Publications
Publications
2023
20. Philipp N, Brinkmann C, Georg J, Schindler D, Berghoff BA (2023). DIGGER-Bac: Prediction of seed regions for high-fidelity construction of synthetic small RNAs in bacteria. Bioinformatics. 39(5):btad285
19. Steube N, Moldenhauer M, Weiland P, Saman D, Kilb A, Ramírez Rojas AA, Garga S, Schindler D, Graumann P, Benesche J, Bange G, Friedrich T, Hochberg GKA (2023). Fortuitously compatible protein surfaces primed allosteric control in cyanobacterial photoprotection. Nat Ecol Evol. 7(5):756-767.
2022
18. Köbel TS, Melo Palhares R, Fromm C, Szymanski W, Angelidou G, Glatter T, Georg J, Berghoff BA, Schindler D (2022). An easy-to-use plasmid toolset for efficient generation and benchmarking of synthetic small RNAs in bacteria. ACS Synth Biol. 11(9):2989-3003.
17. Ramírez Rojas AA, Swidah R, Schindler D (2022). Microbes of traditional fermentation processes as synthetic biology chassis to tackle future food challenges. Front Bioeng Biotechnol. 10:982975.
2021
16. Ong JY, Swidah R, Monti M, Schindler D, Dai J, Cai Y (2021). SCRaMbLE: A study of its robustness and challenges through enhancement of hygromycin B resistance in a semi-synthetic yeast. Bioengineering (Basel). 8(3):42.
15. Luo Z, Yu K, Xie S, Monti M, Schindler D, Fang Y, Zhao S, Liang Z, Jiang S, Luan M, Xiao C, Cai Y, Dai J (2021). Compacting a synthetic yeast chromosome arm. Genome Biol. 22(1):5.
2020
14. Schindler D (2020). Genetic engineering and synthetic genomics in yeast to understand life and boost biotechnology. Bioengineering (Basel). 7(4):137.
13. Zhao Y, Yao Z, Ploessl D, Ghosh S, Monti M, Schindler D, Gao M, Cai Y, Qiao M, Yang C, Cao M, Shao Z (2020). Leveraging the hermes transposon to accelerate the development of nonconventional yeast-based microbial cell factories. ACS Synth Biol. 9(7):1736-1752.
Before 2020
12. Schindler D, Dai J, Cai Y (2018). Synthetic genomics: A new venture to dissect genome fundamentals and engineer new functions.Curr Opin Chem Biol. 46:56-62.
11. Bruhn M, Schindler D, Kemter FS, Wiley MR, Chase K, Koroleva GI, Palacios G, Sozhamannan S, Waldminghaus T (2018). Functionality of two origins of replication in Vibrio cholerae strains with a single chromosome. Front Microbiol. 9:2932.
10. Zumkeller C, Schindler D, Waldminghaus T (2018). Modular assembly of synthetic secondary chromosomes. Methods Mol Biol. 1837:71-94.
9. Schallop N, Milbredt S, Sperlea T, Kemter FS, Bruhn M, Schindler D, Waldminghaus T (2017). Establishing a system for testing replication inhibition of the Vibrio cholerae secondary chromosome in Escherichia coli. Antibiotics (Basel). 7(1):3.
8. Messerschmidt SJ, Schindler D, Zumkeller CM, Kemter FS, Schallop N, Waldminghaus T (2016). Optimization and characterization of the synthetic secondary chromosome synVicII in Escherichia coli. Front Bioeng Biotechnol. 4:96.
7. Schindler D, Milbredt S, Sperlea T, Waldminghaus T (2016). Design and assembly of DNA sequence libraries for chromosomal insertion in bacteria based on a set of modified MoClo vectors. ACS Synth Biol. 5(12):1362-1368.
6. Schindler D, Waldminghaus T (2015). Synthetic chromosomes. FEMS Microbiol Rev. 39(6):871-91.
5. Messerschmidt SJ, Kemter FS, Schindler D, Waldminghaus T (2015). Synthetic secondary chromosomes in Escherichia coli based on the replication origin of chromosome II in Vibrio cholerae. Biotechnol J. 10(2):302-14.
