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2018

Essig, Katharina; Kronbeck, Nina; Guimaraes, Joao C; Lohs, Claudia; Schlundt, Andreas; Hoffmann, Anne; Behrens, Gesine; Brenner, Sven; Kowalska, Joanna; Lopez-Rodriguez, Cristina; Jemielity, Jacek; Holtmann, Helmut; Reiche, Kristin; Hackermüller, Jörg; Sattler, Michael; Zavolan, Mihaela; Heissmeyer, Vigo (2018). Roquin targets mRNAs in a 3'-UTR-specific manner by different modes of regulation. Nature communications, 9 (1), 3810.

Gruber, Andreas J; Gypas, Foivos; Riba, Andrea; Schmidt, Ralf; Zavolan, Mihaela (2018). Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms. Nature methods, 15 (10), 832-836.

Zavolan, Mihaela; Gerber, André P (2018). Mirroring the multifaceted role of RNA and its partners in gene expression. FEBS letters, 592 (17), 2825-2827.

Rzepiela, Andrzej J; Ghosh, Souvik; Breda, Jeremie; Vina-Vilaseca, Arnau; Syed, Afzal P; Gruber, Andreas J; Eschbach, Katja; Beisel, Christian; van Nimwegen, Erik; Zavolan, Mihaela (2018). Single-cell mRNA profiling reveals the hierarchical response of miRNA targets to miRNA induction. Molecular systems biology, 14 (8), e8266.

Gruber, Andreas J; Schmidt, Ralf; Ghosh, Souvik; Martin, Georges; Gruber, Andreas R; van Nimwegen, Erik; Zavolan, Mihaela (2018). Discovery of physiological and cancer-related regulators of 3' UTR processing with KAPAC. Genome biology, 19 (1), 44.

2017

Zavolan, Mihaela; Kanitz, Alexander (2017). RNA splicing and its connection with other regulatory layers in somatic cell reprogramming. Current Opinion in Cell Biology, 52, 8-13.

Essig, Katharina; Hu, Desheng; Guimaraes, Joao C.; Alterauge, Dominik; Edelmann, Stephanie; Raj, Timsse; Kranich, Jan; Behrens, Gesine; Heiseke, Alexander; Floess, Stefan; Klein, Juliane; Maiser, Andreas; Marschall, Susan; Hrabĕ de Angelis, Martin; Leonhardt, Heinrich; Calkhoven, Cornelis F.; Noessner, Elfriede; Brocker, Thomas; Huehn, Jochen; Krug, Anne B.; Zavolan, Mihaela; Baumjohann, Dirk; Heissmeyer, Vigo (2017). Roquin Suppresses the PI3K-mTOR Signaling Pathway to Inhibit T Helper Cell Differentiation and Conversion of Treg to Tfr Cells. Immunity, 47 (6), 1067-1082.e12.

Zavolan, Mihaela; Graveley, Brenton R (2017). RNAs: dynamic and mutable. Genome biology, 18 (1), 226.

Martin, Georges; Schmidt, Ralf; Gruber, Andreas J.; Ghosh, Souvik; Keller, Walter; Zavolan, Mihaela (2017). 3' End Sequencing Library Preparation with A-seq2. Journal of Visualized Experiments (128), e56129.

Mittal, Nitish; Guimaraes, Joao C; Gross, Thomas; Schmidt, Alexander; Vina-Vilaseca, Arnau; Nedialkova, Danny D; Aeschimann, Florian; Leidel, Sebastian A; Spang, Anne; Zavolan, Mihaela (2017). The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan. Nature communications, 8 (1), 457.

Mittal, Nitish; Guimaraes, Joao C.; Gross, Thomas; Schmidt, Alexander; Vina-Vilaseca, Arnau; Nedialkova, Danny D.; Aeschimann, Florian; Leidel, Sebastian A.; Spang, Anne; Zavolan, Mihaela (2017). The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan. Nature Communications, 8, 1-12.

Omidi, Saeed; Zavolan, Mihaela; Pachkov, Mikhail; Breda, Jeremie; Berger, Severin; 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.

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

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

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

2016

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

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

Gruber, Andreas J.; Schmidt, Ralf; Gruber, Andreas R.; Martin, Georges; Ghosh, Souvik; Belmadani, Manuel; Keller, Walter; 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), 1145-1159.

Martin, Georges; Zavolan, Mihaela (2016). Redesigning CLIP for efficiency, accuracy and speed. Nature Methods, 13 (6), 482-3.

