Items where Division is "05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (Zavolan)"

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Dimitrova, Yoana and Gruber, Andreas J. and Mittal, Nitish and Ghosh, Souvik and Dimitriades, Beatrice and Mathow, Daniel and Grandy, William Aaron and Christofori, Gerhard and Zavolan, Mihaela. (2017) TFAP2A is a component of the ZEB1/2 network that regulates TGFB1-induced epithelial to mesenchymal transition. Biology Direct, 12 (1). p. 8.

Gumienny, Rafal and Jedlinski, Dominik J. and Schmidt, Alexander and Gypas, Foivos and Martin, Georges and Vina-Vilaseca, Arnau and Zavolan, Mihaela. (2017) High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq. Nucleic Acids Research, 45 (5). pp. 2341-2353.

Omidi, Saeed and Zavolan, Mihaela and Pachkov, Mikhail and Breda, Jeremie and Berger, Severin and van Nimwegen, Erik. (2017) Automated incorporation of pairwise dependency in transcription factor binding site prediction using dinucleotide weight tensors. PLoS Computational Biology, 13 (7). e1005176.

Riba, Andrea and Emmenlauer, Mario and Chen, Amy and Sigoillot, Frederic and Cong, Feng and Dehio, Christoph and Jenkins, Jeremy and Zavolan, Mihaela. (2017) Explicit Modeling of siRNA-Dependent On- and Off-Target Repression Improves the Interpretation of Screening Results. Cell Systems, 4 (2). pp. 182-193.e4.

Gruber, Andreas J. and Schmidt, Ralf and Gruber, Andreas R. and Martin, Georges and Ghosh, Souvik and Belmadani, Manuel and Keller, Walter and Zavolan, Mihaela. (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, 26 (8). pp. 1145-1159.

Jorjani, Hadi and Kehr, Stephanie and Jedlinski, Dominik J. and Gumienny, Rafal and Hertel, Jana and Stadler, Peter F. and Zavolan, Mihaela and Gruber, Andreas R.. (2016) An updated human snoRNAome. Nucleic Acids Research, 44 (11). pp. 5068-5082.

Martin, Georges and Zavolan, Mihaela. (2016) Redesigning CLIP for efficiency, accuracy and speed. Nature Methods, 13 (6). pp. 482-483.

Janowski, Robert and Heinz, Gitta A. and Schlundt, Andreas and Wommelsdorf, Nina and Brenner, Sven and Gruber, Andreas R. and Blank, Michael and Buch, Thorsten and Buhmann, Raymund and Zavolan, Mihaela and Niessing, Dierk and Heissmeyer, Vigo and Sattler, Michael. (2016) Roquin recognizes a non-canonical hexaloop structure in the 3'-UTR of Ox40. Nature communications, 7. p. 11032.

Guimaraes, Joao C. and Zavolan, Mihaela. (2016) Patterns of ribosomal protein expression specify normal and malignant human cells. Genome biology, 17 (1). p. 236.

Ustianenko, Dmytro and Pasulka, Josef and Feketova, Zuzana and Bednarik, Lukas and Zigackova, Dagmar and Fortova, Andrea and Zavolan, Mihaela and Vanacova, Stepanka. (2016) TUT-DIS3L2 is a mammalian surveillance pathway for aberrant structured non-coding RNAs. The EMBO journal, 35 (20). pp. 2179-2191.

Subasic, Deni and Brümmer, Anneke and Wu, Yibo and Pinto, Sérgio Morgado and Imig, Jochen and Keller, Martin and Jovanovic, Marko and Lightfoot, Helen Louise and Nasso, Sara and Götze, Sandra and Brunner, Erich and Hall, Jonathan and Aebersold, Ruedi and Zavolan, Mihaela and Hengartner, Michael. (2015) Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans. Genome research, 25 (11). pp. 1680-1691.

Zavolan, Mihaela. (2015) Inferring gene expression regulatory networks from high-throughput measurements. Methods, 85. pp. 1-2.

Gumienny, Rafal and Zavolan, Mihaela. (2015) Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G. Nucleic Acids Research, 43 (3). pp. 1380-1391.

Imig, Jochen and Brunschweiger, Andreas and Brümmer, Anneke and Guennewig, Boris and Mittal, Nitish and Kishore, Shivendra and Tsikrika, Panagiota and Gerber, André P. and Zavolan, Mihaela and Hall, Jonathan. (2015) miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. Nature chemical biology, Vol. 11, H. 2. pp. 107-114.

Kanitz, Alexander and Gypas, Foivos and Gruber, Andreas J. and Gruber, Andreas R. and Martin, Georges and Zavolan, Mihaela. (2015) Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data. Genome biology, Vol. 16. p. 150.

Tattikota, Sudhir G. and Rathjen, Thomas and Hausser, Jean and Khedkar, Aditya and Kabra, Uma D. and Pandey, Varun and Sury, Matthias and Wessels, Hans-Hermann and Mollet, Inês G. and Eliasson, Lena and Selbach, Matthias and Zinzen, Robert P. and Zavolan, Mihaela and Kadener, Sebastian and Tschöp, Matthias H. and Jastroch, Martin and Friedländer, Marc R. and Poy, Matthew N.. (2015) miR-184 Regulates Pancreatic β-Cell Function According to Glucose Metabolism. Journal of biological chemistry, Vol. 290, H. 33. pp. 20284-20294.

Zavolan, Mihaela and Keller, Walter. (2015) Reflections on the RNA world. RNA, 21 (4). pp. 531-533.

