Items where Author is "Zavolan, Mihaela"
Jump to: 2017 | August 2016 | 20 June 2016 | June 2016 | March 2016 | 2016 | November 2015 | 1 September 2015 | 2015 | 2014 | 2013 | 2012 | 2011 | 2009 | 2003 Number of items: 50. 2017Omidi, 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. 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. 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. Mittal, Nitish and Guimaraes, Joao C. and Gross, Thomas and Schmidt, Alexander and Vina-Vilaseca, Arnau and Nedialkova, Danny D. and Aeschimann, Florian and Leidel, Sebastian A. and Spang, Anne and Zavolan, Mihaela. (2017) The Gcn4 transcription factor reduces protein synthesis capacity and extends yeast lifespan. Nature Communications, 8. pp. 1-12. August 2016Gruber, 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. 20 June 2016Jorjani, 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. June 2016Martin, Georges and Zavolan, Mihaela. (2016) Redesigning CLIP for efficiency, accuracy and speed. Nature Methods, 13 (6). pp. 482-483. March 2016Janowski, 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. 2016Guimaraes, 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. November 2015Subasic, 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. 1 September 2015Zavolan, Mihaela. (2015) Inferring gene expression regulatory networks from high-throughput measurements. Methods, 85. pp. 1-2. 2015Gumienny, 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. 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. Breda, Jeremie and Rzepiela, Andrzej J. and Gumienny, Rafal and van Nimwegen, Erik and Zavolan, Mihaela. (2015) Quantifying the strength of miRNA-target interactions. Methods, Vol. 85. pp. 90-99. Zavolan, Mihaela and Keller, Walter. (2015) Reflections on the RNA world. RNA, 21 (4). pp. 531-533. 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. 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. 2014Kishore, 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. 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. Stockinger, Heinz and Altenhoff, Adrian M. and Arnold, Konstantin and Bairoch, Amos and Bastian, Frederic and Bergmann, Sven and Bougueleret, Lydie and Bucher, Philipp and Delorenzi, Mauro and Lane, Lydie and Mercier, Philippe Le and Lisacek, Frédérique and Michielin, Olivier and Palagi, Patricia M. and Rougemont, Jacques and Schwede, Torsten and Mering, Christian von and Nimwegen, Erik van and Walther, Daniel and Xenarios, Ioannis and Zavolan, Mihaela and Zdobnov, Evgeny M. and Zoete, Vincent and Appel, Ron D.. (2014) Fifteen years SIB Swiss Institute of Bioinformatics : life science databases, tools and support. Nucleic Acids Research, 42 (W1). W436-W441. 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. 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. 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. 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. 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. Mittal, Nitish and Zavolan, Mihaela. (2014) Seq and CLIP through the miRNA world. Genome biology, Vol. 15, H. 1. p. 202. 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. 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. 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. 2013Khorshid, 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. 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. 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. 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. 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. 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. 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. 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. 2012Jaskiewicz, 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. 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 Zavolan, Mihaela. (2012) Dicer partners expand the repertoire of miRNA targets. Genome biology, Vol. 13, H. 11. p. 179. 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. 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. 2011Suffert, 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. 2009Hausser, 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. 2003Zavolan, 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. |
