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Hess, L., Moos, V., Lauber, A. A., Reiter, W., Schuster, M., Hartl, N., Lackner, D., Boenke, T., Koren, A., Guzzardo, P. M., Gundacker, B., Riegler, A., Vician, P., Miccolo, C., Leiter, S., Chandrasekharan, M. B., Vcelkova, T., Tanzer, A., Jun, J. Q., ... Seiser, C. (2022). A toolbox for class I HDACs reveals isoform specific roles in gene regulation and protein acetylation. PLoS Genetics, 18(8), [e1010376]. https://doi.org/10.1371/journal.pgen.1010376

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

Deforges, J., Reis, R. S., Jacquet, P., Sheppard, S., Gadekar, V. P., Hart-Smith, G., Tanzer, A., Hofacker, I. L., Iseli, C., Xenarios, I., & Poirier, Y. (2019). Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs. Plant Physiology, 180(1), 305-322. https://doi.org/10.1104/pp.19.00043

Tanzer, A., Hofacker, I. L., & Lorenz, R. (2019). RNA modifications in structure prediction – Status quo and future challenges. Methods, 156, 32-39. https://doi.org/10.1016/j.ymeth.2018.10.019

Thiel, B. C., Ochsenreiter, R., Gadekar, V. P., Tanzer, A., & Hofacker, I. L. (2018). RNA structure elements conserved between mouse and 59 other vertebrates. Genes, 9(8), [392]. https://doi.org/10.3390/genes9080392

Tajaddod, M., Tanzer, A., Licht, K., Wolfinger, M. T., Badelt, S., Huber, F., Pusch, O., Schopoff, S., Janisiw, M., Hofacker, I., & Jantsch, M. F. (2016). Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity. Genome Biology, 17(1), [220]. https://doi.org/10.1186/s13059-016-1083-0

Hoelzer, M., Kraehling, V., Amman, F., Barth, E., Bernhart, S. H., Carmelo, V. A. O., Collatz, M., Doose, G., Eggenhofer, F., Ewald, J., Fallmann, J., Feldhahn, L. M., Fricke, M., Gebauer, J., Gruber, A. J., Hufsky, F., Indrischek, H., Kanton, S., Linde, J., ... Marz, M. (2016). Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. Scientific Reports, 6, [34589]. https://doi.org/10.1038/srep34589

Lagarde, J., Uszczynska-Ratajczak, B., Santoyo-Lopez, J., Gonzalez, J. M., Tapanari, E., Mudge, J. M., Steward, C. A., Wilming, L., Tanzer, A., Howald, C., Chrast, J., Vela-Boza, A., Rueda, A., Lopez-Domingo, F. J., Dopazo, J., Reymond, A., Guigo, R., & Harrow, J. (2016). Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq). Nature Communications, 7, [12339]. https://doi.org/10.1038/ncomms12339

Lorenz, R., Wolfinger, M. T., Tanzer, A., & Hofacker, I. L. (2016). Predicting RNA secondary structures from sequence and probing data. Methods, 103, 86-98. https://doi.org/10.1016/j.ymeth.2016.04.004

Sedlyarov, V., Fallmann, J., Ebner, F. D., Huemer, J., Sneezum, L., Ivin, M., Kreiner, K., Tanzer, A., Vogl, C., Hofacker, I., & Kovarik, P. (2016). Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution. Molecular Systems Biology, 12(5), [868]. https://doi.org/10.15252/msb.20156628

Fallmann, J., Sedlyarov, V., Tanzer, A., Kovarik, P., & Hofacker, I. L. (2016). AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements. Nucleic Acids Research, 44(D1), D90-D95. https://doi.org/10.1093/nar/gkv1238

Pervouchine, D. D., Djebali, S., Breschi, A., Davis, C. A., Barja, P. P., Dobin, A., Tanzer, A., Lagarde, J., Zaleski, C., See, L-H., Fastuca, M., Drenkow, J., Wang, H., Bussotti, G., Pei, B., Balasubramanian, S., Monlong, J., Harmanci, A., Gerstein, M., ... Gingeras, T. R. (2015). Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression. Nature Communications, 6, [5903]. https://doi.org/10.1038/ncomms6903

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Mouse ENCODE Consortium, Cheng, Y., Ma, Z., Kim, B-H., Wu, W., Cayting, P., Boyle, A. P., Sundaram, V., Xing, X., Dogan, N., Li, J., Euskirchen, G., Lin, S., Lin, Y., Visel, A., Kawli, T., Yang, X., Patacsil, D., Keller, C. A., ... Tanzer, A. (2014). Principles of regulatory information conservation between mouse and human. Nature, 515(7527), 371-375. https://doi.org/10.1038/nature13985

Gerstein, M. B., Rozowsky, J., Yan, K-K., Wang, D., Cheng, C., Brown, J. B., Davis, C. A., Hillier, L., Sisu, C., Li, J. J., Pei, B., Harmanci, A. O., Duff, M. O., Djebali, S., Alexander, R. P., Alver, B. H., Auerbach, R., Bell, K., Bickel, P. J., ... Waterston, R. (2014). Comparative analysis of the transcriptome across distant species. Nature, 512(7515), 445-448. https://doi.org/10.1038/nature13424

Hoffmann, S., Otto, C., Doose, G., Tanzer, A., Langenberger, D., Christ, S., Kunz, M., Holdt, L. M., Teupser, D., Hackermueller, J., & Stadler, P. F. (2014). A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biology, 15(2), [R34]. https://doi.org/10.1186/gb-2014-15-2-r34

Lorenz, R., Bernhart, S. H., Qin, J., Siederdissen, C. H. Z., Tanzer, A., Amman, F., Hofacker, I. L., & Stadler, P. F. (2013). 2D Meets 4G: G-Quadruplexes in RNA Secondary Structure Prediction. I E E E - A C M Transactions on Computational Biology and Bioinformatics, 10(4), 832-844. https://doi.org/10.1109/TCBB.2013.7