Publications

Cléry, A., Krepl, M., Nguyen, C. K. X., Moursy, A., Jorjani, H., Katsantoni, M., Okoniewski, M., Mittal, N., Zavolan, M., Sponer, J. and Allain, F. H.-T. (2021) “Structure of SRSF1 RRM1 bound to RNA reveals an unexpected bimodal mode of interaction and explains its involvement in SMN1 exon7 splicing”, Nature communications, 12(1), p. 428. doi: 10.1038/s41467-020-20481-w.   
Coto-Llerena, M., Tosti, N., Taha-Mehlitz, S., Kancherla, V., Paradiso, V., Gallon, J., Bianco, G., Garofoli, A., Ghosh, S., Tang, F., Ercan, C., Christofori, G. M., Matter, M. S., Droeser, R. A., Zavolan, M., Soysal, S. D., von Flüe, M., Kollmar, O., Terracciano, L. M., Ng, C. K. Y. and Piscuoglio, S. (2021) “Transcriptional Enhancer Factor Domain Family member 4 Exerts an Oncogenic Role in Hepatocellular Carcinoma by Hippo-Independent Regulation of Heat Shock Protein 70 Family Members”, Hepatology Communications, p. E-pub ahead of print. doi: 10.1002/hep4.1656.   
Börsch, A., Ham, D. J., Mittal, N., Tintignac, L. A., Migliavacca, E., Feige, J. N., Rüegg, M. A. and Zavolan, M. (2021) “Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia”, Communications biology, 4(1), p. 194. doi: 10.1038/s42003-021-01723-z.   
Ho-Xuan, H., Lehmann, G., Glazar, P., Gypas, F., Eichner, N., Heizler, K., Schlitt, H. J., Zavolan, M., Rajewsky, N., Meister, G. and Hackl, C. (2020) “Gene Expression Signatures of a Preclinical Mouse Model during Colorectal Cancer Progression under Low-Dose Metronomic Chemotherapy”, Cancers. MDPI, 13(1), p. 49. doi: 10.3390/cancers13010049.   edoc
Ham, D. J., Börsch, A., Lin, S., Thürkauf, M., Weihrauch, M., Reinhard, J. R., Delezie, J., Battilana, F., Wang, X., Kaiser, M. S., Guridi, M., Sinnreich, M., Rich, M. M., Mittal, N., Tintignac, L. A., Handschin, C., Zavolan, M. and Rüegg, M. A. (2020) “The neuromuscular junction is a focal point of mTORC1 signaling in sarcopenia”, Nature Communications. Nature Publishing Group, 11(1), p. 4510. doi: 10.1038/s41467-020-18140-1.   edoc
Ghosh, S., Guimaraes, J. C., Lanzafame, M., Schmidt, A., Syed, A. P., Dimitriades, B., Börsch, A., Ghosh, S., Mittal, N., Montavon, T., Correia, A. L., Danner, J., Meister, G., Terracciano, L. M., Pfeffer, S., Piscuoglio, S. and Zavolan, M. (2020) “Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation”, The EMBO Journal. Wiley Blackwell, 39(18), p. e103922. doi: 10.15252/embj.2019103922.   edoc
Gruber, A. J. and Zavolan, M. (2020) “Reply to ’A different perspective on alternative cleavage and polyadenylation’”, Nature reviews. Genetics. Nature Publishing Group, 21(1), pp. 63–64. doi: 10.1038/s41576-019-0199-y.   edoc
Liko, D., Rzepiela, A., Vukojevic, V., Zavolan, M. and Hall, M. N. (2020) “Loss of TSC complex enhances gluconeogenesis via upregulation of Dlk1-Dio3 locus miRNAs”, Proceedings of the National Academy of Sciences. National Academy of Sciences, 117(3), pp. 1524–1532. doi: 10.1073/pnas.1918931117.   edoc | Open Access
Guimaraes, J. C., Mittal, N., Gnann, A., Jedlinski, D., Riba, A., Buczak, K., Schmidt, A. and Zavolan, M. (2020) “A rare codon-based translational program of cell proliferation”, Genome biology, 21(1), p. 44. doi: 10.1186/s13059-020-1943-5.   
Hasler, D., Meduri, R., Bąk, M., Lehmann, G., Heizinger, L., Wang, X., Li, Z.-T., Sement, F. M., Bruckmann, A., Dock-Bregeon, A.-C., Merkl, R., Kalb, R., Grauer, E., Kunstmann, E., Zavolan, M., Liu, M.-F., Fischer, U. and Meister, G. (2020) “The Alazami Syndrome-Associated Protein LARP7 Guides U6 Small Nuclear RNA Modification and Contributes to Splicing Robustness”, Molecular cell, 77(5), pp. 1014–1031.e13. doi: 10.1016/j.molcel.2020.01.001.   
Jutzi, D., Campagne, S., Schmidt, R., Reber, S., Mechtersheimer, J., Gypas, F., Schweingruber, C., Colombo, M., von Schroetter, C., Loughlin, F. E., Devoy, A., Hedlund, E., Zavolan, M., Allain, F. H.-T. and Ruepp, M.-D. (2020) “Aberrant interaction of FUS with the U1 snRNA provides a molecular mechanism of FUS induced amyotrophic lateral sclerosis”, Nature communications, 11(1), p. 6341. doi: 10.1038/s41467-020-20191-3.   
