Ausgewählte Publikationen

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Research articles

1.    Trost, N., Rempel, E., Ermakova, O., Tamirisa, S., Parcalabescu, L., Boutros, M., Lohmann, J. U. and Lohmann, I. (2018) WEADE: a workflow for enrichment analysis and data exploration. PLoS One13; e0204016. 

2.    Kim, J. Y.,Yang, W., Forner, J., Lohmann, J. U., Noh, B.,and Noh, Y. S. (2018) Epigenetic reprogramming by histone acetyltransferase HAG1/AtGCN5 is required for pluripotency acquisition in Arabidopsis. EMBO Journal e98726.

3.    Schuerholz, A. K., Lopez-Salmeron, V., Li, Z., Forner, F., Wenzl, C., Gaillochet, C., Augustin, S., Vilches Barro, A., Fuchs, M., Gebert, M., Vermeer J. E. M., Lohmann, J. U. Greb, T., Wolf, S. (2018) A Comprehensive Tool Set for Inducible, Cell Type-Specific Gene Expression in Arabidopsis. Plant Physiology 178, 40-53.

4.    Papagiannouli, F., Tamirisa, S., Rempel, E., Ermakova, O., Trost, N., Zhou, J., Mundorf, J., Brunel, S., Ruhland, N., Boutros, M., Lohmann, J.U., and Lohmann, I. (2018) Decoding the regulatory logic of the Drosophila male stem cell system. Cell Reports 24, 3072-3086. 

5.    Gaillochet, C., Jamge, S., van der Wal, F., Angenent, G., Immink, R., and Lohmann, J. U. (2018) A molecular framework for functional versatility of HECATE transcription factors. Plant Journal95, 57-70. 

6.    Brackmann, K., Qi, J., Gebert, M., Jouannet, V., Schlamp, T., Grünwald, K., Wallner, E. S., Novikova, D.D., Levitsky, V.G., Agustí, J., Sanchez, P., Lohmann, J. U.,Greb, T. (2018) Spatial specificity of auxin responses coordinates wood formation. Nature Communications 9, 875. 

7.    Gaillochet, C., Stiehl, T., Wenzl, C., Ripoll, J. J., Bailey-Steinitz, L. J., Pfeiffer, A., Miotk, A., Hakenjos, J., Forner, J., Yanofsky, M. F., Marciniack-Czochra, A., and Lohmann, J. U. (2017) Control of plant cell fate transitions by transcriptional and hormonal signals. eLife6, e30135.

8.     Luís Balaguer, M. A., Fisher, A. P., Clark, N. M., Fernandez-Espinosa, M. G., Möller, B. K., Weijers, D., Lohmann, J. U., Williams, C., Lorenzo, O., Sozzani, R. (2017) Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells. Proc. Nat. Acad. Sci. USA114, E7632-E7640.

9.    Zhao, X., Bramsiepe, J., Van Durme, M., Komaki, S., Prusicki, M. A., Maruyama, D., Forner, J., Medzihradszky, A., Wijnker, E., Harashima, H., Lu, Y., Schmidt, A., Guthörl, D., Logroño, R. S., Guan, Y., Pochon, G., Grossniklaus, U., Laux, T., Higashiyama, T., Lohmann, J. U., Nowack, M. K., and Schnittger, A. (2017) RETINOBLASTOMA RELATED1 mediates germline entry in ArabidopsisScience 356, eaaf6352.

10.  Pfeiffer, A., Janocha, D., Dong, Y., Medzihradszky, A., Schöne, S., Daum, G., Suzaki, T., Forner, J., Langenecker, T., Rempel, E., Schmid, M., Wirtz, M., Hell, R., and Lohmann J.U. (2016) Integration of light and metabolic signals for stem cell activation at the shoot apical meristem. eLife5, e17023.