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

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

Swiss Institute of Bioinformatics Members, SIB (2016). The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic acids research, 44 (D1), D27-D37.

2015

Subasic, Deni; Brümmer, Anneke; Wu, Yibo; Pinto, Sérgio Morgado; Imig, Jochen; Keller, Martin; Jovanovic, Marko; Lightfoot, Helen Louise; Nasso, Sara; Goetze, Sandra; Brunner, Erich; Hall, Jonathan; Aebersold, Ruedi; Zavolan, Mihaela; Hengartner, Michael O (2015). Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family in C. elegans. Genome research, 25 (11), 1680-91.

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

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

Tattikota, Sudhir G; Rathjen, Thomas; Hausser, Jean; Khedkar, Aditya; Kabra, Uma D; Pandey, Varun; Sury, Matthias; Wessels, Hans-Hermann; Mollet, Inês G; Eliasson, Lena; Selbach, Matthias; Zinzen, Robert P; Zavolan, Mihaela; Kadener, Sebastian; Tschöp, Matthias H; Jastroch, Martin; Friedländer, Marc R; Poy, Matthew N (2015). miR-184 Regulates Pancreatic β-Cell Function According to Glucose Metabolism. Journal of biological chemistry, 290 (33), 20284-94.

Breda, Jeremie; Rzepiela, Andrzej J; Gumienny, Rafal; van Nimwegen, Erik; Zavolan, Mihaela (2015). Quantifying the strength of miRNA-target interactions. Methods, 85, 90-9.

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

Gumienny, Rafal; Zavolan, Mihaela (2015). Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G. Nucleic Acids Research, 43 (3), 1380-91.

Imig, Jochen; Brunschweiger, Andreas; Brümmer, Anneke; Guennewig, Boris; Mittal, Nitish; Kishore, Shivendra; Tsikrika, Panagiota; Gerber, André P; Zavolan, Mihaela; Hall, Jonathan (2015). miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19-miR-106a interaction. Nature chemical biology, 11 (2), 107-14.

2014

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

Schönemann, Lars; Kühn, Uwe; Martin, Georges; Schäfer, Peter; Gruber, Andreas R; Keller, Walter; Zavolan, Mihaela; Wahle, Elmar (2014). Reconstitution of CPSF active in polyadenylation: recognition of the polyadenylation signal by WDR33. Genes & development, 28 (21), 2381-93.

Gruber, Andreas J.; Grandy, William A.; Balwierz, Piotr J.; Dimitrova, Yoana A.; Pachkov, Mikhail; Ciaudo, Constance; van Nimwegen, Erik; Zavolan, Mihaela (2014). Embryonic stem cell-specific microRNAs contribute to pluripotency by inhibiting regulators of multiple differentiation pathways. Nucleic Acids Research, 42 (14), 9313-26.

Hausser, Jean; Zavolan, Mihaela (2014). Identification and consequences of miRNA-target interactions - beyond repression of gene expression. Nature reviews. Genetics, 15 (9), 599-612.

Daubner, Gerrit M.; Brümmer, Anneke; Tocchini, Cristina; Gerhardy, Stefan; Ciosk, Rafal; Zavolan, Mihaela; Allain, Frédéric H.-T. (2014). Structural and functional implications of the QUA2 domain on RNA recognition by GLD-1. Nucleic Acids Research, 42 (12), 8092-105.

Stockinger, Heinz; Altenhoff, Adrian M.; Arnold, Konstantin; Bairoch, Amos; Bastian, Frederic; Bergmann, Sven; Bougueleret, Lydie; Bucher, Philipp; Delorenzi, Mauro; Lane, Lydie; Mercier, Philippe Le; Lisacek, Frédérique; Michielin, Olivier; Palagi, Patricia M.; Rougemont, Jacques; Schwede, Torsten; Mering, Christian von; Nimwegen, Erik van; Walther, Daniel; Xenarios, Ioannis; Zavolan, Mihaela; Zdobnov, Evgeny M.; Zoete, Vincent; Appel, Ron D. (2014). Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. Nucleic Acids Research, 42 (WebServerissue), W436-41.

Latreille, Mathieu; Hausser, Jean; Stützer, Ina; Zhang, Quan; Hastoy, Benoit; Gargani, Sofia; Kerr-Conte, Julie; Pattou, Francois; Zavolan, Mihaela; Esguerra, Jonathan L. S.; Eliasson, Lena; Rülicke, Thomas; Rorsman, Patrik; Stoffel, Markus (2014). MicroRNA-7a regulates pancreatic β cell function. Journal of Clinical Investigation, 124 (6), 2722-35.