Herrmann, C. J., Schmidt, R., Kanitz, A., Artimo, P., Gruber, A. J. and Zavolan, M. (2019) “PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3’ end sequencing”, Nucleic acids research. Oxford University Press, 48(D1), pp. D174-D179. doi: 10.1093/nar/gkz918.   edoc
Riba, A., Di Nanni, N., Mittal, N., Arhné, E., Schmidt, A. and Zavolan, M. (2019) “Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates”, Proceedings of the National Academy of Sciences. National Academy of Sciences, 116(30), pp. 15023–15032. doi: 10.1073/pnas.1817299116.   edoc
Gruber, A. J. and Zavolan, M. (2019) “Alternative cleavage and polyadenylation in health and disease ”, Nature reviews. Genetics. Nature Pub. Group, 20(10), pp. 599–614. doi: 10.1038/s41576-019-0145-z.   edoc
Sendoel, A., Subasic, D., Ducoli, L., Keller, M., Michel, E., Kohler, I., Singh, K. D., Zheng, X., Brümmer, A., Imig, J., Kishore, S., Wu, Y., Kanitz, A., Kaech, A., Mittal, N., Matia-González, A. M., Gerber, A. P., Zavolan, M., Aebersold, R., Hall, J., Allain, F. H.-T. and Hengartner, M. O. (2019) “MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans”, Cell Death & Differentiation subscription. Nature Publishing Group, 26(10), pp. 2157–2178. doi: 10.1038/s41418-019-0291-z.   edoc
Kanitz, A., Syed, A. P., Kaji, K. and Zavolan, M. (2019) “Conserved regulation of RNA processing in somatic cell reprogramming”, BMC genomics. BioMed Central, 20(1), p. 100. doi: 10.1186/s12864-019-5438-2.   edoc
Păunescu, V., Zavolan, M. and Oprea, T. (2019) “In memoriam: Francisc Schneider (1933-2017)”, Journal of cellular and molecular medicine, pp. 3045–3046. doi: 10.1111/jcmm.14173.   edoc
Gruber, A. J., Schmidt, R., Ghosh, S., Martin, G., Gruber, A. R., van Nimwegen, E. and Zavolan, M. (2018) “Discovery of physiological and cancer-related regulators of 3’ UTR processing with KAPAC”, Genome biology, 19(1), p. 44. doi: 10.1186/s13059-018-1415-3.   edoc
Rzepiela, A. J., Ghosh, S., Breda, J., Vina-Vilaseca, A., Syed, A. P., Gruber, A. J., Eschbach, K., Beisel, C., van Nimwegen, E. and Zavolan, M. (2018) “Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction”, Molecular systems biology, 14(8), p. e8266. doi: 10.15252/msb.20188266.   edoc
Zavolan, M. and Gerber, A. P. (2018) “Mirroring the multifaceted role of RNA and its partners in gene expression”, FEBS letters, 592(17), pp. 2825–2827. doi: 10.1002/1873-3468.13230.   edoc
Gruber, A. J., Gypas, F., Riba, A., Schmidt, R. and Zavolan, M. (2018) “Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms”, Nature methods, 15(10), pp. 832–836. doi: 10.1038/s41592-018-0114-z.   edoc
Essig, K., Kronbeck, N., Guimaraes, J. C., Lohs, C., Schlundt, A., Hoffmann, A., Behrens, G., Brenner, S., Kowalska, J., Lopez-Rodriguez, C., Jemielity, J., Holtmann, H., Reiche, K., Hackermüller, J., Sattler, M., Zavolan, M. and Heissmeyer, V. (2018) “Roquin targets mRNAs in a 3’-UTR-specific manner by different modes of regulation”, Nature communications, 9(1), p. 3810. doi: 10.1038/s41467-018-06184-3.   edoc
Zavolan, M. and Kanitz, A. (2018) “RNA splicing and its connection with other regulatory layers in somatic cell reprogramming”, Current Opinion in Cell Biology. Elsevier, 52, pp. 8–13. doi: 10.1016/j.ceb.2017.12.002.   edoc
Zavolan, M. and Graveley, B. R. (2017) “RNAs: dynamic and mutable”, Genome Biology, 18(1), p. 226. doi: 10.1186/s13059-017-1361-5.   edoc | Open Access
Essig, K., Hu, D., Guimaraes, J. C., Alterauge, D., Edelmann, S., Raj, T., Kranich, J., Behrens, G., Heiseke, A., Floess, S., Klein, J., Maiser, A., Marschall, S., Hrabĕ de Angelis, M., Leonhardt, H., Calkhoven, C. F., Noessner, E., Brocker, T., Huehn, J., Krug, A. B., Zavolan, M., Baumjohann, D. and Heissmeyer, V. (2017) “Roquin Suppresses the PI3K-mTOR Signaling Pathway to Inhibit T Helper Cell Differentiation and Conversion of Treg to Tfr Cells”, Immunity. Cell Press, 47(6), pp. 1067–1082.e12. doi: 10.1016/j.immuni.2017.11.008.   edoc
Martin, G., Schmidt, R., Gruber, A. J., Ghosh, S., Keller, W. and Zavolan, M. (2017) “3’ End Sequencing Library Preparation with A-seq2”, Journal of Visualized Experiments. JoVE, (128), p. e56129. doi: 10.3791/56129.   edoc
Gumienny, R., Jedlinski, D. J., Schmidt, A., Gypas, F., Martin, G., Vina-Vilaseca, A. and Zavolan, M. (2017) “High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq”, Nucleic Acids Research. Oxford University Press, 45(5), pp. 2341–2353. doi: 10.1093/nar/gkw1321.   edoc | Open Access
Riba, A., Emmenlauer, M., Chen, A., Sigoillot, F., Cong, F., Dehio, C., Jenkins, J. and Zavolan, M. (2017) “Explicit Modeling of siRNA-Dependent On- and Off-Target Repression Improves the Interpretation of Screening Results”, Cell Systems. Elsevier, 4(2), pp. 182–193. doi: 10.1016/j.cels.2017.01.011.   edoc
Omidi, S., Zavolan, M., Pachkov, M., Breda, J., Berger, S. and van Nimwegen, E. (2017) “Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors”, PLoS Computational Biology. Library of Science, 13(7), p. e1005176. doi: 10.1371/journal.pcbi.1005176.   edoc
Dimitrova, Y., Gruber, A. J., Mittal, N., Ghosh, S., Dimitriades, B., Mathow, D., Grandy, W. A., Christofori, G. and Zavolan, M. (2017) “TFAP2A is a component of the ZEB1/2 network that regulates TGFB1-induced epithelial to mesenchymal transition”, Biology Direct. BioMed Central, 12(1), p. 8. doi: 10.1186/s13062-017-0180-7.   edoc
Mittal, N., Guimaraes, J. C., Gross, T., Schmidt, A., Vina-Vilaseca, A., Nedialkova, D. D., Aeschimann, F., Leidel, S. A., Spang, A. and Zavolan, M. (2017) “The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan”, Nature Communications. Nature Publishing Group, 8(457), pp. 1–12. doi: 10.1038/s41467-017-00539-y.   edoc | Open Access