Balwierz, Piotr J. and Pachkov, Mikhail and Arnold, Phild and Gruber, Andreas J. and Zavolan, Mihaela and van Nimwegen, Erik. (2014) ISMARA: Automated modeling of genomic signals as a democracy of regulatory motifs. Genome research, Vol. 24, H. 5. pp. 869-884.

Daubner, Gerrit M. and Brümmer, Anneke and Tocchini, Cristina and Gerhardy, Stefan and Ciosk, Rafal and Zavolan, Mihaela and Allain, Frédéric H.-T.. (2014) Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1. Nucleic Acids Research, 42 (12). pp. 8092-8105.

Erhard, Florian and Haas, Jürgen and Lieber, Diana and Malterer, Georg and Jaskiewicz, Lukasz and Zavolan, Mihaela and Dölken, Lars and Zimmer, Ralf. (2014) Widespread context-dependency of microRNA-mediated regulation. Genome research, Vol. 24, H. 6. pp. 906-919.

Gruber, Andreas J. and Grandy, William A. and Balwierz, Piotr J. and Dimitrova, Yoana A. and Pachkov, Mikhail and Ciaudo, Constance and van Nimwegen, Erik and Zavolan, Mihaela. (2014) Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways. Nucleic Acids Research, 42 (14). pp. 9313-9326.

Gruber, Andreas R.. (2014) RNA Polymerase III promoter screen uncovers a novel noncoding RNA family conserved in Caenorhabditis and other clade V nematodes. Gene, Vol. 544, H. 2. pp. 236-240.

Gruber, Andreas R. and Martin, Georges and Müller, Philipp and Schmidt, Alexander and Gruber, Andreas J. and Gumienny, Rafal and Mittal, Nitish and Jayachandran, Rajesh and Pieters, Jean and Keller, Walter. (2014) Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells. Nature Communications, 5 (5465). pp. 1-10.

Hausser, Jean and Zavolan, Mihaela. (2014) Identification and consequences of miRNA-target interactions - beyond repression of gene expression. Nature reviews. Genetics, Vol. 15, no. 9. pp. 599-612.

Jorjani, Hadi and Zavolan, Mihaela. (2014) TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data. Bioinformatics, Vol. 30, H. 7. pp. 971-974.

Kishore, Shivendra and Piscuoglio, Salvatore and Kovac, Michal and Gylling, Annette and Wenzel, Friedel and Trapani, Francesca and Altermatt, Hans Joerg and Mele, Valentina and Marra, Giancarlo and Peltomäki, Päivi and Terracciano, Luigi and Zavolan, Mihaela and Heinimann, Karl. (2014) 3'UTR poly(T/U) tract deletions and altered expression of EWSR1 are a hallmark of mismatch repair deficient cancers. Cancer research, Vol. 74,1 , S. 224–234.

Latreille, Mathieu and Hausser, Jean and Stützer, Ina and Zhang, Quan and Hastoy, Benoit and Gargani, Sofia and Kerr-Conte, Julie and Pattou, Francois and Zavolan, Mihaela and Esguerra, Jonathan L. S. and Eliasson, Lena and Rülicke, Thomas and Rorsman, Patrik and Stoffel, Markus. (2014) MicroRNA-7a regulates pancreatic β cell function. Journal of Clinical Investigation, Vol. 124, H. 6. pp. 2722-2735.

Mittal, Nitish and Zavolan, Mihaela. (2014) Seq and CLIP through the miRNA world. Genome biology, Vol. 15, H. 1. p. 202.

Schönemann, Lars and Kühn, Uwe and Martin, Georges and Schäfer, Peter and Gruber, Andreas R. and Keller, Walter and Zavolan, Mihaela and Wahle, Elmar. (2014) Reconstitution of CPSF active in polyadenylation: recognition of the polyadenylation signal by WDR33. Genes & development, Vol. 28. pp. 2381-2393.

Spitzer, Jessica and Hafner, Markus and Landthaler, Markus and Ascano, Manuel and Farazi, Thalia and Wardle, Greg and Nusbaum, Jeff and Khorshid, Mohsen and Burger, Lukas and Zavolan, Mihaela and Tuschl, Thomas. (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, Vol. 539. pp. 113-161.

Brümmer, Anneke and Kishore, Shivendra and Subasic, Deni and Hengartner, Michael and Zavolan, Mihaela. (2013) Modeling the binding specificity of the RNA-binding protein GLD-1 suggests a function of coding region-located sites in translational repression. RNA, Vol. 19, H. 10. pp. 1317-1326.

Gruber, Andreas J. and Zavolan, Mihaela. (2013) Modulation of epigenetic regulators and cell fate decisions by miRNAs. Epigenomics, Vol. 5, H. 6. pp. 671-683.

Gruber, Andreas R. and Martin, Georges and Keller, Walter and Zavolan, Mihaela. (2013) Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors. Wiley Interdisciplinary Reviews. RNA, 5 (2). pp. 183-196.

Hausser, Jean and Syed, Afzal Pasha and Bilen, Biter and Zavolan, Mihaela. (2013) Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation. Genome research, Vol. 23, H. 4. pp. 604-615.

Hausser, Jean and Syed, Afzal Pasha and Selevsek, Nathalie and van Nimwegen, Erik and Jaskiewicz, Lukasz and Aebersold, Ruedi and Zavolan, Mihaela. (2013) Timescales and bottlenecks in miRNA-dependent gene regulation. Molecular systems biology, Vol. 9 , 711.