Erhard, Florian; Haas, Jürgen; Lieber, Diana; Malterer, Georg; Jaskiewicz, Lukasz; Zavolan, Mihaela; Dölken, Lars; Zimmer, Ralf (2014). Widespread context-dependency of microRNA-mediated regulation. Genome research, 24 (6), 906-19.

Spitzer, Jessica; Hafner, Markus; Landthaler, Markus; Ascano, Manuel; Farazi, Thalia; Wardle, Greg; Nusbaum, Jeff; Khorshid, Mohsen; Burger, Lukas; Zavolan, Mihaela; 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, 539, 113-61.

Balwierz, Piotr J; Pachkov, Mikhail; Arnold, Phil; Gruber, Andreas J; Zavolan, Mihaela; van Nimwegen, Erik (2014). ISMARA: Automated modeling of genomic signals as a democracy of regulatory motifs. Genome research, 24 (5), 869-84.

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

Jorjani, Hadi; Zavolan, Mihaela (2014). TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data. Bioinformatics, 30 (7), 971-4.

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, 74,1, S. 224-234 (1), 224-234.

2013

Tattikota, Sudhir G; Rathjen, Thomas; McAnulty, Sarah J; Wessels, Hans-Hermann; Akerman, Ildem; van de Bunt, Martijn; Hausser, Jean; Esguerra, Jonathan L S; Musahl, Anne; Pandey, Amit K; You, Xintian; Chen, Wei; Herrera, Pedro L; Johnson, Paul R; O'Carroll, Donal; Eliasson, Lena; Zavolan, Mihaela; Gloyn, Anna L; Ferrer, Jorge; Shalom-Feuerstein, Ruby; Aberdam, Daniel; Poy, Matthew N (2013). Argonaute2 Mediates Compensatory Expansion of the Pancreatic β Cell. Cell metabolism, 19 (1), 122-34.

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

Gruber, Andreas J; Zavolan, Mihaela (2013). Modulation of epigenetic regulators and cell fate decisions by miRNAs. Epigenomics, 5 (6), 671-83.

Gruber, Andreas R.; Martin, Georges; Keller, Walter; Zavolan, Mihaela (2013). Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors. Wiley Interdisciplinary Reviews. RNA, 5 (2), 183-96.

Brümmer, Anneke; Kishore, Shivendra; Subasic, Deni; Hengartner, Michael; 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, 19 (10), 1317-26.

Zünd, David; Gruber, Andreas R; Zavolan, Mihaela; Mühlemann, Oliver (2013). Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3' UTRs. Nature structural & molecular biology, 20 (8), 936-43.

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

Khorshid, Mohsen; Hausser, Jean; Zavolan, Mihaela; van Nimwegen, Erik (2013). A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets. Nature methods, 10 (3), 253-5.

Hausser, Jean; Syed, Afzal Pasha; Bilen, Biter; Zavolan, Mihaela (2013). Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation. Genome research, 23 (4), 604-15.

2012

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

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

Jaskiewicz, Lukasz; Bilen, Biter; Hausser, Jean; Zavolan, Mihaela (2012). Argonaute CLIP - A method to identify in vivo targets of miRNAs. Methods, 58 (2), 106-12.

Martin, Georges; Gruber, Andreas R.; Keller, Walter; 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), 753-63.

Krützfeldt, Jan; Rösch, Nora; Hausser, Jean; Manoharan, Muthiah; Zavolan, Mihaela; Stoffel, Markus (2012). MicroRNA-194 is a target of transcription factor 1 (Tcf1, Hnf1α) in adult liver and controls expression of frizzled-6. Hepatology, 55 (1), 98-107.

2011

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

Rammelt, Christiane; Bilen, Biter; Zavolan, Mihaela; Keller, Walter (2011). PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif. RNA, 17 (9), 1737-46.

Trajkovski, Mirko; Hausser, Jean; Soutschek, Jürgen; Bhat, Bal; Akin, Akinc; Zavolan, Mihaela; Heim, Markus H; Stoffel, Markus (2011). MicroRNAs 103 and 107 regulate insulin sensitivity. Nature, 474 (7353), 649-53.

Kishore, Shivendra; Jaskiewicz, Lukasz; Burger, Lukas; Hausser, Jean; Khorshid, Mohsen; Zavolan, Mihaela (2011). A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nature Methods, 8 (7), 559-64.

