Items where Division is "05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (Zavolan)"
Jump to: 2024 | 2023 | 2022 | 30 May 2021 | 2021 | 2020 | 2019 | 2018 | 2017 | August 2016 | 20 June 2016 | June 2016 | March 2016 | 2016 | November 2015 | 1 September 2015 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1997 | 1996 | 1994 Number of items at this level: 188. 2024Arnone, Marlon. Evaluation of phenotypic heterogeneity and the role of MRC2 in leukemic stem cells. 2024, Doctoral Thesis, University of Basel, Faculty of Science. Banerjee, Arka. Role of Rpl39l in translation, and consequences for pluripotency and cancer. 2024, Doctoral Thesis, University of Basel, Faculty of Science. 2023Bohmann, 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. Burri, Dominik. Computational methods to identify and characterize the functionality of polyadenylation isoforms. 2023, Doctoral Thesis, University of Basel, Faculty of Science. 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. Katsantoni, Maria. Computational models to infer regulators of gene expression for high-throughput data. 2023, Doctoral Thesis, University of Basel, Faculty of Science. 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. 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. 2022Breda, 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. 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. 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. Schmid, Svenia and Heim-Kupr, Barbara and Pérez-Schindler, Joaquín and Mansingh, Shivani and Beer, Markus and Mittal, Nitish and Ehrenfeuchter, Nikolaus and Handschin, Christoph. (2022) PGC-1β modulates catabolism and fiber atrophy in the fasting-response of specific skeletal muscle beds. Molecular metabolism. p. 101643. 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 2021Ham, 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. 2021Bak, Maciej. Computational analyses of RNA-Sequencing data to identify splicing and polyadenylation regulatory elements. 2021, Doctoral Thesis, University of Basel, Faculty of Science. 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. 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. 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. 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. 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. 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. 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. Grobecker, Pascal. Bayesian methods in transcriptomics. 2021, Doctoral Thesis, University of Basel, Faculty of Science. 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. Mölder, Felix and Jablonski, Kim Philipp and Letcher, Brice and Hall, Michael B. and Tomkins-Tinch, Christopher H. and Sochat, Vanessa and Forster, Jan and Lee, Soohyun and Twardziok, Sven O. and Kanitz, Alexander and Wilm, Andreas and Holtgrewe, Manuel and Rahmann, Sven and Nahnsen, Sven and Köster, Johannes. (2021) Sustainable data analysis with Snakemake. F1000Research, 10. p. 33. Rehm, Heidi L. and Page, Angela J. H. and Smith, Lindsay and Adams, Jeremy B. and Alterovitz, Gil and Babb, Lawrence J. and Barkley, Maxmillian P. and Baudis, Michael and Beauvais, Michael J. S. and Beck, Tim and Beckmann, Jacques S. and Beltran, Sergi and Bernick, David and Bernier, Alexander and Bonfield, James K. and Boughtwood, Tiffany F. and Bourque, Guillaume and Bowers, Sarion R. and Brookes, Anthony J. and Brudno, Michael and Brush, Matthew H. and Bujold, David and Burdett, Tony and Buske, Orion J. and Cabili, Moran N. and Cameron, Daniel L. and Carroll, Robert J. and Casas-Silva, Esmeralda and Chakravarty, Debyani and Chaudhari, Bimal P. and Chen, Shu Hui and Cherry, J. Michael and Chung, Justina and Cline, Melissa and Clissold, Hayley L. and Cook-Deegan, Robert M. and Courtot, Mélanie and Cunningham, Fiona and Cupak, Miro and Davies, Robert M. and Denisko, Danielle and Doerr, Megan J. and Dolman, Lena I. and Dove, Edward S. and Dursi, L. Jonathan and