Sidl, L., Faissner, M., Uhlir, M., Velandia-Huerto, C. A., Waldl, M., Yao, H. T., Hofacker, I. L., & Stadler, P. F. (2025). Computational complexity, algorithmic scope, and evolution. Journal of Physics: Complexity, 6(1), Article 015013. https://doi.org/10.1088/2632-072X/adb928

Rappol, T., Waldl, M., Chugunova, A., Hofacker, I. L., Pauli, A., & Vilardo, E. (2024). tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development. Nucleic Acids Research, 52(17), 10575-10594. https://doi.org/10.1093/nar/gkae595

Thiel, B. C., Bussi, G., Poblete, S., & Hofacker, I. L. (2024). Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data. Nucleic Acids Research, 52(16), e73. https://doi.org/10.1093/nar/gkae602

von Löhneysen, S., Spicher, T., Varenyk, Y., Yao, H. T., Lorenz, R., Hofacker, I., & Stadler, P. F. (2024). Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction. Journal of computational biology : a journal of computational molecular cell biology, 31(6), 549-563. https://doi.org/10.1089/cmb.2024.0519

Beckmann-Schneider, I. K., Waldl, M., Will, S., & Hofacker, I. L. (2024). 3D feasibility of 2D RNA-RNA interaction paths by stepwise folding simulations. RNA, 30(2), 113-123. https://doi.org/10.1261/rna.079756.123

Farman, M. R., Petrackova, D., Kumar, D., Drzmisek, J., Saha, A., Curnova, I., Capek, J., Hejnarova, V., Amman, F., Hofacker, I., & Vecerek, B. (2023). Avirulent phenotype promotes Bordetella pertussis adaptation to the intramacrophage environment. Emerging microbes & infections, 12(1), Article e2146536. https://doi.org/10.1080/22221751.2022.2146536

Yao, H. T., Lorenz, R., Hofacker, I. L., & Stadler, P. F. (2023). Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package. Algorithms for Molecular Biology, 18(1), Article 8. https://doi.org/10.1186/s13015-023-00236-0

Varenyk, Y., Spicher, T., Hofacker, I. L., & Lorenz, R. (2023). Modified RNAs and predictions with the ViennaRNA Package. Bioinformatics, 39(11), Article btad696. https://doi.org/10.1093/bioinformatics/btad696

Waldl, M., Spicher, T., Lorenz, R., Beckmann, I. K., Hofacker, I. L., Von Löhneysen, S., & Stadler, P. F. (2023). Local RNA folding revisited. Journal of Bioinformatics and Computational Biology, 21(4), Article 2350016. https://doi.org/10.1142/S0219720023500166

Mrozowich, T., Park, S. M., Waldl, M., Henrickson, A., Tersteeg, S., Nelson, C. R., De Klerk, A., Demeler, B., Hofacker, I. L., Wolfinger, M. T., & Patel, T. R. (2023). Investigating RNA-RNA interactions through computational and biophysical analysis. Nucleic Acids Research, 51(9), 4588-4601. https://doi.org/10.1093/nar/gkad223

Badelt, S., Lorenz, R., & Hofacker, I. L. (2023). DrTransformer: heuristic cotranscriptional RNA folding using the nearest neighbor energy model. Bioinformatics (Oxford, England), 39(1), Article btad034. https://doi.org/10.1093/bioinformatics/btad034

Gosavi, D., Wower, I., Beckmann-Schneider, I. K., Hofacker, I. L., Wower, J., Wolfinger, M. T., & Sztuba-Solinska, J. (2022). Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus internal Ribosome Entry Site. RNA Biology, 19(1), 496-506. https://doi.org/10.1080/15476286.2022.2058818

Flamm, C., Wielach, J., Wolfinger, M. T., Badelt, S., Lorenz, R., & Hofacker, I. L. (2022). Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction. Frontiers in bioinformatics, 2, Article 835422. https://doi.org/10.3389/fbinf.2022.835422

Zayni, S., Damiati, S., Moreno-Flores, S., Amman, F., Hofacker, I., Jin, D., & Ehmoser, E.-K. (2021). Enhancing the Cell-Free Expression of Native Membrane Proteins by In Silico Optimization of the Coding Sequence-An Experimental Study of the Human Voltage-Dependent Anion Channel. Membranes, 11(10), Article 741. https://doi.org/10.3390/membranes11100741

Entzian, G., Hofacker, I. L., Ponty, Y., Lorenz, R., & Tanzer, A. (2021). RNAxplorer: harnessing the power of guiding potentials to sample RNA landscapes. Bioinformatics, 37(15), 2126-2133. https://doi.org/10.1093/bioinformatics/btab066

Mueller, T., Miladi, M., Hutter, F., Hofacker, I., Will, S., & Backofen, R. (2020). The locality dilemma of Sankoff-like RNA alignments. Bioinformatics, 36, I242-I250. https://doi.org/10.1093/BIOINFORMATICS/BTAA431

Petrackova, D., Farman, M. R., Amman, F., Linhartova, I., Dienstbier, A., Kumar, D., Drzmisek, J., Hofacker, I., Eugenia Rodriguez, M., & Vecerek, B. (2020). Transcriptional profiling of human macrophages during infection with Bordetella pertussis. RNA Biology, 17(5), 731-742. https://doi.org/10.1080/15476286.2020.1727694