2020
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, 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, Epub ahead of print.
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).
Kaposi's Sarcoma Herpesvirus microRNAs Target Caspase 3 and Regulate Apoptosis. PLoS Pathogens, 7 (12), e1002405.
Rammelt, Christiane;
Bilen, Biter;
Zavolan, Mihaela;
Keller, Walter (2011).
PAPD5, a noncanonical poly(A) polymerase with an unusual RNA-binding motif. RNA, 17 (9), 1737-46.
Trajkovski, Mirko;
Hausser, Jean;
Soutschek, Jürgen;
Bhat, Bal;
Akin, Akinc;
Zavolan, Mihaela;
Heim, Markus H;
Stoffel, Markus (2011).
MicroRNAs 103 and 107 regulate insulin sensitivity. Nature, 474 (7353), 649-53.
Kishore, Shivendra;
Jaskiewicz, Lukasz;
Burger, Lukas;
Hausser, Jean;
Khorshid, Mohsen;
Zavolan, Mihaela (2011).
A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins. Nature Methods, 8 (7), 559-64.
Berninger, Philipp;
Jaskiewicz, Lukasz;
Khorshid, Mohsen;
Zavolan, Mihaela (2011).
Conserved generation of short products at piRNA loci. BMC Genomics, 12 (1), 46.
Khorshid, M.;
Rodak, C.;
Zavolan, M. (2011).
CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Research, 39 (Databaseissue), D245-52.
Corioni, M.;
Antih, N.;
Tanackovic, G.;
Zavolan, M.;
Kramer, A. (2011).
Analysis of in situ pre-mRNA targets of human splicing factor SF1 reveals a function in alternative splicing. Nucleic Acids Research, 39 (5), 1868-79.
2010
Kishore, Shivendra;
Luber, Sandra;
Zavolan, Mihaela (2010).
Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression. Briefings in Functional Genomics, 9 (5-6), 391-404.
McGlincy, Nicholas J.;
Tan, Lit-Yeen;
Paul, Nicodeme;
Zavolan, Mihaela;
Lilley, Kathryn S.;
Smith, Christopher W. J. (2010).
Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay. BMC genomics, 11, 565.
Hafner, Markus;
Landthaler, Markus;
Burger, Lukas;
Khorshid, Mohsen;
Hausser, Jean;
Berninger, Philipp;
Rothballer, Andrea;
Ascano, Manuel;
Jungkamp, Anna-Carina;
Munschauer, Mathias;
Ulrich, Alexander;
Wardle, Greg S;
Dewell, Scott;
Zavolan, Mihaela;
Tuschl, Thomas (2010).
PAR-CliP-a method to identify transcriptome-wide the binding sites of RNA binding proteins. Journal of visualized experiments, 41 , 2034 (41), e2034.
Hafner, Markus;
Landthaler, Markus;
Burger, Lukas;
Khorshid, Mohsen;
Hausser, Jean;
Berninger, Philipp;
Rothballer, Andrea;
Ascano, Manuel;
Jungkamp, Anna-Carina;
Munschauer, Mathias;
Ulrich, Alexander;
Wardle, Greg S;
Dewell, Scott;
Zavolan, Mihaela;
Tuschl, Thomas (2010).
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell, 141 (1), 129-41.
Ma, Jun;
Flemr, Matyas;
Stein, Paula;
Berninger, Philipp;
Malik, Radek;
Zavolan, Mihaela;
Svoboda, Petr;
Schultz, Richard M (2010).
MicroRNA activity is suppressed in mouse oocytes. Current biology, 20 (3), 265-70.
Kishore, Shivendra;
Khanna, Amit;
Zhang, Zhaiyi;
Hui, Jingyi;
Balwierz, Piotr J;
Stefan, Mihaela;
Beach, Carol;
Nicholls, Robert D;
Zavolan, Mihaela;
Stamm, Stefan (2010).
The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing. Human molecular genetics, 19 (7), 1153-64.
2009
Hausser, Jean;
Landthaler, Markus;
Jaskiewicz, Lukasz;
Gaidatzis, Dimos;
Zavolan, Mihaela (2009).
Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C-miRNA complexes and the degradation of miRNA targets. Genome research, 19 (11), 2009-2020.
Hutzinger, R.;
Feederle, R.;
Mrazek, J.;
Schiefermeier, N.;
Balwierz, P. J.;
Zavolan, M.;
Polacek, N.;
Delecluse, H. -J.;
Huttenhofer, A. (2009).
