Items where Author is "Zavolan, Mihaela"

2023

Burri, Dominik and Zavolan, Mihaela. (2023) Corrigendum: Shortening of 3' UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism. RNA, 29 (6). p. 863.

Moon, Youngbin and Burri, Dominik and Zavolan, Mihaela. (2023) Identification of experimentally-supported poly(A) sites in single-cell RNA-seq data with SCINPAS. NAR genomics and bioinformatics, 5 (3). lqad079.

de Smalen, Laura M. and Börsch, Anastasiya and Leuchtmann, Aurel B. and Gill, Jonathan F. and Ritz, Danilo and Zavolan, Mihaela and Handschin, Christoph. (2023) Impaired age-associated mitochondrial translation is mitigated by exercise and PGC-1α. Proceedings of the National Academy of Sciences (PNAS), 120 (36). e2302360120.

Katsantoni, Maria and van Nimwegen, Erik and Zavolan, Mihaela. (2023) Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs. Genome Biology, 24 (77). pp. 1-25.

Bohmann, Dirk and O'Connell, Mary and Frendewey, David and Gerber, André and Hernandez, Nouria and Krämer, Angela and Minvielle-Sebastia, Lionel and Shaw, Peter and Wahle, Elmar and Zavolan, Mihaela. (2023) Walter Keller (1938-2023): a tribute from his mentees. RNA, 29 (9). v-xiii.

2022

Breda, Jeremie and Banerjee, Arka and Jayachandran, Rajesh and Pieters, Jean and Zavolan, Mihaela. (2022) A novel approach to single-cell analysis reveals intrinsic differences in immune marker expression in unstimulated BALB/c and C57BL/6 macrophages. FEBS Letters, 596 (20). pp. 2630-2643.

Ghosh, Souvik and Ataman, Meric and Bak, Maciej and Börsch, Anastasiya and Schmidt, Alexander and Buczak, Katarzyna and Martin, Georges and Dimitriades, Beatrice and Herrmann, Christina J. and Kanitz, Alexander and Zavolan, Mihaela. (2022) CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis. Nucleic Acids Research, 50 (6). pp. 3096-3114.

Pignatti, Emanuele and Altinkilic, Emre Murat and Bräutigam, Konstantin and Grössl, Michael and Perren, Aurel and Zavolan, Mihaela and Flück, Christa E.. (2022) Cholesterol deprivation drives DHEA biosynthesis in human adrenals. Endocrinology, 163 (7). bqac076.

Ham, Daniel J. and Börsch, Anastasiya and Chojnowska, Kathrin and Lin, Shuo and Leuchtmann, Aurel B. and Ham, Alexander S. and Thürkauf, Marco and Delezie, Julien and Furrer, Regula and Burri, Dominik and Sinnreich, Michael and Handschin, Christoph and Tintignac, Lionel A. and Zavolan, Mihaela and Mittal, Nitish and Rüegg, Markus A.. (2022) Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle. Nature Communications, 13. p. 2025.

Kaiser, Marco S. and Milan, Giulia and Ham, Daniel J. and Lin, Shuo and Oliveri, Filippo and Chojnowska, Kathrin and Tintignac, Lionel A. and Mittal, Nitish and Zimmerli, Christian E. and Glass, David J. and Zavolan, Mihaela and Rüegg, Markus A.. (2022) Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis. Communications biology, 5 (1). p. 1141.

Streese, Lukas and Demougin, Philippe and Iborra, Paula and Kanitz, Alexander and Deiseroth, Arne and Kröpfl, Julia M. and Schmidt-Trucksäss, Arno and Zavolan, Mihaela and Hanssen, Henner. (2022) Untargeted sequencing of circulating microRNAs in a healthy and diseased older population. Scientific Reports, 12 (1). p. 2991.