11.  Kriegel, A., Andrés, Z., Medzihradszky, A., Krüger, F., Scholl, S., Delang, S., Patir-Nebioglu, M. G., Gute, G., Yang, H., Murphy, A.S., Peer, W. A., Pfeiffer, A., Krebs, W., Lohmann, J. U., and Schumacher, K. (2015) Job sharing in the endomembrane system: vacuolar acidification requires the combined activity of V-ATPase and V-PPase. Plant Cell 27, 3383-96.

12.  Schuster, C., Gaillochet, C., and Lohmann, J.U. (2015) Arabidopsis HECATE genes function in phytohormone control during gynoecium and fruit development. Development 142, 3343-50.

13.  Marín-de la Rosa, N., Pfeiffer, A., Hill, K., Locascio, A., Bhalerao, R., Miskolczi, P., Grønlund, A. L., Wanchoo-Kohli, A., Thomas, S. G., Bennett, M. J., Lohmann J. U., Blázquez,M. A., and Alabadí,D. (2015) Transcriptional co-activation of cytokinin-responsive genes by DELLA proteins. PLOS Genetics7, e1005337.

14.  Forner, J., Pfeiffer, A., Langenecker, A., Manavella, P., and Lohmann, J. U.  (2015) Germline-transmitted genome editing in Arabidopsis thaliana using TAL-Effector-Nucleases. PLOS ONE 10,e0121056.

15. Yang, H., von der Fecht-Bartenbach, J., Friml, J., Lohmann, J. U., Neuhäuser, B., and Ludewig, U. (2015) Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source. Functional Plant Biology 42,239-251.

16.  Daum, G., Medzihradszky, A., Suzaki, T., and Lohmann J.U. (2014) A mechanistic framework of noncell autonomous stem cell induction in Arabidopsis. Proc. Nat. Acad. Sci. USA111, 14619-24.

17.  Vilarrasa-Blasi, J., González-García, M., Frigola, D., Fàbregas, N., Alexiou, K., López-Bigas, N., Rivas, S., Jauneau,A., Lohmann, J. U.,Benfey, P. N., Ibañes, M., and Caño-Delgado, A. (2014) Regulation of plant stem cell quiescence by a novel Brassinosteroid signaling module. Developmental Cell 30, 36-47.

18.  Schuster, C., Gaillochet, C., Medzihradszky, A., Busch, W., Daum, G., Krebs, M., Kehle, A., and Lohmann, J.U.(2014) A regulatory framework for shoot stem cell control integrating metabolic, transcriptional, and phytohormone signals. Developmental Cell 28, 438-49.

19.  Lampropoulos, A., Sutikovic, Z., Wenzl, C., Maegele, I., Lohmann, J.U.*, and Forner, J. (2013) GreenGate – a novel versatile, and efficient cloning system for plant transgenesis. PLOS One 8, e83043.    *corresponding author

20.  Maier, A. T., Stehling-Sun, S. Offenburger, S. L., and Lohmann, J. U. (2011) The bZIP transcription factor PERIANTHIA: A multifunctional hub for meristem control. Frontiers in Plant Science2, 1-17.

21.  Zhao, Z., Andersen, S. U., Ljung, K., Dolezal, K., Miotk, A., Schultheiss, S. J., and Lohmann, J. U.(2010) Hormonal control of the shoot stem cell niche. Nature 465, 1089-92.

22.  Busch, W., Miotk, A., Ariel, F. D., Zhao, Z., Forner, J., Daum, G., Suzaki, T., Schuster, C., Schultheiß, S. J., Leibfried, A., Haubeiß, S., Ha, N., Chan, R. L., and Lohmann, J. U. (2010) Transcriptional regulation of a plant stem cell niche. Developmental Cell 18, 849-61.

23.  Buechel, S., Leibfried, A., To, J.P.C., Zhao, Z., Andersen, S. U., Kieber, J. J., and Lohmann, J. U.(2010) Role of A-type ARABIDOPSIS RESPONSE REGULATORS in meristem maintenance and regeneration. European Journal of Cell Biology 89, 279-84.

