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Publications

Submitted
Papers
Florian Erhard, Ralf Zimmer. Context-dependent rescoring of Tandem-MS spectra dramatically increases peptide identification rates. ISMB 2011, submitted, Submitted.
    2013
    Papers
    Florian Erhard, Lars Dölken, Ralf Zimmer. RIP-chip enrichment analysis. Bioinformatics, vol 29, no. 1, pp. 77--83, September 2012, Basel, Switzerland, Jan 2013.
    2012
    Papers
    Florian Erhard, Ralf Zimmer. Detecting outlier peptides in quantitative high-throughput mass spectrometry data. Journal of Proteomics, vol 75, no. 11, pp. 3230-9, 2012 Jun 18 2012.
    2011
    Papers
    Florian Erhard, Ralf Zimmer. Detecting outlier peptides in quantitative high-throughput mass spectrometry data. Detecting outlier peptides in quantitative high-throughput mass spectrometry data, September 2011, Weihenstephan, Germany, 2011.
      2010
      Papers
      Caroline C. Friedel, Stefanie Kaufmann, Lars Dölken, Ralf Zimmer. HALO - A Java framework for precise transcript half-life determination. Bioinformatics, vol 26, no. 9, pp. 1264-1266, May 2010.
      Lars Dölken, Georg Malterer, Florian Erhard, Sheila Kothe, Caroline C. Friedel, Guillaume Suffert, Lisa Marcinowski, Natalie Motsch, Stephanie Barth, Michaela Beizinger, Diana Lieber, Susanne M. Bailer, Reinhard Hoffmann, Zsolt Ruzsics, Elisabeth Kremmer, Sebastien Pfeffer, Ralf Zimmer, Ulrich H. Koszinowski, Friedrich Grässer, Gunter Meister, Jürgen Haas. Systemic Analysis of Viral and Cellular miRNA Targets in Cells Latently Infected with Human gamma-Herpesviruses through RISC Immunoprecipitation Assays. Cell Host & Microbe, vol 7, no. 4, pp. 324-334, April 2010.
      Florian Erhard, Ralf Zimmer. Classification of ncRNAs using position and size information in deep sequencing data. Bioinformatics, vol 26, no. 18, pp. i426-i432, September 2010.
      J. Szczyrba, E. Loprich, S. Wach, V. Jung, G. Unteregger, S. Barth, R. Grobholz, W. Wieland, R. Stohr, A. Hartmann, B. Wullich, F. Grasser. The microRNA profile of prostate carcinoma obtained by deep sequencing. Mol. Cancer Res., vol 8, pp. 529–538, Apr 2010.
        B. Steer, B. Adler, S. Jonjic, J.P. Stewart, H. Adler. A gammaherpesvirus complement regulatory protein promotes initiation of infection by activation of protein kinase Akt/PKB. PLoS ONE, vol 5, no. 7, pp. e11672, 2010.
          J.Y. Zhu, M. Strehle, A. Frohn, E. Kremmer, K.P. Höfig, G. Meister, H. Adler. Identification and analysis of expression of novel microRNAs of murine gammaherpesvirus 68. J. of Virology, vol 84, no. 19, pp. 10266-10275, 2010.
            2009
            Papers
            Caroline C. Friedel, Lars Dölken, Zsolt Ruzsics, Ulrich Koszinowski, Ralf Zimmer. Conserved principles of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Research, vol 37, no. 17, pp. e115, Sep 2009.
            Caroline C. Friedel, Lars Dölken. Metabolic tagging and purification of nascent RNA: Implications for transcriptomics. Molecular BioSystems, vol 5, no. 11, pp. 1271-8, Nov 2009.
            Dölken L, Jonjic S. All for one and one for all: herpesviral microRNAs close in on their prey. Cell Host Microbe, vol 5, no. 4, pp. 315-317, Apr 2009.
              Weinmann L, Höck J, Ivacevic T, Ohrt T, Mütze J, Schwille P, Kremmer E, Benes V, Urlaub H, Meister G. Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs. Cell, vol 136, no. 3, pp. 496-507, 2009.
                Zhu JY, Pfuhl T, Motsch N, Barth S, Nicholls J, Grässer F, Meister G. Identification of novel Epstein-Barr virus microRNA genes from nasopharyngeal carcinomas. J Virol, vol 83, no. 7, pp. 3333-3341, 2009.
                  Esslinger S, Förstemann K. MicroRNAs repress mainly through mRNA decay. Angew Chem Int Ed Engl, vol 48, no. 5, pp. 853-855, 2009.
