1 Corresponding author

2 Shared senior authorship


Rich, C., Reitz, M.U., Eichmann, R., Hermann, S., Woolley-Allen, K., Esteban, E., Pasha, A., Kogel, K.H., Provart, N.J., Ott, S.1, Schäfer, P.1,2 Cell type identity determines transcriptomic immurrrne responses in Arabidopsis thaliana roots. bioRxiv


Schang, A.L., van Steenwinckel, J., Lipecki, J., Rich, C., Woolley-Allen, K., Dyer, N., Le Charpentier, T., Fleiss, B., Schäfer, P., Ott, S., Mezger, V., Saberan-Djoneidi, D., Gressens, P. (2018) Discordant perturbations of transcriptome and epigenome landscapes highlight dual roles of proinflammatory players in normal and IL1B-compromised OPC maturation trajectory in a prenatal model of diffuse white matter injury. bioRxiv


Rich, C., Stechemesser, A.H., Finch, J., Lucas, E.S., Ott, S., Schäfer, P. (2020) Single-cell transcriptomics - a high-resolution avenue for plant functional genomics. Trends in Plant Science 25:186-197.


Li, T., Wang, Q., Feng, R., Fan, G., Li, W., Du, Y., Zhang, M., Schäfer, P., Tyler, B.M., Shan, W. (2019) Negative regulators of plant immunity derived from cinnamyl alcohol dehydrogenases are targeted by multiple Phytophthora Avr3a-like effectors. Accepted in New Phytologist


Lagunas, B., Achom, M., Bonyadi-Pour, R., Pardal, A.J., Richmond, B.L., Sergaki, C., Vázquez, S., Schäfer, P., Ott, S., Hammond, J.P, Gifford, M.L (2019) Regulation of resource partitioning coordinates nitrogen and rhizobia responses and autoregulation of nodulation in the legume Medicago truncatula. Molecular Plant 12: 833-846.


Jiang, X., Zerfaß, C., Feng, S., Eichmann, R., Asally, M., Schäfer, P.1,2, Soyer, OS1,2. (2018) Impact of spatial organization on a novel auxotrophic interaction among soil microbes. ISME J 12:1443-1456.


Quareshy, M., Prusinska, J., Kieffer, M., Fukui, K., Pardal Bermejo, A., Lehmann, S., Schäfer, P., del Genio, C., Kepinski, S., Hayashi, K., Marsh, A., Napier, R. (2018) The tetrazole analogue of the auxin indole-3-acetic acid binds preferentially to TIR1 and not AFB5. ACS Chemical Biology 13: 2585-2594.


Sergaki, C., Lagunas, B., Lidbury, I., Gifford, M.L., Schäfer, P. (2018) Challenges and approaches in microbiome research: from fundamental to applied. Frontiers in Plant Science 9: 1205.


Acevedo-Garcia, J., Gruner, K., Reinstädler, A., Kemen, A., Kemen, E., Cao, L., Takken, F.L.W., Reitz, M.U., Schäfer, P., O'Connell, R.J., Kusch, S., Kuhn, H., Panstruga, R. (2017) The powdery mildew-resistant Arabidopsis mlo2 mlo6 mlo12 triple mutant displays altered infection phenotypes with diverse types of phytopathogens. Scientific Reports 7:9319.


Lareen A, Burton F, Schäfer P (2016) Plant root-microbe communication in shaping root microbiomes. Plant Molecular Biology 90:575-87.


Eichmann, R., Schäfer, P. (2015) Growth versus immunity-a redirection of the cell cycle? Current Opinion in Plant Biology 26:106-112.


Patron, N., Orzaez, D., Marillonnet, S., Warzecha, H., Matthewman, C., Youles, M., Raitskin, O., Leveau, A., Farre-Martinez, G., Rogers, C., Smith, A., Hibberd, J., Webb, A., Locke, J., Schornack, S., Ajioka, J., Baulcombe, D., Zipfel, C., Kamoun, S., Jones, J., Kuhn, H., Robatzek, S., Van Esse, H.P., Oldroyd, G., Sanders, D., Martin, C., Field, R., O'Connor, S., Fox, S., Wulff, B., Miller, B., Breakspear, A., Radhakrishnan, G., Delaux, P.M., Loque, D., Granell, A., Tissier, A., Shih, P., Brutnell, T., Quick, P., Rischer, H., Fraser, P., Aharoni, A., Raines, C., South, P., Ané, J.M., Hamberger, B., Langdale, J., Stougaard, J., Bouwmeester, H., Udvardi, M., Murray, J., Ntoukakis, V., Schäfer, P., Denby, K., Edwards, K., Osbourn, A., Haseloff, J. (2015) Standards for Plant Synthetic Biology: A Common Syntax for Exchange of DNA Parts. New Phytologist 208:13-19.