Expression and processing of a small nucleolar RNA from the Epstein-Barr virus genome. PLoS Pathogens, 5 (8), e1000547.
Hausser, Jean;
Berninger, Philipp;
Rodak, Christoph;
Jantscher, Yvonne;
Wirth, Stefan;
Zavolan, Mihaela (2009).
MirZ: an integrated microRNA expression atlas and target prediction resource. Nucleic Acids Research, 37 (WebServerissue), W266-72.
Poy, Matthew N;
Hausser, Jean;
Trajkovski, Mirko;
Braun, Matthias;
Collins, Stephan;
Rorsman, Patrik;
Zavolan, Mihaela;
Stoffel, Markus (2009).
miR-375 maintains normal pancreatic alpha- and beta-cell mass. Proceedings of the National Academy of Sciences of the United States of America, 106 (14), 5813-8.
Pena, John T G;
Sohn-Lee, Cherin;
Rouhanifard, Sara H;
Ludwig, Janos;
Hafner, Markus;
Mihailovic, Aleksandra;
Lim, Cindy;
Holoch, Daniel;
Berninger, Philipp;
Zavolan, Mihaela;
Tuschl, Thomas (2009).
miRNA in situ hybridization in formaldehyde and EDC-fixed tissues. Nature Methods, 6 (2), 139-41.
FANTOM Consortium,;
Suzuki, Harukazu;
Forrest, Alistair R R;
van Nimwegen, Erik;
Daub, Carsten O;
Balwierz, Piotr J;
Irvine, Katharine M;
Lassmann, Timo;
Ravasi, Timothy;
Hasegawa, Yuki;
de Hoon, Michiel J L;
Katayama, Shintaro;
Schroder, Kate;
Carninci, Piero;
Tomaru, Yasuhiro;
Kanamori-Katayama, Mutsumi;
Kubosaki, Atsutaka;
Akalin, Altuna;
Ando, Yoshinari;
Arner, Erik;
Asada, Maki;
Asahara, Hiroshi;
Bailey, Timothy;
Bajic, Vladimir B;
Bauer, Denis;
Beckhouse, Anthony G;
Bertin, Nicolas;
Björkegren, Johan;
Brombacher, Frank;
Bulger, Erika;
Chalk, Alistair M;
Chiba, Joe;
Cloonan, Nicole;
Dawe, Adam;
Dostie, Josee;
Engström, Pär G;
Essack, Magbubah;
Faulkner, Geoffrey J;
Fink, J Lynn;
Fredman, David;
Fujimori, Ko;
Furuno, Masaaki;
Gojobori, Takashi;
Gough, Julian;
Grimmond, Sean M;
Gustafsson, Mika;
Hashimoto, Megumi;
Hashimoto, Takehiro;
Hatakeyama, Mariko;
Heinzel, Susanne;
Hide, Winston;
Hofmann, Oliver;
Hörnquist, Michael;
Huminiecki, Lukasz;
Ikeo, Kazuho;
Imamoto, Naoko;
Inoue, Satoshi;
Inoue, Yusuke;
Ishihara, Ryoko;
Iwayanagi, Takao;
Jacobsen, Anders;
Kaur, Mandeep;
Kawaji, Hideya;
Kerr, Markus C;
Kimura, Ryuichiro;
Kimura, Syuhei;
Kimura, Yasumasa;
Kitano, Hiroaki;
Koga, Hisashi;
Kojima, Toshio;
Kondo, Shinji;
Konno, Takeshi;
Krogh, Anders;
Kruger, Adele;
Kumar, Ajit;
Lenhard, Boris;
Lennartsson, Andreas;
Lindow, Morten;
Lizio, Marina;
Macpherson, Cameron;
Maeda, Norihiro;
Maher, Christopher A;
Maqungo, Monique;
Mar, Jessica;
Matigian, Nicholas A;
Matsuda, Hideo;
Mattick, John S;
Meier, Stuart;
Miyamoto, Sei;
Miyamoto-Sato, Etsuko;
Nakabayashi, Kazuhiko;
Nakachi, Yutaka;
Nakano, Mika;
Nygaard, Sanne;
Okayama, Toshitsugu;
Okazaki, Yasushi;
Okuda-Yabukami, Haruka;
Orlando, Valerio;
Otomo, Jun;
Pachkov, Mikhail;
Petrovsky, Nikolai;
Plessy, Charles;
Quackenbush, John;
Radovanovic, Aleksandar;
