.; Brinkmann, C. K.; Schindler, D.: Validation of Golden Gate Assemblies using highly multiplexed nanopore amplicon sequencing. In: Golden Gate Cloning. Methods in Molecular Biology, Vol. 2850, pp. 171 - 196 (Ed. Schindler, D.). Humana, New York, NY (2025)

Sendker, F. L.; Schlotthauer, T. J.; Mais, C.-N.; Lo, Y. K.; Girbig, M.; Bohn, S.; Heimerl, T.; Schindler, D.; Weinstein, A.; Metzger, B. P. H. et al.; Thornton, J. W.; Pillai, A.; Bange, G.; Schuller, J. M.; Hochberg, G. K. A.: Frequent transitions in self-assembly across the evolution of a central metabolic enzyme. Nature Communications 15 (1), 10515 (2024)

de Vries, S. T.; Köbel, T. S.; Sanal, A.; Schindler, D.: In- & Out-Cloning: plasmid toolboxes for scarless transcription unit and modular Golden Gate acceptor plasmid assembly. Synthetic Biology 9 (1), ysae016 (2024)

He, H.; Gómez-Coronado, P. A.; Zarzycki, J.; Barthel, S.; Kahnt, J.; Claus, P.; Klein, M.; Klose, M.; de Crécy-Lagard, V.; Schindler, D. et al.; Paczia, N.; Glatter, T.; Erb, T. J.: Adaptive laboratory evolution recruits the promiscuity of succinate semialdehyde dehydrogenase to repair different metabolic deficiencies. Nature Communications 15 (1), 8898 (2024)

Pozhydaieva, N.; Billau, F. A.; Wolfram-Schauerte, M.; Ramírez Rojas, A. A.; Paczia, N.; Schindler, D.; Höfer, K.: Temporal epigenome modulation enables efficient bacteriophage engineering and functional analysis of phage DNA modifications. PLOS Genetics 20 (9), e1011384 (2024)

Su, L.; Huber, E. M.; Westphalen, M.; Gellner, J.; Bode, E.; Köbel, T.; Grün, P.; Alanjary, M. M.; Glatter, T.; Cirnski, K. et al.; Müller, R.; Schindler, D.; Groll, M.; Bode, H. B.: Isofunctional but structurally different methyltransferases for dithiolopyrrolone diversification. Angewandte Chemie International Edition, e202410799 (2024)

Brück, M.; Köbel, T. S.; Dittmar, S.; Ramírez Rojas, A. A.; Georg, J.; Berghoff, B. A.; Schindler, D.: A library-based approach allows systematic and rapid evaluation of seed region length and reveals design rules for synthetic bacterial small RNAs. iScience 27 (9), 110774 (2024)

Zumkeller, C.; Schindler, D.; Felder, J.; Waldminghaus, T.: Modular Assembly of Synthetic Secondary Chromosomes. In: Bacterial Chromatin. Methods in Molecular Biology,, Vol. 2819, 2819 Ed., pp. 157 - 187 (Ed. Dame, R. T.). Humana, New York, NY (2024)

Szymanski, E. A.; Schindler, D.: A (metaphorical) moment for RNA-based biotechnology?: Current metaphors for RNA limit development of and public communication about RNA-based technologies. EMBO Reports 25, pp. 3182 - 3186 (2024)

Ramming, L.; Stukenberg, D.; Sanchez Olmos, M. d. C.; Glatter, T.; Becker, A.; Schindler, D.: Rationally designed chromosome fusion does not prevent rapid growth of Vibrio natriegens. Communications Biology 7 (1), 519 (2024)

Lindeboom, T. A.; Sanchez Olmos, M. d. C.; Schulz, K.; Brinkmann, C. K.; Ramírez Rojas, A. A.; Hochrein, L.; Schindler, D.: An optimized genotyping workflow for identifying highly SCRaMbLEd synthetic yeasts. ACS Synthetic Biology 13 (4), pp. 1116 - 1127 (2024)

Sendker, F. L.; Lo, Y. K.; Heimerl, T.; Bohn, S.; Persson, L. J.; Mais, C.-N.; Sadowska, W.; Paczia, N.; Nußbaum, E.; del Carmen Sánchez Olmos, M. et al.; Forchhammer, K.; Schindler, D.; Erb, T. J.; Benesch, J. L. P.; Marklund, E. G.; Bange, G.; Schuller, J. M.; Hochberg, G. K. A.: Emergence of fractal geometries in the evolution of a metabolic enzyme. Nature 628 (8009), pp. 894 - 900 (2024)

Wolfram-Schauerte, M.; Moskalchuk, A.; Pozhydaieva, N.; Ramírez Rojas, A. A.; Schindler, D.; Kaiser, S.; Paczia, N.; Höfer, K.: T4 phage RNA is NAD-capped and alters the NAD-cap epitranscriptome of Escherichia coli during infection through a phage-encoded decapping enzyme. bioRxiv: the preprint server for biology, 2024.04.04.588121 (2024)

Brück, M.; Berghoff, B. A.; Schindler, D.: In Silico Design, In Vitro Construction, and In Vivo Application of Synthetic Small Regulatory RNAs in Bacteria. In: Synthetic Biology. Methods in Molecular Biology, Vol. 2760 (Ed. Braman, J. C.). Humana, New York, NY. (2024)

Ramírez Rojas, A. A.; Brinkmann, C. K.; Köbel, T. S.; Schindler, D.: DuBA.flow─A low-cost, long-read amplicon sequencing workflow for the validation of synthetic DNA constructs. ACS Synthetic Biology (2024)