4. Schindler D, Waldminghaus T (2014). “Non-canonical protein-DNA interactions identified by ChIP are not artifacts”: response. BMC genomics 14:638.
3. Schindler D, Nowrousian M (2014). The polyketide synthase gene pks4 is essential for sexual development and regulates fruiting body morphology in Sordaria macrospora. Fungal Genet Biol. 68:48-59.
2. Gesing S, Schindler D, Nowrousian M (2013). Suppression subtractive hybridization and comparative expression analysis to identify developmentally regulated genes in filamentous fungi. J Basic Microbiol. 2013. 53(9):742-51.
1. Gesing S, Schindler D, Fränzel B, Wolters D, Nowrousian M (2012). The histone chaperone ASF1 is essential for sexual development in the filamentous fungus Sordaria macrospora. Mol Microbiol. 84(4):748-65.
Preprints
2023
9. Abramczyk D, Sánchez Olmos MdC, Ramírez Rojas AA, Schindler D, Robertson D, McColm S, Marston A, Barlow P (2023). A supernumerary synthetic chromosome in Komagataella phaffii as a repository for extraneous genetic material. bioRxiv.
8. Köbel TS, Schindler D (2023). Automation and miniaturization of Golden Gate DNA assembly reactions using acoustic dispensers. arXiv.
7. Ramming L, Stukenberg D, Sánchez Olmos MdC, Becker A, Schindler D (2023). DNA replication is not a limiting factor for the rapid growth of Vibrio natriegens. bioRxiv.
6. Li T, Zhao S, Cheng L, Hou S, Luo Z, Xu J, Yu W, Jiang S, Monti M, Schindler S, Zhang W, Hou C, Ma Y, Cai Y, Boeke JD, Dai J (2023). Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae. bioRxiv.
5. Brueck M, Berghoff BA, Schindler D (2023). In silico design, in vitro construction and in vivo application of synthetic small regulatory RNAs in bacteria. arXiv.
2022
4. Lindeboom TA, Sánchez Olmos MdC, Schulz K, Brinkmann CK, Ramírez Rojas AA, Hochrein L, Schindler D (2022). L-SCRaMbLE creates large-scale genome rearrangements in synthetic Sc2. 0 chromosomes. bioRxiv, 2022-12.
3. Jiang S, Luo Z, Yu K, Zhao S, Cai Z, Yu W, Wang H, Cheng L, Liang Z, Gao H, Monti M, Schindler D, Huang L, Zeng C, Zhang W, Zhou C, Tang Y, Li T, Ma Y, Cai Y, Boeke JD, Dai J (2022). Reconstruct a eukaryotic chromosome arm by de novo design and synthesis. bioRxiv.
2. Schindler D, Walker RSK, Jiang S, Brooks AN, Wang Y, Müller CA, Cockram C, Luo Y, García Martínez A, Schraivogel D, Mozziconacci J, Blount BA, Cai J, Ogunlana L, Liu W, JönnsonK, Abramczyk D, Garcia-Ruiz E, Swidah R, Ellis T, Antequera F, Shen Y, Nieduszynski CA, Koszul R, Dai J, Steinmetz LM, Boeke JD, Cai Y (2022). Design, construction, and functional characterization of a tRNA neochromosome in yeast. bioRxiv.
1. Shen Y, Gao F, Wang Y, Wang Y, Zheng J, Gong J, Zhang J, Luo Z, Schindler D, Deng Y, Ding W, Lin T, Swidah R, Zhao H, Jiang S, Zeng C, Chen S, Chen T, Wang Y, Luo Y, Mitchell L, Bader JS, Zhang G, Shen X, Wang J, Fu X, Dai J, Boeke JD, Yang H, Xu X, Cai Y (2022). Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast. bioRxiv.