24.  Schultheiss, S. J., Busch, W., Lohmann, J. U., Kohlbacher, O., and Rätsch, G. (2009) KIRMES: Kernel-based identification of regulatory modules in euchromatic sequences. Bioinformatics 25, 2126-33. 

25.  Maier, A. T., Stehling-Sun, S., Wollmann, H., Demar, M., Hong, R. L., Haubeiß, S., Weigel, D., and Lohmann, J. U.(2009) Dual roles of the bZIP transcription factor PERIANTHIA in the control of floral architecture and homeotic gene expression. Development 136, 1613-20.

26. Fulton, L., Batoux, M., Vaddepalli, P., Yadav, R. K., Busch, W., Andersen, S. U., Lohmann, J. U., and Schneitz, K. (2009) DETORQUEO, QUIRKY, and ZERZAUSTRepresent Novel Components Involved in Organ Development Mediated by the Receptor-like Kinase STRUBBELIG in Arabidopsis thaliana. PLOS Genetics 5, e1000355.

27.  Geier, F., Lohmann J. U*., Gerstung, M., Maier, A. T., Timmer J., and Fleck, C. (2008) A quantitative and dynamic model for plant stem cell regulation.  PLOS ONE3, e3553. *corresponding author

28.  Skirycz, A., Radziejwoski, A., Busch, W., Hannah, M.A., Czeszejko, J., Kwasniewski, M., Zanor, M.I., Lohmann, J.U., De Veylder, L., Witt, I., Mueller-Roeber, B. (2008) DOF Transcription Factor OBP1 is Involved in Cell Cycle Regulation in Arabidopsis thaliana. Plant Journal 56, 779-92.

29.  Laubinger, S., Sachsenberg, T., Zeller, G., Busch, W., Lohmann, J. U., Rätsch, G., and Weigel, D. (2008) Dual roles of the nuclear cap binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Proc. Nat. Acad. Sci. USA 105, 8795-800.

30.  Brüx, A. Liu, T. Y., Krebs, M., Stierhof, Y. D.,Lohmann, J. U., Miersch, O., Wasternack, C., and Schumacher, K. (2008) Reduced V-ATPase activity in the trans-Golgi network causes oxylipindependent hypocotyl growth inhibition. Plant Cell 20, 1088-100.

31.  Andersen, S. U., Buechel, S., Zhao, Z., Ljung,K., Novák, O., Busch, W., Schuster, C., and Lohmann, J. U.(2008) Requirement of B2-Type Cyclin Dependent Kinases for meristem integrity in Arabidopsis thaliana. Plant Cell 20, 88-100.

32.  Henz, S. R., Cumbie, J., Kasschau, K. D., Lohmann, J. U., Carrington, J. C., Weigel, D., Schmid, M. (2007) Distinct expression patterns of natural antisense transcripts in Arabidopsis. Plant Physiology 144, 1247–55.

33.  Levesque, M. P., Vernoux, T., Busch, W., Cui, H., Wang, J. Y., Blilou, I., Hassan, H., Nakajima, K., Matsumoto, N., Lohmann, J. U., Scheres, B., and Benfey, P. N. (2006) Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLOS Biology 4, 739-52.

34.  Wittlieb, J., Khalturin, K., Lohmann, J. U., Anton-Erxleben, F., and Bosch, T.C.G. (2006) Transgenic Hydra allow in vivo tracking of individual stem cells during morphogenesis in a basal metazoan. Proc. Nat. Acad. Sci. USA 103, 6208-11.

35.  Leibfried, A., To, J. P. C., Stehling, S., Busch, W., Kehle, A., Demar, M., Kieber, J. J., and Lohmann, J. U.(2005) WUSCHEL controls meristem function by direct regulation of cytokinin inducible response regulators. Nature 438,1172-75.