Reitz, M.U., Gifford, M.L., Schäfer, P. (2015) Hormone activities and the cell cycle machinery in immunity-triggered growth inhibition. Journal of Experimental Botany 66:2187-97.


Lagunas, B., Schäfer, P., Gifford, M.L. (2015) Housing helpful invaders: the evolutionary and molecular architecture underlying plant root-mutualist microbe interactions. Journal of Experimental Botany 66:2177-86.


Döhlemann, G., Requena, N., Schäfer, P., Brunner, F., O’Connell, R., Parker, J.E. (2014) Reprogramming of plant cells by filamentous plant-colonising microbes. New Phytologist 204:803-14.


Brandizzi, F., Frigerio, L., Howell, S.H., Schäfer, P. (2014) Endoplasmic reticulum – shape and function in stress translation. Frontiers in Plant Science 5:1-2.


Reitz, M.U., Pai, S., Imani, J., Schäfer, P. (2013) New insights into the subcellular localization of Tubby-like proteins and their participation in the Arabidopsis-Piriformospora indica interaction. Plant Signaling and Behaviour 8:doi:pii:e25198.


Khatabi, B., Schäfer, P. (2012) Ethylene in mutualistic symbioses. Plant Signaling and Behaviour 12:1634-38.


Eichmann, R., Schäfer, P. (2012) The endoplasmic reticulum in plant immunity and cell death. Frontiers in Plant Proteomics 3:200.


Reitz, M.U., Bissue, J.K., Zocher, K., Attard, A., Hückelhoven, R., Becker, K., Imani, J., Eichmann, R., Schäfer, P. (2012) The subcellular localization of Tubby-like proteins and participation in stress signaling and root colonization by the mutualist Piriformospora indica. Plant Physiology 160:1-16.


Khatabi, B., Molitor, A., Lindermayr, C., Pfiffi, S., Durner, J., von Wettstein, D., Kogel, K.H., Schäfer, P. (2012) Ethylene supports colonization of plant roots by the beneficial fungus Piriformospora indica. PLoS One 7:e35502.


Qiang, X., Zechmann, B,. Reitz, M.U., Kogel, K.H., Schäfer, P. (2012) The mutualistic fungus Piriformospora indica colonizes Arabidopsis roots by inducing an endoplasmic reticulum stress-triggered caspase-dependent cell death. Plant Cell 24:794-809. Featured by Faculty of 1000.


Qiang, X., Weiß, M., Kogel, K.H., Schäfer, P. (2012) Piriformospora indica – a mutualistic basidiomycete with an exceptionally large plant host range. Molecular Plant Pathology 13:508-518.


Jacobs, S., Zechmann, B., Molitor, A., Trujillo, M., Petutschnig, E., Lipka, V., Kogel, K.H., Schäfer, P. (2011) Broad spectrum suppression of innate immunity is required for colonization of Arabidopsis roots by the beneficial fungus Piriformospora indica. Plant Physiology 156:726-40.

Imani, J., Li, L., Schäfer, P.1,2, Kogel, K.H.1 (2011) STARTS – A stable root transformation system for rapid functional analyses of proteins in roots of the monocot model plant barley. Plant Journal 67:726-735.


Kogel, K.H., Voll, L.M., Schäfer, P., Jansen, C., Wu, Y., Langen, G., Imani, J., Hofmann, J., Schmiedl, A., Sonnewald, S., von Wettstein, D., Cook, R.J., Sonnewald, U. (2010) Transcriptome and metabolome profiling of field-grown transgenic barley lack induced differences but show cultivar-specific variations. Proceeding of the National Academy of Sciences of the United States of America 107:6198-6203.


Schäfer, P. 1, Pfiffi, S., Voll, L.M., Zajic, D., Chandler, P.M., Waller, F., Scholz, U., Pons-Kühnemann, J., Sonnewald, S., Sonnewald, U., Kogel, K.H. (2009) Manipulation of plant innate immunity and gibberellin as factor of compatibility in the mutualistic association of barley roots with Piriformospora indica. Plant Journal 59:461-474.