Rehli, Michael;
Saito, Rintaro;
Sandelin, Albin;
Schmeier, Sebastian;
Schönbach, Christian;
Schwartz, Ariel S;
Semple, Colin A;
Sera, Miho;
Severin, Jessica;
Shirahige, Katsuhiko;
Simons, Cas;
St Laurent, George;
Suzuki, Masanori;
Suzuki, Takahiro;
Sweet, Matthew J;
Taft, Ryan J;
Takeda, Shizu;
Takenaka, Yoichi;
Tan, Kai;
Taylor, Martin S;
Teasdale, Rohan D;
Tegnér, Jesper;
Teichmann, Sarah;
Valen, Eivind;
Wahlestedt, Claes;
Waki, Kazunori;
Waterhouse, Andrew;
Wells, Christine A;
Winther, Ole;
Wu, Linda;
Yamaguchi, Kazumi;
Yanagawa, Hiroshi;
Yasuda, Jun;
Zavolan, Mihaela;
Hume, David A;
Riken Omics Science Center,;
Arakawa, Takahiro;
Fukuda, Shiro;
Imamura, Kengo;
Kai, Chikatoshi;
Kaiho, Ai;
Kawashima, Tsugumi;
Kawazu, Chika;
Kitazume, Yayoi;
Kojima, Miki;
Miura, Hisashi;
Murakami, Kayoko;
Murata, Mitsuyoshi;
Ninomiya, Noriko;
Nishiyori, Hiromi;
Noma, Shohei;
Ogawa, Chihiro;
Sano, Takuma;
Simon, Christophe;
Tagami, Michihira;
Takahashi, Yukari;
Kawai, Jun;
Hayashizaki, Yoshihide (2009).
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature genetics, 41 (5), 553-62.
2008
Sinkkonen, Lasse;
Hugenschmidt, Tabea;
Berninger, Philipp;
Gaidatzis, Dimos;
Mohn, Fabio;
Artus-Revel, Caroline G;
Zavolan, Mihaela;
Svoboda, Petr;
Filipowicz, Witold (2008).
MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells. Nature structural & molecular biology, 15 (3), 259-67.
Landthaler, Markus;
Gaidatzis, Dimos;
Rothballer, Andrea;
Chen, Po Yu;
Soll, Steven Joseph;
Dinic, Lana;
Ojo, Tolulope;
Hafner, Markus;
Zavolan, Mihaela;
Tuschl, Thomas (2008).
Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. RNA, 14 (12), 2580-96.
Galgano, A.;
Forrer, M.;
Jaskiewicz, L.;
Kanitz, A.;
Zavolan, M.;
Gerber, A. P. (2008).
Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system. PLoS ONE, 3 (9), e3164.
Connolly, Erin;
Melegari, Margherita;
Landgraf, Pablo;
Tchaikovskaya, Tatyana;
Tennant, Bud C;
Slagle, Betty L;
Rogler, Leslie E;
Zavolan, Mihaela;
Tuschl, Thomas;
Rogler, Charles E (2008).
Elevated expression of the miR-17-92 polycistron and miR-21 in hepadnavirus-associated hepatocellular carcinoma contributes to the malignant phenotype. American Journal of Pathology, 173 (3), 856-64.
Chen, Po Yu;
Weinmann, Lasse;
Gaidatzis, Dimos;
Pei, Yi;
Zavolan, Mihaela;
Tuschl, Thomas;
Meister, Gunter (2008).
Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity. RNA, 14 (2), 263-74.
Berninger, Philipp;
Gaidatzis, Dimos;
van Nimwegen, Erik;
Zavolan, Mihaela (2008).
Computational analysis of small RNA cloning data. Methods, 44 (1), 13-21.
Chern, Tzu-Ming;
Paul, Nicodeme;
van Nimwegen, Erik;
Zavolan, Mihaela (2008).
Computational analysis of full-length cDNAs reveals frequent coupling between transcriptional and splicing programs. DNA research, 15 (2), 63-72.
