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Take a look at the publications by the Experimental and Computational Plant Development research group. We are currently updating this section

Preprints

Eva E. Deinum, Athanasius F. M. Marée, Yoselin Benitez-Alfonso, Verônica A. Grieneisen (2025). Modelling symplasmic transport: from biophysical basics to steeper root gradients. bioRxiv 2025.01.01.631002; doi: 

Leonardo Jo, Rianne Kluck, Sara Buti, Julia Holbein, Himanshu Chhillar, Pingtao Ding, Rochus Benni Franke, Kaisa Kajala. (2025) ABA-induced MYB transcriptional module regulates the differentiation trajectory of chickpea exodermis. bioRxiv 2025.01.03.631192; doi: 

Li, L., Helming, T., Wonder, J., van Asselt, G., Pantazopoulou, C. K., van de Kaa, Y. T. R., Kohlen, W., Pierik, R., & Kajala, K. (2024). Brassinosteroid and gibberellin signaling are required for Tomato internode elongation in response to low red: far-red light. bioRxiv, 2024.02.29.582690.

2025

Panicucci, G., Barreto, P., Herzog, M., Lichtenauer, S., Schwarzländer, M., Pedersen, O., & Weits, D. A. (2025). Tools to understand hypoxia responses in plant tissues. Plant Physiology, 197(1), Article kiae624. 

2024

Van Den Herik B, Bergonzi S, Li Y, Bachem CW, Ten Tusscher KH. 2024. A coordinated switch in sucrose and callose metabolism enables enhanced symplastic unloading in potato tubers. Quantitative Plant Biology. 5:Article e4.

Oskam L, Snoek BL, Pantazopoulou CK, van Veen H, Matton SEA, Dijkhuizen R, Pierik R. 2024. A low-cost open-source imaging platform reveals spatiotemporal insight into leaf elongation and movement. Plant Physiology. 195(3):1866-1879.

Cantó-Pastor A, Kajala K, Shaar-Moshe L, Manzano C, Timilsena P, De Bellis D, Gray S, Holbein J, Yang H, Mohammad S, et al. 2024. A suberized exodermis is required for tomato drought tolerance. Nature Plants. 10(1):118-130.

Herrera J, Bensussen A, García-Gómez ML, Garay-Arroyo A, Álvarez-Buylla ER. 2024. A system-level model reveals that transcriptional stochasticity is required for hematopoietic stem cell differentiation. npj Systems Biology and Applications. 10(1):1-21.

Garcia Gomez M, ten Tusscher K. 2024. Computational Root Biology: Illuminating Patterning and Growth Decisions. In Plant Roots: The Hidden Half. CRC Press. pp. 499-514.

Rankenberg T, van Veen H, Sedaghatmehr M, Liao CY, Devaiah MB, Stouten EA, Balazadeh S, Sasidharan R. 2024. Differential leaf flooding resilience in Arabidopsis thaliana is controlled by ethylene signaling-activated and age-dependent phosphorylation of ORESARA1. Plant Communications. 5(6):Article 100848.

Taylor T, Daksa J, Shimels MZ, Etalo DW, Thiombiano B, Walmsey A, Chen AJ, Bouwmeester HJ, Raaijmakers JM, Brady SM, et al. 2024. Evaluating Mechanisms of Soil Microbiome Suppression of Striga Infection in Sorghum. Bioprotocol. 14(17):Article e5058.

Li L, Wonder J, Helming T, van Asselt G, Pantazopoulou CK, van de Kaa Y, Kohlen W, Pierik R, Kajala K. 2024. Evaluation of the roles of brassinosteroid, gibberellin and auxin for tomato internode elongation in response to low red:farred light. Physiologia Plantarum. 176(5):Article e14558.

Huber M, de Boer HJ, Romanowski A, van Veen H, Buti S, Kahlon PS, van der Meijden J, Koch J, Pierik R. 2024. Far-red light enrichment affects gene expression and architecture as well as growth and photosynthesis In rice. Plant Cell and Environment. 47(8):2936-2953.

Jiménez JDLC, Mustroph A, Pedersen O, Weits DA, Schmidt-Schippers R. 2024. Flooding stress and responses to hypoxia in plants. Functional Plant Biology. 51(4):Article FP24061.

Jo L, Kajala K. 2024. ggPlantmap: an open-source R package for the creation of informative and quantitative ggplot maps derived from plant images. Journal of Experimental Botany. 75(17):5366-5376.

