2013
71 Blanc, M., Hsieh, W.Y., Robertson, K.A., Kropp K.A., Forster, T., Shui, G., Lacaze, P., Watterson, S., Griffiths, S.J., Spann, N.J., Meljon, A., Talbot, S., Krishnan, K., Douglas F Covey, D.F., Wenk, M.R., Craigon, M., Ruzsics, Z., Haas, J., Angulo, A., Griffiths, W.J., Glass, C.K., Wang, Y., Ghazal, P. The transcription factor STAT-1 couples macrophage synthesis of 25-hydroxycholesterol to the interferon antiviral response. Immunity. 2013 Jan 24;38(1):106-18. doi: 10.1016/j.immuni.2012.11.004. Epub 2012 Dec 27.
70 Che, X., Oliver, S.L., Reichelt, M., Sommer, M.H., Haas, J., Rovi? , T.L., Arvin A.M. ORF11 Protein Interacts with the ORF9 Essential Tegument Protein in Varicella-Zoster Virus Infection. J Virol. 2013 May;87(9):5106-17. doi: 10.1128/JVI.00102-13. Epub 2013 Feb 20.
69 Conrad KD, Giering F, Erfurth C, Neumann A, Fehr C, Meister G, Niepmann M. MicroRNA-122 dependent binding of Ago2 protein to hepatitis C virus RNA is associated with enhanced RNA stability and translation stimulation. PLOS One, 8(2):e56272.
68 Daschkey S., Röttger S., Giri A., Bradtke J., Teigler-Sclegel A., Meister G., Borkhatdt A., Landgraf P. MicroRNAs distinguish cytogenetic subgroups in pediatric AML and contribute to complex regulatory networks in AML-relevant pathways. PLOS One, 8(2):e56334.
67 Jing, L., Chong, T.M., Bruckner, J., Davies, D.H., Felgner, P.L., Wald, A., Haas, J., Verjans, G.M.G.M., Koelle, D.M. Memory CD4 T-cell responses in humans are independent of pathogen persistence and show prolonged maintenance of subdominant specificities. J Immunol. in press.
66 Lankisch P, H. Adler and A. Borkhardt Testing for herpesvirus infection is essential in children with chromosomal-instability syndromes. J of Virology, 87 (2013): 3616-3617.
65 Lenac Roviš T, Bailer SM, Pothineni VR, Ouwendijk WJ, Šimi? H, Babi? M, Mikli? K, Mali? S, Verweij MC, Baiker A, Gonzalez O, von Brunn A, Zimmer R, Früh K, Verjans GM, Jonji? S, Haas J. A comprehensive analysis of Varicella Zoster virus (VZV) proteins using a monoclonal antibody collection. J Virol In press
64 Loedige I., Gaidatzis D., Sack R., Meister G. & Filipowicz W. The mammalian TRIM-NKL protein Trim71/LIN41 is a repressor of mRNA function. Nucleic Acids Research, 1(2):141-55.
63 Russell CD, Haas J. Cyclosporine has a potential role in the treatment of SARS. J Infect. 2013 Feb 6.
62 Sarek G, Ma L, Enbäck J, Järviluoma A, Moreau P, Haas J, Gessain A, Koskinen PJ, Laakkonen P, Ojala PM. Kaposi's sarcoma herpesvirus lytic replication compromises apoptotic response to p53 reactivation in virus-induced lymphomas. Oncogene. 2013 Feb 28;32(9):1091-8.
61 SScholz, B.A., Harth-Hertle, M.L., Malterer, G. Haas, J., Ellwart, J., Schulz, T.F., Kempkes, B. Abortive lytic reactivation of KSHV in CBF1 deficient human B cell lines. PLOS Pathogens. in press.
60 Tahoun, A., Mahajan, S., Paxton, E., Malterer, G., Donaldson, D., O?Shea, M., Roe, A.J., Shaw, D.J., Gally, D.L., Lengeling, A., Mabbott, N., Haas, J. and Mahajan, A. Salmonella transform follicle-associated epithelial cells into antigen sampling M cells to promote their intestinal invasion. Cell Host & Microbe 12(5):645-5669.