2007
Landgraf, P.;
Rusu, M.;
Sheridan, R.;
Sewer, A.;
Iovino, N.;
Aravin, A.;
Pfeffer, S.;
Rice, A.;
Kamphorst, A. O.;
Landthaler, M.;
Lin, C.;
Socci, N. D.;
Hermida, L.;
Fulci, V.;
Chiaretti, S.;
Foa, R.;
Schliwka, J.;
Fuchs, U.;
Novosel, A.;
Muller, R. -U.;
Schermer, B.;
Bissels, U.;
Inman, J.;
Phan, Q.;
Chien, M.;
Weir, D. B.;
Choksi, R.;
De Vita, G.;
Frezzetti, D.;
Trompeter, H. -I.;
Hornung, V.;
Teng, G.;
Hartmann, G.;
Palkovits, M.;
Di Lauro, R.;
Wernet, P.;
Macino, G.;
Rogler, C. E.;
Nagle, J. W.;
Ju, J.;
Papavasiliou, F. N.;
Benzing, T.;
Lichter, P.;
Tam, W.;
Brownstein, M. J.;
Bosio, A.;
Borkhardt, A.;
Russo, J. J.;
Sander, C.;
Zavolan, M.;
Tuschl, T. (2007).
A mammalian microRNA expression atlas based on small RNA library sequencing. Cell, 129 (7), 1401-1414.
Peyer, Anne-Kathrin;
Jung, Diana;
Beer, Markus;
Gnerre, Carmela;
Keogh, Adrian;
Stroka, Deborah;
Zavolan, Mihaela;
Meyer, Urs-A (2007).
Regulation of human liver delta-aminolevulinic acid synthase by bile acids. Hepatology, 46 (6), 1960-70.
Yao, Yongxiu;
Zhao, Yuguang;
Xu, Hongtao;
Smith, Lorraine P;
Lawrie, Charles H;
Sewer, Alain;
Zavolan, Mihaela;
Nair, Venugopal (2007).
Marek's disease virus type 2 (MDV-2) encoded microRNAs show no sequence conservation with those encoded by MDV-1. Journal of virology, 81 (13), 7164-70.
Randall, Glenn;
Panis, Maryline;
Cooper, Jacob D;
Tellinghuisen, Timothy L;
Sukhodolets, Karen E;
Pfeffer, Sebastien;
Landthaler, Markus;
Landgraf, Pablo;
Kan, Sherry;
Lindenbach, Brett D;
Chien, Minchen;
Weir, David B;
Russo, James J;
Ju, Jingyue;
Brownstein, Michael J;
Sheridan, Robert;
Sander, Chris;
Zavolan, Mihaela;
Tuschl, Thomas;
Rice, Charles M (2007).
Cellular cofactors affecting hepatitis C virus infection and replication. Proceedings of the National Academy of Sciences of the United States of America, 104 (31), 12884-9.
Fulci, Valerio;
Chiaretti, Sabina;
Goldoni, Marina;
Azzalin, Gianluca;
Carucci, Nicoletta;
Tavolaro, Simona;
Castellano, Leandro;
Magrelli, Armando;
Citarella, Franca;
Messina, Monica;
Maggio, Roberta;
Peragine, Nadia;
Santangelo, Simona;
Mauro, Francesca Romana;
Landgraf, Pablo;
Tuschl, Thomas;
Weir, David B;
Chien, Minchen;
Russo, James J;
Ju, Jingyue;
Sheridan, Robert;
Sander, Chris;
Zavolan, Mihaela;
Guarini, Anna;
Fo (2007).
Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia. Blood, 109 (11), 4944-51.
Gaidatzis, Dimos;
van Nimwegen, Erik;
Hausser, Jean;
Zavolan, Mihaela (2007).
Inference of miRNA targets using evolutionary conservation and pathway analysis. BMC bioinformatics, 8, 69.
2006
Sood, Pranidhi;
Krek, Azra;
Zavolan, Mihaela;
Macino, Giuseppe;
Rajewsky, Nikolaus (2006).
Cell-type-specific signatures of microRNAs on target mRNA expression. Proceedings of the National Academy of Sciences of the United States of America, 103 (8), 2746-51.
Schmitter, D.;
Filkowski, J.;
Sewer, A.;
Pillai, R. S.;
Oakeley, E. J.;
Zavolan, M.;
Svoboda, P.;
Filipowicz, W. (2006).
Effects of Dicer and Argonaute down-regulation on mRNA levels in human HEK293 cells. Nucleic Acids Research, 34 (17), 4801-15.
Nair, Venugopal;
Zavolan, Mihaela (2006).
Virus-encoded microRNAs : novel regulators of gene expression. Trends in microbiology, 14 (4), 169-75.
