References

To cite the work that made TripLexicon possible, please use:

Warwick, T., Seredinski, S., Krause, N. M., Bains, J. K., Althaus, L., Oo, J. A., … & Brandes, R. P. (2022). A universal model of RNA:DNA::DNA triplex formation accurately predicts genome-wide RNA–DNA interactions. Briefings in Bioinformatics, 23(6), bbac445.

Baumgarten, N., Hecker, D., Karunanithi, S., Schmidt, F., List, M., & Schulz, M. H. (2020). EpiRegio: analysis and retrieval of regulatory elements linked to genes. Nucleic Acids Research, 48(W1), W193-W199.

Additionally, see the following works on RNA:DNA:DNA triplex formation and its consequences:

Warwick, T., Brandes, R. P., & Leisegang, M. S. (2023). Computational methods to study DNA:DNA:RNA triplex formation by lncRNAs. Non-coding RNA, 9(1), 10.

Leisegang, M. S., Warwick, T., Stötzel, J., & Brandes, R. P. (2024). RNA-DNA triplexes: molecular mechanisms and functional relevance. Trends in Biochemical Sciences.

Leisegang, M. S., Bains, J. K., Seredinski, S., Oo, J. A., Krause, N. M., Kuo, C. C., … & Brandes, R. P. (2022). HIF1α-AS1 is a DNA:DNA:RNA triplex-forming lncRNA interacting with the HUSH complex. Nature Communications, 13(1), 6563.

Trembinski, D. J., Bink, D. I., Theodorou, K., Sommer, J., Fischer, A., van Bergen, A., … & Boon, R. A. (2020). Aging-regulated anti-apoptotic long non-coding RNA Sarrah augments recovery from acute myocardial infarction. Nature Communications, 11(1), 2039.