Publications

Preprints

• Vijayan A, Mody TA, Yu Q, Wolny A, Cerrone L, Strauss S, Tsiantis M, Smith RS, Hamprecht FA, Kreshuk A, et al (2024) A deep learning-based toolkit for 3D nuclei segmentation and quantitative analysis in cellular and tissue context. BioRxiv: 2024.02.19.580954
• Ramos JRD, Reyes-Hernandez BJ, Alim K & Maizel A (2023) Mechanotransduction in Lateral Root Initiation: A Model Integrating Growth Mechanics and Auxin Signaling. BioRxiv
• Berthet, Beatrice., Bald, L., Louveaux, M., and Maizel, A. (2022). Progressive maturation of the root apical meristem in Arabidopsis thaliana lateral roots. BioRxiv.

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Projects publications

2024

• Mosca G, Eng RC, Adibi M, Yoshida S, Lane B, Bergheim L, Weber G, Smith RS & Hay A (2024) Growth and tension in explosive fruit. Curr Biol

2023

• Ivan Lebovka, Bruno Hay Mele, Xiaomin Liu, Alexandra Zakieva, Theresa Schlamp, Nial Rau Gursanscky, Roeland MH Merks, Ruth Großeholz, Thomas Greb (2023) Computational modelling of cambium activity provides a regulatory framework for simulating radial plant growth eLife 12:e66627
• Bhatia N, Wilson-Sánchez D, Strauss S, Vuolo F, Pieper B, Hu Z, Rambaud-Lavigne L & Tsiantis M (2023) Interspersed expression of CUP-SHAPED COTYLEDON2 and REDUCED COMPLEXITY shapes Cardamine hirsuta complex leaf form. Curr Biol 33: 2977–2987.e6
• Piepers M, Erbstein K, Reyes-Hernandez J, Song C, Tessi T, Petrasiunaite V, Faerber N, Distel K & Maizel A (2023) GreenGate 2.0: Backwards compatible addons for assembly of complex transcriptional units and their stacking with GreenGate. PLoS One 18: e0290097
• Stitz M, Kuster D, Reinert M, Schepetilnikov M, Berthet B, Reyes-Hernández J, Janocha D, Artins A, Boix M, Henriques R, et al (2023) TOR acts as a metabolic gatekeeper for auxin-dependent lateral root initiation in Arabidopsis thaliana. EMBO J 42: e111273
• Zakieva A, Cerrone L & Greb T (2023) Deep machine learning for cell segmentation and quantitative analysis of radial plant growth. Cells & Development: 203842
• Reyes-Hernández BJ & Maizel A (2023) Tunable recurrent priming of lateral roots in Arabidopsis: More than just a clock? Curr Opin Plant Biol 76: 102479

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
• Stöckle, D., Reyes-Hernández, B.J., Barro, A.V., Nenadić, M., Winter, Z., Marc-Martin, S., Bald, L., Ursache, R., Fujita, S., Maizel, A., et al. (2022). Microtubule-based perception of mechanical conflicts controls plant organ morphogenesis. Sci Adv 8, eabm4974. 10.1126/sciadv.abm4974.
• Sören Strauss, Adam Runions, Brendan Lane, Dennis Eschweiler, Namrata Bajpai, Nicola Trozzi, Anne-Lise Routier-Kierzkowska, Saiko Yoshida, Sylvia Rodrigues da Silveira, Athul Vijayan, Rachele Tofanelli, Mateusz Majda, Emillie Echevin, Constance Le Gloanec, Hana Bertrand-Rakusova, Milad Adibi, Kay Schneitz, George W Bassel, Daniel Kierzkowski, Johannes Stegmaier, Miltos Tsiantis, Richard S Smith (2022) Using positional information to provide context for biological image analysis with MorphoGraphX 2.0 eLife 11:e72601
• Wolny, A., Yu, Q., Pape,. C., Kreshuk., A. (2022). Sparse Object-level Supervision for Instance Segmentation with Pixel Embeddings. CVPR2022
• Pérez-Antón M, Schneider I, Kroll P, Hofhuis H, Metzger S, Pauly M & Hay A (2022) Explosive seed dispersal depends on SPL7 to ensure sufficient copper for localized lignin deposition via laccases. Proc Natl Acad Sci U S A 119: e2202287119
• Emonet A & Hay A (2022) Development and diversity of lignin patterns. Plant Physiol 190: 31–43
• Petrella R, Gabrieli F, Cavalleri A, Schneitz K, Colombo L & Cucinotta M (2022) Pivotal role of STIP in ovule pattern formation and female germline development in Arabidopsis thaliana. Development 149

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

• Galvan-Ampudia CS, Cerutti G, Legrand J, Brunoud G, Martin-Arevalillo R, Azais R, Bayle V, Moussu S, Wenzl C, Jaillais Y, Lohmann JU, Godin C, Vernoux T. Temporal integration of auxin information for the regulation of patterning. Elife. 2020 May 7;9:e55832. doi: 10.7554/eLife.55832.
• 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.
• 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