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  • Fischer T, Tschernig T, Drews F, Brix K, Meier C,  Simon M, Kautenburger R, Schneider M
    siRNA delivery to macrophages using aspherical, nanostructured microparticles as a delivery system for pulmonary administration
    European Journal of Pharmaceutics and Biopharmaceutics,
  • Drews F, Karunanithi S, Götz U, Marker S, deWijn R, Pirritano M, Rodrigues-Viana AM, Jung M, Gasparoni G, Schulz MH, Simon M
    Two Piwis with Ago-like functions silence somatic genes at the chromatin level
  • Karunanithi S, Oruganti V, deWijn R, Drews F, Cheaib M, Nordström K, Simon M*, Schulz MH*
    Feeding exogenous dsRNA interferes with endogenous sRNA accumulation in Paramecium
    DNA Research, 27  dsaa005, *co-corresponding authors
  • Pirritano M, Zaburannyi N, Grosser K, Gasparoni G, Müller R, Simon M*, Schrallhammer M*
    Dual-seq revearls genome and transcriptome of Caedibacter taeniospiralis, obligate endosymbiont of Paramecium
    Scientific reports, 10  DOI: 10.1038/s41598-020-65894-1  *co-corresponding authors



  • Giehr S, Simon M, Gasparoni G, Khalifa S, Schulz MH, Schmitt MJ, Breinig F.
    Yeast viral killer toxin K1 induces specific host cell adaptions via intrinsic selection pressure
    Applied and Environmental Microbiology, doi: 10.1128/AEM.02446-19. 2019.
  • Meistertzheim M, Fehlmann T, Drews F, Pirritano M, Gasparoni G, Keller A, Simon M.
    Comparative analysis of biochemical biases by ligation- and templateswitch-based small RNA library peparation methods
    Clinical Chemistry, 65:1581-1591. 2019.
  • Hickl D, Drews F, Girke C, Zimmer D, Muehlhaus T, Hauth J, Nordström K, Trentmann O, Neuhaus E, Fehlmann T, Keller A, Simon M, Möhlmann T.
    Differential degradation of RNA species by autophagy related pathways in plants
  • Blum A, Khalifa S, Nordström K, Simon M, Schulz M, Schmitt MJ.
    Transcriptomics of a KDELR1 knockout cell line reveals modulated cell adhesion properties
    Scientific Reports 9; Doi:10.1038/s41598-019-47027-5. 2019.
  • Karunanithi S, Oruganti V, Marker S, Rodriguez-Viana AM, Drews F, Pirritano M, Nordström K, Simon M*, Schulz MJ*.
    Exogenous RNAI mechanisms contribute to transcriptome adaptation by phased siRNA clusters in Paramecium
    Nucleic Acids Research 47: doi: 10.1093/ner/gkz227. 2019. *co-corresponding authors
  • Giehr S, Simon M, Nordström K, Khalifa S, Schulz MH, Schmitt MJ, Breinig F.
    Transcriptome Kinetics of Saccharomyces cerevisiae in response to viral killer toxin K1
    Frontiers in microbiology 10 Doi:10..3389/fmicb.2019.01102. 2019.
  • Karunanithi S, Simon M, Schulz MH
    Automated anlysis of small RNA datasets with RAPID
    Peer Journal 7:e6710. 2019.
  • Fehlmann T, Backes C, Pirritano M, Laufer T, Galata V, Hern F, Kahraman M, Gasparoni G, Ludwig N, Lenhof H-P, Gregersen HAA, Franke R, Meese E, Simon M, Keller A.
    The sncRNA Zoo: a repository for circulating small noncoding RNAs in animals
    Nucleic Acids Research 47: 4431-4441. 2019.



  • Pirritano M, Fehlmann T, Laufer T, Ludwig N, Gasparoni G, Li Y, Meese E, Keller A, Simon M.
    NGS analysis of total small non coding RNAs from low input RNA from dried blood sampling
    Analytical Chemistry, 16: 11791-11796. 2018.
  • Dehghani Amirabad A, Ramasamy P, Wierz M, Nordström K, Kessler SM, Schulz MH, Simon M.
    Transgenic expression of the RNA binding protein IMP2 stabilizes miRNA targets in murine microsteatosis
    BBA - Molecular Basis of Disease doi:10.1016/j.bbadis.2018.05.024 . 2018.
  • Pirritano M, Götz U, Karunanithi S, Nordström K, Schulz MH, Simon M.
    Environmental temperature controls accumulation of transcacting siRNAs invovled in heterochromatin formation
    Genes, 9(2), 117 . 2108.
  • Grosser K, Ramasamy P, Amirabad A, Schulz MH, Gasparoni G, Simon M, Schrallhammer M.
    More than the 'killer trait': infection with the bacterial endosymbiont Caedibacter taeniospiralis causes transcriptomic modulation in Paramecium host
    Genome Biology and Evolution DOI10.1093/gbe/evy024. 2018.
  • Zaburannyi N, Grosser K, Gasparoni G, Müller G, Schrallhammer M, Simon M.
    Draft Genome Sequence and Annotation of the Obligate Bacterial Endosymbiont Caedibacter taeniospiralis , Causative Agent of the Killer Phenotype in Paramecium tetraurelia
    Genome Announcements 6(3):e01418-17. 2018


