Publications

Preprints

• Lebovka, I., Mele, B.H., Zakieva, A., Gursanscky, N., Merks, R.M.H., and Greb, T. (2020). Computational modelling of cambium activity provides a regulatory framework for simulating radial plant growth. BioRxiv
• Strauss, S., Runions, A., Lande, B., Eschweiler, D., Bajpai, N., Trozzi, N., Routier-Kierzkwoska, A., Yoshida, S., Rodrigues da Silveira, S., Vijayan, A., Tofanelli, R., Majda, M., Echevin, E., Le Gloanec, C., Bertrand-Rakusova, H., Adibi, M., Schneitz, K., Bassel, G., Kierzkwoski, D., Stegmeier, J., Tsiantis, M., and Smith, R. S., 2021. MorphoGraphX 2.0: Providing context for biological image analysis with positional information. BioRxiv
• Stöckle, D., Reyes-Hernández, B. J., Barro, A. V., Nenadic, M., Winter, Z., Marc-Martin, S., Bald, L., Ursache, R., Fujita, S., Maizel, A., and Vermeer, J. E. (2021) Microtubule-based perception of mechanical conflicts controls plant organ morphogenesis. BioRxiv
• Vijayan, A., Strauss, S., Tofanelli, R., Mody, T. A, Lee, K., Tsiantis, M., Smith, R. S. and Schneitz, K. (2021). The annotation and analysis of complex 3D plant organs using 3DCoordX. BioRxiv
• Wolny, A., Yu, Q., Pape,. C., Kreshuk., A. (2021). Sparse Object-level Supervision for Instance Segmentation with Pixel Embeddings. arXiv:2103.14572v2
• Berthet, Beatrice., Bald, L., Louveaux, M., and Maizel, A. (2022). Progressive maturation of the root apical meristem in Arabidopsis thaliana lateral roots. BioRxiv.
• Stitz, Michael., Kuster, D., Reinert, M., Schepetilnikov, M., Berthet, B., Janocha, D., Artins, A., Boix, M., Henriques, R., Pfeiffer, A., Lohmann, J., Gaquerel, E., Maizel, A. (2022). TOR acts as metabolic gatekeeper for auxin-dependent lateral root initiation in Arabidopsis thaliana. BioRxiv.

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Projects publications

2022

• Athul Vijayan, Soeren Strauss, Rachele Tofanelli, Tejasvinee Atul Mody, Karen Lee, Miltos Tsiantis, Richard S Smith, Kay Schneitz, The annotation and analysis of complex 3D plant organs using 3DCoordX, Plant Physiology, (2022), kiac145, https://doi.org/10.1093/plphys/kiac145

2021

• Vijayan, A., Tofanelli, R., Strauss, S., Cerrone, L., Wolny, A., Strohmeier, J., Kreshuk, A., Hamprecht, F., Smith, R. and Schneitz, K., 2021. A digital 3D reference atlas reveals cellular growth patterns shaping the Arabidopsis ovule. eLife (2021);10:e63262 DOI: 10.7554/eLife.63262
• D. Ramos, J.R., Maizel, A. & Alim, K. Tissue-wide integration of mechanical cues promotes effective auxin patterning. Eur. Phys. J. Plus 136, 250 (2021). https://doi.org/10.1140/epjp/s13360-021-01204-6
• Lilli Marie Schütz, Marion Louveaux, Amaya Vilches Barro, Sami Bouziri, Lorenzo Cerrone, Adrian Wolny, Anna Kreshuk, Fred A Hamprecht, Alexis Maizel, Integration of Cell Growth and Asymmetric Division During Lateral Root Initiation In Arabidopsis thaliana, Plant and Cell Physiology, (2021). pcab038, https://doi.org/10.1093/pcp/pcab038

2020

• Chaudhary, A., Chen, X., Gao, J., Leśniewska, B., Hammerl, R., Dawid, C. and Schneitz, K. (2020). The receptor kinase STRUBBELIG promotes the response to cellulose deficiency in Arabidopsis thaliana. PLoS Genetics
• Galvan-Ampudia, Carlos S, Guillaume Cerutti, Jonathan Legrand, Géraldine Brunoud, Raquel Martin-Arevalillo, Romain Azais, and Vincent Bayle et al. (2020). Temporal Integration Of Auxin Information For The Regulation Of Patterning. Elife 9. doi:10.7554/elife.55832.
• Escamez, S., André, D., Sztojka, B., Bollhöner, B., Hall, H., Berthet, B., Voß, U., Lers, A., Maizel, A., Andersson, M., et al. (2020). Cell Death in Cells Overlying Lateral Root Primordia Facilitates Organ Growth in Arabidopsis. Current Biology S0960982219315805.
• Wolny, A., Cerrone, L., Vijayan, A., Barro, A. V., Louveaux, M., Wenzl, C., Strauss, S., Wilson-Sanchéz, W., Lymbouridou, R., Steigleder, S., Pape, et al. (2020). “Accurate And Versatile 3D Segmentation Of Plant Tissues At Cellular Resolution.” Elife 9. doi: 10.7554/eLife.57613