Berninger, Philipp; Jaskiewicz, Lukasz; Khorshid, Mohsen; Zavolan, Mihaela (2011). Conserved generation of short products at piRNA loci. BMC Genomics, 12 (1), 46.

Khorshid, M.; Rodak, C.; Zavolan, M. (2011). CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Research, 39 (Databaseissue), D245-52.

Corioni, M.; Antih, N.; Tanackovic, G.; Zavolan, M.; 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), 1868-79.

2010

Kishore, Shivendra; Luber, Sandra; Zavolan, Mihaela (2010). Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression. Briefings in Functional Genomics, 9 (5-6), 391-404.

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, 11, 565.

Hafner, Markus; Landthaler, Markus; Burger, Lukas; Khorshid, Mohsen; Hausser, Jean; Berninger, Philipp; Rothballer, Andrea; Ascano, Manuel; Jungkamp, Anna-Carina; Munschauer, Mathias; Ulrich, Alexander; Wardle, Greg S; Dewell, Scott; Zavolan, Mihaela; Tuschl, Thomas (2010). PAR-CliP-a method to identify transcriptome-wide the binding sites of RNA binding proteins. Journal of visualized experiments, 41, 2034 (41), e2034.

Hafner, Markus; Landthaler, Markus; Burger, Lukas; Khorshid, Mohsen; Hausser, Jean; Berninger, Philipp; Rothballer, Andrea; Ascano, Manuel; Jungkamp, Anna-Carina; Munschauer, Mathias; Ulrich, Alexander; Wardle, Greg S; Dewell, Scott; Zavolan, Mihaela; Tuschl, Thomas (2010). Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell, 141 (1), 129-41.

Ma, Jun; Flemr, Matyas; Stein, Paula; Berninger, Philipp; Malik, Radek; Zavolan, Mihaela; Svoboda, Petr; Schultz, Richard M (2010). MicroRNA activity is suppressed in mouse oocytes. Current biology, 20 (3), 265-70.

Kishore, Shivendra; Khanna, Amit; Zhang, Zhaiyi; Hui, Jingyi; Balwierz, Piotr J; Stefan, Mihaela; Beach, Carol; Nicholls, Robert D; Zavolan, Mihaela; Stamm, Stefan (2010). The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Human molecular genetics, 19 (7), 1153-64.

2009

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, 19 (11), 2009-20.

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

Hausser, Jean; Berninger, Philipp; Rodak, Christoph; Jantscher, Yvonne; Wirth, Stefan; Zavolan, Mihaela (2009). MirZ: an integrated microRNA expression atlas and target prediction resource. Nucleic Acids Research, 37 (WebServerissue), W266-72.

Poy, Matthew N; Hausser, Jean; Trajkovski, Mirko; Braun, Matthias; Collins, Stephan; Rorsman, Patrik; Zavolan, Mihaela; Stoffel, Markus (2009). miR-375 maintains normal pancreatic alpha- and beta-cell mass. Proceedings of the National Academy of Sciences of the United States of America, 106 (14), 5813-8.

Pena, John T G; Sohn-Lee, Cherin; Rouhanifard, Sara H; Ludwig, Janos; Hafner, Markus; Mihailovic, Aleksandra; Lim, Cindy; Holoch, Daniel; Berninger, Philipp; Zavolan, Mihaela; Tuschl, Thomas (2009). miRNA in situ hybridization in formaldehyde and EDC-fixed tissues. Nature Methods, 6 (2), 139-41.