  • Staudt E, Ramasamy P, Plattner H, Simon M.
    Differential subcellular distribution of four phospholipase C isoforms and secretion of GPI-PLC activity
    BBA - Biomembranes, 1858: 3157-3168. 2016.
  • Götz U, Marker S, Cheaib M, Andresen K, Shreshtha S, Durai D, Nordström K, Schulz MH, Simon M.
    Two sets of RNAi components are required for heterochromatin formation in trans by truncated transgenes
    Nucleic Acids Reseach, doi: 10.1093/nar/gkw267 2016.


  • Cheaib M, Dehghani Amirabad A, Nordström KJV, Schulz MH, Simon M.
    Epigenetic regualtion of serotype expression antagonizes transcriptome dynamics in Paramecium tetraurelia
    DNA Research, 22(4): 1–13.2015.
  • Carradec Q. Götz U, Arnaiz O, Pouch J, Simon M, Meyer E, Marker S.
    Genetic dissection of primary and secondary siRNA biosynthesis in the ciliate Paramecium tetraurelia.
    Nucleic Acids Research, 43: 1818-1833. 2015.


  • Baranasic D, Oppermann T, Cheaib M, Cullum J, Schmidt H, Simon M.
    Genomic characterization of variable surface antigens reveals a telomere position effect as a prerequisite for RNAi-mediated silencing in Paramecium tetraurelia.
    mBio 5: e01328-14. 2014.
  • Simon M, Plattner H.
    Unicellular eukaryotes as models in basic cell and molecular biology – A critical appraisal of their past and future value.
    International Review of Cell and Molecular Biology, 309: 141-198. 2014.


  • Cheaib M, Simon M.
    Dynamic chromatin remodeling of ciliate macronuclear DNA as determined by an optimized Chromatin Immunoprecipitation (ChIP) method for Paramecium tetraurelia.
    Applied Microbiology and Biotechnology, 97: 2661-2670. 2013.
  • Simon M, Kusch J.
    Communicative functions of GPI-anchored surface proteins in unicellular eukaryotes.
    Critical Reviews in Microbiology, doi:10.3109/1040841X.2012.691459 . 2013.


  • Müller A, Klöppel T, Valentine M, VanHouten JL, Simon M.
    Selective and programmed cleavage of GPI-anchored proteins from the surface membrane by phospholipase C.
    Biochimica et Biophysica Acta - Biomembranes, 1818: 117-124. 2012.


  • Marker S, Le Mouël A, Meyer E, Simon M.
    Distinct RNA-dependent RNA polymerases are required for RNAi triggered by double-stranded RNA versus truncated transgenes in Paramecium tetraurelia.
    Nucleic Acids Research, 38: 4092-4107. 2010.
  • Sarathi M, Simon M, Venkatesan C, Thomas J, Ravi M, Madan N, Thiyagarajan S, Hameed ASH.
    Efficacy of bacterially expressed dsRNA specific to different structural genes of white spot syndrome virus (WSSV) to protect shrimp from WSSV infection.
    Journal of Fish Disease 33: 603-607. 2010.


  • Klöppel T, Müller, A, Marker S, Simon M.
    Two isoforms of eukaryotic phospholipase C affecting transport and release of GPI-anchored proteins in vivo.
    European Journal of Cell Biology 88: 577-592. 2009.


  • Sarathi M, Simon M, Ahmed VP, Kumar SR, Hameed AS.
    Silencing VP28 gene of white spot syndrome virus of shrimp by bacterially expressed dsRNA.
    Marine Biotechnology 10: 198-206. 2008.
  • Sarathi M, Simon M, Venkatesan C, Hameed AS.
    Oral administration of bacterially expressed VP28 dsRNA to protect Penaeus monodon from white spot syndrome virus.
    Marine Biotechnology 10: 242-9. 2008.


  • Simon M, Schmidt HJ.
    Antigenic Variation in Ciliates: Antigen, Structure, Function, Expression.
    Journal of Eukaryotic Microbiology 54: 1-7. 2007.


  • Simon M, Marker S, Schmidt HJ.
    Inefficient Serotype Knock Down Leads to Stable Coexistence of Different Surface Antigens on the Outer Membrane in Paramecium tetraurelia.
    European Journal of Protistology 42: 49-53. 2006a.
  • Simon M, Marker S, Schmidt HJ.
    Post-transcriptional control is a strong factor enabling exclusive expression of surface antigens in Paramecium tetraurelia.
    Gene Expression 13: 167-78. 2006b.


  • Simon M, Schmidt HJ.
    Variety of Serotypes of Paramecium primaurelia: Single Epitopes are Responsible for Immunological Differentiation.
    Journal of Eukaryotic Microbiology 52: 319-327. 2005.