30 May 2021

Ham, Daniel J. and Börsch, Anastasyia and Chojnowska, Kathrin and Lin, Shuo and Leuchtmann, Aurel B. and Ham, Alexander S. and Thürkauf, Marco and Delezie, Julien and Furrer, Regula and Burri, Dominik and Sinnreich, Michael and Handschin, Christoph and Tintignac, Lionel A. and Zavolan, Mihaela and Mittal, Nitish and Rüegg, Markus A.. (2021) Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle.

2021

Breda, Jérémie and Zavolan, Mihaela and van Nimwegen, Erik. (2021) Bayesian inference of gene expression states from single-cell RNA-seq data. Nature Biotechnology, 39 (8). pp. 1008-1016.

Kaiser, Marco S. and Milan, Giulia and Lin, Shuo and Oliveri, Filippo and Chojnowska, Kathrin and Tintignac, Lionel A. and Mittal, Nitish and Zimmerli, Christian E. and Glass, David J. and Zavolan, Mihaela and Ham, Daniel J. and Rüegg, Markus A.. (2021) Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis. bioRxiv. pp. 1-39.

Börsch, Anastasiya and Ham, Daniel J. and Mittal, Nitish and Tintignac, Lionel A. and Migliavacca, Eugenia and Feige, Jérôme N. and Rüegg, Markus A. and Zavolan, Mihaela. (2021) Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia. Communications Biology, 4 (1). p. 194.

Karousis, Evangelos D. and Gypas, Foivos and Zavolan, Mihaela and Mühlemann, Oliver. (2021) Nanopore sequencing reveals endogenous NMD-targeted isoforms in human cells. Genome Biology, 22 (1). p. 223.

Burri, Dominik and Zavolan, Mihaela. (2021) Shortening of 3p UTRs in most cell types composing tumor tissues implicates alternative polyadenylation in protein metabolism. RNA (New York, N.Y.), 27 (12). pp. 1459-1470.

Cléry, Antoine and Krepl, Miroslav and Nguyen, Cristina K. X. and Moursy, Ahmed and Jorjani, Hadi and Katsantoni, Maria and Okoniewski, Michal and Mittal, Nitish and Zavolan, Mihaela and Sponer, Jiri and Allain, Frédéric H.-T.. (2021) Structure of SRSF1 RRM1 bound to RNA reveals an unexpected bimodal mode of interaction and explains its involvement in SMN1 exon7 splicing. Nature Communications, 12 (1). p. 428.

Ghosh, Souvik and Börsch, Anastasiya and Ghosh, Shreemoyee and Zavolan, Mihaela. (2021) The transcriptional landscape of a hepatoma cell line grown on scaffolds of extracellular matrix proteins. BMC Genomics, 22 (1). p. 238.

Börsch, Anastasiya and Zavolan, Mihaela. (2021) Transcription factor motif activity as a biomarker of muscle aging. American journal of aging science and research, 2 (1). pp. 19-23.

Coto-Llerena, Mairene and Tosti, Nadia and Taha-Mehlitz, Stephanie and Kancherla, Venkatesh and Paradiso, Viola and Gallon, John and Bianco, Gaia and Garofoli, Andrea and Ghosh, Souvik and Tang, Fengyuan and Ercan, Caner and Christofori, Gerhard M. and Matter, Matthias S. and Droeser, Raoul A. and Zavolan, Mihaela and Soysal, Savas D. and von Flüe, Markus and Kollmar, Otto and Terracciano, Luigi M. and Ng, Charlotte K. Y. and Piscuoglio, Salvatore. (2021) Transcriptional Enhancer Factor Domain Family member 4 Exerts an Oncogenic Role in Hepatocellular Carcinoma by Hippo-Independent Regulation of Heat Shock Protein 70 Family Members. Hepatology Communications, 5 (4). pp. 661-674.

2020

Guimaraes, Joao C. and Mittal, Nitish and Gnann, Alexandra and Jedlinski, Dominik and Riba, Andrea and Buczak, Katarzyna and Schmidt, Alexander and Zavolan, Mihaela. (2020) A rare codon-based translational program of cell proliferation. Genome Biology, 21 (1). p. 44.