FANTOM Consortium,; Suzuki, Harukazu; Forrest, Alistair R R; van Nimwegen, Erik; Daub, Carsten O; Balwierz, Piotr J; Irvine, Katharine M; Lassmann, Timo; Ravasi, Timothy; Hasegawa, Yuki; de Hoon, Michiel J L; Katayama, Shintaro; Schroder, Kate; Carninci, Piero; Tomaru, Yasuhiro; Kanamori-Katayama, Mutsumi; Kubosaki, Atsutaka; Akalin, Altuna; Ando, Yoshinari; Arner, Erik; Asada, Maki; Asahara, Hiroshi; Bailey, Timothy; Bajic, Vladimir B; Bauer, Denis; Beckhouse, Anthony G; Bertin, Nicolas; Björkegren, Johan; Brombacher, Frank; Bulger, Erika; Chalk, Alistair M; Chiba, Joe; Cloonan, Nicole; Dawe, Adam; Dostie, Josee; Engström, Pär G; Essack, Magbubah; Faulkner, Geoffrey J; Fink, J Lynn; Fredman, David; Fujimori, Ko; Furuno, Masaaki; Gojobori, Takashi; Gough, Julian; Grimmond, Sean M; Gustafsson, Mika; Hashimoto, Megumi; Hashimoto, Takehiro; Hatakeyama, Mariko; Heinzel, Susanne; Hide, Winston; Hofmann, Oliver; Hörnquist, Michael; Huminiecki, Lukasz; Ikeo, Kazuho; Imamoto, Naoko; Inoue, Satoshi; Inoue, Yusuke; Ishihara, Ryoko; Iwayanagi, Takao; Jacobsen, Anders; Kaur, Mandeep; Kawaji, Hideya; Kerr, Markus C; Kimura, Ryuichiro; Kimura, Syuhei; Kimura, Yasumasa; Kitano, Hiroaki; Koga, Hisashi; Kojima, Toshio; Kondo, Shinji; Konno, Takeshi; Krogh, Anders; Kruger, Adele; Kumar, Ajit; Lenhard, Boris; Lennartsson, Andreas; Lindow, Morten; Lizio, Marina; Macpherson, Cameron; Maeda, Norihiro; Maher, Christopher A; Maqungo, Monique; Mar, Jessica; Matigian, Nicholas A; Matsuda, Hideo; Mattick, John S; Meier, Stuart; Miyamoto, Sei; Miyamoto-Sato, Etsuko; Nakabayashi, Kazuhiko; Nakachi, Yutaka; Nakano, Mika; Nygaard, Sanne; Okayama, Toshitsugu; Okazaki, Yasushi; Okuda-Yabukami, Haruka; Orlando, Valerio; Otomo, Jun; Pachkov, Mikhail;0 Petrovsky, Nikolai;1 Plessy, Charles;2 Quackenbush, John;3 Radovanovic, Aleksandar;4 Rehli, Michael;5 Saito, Rintaro;6 Sandelin, Albin;7 Schmeier, Sebastian;8 Schönbach, Christian;9 Schwartz, Ariel S;0 Semple, Colin A;1 Sera, Miho;2 Severin, Jessica;3 Shirahige, Katsuhiko;4 Simons, Cas;5 St Laurent, George;6 Suzuki, Masanori;7 Suzuki, Takahiro;8 Sweet, Matthew J;9 Taft, Ryan J;0 Takeda, Shizu;1 Takenaka, Yoichi;2 Tan, Kai;3 Taylor, Martin S;4 Teasdale, Rohan D;5 Tegnér, Jesper;6 Teichmann, Sarah;7 Valen, Eivind;8 Wahlestedt, Claes;9 Waki, Kazunori;0 Waterhouse, Andrew;1 Wells, Christine A;2 Winther, Ole;3 Wu, Linda;4 Yamaguchi, Kazumi;5 Yanagawa, Hiroshi;6 Yasuda, Jun;7 Zavolan, Mihaela;8 Hume, David A;9 Riken Omics Science Center,;0 Arakawa, Takahiro;1 Fukuda, Shiro;2 Imamura, Kengo;3 Kai, Chikatoshi;4 Kaiho, Ai;5 Kawashima, Tsugumi;6 Kawazu, Chika;7 Kitazume, Yayoi;8 Kojima, Miki;9 Miura, Hisashi;0 Murakami, Kayoko;1 Murata, Mitsuyoshi;2 Ninomiya, Noriko;3 Nishiyori, Hiromi;4 Noma, Shohei;5 Ogawa, Chihiro;6 Sano, Takuma;7 Simon, Christophe;8 Tagami, Michihira;9 Takahashi, Yukari;0 Kawai, Jun;1 Hayashizaki, Yoshihide;2 (2009). The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature genetics, 41 (5), 553-62.

2008

Sinkkonen, Lasse; Hugenschmidt, Tabea; Berninger, Philipp; Gaidatzis, Dimos; Mohn, Fabio; Artus-Revel, Caroline G; Zavolan, Mihaela; Svoboda, Petr; Filipowicz, Witold (2008). MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nature structural & molecular biology, 15 (3), 259-67.

Landthaler, Markus; Gaidatzis, Dimos; Rothballer, Andrea; Chen, Po Yu; Soll, Steven Joseph; Dinic, Lana; Ojo, Tolulope; Hafner, Markus; Zavolan, Mihaela; Tuschl, Thomas (2008). Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA, 14 (12), 2580-96.

Galgano, A.; Forrer, M.; Jaskiewicz, L.; Kanitz, A.; Zavolan, M.; Gerber, A. P. (2008). Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PLoS ONE, 3 (9), e3164.

