Kleinova, R., Rajendra, V., Leuchtenberger, A. F., Lo Giudice, C., Vesely, C., Kapoor, U., Tanzer, A., Derdak, S., Picardi, E., & Jantsch, M. F. (2023). The ADAR1 editome reveals drivers of editing-specificity for ADAR1-isoforms. Nucleic Acids Research, 51(9), 4191-4207. https://doi.org/10.1093/nar/gkad265

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), Artikel 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), Artikel 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), Artikel 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, Artikel 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, Artikel 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), Artikel 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, Artikel 5903. https://doi.org/10.1038/ncomms6903

Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B. D., Shen, Y., Pervouchine, D. D., Djebali, S., Thurman, R. E., Kaul, R., Rynes, E., Kirilusha, A., Marinov, G. K., Williams, B. A., ... Mouse ENCODE Consortium (2014). A comparative encyclopedia of DNA elements in the mouse genome. Nature, 515(7527), 355-364. https://doi.org/10.1038/nature13992

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), Artikel 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