Lorenz, R., Hofacker, I., & Bernhart, S. (2012). Folding RNA/DNA hybrid duplexes. Bioinformatics, 28(19), 2530-2531. https://doi.org/10.1093/bioinformatics/bts466

Will, S., Joshi, T., Hofacker, I., Stadler, P., & Backofen, R. (2012). LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs. RNA, 18(5), 900-914. https://doi.org/10.1261/rna.029041.111

Amman, F., Flamm, C., & Hofacker, I. (2012). Modelling Translation Initiation under the Influence of sRNA. International Journal of Molecular Sciences, 13(12), 16223-16240. https://doi.org/10.3390/ijms131216223

Hofacker, I., Reidys, C. M., & Stadler, P. (2012). Symmetric circular matchings and RNA folding. Discrete Mathematics, 312(1), 100-112.

Marz, M., Gruber, A., Höner zu Siederdissen, C., Amman, F., Badelt, S., Bartschat, S., Bernhart, S., Kehr, S., Lorenz, R., Tanzer, A., Yusuf, D., Tafer, H., Hofacker, I., & Stadler, P. (2011). Animal snoRNAs and scaRNAs with exceptional structures. RNA Biology, 8(6), 938-946.

Gruber, A., Fallmann, J., Kratochvill, F., Kovarik, P., & Hofacker, I. (2011). AREsite: a database for the comprehensive investigation of AU-rich elements. Nucleic Acids Research, 39(Suppl.1), 66-69. https://doi.org/10.1093/nar/gkq990

Tafer, H., Amman, F., Eggenhofer, F., Stadler, P., & Hofacker, I. (2011). Fast accessibility-based prediction of RNA-RNA interactions. Bioinformatics, 27(14), 1934-1940.

Gorodkin, J., & Hofacker, I. (2011). From Structure Prediction to Genomic Screens for Novel Non-Coding RNAs. PLoS Computational Biology, 7(8). https://doi.org/10.1371/journal.pcbi.1002100

Hackl, M., Jakobi, T., Blom, J., Doppmeier, D., Brinkrolf, K., Bernhart, S., Höner zu Siederdissen, C., Bort, J. A. H., Wieser, M., Kunert, R., Jeffs, S., Hofacker, I., Goesmann, A., Puehler, A., Borth, N., & Grillari, J. (2011). Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of Biotechnology, 153(1-2), 62-75.

Bernhart, S., Mückstein, U., & Hofacker, I. (2011). RNA Accessibility in cubic time. Algorithms for Molecular Biology, 6(1). https://doi.org/10.1186/1748-7188-6-3

Washietl, S., Findeiss, S., Müller, S. A., Kalkhof, S., von Bergen, M., Hofacker, I., Stadler, P., & Goldman, N. (2011). RNAcode: Robust discrimination of coding and noncoding regions in comparative sequence data. RNA, 17(4), 578-594. https://doi.org/10.1261/rna.2536111

Eggenhofer, F., Tafer, H., Stadler, P., & Hofacker, I. (2011). RNApredator: fast accessibility-based prediction of sRNA targets. Nucleic Acids Research, 39(Suppl 2), 149-154. https://doi.org/10.1093/nar/gkr467

Kratochvill, F., Machacek, C. N., Vogl, C., Ebner, F. D., Sedlyarov, V., Gruber, A., Hartweger, H., Vielnascher, R., Karaghiosoff, M., Rülicke, T., Müller, M., Hofacker, I., Lang, R., & Kovarik, P. (2011). Tristetraprolin-driven regulatory circuit controls quality and timing of mRNA decay in inflammation. Molecular Systems Biology, 7. https://doi.org/10.1038/msb.2011.93

Lorenz, R., Bernhart, S. H. F., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P., & Hofacker, I. (2011). ViennaRNA Package 2.0. Algorithms for Molecular Biology, 6. https://doi.org/10.1186/1748-7188-6-26

Hofacker, I., Flamm, C., Heine, C., Wolfinger, M., Scheuermann, G., & Stadler, P. (2010). BarMap: RNA folding on dynamic energy landscapes. RNA, 16(7), 1308-1316. https://doi.org/10.1261/rna.2093310

Yusuf, D., Marz, M., Stadler, P., & Hofacker, I. (2010). Bcheck: a wrapper tool for detecting RNase P RNA genes. BMC Genomics, 11(Art. 432). https://doi.org/10.1186/1471-2164-11-432

Gorodkin, J., Hofacker, I., Torarinsson, E., Yao, Z., Havgaard, J. H., & Ruzzo, W. L. (2010). De novo prediction of structured RNAs from genomic sequences. Trends in Biotechnology, 28(1), 9-19. https://doi.org/10.1016/j.tibtech.2009.09.006