Khorshid, Mohsen and Hausser, Jean and Zavolan, Mihaela and van Nimwegen, Erik. (2013) A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nature methods, Vol. 10, H. 3. pp. 253-255.

Kishore, Shivendra and Gruber, Andreas R. and Jedlinski, Dominik J. and Syed, Afzal P. and Jorjani, Hadi and Zavolan, Mihaela. (2013) Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing. Genome biology, Vol. 14, H. 5 , R45.

Tattikota, Sudhir G. and Rathjen, Thomas and McAnulty, Sarah J. and Wessels, Hans-Hermann and Akerman, Ildem and van de Bunt, Martijn and Hausser, Jean and Esguerra, Jonathan L. S. and Musahl, Anne and Pandey, Amit K. and You, Xintian and Chen, Wei and Herrera, Pedro L. and Johnson, Paul R. and O'Carroll, Donal and Eliasson, Lena and Zavolan, Mihaela and Gloyn, Anna L. and Ferrer, Jorge and Shalom-Feuerstein, Ruby and Aberdam, Daniel and Poy, Matthew N.. (2013) Argonaute2 Mediates Compensatory Expansion of the Pancreatic β Cell. Cell metabolism, Vol. 19, H. 1. pp. 122-134.

Zünd, David and Gruber, Andreas R. and Zavolan, Mihaela and Mühlemann, Oliver. (2013) Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3' UTRs. Nature structural & molecular biology, Vol. 20, H. 8 , S. 936–943.

Gruber, Andreas R. and Martin, Georges and Keller, Walter and Zavolan, Mihaela. (2012) Cleavage factor Im is a key regulator of 3' UTR length. RNA Biology, 9 (12). pp. 1405-1412.

Jaskiewicz, Lukasz and Bilen, Biter and Hausser, Jean and Zavolan, Mihaela. (2012) Argonaute CLIP - A method to identify in vivo targets of miRNAs. Methods, Vol. 58, no. 2. pp. 106-112.

Jaskiewicz, Lukasz and Zavolan, Mihaela. (2012) Dicer partners expand the repertoire of miRNA targets. Genome biology, Vol. 13, H. 11. p. 179.

Krützfeldt, Jan and Rösch, Nora and Hausser, Jean and Manoharan, Muthiah and Zavolan, Mihaela and Stoffel, Markus. (2012) MicroRNA-194 is a target of transcription factor 1 (Tcf1, Hnf1α) in adult liver and controls expression of frizzled-6. Hepatology, Vol. 55, No. 1. pp. 98-107.

Martin, Georges and Gruber, Andreas R. and Keller, Walter and Zavolan, Mihaela. (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, 1 (6). pp. 753-763.

Berninger, P. and Jaskiewicz, L. and Khorshid, M. and Zavolan, M.. (2011) Conserved generation of short products at piRNA loci. BMC Genomics, Vol. 12, H. 1 , 46.

Corioni, M. and Antih, N. and Tanackovic, G. and 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, 39 (5). pp. 1868-1879.

Khorshid, M. and Rodak, C. and Zavolan, M.. (2011) CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Research, 39 (1 Supplement). D245-D252.

Kishore, S. and Jaskiewicz, L. and Burger, L. and Hausser, J. and Khorshid, M. and Zavolan, M.. (2011) A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nature Methods, Vol. 8, H. 7. pp. 559-564.

Rammelt, C. and Bilen, B. and Zavolan, M. and Keller, W.. (2011) PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif. RNA, Vol. 17. pp. 1737-1746.

Suffert, Guillaume and Malterer, Georg and Hausser, Jean and Viiliäinen, Johanna and Fender, Aurélie and Contrant, Maud and Ivacevic, Tomi and Benes, Vladimir and Gros, Frédéric and Voinnet, Olivier and Zavolan, Mihaela and Ojala, Päivi M. and Haas, Juergen G. and Pfeffer, Sébastien. (2011) Kaposi's Sarcoma Herpesvirus microRNAs Target Caspase 3 and Regulate Apoptosis. PLoS Pathogens, Vol. 7, H. 12 , e1002405.

Trajkovski, Mirko and Hausser, Jean and Soutschek, Jürgen and Bhat, Bal and Akin, Akinc and Zavolan, Mihaela and Heim, Markus H. and Stoffel, Markus. (2011) MicroRNAs 103 and 107 regulate insulin sensitivity. Nature, Vol. 474, H. 7353. pp. 649-653.

Hafner, M. and Landthaler, M. and Burger, L. and Khorshid, M. and Hausser, J. and Berninger, P. and Rothballer, A. and Ascano, M. and Jungkamp, A. -C. and Munschauer, M. and Ulrich, A. and Wardle, G. S. and Dewell, S. and 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, H. 41 , 2034.

Hafner, M. and Landthaler, M. and Burger, L. and Khorshid, M. and Hausser, J. and Berninger, P. and Rothballer, A. and Ascano, M. J. and Jungkamp, A. -C. and Munschauer, M. and Ulrich, A. and Wardle, G. S. and Dewell, S. and Zavolan, M. and Tuschl, T.. (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell, Vol. 141, H. 1. pp. 129-141.

Kishore, S. and Khanna, A. and Zhang, Z. and Hui, J. and Balwierz, P. J. and Stefan, M. and Beach, C. and Nicholls, R. D. and Zavolan, M. and Stamm, S.. (2010) The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Human Molecular Genetics, Vol. 19, H. 7. pp. 1153-1164.