Su, L.; Huber, E. M.; Westphalen, M.; Gellner, J.; Bode, E.; Köbel, T.; Grün, P.; Alanjary, M. M.; Glatter, T.; Schindler, D. et al.; Groll, M.; Bode, H. B.: Identification, structure and function of the methyltransferase involved in the biosynthesis of the dithiolopyrrolone antibiotic xenorhabdin. bioRxiv: the preprint server for biology, 2024.01.12.575338 (2024)

de Vries, S. T.; Köbel, T. S.; Sanal, A.; Schindler, D.: In- & Out-Cloning: plasmid toolboxes for scarless transcription unit and modular Golden Gate acceptor plasmid assembly. Synthetic Biology 9 (1), ysae016 (2024)

Ramírez Rojas, A. A.: Title not yet available. Dissertation, Philipps-Universität Marburg, Marburg (2024)

Schindler, D.; Walker, R. S.K.; Cai, Y.: Methodological advances enabled by the construction of a synthetic yeast genome. Cell Reports Methods 4 (4), 100761 (2024)

Schwarz, M.: Title not yet available. Bachelor, Philipps-Universität Marburg, Marburg (2024)

Philipp, N.; Brinkmann, C. K.; Georg, J.; Schindler, D.; Berghoff, B. A.: DIGGER-Bac: prediction of seed regions for high-fidelity construction of synthetic small RNAs in bacteria. Bioinformatics 39 (5), btad285 (2023)

Abramczyk, D.; Sanchez Olmos, M. d. C.; Ramírez Rojas, A. A.; Schindler, D.; Robertson, D.; McColm, S.; Marston, A. L.; Barlow, P. N.: A supernumerary synthetic chromosome in Komagataella phaffii as a repository for extraneous genetic material. Microbial Cell Factories 22 (1), 259 (2023)

Luo, S.; Diehl, C.; He, H.; Bae, Y.; Klose, M.; Claus, P.; Cortina, N. S.; Fernandez, C. A.; Schulz-Mirbach, H. A. M.; McLean, R. et al.; Ramírez Rojas, A. A.; Schindler, D.; Paczia, N.; Erb, T. J.: Construction and modular implementation of the THETA cycle for synthetic CO₂ fixation. Nature Catalysis 6 (12), pp. 1228 - 1240 (2023)

Ramming, L. C.: Title not yet available. Master, Philipps-Universität Marburg, Marburg (2023)

Schindler, D.; Walker, R. S.K.; Jiang, S.; Brooks, A. N.; Wang, Y.; Müller, C. A.; Cockram, C.; Luo, Y.; García, A.; Schraivogel, D. et al.; Mozziconacci, J.; Pena, N.; Assari, M.; Olmos, S.; Carmen, M. d.; Zhao, Y.; Ballerini, A.; Blount, B. A.; Cai, J.; Ogunlana, L.; Liu, W.; Jönsson, K.; Abramczyk, D.; Garcia-Ruiz, E.; Turowski, T. W.; Swidah, R.; Ellis, T.; Pan, T.; Antequera, F.; Shen, Y.; Nieduszynski, C. A.; Koszul, R.; Dai, J.; Steinmetz, L. M.; Boeke, J. D.; Cai, Y.: Design, construction, and functional characterization of a tRNA neochromosome in yeast. Cell 186 (24), pp. 5237 - 5253.e22 (2023)

Shen, Y.; Gao, F.; Wang, Y.; Wang, Y.; Zheng, J.; Gong, J.; Zhang, J.; Luo, Z.; Schindler, D.; Deng, Y. et al.; Ding, W.; Lin, T.; Swidah, R.; Zhao, H.; Jiang, S.; Zeng, C.; Chen, S.; Chen, T.; Wang, Y.; Luo, Y.; Mitchell, L.; Bader, J. S.; Zhang, G.; Shen, X.; Wang, J.; Fu, X.; Dai, J.; Boeke, J. D.; Yang, H.; Xu, X.; Cai, Y.: Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast. Cell genomics 3 (11), 100364 (2023)

Steube, N.; Moldenhauer, M.; Weiland, P.; Saman, D.; Kilb, A.; Ramírez Rojas, A. A.; Garg, S.; Schindler, D.; Graumann, P. L.; Benesch, J. L. P. et al.; Bange, G.; Friedrich, T.; Hochberg, G. K. A.: Fortuitously compatible protein surfaces primed allosteric control in cyanobacterial photoprotection. Nature Ecology & Evolution 7, pp. 756 - 767 (2023)

Ramírez Rojas, A. A.; Swidah, R.; Schindler, D.: Microbes of traditional fermentation processes as synthetic biology chassis to tackle future food challenges. Frontiers in Bioengineering and Biotechnology 10, 982975 (2022)

Koebel, T. S.; Palhares, R. M.; Fromm, C.; Szymanski, W. G.; Angelidou, G.; Glatter, T.; Georg, J.; Berghoff, B. A.; Schindler, D.: An easy-to-use plasmid toolset for efficient generation and benchmarking of synthetic small RNAs in bacteria. ACS Synthetic Biology 11 (9), pp. 2989 - 3003 (2022)

Ong, J. Y.; Swidah, R.; Monti, M.; Schindler, D.; Dai, J.; Cai, Y.: SCRaMbLE: A study of its robustness and challenges through enhancement of Hygromycin B resistance in a semi-synthetic yeast. Bioengineering 8 (3), 42 (2021)

Schindler, D.: Genetic Engineering and Synthetic Genomics in Yeast to Understand Life and Boost Biotechnology. Bioengineering-Basel 7 (4), pp. 137 - Article No.: 137 (2020)