[{"ddc":["530"],"has_accepted_license":"1","file":[{"success":1,"creator":"dernst","date_created":"2025-05-12T09:31:22Z","file_name":"2025_PhysicsFluids_Bartolucci.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"242d05898aa0a2348b9c108747adb5ce","file_size":4926853,"date_updated":"2025-05-12T09:31:22Z","file_id":"19681"}],"quality_controlled":"1","publication":"Physics of Fluids","issue":"4","doi":"10.1063/5.0255841","publication_identifier":{"issn":["1070-6631"],"eissn":["1089-7666"]},"article_number":"044122","year":"2025","date_created":"2025-05-11T22:02:40Z","title":"Phase behavior of Cacio e Pepe sauce","abstract":[{"text":"“Pasta alla Cacio e pepe” is a traditional Italian dish made with pasta, pecorino cheese, and pepper. Despite its simple ingredient list, achieving the perfect texture and creaminess of the sauce can be challenging. In this study, we systematically explore the phase behavior of Cacio e pepe sauce, focusing on its stability at increasing temperatures for various proportions of cheese, water, and starch. We identify starch concentration as the key factor influencing sauce stability, with direct implications for practical cooking. Specifically, we delineate a regime where starch concentrations below 1% (relative to cheese mass) lead to the formation of system-wide clumps, a condition determining what we term the “Mozzarella Phase” and corresponding to an unpleasant and separated sauce. Additionally, we examine the impact of cheese concentration relative to water at a fixed starch level, observing a lower critical solution temperature that we theoretically rationalized by means of a minimal effective free-energy model. We further analyze the effect of a less traditional stabilizer, trisodium citrate, and observe a sharp transition from the Mozzarella Phase to a completely smooth and stable sauce, in contrast to starch-stabilized mixtures, where the transition is more gradual. Finally, we present a scientifically optimized recipe based on our findings, enabling a consistently flawless execution of this classic dish.","lang":"eng"}],"external_id":{"arxiv":["2501.00536"],"isi":["001482986200001"]},"publication_status":"published","article_processing_charge":"Yes (in subscription journal)","related_material":{"link":[{"description":"News on ISTA","url":"https://ista.ac.at/en/news/2025-ig-nobel-prize-for-perfect-pasta-sauce/","relation":"press_release"}]},"OA_place":"publisher","volume":37,"author":[{"first_name":"G.","last_name":"Bartolucci","full_name":"Bartolucci, G."},{"full_name":"Busiello, D. M.","last_name":"Busiello","first_name":"D. M."},{"first_name":"M.","last_name":"Ciarchi","full_name":"Ciarchi, M."},{"full_name":"Corticelli, A.","last_name":"Corticelli","first_name":"A."},{"first_name":"I.","last_name":"Di Terlizzi","full_name":"Di Terlizzi, I."},{"id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","full_name":"Olmeda, Fabrizio","last_name":"Olmeda","first_name":"Fabrizio"},{"last_name":"Revignas","first_name":"D.","full_name":"Revignas, D."},{"last_name":"Schimmenti","first_name":"V. M.","full_name":"Schimmenti, V. M."}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"chicago":"Bartolucci, G., D. M. Busiello, M. Ciarchi, A. Corticelli, I. Di Terlizzi, Fabrizio Olmeda, D. Revignas, and V. M. Schimmenti. “Phase Behavior of Cacio e Pepe Sauce.” <i>Physics of Fluids</i>. AIP Publishing, 2025. <a href=\"https://doi.org/10.1063/5.0255841\">https://doi.org/10.1063/5.0255841</a>.","apa":"Bartolucci, G., Busiello, D. M., Ciarchi, M., Corticelli, A., Di Terlizzi, I., Olmeda, F., … Schimmenti, V. M. (2025). Phase behavior of Cacio e Pepe sauce. <i>Physics of Fluids</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0255841\">https://doi.org/10.1063/5.0255841</a>","mla":"Bartolucci, G., et al. “Phase Behavior of Cacio e Pepe Sauce.” <i>Physics of Fluids</i>, vol. 37, no. 4, 044122, AIP Publishing, 2025, doi:<a href=\"https://doi.org/10.1063/5.0255841\">10.1063/5.0255841</a>.","short":"G. Bartolucci, D.M. Busiello, M. Ciarchi, A. Corticelli, I. Di Terlizzi, F. Olmeda, D. Revignas, V.M. Schimmenti, Physics of Fluids 37 (2025).","ieee":"G. Bartolucci <i>et al.