Publications

Dissertations

  • Mathematical Modelling of the Floral Transition. PhD thesis. Jean-Louis Dinh (http://eprints.nottingham.ac.uk/id/eprint/45106). Defense on 24/04/2017.
  • The analysis of PWWP INTERACTOR OF POLYCOMBS 1 (PWO1), a putative link between Polycomb-mediated repression and nuclear periphery. Evolutionary studies of Polycomb-mediated repression in the unicellular algae. Pawel Mikulski. Defense on 31/03/2017.
  • Characterisation of transcriptional and chromatin events in relation to floral transition and identification of nuclear organisation determinants. PhD thesis. Stefania Del Prete (unpublished). Defense on 21/03/2017.
  • Statistical analysis and modelling of nuclear architecture in Arabidopsis thaliana. PhD thesis. Javier Arpón. Defense on 09/11/2016.
  • Characterization of transcriptional enhancers in plants using Arabidopsis thaliana and Zea mays as models. PhD thesis. Johan Zicola (unpublished). Defense on 06/06/2016.

Publications

  • Weber, B.*, Oka, R.*, Zicola, J.*, Stam, M. (2016). Plant Enhancers: A Call for Discovery. Trends in Plant Science 21 (2016), pp. 974-987. doi: 10.1016/j.tplants.2016.07.013. *co-first authors.
  • Rurika Oka*, Johan Zicola*,Blaise Weber*, Charlie Hodgman, Jonathan Gent, Jan-Jaap Wesselink, Huub C.J. Hoefsloot, Franziska Turk, Maike Stam (2017). Genome-wide Mapping of Transcriptional Enhancers Using Chromatin Features in Zea mays.  Genome Biology 18:137. doi: 10.1186/s13059-017-1273-4. *co-first authors.
  • Hohenstatt ML*, Mikulski P*, Komarynets O, Klose C, Kycia I, Jeltsch A, Farrona S**, Schubert D**. PWWP-DOMAIN INTERACTOR OF POLYCOMBS11 interacts with Polycomb-group proteins and histones and regulates Arabidopsis flowering and development. Plant Cell. 2018 Jan 12. pii: tpc.00117.2017. doi: 10.1105/tpc.17.00117. (* and ** = equal contribution).
  • Mikulski P*, Hohenstatt ML*, Farrona S, Smaczniak C, Kaufmann K, Angenent G, Schubert D. PWWP INTERACTOR OF POLYCOMBS (PWO1) links PcG-mediated gene repression to the nuclear lamina in Arabidopsis. BioRxiv. 2017 Nov 16. doi: https://doi.org/10.1101/220541. (* = equal contribution)
  • Mikulski P, Komarynets O, Fachinelli F, Weber APM, Schubert D. Characterization of the Polycomb-Group Mark H3K27me3 in Unicellular Algae. Front Plant Sci. 2017 Apr 26;8:607. doi: 10.3389/fpls.2017.00607.
  • Weber, B.*, Jamge. S.*, Stam, M.E. 3C in Maize and Arabidopsis (2017). Marian Bemer and Celia Baroux (eds.), Plant Chromatin Dynamics: Methods and Protocols, Methods in Molecular Biology, vol. 1675, pp 247-270. DOI 10.1007/978-1-4939-7318-7_15. *co-first authors.
  • Weber, B.*, Jamge. S.*, Stam, M.E. 3C in Maize and Arabidopsis (2017). Marian Bemer and Celia Baroux (eds.), Plant Chromatin Dynamics: Methods and Protocols, Methods in Molecular Biology, vol. 1675, pp 247-270. DOI 10.1007/978-1-4939-7318-7_15. *co-first authors.
  • Jamge S., Angenent G.C, Bemer M. Identification of in planta protein-protein interactions using IP-MS.  Marian Bemer and Celia Baroux (eds.), Plant Chromatin Dynamics: Methods and Protocols, Methods in Molecular Biology, vol. 1675, pp 315-329. DOI 10.1007/978-1-4939-7318-7_18.