Connolly, Erin; Melegari, Margherita; Landgraf, Pablo; Tchaikovskaya, Tatyana; Tennant, Bud C; Slagle, Betty L; Rogler, Leslie E; Zavolan, Mihaela; Tuschl, Thomas; Rogler, Charles 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, 173 (3), 856-64.

Chen, Po Yu; Weinmann, Lasse; Gaidatzis, Dimos; Pei, Yi; Zavolan, Mihaela; Tuschl, Thomas; Meister, Gunter (2008). Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity. RNA, 14 (2), 263-74.

Berninger, Philipp; Gaidatzis, Dimos; van Nimwegen, Erik; Zavolan, Mihaela (2008). Computational analysis of small RNA cloning data. Methods, 44 (1), 13-21.

Chern, Tzu-Ming; Paul, Nicodeme; van Nimwegen, Erik; Zavolan, Mihaela (2008). Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs. DNA research, 15 (2), 63-72.

2007

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.; Tuschl, T. (2007). A mammalian microRNA expression atlas based on small RNA library sequencing. Cell, 129 (7), 1401-1414.

Peyer, Anne-Kathrin; Jung, Diana; Beer, Markus; Gnerre, Carmela; Keogh, Adrian; Stroka, Deborah; Zavolan, Mihaela; Meyer, Urs-A (2007). Regulation of human liver delta-aminolevulinic acid synthase by bile acids. Hepatology, 46 (6), 1960-70.

Yao, Yongxiu; Zhao, Yuguang; Xu, Hongtao; Smith, Lorraine P; Lawrie, Charles H; Sewer, Alain; Zavolan, Mihaela; Nair, Venugopal (2007). Marek's disease virus type 2 (MDV-2) encoded microRNAs show no sequence conservation with those encoded by MDV-1. Journal of virology, 81 (13), 7164-70.

Randall, Glenn; Panis, Maryline; Cooper, Jacob D; Tellinghuisen, Timothy L; Sukhodolets, Karen E; Pfeffer, Sebastien; Landthaler, Markus; Landgraf, Pablo; Kan, Sherry; Lindenbach, Brett D; Chien, Minchen; Weir, David B; Russo, James J; Ju, Jingyue; Brownstein, Michael J; Sheridan, Robert; Sander, Chris; Zavolan, Mihaela; Tuschl, Thomas; Rice, Charles M (2007). Cellular cofactors affecting hepatitis C virus infection and replication. Proceedings of the National Academy of Sciences of the United States of America, 104 (31), 12884-9.

Fulci, Valerio; Chiaretti, Sabina; Goldoni, Marina; Azzalin, Gianluca; Carucci, Nicoletta; Tavolaro, Simona; Castellano, Leandro; Magrelli, Armando; Citarella, Franca; Messina, Monica; Maggio, Roberta; Peragine, Nadia; Santangelo, Simona; Mauro, Francesca Romana; Landgraf, Pablo; Tuschl, Thomas; Weir, David B; Chien, Minchen; Russo, James J; Ju, Jingyue; Sheridan, Robert; Sander, Chris; Zavolan, Mihaela; Guarini, Anna; Fo (2007). Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia. Blood, 109 (11), 4944-51.

Gaidatzis, Dimos; van Nimwegen, Erik; Hausser, Jean; Zavolan, Mihaela (2007). Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC bioinformatics, 8, 69.

2006

Sood, Pranidhi; Krek, Azra; Zavolan, Mihaela; Macino, Giuseppe; Rajewsky, Nikolaus (2006). Cell-type-specific signatures of microRNAs on target mRNA expression. Proceedings of the National Academy of Sciences of the United States of America, 103 (8), 2746-51.

Schmitter, D.; Filkowski, J.; Sewer, A.; Pillai, R. S.; Oakeley, E. J.; Zavolan, M.; Svoboda, P.; Filipowicz, W. (2006). Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells. Nucleic Acids Research, 34 (17), 4801-15.

Nair, Venugopal; Zavolan, Mihaela (2006). Virus-encoded microRNAs: novel regulators of gene expression. Trends in microbiology, 14 (4), 169-75.