36.  Wigge, P. A., Kim, M.C., Jaeger, K. E., Busch, W., Schmid, M., Lohmann, J. U., and Weigel, D. (2005) Integration of spatial and temporal information during floral induction in Arabidopsis. Science 309, 1056-59.

37.  Schmid, M., Davison, T. S., Henz, S. R., Pape, U. J., Demar, M., Vingron, M., Schölkopf, B., Weigel, D., and Lohmann, J. U. (2005) A gene expression map of Arabidopsis thaliana development. Nature Genetics 37, 501-06.

38.  Schmid, M., Uhlenhaut, N. H., Godard, F., Demar, M., Bressan, R., Weigel, D., and Lohmann J. U.(2003) Dissection of floral induction pathways using global expression analysis. Development 130, 6001-12.

39.  Bosch, T. C. G., Augustin, R., Gellner, K., Khalturin, K., and Lohmann, J. U.(2002) In vivo electroporation for genetic manipulations of whole Hydra polyps. Differentiation 70, 140-47.

40.  Lohmann, J. U., Hong, R., Hobe, M., Busch, M. A., Parcy, F., Simon, R., and Weigel, D. (2001) A molecular link between stem cell regulation and floral patterning in Arabidopsis. Cell 105, 793-803.

41.  Lohmann, J. U.,and Bosch, T. C. G. (2000) The novel peptide HEADY specifies apical fate in a simple radially symmetric metazoan. Genes & Development 14, 2771-77.

42.  Lohmann, J. U., Endl, I., and Bosch, T. C. G. (1999) Silencing of developmental genes in Hydra. Developmental Biology 214, 211-14.

43.  Hampe, W., Urny, J., Franke, I., Hoffmeister-Ullerich, S. A. H., Herrmann, D., Petersen, C. M., Lohmann, J., and Schaller, H. C. (1999) A head-activator binding protein is present in hydra in a soluble and a membrane-anchored form. Development 126, 4077-86.

44.  Endl, I., Lohmann, J. U., and Bosch, T. C. G. (1999) Head-specific gene expression in Hydra: Complexity of DNA-protein interactions at the promoter of ks1 is inversely correlated to the head activation potential. Proc. Natl. Acad. Sci. USA 96, 1445-50.

45.  Takahashi T., Muneoka, Y., Lohmann, J., de Haro, M., Bosch, T. C. G., David, C., Bode, H., Koizumi, O., Shimizu, H., Hatta, M., Fujisawa, T., and Sugiyama, T. (1997) Systematic isolation of peptide signal molecules regulating development in hydra: LWamide and PW families. Proc. Natl. Acad. Sci. USA 94, 1241-46.

46.  Lohmann, J., Schickle, H. P., and Bosch, T. C. G. (1995) REN, a rapid, efficient and non-radioactive method for differential display and isolation of mRNA. BioTechniques 18, 200-202.

Reviews, book chapters and technical reports:

1.     Janocha, D., and Lohmann, J. U. (2018) From signals to stem cells and back again. Current Opinion in Plant Biology 45, 136-142.

2.    Lohmann, J. U., and Janzig, D. (2018) Identification of Causal Dependences in Gene Regulatory Networks using Algorithmic Information Theory. In “Information- and Communication Theory in Molecular Biology” (ed. M. Bossert); Springer Lecture Notes in Bioengineering. Springer Verlag, Heidelberg.

3.     Peiffer, A., Wenzl, C., and Lohmann, J. U.(2017) Beyond flexibility: Controlling stem cells in an ever-changing environment. Current Opinion in Plant Biology35, 117-123. 

4.     Lohmann, J. U., and Janzig, D. (2017) Identification of Causal Dependences in Gene Regulatory Networks using Algorithmic Information Theory. In “Information- and Communication Theory in Molecular Biology” (ed. M. Bossert); Springer Lecture Notes in Bioengineering. Springer Verlag, Heidelberg.