59 Vidy A, T. Sacher, H. Adler, S. Jordan, U. H. Koszinowski and Z. Ruzsics Systemic and local infection routes govern different cellular dissemination pathways during gamma-herpesvirus infection in vivo. J Virol, 87 (2013): 4596-4608.
58 Yu X, Seitz S, Pointon T, Bowlin JL, Cohrs RJ, Jonji? S, Haas J, Wellish M, Gilden D. Varicella zoster virus infection of highly pure terminally differentiated human neurons. J Neurovirol. 2013 Feb;19(1):75-81.
2012
57 Bonilla WV, A. Fröhlich, K. Senn, S. Kallert, M. Fernandez, S. Johnson, M. Kreutzfeldt, A. N. Hegazy, C. Schrick, P. G. Fallon, R. Klemenz, S. Nakae, H. Adler, D. Merkler, M. Löhning and D. D. Pinschewer. The Alarmin Interleukin-33 Drives Protective Antiviral CD8+ T Cell Responses Science, 335 (2012): 984-989.
56 Dittmer A, Förstemann K MCMV infection of cultured mouse cells induces expression of miR-7a. J Gen Virol. Mar 21.
55 Dueck A., Ziegler C., Eichner A., Berezikov E. & Meister G. MicroRNAs associated with the different human Argonaute proteins. Nucleic Acids Research, 40(19):9850-62.
54 Erhard F, Lars Dölken, and Ralf Zimmer. RIP-chip enrichment analysis. Bioinformatics, 29(1):77-83 (2013).
53 Erhard, F. and R. Zimmer. Detecting outlier peptides in quantitative high-throughput mass spectrometry data. Journal of Proteomics, 75(11):3230?3239, DOI: 10.1016/j.jprot.2012.03.032.
52 Frohn A., Eberl H.C., Stöhr J., Glasmacher E., Rüdel S., Heismeyer V., Mann M. & Meister G. Dicer-dependent and -independent Argonaute2 protein interaction networks in mammalian cells. Molecular and Cellular proteomics, 11(11):1442-56.
51 Jing, L., Haas, J., Chong, T.M., Bruckner, J.J., Dann, G.C., Dong, L.,Marshak, J.O., McClurkan, C.L., Yamamoto, T.N., Bailer, S.M., Laing, K.J., Wald, A., Verjans, G.M.G.M. and Koelle, D.M. Cross-presentation and genome-wide screening reveal candidate T cells antigens for a herpes simplex virus type 1 vaccine J Clin Invest. 2012 Feb 1;122(2):654-73. doi: 10.1172/JCI60556. Epub 2012 Jan 3.
50 Kappelmann M., Kuphal S., Meister G., Varidom L. & Bosserhoff A.K. MicroRNA miR-125b controls melanoma progression by direct regulation of c-Jun protein expression. Oncogene, in press. doi: 10.1038/onc.2012.307.
49 Li Z., Ender C., Meister G., Moore P.S., Chang Y. & John B. Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Research, 40(14):6787-99.
48 Marcinowski L, Lidschreiber M, Windhager L, Rieder M, Bosse JB, Rädle B, Bonfert T, Györy I, de Graaf M, Prazeres da Costa O, Rosenstiel P, Friedel CC, Zimmer R, Ruzsics Z, Dölken L. Real-time transcriptional profiling of cellular and viral gene expression during lytic cytomegalovirus infection. PLoS Pathogens 2012 Sep;8(9):e1002908.
47 Marcinowski L, Tanguy M, Krmpotic A, Rädle B, Juranic V, Tuddenham L, Chane-Woon-Ming B, Ruzsics Z, Erhard F, Benkartek C, Babic M, Zimmer R, Trgovcich J, Koszinowski UH, Jonjic S, Pfeffer S, Dölken L. Degradation of cellular miR-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo. PLoS Pathog. 2012 Feb;8(2):e1002510. Epub 2012 Feb 9.
46 Motsch N., Imig J., Zhu J.Y., Barth S., Reineke T., Tinguely M., Dueck A., Meister G., Renner C. & Graesser F. MicroRNA profiling of Epstein-Barr Virus-associated NK/T-cell lymphomas by deep sequencing. Plos One, 7(8):e42193.