Gruber, A. J., Schmidt, R., Gruber, A. R., Martin, G., Ghosh, S., Belmadani, M., Keller, W. and Zavolan, M. (2016) “A comprehensive analysis of 3’ end sequencing data sets reveals novel polyadenylation signals and the repressive role of heterogeneous ribonucleoprotein C on cleavage and polyadenylation”, Genome Research. Cold Spring Harbor Laboratory Press, 26(8), pp. 1145–1159. doi: 10.1101/gr.202432.115.   edoc | Open Access
Jorjani, H., Kehr, S., Jedlinski, D. J., Gumienny, R., Hertel, J., Stadler, P. F., Zavolan, M. and Gruber, A. R. (2016) “An updated human snoRNAome”, Nucleic Acids Research. Oxford University Press, 44(11), pp. 5068–5082. doi: 10.1093/nar/gkw386.   edoc | Open Access
Martin, G. and Zavolan, M. (2016) “Redesigning CLIP for efficiency, accuracy and speed”, Nature Methods. Nature Publishing Group, 13(6), pp. 482–483. doi: 10.1038/nmeth.3870.   edoc
Janowski, R., Heinz, G. A., Schlundt, A., Wommelsdorf, N., Brenner, S., Gruber, A. R., Blank, M., Buch, T., Buhmann, R., Zavolan, M., Niessing, D., Heissmeyer, V. and Sattler, M. (2016) “Roquin recognizes a non-canonical hexaloop structure in the 3’-UTR of Ox40”, Nature communications. Nature Publishing Group, 7, p. 11032. doi: 10.1038/ncomms11032.   edoc
Guimaraes, J. C. and Zavolan, M. (2016) “Patterns of ribosomal protein expression specify normal and malignant human cells”, Genome biology. BioMed Central, 17(1), p. 236. doi: 10.1186/s13059-016-1104-z.   edoc
Ustianenko, D., Pasulka, J., Feketova, Z., Bednarik, L., Zigackova, D., Fortova, A., Zavolan, M. and Vanacova, S. (2016) “TUT-DIS3L2 is a mammalian surveillance pathway for aberrant structured non-coding RNAs”, The EMBO journal. EMBO Press, 35(20), pp. 2179–2191. doi: 10.15252/embj.201694857.   edoc
Subasic, D., Brümmer, A., Wu, Y., Pinto, S. M., Imig, J., Keller, M., Jovanovic, M., Lightfoot, H. L., Nasso, S., Götze, S., Brunner, E., Hall, J., Aebersold, R., Zavolan, M. and Hengartner, M. (2015) “Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans”, Genome research. Cold Spring Harbor Laboratory Press, 25(11), pp. 1680–1691. doi: 10.1101/gr.183160.114.   edoc
Zavolan, M. (2015) “Inferring gene expression regulatory networks from high-throughput measurements”, Methods. Academic Press, pp. 1–2. doi: 10.1016/j.ymeth.2015.07.006.   edoc
Gumienny, R. and Zavolan, M. (2015) “Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G”, Nucleic Acids Research. Oxford University Press, 43(3), pp. 1380–1391. doi: 10.1093/nar/gkv050.   edoc | Open Access
Tattikota, S. G., Rathjen, T., Hausser, J., Khedkar, A., Kabra, U. D., Pandey, V., Sury, M., Wessels, H.-H., Mollet, I. G., Eliasson, L., Selbach, M., Zinzen, R. P., Zavolan, M., Kadener, S., Tschöp, M. H., Jastroch, M., Friedländer, M. R. and Poy, M. N. (2015) “miR-184 Regulates Pancreatic β-Cell Function According to Glucose Metabolism”, Journal of biological chemistry. American Society of Biological Chemists, Vol. 290, H. 33, pp. 20284–20294. doi: 10.1074/jbc.M115.658625.   edoc
Zavolan, M. and Keller, W. (2015) “Reflections on the RNA world”, RNA. Cambridge University Press, 21(4), pp. 531–533. doi: 10.1261/rna.049999.115.   edoc | Open Access
Kanitz, A., Gypas, F., Gruber, A. J., Gruber, A. R., Martin, G. and Zavolan, M. (2015) “Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data”, Genome biology. BioMed Central, Vol. 16, p. 150. doi: 10.1186/s13059-015-0702-5.   edoc
Breda, J., Rzepiela, A. J., Gumienny, R., van Nimwegen, E. and Zavolan, M. (2015) “Quantifying the strength of miRNA-target interactions”, Methods. Academic Press, Vol. 85, pp. 90–99. doi: 10.1016/j.ymeth.2015.04.012.   edoc
Imig, J., Brunschweiger, A., Brümmer, A., Guennewig, B., Mittal, N., Kishore, S., Tsikrika, P., Gerber, A. P., Zavolan, M. and Hall, J. (2015) “miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction”, Nature chemical biology. Nature Publishing Group, Vol. 11, H. 2, pp. 107–114. doi: 10.1038/nchembio.1713.   edoc
Gruber, A. R., Martin, G., Müller, P., Schmidt, A., Gruber, A. J., Gumienny, R., Mittal, N., Jayachandran, R., Pieters, J., Keller, W., van Nimwegen, E. and Zavolan, M. (2014) “Global 3’ UTR shortening has a limited effect on protein abundance in proliferating T cells”, Nature Communications. Nature Publishing Group, 5(5465), pp. 1–10. doi: 10.1038/ncomms6465.   edoc | Open Access
Schönemann, L., Kühn, U., Martin, G., Schäfer, P., Gruber, A. R., Keller, W., Zavolan, M. and Wahle, E. (2014) “Reconstitution of CPSF active in polyadenylation: recognition of the polyadenylation signal by WDR33”, Genes & development. Cold Spring Harbor Laboratory, Vol. 28, pp. 2381–2393. doi: 10.1101/gad.250985.114.   edoc | Open Access
Gruber, A. J., Grandy, W. A., Balwierz, P. J., Dimitrova, Y. A., Pachkov, M., Ciaudo, C., van Nimwegen, E. and Zavolan, M. (2014) “Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways”, Nucleic Acids Research. Oxford University Press, 42(14), pp. 9313–9326. doi: 10.1093/nar/gku544.   edoc | Open Access
Hausser, J. and Zavolan, M. (2014) “Identification and consequences of miRNA-target interactions - beyond repression of gene expression”, Nature reviews. Genetics. Nature Publishing Group, Vol. 15, no. 9, pp. 599–612.   edoc
Daubner, G. M., Brümmer, A., Tocchini, C., Gerhardy, S., Ciosk, R., Zavolan, M. and Allain, F. H.-T. (2014) “Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1”, Nucleic Acids Research. Oxford University Press, 42(12), pp. 8092–8105. doi: 10.1093/nar/gku445.   edoc | Open Access
