ENCODE Project Consortium, Dunham, I., Kundaje, A., Aldred, S. F., Collins, P. J., Davis, C. A., Doyle, F., Epstein, C. B., Frietze, S., Harrow, J., Kaul, R., Khatun, J., Lajoie, B. R., Landt, S. G., Lee, B. K., Pauli, F., Rosenbloom, K. R., Sabo, P., Safi, A., ... Valencia, A. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57-74. https://doi.org/10.1038/nature11247

Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., Xue, C., Marinov, G. K., Khatun, J., Williams, B. A., Zaleski, C., Rozowsky, J., Röder, M., Kokocinski, F., Abdelhamid, R. F., ... King, B. (2012). Landscape of transcription in human cells. Nature, 489(7414), 101-108. https://doi.org/10.1038/nature11233

Pei, B., Sisu, C., Frankish, A., Howald, C., Habegger, L., Mu, X. J., Harte, R., Balasubramanian, S., Tanzer, A., Diekhans, M., Reymond, A., Hubbard, T. J., Harrow, J., & Gerstein, M. B. (2012). The GENCODE pseudogene resource. Genome Biology, 13(9), [R51]. https://doi.org/10.1186/gb-2012-13-9-r51

Howald, C., Tanzer, A., Chrast, J., Kokocinski, F., Derrien, T., Walters, N., Gonzalez, J. M., Frankish, A., Aken, B. L., Hourlier, T., Vogel, J. H., White, S., Searle, S., Harrow, J., Hubbard, T. J., Guigó, R., & Reymond, A. (2012). Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Research, 22(9), 1698-1710. https://doi.org/10.1101/gr.134478.111

Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., Barnes, I., Bignell, A., Boychenko, V., Hunt, T., Kay, M., Mukherjee, G., Rajan, J., Despacio-Reyes, G., Saunders, G., ... Hubbard, T. J. (2012). GENCODE: The reference human genome annotation for the ENCODE project. Genome Research, 22(9), 1760-1774. https://doi.org/10.1101/gr.135350.111

Derrien, T., Johnson, R., Bussotti, G., Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., Lagarde, J., Veeravalli, L., Ruan, X., Ruan, Y., Lassmann, T., Carninci, P., Brown, J. B., Lipovich, L., Gonzalez, J. M., ... Guigó, R. (2012). The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Research, 22(9), 1775-1789. https://doi.org/10.1101/gr.132159.111

ENCODE Project Consortium, Myers, R. M., Stamatoyannopoulos, J., Snyder, M., Dunham, I., Hardison, R. C., Bernstein, B. E., Gingeras, T. R., Kent, W. J., Birney, E., Wold, B., Crawford, G. E., Bernstein, B. E., Epstein, C. B., Shoresh, N., Ernst, J., Mikkelsen, T. S., Kheradpour, P., Zhang, X., ... Wang, J. (2011). A User's Guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biology, 9(4), [e1001046]. https://doi.org/10.1371/journal.pbio.1001046

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.

Boria, I., Gruber, A., Tanzer, A., Bernhart, S., Lorenz, R., Müller, M., Hofacker, I., & Stadler, P. (2010). Nematode sbRNAs: Homologs of vertebrate Y RNAs. Journal of Molecular Evolution, 70(4), 346-358. https://doi.org/10.1007/s00239-010-9332-4

Lam, H. Y. K., Mu, X. J., Stütz, A. M., Tanzer, A., Cayting, P. D., Snyder, M., Kim, P. M., Korbel, J. O., & Gerstein, M. B. (2010). Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. Nature Biotechnology, 28(1), 47-55. https://doi.org/10.1038/nbt.1600

Rederstorff, M., Bernhart, S., Tanzer, A., Zywicki, M., Perfler, K., Lukasser, M., Hofacker, I., & Hüttenhofer, A. (2010). RNPomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles. Nucleic Acids Research, 38(10). https://doi.org/10.1093/nar/gkq057

Tafer, H., Stadler, P., Tanzer, A., Rose, D., Marz, M., Schierwater, B., Jong, D. D., & Hertel, J. (2009). Non-Coding RNA Annotation of the Genome of Trichoplax adhaerens. Nucleic Acids Research, 37(5), 1602-1615.

Lynch, V. J., Tanzer, A., Wang, Y., Leung, F., Gellersen, B., Emera, D., & Wagner, G. P. (2008). Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 105(39), 14928-14933. http://www.pnas.org/content/105/39/14928.abstract

Wolfinger, M., Tanzer, A., Hofacker, I., Mandl, C., Flamm, C., Thurner, C., Geis, M., Middendorf, M., & Stadler, P. F. (2008). Folding kinetics of large RNAs. Journal of Molecular Biology, 379, 160-173.

Korbel, J. O., Urban, A. E., Affourtit, J. P., Godwin, B., Grubert, F., Simons, J. F., Kim, P. M., Palejev, D., Carriero, N. J., Du, L., Taillon, B. E., Chen, Z., Tanzer, A., Saunders, A. C. E., Chi, J., Yang, F., Carter, N. P., Hurles, M. E., Weissman, S. M., ... Snyder, M. (2007). Paired-end mapping reveals extensive structural variation in the human genome. Science, 318(5849), 420-426. https://doi.org/10.1126/science.1149504

Backofen, R., Bernhart, S., Flamm, C., Fried, C., Fritscher, C., Hackermüller, J., Hertel, J., Hofacker, I., Missal, K., Mosig, A., Prohaska, S. J., Rose, D., Stadler, P., Tanzer, A., Washietl, S., & Will, S. (2007). RNAs everywhere: Genome-wide annotation of structured RNAs. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 308(1), 1-25. http://www3.interscience.wiley.com/cgi-bin/abstract/113521524/ABSTRACT

Stadler, P., Gruber, A., Washietl, S., Stocsits, C., Tanzer, A., Hofacker, I., Hertel, J., Reiche, K., & Hackermüller, J. (2007). Structured RNAs in the ENCODE selected regions of the human genome. Genome Research, 17, 852-864. https://doi.org/10.1101/gr.5650707

Tanzer, A., & Stadler, P. F. (2006). Evolution of microRNAs. Methods in Molecular Biology, 342, 335-50. https://doi.org/10.1385/1-59745-123-1:335

Hertel, J., Lindemeyer, M., Missal, K., Fried, C., Tanzer, A., Flamm, C., Hofacker, I., & Stadler, P. (2006). The expansion of the metazoan microRNA repertoire. BMC Genomics, 7(25), 1-15. http://www.biomedcentral.com/1471-2164/7/25