Aravin, Alexei;
Gaidatzis, Dimos;
Pfeffer, Sébastien;
Lagos-Quintana, Mariana;
Landgraf, Pablo;
Iovino, Nicola;
Morris, Patricia;
Brownstein, Michael J;
Kuramochi-Miyagawa, Satomi;
Nakano, Toru;
Chien, Minchen;
Russo, James J;
Ju, Jingyue;
Sheridan, Robert;
Sander, Chris;
Zavolan, Mihaela;
Tuschl, Thomas (2006).
A novel class of small RNAs bind to MILI protein in mouse testes. Nature, 442 (7099), 203-7.
van Nimwegen, Erik;
Paul, Nicodeme;
Sheridan, Robert;
Zavolan, Mihaela (2006).
SPA : a probabilistic algorithm for spliced alignment. PLoS genetics, 2 (4), e24.
Chern, Tzu-Ming;
van Nimwegen, Erik;
Kai, Chikatoshi;
Kawai, Jun;
Carninci, Piero;
Hayashizaki, Yoshihide;
Zavolan, Mihaela (2006).
A simple physical model predicts small exon length variations. PLoS genetics, 2 (4), e45.
Zavolan, Mihaela;
van Nimwegen, Erik (2006).
The types and prevalence of alternative splice forms. Current opinion in structural biology, 16 (3), 362-7.
2005
Pfeffer, Sébastien;
Sewer, Alain;
Lagos-Quintana, Mariana;
Sheridan, Robert;
Sander, Chris;
Grässer, Friedrich A;
van Dyk, Linda F;
Ho, C Kiong;
Shuman, Stewart;
Chien, Minchen;
Russo, James J;
Ju, Jingyue;
Randall, Glenn;
Lindenbach, Brett D;
Rice, Charles M;
Simon, Viviana;
Ho, David D;
Zavolan, Mihaela;
Tuschl, Thomas (2005).
Identification of microRNAs of the herpesvirus family. Nature Methods, 2 (4), 269-76.
Gomes, A R;
Vinga, S;
Zavolan, M;
de Lencastre, H (2005).
Analysis of the genetic variability of virulence-related loci in epidemic clones of methicillin-resistant Staphylococcus aureus. Antimicrobial Agents and Chemotherapy, 49 (1), 366-79.
Chen, Po Yu;
Manninga, Heiko;
Slanchev, Krasimir;
Chien, Minchen;
Russo, James J;
Ju, Jingyue;
Sheridan, Robert;
John, Bino;
Marks, Debora S;
Gaidatzis, Dimos;
Sander, Chris;
Zavolan, Mihaela;
Tuschl, Thomas (2005).
The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes & development, 19 (11), 1288-93.
Sewer, Alain;
Paul, Nicodème;
Landgraf, Pablo;
Aravin, Alexei;
Pfeffer, Sébastien;
Brownstein, Michael J;
Tuschl, Thomas;
van Nimwegen, Erik;
Zavolan, Mihaela (2005).
Identification of clustered microRNAs using an ab initio prediction method. BMC bioinformatics, 6, 267.
Speirs, Christina;
van Nimwegen, Erik;
Bolton, Diane;
Zavolan, Mihaela;
Duvall, Melody;
Angleman, Sara;
Siegel, Richard;
Perelson, Alan S;
Lenardo, Michael J (2005).
Analysis of human immunodeficiency virus cytopathicity by using a new method for quantitating viral dynamics in cell culture. Journal of virology, 79 (7), 4025-32.