Dyke, Stephanie O. M. and Eddy, James A. and Eilbeck, Karen and Ellrott, Kyle P. and Fairley, Susan and Fakhro, Khalid A. and Firth, Helen V. and Fitzsimons, Michael S. and Fiume, Marc and Flicek, Paul and Fore, Ian M. and Freeberg, Mallory A. and Freimuth, Robert R. and Fromont, Lauren A. and Fuerth, Jonathan and Gaff, Clara L. and Gan, Weiniu and Ghanaim, Elena M. and Glazer, David and Green, Robert C. and Griffith, Malachi and Griffith, Obi L. and Grossman, Robert L. and Groza, Tudor and Guidry Auvil, Jaime M. and Guigó, Roderic and Gupta, Dipayan and Haendel, Melissa A. and Hamosh, Ada and Hansen, David P. and Hart, Reece K. and Hartley, Dean Mitchell and Haussler, David and Hendricks-Sturrup, Rachele M. and Ho, Calvin W. L. and Hobb, Ashley E. and Hoffman, Michael M. and Hofmann, Oliver M. and Holub, Petr and Hsu, Jacob Shujui and Hubaux, Jean-Pierre and Hunt, Sarah E. and Husami, Ammar and Jacobsen, Julius O. and Jamuar, Saumya S. and Janes, Elizabeth L. and Jeanson, Francis and Jené, Aina and Johns, Amber L. and Joly, Yann and Jones, Steven J. M. and Kanitz, Alexander and Kato, Kazuto and Keane, Thomas M. and Kekesi-Lafrance, Kristina and Kelleher, Jerome and Kerry, Giselle and Khor, Seik-Soon and Knoppers, Bartha M. and Konopko, Melissa A. and Kosaki, Kenjiro and Kuba, Martin and Lawson, Jonathan and Leinonen, Rasko and Li, Stephanie and Lin, Michael F. and Linden, Mikael and Liu, Xianglin and Liyanage, Isuru Udara and Lopez, Javier and Lucassen, Anneke M. and Lukowski, Michael and Mann, Alice L. and Marshall, John and Mattioni, Michele and Metke-Jimenez, Alejandro and Middleton, Anna and Milne, Richard J. and Molnár-Gábor, Fruzsina and Mulder, Nicola and Munoz-Torres, Monica C. and Nag, Rishi and Nakagawa, Hidewaki and Nasir, Jamal and Navarro, Arcadi and Nelson, Tristan H. and Niewielska, Ania and Nisselle, Amy and Niu, Jeffrey and Nyrönen, Tommi H. and O'Connor, Brian D. and Oesterle, Sabine and Ogishima, Soichi and Wang, Vivian Ota and Paglione, Laura A. D. and Palumbo, Emilio and Parkinson, Helen E. and Philippakis, Anthony A. and Pizarro, Angel D. and Prlic, Andreas and Rambla, Jordi and Rendon, Augusto and Rider, Renee A. and Robinson, Peter N. and Rodarmer, Kurt W. and Rodriguez, Laura Lyman and Rubin, Alan F. and Rueda, Manuel and Rushton, Gregory A. and Ryan, Rosalyn S. and Saunders, Gary I. and Schuilenburg, Helen and Schwede, Torsten and Scollen, Serena and Senf, Alexander and Sheffield, Nathan C. and Skantharajah, Neerjah and Smith, Albert V. and Sofia, Heidi J. and Spalding, Dylan and Spurdle, Amanda B. and Stark, Zornitza and Stein, Lincoln D. and Suematsu, Makoto and Tan, Patrick and Tedds, Jonathan A. and Thomson, Alastair A. and Thorogood, Adrian and Tickle, Timothy L. and Tokunaga, Katsushi and Törnroos, Juha and Torrents, David and Upchurch, Sean and Valencia, Alfonso and Guimera, Roman Valls and Vamathevan, Jessica and Varma, Susheel and Vears, Danya F. and Viner, Coby and Voisin, Craig and Wagner, Alex H. and Wallace, Susan E. and Walsh, Brian P. and Williams, Marc S. and Winkler, Eva C. and Wold, Barbara J. and Wood, Grant M. and Woolley, J. Patrick and Yamasaki, Chisato and Yates, Andrew D. and Yung, Christina K. and Zass, Lyndon J. and Zaytseva, Ksenia and Zhang, Junjun and Goodhand, Peter and North, Kathryn and Birney, Ewan. (2021) GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genomics, 1 (2). p. 100029. Wang, Yuluan and Soneson, Charlotte and Malinowska, Anna L. and Laski, Artur and Ghosh, Souvik and Kanitz, Alexander and Gebert, Luca F. R. and Robinson, Mark D. and Hall, Jonathan. (2021) MiR-CLIP reveals iso-miR selective regulation in the miR-124 targetome. Nucleic Acids Research, 49 (1). pp. 25-37. 2020Ghosh, 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. 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. 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. 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. 