  • Suraj Jamge, Maike E. Stam, Richard G.H. Immink, Gerco C. Angenent. (2017) A cautionary note on the use of chromosome conformation capture in plants. Plant Methods 13: 101. DOI 10.1186/s13007-017-0251-x.
  • Kathrin Lauss, René Wardenaar, Rurika Oka, Marieke H.A. van Hulten, Damar T. Anggoro, Frank Becker, Victor Guryev, Joost J.B. Keurentjes, Maike Stam*, Frank Johannes*. Parental DNA methylation states are associated with heterosis in epigenetic hybrids. *Corresponding co-last authors. Plant Physiology. doi: 10.1104/pp.17.01054.
  • Damar Tri Anggoro, MariliisTark-Dame, Aimee Walmsley, Rurika Oka, Mara de Sain, Maike Stam (2017). BIBAC-GW-based vectors for generating reporter lines for site-specific genome editing in planta. Plasmid 89, pp. 27-36. doi.org/10.1016/j.plasmid.2016.12.002
  • Bey T, Koini M, and Fransz P: Fluorescence in situ hybridization and immunolabeling on 3-dimensionally preserved nuclei. Marian Bemer and Celia Baroux (eds.), Plant Chromatin Dynamics: Methods and Protocols, Methods in Molecular Biology, vol. 1675, pp 467-480. DOI 10.1007/978-1-4939-7318-7_27.
  • Molitor, A., Latrasse, D., Zytnicki, M., Andrey, P., Houba-Herin, N., Hachet, M., Battail, C., Del Prete, S., Alberti, A., Quesneville, H., and Gaudin, V. (2016). The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 subunit LHP1 function in concert to regulate the transcription of stress-responsive genes. Plant Cell 28, 2197-2211.
  • Javier Arpon, Valérie Gaudin and Philippe Andrey. A method for testing random spatial models on nuclear object distributions. Marian Bemer and Celia Baroux (eds.), Plant Chromatin Dynamics: Methods and Protocols, Methods in Molecular Biology, vol. 1675, pp 493-507. DOI 10.1007/978-1-4939-7318-7_29
  • JL Dinh, E Farcot, C Hodgman (2017). The logic of the floral transition: reverse-engineering the switch controlling the identity of lateral organs. PLoS Computational Biology 13 (9): e1005744. doi.org/10.1371/journal.pcbi.1005744
  • Weber B., Zicola J., Oka R., Stam M. Plant enhancers: A call for discovery. Accepted on July 29th 2016 by Trends in Plant Science.
  • Till Bey, Suraj Jamge, Sonja Klemme, Dorota Natalia Komar, Sabine Le Gall, Pawel Mikulski, Martin Schmidt, Johan Zicola & Alexandre Berr, 2016. Chromatin and epigenetics in all their states: Meeting report of the first conference on Epigenetic and Chromatin Regulation of Plant Traits – January 14 – 15, 2016 – Strasbourg, France. Epigenetics, 2016: ISSN: 1559-2294,  http://www.tandfonline.com/doi/full/10.1080/15592294.2016.1185580
  • Komar, D. N., Mouriz, A., Jarillo, J. A., Piñeiro, M. Chromatin Immunoprecipitation Assay for the Identification of Arabidopsis Protein-DNA Interactions In Vivo. J. Vis. Exp. (107), 2016, e53422, doi:10.3791/53422.
  • Del Prete S, Mikulski P, Schubert D, Gaudin V. One, Two, Three: Polycomb Proteins Hit All Dimensions of Gene Regulation. Genes (Basel). 2015 Jul 10;6(3):520-42, 2015.3390/genes6030520
  • Le Roux C, Del Prete S, Boutet-Mercey S, Perreau F, Balague C, Roby D, Fagard M, Gaudin V. The hnRNP-Q protein LIF2 participates in the plant immune response. PLoS One 9;6:e99343, 2014.
  • Del Prete S, Arpón J, Sakai K, Andrey P, Gaudin V. Nuclear architecture and chromatin dynamics in interphase nuclei of Arabidopsis thaliana. Cytogenetic and Genome Research, 143, 28–50, 2014.