</i>, “Phase behavior of Cacio e Pepe sauce,” <i>Physics of Fluids</i>, vol. 37, no. 4. AIP Publishing, 2025.","ama":"Bartolucci G, Busiello DM, Ciarchi M, et al. Phase behavior of Cacio e Pepe sauce. <i>Physics of Fluids</i>. 2025;37(4). doi:<a href=\"https://doi.org/10.1063/5.0255841\">10.1063/5.0255841</a>","ista":"Bartolucci G, Busiello DM, Ciarchi M, Corticelli A, Di Terlizzi I, Olmeda F, Revignas D, Schimmenti VM. 2025. Phase behavior of Cacio e Pepe sauce. Physics of Fluids. 37(4), 044122."},"day":"01","status":"public","OA_type":"hybrid","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"arxiv":1,"publisher":"AIP Publishing","department":[{"_id":"EdHa"}],"date_updated":"2026-04-28T13:24:53Z","month":"04","language":[{"iso":"eng"}],"date_published":"2025-04-01T00:00:00Z","oa":1,"file_date_updated":"2025-05-12T09:31:22Z","isi":1,"_id":"19670","scopus_import":"1","type":"journal_article","acknowledgement":"he authors thank Frank Jülicher, for supporting the initiative and stimulating discussions. We thank Tetsuya Spippayashi for enlightening clarifications on the historical origins of Cacio e pepe and Giuseppe Ricchitelli for helping with the construction of the experimental apparatus. We further thank Martina Gaiba, Alessandro Gaiba, John D. Treado, Virginia Lepore, Eleonora Nanu, Julia Kirsch, Lara Koehler, Burak Budanur, Irina Pi-Jaumà, Elizabeth Brückner, M.J. Franco Oñate, Giorgio Nicoletti, and Marco Salvalaglio for their support and for eating up the sample leftovers. Finally, we thank Simone Frau for taking the photograph in Fig. 1(a).","article_type":"original","oa_version":"Published Version","intvolume":"        37"},{"project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"}],"citation":{"short":"S.B.P. Mclaren, S. Xue, S. Ding, A.K. Winkel, O. Baldwin, S. Dwarakacherla, K. Franze, E.B. Hannezo, F. Xiong, Developmental Cell 60 (2025) 2237–2247.e4.","ieee":"S. B. P. Mclaren <i>et al.</i>, “Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord,” <i>Developmental Cell</i>, vol. 60, no. 17. Elsevier, p. 2237–2247.e4, 2025.","ista":"Mclaren SBP, Xue S, Ding S, Winkel AK, Baldwin O, Dwarakacherla S, Franze K, Hannezo EB, Xiong F. 2025. Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord. Developmental Cell. 60(17), 2237–2247.e4.","ama":"Mclaren SBP, Xue S, Ding S, et al. Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord. <i>Developmental Cell</i>. 2025;60(17):2237-2247.e4. doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">10.1016/j.devcel.2025.04.010</a>","apa":"Mclaren, S. B. P., Xue, S., Ding, S., Winkel, A. K., Baldwin, O., Dwarakacherla, S., … Xiong, F. (2025). Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">https://doi.org/10.1016/j.devcel.2025.04.010</a>","chicago":"Mclaren, Susannah B.P., Shi-lei Xue, Siyuan Ding, Alexander K. Winkel, Oscar Baldwin, Shreya Dwarakacherla, Kristian Franze, Edouard B Hannezo, and Fengzhu Xiong. “Differential Tissue Deformability Underlies Fluid Pressure-Driven Shape Divergence of the Avian Embryonic Brain and Spinal Cord.” <i>Developmental Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">https://doi.org/10.1016/j.devcel.2025.04.010</a>.","mla":"Mclaren, Susannah B. P., et al. “Differential Tissue Deformability Underlies Fluid Pressure-Driven Shape Divergence of the Avian Embryonic Brain and Spinal Cord.” <i>Developmental Cell</i>, vol. 60, no. 17, Elsevier, 2025, p. 2237–2247.e4, doi:<a href=\"https://doi.org/10.1016/j.devcel.2025.04.010\">10.1016/j.devcel.2025.04.010</a>."