Kishore, S. and 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, Vol. 9, no. 5. pp. 391-404.

Ma, J. and Flemr, M. and Stein, P. and Berninger, P. and Malik, R. and Zavolan, M. and Svoboda, P. and Schultz, R. M.. (2010) MicroRNA activity is suppressed in mouse oocytes. Current biology, Vol. 20, H. 3. pp. 265-270.

McGlincy, N. J. and Tan, L. -Y. and Paul, N. and Zavolan, M. and 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, Vol. 11 , 565.

Hausser, Jean and Berninger, Philipp and Rodak, Christoph and Jantscher, Yvonne and Wirth, Stefan and Zavolan, Mihaela. (2009) MirZ: an integrated microRNA expression atlas and target prediction resource. Nucleic Acids Research, 37 (2 Supplement). W266-W272.

Hausser, Jean and Landthaler, Markus and Jaskiewicz, Lukasz and Gaidatzis, Dimos and Zavolan, Mihaela. (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, Vol. 19, H. 11. pp. 2009-2020.

Hutzinger, R. and Feederle, R. and Mrazek, J. and Schiefermeier, N. and Balwierz, P. J. and Zavolan, M. and Polacek, N. and Delecluse, H. -J. and Huttenhofer, A.. (2009) Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome. PLoS Pathogens, Vol. 5, H. 8 , e1000547.

Pena, J. T. G. and Sohn-Lee, C. and Rouhanifard, S. H. and Ludwig, J. and Hafner, M. and Mihailovic, A. and Lim, C. and Holoch, D. and Berninger, P. and 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.

Poy, M. N. and Hausser, J. and Trajkovski, M. and Braun, M. and Collins, S. and Rorsman, P. and 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, Vol. 106, H. 14. pp. 5813-5818.

Suzuki, H. and Forrest, A. R. and van Nimwegen, E. and Daub, C. O. and Balwierz, P. J. and Irvine, K. M. and Lassmann, T. and Ravasi, T. and Hasegawa, Y. and de Hoon, M. J. and Katayama, S. and Schroder, K. and Carninci, P. and Tomaru, Y. and Kanamori-Katayama, M. and Kubosaki, A. and Akalin, A. and Ando, Y. and Arner, E. and Asada, M. and Asahara, H. and Bailey, T. and Bajic, V. B. and Bauer, D. and Beckhouse, A. G. and Bertin, N. and Bjorkegren, J. and Brombacher, F. and Bulger, E. and Chalk, A. M. and Chiba, J. and Cloonan, N. and Dawe, A. and Dostie, J. and Engstrom, P. G. and Essack, M. and Faulkner, G. J. and Fink, J. L. and Fredman, D. and Fujimori, K. and Furuno, M. and Gojobori, T. and Gough, J. and Grimmond, S. M. and Gustafsson, M. and Hashimoto, M. and Hashimoto, T. and Hatakeyama, M. and Heinzel, S. and Hide, W. and Hofmann, O. and Hornquist, M. and Huminiecki, L. and Ikeo, K. and Imamoto, N. and Inoue, S. and Inoue, Y. and Ishihara, R. and Iwayanagi, T. and Jacobsen, A. and Kaur, M. and Kawaji, H. and Kerr, M. C. and Kimura, R. and Kimura, S. and Kimura, Y. and Kitano, H. and Koga, H. and Kojima, T. and Kondo, S. and Konno, T. and Krogh, A. and Kruger, A. and Kumar, A. and Lenhard, B. and Lennartsson, A. and Lindow, M. and Lizio, M. and Macpherson, C. and Maeda, N. and Maher, C. A. and Maqungo, M. and Mar, J. and Matigian, N. A. and Matsuda, H. and Mattick, J. S. and Meier, S. and Miyamoto, S. and Miyamoto-Sato, E. and Nakabayashi, K. and Nakachi, Y. and Nakano, M. and Nygaard, S. and Okayama, T. and Okazaki, Y. and Okuda-Yabukami, H. and Orlando, V. and Otomo, J. and Pachkov, M. and Petrovsky, N. and Plessy, C. and Quackenbush, J. and Radovanovic, A. and Rehli, M. and Saito, R. and Sandelin, A. and Schmeier, S. and Schonbach, C. and Schwartz, A. S. and Semple, C. A. and Sera, M. and Severin, J. and Shirahige, K. and Simons, C. and St Laurent, G. and Suzuki, M. and Suzuki, T. and Sweet, M. J. and Taft, R. J. and Takeda, S. and Takenaka, Y. and Tan, K. and Taylor, M. S. and Teasdale, R. D. and Tegner, J. and Teichmann, S. and Valen, E. and Wahlestedt, C. and Waki, K. and Waterhouse, A. and Wells, C. A. and Winther, O. and Wu, L. and Yamaguchi, K. and Yanagawa, H. and Yasuda, J. and Zavolan, M. and Hume, D. A. and Arakawa, T. and Fukuda, S. and Imamura, K. and Kai, C. and Kaiho, A. and Kawashima, T. and Kawazu, C. and Kitazume, Y. and Kojima, M. and Miura, H. and Murakami, K. and Murata, M. and Ninomiya, N. and Nishiyori, H. and Noma, S. and Ogawa, C. and Sano, T. and Simon, C. and Tagami, M. and Takahashi, Y. and Kawai, J. and Hayashizaki, Y.. (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature genetics, Vol. 41, H. 5. pp. 553-562.