Carninci, P;
Kasukawa, T;
Katayama, S;
Gough, J;
Frith, M C;
Maeda, N;
Oyama, R;
Ravasi, T;
Lenhard, B;
Wells, C;
Kodzius, R;
Shimokawa, K;
Bajic, V B;
Brenner, S E;
Batalov, S;
Forrest, A R R;
Zavolan, M;
Davis, M J;
Wilming, L G;
Aidinis, V;
Allen, J E;
Ambesi-Impiombato, A;
Apweiler, R;
Aturaliya, R N;
Bailey, T L;
Bansal, M;
Baxter, L;
Beisel, K W;
Bersano, T;
Bono, H;
Chalk, A M;
Chiu, K P;
Choudhary, V;
Christoffels, A;
Clutterbuck, D R;
Crowe, M L;
Dalla, E;
Dalrymple, B P;
de Bono, B;
Della Gatta, G;
di Bernardo, D;
Down, T;
Engstrom, P;
Fagiolini, M;
Faulkner, G;
Fletcher, C F;
Fukushima, T;
Furuno, M;
Futaki, S;
Gariboldi, M;
Georgii-Hemming, P;
Gingeras, T R;
Gojobori, T;
Green, R E;
Gustincich, S;
Harbers, M;
Hayashi, Y;
Hensch, T K;
Hirokawa, N;
Hill, D;
Huminiecki, L;
Iacono, M;
Ikeo, K;
Iwama, A;
Ishikawa, T;
Jakt, M;
Kanapin, A;
Katoh, M;
Kawasawa, Y;
Kelso, J;
Kitamura, H;
Kitano, H;
Kollias, G;
Krishnan, S P T;
Kruger, A;
Kummerfeld, S K;
Kurochkin, I V;
Lareau, L F;
Lazarevic, D;
Lipovich, L;
Liu, J;
Liuni, S;
McWilliam, S;
Madan Babu, M;
Madera, M;
Marchionni, L;
Matsuda, H;
Matsuzawa, S;
Miki, H;
Mignone, F;
Miyake, S;
Morris, K;
Mottagui-Tabar, S;
Mulder, N;
Nakano, N;
Nakauchi, H;
Ng, P;
Nilsson, R;
Nishiguchi, S;
Nishikawa, S;
Nori, F;
Ohara, O;
Okazaki, Y;
Orlando, V;
Pang, K C;
Pavan, W J;
Pavesi, G;
Pesole, G;
Petrovsky, N;
Piazza, S;
Reed, J;
Reid, J F;
Ring, B Z;
Ringwald, M;
Rost, B;
Ruan, Y;
Salzberg, S L;
Sandelin, A;
Schneider, C;
Schönbach, C;
Sekiguchi, K;
Semple, C A M;
Seno, S;
Sessa, L;
Sheng, Y;
Shibata, Y;
Shimada, H;
Shimada, K;
Silva, D;
Sinclair, B;
Sperling, S;
Stupka, E;
Sugiura, K;
Sultana, R;
Takenaka, Y;
Taki, K;
Tammoja, K;
Tan, S L;
Tang, S;
Taylor, M S;
Tegner, J;
Teichmann, S A;
Ueda, H R;
van Nimwegen, E;
Verardo, R;
Wei, C L;
Yagi, K;
Yamanishi, H;
Zabarovsky, E;
Zhu, S;
Zimmer, A;
Hide, W;
Bult, C;
Grimmond, S M;
Teasdale, R D;
Liu, E T;
Brusic, V;
Quackenbush, J;
Wahlestedt, C;
Mattick, J S;
Hume, D A;
Kai, C;
Sasaki, D;
Tomaru, Y;
Fukuda, S;
Kanamori-Katayama, M;
Suzuki, M;
Aoki, J;
Arakawa, T;
Iida, J;
Imamura, K;
Itoh, M;
Kato, T;
Kawaji, H;
Kawagashira, N;
Kawashima, T;
Kojima, M;
Kondo, S;
Konno, H;
Nakano, K;
Ninomiya, N;
Nishio, T;
Okada, M;
Plessy, C;
Shibata, K;
Shiraki, T;
Suzuki, S;
Tagami, M;
Waki, K;
Watahiki, A;
Okamura-Oho, Y;
Suzuki, H;
Kawai, J;
Hayashizaki, Y;
FANTOM Consortium,;
RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group), (2005).
The transcriptional landscape of the mammalian genome. Science, 309 (5740), 1559-63.
2004
Pfeffer, S;
Zavolan, M;
Grasser, FA;
Chien, MC;
Russo, JJ;
Ju, JY;
John, B;
Enright, AJ;
Marks, D;
Sander, C;
Tuschl, T (2004).
Identification of virus-encoded microRNAs. Science, 304 (5671), 734-736.
2003
Zavolan, Mihaela;
Socci, Nicholas D;
Rajewsky, Nikolaus;
Gaasterlamd, Terry (2003).
SMASHing regulatory sites in DNA by human-mouse sequence comparisons. Proceedings / IEEE Computer Society Bioinformatics Conference. IEEE Computer Society Bioinformatics Conference, 2, 277-86.
