Publications


Publications

# = corresponding author, § = equal contribution

2024

32. Ramming L§, Stukenberg D§, Sánchez Olmos MdC, Glatter T, Becker A, Schindler D# (2024) Rationally designed chromosome fusion does not prevent rapid growth of Vibrio natriegens. Commun Biol. 7:519

31. Schindler D#, §, Walker RSK§, Cai Y# (2024) Methodological advances enabled by the construction of a synthetic yeast genome. Cell Rep Methods. 4(4):100761.

30. Sendker FL, Lo YK, Heimerl T, Bohn S, Persson L, Mais CN, Sadowska W, Paczia N, Sánchez Olmos MdC, Forchhammer K, Schindler D, Erb TJ, Benesch JLP, Marklund EG, Bange G, Schuller JM, Hochberg GKA (2024) Emergence of fractal geometries in the evolution of a metabolic enzyme. Nature. 628(8009):894-900.

29. Lindeboom TA§, Sánchez Olmos MdC§, Schulz K, Brinkmann CK, Ramírez Rojas AA, Hochrein L#, Schindler D# (2024) An optimized genotyping workflow for identifying highly SCRaMbLEd synthetic yeasts. ACS Synth Biol. 13(4):1116-1127.

28. Brück M, Berghoff BA, Schindler D# (2024) In silico design, in vitro construction and in vivo application of synthetic small regulatory RNAs in bacteria. Methods Mol Biol. 2760:479-507.

27. Cheng L, Zhao S, Li T, Hou S, Luo Z, Xu J, Yu W, Jiang S, Monti M, Schindler D, Zhang W,  Hou C, Ma Y, Cai Y, Boeke JD, Dai J (2024) Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae. Nat Commun. 15(1):770.

26. Ramírez Rojas AA§, Brinkmann CK§, Köbel TS, Schindler D# (2024) DuBA.flow – A low-cost, long-read amplicon sequencing workflow for the validation of synthetic DNA constructs. ACS Synth Biol. 13(2):457-465.

2023

25. 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. Microb Cell Fact. 22(1):259.

24. Luo S, Diehl C, He H, Jun Bae Y, Klose M, Claus P, Socorro Cortina N, Fernandez CA, Schulz-Mirbach H, McLean R, Ramírez Rojas AA, Schindler D, Paczia N, Erb TJ (2023) Construction and modular implementation of the synthetic THETA cycle for CO2-fixation in vitro and in vivo. Nature Cat. 6:1228–1240.

23. Jiang S, Luo Z, Wu J, 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, Zhao Q, Dai J (2023) Building a eukaryotic chromosome arm by de novo design and synthesis. Nat Commun. 14(1):7886.

22. Schindler D§, Walker RSK§, Jiang S, Brooks AN, Wang Y, Müller CA, Cockram C, Luo Y, García Martínez A, Schraivogel D, Mozziconacci J, Pena N, Assari M, Sánchez Olmos MdC, Zhao Y, Ballerini A, 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 (2023) Design, construction, and functional characterization of a tRNA neochromosome in yeast. Cell. 186(24):5237-5253.e22.

21. 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 (2023) Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast. Cell Genom. 3(11):100364.

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

# = corresponding author, § = equal contribution, 8 of 15 preprints are published in peer-reviewed journals

2024

15. Brück M, Köbel TS, Dittmar S, Ramírez Rojas AA, Georg J, Berghoff BA#, Schindler D# (2024) A library-based approach for systematic modulation of the seed region length reveals design rules for synthetic small RNAs in bacteria. bioRxiv.

14. Wolfram-Schauerte M, Moskalchuk A, Pozhydaieva N, Ramírez Rojas AA, Schindler D, Kaiser S, Pazcia N, Höfer K (2024) T4 phage RNA is NAD-capped and alters the NAD-cap epitranscriptome of Escherichia coli during infection through a phage-encoded decapping enzyme. bioRxiv.

13. Pozhydaieva N, Billau FA, Wolfram-Schauerte M, Ramírez Rojas AA, Paczia N, Schindler D, Höfer K (2024) Temporal epigenome modulation enables efficient bacteriophage engineering and functional analysis of phage DNA modifications. bioRxiv.

12. de Vries ST, Kley L, Schindler D# (2024) Use of a Golden Gate plasmid set enabling scarless MoClo-compatible transcription unit assembly. arXiv.

11. Ramírez Rojas AA, Brinkmann CK, Schindler D# (2024) Validation of Golden Gate assemblies using highly multiplexed Nanopore amplicon sequencing. arXiv.

10. Su L, Huber EM, Westphalen M, Gellner J, Bode E, Köbel T, Grün P, Alanjary MM, Glatter T, Schindler D, Groll M, Bode HB (2024) Identification, structure and function of the methyltransferase involved in the biosynthesis of the dithiolopyrrolone antibiotic xenorhabdin. bioRxiv.

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. [published in Microbial Cell Factories]

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. [published in Communications Biology]

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. [published in Nature Communications]

5. Brück M, Berghoff BA, Schindler D# (2023). In silico design, in vitro construction and in vivo application of synthetic small regulatory RNAs in bacteria. arXiv. [published in Methods in Molecular Biology]

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. [published in ACS Synthetic Biology]

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. [published in Nature Communications]

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. [published in Cell]

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. [published in Cell Genomics]