Aravin, Alexei; Gaidatzis, Dimos; Pfeffer, Sébastien; Lagos-Quintana, Mariana; Landgraf, Pablo; Iovino, Nicola; Morris, Patricia; Brownstein, Michael J; Kuramochi-Miyagawa, Satomi; Nakano, Toru; Chien, Minchen; Russo, James J; Ju, Jingyue; Sheridan, Robert; Sander, Chris; Zavolan, Mihaela; Tuschl, Thomas (2006). A novel class of small RNAs bind to MILI protein in mouse testes. Nature, 442 (7099), 203-7.

van Nimwegen, Erik; Paul, Nicodeme; Sheridan, Robert; Zavolan, Mihaela (2006). SPA: a probabilistic algorithm for spliced alignment. PLoS genetics, 2 (4), e24.

Chern, Tzu-Ming; van Nimwegen, Erik; Kai, Chikatoshi; Kawai, Jun; Carninci, Piero; Hayashizaki, Yoshihide; Zavolan, Mihaela (2006). A simple physical model predicts small exon length variations. PLoS genetics, 2 (4), e45.

Zavolan, Mihaela; van Nimwegen, Erik (2006). The types and prevalence of alternative splice forms. Current opinion in structural biology, 16 (3), 362-7.

2005

Pfeffer, Sébastien; Sewer, Alain; Lagos-Quintana, Mariana; Sheridan, Robert; Sander, Chris; Grässer, Friedrich A; van Dyk, Linda F; Ho, C Kiong; Shuman, Stewart; Chien, Minchen; Russo, James J; Ju, Jingyue; Randall, Glenn; Lindenbach, Brett D; Rice, Charles M; Simon, Viviana; Ho, David D; Zavolan, Mihaela; Tuschl, Thomas (2005). Identification of microRNAs of the herpesvirus family. Nature Methods, 2 (4), 269-76.

Gomes, A R; Vinga, S; Zavolan, M; 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, 49 (1), 366-79.

Chen, Po Yu; Manninga, Heiko; Slanchev, Krasimir; Chien, Minchen; Russo, James J; Ju, Jingyue; Sheridan, Robert; John, Bino; Marks, Debora S; Gaidatzis, Dimos; Sander, Chris; Zavolan, Mihaela; Tuschl, Thomas (2005). The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes & development, 19 (11), 1288-93.

Sewer, Alain; Paul, Nicodème; Landgraf, Pablo; Aravin, Alexei; Pfeffer, Sébastien; Brownstein, Michael J; Tuschl, Thomas; van Nimwegen, Erik; Zavolan, Mihaela (2005). Identification of clustered microRNAs using an ab initio prediction method. BMC bioinformatics, 6, 267.

Speirs, Christina; van Nimwegen, Erik; Bolton, Diane; Zavolan, Mihaela; Duvall, Melody; Angleman, Sara; Siegel, Richard; Perelson, Alan S; Lenardo, Michael J (2005). Analysis of human immunodeficiency virus cytopathicity by using a new method for quantitating viral dynamics in cell culture. Journal of virology, 79 (7), 4025-32.

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;0 Nori, F;1 Ohara, O;2 Okazaki, Y;3 Orlando, V;4 Pang, K C;5 Pavan, W J;6 Pavesi, G;7 Pesole, G;8 Petrovsky, N;9 Piazza, S;0 Reed, J;1 Reid, J F;2 Ring, B Z;3 Ringwald, M;4 Rost, B;5 Ruan, Y;6 Salzberg, S L;7 Sandelin, A;8 Schneider, C;9 Schönbach, C;0 Sekiguchi, K;1 Semple, C A M;2 Seno, S;3 Sessa, L;4 Sheng, Y;5 Shibata, Y;6 Shimada, H;7 Shimada, K;8 Silva, D;9 Sinclair, B;0 Sperling, S;1 Stupka, E;2 Sugiura, K;3 Sultana, R;4 Takenaka, Y;5 Taki, K;6 Tammoja, K;7 Tan, S L;8 Tang, S;9 Taylor, M S;0 Tegner, J;1 Teichmann, S A;2 Ueda, H R;3 van Nimwegen, E;4 Verardo, R;5 Wei, C L;6 Yagi, K;7 Yamanishi, H;8 Zabarovsky, E;9 Zhu, S;0 Zimmer, A;1 Hide, W;2 Bult, C;3 Grimmond, S M;4 Teasdale, R D;5 Liu, E T;6 Brusic, V;7 Quackenbush, J;8 Wahlestedt, C;9 Mattick, J S;0 Hume, D A;1 Kai, C;2 Sasaki, D;3 Tomaru, Y;4 Fukuda, S;5 Kanamori-Katayama, M;6 Suzuki, M;7 Aoki, J;8 Arakawa, T;9 Iida, J;0 Imamura, K;1 Itoh, M;2 Kato, T;3 Kawaji, H;4 Kawagashira, N;5 Kawashima, T;6 Kojima, M;7 Kondo, S;8 Konno, H;9 Nakano, K;0 Ninomiya, N;1 Nishio, T;2 Okada, M;3 Plessy, C;4 Shibata, K;5 Shiraki, T;6 Suzuki, S;7 Tagami, M;8 Waki, K;9 Watahiki, A;0 Okamura-Oho, Y;1 Suzuki, H;2 Kawai, J;3 Hayashizaki, Y;4 FANTOM Consortium,;5 RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group),;6 (2005). The transcriptional landscape of the mammalian genome. Science, 309 (5740), 1559-63.