Jutzi, Daniel and Campagne, Sébastien and Schmidt, Ralf and Reber, Stefan and Mechtersheimer, Jonas and Gypas, Foivos and Schweingruber, Christoph and Colombo, Martino and von Schroetter, Christine and Loughlin, Fionna E. and Devoy, Anny and Hedlund, Eva and Zavolan, Mihaela and Allain, Frédéric H.-T. and Ruepp, Marc-David. (2020) Aberrant interaction of FUS with the U1 snRNA provides a molecular mechanism of FUS induced amyotrophic lateral sclerosis. Nature Communications, 11 (1). p. 6341.

Ho-Xuan, Hung and Lehmann, Gerhard and Glazar, Petar and Gypas, Foivos and Eichner, Norbert and Heizler, Kevin and Schlitt, Hans Jürgen and Zavolan, Mihaela and Rajewsky, Nikolaus and Meister, Gunter and Hackl, Christina. (2020) Gene Expression Signatures of a Preclinical Mouse Model during Colorectal Cancer Progression under Low-Dose Metronomic Chemotherapy. Cancers, 13 (1). p. 49.

Liko, Dritan and Rzepiela, Andrzej and Vukojevic, Vanja and Zavolan, Mihaela and Hall, Michael N.. (2020) Loss of TSC complex enhances gluconeogenesis via upregulation of Dlk1-Dio3 locus miRNAs. Proceedings of the National Academy of Sciences, 117 (3). pp. 1524-1532.

Ghosh, Souvik and Guimaraes, Joao C. and Lanzafame, Manuela and Schmidt, Alexander and Syed, Afzal Pasha and Dimitriades, Beatrice and Börsch, Anastasiya and Ghosh, Shreemoyee and Mittal, Nitish and Montavon, Thomas and Correia, Ana Luisa and Danner, Johannes and Meister, Gunter and Terracciano, Luigi M. and Pfeffer, Sébastien and Piscuoglio, Salvatore and Zavolan, Mihaela. (2020) Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation. The EMBO Journal, 39 (18). e103922.

Gruber, Andreas J. and Zavolan, Mihaela. (2020) Reply to 'A different perspective on alternative cleavage and polyadenylation'. Nature reviews. Genetics, 21 (1). pp. 63-64.

Hasler, Daniele and Meduri, Rajyalakshmi and Bąk, Maciej and Lehmann, Gerhard and Heizinger, Leonhard and Wang, Xin and Li, Zhi-Tong and Sement, François M. and Bruckmann, Astrid and Dock-Bregeon, Anne-Catherine and Merkl, Rainer and Kalb, Reinhard and Grauer, Eva and Kunstmann, Erdmute and Zavolan, Mihaela and Liu, Mo-Fang and Fischer, Utz and Meister, Gunter. (2020) The Alazami Syndrome-Associated Protein LARP7 Guides U6 Small Nuclear RNA Modification and Contributes to Splicing Robustness. Molecular Cell, 77 (5). pp. 1014-1031.e13.

Ham, Daniel J. and Börsch, Anastasiya and Lin, Shuo and Thürkauf, Marco and Weihrauch, Martin and Reinhard, Judith R. and Delezie, Julien and Battilana, Fabienne and Wang, Xueyong and Kaiser, Marco S. and Guridi, Maitea and Sinnreich, Michael and Rich, Mark M. and Mittal, Nitish and Tintignac, Lionel A. and Handschin, Christoph and Zavolan, Mihaela and Rüegg, Markus A.. (2020) The neuromuscular junction is a focal point of mTORC1 signaling in sarcopenia. Nature Communications, 11 (1). p. 4510.

2019

Gruber, Andreas J. and Zavolan, Mihaela. (2019) Alternative cleavage and polyadenylation in health and disease. Nature reviews. Genetics, 20 (10). pp. 599-614.

