Publications of Daniel Schindler

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)

Luo, Z.; Yu, K.; Xie, S.; Monti, M.; Schindler, D.; Fang, Y.; Zhao, S.; Liang, Z.; Jiang, S.; Luan, M. et al.; Xiao, C.; Cai, Y.; Dai, J.: Compacting a synthetic yeast chromosome arm. Genome Biology: Biology for the Post-Genomic Era 22 (1), 5 (2021)

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)

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)

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)

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)

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)

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. bioRxiv: the preprint server for biology, 2025.02.11.637667 (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. et al.; Thornton, J. W.; Pillai, A.; Bange, G.; Schuller, J.; Hochberg, G. K. A.: Frequent transitions in self-assembly across the evolution of a central metabolic enzyme. bioRxiv: the preprint server for biology, 2024.07.05.602260 (2024)

de Vries, S. T.; Koebel, T. S.; Sanal, A.; Schindler, D.: In- & Out-Cloning: Plasmid toolboxes for scarless transcription unit and modular Golden Gate acceptor plasmid assembly. bioRxiv: the preprint server for biology, 2024.06.22.600171 (2024)

Brueck, M.; Koebel, 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. bioRxiv: the preprint server for biology, 2024.04.24.590872 (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)

de Vries, S. T.; Kley, L.; Schindler, D.: Use of a Golden Gate plasmid set enabling scarless MoClo-compatible transcription unit assembly. arXiv, arXiv.2402.03410 (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. bioRxiv: the preprint server for biology, 2024.01.28.577628 (2024)

Rojas, A. A. R.; Brinkmann, C. K.; Schindler, D.: Validation of Golden Gate assemblies using highly multiplexed Nanopore amplicon sequencing. arXiv, arXiv:2401.14191 (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)

Köbel, T. S.; Schindler, D.: Automation and miniaturization of Golden Gate DNA assembly reactions using acoustic dispensers. arXiv, arXiv.2310.00325 (2023)

Brueck, M.; Berghoff, B. A.; Schindler, D.: In silico design, in vitro construction and in vivo application of synthetic small regulatory RNAs in bacteria. arXiv, arXiv.2304.14932 (2023)

Abramczyk, D.; Sanchez Olmos, M. d. C.; Ramírez Rojas, A. A.; Schindler, D.; Robertson, D.; McColm, S.; Marston, A.; Barlow, P.: A supernumerary synthetic chromosome in Komagataella phaffii as a repository for extraneous genetic material. bioRxiv: the preprint server for biology, 2023.10.05.561004 (2023)