2004

Pfeffer, S; Zavolan, M; Grasser, FA; Chien, MC; Russo, JJ; Ju, JY; John, B; Enright, AJ; Marks, D; Sander, C; Tuschl, T (2004). Identification of virus-encoded microRNAs. Science, 304 (5671), 734-736.

2003

Zavolan, Mihaela; Socci, Nicholas D; Rajewsky, Nikolaus; Gaasterlamd, Terry (2003). SMASHing regulatory sites in DNA by human-mouse sequence comparisons. Proceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference, 2, 277-86.

Zavolan, Mihaela; Kondo, Shinji; Schonbach, Christian; Adachi, Jun; Hume, David A; Hayashizaki, Yoshihide; Gaasterland, Terry; RIKEN GER Group,; GSL Members, (2003). Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome research, 13 (6B), 1290-300.

Ravasi, Timothy; Huber, Thomas; Zavolan, Mihaela; Forrest, Alistair; Gaasterland, Terry; Grimmond, Sean; Hume, David A; RIKEN GER Group,; GSL Members, (2003). Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. Genome research, 13 (6B), 1430-42.

Aravin, Alexei A; Lagos-Quintana, Mariana; Yalcin, Abdullah; Zavolan, Mihaela; Marks, Debora; Snyder, Ben; Gaasterland, Terry; Meyer, Jutta; Tuschl, Thomas (2003). The small RNA profile during Drosophila melanogaster development. Developmental cell, 5 (2), 337-50.

Yang, Edward; van Nimwegen, Erik; Zavolan, Mihaela; Rajewsky, Nikolaus; Schroeder, Mark; Magnasco, Marcelo; Darnell, James E (2003). Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes. Genome research, 13 (8), 1863-72.

2002

Okazaki, Y; Furuno, M; Kasukawa, T; Adachi, J; Bono, H (2002). Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420 (6915), 563-73.

Zavolan, Mihaela; van Nimwegen, Erik; Gaasterland, Terry (2002). Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. Genome research, 12 (9), 1377-85.

van Nimwegen, Erik; Zavolan, Mihaela; Rajewsky, Nikolaus; Siggia, Eric 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, 99 (11), 7323-8.

2001

De Boer, Rob J.; Oprea, Mihaela; Antia, Rustom; Murali-Krishna, Kaja; Ahmed, Rafi; 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), 10663-9.

Gaasterland, Terry; Oprea, Mihaela (2001). Whole-genome analysis: annotations and updates. Current Opinion in Structural Biology, 11 (3), 377-81.

Kepler, Thomas B.; Oprea, Mihaela (2001). Improved inference of mutation rates: I. An integral representation for the Luria-Delbrück distribution. Theoretical population biology, 59 (1), 41-8.

Oprea, Mihaela; 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), 49-59.

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

Zavolan, M; Kepler, T B (2001). Statistical inference of sequence-dependent mutation rates. Current opinion in genetics & development, 11 (6), 612-5.

2000

Oprea, Mihaela; van Nimwegen, Erik; Perelson, Alan S. (2000). Dynamics of one-pass germinal center models: implications for affinity maturation. Bulletin of Mathematical Biology, 62 (1), 121-53.

1999

Oprea, Mihaela; Kepler, Thomas B. (1999). Genetic plasticity of V genes under somatic hypermutation: statistical analyses using a new resampling-based methodology. Genome Research, 9 (12), 1294-304.

1997

Oprea, Mihaela; Perelson, A. S. (1997). Somatic mutation leads to efficient affinity maturation when centrocytes recycle back to centroblasts. Journal of Immunology, 158 (11), 5155-62.

1996

Oprea, M.; Perelson, A. S. (1996). Exploring the mechanisms of primary antibody responses to T cell-dependent antigens. Journal of Theoretical Biology, 181 (3), 215-36.

1994

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


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