Kanitz, Alexander and Syed, Afzal Pasha and Kaji, Keisuke and Zavolan, Mihaela. (2019) Conserved regulation of RNA processing in somatic cell reprogramming. BMC genomics, 20 (1). p. 100.

Păunescu, Virgil and Zavolan, Mihaela and Oprea, Tudor. (2019) In memoriam: Francisc Schneider (1933-2017). Journal of cellular and molecular medicine. pp. 3045-3046.

Sendoel, Ataman and Subasic, Deni and Ducoli, Luca and Keller, Martin and Michel, Erich and Kohler, Ines and Singh, Kapil Dev and Zheng, Xue and Brümmer, Anneke and Imig, Jochen and Kishore, Shivendra and Wu, Yibo and Kanitz, Alexander and Kaech, Andres and Mittal, Nitish and Matia-González, Ana M. and Gerber, André P. and Zavolan, Mihaela and Aebersold, Ruedi and Hall, Jonathan and Allain, Frédéric H.-T. and Hengartner, Michael O.. (2019) MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans. Cell Death & Differentiation subscription, 26 (10). pp. 2157-2178.

Herrmann, Christina J. and Schmidt, Ralf and Kanitz, Alexander and Artimo, Panu and Gruber, Andreas J. and Zavolan, Mihaela. (2019) PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3' end sequencing. Nucleic acids research, 48 (D1). D174-D179.

Riba, Andrea and Di Nanni, Noemi and Mittal, Nitish and Arhné, Erik and Schmidt, Alexander and Zavolan, Mihaela. (2019) Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates. Proceedings of the National Academy of Sciences, 116 (30). pp. 15023-15032.

2018

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

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

Zavolan, Mihaela and Kanitz, Alexander. (2018) RNA splicing and its connection with other regulatory layers in somatic cell reprogramming. Current Opinion in Cell Biology, 52. pp. 8-13.

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

Rzepiela, Andrzej J. and Ghosh, Souvik and Breda, Jeremie and Vina-Vilaseca, Arnau and Syed, Afzal P. and Gruber, Andreas J. and Eschbach, Katja and Beisel, Christian and van Nimwegen, Erik and 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. and Gypas, Foivos and Riba, Andrea and Schmidt, Ralf and Zavolan, Mihaela. (2018) Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms. Nature methods, 15 (10). pp. 832-836.

2017

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

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.

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.

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

Essig, Katharina and Hu, Desheng and Guimaraes, Joao C. and Alterauge, Dominik and Edelmann, Stephanie and Raj, Timsse and Kranich, Jan and Behrens, Gesine and Heiseke, Alexander and Floess, Stefan and Klein, Juliane and Maiser, Andreas and Marschall, Susan and Hrabĕ de Angelis, Martin and Leonhardt, Heinrich and Calkhoven, Cornelis F. and Noessner, Elfriede and Brocker, Thomas and Huehn, Jochen and Krug, Anne B. and Zavolan, Mihaela and Baumjohann, Dirk and 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). pp. 1067-1082.e12.

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 (457). pp. 1-12.

August 2016

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.

20 June 2016

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.

June 2016

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

March 2016

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.

2016

Breda, Jeremie and Rzepiela, Andrzej J. and Gumienny, Rafal and van Nimwegen, Erik and Zavolan, Mihaela. (2016) Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99]. Methods, 104. pp. 204-205.

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.

November 2015

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.

1 September 2015

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

2015

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.

Gumienny, Rafal and Zavolan, Mihaela. (2015) Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G. (erratum). Nucleic Acids Research, 43 (18). p. 9095.

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.

2014

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, 74 (1). pp. 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.

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 and van Nimwegen, Erik and Zavolan, Mihaela. (2014) Global 3' UTR shortening has a limited effect on protein abundance in proliferating T cells. Nature Communications, 5 (5465). pp. 1-10.

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.

2013

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.

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.

2012

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.

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.

2011

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.

2009

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.

2003

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.