5.     Greb, T. and Lohmann, J. U.(2016) Plant Stem Cells. Current Biology26, R816-R821.

6.     Gaillochet, C., and Lohmann, J. U.(2015) The never-ending story: from pluripotency to plant developmental plasticity. Development142, 2237-49.

7.    Gaillochet, C., Daum, D., and Lohmann, J. U.(2015) O Cell, Where Art Thou? The mechanisms of shoot meristem patterning. Current Opinion in Plant Biology23, 91-97. 

8.    Medzihradszky, A., Schneitz, K., and Lohmann, J. U.(2014) Detection of mRNA expression patterns by non-radioactive in situhybridization on histological sections of floral tissue. Methods in Molecular Biology1110, 275-93.

9.    von Wangenheim, D., Daum, G., Lohmann, J. U.,Stelzer, E. K., and Maizel, A.(2014) Live Imaging of Arabidopsis Development. Methods in Molecular Biology 1062, 539-50.

10.  Lohmann J.U., and Maizel, A. (2013) Developmental plasticity and adaptation in plants. Mechanisms of Development130, 1.

11.  Somorjai, I.M., Lohmann, J.U., Holstein, T.W. and Zhao, Z. (2012) Stem Cells: a view from the roots. Biotechnology Journal.7,704-22. 

12.  Parcy, F., Lohmann, J.U.(2011) June Bloom in Maratea. Development138, 4335-40.

13.  Lohmann, J.U., and Nemhauser, J.L. (2009) Cell signaling and gene regulation. Current Opinion in Plant Biology12, 517-19.

14.  Lohmann J.U.(2008) Plant Stem Cells: Divide et impera. In "Stem cells: from Hydra to man"; Springer Verlag.

15.  Busch, W., and Lohmann, J. U.(2007) Profiling a plant: Expression analysis in Arabidopsis. Current Opinion in Plant Biology10,136–41.

16.  Lohmann, J. U., and Weigel, D. (2004) From though nuts to touch-me-nots. Cell 116, 763-64.

17.  Lohmann, J. U., and Weigel, D. (2002) Building beauty. The genetic control of floral patterning. Developmental Cell2, 135-42.

18.  Bosch, T. C. G., and Lohmann, J. U.(2000) Non-radioactive differential display of messenger RNA. Nucleic Acid Protocols Handbook, 645-51 (ed. R. Rapley). Humana Press, Totowa, NJ.

19.  Reinhardt, B., Frank, U., Gellner, K., Lohmann, J. U., and Bosch, T. C. G. (1999) High resolution, fluorescent-based differential display on a DNA sequencer followed by band excision. BioTechniques 27, 268-71.

20.  Lohmann, J., Schickle, H. P. and Bosch, T. C. G. (1999) Update to: REN, a rapid, efficient and non-radioactive method for differential display and mRNA isolation. BioTechniques Update Series. Expression genetics: Differential display, 327-328 (ed.  A. Pardee and M. McClelland). BioTechniques BooksEaton Publishing, Westborough, MA.

21.  Bosch, T. C. G., and Lohmann, J. U.(1998) Identification of differentially expressed genes by nonradioactive differential display of messenger RNA. Methods in Molecular Biology86, 153-60 (ed. R. Rapley and D.L. Manning), Humana Press, Totowa, NJ.

22.  Lohmann, J. U., Solleder, G., und Bosch, T. C. G. (1997) Identifikation differentiell exprimierter Gene. Laborpraxis10, 18-21.

23.  Bosch, T. C. G., Lohmann, J.(1997) Nonradioactive differential display of messenger RNA. Fingerprinting methods based on arbitrarily primed PCR: 295-304. Springer Lab Manual (ed. MR Micheli and R. Bova). Springer Verlag, Heidelberg.

24.  Lohmann, J., Schickle, H. P., und Bosch, T. C. G. (1997) Nicht-radioaktive „Differential Display“ PCR mit horizontalen Polyacrylamidgelen. Laborpraxis2, 74-78.