Berninger, P. and Gaidatzis, D. and van Nimwegen, E. and Zavolan, M.. (2008) Computational analysis of small RNA cloning data. Methods, Vol. 44, no. 1. pp. 13-21.

Chen, P. Y. and Weinmann, L. and Gaidatzis, D. and Pei, Y. and Zavolan, M. and Tuschl, T. and Meister, G.. (2008) Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity. RNA, Vol. 14, H. 2. pp. 263-274.

Chern, T. -M. and Paul, N. and van Nimwegen, E. and Zavolan, M.. (2008) Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs. DNA research, Vol. 15, H. 2. pp. 63-72.

Connolly, E. and Melegari, M. and Landgraf, P. and Tchaikovskaya, T. and Tennant, B. C. and Slagle, B. L. and Rogler, L. E. and Zavolan, M. and 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, Vol. 173, no. 3. pp. 856-864.

Galgano, A. and Forrer, M. and Jaskiewicz, L. and Kanitz, A. and 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, Vol. 3, H. 9 , e3164.

Landthaler, M. and Gaidatzis, D. and Rothballer, A. and Chen, P. Y. and Soll, S. J. and Dinic, L. and Ojo, T. and Hafner, M. and Zavolan, M. and Tuschl, T.. (2008) Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA, Vol. 14, H. 12 , S. 2580–2596 : 2008.

Sinkkonen, L. and Hugenschmidt, T. and Berninger, P. and Gaidatzis, D. and Mohn, F. and Artus-Revel, C. G. and Zavolan, M. and 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, Vol. 15, no. 3. pp. 259-267.

Fulci, V. and Chiaretti, S. and Goldoni, M. and Azzalin, G. and Carucci, N. and Tavolaro, S. and Castellano, L. and Magrelli, A. and Citarella, F. and Messina, M. and Maggio, R. and Peragine, N. and Santangelo, S. and Mauro, F. R. and Landgraf, P. and Tuschl, T. and Weir, D. B. and Chien, M. and Russo, J. J. and Ju, J. and Sheridan, R. and Sander, C. and Zavolan, M. and Guarini, A. and 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.

Gaidatzis, D. and van Nimwegen, E. and Hausser, J. and Zavolan, M.. (2007) Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC bioinformatics, Vol. 8 , 69.

Landgraf, P. and Rusu, M. and Sheridan, R. and Sewer, A. and Iovino, N. and Aravin, A. and Pfeffer, S. and Rice, A. and Kamphorst, A. O. and Landthaler, M. and Lin, C. and Socci, N. D. and Hermida, L. and Fulci, V. and Chiaretti, S. and Foa, R. and Schliwka, J. and Fuchs, U. and Novosel, A. and Muller, R. -U. and Schermer, B. and Bissels, U. and Inman, J. and Phan, Q. and Chien, M. and Weir, D. B. and Choksi, R. and De Vita, G. and Frezzetti, D. and Trompeter, H. -I. and Hornung, V. and Teng, G. and Hartmann, G. and Palkovits, M. and Di Lauro, R. and Wernet, P. and Macino, G. and Rogler, C. E. and Nagle, J. W. and Ju, J. and Papavasiliou, F. N. and Benzing, T. and Lichter, P. and Tam, W. and Brownstein, M. J. and Bosio, A. and Borkhardt, A. and Russo, J. J. and Sander, C. and Zavolan, M. and Tuschl, T.. (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell, Vol. 129, H. 7. pp. 1401-1414.

Peyer, A. -K. and Jung, D. and Beer, M. and Gnerre, C. and Keogh, A. and Stroka, D. and Zavolan, M. and Meyer, U. -A.. (2007) Regulation of human liver delta-aminolevulinic acid synthase by bile acids. Hepatology, Vol. 46, No. 6. pp. 1960-1970.

Randall, G. and Panis, M. and Cooper, J. D. and Tellinghuisen, T. L. and Sukhodolets, K. E. and Pfeffer, S. and Landthaler, M. and Landgraf, P. and Kan, S. and Lindenbach, B. D. and Chien, M. and Weir, D. B. and Russo, J. J. and Ju, J. and Brownstein, M. J. and Sheridan, R. and Sander, C. and Zavolan, M. and 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, Vol. 104, H. 31. pp. 12884-12889.

Yao, Y. and Zhao, Y. and Xu, H. and Smith, L. P. and Lawrie, C. H. and Sewer, A. and 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, Vol. 81, H. 13. pp. 7164-7170.

Aravin, A. and Gaidatzis, D. and Pfeffer, S. and Lagos-Quintana, M. and Landgraf, P. and Iovino, N. and Morris, P. and Brownstein, M. J. and Kuramochi-Miyagawa, S. and Nakano, T. and Chien, M. and Russo, J. J. and Ju, J. and Sheridan, R. and Sander, C. and Zavolan, M. and Tuschl, T.. (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature, Vol. 442. pp. 203-207.

Chern, T. -M. and van Nimwegen, E. and Kai, C. and Kawai, J. and Carninci, P. and Hayashizaki, Y. and Zavolan, M.. (2006) A simple physical model predicts small exon length variations. PLoS genetics, Vol. 2, H. 4 , e45.

Nair, V. and Zavolan, M.. (2006) Virus-encoded microRNAs : novel regulators of gene expression. Trends in microbiology, Vol. 14, H. 4. pp. 169-175.

Schmitter, D. and Filkowski, J. and Sewer, A. and Pillai, R. S. and Oakeley, E. J. and Zavolan, M. and Svoboda, P. and Filipowicz, W.. (2006) Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells. Nucleic Acids Research, 34 (17). pp. 4801-4815.