},"PlanS_conform":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid","ec_funded":1,"status":"public","day":"08","file_date_updated":"2025-12-29T13:45:05Z","oa":1,"isi":1,"date_updated":"2025-12-29T14:58:14Z","department":[{"_id":"EdHa"}],"publisher":"Elsevier","date_published":"2025-09-08T00:00:00Z","month":"09","language":[{"iso":"eng"}],"acknowledgement":"We thank A. Dimitracopoulos, K. Kawaguchi, J. Vidigueira, B. Baum, I. McLaren, D. St Johnston, and members of the Buckley, Scarpa, Steventon, Kawaguchi, and Xiong labs for technical assistance and constructive feedback. We thank Ryan Greenhalgh for methods developed to obtain fluidity values from AFM data. We thank Nicola Lawrence, Alex Sossick, and Sargon Gross-Thebing from the Gurdon Institute Imaging Facility for microscopy support. Funding: this work was supported by a Wellcome Trust/Royal Society Sir Henry Dale Fellowship (215439/Z/19/Z) and UKRI-EPSRC Frontier Research Grant (EP/X023761/1, originally selected as an ERC Starting Grant) to F.X.; an ERC Consolidator Grant (772426), ERC Synergy Grant 101118729 UNFOLD, and Alexander von Humboldt Professorship ( Alexander von Humboldt Foundation) to K.F.; and an ERC Starting Grant (851288) to E.H.","type":"journal_article","oa_version":"Published Version","intvolume":"        60","article_type":"original","scopus_import":"1","_id":"19703","quality_controlled":"1","file":[{"content_type":"application/pdf","file_name":"2025_DevelopmentalCell_McLaren.pdf","date_created":"2025-12-29T13:45:05Z","success":1,"creator":"dernst","file_id":"20872","file_size":12564806,"date_updated":"2025-12-29T13:45:05Z","access_level":"open_access","relation":"main_file","checksum":"1ca6f0822c1cbd430686d5e2a4f96401"}],"ddc":["570"],"has_accepted_license":"1","date_created":"2025-05-18T22:02:50Z","year":"2025","publication":"Developmental Cell","publication_identifier":{"eissn":["1878-1551"],"issn":["1534-5807"]},"doi":"10.1016/j.devcel.2025.04.010","issue":"17","publication_status":"published","external_id":{"pmid":["40347948"],"isi":["001570502100005"]},"abstract":[{"lang":"eng","text":"An enlarged brain underlies the complex central nervous system of vertebrates. The dramatic expansion of the brain that diverges its shape from the spinal cord follows neural tube closure during embryonic development. Here, we show that this differential deformation is encoded by a pre-pattern of tissue material properties in chicken embryos. Using magnetic droplets and atomic force microscopy, we demonstrate that the dorsal hindbrain is more fluid than the dorsal spinal cord, resulting in a thinning versus a resisting response to increasing lumen pressure, respectively. The dorsal hindbrain exhibits reduced apical actin and a disorganized laminin matrix consistent with tissue fluidization. Blocking the activity of neural-crest-associated matrix metalloproteinases inhibits hindbrain expansion. Transplanting dorsal hindbrain cells to the spinal cord can locally create an expanded brain-like morphology in some cases. Our findings raise questions in vertebrate head evolution and suggest a general role of mechanical pre-patterning in sculpting epithelial tubes."}],"article_processing_charge":"Yes (in subscription journal)","page":"2237-2247.e4","title":"Differential tissue deformability underlies fluid pressure-driven shape divergence of the avian embryonic brain and spinal cord","OA_place":"publisher","volume":60,"author":[{"full_name":"Mclaren, Susannah B.P.","last_name":"Mclaren","first_name":"Susannah B.P."},{"id":"31D2C804-F248-11E8-B48F-1D18A9856A87","full_name":"Xue, Shi-lei","last_name":"Xue","first_name":"Shi-lei"},{"first_name":"Siyuan","last_name":"Ding","full_name":"Ding, Siyuan"},{"last_name":"Winkel","first_name":"Alexander K.","full_name":"Winkel, Alexander K."