============
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 <https://academic.oup.com/bib/article/23/6/bbac445/6760135>`_, 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 <https://academic.oup.com/nar/article/48/W1/W193/5847772>`_, 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 <https://www.mdpi.com/2311-553X/9/1/10>`_, 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 <https://www.cell.com/trends/biochemical-sciences/fulltext/S0968-0004(24)00075-6>`_.

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 <https://www.nature.com/articles/s41467-022-34252-2>`_, 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 <https://www.nature.com/articles/s41467-020-15995-2>`_, 11(1), 2039.