Stockinger, H., Altenhoff, A. M., Arnold, K., Bairoch, A., Bastian, F., Bergmann, S., Bougueleret, L., Bucher, P., Delorenzi, M., Lane, L., Mercier, P. L., Lisacek, F., Michielin, O., Palagi, P. M., Rougemont, J., Schwede, T., Mering, C. von, Nimwegen, E. van, Walther, D., Xenarios, I., Zavolan, M., Zdobnov, E. M., Zoete, V. and Appel, R. D. (2014) “Fifteen years SIB Swiss Institute of Bioinformatics : life science databases, tools and support”, Nucleic Acids Research. Oxford University Press, 42(W1), pp. W436-W441. doi: 10.1093/nar/gku380.   edoc | Open Access
Balwierz, P. J., Pachkov, M., Arnold, P., Gruber, A. J., Zavolan, M. and van Nimwegen, E. (2014) “ISMARA: Automated modeling of genomic signals as a democracy of regulatory motifs”, Genome research. Cold Spring Harbor Laboratory Press, Vol. 24, H. 5, pp. 869–884. doi: 10.1101/gr.169508.113.   edoc
Erhard, F., Haas, J., Lieber, D., Malterer, G., Jaskiewicz, L., Zavolan, M., Dölken, L. and Zimmer, R. (2014) “Widespread context-dependency of microRNA-mediated regulation”, Genome research. Cold Spring Harbor Laboratory Press, Vol. 24, H. 6, pp. 906–919. doi: 10.1101/gr.166702.113.   edoc
Latreille, M., Hausser, J., Stützer, I., Zhang, Q., Hastoy, B., Gargani, S., Kerr-Conte, J., Pattou, F., Zavolan, M., Esguerra, J. L. S., Eliasson, L., Rülicke, T., Rorsman, P. and Stoffel, M. (2014) “MicroRNA-7a regulates pancreatic β cell function”, Journal of Clinical Investigation. American Society for Clinical Investigation, Vol. 124, H. 6, pp. 2722–2735. doi: 10.1172/JCI73066.   edoc
Jorjani, H. and Zavolan, M. (2014) “TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data”, Bioinformatics. Oxford University Press, Vol. 30, H. 7, pp. 971–974. doi: 10.1093/bioinformatics/btt752.   edoc
Spitzer, J., Hafner, M., Landthaler, M., Ascano, M., Farazi, T., Wardle, G., Nusbaum, J., Khorshid, M., Burger, L., Zavolan, M. and Tuschl, T. (2014) “PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation) : a Step-By-Step Protocol to the Transcriptome-Wide Identification of Binding Sites of RNA-Binding Proteins”, Methods in enzymology. Elsevier, Vol. 539, pp. 113–161. doi: 10.1016/B978-0-12-420120-0.00008-6.   edoc
Mittal, N. and Zavolan, M. (2014) “Seq and CLIP through the miRNA world”, Genome biology. BioMed Central, Vol. 15, H. 1, p. 202. doi: 10.1186/gb4151.   edoc
Kishore, S., Piscuoglio, S., Kovac, M., Gylling, A., Wenzel, F., Trapani, F., Altermatt, H. J., Mele, V., Marra, G., Peltomäki, P., Terracciano, L., Zavolan, M. and Heinimann, K. (2014) “3’UTR poly(T/U) tract deletions and altered expression of EWSR1 are a hallmark of mismatch repair deficient cancers”, Cancer research. American Association for Cancer Research, 74(1), pp. 224–234. doi: 10.1158/0008-5472.CAN-13-2100.   edoc
Gruber, A. R., Martin, G., Keller, W. and Zavolan, M. (2013) “Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors”, Wiley Interdisciplinary Reviews. RNA. Wiley-Blackwell, 5(2), pp. 183–196. doi: 10.1002/wrna.1206.   edoc | Open Access
Tattikota, S. G., Rathjen, T., McAnulty, S. J., Wessels, H.-H., Akerman, I., van de Bunt, M., Hausser, J., Esguerra, J. L. S., Musahl, A., Pandey, A. K., You, X., Chen, W., Herrera, P. L., Johnson, P. R., O’Carroll, D., Eliasson, L., Zavolan, M., Gloyn, A. L., Ferrer, J., Shalom-Feuerstein, R., Aberdam, D. and Poy, M. N. (2013) “Argonaute2 Mediates Compensatory Expansion of the Pancreatic β Cell”, Cell metabolism. Cell Press, Vol. 19, H. 1, pp. 122–134. doi: 10.1016/j.cmet.2013.11.015.   edoc
Hausser, J., Syed, A. P., Selevsek, N., van Nimwegen, E., Jaskiewicz, L., Aebersold, R. and Zavolan, M. (2013) “Timescales and bottlenecks in miRNA-dependent gene regulation”, Molecular systems biology. EMBO, Vol. 9 , 711. doi: 10.1038/msb.2013.68.   edoc
Gruber, A. J. and Zavolan, M. (2013) “Modulation of epigenetic regulators and cell fate decisions by miRNAs”, Epigenomics. Future Medicine, Vol. 5, H. 6, pp. 671–683. doi: 10.2217/epi.13.65.   edoc
Brümmer, A., Kishore, S., Subasic, D., Hengartner, M. and Zavolan, M. (2013) “Modeling the binding specificity of the RNA-binding protein GLD-1 suggests a function of coding region-located sites in translational repression”, RNA. Cambridge University Press, Vol. 19, H. 10, pp. 1317–1326. doi: 10.1261/rna.037531.112.   edoc
Zünd, D., Gruber, A. R., Zavolan, M. and Mühlemann, O. (2013) “Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3’ UTRs”, Nature structural & molecular biology. Nature Publ. Group, Vol. 20, H. 8 , S. 936–943. doi: 10.1038/nsmb.2635.   edoc
Kishore, S., Gruber, A. R., Jedlinski, D. J., Syed, A. P., Jorjani, H. and Zavolan, M. (2013) “Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing”, Genome biology. BioMed Central, Vol. 14, H. 5 , R45. doi: 10.1186/gb-2013-14-5-r45.   edoc
Khorshid, M., Hausser, J., Zavolan, M. and van Nimwegen, E. (2013) “A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets”, Nature methods. Nature Publishing Group, Vol. 10, H. 3, pp. 253–255. doi: 10.1038/nmeth.2341.   edoc
Hausser, J., Syed, A. P., Bilen, B. and Zavolan, M. (2013) “Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation”, Genome research. Cold Spring Harbor Laboratory Press, Vol. 23, H. 4, pp. 604–615. doi: 10.1101/gr.139758.112.   edoc
Gruber, A. R., Martin, G., Keller, W. and Zavolan, M. (2012) “Cleavage factor Im is a key regulator of 3’ UTR length”, RNA Biology. Landes Bioscience, 9(12), pp. 1405–1412. doi: 10.4161/rna.22570.   edoc | Open Access
Jaskiewicz, L. and Zavolan, M. (2012) “Dicer partners expand the repertoire of miRNA targets”, Genome biology. BioMed Central, Vol. 13, H. 11, p. 179. doi: 10.1186/gb-2012-13-11-179.   edoc