},{"first_name":"Oscar","last_name":"Baldwin","full_name":"Baldwin, Oscar"},{"first_name":"Shreya","last_name":"Dwarakacherla","full_name":"Dwarakacherla, Shreya"},{"first_name":"Kristian","last_name":"Franze","full_name":"Franze, Kristian"},{"first_name":"Edouard B","last_name":"Hannezo","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"last_name":"Xiong","first_name":"Fengzhu","full_name":"Xiong, Fengzhu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"OA_type":"gold","day":"01","status":"public","citation":{"ieee":"S. Jouveshomme, M. Lizée, P. Robin, and L. Bocquet, “Multiple ionic memories in asymmetric nanochannels revealed by mem-spectrometry,” <i>New Journal of Physics</i>, vol. 27, no. 6. IOP Publishing, 2025.","short":"S. Jouveshomme, M. Lizée, P. Robin, L. Bocquet, New Journal of Physics 27 (2025).","ama":"Jouveshomme S, Lizée M, Robin P, Bocquet L. Multiple ionic memories in asymmetric nanochannels revealed by mem-spectrometry. <i>New Journal of Physics</i>. 2025;27(6). doi:<a href=\"https://doi.org/10.1088/1367-2630/ade61b\">10.1088/1367-2630/ade61b</a>","ista":"Jouveshomme S, Lizée M, Robin P, Bocquet L. 2025. Multiple ionic memories in asymmetric nanochannels revealed by mem-spectrometry. New Journal of Physics. 27(6), 065001.","apa":"Jouveshomme, S., Lizée, M., Robin, P., &#38; Bocquet, L. (2025). Multiple ionic memories in asymmetric nanochannels revealed by mem-spectrometry. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ade61b\">https://doi.org/10.1088/1367-2630/ade61b</a>","chicago":"Jouveshomme, Simon, Mathieu Lizée, Paul Robin, and Lydéric Bocquet. “Multiple Ionic Memories in Asymmetric Nanochannels Revealed by Mem-Spectrometry.” <i>New Journal of Physics</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/1367-2630/ade61b\">https://doi.org/10.1088/1367-2630/ade61b</a>.","mla":"Jouveshomme, Simon, et al. “Multiple Ionic Memories in Asymmetric Nanochannels Revealed by Mem-Spectrometry.” <i>New Journal of Physics</i>, vol. 27, no. 6, 065001, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/1367-2630/ade61b\">10.1088/1367-2630/ade61b</a>."},"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"intvolume":"        27","oa_version":"Published Version","article_type":"original","acknowledgement":"The authors acknowledge ERC n-AQUA for funding. S J acknowledges CNRS for funding. The authors thank Hummink for pipette supply and characterization. P R acknowledges funding from the European Union Horizon 2020 research and innovation program under the Marie Skodowska-Curie Grant Agreement No. 101034413.","type":"journal_article","scopus_import":"1","_id":"19966","isi":1,"file_date_updated":"2025-07-08T06:11:59Z","DOAJ_listed":"1","oa":1,"date_published":"2025-06-01T00:00:00Z","month":"06","language":[{"iso":"eng"}],"date_updated":"2025-09-30T13:47:45Z","publisher":"IOP Publishing","department":[{"_id":"EdHa"}],"date_created":"2025-07-06T22:01:23Z","year":"2025","article_number":"065001","publication_identifier":{"eissn":["1367-2630"]},"doi":"10.1088/1367-2630/ade61b","issue":"6","publication":"New Journal of Physics","quality_controlled":"1","file":[{"date_created":"2025-07-08T06:11:59Z","content_type":"application/pdf","file_name":"2025_NewJourPhysics_Jouveshomme.pdf","creator":"dernst","success":1,"file_id":"19973","relation":"main_file","checksum":"e0e11aa01c54b20ee6cdd1f6b999571f","access_level":"open_access","file_size":1296141,"date_updated":"2025-07-08T06:11:59Z"}],"has_accepted_license":"1","ddc":["530"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Jouveshomme","first_name":"Simon","full_name":"Jouveshomme, Simon"},{"first_name":"Mathieu","last_name":"Lizée","full_name":"Lizée, Mathieu"},{"full_name":"Robin, Paul","orcid":"0000-0002-5728-9189","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","last_name":"Robin","first_name":"Paul"},{"last_name":"Bocquet","first_name":"Lydéric","full_name":"Bocquet, Lydéric"}],"OA_place":"publisher","volume":27,"article_processing_charge":"Yes","external_id":{"isi":["001517731700001"]},"publication_status":"published","abstract":[{"text":"Recently