Zavolan, Mihaela;
Kondo, Shinji;
Schonbach, Christian;
Adachi, Jun;
Hume, David A;
Hayashizaki, Yoshihide;
Gaasterland, Terry;
RIKEN GER Group,;
GSL Members, (2003).
Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome research, 13 (6B), 1290-300.
Ravasi, Timothy;
Huber, Thomas;
Zavolan, Mihaela;
Forrest, Alistair;
Gaasterland, Terry;
Grimmond, Sean;
Hume, David A;
RIKEN GER Group,;
GSL Members, (2003).
Systematic characterization of the zinc-finger-containing proteins in the mouse transcriptome. Genome research, 13 (6B), 1430-42.
Aravin, Alexei A;
Lagos-Quintana, Mariana;
Yalcin, Abdullah;
Zavolan, Mihaela;
Marks, Debora;
Snyder, Ben;
Gaasterland, Terry;
Meyer, Jutta;
Tuschl, Thomas (2003).
The small RNA profile during Drosophila melanogaster development. Developmental cell, 5 (2), 337-50.
Yang, Edward;
van Nimwegen, Erik;
Zavolan, Mihaela;
Rajewsky, Nikolaus;
Schroeder, Mark;
Magnasco, Marcelo;
Darnell, James E (2003).
Decay rates of human mRNAs : correlation with functional characteristics and sequence attributes. Genome research, 13 (8), 1863-72.
2002
Okazaki, Y;
Furuno, M;
Kasukawa, T;
Adachi, J;
Bono, H (2002).
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420 (6915), 563-73.
Zavolan, Mihaela;
van Nimwegen, Erik;
Gaasterland, Terry (2002).
Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. Genome research, 12 (9), 1377-85.
van Nimwegen, Erik;
Zavolan, Mihaela;
Rajewsky, Nikolaus;
Siggia, Eric D (2002).
Probabilistic clustering of sequences : inferring new bacterial regulons by comparative genomics. Proceedings of the National Academy of Sciences of the United States of America, 99 (11), 7323-8.
2001
De Boer, Rob J.;
Oprea, Mihaela;
Antia, Rustom;
Murali-Krishna, Kaja;
Ahmed, Rafi;
Perelson, Alan S. (2001).
Recruitment times, proliferation, and apoptosis rates during the CD8(+) T-cell response to lymphocytic choriomeningitis virus. Journal of virology, 75 (22), 10663-9.
Gaasterland, Terry;
Oprea, Mihaela (2001).
Whole-genome analysis: annotations and updates. Current Opinion in Structural Biology, 11 (3), 377-81.
Kepler, Thomas B.;
Oprea, Mihaela (2001).
Improved inference of mutation rates: I. An integral representation for the Luria-Delbrück distribution. Theoretical population biology, 59 (1), 41-8.
Oprea, Mihaela;
Kepler, Thomas B. (2001).
Improved inference of mutation rates: II. Generalization of the Luria-Delbrück distribution for realistic cell-cycle time distributions. Theoretical population biology, 59 (1), 49-59.
Oprea, Mihaela;
Cowell, Lindsay G.;
Kepler, Thomas B. (2001).
The targeting of somatic hypermutation closely resembles that of meiotic mutation. Journal of Immunology, 166 (2), 892-899.
Zavolan, M;
Kepler, T B (2001).
Statistical inference of sequence-dependent mutation rates. Current opinion in genetics & development, 11 (6), 612-5.
2000
Oprea, Mihaela;
van Nimwegen, Erik;
Perelson, Alan S. (2000).
Dynamics of one-pass germinal center models: implications for affinity maturation. Bulletin of Mathematical Biology, 62 (1), 121-53.
1999
Oprea, Mihaela;
Kepler, Thomas B. (1999).
Genetic plasticity of V genes under somatic hypermutation: statistical analyses using a new resampling-based methodology. Genome Research, 9 (12), 1294-304.
1997
Oprea, Mihaela;
Perelson, A. S. (1997).
Somatic mutation leads to efficient affinity maturation when centrocytes recycle back to centroblasts. Journal of Immunology, 158 (11), 5155-62.
1996
Oprea, M.;
Perelson, A. S. (1996).
Exploring the mechanisms of primary antibody responses to T cell-dependent antigens. Journal of Theoretical Biology, 181 (3), 215-36.
1994
Weisbuch, Gérard;
Oprea, Mihaela (1994).
Capacity of a model immune network. Bulletin of Mathematical Biology, 56 (5), 899-921.