Jaskiewicz, L., Bilen, B., Hausser, J. and Zavolan, M. (2012) “Argonaute CLIP - A method to identify in vivo targets of miRNAs”, Methods. Academic Press, Vol. 58, no. 2, pp. 106–112. doi: 10.1016/j.ymeth.2012.09.006.   edoc
Martin, G., Gruber, A. R., Keller, W. and Zavolan, M. (2012) “Genome-wide Analysis of Pre-mRNA 3′ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3′ UTR Length”, Cell Reports. Cell Press, 1(6), pp. 753–763. doi: 10.1016/j.celrep.2012.05.003.   edoc | Open Access
Krützfeldt, J., Rösch, N., Hausser, J., Manoharan, M., Zavolan, M. and Stoffel, M. (2012) “MicroRNA-194 is a target of transcription factor 1 (Tcf1, Hnf1α) in adult liver and controls expression of frizzled-6”, Hepatology. Saunders, Vol. 55, No. 1, pp. 98–107. doi: 10.1002/hep.24658.   edoc
Suffert, G., Malterer, G., Hausser, J., Viiliäinen, J., Fender, A., Contrant, M., Ivacevic, T., Benes, V., Gros, F., Voinnet, O., Zavolan, M., Ojala, P. M., Haas, J. G. and Pfeffer, S. (2011) “Kaposi’s Sarcoma Herpesvirus microRNAs Target Caspase 3 and Regulate Apoptosis”, PLoS Pathogens. Public Library of Science, Vol. 7, H. 12 , e1002405. doi: 10.1371/journal.ppat.1002405.   edoc
Berninger, P., Jaskiewicz, L., Khorshid, M. and Zavolan, M. (2011) “Conserved generation of short products at piRNA loci”, BMC Genomics. BioMed Central, Vol. 12, H. 1 , 46. doi: 10.1186/1471-2164-12-46.   edoc
Trajkovski, M., Hausser, J., Soutschek, J., Bhat, B., Akin, A., Zavolan, M., Heim, M. H. and Stoffel, M. (2011) “MicroRNAs 103 and 107 regulate insulin sensitivity”, Nature. Macmillan, Vol. 474, H. 7353, pp. 649–653. doi: 10.1038/nature10112.   edoc
Kishore, S., Jaskiewicz, L., Burger, L., Hausser, J., Khorshid, M. and Zavolan, M. (2011) “A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins”, Nature Methods. Nature Publishing Group, Vol. 8, H. 7, pp. 559–564. doi: 10.1038/nmeth.1608.   edoc
Rammelt, C., Bilen, B., Zavolan, M. and Keller, W. (2011) “PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif”, RNA. Cambridge University Press, Vol. 17, pp. 1737–1746. doi: 10.1261/rna.2787011.   edoc | Open Access
Corioni, M., Antih, N., Tanackovic, G., Zavolan, M. and Kramer, A. (2011) “Analysis of in situ pre-mRNA targets of human splicing factor SF1 reveals a function in alternative splicing”, Nucleic Acids Research. Oxford University Press, 39(5), pp. 1868–1879. doi: 10.1093/nar/gkq1042.   edoc | Open Access
Khorshid, M., Rodak, C. and Zavolan, M. (2011) “CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins”, Nucleic Acids Research. Oxford University Press, 39(1 Supplement), pp. D245-D252. doi: 10.1093/nar/gkq940.   edoc | Open Access
McGlincy, N. J., Tan, L. .-Y., Paul, N., Zavolan, M., Lilley, K. S. and Smith, C. W. J. (2010) “Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay”, BMC genomics. BioMed Central, Vol. 11 , 565. doi: 10.1186/1471-2164-11-565.   edoc
Kishore, S., Khanna, A., Zhang, Z., Hui, J., Balwierz, P. J., Stefan, M., Beach, C., Nicholls, R. D., Zavolan, M. and Stamm, S. (2010) “The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing”, Human molecular genetics. Oxford Univ. Press, Vol. 19, H. 7, pp. 1153–1164. doi: 10.1093/hmg/ddp585.   edoc
Ma, J., Flemr, M., Stein, P., Berninger, P., Malik, R., Zavolan, M., Svoboda, P. and Schultz, R. M. (2010) “MicroRNA activity is suppressed in mouse oocytes”, Current biology. Cell Press, Vol. 20, H. 3, pp. 265–270. doi: 10.1016/j.cub.2009.12.042.   edoc
Hafner, M., Landthaler, M., Burger, L., Khorshid, M., Hausser, J., Berninger, P., Rothballer, A., Ascano, M., Jungkamp, A. .-C., Munschauer, M., Ulrich, A., Wardle, G. S., Dewell, S., Zavolan, M. and Tuschl, T. (2010) “PAR-CliP-a method to identify transcriptome-wide the binding sites of RNA binding proteins”, Journal of visualized experiments. JoVE, H. 41 , 2034. doi: 10.3791/2034.   edoc
Kishore, S., Luber, S. and Zavolan, M. (2010) “Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression”, Briefings in Functional Genomics. Oxford Univ. Press, Vol. 9, no. 5, pp. 391–404. doi: 10.1093/bfgp/elq028.   edoc
Hafner, M., Landthaler, M., Burger, L., Khorshid, M., Hausser, J., Berninger, P., Rothballer, A., Ascano, M. J., Jungkamp, A. .-C., Munschauer, M., Ulrich, A., Wardle, G. S., Dewell, S., Zavolan, M. and Tuschl, T. (2010) “Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP”, Cell. Cell Press, Vol. 141, H. 1, pp. 129–141. doi: 10.1016/j.cell.2010.03.009.   edoc
Hausser, J., Berninger, P., Rodak, C., Jantscher, Y., Wirth, S. and Zavolan, M. (2009) “MirZ: an integrated microRNA expression atlas and target prediction resource”, Nucleic Acids Research. Oxford University Press, 37(2 Supplement), pp. W266-W272. doi: 10.1093/nar/gkp412.   edoc | Open Access
Hausser, J., Landthaler, M., Jaskiewicz, L., Gaidatzis, D. and Zavolan, M. (2009) “Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets”, Genome research. Cold Spring Harbor Laboratory Press, Vol. 19, H. 11, pp. 2009–2020. doi: 10.1101/gr.091181.109.   edoc
Pena, J. T. G., Sohn-Lee, C., Rouhanifard, S. H., Ludwig, J., Hafner, M., Mihailovic, A., Lim, C., Holoch, D., Berninger, P., Zavolan, M. and Tuschl, T. (2009) “miRNA in situ hybridization in formaldehyde and EDC-fixed tissues”, Nature Methods, Vol. 6, no. 2, pp. 139–141.   edoc
Hutzinger, R., Feederle, R., Mrazek, J., Schiefermeier, N., Balwierz, P. J., Zavolan, M., Polacek, N., Delecluse, H. .-J. and Huttenhofer, A. (2009) “Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome”, PLoS Pathogens. Public Library of Science, Vol. 5, H. 8 , e1000547.   edoc