Sood, P. and Krek, A. and Zavolan, M. and 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, Vol. 103, H. 8. pp. 2746-2751.

Zavolan, M. and van Nimwegen, E.. (2006) The types and prevalence of alternative splice forms. Current opinion in structural biology, Vol. 16, H. 3. pp. 362-367.

van Nimwegen, E. and Paul, N. and Sheridan, R. and Zavolan, M.. (2006) SPA : a probabilistic algorithm for spliced alignment. PLoS genetics, Vol. 2, H. 4 , e24.

Carninci, P. and Kasukawa, T. and Katayama, S. and Gough, J. and Frith, M. C. and Maeda, N. and Oyama, R. and Ravasi, T. and Lenhard, B. and Wells, C. and Kodzius, R. and Shimokawa, K. and Bajic, V. B. and Brenner, S. E. and Batalov, S. and Forrest, A. R. R. and Zavolan, M. and Davis, M. J. and Wilming, L. G. and Aidinis, V. and Allen, J. E. and Ambesi-Impiombato, A. and Apweiler, R. and Aturaliya, R. N. and Bailey, T. L. and Bansal, M. and Baxter, L. and Beisel, K. W. and Bersano, T. and Bono, H. and Chalk, A. M. and Chiu, K. P. and Choudhary, V. and Christoffels, A. and Clutterbuck, D. R. and Crowe, M. L. and Dalla, E. and Dalrymple, B. P. and de Bono, B. and Della Gatta, G. and di Bernardo, D. and Down, T. and Engstrom, P. and Fagiolini, M. and Faulkner, G. and Fletcher, C. F. and Fukushima, T. and Furuno, M. and Futaki, S. and Gariboldi, M. and Georgii-Hemming, P. and Gingeras, T. R. and Gojobori, T. and Green, R. E. and Gustincich, S. and Harbers, M. and Hayashi, Y. and Hensch, T. K. and Hirokawa, N. and Hill, D. and Huminiecki, L. and Iacono, M. and Ikeo, K. and Iwama, A. and Ishikawa, T. and Jakt, M. and Kanapin, A. and Katoh, M. and Kawasawa, Y. and Kelso, J. and Kitamura, H. and Kitano, H. and Kollias, G. and Krishnan, S. P. T. and Kruger, A. and Kummerfeld, S. K. and Kurochkin, I. V. and Lareau, L. F. and Lazarevic, D. and Lipovich, L. and Liu, J. and Liuni, S. and McWilliam, S. and Madan Babu, M. and Madera, M. and Marchionni, L. and Matsuda, H. and Matsuzawa, S. and Miki, H. and Mignone, F. and Miyake, S. and Morris, K. and Mottagui-Tabar, S. and Mulder, N. and Nakano, N. and Nakauchi, H. and Ng, P. and Nilsson, R. and Nishiguchi, S. and Nishikawa, S. and Nori, F. and Ohara, O. and Okazaki, Y. and Orlando, V. and Pang, K. C. and Pavan, W. J. and Pavesi, G. and Pesole, G. and Petrovsky, N. and Piazza, S. and Reed, J. and Reid, J. F. and Ring, B. Z. and Ringwald, M. and Rost, B. and Ruan, Y. and Salzberg, S. L. and Sandelin, A. and Schneider, C. and Schonbach, C. and Sekiguchi, K. and Semple, C. A. M. and Seno, S. and Sessa, L. and Sheng, Y. and Shibata, Y. and Shimada, H. and Shimada, K. and Silva, D. and Sinclair, B. and Sperling, S. and Stupka, E. and Sugiura, K. and Sultana, R. and Takenaka, Y. and Taki, K. and Tammoja, K. and Tan, S. L. and Tang, S. and Taylor, M. S. and Tegner, J. and Teichmann, S. A. and Ueda, H. R. and van Nimwegen, E. and Verardo, R. and Wei, C. L. and Yagi, K. and Yamanishi, H. and Zabarovsky, E. and Zhu, S. and Zimmer, A. and Hide, W. and Bult, C. and Grimmond, S. M. and Teasdale, R. D. and Liu, E. T. and Brusic, V. and Quackenbush, J. and Wahlestedt, C. and Mattick, J. S. and Hume, D. A. and Kai, C. and Sasaki, D. and Tomaru, Y. and Fukuda, S. and Kanamori-Katayama, M. and Suzuki, M. and Aoki, J. and Arakawa, T. and Iida, J. and Imamura, K. and Itoh, M. and Kato, T. and Kawaji, H. and Kawagashira, N. and Kawashima, T. and Kojima, M. and Kondo, S. and Konno, H. and Nakano, K. and Ninomiya, N. and Nishio, T. and Okada, M. and Plessy, C. and Shibata, K. and Shiraki, T. and Suzuki, S. and Tagami, M. and Waki, K. and Watahiki, A. and Okamura-Oho, Y. and Suzuki, H. and Kawai, J. and Hayashizaki, Y.. (2005) The transcriptional landscape of the mammalian genome. Science, Vol. 309, no. 5740. pp. 1559-1563.

Chen, P. Y. and Manninga, H. and Slanchev, K. and Chien, M. and Russo, J. J. and Ju, J. and Sheridan, R. and John, B. and Marks, D. S. and Gaidatzis, D. and Sander, C. and Zavolan, M. and Tuschl, T.. (2005) The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes & development, Vol. 19, H. 11. pp. 1288-1293.