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. Iadevaia, Valentina and Wouters, Maikel D. and Kanitz, Alexander and Matia-González, Ana M. and Laing, Emma E. and Gerber, André P.. (2020) Tandem RNA isolation reveals functional rearrangement of RNA-binding proteins on; CDKN1B/p27; Kip1; 3'UTRs in cisplatin treated cells. RNA Biology, 17 (1). pp. 33-46. 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. 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. 2019Gruber, Andreas J. and Zavolan, Mihaela. (2019) Alternative cleavage and polyadenylation in health and disease. Nature reviews. Genetics, 20 (10). pp. 599-614. 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. 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. Koç, Baran. Identification of non-coding RNAs associated with autism spectrum disorder and cognitive assessment of NMDA receptor modulators in mouse. 2019, Doctoral Thesis, University of Basel, Faculty of Science. Păunescu, Virgil and Zavolan, Mihaela and Oprea, Tudor. (2019) In memoriam: Francisc Schneider (1933-2017). Journal of cellular and molecular medicine. pp. 3045-3046. 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. 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. 2018Essig, 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. 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. 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. Gypas, Foivos. Computational methods for the identification and quantification of transcript isoforms from next generation sequencing data. 2018, Doctoral Thesis, University of Basel, Faculty of Science. 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. Schmidt, Ralf. To what end? - Computational tools to uncover regulators of pre-mRNA polyadenylation site selection. 2018, Doctoral Thesis, University of Basel, Faculty of Science. 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. 2017Brancati, Giovanna. Molecular determinants of miRNA target specificity and tissue-specific studies in C. elegans. 2017, Doctoral Thesis, University of Basel, Faculty of Science. 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. 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. 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. 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. 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. 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. Zavolan, Mihaela and Graveley, Brenton R.. (2017) RNAs: dynamic and mutable. Genome Biology, 18 (1). p. 226. 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. 2016Aeschimann, Florian. The mRNA silencing dual activity of the RNA-binding protein LIN41 and the role of its targets in C. elegans development. 2016, Doctoral Thesis, University of Basel, Faculty of Science. 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. Gumienny, Rafał Wojciech. Identification of small non-coding RNA targets using computational predictions and high throughput sequencing data. 2016, Doctoral Thesis, University of Basel, Faculty of Science. Jedlinski, Dominik Jan. Deciphering the landscape of snoRNA-mediated RNA modifications with high-throughput sequencing approaches. 2016, Doctoral Thesis, University of Basel, Faculty of Science. 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. 2015Dimitrova, Yoana. Robustness and plasticity of epithelial cell state in development and malignancy. 2015, Doctoral Thesis, University of Basel, Faculty of Science. Gruber, Andreas J.. Computational analysis of transcriptional and post-transcriptional regulation of gene expression. 2015, Doctoral Thesis, University of Basel, Faculty of Science. 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. Hendriks, Gerardus Johannes. Extensive oscillatory gene expression during "C. elegans" larval development. 2015, Doctoral Thesis, University of Basel, Faculty of Science. 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. 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. Syed, Afzal Pasha. 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