2021
Börsch, Anastasiya;
Ham, Daniel J;
Mittal, Nitish;
Tintignac, Lionel A;
Migliavacca, Eugenia;
Feige, Jérôme N;
Rüegg, Markus A;
Zavolan, Mihaela (2021).
Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia. Communications biology, 4 (1), 194.
Cléry, Antoine;
Krepl, Miroslav;
Nguyen, Cristina K X;
Moursy, Ahmed;
Jorjani, Hadi;
Katsantoni, Maria;
Okoniewski, Michal;
Mittal, Nitish;
Zavolan, Mihaela;
Sponer, Jiri;
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), 428.
Coto-Llerena, Mairene;
Tosti, Nadia;
Taha-Mehlitz, Stephanie;
Kancherla, Venkatesh;
Paradiso, Viola;
Gallon, John;
Bianco, Gaia;
Garofoli, Andrea;
Ghosh, Souvik;
Tang, Fengyuan;
Ercan, Caner;
Christofori, Gerhard M.;
Matter, Matthias S.;
Droeser, Raoul A.;
Zavolan, Mihaela;
Soysal, Savas D.;
von Flüe, Markus;
Kollmar, Otto;
Terracciano, Luigi M.;
Ng, Charlotte K. Y.;
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, E-pub ahead of print.
2020
Ho-Xuan, Hung;
Lehmann, Gerhard;
Glazar, Petar;
Gypas, Foivos;
Eichner, Norbert;
Heizler, Kevin;
Schlitt, Hans Jürgen;
Zavolan, Mihaela;
Rajewsky, Nikolaus;
Meister, Gunter;
Hackl, Christina (2020).
Gene Expression Signatures of a Preclinical Mouse Model during Colorectal Cancer Progression under Low-Dose Metronomic Chemotherapy. Cancers, 13 (1), 49.
Jutzi, Daniel;
Campagne, Sébastien;
Schmidt, Ralf;
Reber, Stefan;
Mechtersheimer, Jonas;
Gypas, Foivos;
Schweingruber, Christoph;
Colombo, Martino;
von Schroetter, Christine;
Loughlin, Fionna E;
Devoy, Anny;
Hedlund, Eva;
Zavolan, Mihaela;
Allain, Frédéric H-T;
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), 6341.
Ham, Daniel J.;
Börsch, Anastasiya;
Lin, Shuo;
Thürkauf, Marco;
Weihrauch, Martin;
Reinhard, Judith R.;
Delezie, Julien;
Battilana, Fabienne;
Wang, Xueyong;
Kaiser, Marco S.;
Guridi, Maitea;
Sinnreich, Michael;
Rich, Mark M.;
Mittal, Nitish;
Tintignac, Lionel A.;
Handschin, Christoph;
Zavolan, Mihaela;
Rüegg, Markus A. (2020).
The neuromuscular junction is a focal point of mTORC1 signaling in sarcopenia. Nature Communications, 11 (1), 4510.
Ghosh, Souvik;
Guimaraes, Joao C.;
Lanzafame, Manuela;
Schmidt, Alexander;
Syed, Afzal Pasha;
Dimitriades, Beatrice;
Börsch, Anastasiya;
Ghosh, Shreemoyee;
Mittal, Nitish;
Montavon, Thomas;
Correia, Ana Luisa;
Danner, Johannes;
Meister, Gunter;
Terracciano, Luigi M.;
Pfeffer, Sébastien;
Piscuoglio, Salvatore;
Zavolan, Mihaela (2020).
Prevention of dsRNA-induced interferon signaling by AGO1x is linked to breast cancer cell proliferation. The EMBO Journal, 39 (18), e103922.
Guimaraes, Joao C;
Mittal, Nitish;
Gnann, Alexandra;
Jedlinski, Dominik;
Riba, Andrea;
Buczak, Katarzyna;
Schmidt, Alexander;
Zavolan, Mihaela (2020).
A rare codon-based translational program of cell proliferation. Genome biology, 21 (1), 44.
Hasler, Daniele;
Meduri, Rajyalakshmi;
Bąk, Maciej;
Lehmann, Gerhard;
Heizinger, Leonhard;
Wang, Xin;
Li, Zhi-Tong;
Sement, François M;
Bruckmann, Astrid;
Dock-Bregeon, Anne-Catherine;
Merkl, Rainer;
Kalb, Reinhard;
Grauer, Eva;
Kunstmann, Erdmute;
Zavolan, Mihaela;
Liu, Mo-Fang;
Fischer, Utz;
Meister, Gunter (2020).