discovered nanofluidic memristors, have raised promises for the development of iontronics and neuromorphic computing with ions. Ionic memory effects are related to ion dynamics inside nanochannels, with timescales associated with the manifold physicochemical phenomena occurring at confined interfaces. Here, we explore experimentally the frequency-dependent current–voltage response of model nanochannels—namely glass nanopipettes—to investigate memory effects in ion transport. This characterisation, which we refer to as mem-spectrometry, highlights two characteristic frequencies, associated with short and long timescales of the order of 50 ms and 50 s in the present system. Whereas the former can be associated with ionic diffusion, very long timescales are difficult to explain with conventional transport phenomena. We develop a minimal model accounting for these mem-spectrometry results, pointing to surface charge regulation and ionic adsorption-desorption as possible origins for the long-term memory. Our work demonstrates the relevance of mem-spectrometry to highlight subtle ion transport properties in nanochannels, giving hereby new insights on the mechanisms governing ion transport and current rectification in charged conical nanopores.","lang":"eng"}],"title":"Multiple ionic memories in asymmetric nanochannels revealed by mem-spectrometry"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2205.02645"}],"quality_controlled":"1","issue":"4","doi":"10.1086/734083","publication_identifier":{"eissn":["1537-5323"],"issn":["0003-0147"]},"publication":"The American Naturalist","year":"2025","date_created":"2025-07-21T08:37:27Z","title":"Discovering stochastic dynamical equations from ecological time series data","page":"E100-E117","article_processing_charge":"No","abstract":[{"text":"Theoretical studies have shown that stochasticity can affect the dynamics of ecosystems in counterintuitive ways. However, without knowing the equations governing the dynamics of populations or ecosystems, it is difficult to ascertain the role of stochasticity in real datasets. Therefore, the inverse problem of inferring the governing stochastic equations from datasets is important. Here, we present an equation discovery methodology that takes time series data of state variables as input and outputs a stochastic differential equation. We achieve this by combining traditional approaches from stochastic calculus with the equation discovery techniques. We demonstrate the generality of the method via several applications. First, we deliberately choose various stochastic models with fundamentally different governing equations, yet they produce nearly identical steady-state distributions. We show that we can recover the correct underlying equations, and thus infer the structure of their stability, accurately from the analysis of time series data alone. We demonstrate our method on two real-world datasets—fish schooling and single-cell migration—that have vastly different spatiotemporal scales and dynamics. We illustrate various limitations and potential pitfalls of the method and how to overcome them via diagnostic measures. Finally, we provide our open-source code via a package named PyDaDDy (Python Library for Data-Driven