2019

• Berg, S., Kutra, D., Kroeger, T., Straehle, C.N., Kausler, B.X., Haubold, C., Schiegg, M., Ales, J., Beier, T., Rudy, M., et al. (2019). ilastik: interactive machine learning for (bio)image analysis. Nat Methods.
• Cerrone, L., Zeilmann, A., and Hamprecht, F.A. (2019). End-To-End Learned Random Walker for Seeded Image Segmentation. Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition pp. 12559–12568.
• Khadka, J., Julien, J.-D., Alim, K. (2019) Feedback from tissue mechanics self-organizes efficient outgrowth of plant organ. Biophysical Journal
• Kierzkowski, D., Runions, A., Vuolo, F., Strauss, S., Lymbouridou, R., Routier-Kierzkowska, A.-L., Wilson-Sánchez, D., Jenke, H., Galinha, C., Mosca, G., et al. (2019). A Growth-Based Framework for Leaf Shape Development and Diversity. Cell 177, 1405-1418.e17.
• Pape, C., Matskevych, A., Wolny, A., Hennies, J., Mizzon, G., Louveaux, M., Musser, J., Maizel, A., Arendt, D., Kreshuk, A. (2019). Leveraging Domain Knowledge to Improve Microscopy Image Segmentation with Lifted Multicuts. Frontiers in Computer Science.
• Ramakrishna, P., Duarte, P.R., Rance, G.A., Schubert, M., Vordermaier, V., Vu, L.D., Murphy, E., Barro, A.V., Swarup, K., Moirangthem, K., et al. (2019). EXPANSIN A1-mediated radial swelling of pericycle cells positions anticlinal cell divisions during lateral root initiation. PNAS 116, 8597–8602.
• Tofanelli, R., Vijayan, A., Scholz, S., and Schneitz, K. (2019). Protocol for rapid clearing and staining of fixed Arabidopsis ovules for improved imaging by confocal laser scanning microscopy. Plant Methods 15, 120.
• Vilches Barro, A., Stöckle, D., Thellmann, M., Ruiz-Duarte, P., Bald, L., Louveaux, M., von Born, P., Denninger, P., Goh, T., Fukaki, H., et al. (2019). Cytoskeleton Dynamics Are Necessary for Early Events of Lateral Root Initiation in Arabidopsis. Current Biology 29, 2443-2454.e5.

2018

• Chaudhary, A., Gao, J. and Schneitz, K. (2018). The genetic control of ovule development. Reference Module in Life Sciences, doi:10.1016/B978-0-12-809633-8.20737-1.
• Vuolo, F., Kierzkowski, D., Runions, A., Hajheidari, M., Mentink, R.A., Gupta, M.D., Zhang, Z., Vlad, D., Wang, Y., Pecinka, A., et al. (2018). LMI1 homeodomain protein regulates organ proportions by spatial modulation of endoreduplication. Genes Dev. 32, 1361–1366.

2017

• Runions, A. and Tsiantis, M. (2017), The shape of things to come: From typology to predictive models for leaf diversity. American Journal of Botany, 104: 1437-1441.

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Related publications

• Mergner, J., Frejno, M., List, M., Papacek, M., Chen, X., Chaudhary, A., Samara, P., Richter, S., Shikata, H., Messerer, M., Lang, D., Altmann, S., Cyprys, P., Zolg, D., Mathieson, T., Bantscheff, M., Hazarika, R., Dawid, C., Dunkel, A., Hofmann, T., Sprunck, S., Falter-Braun, P., Johannes, F., Mayer, K., Jürgens, G., Wilhelm, M., Baumbach, J., Grill, E., Schneitz, K., Schwechheimer, C. and Küster, B. (2020). “Mass-spectrometry-based draft of the Arabidopsis proteome.” Nature, in press.
• Thomas Montenegro-Johnson, Soeren Strauss, Matthew DB Jackson, Liam Walker, Richard S Smith, George W Bassel (2019) 3DCellAtlas Meristem: a tool for the global cellular annotation of shoot apical meristems. Plant Methods, 15:1.
• Sapala, A., Runions, A., Routier-Kierzkowska, A.-L., Das Gupta, M., Hong, L., Hofhuis, H., Verger, S., Mosca, G., Li, C.-B., Hay, A., Hamant, O., Roeder, A., Tsiantis, M., Prusinkiewicz, R., & Smith, R. S. (2018). Why plants make puzzle cells, and how their shape emerges. eLife, 7: e32794.
• Scholz, S., Pleßmann, J., Enugutti, B., Hüttl, R., Wassmer, K. and Schneitz, K. (2019). The AGC protein kinase UNICORN controls planar growth by attenuating PDK1 in Arabidopsis thaliana. PLoS Genet, 15: e1007927