The Alazami Syndrome-Associated Protein LARP7 Guides U6 Small Nuclear RNA Modification and Contributes to Splicing Robustness. Molecular cell, 77 (5), 1014-1031.e13.
Liko, Dritan;
Rzepiela, Andrzej;
Vukojevic, Vanja;
Zavolan, Mihaela;
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), 1524-1532.
Gruber, Andreas J.;
Zavolan, Mihaela (2020).
Reply to 'A different perspective on alternative cleavage and polyadenylation'. Nature reviews. Genetics, 21 (1), 63-64.
2019
Herrmann, Christina J.;
Schmidt, Ralf;
Kanitz, Alexander;
Artimo, Panu;
Gruber, Andreas J.;
Zavolan, Mihaela (2019).
PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3' end sequencing. Nucleic acids research, 48 (D1), D174-D179.
Gruber, Andreas J.;
Zavolan, Mihaela (2019).
Alternative cleavage and polyadenylation in health and disease. Nature reviews. Genetics, 20 (10), 599-614.
Păunescu, Virgil;
Zavolan, Mihaela;
Oprea, Tudor (2019).
In memoriam: Francisc Schneider (1933-2017). Journal of cellular and molecular medicine, 23 (4), 3045-3046.
Sendoel, Ataman;
Subasic, Deni;
Ducoli, Luca;
Keller, Martin;
Michel, Erich;
Kohler, Ines;
Singh, Kapil Dev;
Zheng, Xue;
Brümmer, Anneke;
Imig, Jochen;
Kishore, Shivendra;
Wu, Yibo;
Kanitz, Alexander;
Kaech, Andres;
Mittal, Nitish;
Matia-González, Ana M.;
Gerber, André P.;
Zavolan, Mihaela;
Aebersold, Ruedi;
Hall, Jonathan;
Allain, Frédéric H.-T.;
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), 2157-2178.
Kanitz, Alexander;
Syed, Afzal Pasha;
Kaji, Keisuke;
Zavolan, Mihaela (2019).
Conserved regulation of RNA processing in somatic cell reprogramming. BMC genomics, 20 (1), 100.
Riba, Andrea;
Di Nanni, Noemi;
Mittal, Nitish;
Arhné, Erik;
Schmidt, Alexander;
Zavolan, Mihaela (2019).
Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates. Proceedings of the National Academy of Sciences, 116 (30), 15023-15032.
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.
Zavolan, Mihaela;
Kanitz, Alexander (2018).
RNA splicing and its connection with other regulatory layers in somatic cell reprogramming. Current Opinion in Cell Biology, 52, 8-13.
2017
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 (457), 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.
Kishore, Shivendra;
Piscuoglio, Salvatore;
Kovac, Michal;
Gylling, Annette;
Wenzel, Friedel;
Trapani, Francesca;
Altermatt, Hans Joerg;
Mele, Valentina;
Marra, Giancarlo;
Peltomäki, Päivi;
Terracciano, Luigi;
Zavolan, Mihaela;
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), 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).
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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;
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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.
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Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. Genome research, 13 (6B), 1430-42.
Aravin, Alexei A;
Lagos-Quintana, Mariana;
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Meyer, Jutta;
Tuschl, Thomas (2003).
The small RNA profile during Drosophila melanogaster development. Developmental cell, 5 (2), 337-50.
Yang, Edward;
van Nimwegen, Erik;
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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;
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Kasukawa, T;
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Bono, H (2002).
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420 (6915), 563-73.
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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.;
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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.
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Whole-genome analysis: annotations and updates. Current Opinion in Structural Biology, 11 (3), 377-81.
Kepler, Thomas B.;
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Improved inference of mutation rates: I. An integral representation for the Luria-Delbrück distribution. Theoretical population biology, 59 (1), 41-8.
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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.
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The targeting of somatic hypermutation closely resembles that of meiotic mutation. Journal of Immunology, 166 (2), 892-899.
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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;
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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;
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Somatic mutation leads to efficient affinity maturation when centrocytes recycle back to centroblasts. Journal of Immunology, 158 (11), 5155-62.
1996
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Exploring the mechanisms of primary antibody responses to T cell-dependent antigens. Journal of Theoretical Biology, 181 (3), 215-36.
1994
Weisbuch, Gérard;
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Capacity of a model immune network. Bulletin of Mathematical Biology, 56 (5), 899-921.
