On-line single cell Browser tool:

https://bioit3.irc.ugent.be/plant-sc-atlas/

Published benchmarks, protocols and resources:

  • Carolin Grones, Thomas Eekhout, Dongbo Shi,  Manuel Neumann,  Lea S. Berg, Yuji Ke, Rachel Shahan, Kevin L. Cox Jr, Hilde Nelissen, Jan U. Lohmann, Stefania Giacomello, Olivier C. Martin, Benjamin Cole, Jia-Wei Wang, Kerstin Kaufmann, Michael T. Raissig, Gergo Palfalvi, Thomas Greb, Marc Libault and Bert De Rybel (2024). Best practices for the execution, analysis and data storage of plant single cell/nucleus transcriptomics. Plant Cell link
  • Ke Y, Minne M, Eekhout T and De Rybel B. (2023) Single Cell RNA-Sequencing in Arabidopsis Root Tissues. In Methods Mol Biol. 2023;2698:41-56.
  • Chang Su, Munan Lyu, A.P. Mähönen, Ykä Helariutta, Bert De Rybel and Sampo Muranen (2023) Cella: 3D data visualization for plant single-cell transcriptomics in Blender. Physiologia Plantarum

Published reviews and research papers from the group involving single cell omics:

  • Claudia von der Mark, Max Minne and Bert De Rybel (2024). Studying plant vascular development using single-cell approaches. Current Opinion in Plant Biology
  • Minne M.°, Ke Y.°, Saura-Sanchez M.° and De Rybel B.* (2022). Advancing root developmental research through single-cell technologies. Curr. Opin. Plant Biol. 65, 102113. 
  • Yang B.*, Minne M., Brunoni F., Plačková L., Petřík I., Sun Y., Nolf J., Smet W., Verstaen K., Wendrich J.R., Eekhout T., Hoyerová K., Van Isterdael G., Haustraete J., Bishopp A., Farcot E., Novák O., Saeys Y. and De Rybel B.* (2021). Non-cell autonomous and spatiotemporal signalling from a tissue organizer orchestrates root vascular development. Nat. Plants 7, 1485-1494. 
  • Seyfferth C.°, Renema J.°, Wendrich J.R., Eekhout T., Seurinck R., Vandamme N., Blob B., Saeys Y., Helariutta Y., Birnbaum K.D.* and De Rybel B.* (2021). Advances and opportunities of single-cell transcriptomics for plant research. Annu. Rev. Plant Biol. 72, 847-866. 
  • Wendrich J.R. °, Yang B.J. °, Vandamme N. °, Verstaen K., Smet W., Van de Velde C., Minne, M., Wybouw B., Mor E., Arents H.E., Nolf J., Van Duyse J., Van Isterdael G., Maere S., Saeys Y.* and De Rybel B.* (2020) Vascular transcription factors control epidermal responses to environmental conditions. Science 370, eaay4970. 

Collaborative publications involving our single cell platform:

  • Xilan Yang, Ward Poelmans, Carolin Grones, Abdellah Lakehal, Julie Pevernagie, Michiel Van Bel, Maria Njo, Lin Xu, Hilde Nelissen, Bert De Rybel, Hans Motte*# and Tom Beeckman*# (2023) Spatial transcriptomics of a lycophyte root sheds light on root evolution Current Biology
  • Eun-Ji Kim, Cheng Zhang, Boyu Guo, Thomas Eekhout, Anaxi Houbaert, Jos R. Wendrich, Niels Vandamme, Manish Tiwari, Claire Simon Vezo, Isabelle Vanhoutte, Yvan Saeys, Kun Wang, Yuxian Zhu, Bert De Rybel, and Eugenia Russinova (2023) Cell type-specific attenuation of brassinosteroid signalling precedes stomatal asymmetric cell division PNAS
  • Trang Hieu Nguyen, Louis Thiers, Alex Van Moerkercke, Yuechen Bai, Patricia Fernández-Calvo, Max Minne, Thomas Depuydt, Kevin Verstaen, Gert Van Isterdael, Hans-Wilhelm Nützmann, Anne Osbourn, Yvan Saeys, Bert De Rybel, Klaas Vandepoele, Andrés Ritter# and Alain Goossens* (2023) A redundant transcription factor network steers spatiotemporal Arabidopsis triterpene synthesis Nat. Plants
  • Roszak P.°, Heo J.-o.°, Blob B.°, Toyokura K.°, Sugiyama Y.§, Angels de Luis Balaguer M.§, Lau W.W.Y.§, Hamey F.§, Cirrone J.§, Madej E., Bouatta A.M., Wang X., Guichard M., Ursache R., Tavares H., Verstaen K., Wendrich J., Melnyk C.W., Oda Y., Shasha D., Ahnert S.E., Saeys Y., De Rybel B., Heidstra R., Scheres B., Grossmann G., Mähönen A.P., Denninger P., Göttgens B., Sozzani R.*, Birnbaum K.D.* and Helariutta Y.* (2021). Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization. Science 374, eaba5531. 
  • Graeff M., Rana S., Wendrich J., Dorier J., Eekhout T., Aliaga Fandino A.C., Guex N., Bassel G., De Rybel B. and Hardtke C.* (2021). A single-cell morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root. Mol. Plant, S1674-2052(21)00312-9.