Eswaran G, Zhang X, Rutten JP, Han J, Iida H, López Ortiz J, Mäkilä R, Wybouw B, Planterose Jiménez B, Vainio L, et al. 2024. Identification of cambium stem cell factors and their positioning mechanism. Science (New York, N.Y.). 386(6722):646-653.

Gautrat P, Matton SEA, Oskam L, Shetty SS, van der Velde KJ, Pierik R. 2024. Lights, location, action: shade avoidance signalling over spatial scales. Journal of Experimental Botany.

García-Gómez ML, ten Tusscher K. 2024. Multi-scale mechanisms driving root regeneration: From regeneration competence to tissue repatterning. Plant Journal. 119(3):1183-1196.

Gautrat P, Buti S, Romanowski A, Lammers M, Matton SEA, Buijs G, Pierik R. 2024. Phytochrome-dependent responsiveness to root-derived cytokinins enables coordinated elongation responses to combined light and nitrate cues. Nature Communications. 15(1):Article 8489.

Manzano C, Morimoto KW, Shaar-Moshe L, Mason GA, Cantó-Pastor A, Gouran M, De Bellis D, Ursache R, Kajala K, Sinha N, et al. 2024. Regulation and function of a polarly localized lignin barrier in the exodermis. Nature Plants.

Noordijk B, Garcia Gomez ML, ten Tusscher KHWJ, de Ridder D, van Dijk ADJ, Smith RW. 2024. The rise of scientific machine learning: a perspective on combining mechanistic modelling with machine learning for systems biology. Frontiers in Systems Biology. 4:Article 1407994.

Kawa D, Thiombiano B, Shimels MZ, Taylor T, Walmsley A, Vahldick HE, Rybka D, Leite MFA, Musa Z, Bucksch A, et al. 2024. The soil microbiome modulates the sorghum root metabolome and cellular traits with a concomitant reduction of Striga infection. Cell Reports. 43(4):Article 113971.

Li L. 2024. Tomato Shade Avoidance: Unraveling Internode Elongation and Hormonal Harmony. Utrecht ľ�ϸ���Ӱ��. 259 p.

Jo L, Nodine MD. 2024. "To remember or forget: Insights into the mechanisms of epigenetic reprogramming and priming in early plant embryos". Current Opinion in Plant Biology. 81:Article 102612.

Janacek DP, Kolb M, Schulz L, Mergner J, Kuster B, Glanc M, Friml J, ten Tusscher K, Schwechheimer C, Hammes UZ. 2024. Transport properties of canonical PIN-FORMED proteins from Arabidopsis and the role of the loop domain in auxin transport. Developmental Cell. 59(24):3259-3271.e4.

2023

Pantazopoulou, C. K., Buti, S., Nguyen, C. T., Oskam, L., Weits, D. A., Farmer, E. E., et al. (2023). Mechanodetection of neighbor plants elicits adaptive leaf movements through calcium dynamics. Nature Communications, 14(1), 5827.

Dalle Carbonare, L., Basile, A., Rindi, L., Bulleri, F., Hamedeh, H., Iacopino, S., et al. (2023). Dim artificial light at night alters gene expression rhythms and growth in a key seagrass species (Posidonia oceanica). Scientific Reports, 13(1), 10620.

Kunkowska, A. B., Fontana, F., Betti, F., Soeur, R., Beckers, G. J. M., Meyer, C., et al. (2023). Target of rapamycin signaling couples energy to oxygen sensing to modulate hypoxic gene expression in Arabidopsis. Proceedings of the National Academy of Sciences, 120(3), e2212474120.

Weits, D. A., Zhou, L., Giuntoli, B., Carbonare, L. D., Iacopino, S., Piccinini, L., Lombardi, L., Shukla, V., Bui, L. T., Novi, G., van Dongen, J. T., & Licausi, F. (2023). Acquisition of hypoxia inducibility by oxygen sensing N-terminal cysteine oxidase in spermatophytes. Plant Cell Environ, 46(1), 322-338. doi: 10.1111/pce.14440.

Caspi, Y., Pantazopoulou, C. K., Prompers, J. J., Pieterse, C. M. J., Pol, H. H., & Kajala, K. (2023). Why did glutamate, GABA, and melatonin become intercellular signalling molecules in plants? eLife, 12, e83361.

Jo, L., & Kajala, K. (2023). ggPlantmap: an R package for creation of informative and quantitative ggplot maps derived from plant images. doi: .