Gomes, A. R. and Vinga, S. and 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, Vol. 49, H. 1. pp. 366-379.

Pfeffer, S. and Sewer, A. and Lagos-Quintana, M. and Sheridan, R. and Sander, C. and Grasser, F. A. and van Dyk, L. F. and Ho, C. K. and Shuman, S. and Chien, M. and Russo, J. J. and Ju, J. and Randall, G. and Lindenbach, B. D. and Rice, C. M. and Simon, V. and Ho, D. D. and Zavolan, M. and Tuschl, T.. (2005) Identification of microRNAs of the herpesvirus family. Nature Methods, Vol. 2, no. 4. pp. 269-276.

Sewer, A. and Paul, N. and Landgraf, P. and Aravin, A. and Pfeffer, S. and Brownstein, M. J. and Tuschl, T. and van Nimwegen, E. and Zavolan, M.. (2005) Identification of clustered microRNAs using an ab initio prediction method. BMC bioinformatics, Vol. 6, , 267.

Speirs, C. and van Nimwegen, E. and Bolton, D. and Zavolan, M. and Duvall, M. and Angleman, S. and Siegel, R. and 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, Vol. 79, H. 7. pp. 4025-4032.

Pfeffer, S. and Zavolan, M. and Grasser, F. A. and Chien, M. and Russo, J. J. and Ju, J. and John, B. and Enright, A. J. and Marks, D. and Sander, C. and Tuschl, T.. (2004) Identification of virus-encoded microRNAs. Science, Vol. 304, no. 5671. pp. 734-736.

Aravin, A. A. and Lagos-Quintana, M. and Yalcin, A. and Zavolan, M. and Marks, D. and Snyder, B. and Gaasterland, T. and Meyer, J. and Tuschl, T.. (2003) The small RNA profile during Drosophila melanogaster development. Developmental cell, Vol. 5, H. 2. pp. 337-350.

Ravasi, T. and Huber, T. and Zavolan, M. and Forrest, A. and Gaasterland, T. and Grimmond, S. and Hume, D. A.. (2003) Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. Genome research, Vol. 13, H. 6b. pp. 1430-1442.

Yang, E. and van Nimwegen, E. and Zavolan, M. and Rajewsky, N. and Schroeder, M. and Magnasco, M. and Darnell, J. E. J.. (2003) Decay rates of human mRNAs : correlation with functional characteristics and sequence attributes. Genome research, Vol. 13, H. 8. pp. 1863-1872.

Zavolan, M. and Kondo, S. and Schonbach, C. and Adachi, J. and Hume, D. A. and 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, Vol. 13, H. 6b. pp. 1290-1300.

Zavolan, Mihaela and Socci, Nicholas D. and Rajewsky, Nikolaus and Gaasterlamd, Terry. (2003) SMASHing regulatory sites in DNA by human-mouse sequence comparisons. Proceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference, Vol. 2. pp. 277-286.

Okazaki, Y. and Furuno, M. and Kasukawa, T. and Adachi, J. and Bono, H. and Kondo, S. and Nikaido, I. and Osato, N. and Saito, R. and Suzuki, H. and Yamanaka, I. and Kiyosawa, H. and Yagi, K. and Tomaru, Y. and Hasegawa, Y. and Nogami, A. and Schonbach, C. and Gojobori, T. and Baldarelli, R. and Hill, D. P. and Bult, C. and Hume, D. A. and Quackenbush, J. and Schriml, L. M. and Kanapin, A. and Matsuda, H. and Batalov, S. and Beisel, K. W. and Blake, J. A. and Bradt, D. and Brusic, V. and Chothia, C. and Corbani, L. E. and Cousins, S. and Dalla, E. and Dragani, T. A. and Fletcher, C. F. and Forrest, A. and Frazer, K. S. and Gaasterland, T. and Gariboldi, M. and Gissi, C. and Godzik, A. and Gough, J. and Grimmond, S. and Gustincich, S. and Hirokawa, N. and Jackson, I. J. and Jarvis, E. D. and Kanai, A. and Kawaji, H. and Kawasawa, Y. and Kedzierski, R. M. and King, B. L. and Konagaya, A. and Kurochkin, I. V. and Lee, Y. and Lenhard, B. and Lyons, P. A. and Maglott, D. R. and Maltais, L. and Marchionni, L. and McKenzie, L. and Miki, H. and Nagashima, T. and Numata, K. and Okido, T. and Pavan, W. J. and Pertea, G. and Pesole, G. and Petrovsky, N. and Pillai, R. and Pontius, J. U. and Qi, D. and Ramachandran, S. and Ravasi, T. and Reed, J. C. and Reed, D. J. and Reid, J. and Ring, B. Z. and Ringwald, M. and Sandelin, A. and Schneider, C. and Semple, C. A. M. and Setou, M. and Shimada, K. and Sultana, R. and Takenaka, Y. and Taylor, M. S. and Teasdale, R. D. and Tomita, M. and Verardo, R. and Wagner, L. and Wahlestedt, C. and Wang, Y. and Watanabe, Y. and Wells, C. and Wilming, L. G. and Wynshaw-Boris, A. and Yanagisawa, M. and Yang, I. and Yang, L. and Yuan, Z. and Zavolan, M. and Zhu, Y. and Zimmer, A. and Carninci, P. and Hayatsu, N. and Hirozane-Kishikawa, T. and Konno, H. and Nakamura, M. and Sakazume, N. and Sato, K. and Shiraki, T. and Waki, K. and Kawai, J. and Aizawa, K. and Arakawa, T. and Fukuda, S. and Hara, A. and Hashizume, W. and Imotani, K. and Ishii, Y. and Itoh, M. and Kagawa, I. and Miyazaki, A. and Sakai, K. and Sasaki, D. and Shibata, K. and Shinagawa, A. and Yasunishi, A. and Yoshino, M. and Waterston, R. and Lander, E. S. and Rogers, J. and Birney, E. and Hayashizaki, Y.. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, Vol. 420 No. 6915. pp. 563-573.