                    C. Nandy, J. Mrazek, H. Stoiber, F.A. Grasser, A. Huttenhofer, N. Polacek. Epstein-barr virus-induced expression of a novel human vault RNA. J. Mol. Biol., vol 388, pp. 776–784, May 2009.
                      Kocks JR, Adler H, Danzer H, Hoffmann K, Jonigk D, Lehmann U, Förster R. Chemokine receptor CCR7 contributes to a rapid and efficient clearance of lytic murine gamma-herpes virus 68 from the lung, whereas bronchus-associated lymphoid tissue harbors virus during latency.. J Immunol. , vol 182, no. 11, pp. 6861-6869, Jun 1 2009.
                        Flach B, Steer B, Thakur NN, Haas J, Adler H. The M10 locus of murine gammaherpesvirus 68 contributes to both the lytic and the latent phases of infection.. J Virol., vol 83, no. 16, pp. 8163-8172, 2009.
                          Adler H, El-Gogo S, Guggemoos S, Zimmermann W, Beauchemin N, Kammerer R. Perturbation of lytic and latent gammaherpesvirus infection in the absence of the inhibitory receptor CEACAM1.. PLoS One, vol 4, no. 7, pp. e6317, Jul 21 2009.
                          J.V. Hartig, S. Esslinger, R. Bottcher, K. Saito, K. Forstemann. Endo-siRNAs depend on a new isoform of loquacious and target artificially introduced, high-copy sequences. EMBO J., vol 28, pp. 2932–2944, Oct 2009.
                            2008
                            Papers
                            Dölken L, Haas J. Small noncoding RNA: novel targets for antiviral therapy. Future Microbiol., vol 3, no. 6, pp. 585-588, 2008.
                              Ender C, Krek A, Friedländer MR, Beitzinger M, Weinmann L, Chen W, Pfeffer S, Rajewsky N, Meister G. A human snoRNA with microRNA-like functions. Mol Cell, vol 32, no. 4, pp. 519-528, 2008.
                                Shah C, Förstemann K. Monitoring miRNA-mediated silencing in Drosophila melanogaster S2-cells. Biochim Biophys Acta, vol 1779, no. 11, pp. 766-772, 2008.
                                  Aumiller V, Förstemann K. Roles of microRNAs beyond development--metabolism and neural plasticity. . ;1779(11):. Biochim Biophys Acta, vol 1779, no. 11, pp. 692-696, 2008.
                                    S. Barth, T. Pfuhl, A. Mamiani, C. Ehses, K. Roemer, E. Kremmer, C. Jaker, J. Hock, G. Meister, F.A. Grasser. Epstein-Barr virus-encoded microRNA miR-BART2 down-regulates the viral DNA polymerase BALF5. Nucleic Acids Res., vol 36, pp. 666–675, Feb 2008.
                                      El-Gogo S, Flach B, Staib C, Sutter G, Adler H. In vivo attenuation of recombinant murine gammaherpesvirus 68 (MHV-68) is due to the expression and immunogenicity but not to the insertion of foreign sequences.. Virology, vol 380, no. 2, pp. 322-327, Oct 25 2008.
                                        2007
                                        Papers
                                        N. Motsch, T. Pfuhl, J. Mrazek, S. Barth, F.A. Grasser. Epstein-Barr virus-encoded latent membrane protein 1 (LMP1) induces the expression of the cellular microRNA miR-146a. RNA Biol, vol 4, pp. 131–137, Nov 2007.
                                          J. Mrazek, S.B. Kreutmayer, F.A. Grasser, N. Polacek, A. Huttenhofer. Subtractive hybridization identifies novel differentially expressed ncRNA species in EBV-infected human B cells. Nucleic Acids Res., vol 35, pp. e73, 2007.
                                            2005
                                            Papers
                                            S. Pfeffer, A. Sewer, M. Lagos-Quintana, R. Sheridan, C. Sander, F.A. Grasser, vanL.F. Dyk, C.K. Ho, S. Shuman, M. Chien, J.J. Russo, J. Ju, G. Randall, B.D. Lindenbach, C.M. Rice, V. Simon, D.D. Ho, M. Zavolan, T. Tuschl. Identification of microRNAs of the herpesvirus family. Nat. Methods, vol 2, pp. 269–276, Apr 2005.
                                              2004
                                              Papers
                                              S. Pfeffer, M. Zavolan, F.A. Grasser, M. Chien, J.J. Russo, J. Ju, B. John, A.J. Enright, D. Marks, C. Sander, T. Tuschl. Identification of virus-encoded microRNAs. Science, vol 304, pp. 734–736, Apr 2004.
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