Suzuki, H., Forrest, A. R., van Nimwegen, E., Daub, C. O., Balwierz, P. J., Irvine, K. M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M. J., Katayama, S., Schroder, K., Carninci, P., Tomaru, Y., Kanamori-Katayama, M., Kubosaki, A., Akalin, A., Ando, Y., Arner, E., Asada, M., Asahara, H., Bailey, T., Bajic, V. B., Bauer, D., Beckhouse, A. G., Bertin, N., Bjorkegren, J., Brombacher, F., Bulger, E., Chalk, A. M., Chiba, J., Cloonan, N., Dawe, A., Dostie, J., Engstrom, P. G., Essack, M., Faulkner, G. J., Fink, J. L., Fredman, D., Fujimori, K., Furuno, M., Gojobori, T., Gough, J., Grimmond, S. M., Gustafsson, M., Hashimoto, M., Hashimoto, T., Hatakeyama, M., Heinzel, S., Hide, W., Hofmann, O., Hornquist, M., Huminiecki, L., Ikeo, K., Imamoto, N., Inoue, S., Inoue, Y., Ishihara, R., Iwayanagi, T., Jacobsen, A., Kaur, M., Kawaji, H., Kerr, M. C., Kimura, R., Kimura, S., Kimura, Y., Kitano, H., Koga, H., Kojima, T., Kondo, S., Konno, T., Krogh, A., Kruger, A., Kumar, A., Lenhard, B., Lennartsson, A., Lindow, M., Lizio, M., Macpherson, C., Maeda, N., Maher, C. A., Maqungo, M., Mar, J., Matigian, N. A., Matsuda, H., Mattick, J. S., Meier, S., Miyamoto, S., Miyamoto-Sato, E., Nakabayashi, K., Nakachi, Y., Nakano, M., Nygaard, S., Okayama, T., Okazaki, Y., Okuda-Yabukami, H., Orlando, V., Otomo, J., Pachkov, M., Petrovsky, N., Plessy, C., Quackenbush, J., Radovanovic, A., Rehli, M., Saito, R., Sandelin, A., Schmeier, S., Schonbach, C., Schwartz, A. S., Semple, C. A., Sera, M., Severin, J., Shirahige, K., Simons, C., St Laurent, G., Suzuki, M., Suzuki, T., Sweet, M. J., Taft, R. J., Takeda, S., Takenaka, Y., Tan, K., Taylor, M. S., Teasdale, R. D., Tegner, J., Teichmann, S., Valen, E., Wahlestedt, C., Waki, K., Waterhouse, A., Wells, C. A., Winther, O., Wu, L., Yamaguchi, K., Yanagawa, H., Yasuda, J., Zavolan, M., Hume, D. A., Arakawa, T., Fukuda, S., Imamura, K., Kai, C., Kaiho, A., Kawashima, T., Kawazu, C., Kitazume, Y., Kojima, M., Miura, H., Murakami, K., Murata, M., Ninomiya, N., Nishiyori, H., Noma, S., Ogawa, C., Sano, T., Simon, C., Tagami, M., Takahashi, Y., Kawai, J. and Hayashizaki, Y. (2009) “The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line”, Nature genetics. Nature Publ, Vol. 41, H. 5, pp. 553–562. doi: 10.1038/ng.375.   edoc
Poy, M. N., Hausser, J., Trajkovski, M., Braun, M., Collins, S., Rorsman, P., Zavolan, M. and Stoffel, M. (2009) “miR-375 maintains normal pancreatic alpha- and beta-cell mass”, Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, Vol. 106, H. 14, pp. 5813–5818.   edoc
Berninger, P., Gaidatzis, D., van Nimwegen, E. and Zavolan, M. (2008) “Computational analysis of small RNA cloning data”, Methods. Academic Press, Vol. 44, no. 1, pp. 13–21. doi: 10.1016/j.ymeth.2007.10.002.   edoc
Connolly, E., Melegari, M., Landgraf, P., Tchaikovskaya, T., Tennant, B. C., Slagle, B. L., Rogler, L. E., Zavolan, M., Tuschl, T. and Rogler, C. E. (2008) “Elevated expression of the miR-17-92 polycistron and miR-21 in hepadnavirus-associated hepatocellular carcinoma contributes to the malignant phenotype”, American Journal of Pathology. American Society for Investigative Pathology, Vol. 173, no. 3, pp. 856–864.   edoc
Sinkkonen, L., Hugenschmidt, T., Berninger, P., Gaidatzis, D., Mohn, F., Artus-Revel, C. G., Zavolan, M., Svoboda, P. and Filipowicz, W. (2008) “MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells”, Nature structural & molecular biology. Nature Publ. Group, Vol. 15, no. 3, pp. 259–267.   edoc
Chern, T. .-M., Paul, N., van Nimwegen, E. and Zavolan, M. (2008) “Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs”, DNA research. Oxford University Press, Vol. 15, H. 2, pp. 63–72. doi: 10.1093/dnares/dsm036.   edoc
Galgano, A., Forrer, M., Jaskiewicz, L., Kanitz, A., Zavolan, M. and Gerber, A. P. (2008) “Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system”, PLoS ONE. Public Library of Science, Vol. 3, H. 9 , e3164.   edoc
Chen, P. Y., Weinmann, L., Gaidatzis, D., Pei, Y., Zavolan, M., Tuschl, T. and Meister, G. (2008) “Strand-specific 5’-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity”, RNA. Cambridge University Press, Vol. 14, H. 2, pp. 263–274.   edoc
Landthaler, M., Gaidatzis, D., Rothballer, A., Chen, P. Y., Soll, S. J., Dinic, L., Ojo, T., Hafner, M., Zavolan, M. and Tuschl, T. (2008) “Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs”, RNA. Cambridge University Press, Vol. 14, H. 12 , S. 2580–2596 : 2008.   edoc
Peyer, A. .-K., Jung, D., Beer, M., Gnerre, C., Keogh, A., Stroka, D., Zavolan, M. and Meyer, U. .-A. (2007) “Regulation of human liver delta-aminolevulinic acid synthase by bile acids”, Hepatology. Saunders, Vol. 46, No. 6, pp. 1960–1970.   edoc
Gaidatzis, D., van Nimwegen, E., Hausser, J. and Zavolan, M. (2007) “Inference of miRNA targets using evolutionary conservation and pathway analysis”, BMC bioinformatics. BioMed Central, Vol. 8 , 69. doi: 10.1186/1471-2105-8-69.   edoc
Fulci, V., Chiaretti, S., Goldoni, M., Azzalin, G., Carucci, N., Tavolaro, S., Castellano, L., Magrelli, A., Citarella, F., Messina, M., Maggio, R., Peragine, N., Santangelo, S., Mauro, F. R., Landgraf, P., Tuschl, T., Weir, D. B., Chien, M., Russo, J. J., Ju, J., Sheridan, R., Sander, C., Zavolan, M., Guarini, A., Foa, R. and Macino, G. (2007) “Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia”, Blood, Vol. 109, H. 11, pp. 4944–4951.   edoc
Yao, Y., Zhao, Y., Xu, H., Smith, L. P., Lawrie, C. H., Sewer, A., Zavolan, M. and Nair, V. (2007) “Marek’s disease virus type 2 (MDV-2) encoded microRNAs show no sequence conservation with those encoded by MDV-1”, Journal of virology. American Society for Microbiology, Vol. 81, H. 13, pp. 7164–7170.   edoc