45 Petri, T., Berchtold, E., Zimmer, R. and C. Friedel. Detection and correction of probe-level artefacts on microarrays BMC Bioinformatics. 2012 May 30;13:114. doi: 10.1186/1471-2105-13-114.
44 R. Ruiss, S. Ohno, B. Steer, R. Zeidler and H. Adler. Murine gammaherpesvirus 68 glycoprotein 150 does not contribute to latency amplification in vivo. Virology Journal, 9 (2012): 107.
43 S. Ohno, B. Steer, C. Sattler and H. Adler. Open reading frame 23 of murine gammaherpesvirus 68 is nonessential for in vitro and in vivo infection Journal of General Virology, 93 (2012): 1076-1080.
42 Sarek, G. Enbaeck, J., Haas, J., Gessain, A. Laakkonen, P. and Ojala, P. Regression of primary effusion lymphoma tumors in vivo requires the restoration of p53 function. Oncogene 2012 Apr 2. doi: 10.1038/onc.2012.118.
41 Treiber T, Treiber N. & Meister G. Regulation of microRNA biogenesis and function. Thromb Haemost, 107(4):605-10.
40 Tuddenham L, Jung JS, Chane-Woon-Ming B, Dölken L, Pfeffer S. Small RNA deep sequencing identifies microRNAs and other small noncoding RNAs from human herpesvirus 6B. Journal of Virology Virol. 2012 Feb; 86(3):1638-49. Epub 2011 Nov 23.
39 Wash, R., Calabressi, S., Franz, S., Goulding, D., Tan, E.P., Nikolov, N., Skarnes, B., Bradley, A., Digard, P., Barclay, W., Haas, J., Efstathiou, S., Kellam, P. Permissive and restricted virus infection of murine embryonic stem cells. J Gen Virol. 93 :2118-30.
38 Windhager L, Bonfert T, Burger K, Ruzsics Z, Krebs S, Kaufmann S, Malterer G, L'hernault A, Schilhabel M, Schreiber S, Rosenstiel P, Zimmer R, Eick D, Friedel CC, Dölken L. Ultra short and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution. Genome Research 2012 Apr 26.
2011
37 Barth S., Meister G. & Grässer F.A. (2011). EBV-encoded miRNAs. Biochim. Biophys. Acta, 1808(11-12):631-640.
36 Erhard, F. and R. Zimmer. Classification of ncRNAs using position and size information in deep sequencing data. Bioinformatics. 26: 18.
35 Geistlinger, L., G. Csaba, R. Küffner, N. Mulder, R. Zimmer. From Sets to Graphs: Towards a Realistic Enrichment Analysis of Transcriptomic Systems. Bioinformatics (2011) 27 (13): i366-i373. doi: 10.1093/bioinformatics/btr228
34 Gonzalez, O. and R. Zimmer. Contextual Analysis of RNAi-based Functional Screens Using Interaction Networks.' Bioinformatics. 2011 Oct 1;27(19):2707-13. Epub 2011 Aug 10.
33 Halenius A, Hauka S, Dölken L, Stindt J, Reinhard H, Wiek C, Hanenberg H, Koszinowski UH, Momburg F, Hengel H. Human cytomegalovirus disrupts the major histocompatibility complex class I Peptide-loading complex and inhibits tapasin gene transcription. J Virol. 2011 Apr;85(7):3473-85. Epub 2011 Jan 19.
32 Imig J., Motsch N., Zhu J.Y., Barth S., Okoniewski M., Reineke T., Tinguely M., Faggioni A., Trivedi P., Meister G., Renner C. & Grässer F.A. microRNA profiling in Epstein-Barr virus-associated B-cell lymphoma. Nucleic Acids Research, 39(5):1880-1893.
31 Küffner, R., T. Petri, P. Tavakkolkhah, L. Windhager, R. Zimmer. Inferring Gene Regulatory Networks by ANOVA. Bioinformatics. 2012 May 15;28(10):1376-82. Epub 2012 Mar 30.