Zavolan, M. and van Nimwegen, E. and Gaasterland, T.. (2002) Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. Genome research, Vol. 12, H. 9. pp. 1377-1385.

van Nimwegen, E. and Zavolan, M. and 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, Vol. 99, No. 11. pp. 7323-7328.

De Boer, Rob J. and Oprea, Mihaela and Antia, Rustom and Murali-Krishna, Kaja and Ahmed, Rafi and Perelson, Alan S.. (2001) Recruitment times, proliferation, and apoptosis rates during the CD8(+) T-cell response to lymphocytic choriomeningitis virus. Journal of virology, 75 (22). pp. 10663-10669.

Gaasterland, Terry and Oprea, Mihaela. (2001) Whole-genome analysis: annotations and updates. Current Opinion in Structural Biology, 11 (3). pp. 377-381.

Kepler, Thomas B. and Oprea, Mihaela. (2001) Improved inference of mutation rates: I. An integral representation for the Luria-Delbrück distribution. Theoretical population biology, 59 (1). pp. 41-48.

Oprea, Mihaela and Cowell, Lindsay G. and Kepler, Thomas B.. (2001) The targeting of somatic hypermutation closely resembles that of meiotic mutation. Journal of Immunology, 166 (2). pp. 892-899.

Oprea, Mihaela and Kepler, Thomas B.. (2001) Improved inference of mutation rates: II. Generalization of the Luria-Delbrück distribution for realistic cell-cycle time distributions. Theoretical population biology, 59 (1). pp. 49-59.

Zavolan, M. and Kepler, T. B.. (2001) Statistical inference of sequence-dependent mutation rates. Current opinion in genetics & development, Vol. 11, H. 6. pp. 612-615.

Oprea, Mihaela and van Nimwegen, Erik and Perelson, Alan S.. (2000) Dynamics of one-pass germinal center models: implications for affinity maturation. Bulletin of Mathematical Biology, 62 (1). pp. 121-153.

Oprea, Mihaela and Kepler, Thomas B.. (1999) Genetic plasticity of V genes under somatic hypermutation: statistical analyses using a new resampling-based methodology. Genome Research, 9 (12). pp. 1294-1304.

Oprea, Mihaela and Perelson, A. S.. (1997) Somatic mutation leads to efficient affinity maturation when centrocytes recycle back to centroblasts. Journal of Immunology, 158 (11). pp. 5155-5162.

Oprea, M. and Perelson, A. S.. (1996) Exploring the mechanisms of primary antibody responses to T cell-dependent antigens. Journal of Theoretical Biology, 181 (3). pp. 215-236.

Weisbuch, Gérard and Oprea, Mihaela. (1994) Capacity of a model immune network. Bulletin of Mathematical Biology, 56 (5). pp. 899-921.

No

Rausch, Magdalene. Differential roles of the microRNA let-7 in C. elegans tissue development. 2015, Doctoral Thesis, University of Basel, Faculty of Science.

Richter, Hannes. Functional and structural analysis of the C. elegans PAXT-1-XRN2 complex. 2015, Doctoral Thesis, University of Basel, Faculty of Science.

Bilen, Biter. Development of methods for the analysis of deep sequencing data; applications to the discovery of functions of RNA-binding proteins. 2014, Doctoral Thesis, University of Basel, Faculty of Science.

Jorjani, Hadi. Computational analysis of next generation sequencing data : from transcription start sites in bacteria to human non-coding RNAS. 2014, Doctoral Thesis, University of Basel, Faculty of Science.

Mathys, Hansruedi. The role of GW182 proteins in microRNA-mediated gene silencing. 2013, Doctoral Thesis, University of Basel, Faculty of Science.

Mohsen, Khorshid. Characterization of post-transcriptional regulatory network of RNA-binding proteins using computational predictions and deep sequencing data. 2013, Doctoral Thesis, University of Basel, Faculty of Science.

Hurschler, Benjamin. The type II poly(A)-binding protein PABP-2 is a downstream target of the "let-7" microRNA in the heterochronic pathway of "Caenorhabditis elegans" : mechanisms of microRNA-mediated gene silencing in "Caenorhabditis elegans". 2012, Doctoral Thesis, University of Basel, Faculty of Science.

Berninger, Philipp Friedrich. Computational methods for analyzing small RNAs and their interaction partners with large-scale techniques. 2011, Doctoral Thesis, University of Basel, Faculty of Science.

Hausser, Jean Albert René. Regulation of gene expression by micrornas : targeting specificity, kinetics and function. 2011, Doctoral Thesis, University of Basel, Faculty of Science.

Chern, Tzu-Ming. A trio of unique alternative splicing patterns : the splicing of tandem NAGNAG acceptors, transcription-start-site-dependent and mutually dependent cassette exons. 2008, Doctoral Thesis, University of Basel, Faculty of Science.

Gaidatzis, Dimosthenis. Computational discovery of animal small RNA genes and targets. 2007, Doctoral Thesis, University of Basel, Faculty of Science.