Landgraf, P., Rusu, M., Sheridan, R., Sewer, A., Iovino, N., Aravin, A., Pfeffer, S., Rice, A., Kamphorst, A. O., Landthaler, M., Lin, C., Socci, N. D., Hermida, L., Fulci, V., Chiaretti, S., Foa, R., Schliwka, J., Fuchs, U., Novosel, A., Muller, R. .-U., Schermer, B., Bissels, U., Inman, J., Phan, Q., Chien, M., Weir, D. B., Choksi, R., De Vita, G., Frezzetti, D., Trompeter, H. .-I., Hornung, V., Teng, G., Hartmann, G., Palkovits, M., Di Lauro, R., Wernet, P., Macino, G., Rogler, C. E., Nagle, J. W., Ju, J., Papavasiliou, F. N., Benzing, T., Lichter, P., Tam, W., Brownstein, M. J., Bosio, A., Borkhardt, A., Russo, J. J., Sander, C., Zavolan, M. and Tuschl, T. (2007) “A mammalian microRNA expression atlas based on small RNA library sequencing”, Cell. Cell Press, 129(7), pp. 1401–1414. doi: 10.1016/j.cell.2007.04.040.   edoc | Open Access
Randall, G., Panis, M., Cooper, J. D., Tellinghuisen, T. L., Sukhodolets, K. E., Pfeffer, S., Landthaler, M., Landgraf, P., Kan, S., Lindenbach, B. D., Chien, M., Weir, D. B., Russo, J. J., Ju, J., Brownstein, M. J., Sheridan, R., Sander, C., Zavolan, M., Tuschl, T. and Rice, C. M. (2007) “Cellular cofactors affecting hepatitis C virus infection and replication”, Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, Vol. 104, H. 31, pp. 12884–12889.   edoc
van Nimwegen, E., Paul, N., Sheridan, R. and Zavolan, M. (2006) “SPA : a probabilistic algorithm for spliced alignment”, PLoS genetics. Public Library of Science, Vol. 2, H. 4 , e24. doi: 10.1371/journal.pgen.0020024.   edoc
Nair, V. and Zavolan, M. (2006) “Virus-encoded microRNAs : novel regulators of gene expression”, Trends in microbiology. Elsevier, Vol. 14, H. 4, pp. 169–175.   edoc
Chern, T. .-M., van Nimwegen, E., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y. and Zavolan, M. (2006) “A simple physical model predicts small exon length variations”, PLoS genetics. Public Library of Science, Vol. 2, H. 4 , e45. doi: 10.1371/journal.pgen.0020045.   edoc
Schmitter, D., Filkowski, J., Sewer, A., Pillai, R. S., Oakeley, E. J., Zavolan, M., Svoboda, P. and Filipowicz, W. (2006) “Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells”, Nucleic Acids Research. Oxford University Press, 34(17), pp. 4801–4815. doi: 10.1093/nar/gkl646.   edoc | Open Access
Sood, P., Krek, A., Zavolan, M., Macino, G. and Rajewsky, N. (2006) “Cell-type-specific signatures of microRNAs on target mRNA expression”, Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, Vol. 103, H. 8, pp. 2746–2751.   edoc
Zavolan, M. and van Nimwegen, E. (2006) “The types and prevalence of alternative splice forms”, Current opinion in structural biology. Current Biology, Vol. 16, H. 3, pp. 362–367. doi: 10.1016/j.sbi.2006.05.002.   edoc
Aravin, A., Gaidatzis, D., Pfeffer, S., Lagos-Quintana, M., Landgraf, P., Iovino, N., Morris, P., Brownstein, M. J., Kuramochi-Miyagawa, S., Nakano, T., Chien, M., Russo, J. J., Ju, J., Sheridan, R., Sander, C., Zavolan, M. and Tuschl, T. (2006) “A novel class of small RNAs bind to MILI protein in mouse testes”, Nature. Macmillan, Vol. 442, pp. 203–207.   edoc
Sewer, A., Paul, N., Landgraf, P., Aravin, A., Pfeffer, S., Brownstein, M. J., Tuschl, T., van Nimwegen, E. and Zavolan, M. (2005) “Identification of clustered microRNAs using an ab initio prediction method”, BMC bioinformatics. BioMed Central, Vol. 6, , 267. doi: 10.1186/1471-2105-6-267.   edoc
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C., Kodzius, R., Shimokawa, K., Bajic, V. B., Brenner, S. E., Batalov, S., Forrest, A. R. R., Zavolan, M., Davis, M. J., Wilming, L. G., Aidinis, V., Allen, J. E., Ambesi-Impiombato, A., Apweiler, R., Aturaliya, R. N., Bailey, T. L., Bansal, M., Baxter, L., Beisel, K. W., Bersano, T., Bono, H., Chalk, A. M., Chiu, K. P., Choudhary, V., Christoffels, A., Clutterbuck, D. R., Crowe, M. L., Dalla, E., Dalrymple, B. P., de Bono, B., Della Gatta, G., di Bernardo, D., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G., Fletcher, C. F., Fukushima, T., Furuno, M., Futaki, S., Gariboldi, M., Georgii-Hemming, P., Gingeras, T. R., Gojobori, T., Green, R. E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, T. K., Hirokawa, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Kelso, J., Kitamura, H., Kitano, H., Kollias, G., Krishnan, S. P. T., Kruger, A., Kummerfeld, S. K., Kurochkin, I. V., Lareau, L. F., Lazarevic, D., Lipovich, L., Liu, J., Liuni, S., McWilliam, S., Madan Babu, M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mulder, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., Nishikawa, S., Nori, F., Ohara, O., Okazaki, Y., Orlando, V., Pang, K. C., Pavan, W. J., Pavesi, G., Pesole, G., Petrovsky, N., Piazza, S., Reed, J., Reid, J. F., Ring, B. Z., Ringwald, M., Rost, B., Ruan, Y., Salzberg, S. L., Sandelin, A., Schneider, C., Schonbach, C., Sekiguchi, K., Semple, C. A. M., Seno, S., Sessa, L., Sheng, Y., Shibata, Y., Shimada, H., Shimada, K., Silva, D., Sinclair, B., Sperling, S., Stupka, E., Sugiura, K., Sultana, R., Takenaka, Y., Taki, K., Tammoja, K., Tan, S. L., Tang, S., Taylor, M. S., Tegner, J., Teichmann, S. A., Ueda, H. R., van Nimwegen, E., Verardo, R., Wei, C. L., Yagi, K., Yamanishi, H., Zabarovsky, E., Zhu, S., Zimmer, A., Hide, W., Bult, C., Grimmond, S. M., Teasdale, R. D., Liu, E. T., Brusic, V., Quackenbush, J., Wahlestedt, C., Mattick, J. S., Hume, D. A., Kai, C., Sasaki, D., Tomaru, Y., Fukuda, S., Kanamori-Katayama, M., Suzuki, M., Aoki, J., Arakawa, T., Iida, J., Imamura, K., Itoh, M., Kato, T., Kawaji, H., Kawagashira, N., Kawashima, T., Kojima, M., Kondo, S., Konno, H., Nakano, K., Ninomiya, N., Nishio, T., Okada, M., Plessy, C., Shibata, K., Shiraki, T., Suzuki, S., Tagami, M., Waki, K., Watahiki, A., Okamura-Oho, Y., Suzuki, H., Kawai, J. and Hayashizaki, Y. (2005) “The transcriptional landscape of the mammalian genome”, Science. American Association for the Advancement of Science, Vol. 309, no. 5740, pp. 1559–1563. doi: 10.1126/science.1112014.   edoc