30 Malterer G, Dölken L, Haas J. The miRNA-targetome of KSHV and EBV in human B-cells. RNA Biol. 2011 Jan 1;8(1). [Epub ahead of print]
29 Meister G. Vision: Dicer leaps into view. Nature, 471(7338):308-9.
28 Miller C, Schwalb B, Maier K, Schulz D, Dümcke S, Zacher B, Mayer A, Sydow J, Marcinowski L, Dölken L*, Martin DE, Tresch A*, Cramer P*.* = joined corresponding authors. Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol. 2011 Jan 4;7:458.
27 Röther S. & Meister G. Small RNAs derived from longer non-coding RNAs. Biochimie, 93(11): 1905-1915.
26 Suffert G, Malterer G, Hausser J, Viiliäinen J, Fender A, Contrant M, Ivacevic T, Benes V, Gros F, Voinnet O, Zavolan M, Ojala PM, Haas JG, Pfeffer S. Kaposi's sarcoma herpesvirus microRNAs target caspase 3 and regulate apoptosis. PLoS Pathog. 2011 Dec;7(12):e1002405. Epub 2011 Dec 8.
25 Valen E., Preker P., Andersen P.R., Zhao X., Chen Y., Ender C., Dueck A., Meister G., Sandelin A. & Jensen T.H. Biogenic mechanisms and utilization of small RNAs from human protein-coding genes. Nat. Struct. Mol. Biol., 18(9):1075-82.
2010
24 Adler H. Comment on: Induction of TGF-beta1, not regulatory T cells, impairs antiviral immunity in the lung following bone marrow transplant. (J. of Immunology, 185 (2010): 1350-1351).
23 Buck AH, Perot J, Chisholm MA, Kumar DS, Tuddenham L, Cognat V, Marcinowski L, Dölken L, Pfeffer S. Post-transcriptional regulation of miR-27 in murine cytomegalovirus infection. RNA. 2010 Feb;16(2):307-15. Epub 2010 Jan 4. PubMedPMID: 20047990; PubMed Central PMCID: PMC2811660.
22 Dölken L, Krmpotic A, Kothe S, Tuddenham L, Tanguy M, Marcinowski L, Ruzsics Z, Elefant N, Altuvia Y, Margalit H, Koszinowski UH, Jonjic S, Pfeffer S. Cytomegalovirus microRNAs facilitate persistent virus infection in salivary glands..PLoS Pathog. 2010 Oct 14;6(10):e1001150.
21 Dölken, L., G. Malterer, F. Erhard, S. Kothe, C. C. Friedel, G. Suffert, L. Marcinowski, N. Motsch, S. Barth, M. Beizinger, D. Lieber, S. Bailer, R. Hoffmann, Z. Ruzsics, E. Kremmer, S. Pfeffer, R. Zimmer, U. H. Koszinowski, F. Grässer, G. Meister and J. Haas. Systemic Analysis of Viral and Cellular miRNA Targets in Cells Latently Infected with Human gamma-Herpesviruses through RISC Immunoprecipitation Assays.' Cell Host & Microbe, 7(4): 324-334.
20 Friedel CC, Kaufmann S, Dölken L, Zimmer R. HALO - A Java framework forprecise transcript half-life determination. Bioinformatics. 2010 Mar 17. [Epubahead of print] PubMed PMID: 20299326.
19 Imig, J., Motsch, N., Zhu, J. Y., Barth, S., Okoniewski, M., Reineke, T., Tinguely, M., Faggioni, A., Trivedi, P., Meister, G., Renner, C., and Grässer, F. A. microRNA profiling in Epstein-Barr virus-associated B-cell lymphoma. Nucleic Acids Res.
18 Petri Nets with Fuzzy Logic (PNFL): reverse engineering and parametrization.' PLoS One 5(9): e12807. Kuffner, R., T. Petri, L. Windhager, R. Zimmer
17 Naeem, H., R. Küffner, G. Csaba and R. Zimmer. miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature.' BMC Bioinformatics. 11: 135.