Schäfer, P. 1, Pfiffi, S., Voll, L.M., Zajic, D., Chandler, P.M., Waller, F., Scholz, U., Pons-Kühnemann, J., Sonnewald, S., Sonnewald, U., Kogel, K.H. (2009) Phytohormones in plant root-Piriformospora indica mutualism. Plant Signaling & Behavior 4:669-671. 1Corresponding author.


Sharma, M., Schmid, M., Rothballer, M., Hause, G., Zuccaro, A., Imani, J., Kämpfer, P., Schäfer, P., Hartmann, A., Kogel, K.H. (2008) Detection and identification of mycorrhiza helper bacteria intimately associated with representatives of the order Sebacinales. Cellular Microbiology 10:2235-2246.


Baltruschat, H., Fodor, J., Harrach, B.D., Niemczyk, E., Barna, B., Gullner, G., Janeczko, A., Kogel, K.H., Schäfer, P., Schwarczinger, I., Zuccaro, A., Skoczowski, A. (2008). Salt tolerance of barley induced by the root endophyte Piriformospora indica is associated with a strong increase in antioxidants. New Phytologist 180:501-510.


Waller, F., Mukherjee, K., Achatz, B., Deshmukh, S., Sharma, M., Schäfer, P., Kogel, K.H. (2008) Local and systemic modulation of plant responses by Piriformospora indica and related Sebacinales species. Journal of Plant Physiology 165:60-70.


Felle, H.H., Herrmann, A., Schäfer, P., Hückelhoven, R., Kogel, K.H. (2008) Interactive signal transfer between host and pathogen during successful infection of barley leaves by Blumeria graminis and Bipolaris sorokiniana. Journal of Plant Physiology 165:52-59.


Schäfer, P., Khatabi, B., Kogel, K.H. (2007) Root cell death and systemic effects of Piriformospora indica: a study on mutualism. FEMS Microbiology Letters 275:1-7.


Deshmukh, S.D., Hückelhoven, R., Schäfer, P., Imani, J., Sharma, M., Weiß, M., Waller, F., Kogel, K.H. (2006) The root endophytic fungus Piriformospora indica requires host cell death for proliferation during mutualistic symbiosis with barley. Proceeding of the National Academy of Sciences of the United States of America 103:18450-18457.


Eichmann, R., Biemelt, S., Schäfer, P., Scholz, U., Jansen, C., Felk, A., Schäfer, W., Langen, G., Sonnewald, U., Kogel, K.H., Hückelhoven, R. (2006) Macroarray expression analysis of barley susceptibility and nonhost resistance to Blumeria graminis. Journal of Plant Physiology 163:657-70.


Ibeagha, A.E., Hückelhoven, R., Schäfer, P., Singh, D.P., Kogel, K.H. (2005) Model wheat genotypes as tools to uncover effective defense mechanisms against the hemibiotrophic fungus Bipolaris sorokiniana. Phytopathology 95:528-532.


Schäfer, P., Hückelhoven, R., Kogel, K.H. (2004) The white barley mutant albostrians shows a supersusceptible but symptomless interaction phenotype with the hemibiotrophic fungus Bipolaris sorokiniana. Molecular Plant Microbe Interaction 17:366-73.


Kumar, J., Schäfer, P., Hückelhoven, R., Langen, G., Baltruschat, H., Stein, E., Nagarajan, S., Kogel, K.H. (2002) Bipolaris sorokiniana, a cereal pathogen of global concern: cytological and molecular approaches towards better control. Molecular Plant Pathology 3:185-95.



Book chapters


Jacobs, S., Kogel, K.H., Schäfer, P. (2013) Root-based innate immunity in pathogenic and mutualistic plant-microbe interactions. In: Piriformospora indica - Sebacinales and their Biotechnological Applications (p. 223-238). Ralf Oelmüller, Gerhard Kost and Ajit Varma (Editors). Soil Biology series. Springer Verlag.


Schäfer, P., Kogel, K.H. (2009) The sebacinoid fungus Piriformospora indica: an orchid mycorrhiza which may increase host plant reproduction and fitness. The Mycota, Vol. 5, Plant Relationships. H.B. Deising and K. Esser. eds. Springer-Verlag, Heidelberg. 14 pages.