Pfeffer, S., Sewer, A., Lagos-Quintana, M., Sheridan, R., Sander, C., Grasser, F. A., van Dyk, L. F., Ho, C. K., Shuman, S., Chien, M., Russo, J. J., Ju, J., Randall, G., Lindenbach, B. D., Rice, C. M., Simon, V., Ho, D. D., Zavolan, M. and Tuschl, T. (2005) “Identification of microRNAs of the herpesvirus family”, Nature Methods. Nature Publishing Group, Vol. 2, no. 4, pp. 269–276.   edoc
Gomes, A. R., Vinga, S., Zavolan, M. and de Lencastre, H. (2005) “Analysis of the genetic variability of virulence-related loci in epidemic clones of methicillin-resistant Staphylococcus aureus”, Antimicrobial Agents and Chemotherapy. American Society for Microbiology, Vol. 49, H. 1, pp. 366–379.   edoc
Chen, P. Y., Manninga, H., Slanchev, K., Chien, M., Russo, J. J., Ju, J., Sheridan, R., John, B., Marks, D. S., Gaidatzis, D., Sander, C., Zavolan, M. and Tuschl, T. (2005) “The developmental miRNA profiles of zebrafish as determined by small RNA cloning”, Genes & development. Cold Spring Harbor Laboratory, Vol. 19, H. 11, pp. 1288–1293.   edoc
Speirs, C., van Nimwegen, E., Bolton, D., Zavolan, M., Duvall, M., Angleman, S., Siegel, R., Perelson, A. S. and Lenardo, M. J. (2005) “Analysis of human immunodeficiency virus cytopathicity by using a new method for quantitating viral dynamics in cell culture”, Journal of virology. American Society for Microbiology, Vol. 79, H. 7, pp. 4025–4032. doi: 10.1128/JVI.79.7.4025-4032.2005.   edoc
Pfeffer, S., Zavolan, M., Grasser, F. A., Chien, M., Russo, J. J., Ju, J., John, B., Enright, A. J., Marks, D., Sander, C. and Tuschl, T. (2004) “Identification of virus-encoded microRNAs”, Science. American Association for the Advancement of Science, Vol. 304, no. 5671, pp. 734–736.   edoc
Zavolan, M., Socci, N. D., Rajewsky, N. and Gaasterlamd, T. (2003) “SMASHing regulatory sites in DNA by human-mouse sequence comparisons”, Proceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Press, Vol. 2, pp. 277–286.   edoc
Zavolan, M., Kondo, S., Schonbach, C., Adachi, J., Hume, D. A., Hayashizaki, Y. and Gaasterland, T. (2003) “Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome”, Genome research. Cold Spring Harbor Laboratory Press, Vol. 13, H. 6b, pp. 1290–1300.   edoc
Yang, E., van Nimwegen, E., Zavolan, M., Rajewsky, N., Schroeder, M., Magnasco, M. and Darnell, J. E. J. (2003) “Decay rates of human mRNAs : correlation with functional characteristics and sequence attributes”, Genome research. Cold Spring Harbor Laboratory Press, Vol. 13, H. 8, pp. 1863–1872.   edoc
Ravasi, T., Huber, T., Zavolan, M., Forrest, A., Gaasterland, T., Grimmond, S. and Hume, D. A. (2003) “Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome”, Genome research. Cold Spring Harbor Laboratory Press, Vol. 13, H. 6b, pp. 1430–1442.   edoc
Aravin, A. A., Lagos-Quintana, M., Yalcin, A., Zavolan, M., Marks, D., Snyder, B., Gaasterland, T., Meyer, J. and Tuschl, T. (2003) “The small RNA profile during Drosophila melanogaster development”, Developmental cell. Cell Press, Vol. 5, H. 2, pp. 337–350.   edoc
van Nimwegen, E., Zavolan, M., Rajewsky, N. and Siggia, E. D. (2002) “Probabilistic clustering of sequences : inferring new bacterial regulons by comparative genomics”, Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, Vol. 99, No. 11, pp. 7323–7328. doi: 10.1073/pnas.112690399.   edoc
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Kepler, T. B. and Oprea, M. (2001) “Improved inference of mutation rates: I. An integral representation for the Luria-Delbrück distribution”, Theoretical population biology. Academic Press, 59(1), pp. 41–48. doi: 10.1006/tpbi.2000.1498.   edoc
Oprea, M. and Kepler, T. B. (2001) “Improved inference of mutation rates: II. Generalization of the Luria-Delbrück distribution for realistic cell-cycle time distributions”, Theoretical population biology. Academic Press, 59(1), pp. 49–59. doi: 10.1006/tpbi.2000.1504.   edoc
Gaasterland, T. and Oprea, M. (2001) “Whole-genome analysis: annotations and updates”, Current Opinion in Structural Biology. Elsevier, 11(3), pp. 377–381. doi: 10.1016/S0959-440X(00)00213-X.   edoc
De Boer, R. J., Oprea, M., Antia, R., Murali-Krishna, K., Ahmed, R. . and Perelson, A. S. (2001) “Recruitment times, proliferation, and apoptosis rates during the CD8(+) T-cell response to lymphocytic choriomeningitis virus”, Journal of virology. American Society of Microbiology, 75(22), pp. 10663–10669. doi: 10.1128/JVI.75.22.10663-10669.2001.   edoc
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Oprea, M., van Nimwegen, E. . and Perelson, A. S. (2000) “Dynamics of one-pass germinal center models: implications for affinity maturation”, Bulletin of Mathematical Biology. Springer, 62(1), pp. 121–153. doi: 10.1006/bulm.1999.0144.   edoc
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Oprea, M. and Perelson, A. S. (1997) “Somatic mutation leads to efficient affinity maturation when centrocytes recycle back to centroblasts”, Journal of Immunology. American Association of Immunologists, 158(11), pp. 5155–5162.   edoc
Oprea, M. and Perelson, A. S. (1996) “Exploring the mechanisms of primary antibody responses to T cell-dependent antigens”, Journal of Theoretical Biology. Elsevier, 181(3), pp. 215–236. doi: 10.1006/jtbi.1996.0127.   edoc
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