16 Steer, B. Adler, S. Jonjic, J. P. Stewart, and H. Adler. A gammaherpesvirus complement regulatory protein promotes initiation of infection by activation of protein kinase Akt/PKB (PLoS ONE, 5 (7) (2010): e11672).
15 Szczyrba, J., Loprich, E., Wach, S., Jung, V., Unteregger, G., Barth, S., Grobholz, R., Wieland, W., Stohr, R., Hartmann, A., Wullich, B., and Grässer, F. The MicroRNA Profile of Prostate Carcinoma Obtained by Deep Sequencing. Mol Cancer Res 8(4), 529-38.
14 Weintz G, Olsen JV, Frühauf K, Niedzielska M, Amit I,Jantsch J, Mages J, Frech C, Dölken L, Mann M, Lang R. The Phosphoproteome of Toll-like Receptor (TLR)-Activated Macrophages, Molecular Systemsbiology,accepted 4/2010
13 Zhu J.Y., Strehle M., Frohn A., Kremmer E., Höfig K.P., Meister G. & Adler H. Identification and analysis of expression of novel microRNAs of murine gammaherpesvirus 68. J. Virol., 84(19): 10266-75.
2009
12 Adler H., S. El-Gogo, K. Freimüller, S. Guggemoos, W. Zimmermann, N. Beauchemin and Kammerer, R.: Perturbation of lytic and latent gammaherpesvirus infection in the absence of the inhibitory receptor CEACAM1. PLoS One, 4 (7) (2009): e6317. doi:10.1371/ journal.pone.0006317
11 Dölken L, Jonjic S. All for one and one for all: herpesviral microRNAs closein on their prey. Cell Host Microbe. 2009 Apr 23;5(4):315-7. PubMed PMID:19380110.
10 Dölken L, Pfeffer S, Koszinowski UH. Cytomegalovirus microRNAs. Virus Genes.2009 Jun;38(3):355-64. Epub 2009 Mar 17. Review. PubMed PMID: 19291384.
9 Flach B., B. Steer, N. N. Thakur, J. Haas and Adler, H.: The M10 locus of murine gammaherpesvirus 68 contributes to both the lytic and latent phases of infection. J. of Virology 83 (2009): 8163-8172
8 Friedel CC, Dölken L, Ruzsics Z, Koszinowski UH, Zimmer R. Conservedprinciples of mammalian transcriptional regulation revealed by RNA half-life. Nucleic Acids Res. 2009 Sep;37(17):e115. Epub 2009 Jun 26. PubMed PMID: 19561200;PubMed Central PMCID: PMC2761256.
7 Friedel CC, Dölken L. Metabolic tagging and purification of nascent RNA:implications for transcriptomics. Mol Biosyst. 2009 Nov;5(11):1271-8. Epub 2009Aug 26. Review. PubMed PMID: 19823741.
6 Kocks J.R., H. Adler, H. Danzer, K. Hoffmann, D. Jonigk, U. Lehmann and Förster R.: Chemokine receptor CCR7 contributes to a rapid and efficient clearance of lytic MHV-68 from the lung while bronchus-associated lymphoid tissue harbours virus during latency. J. of Immunology 182 (2009): 6861-6869
5 Zhu J.Y., Pfuhl T., Motsch N., Barth S., Nicholls J., Grässer F. & Meister G. (2009) Identification of novel Epstein-Barr Virus microRNA genes from Nasopharyngeal Carcinomas. Journal of Virology, 83(7):3333-41.
2008
4 Dölken L, Haas J. Small noncoding RNA: novel targets for antiviral therapy. Future Microbiol. 2008 Dec;3(6):585-8. PubMed PMID: 19072174.
3 Dölken L., Z. Ruzsics, B. Radle, C. C. Friedel, R. Zimmer, J. Mages, R. Hoffmann, P. Dickinson, T. Forster, P. Ghazal and U. H. Koszinowski (2008). High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA 14(9): 1959-72.
2 El-Gogo S., B. Flach, C. Staib, G. Sutter and 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 380 (2008): 322-327
1 Erhard, F., C. C. Friedel and R. Zimmer (2008). FERN - a Java framework for stochastic simulation and evaluation of reaction networks. BMC Bioinformatics 9: 356.