Dynamics).","lang":"eng"}],"publication_status":"published","external_id":{"isi":["001433250500001"],"pmid":["40179429"],"arxiv":["2205.02645"]},"related_material":{"record":[{"status":"public","id":"20121","relation":"software"}]},"pmid":1,"author":[{"last_name":"Nabeel","first_name":"Arshed","full_name":"Nabeel, Arshed"},{"full_name":"Karichannavar, Ashwin","first_name":"Ashwin","last_name":"Karichannavar"},{"full_name":"Palathingal, Shuaib","first_name":"Shuaib","last_name":"Palathingal"},{"full_name":"Jhawar, Jitesh","last_name":"Jhawar","first_name":"Jitesh"},{"first_name":"David","last_name":"Brückner","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975"},{"first_name":"Danny","last_name":"Raj M","full_name":"Raj M, Danny"},{"full_name":"Guttal, Vishwesha","first_name":"Vishwesha","last_name":"Guttal"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":205,"OA_place":"repository","citation":{"mla":"Nabeel, Arshed, et al. “Discovering Stochastic Dynamical Equations from Ecological Time Series Data.” <i>The American Naturalist</i>, vol. 205, no. 4, University of Chicago Press, 2025, pp. E100–17, doi:<a href=\"https://doi.org/10.1086/734083\">10.1086/734083</a>.","apa":"Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Raj M, D., &#38; Guttal, V. (2025). Discovering stochastic dynamical equations from ecological time series data. <i>The American Naturalist</i>. University of Chicago Press. <a href=\"https://doi.org/10.1086/734083\">https://doi.org/10.1086/734083</a>","chicago":"Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar, David Brückner, Danny Raj M, and Vishwesha Guttal. “Discovering Stochastic Dynamical Equations from Ecological Time Series Data.” <i>The American Naturalist</i>. University of Chicago Press, 2025. <a href=\"https://doi.org/10.1086/734083\">https://doi.org/10.1086/734083</a>.","ista":"Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Raj M D, Guttal V. 2025. Discovering stochastic dynamical equations from ecological time series data. The American Naturalist. 205(4), E100–E117.","ama":"Nabeel A, Karichannavar A, Palathingal S, et al. Discovering stochastic dynamical equations from ecological time series data. <i>The American Naturalist</i>. 2025;205(4):E100-E117. doi:<a href=\"https://doi.org/10.1086/734083\">10.1086/734083</a>","ieee":"A. Nabeel <i>et al.</i>, “Discovering stochastic dynamical equations from ecological time series data,” <i>The American Naturalist</i>, vol. 205, no. 4. University of Chicago Press, pp. E100–E117, 2025.","short":"A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, D. Raj M, V. Guttal, The American Naturalist 205 (2025) E100–E117."},"project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"day":"01","status":"public","OA_type":"green","month":"04","language":[{"iso":"eng"}],"date_published":"2025-04-01T00:00:00Z","department":[{"_id":"EdHa"}],"arxiv":1,"publisher":"University of Chicago Press","date_updated":"2025-09-30T14:14:43Z","isi":1,"oa":1,"_id":"20056","article_type":"original","oa_version":"Preprint","intvolume":"       205","acknowledgement":"V.G. acknowledges support from the Science and Engi-neering Research Board, Department of Biotechnology,and the Indo-French Centre for the Promotion of Ad-vanced Research (64T4-1). D.R.M. acknowledges supportfrom a Department of Science and Technology (DST) In-novation in Science Pursuit for Inspired Research (IN-SPIRE) Faculty Award. J.J. acknowledges support froma Humboldt postdoctoral fellowship and the Heidelber-ger Akademie der Wissenschaften, Heidelberg, Germany.D.B.B. acknowledges support from the NOMIS Founda-tion and an European Molecular Biology Organization(EMBO) postdoctoral fellowship (ALTF 343-2022). A.N.and S.P. acknowledge support from Ministry of Educa-tion (MoE) PhD fellowships. We thank Ashrit Mangal-wedhekar, Vivek Jadhav, Shikhara Bhat, Cassandre Aimon,and Harishankar Muppirala for comments on the manu-script and code. We thank Kollegala Sharma for his inputon the Kannada translation of the title and abstract.Data-Driven Model Discovery E115","type":"journal_article"},{"scopus_import":"1","_id":"20080","intvolume":"        16","oa_version":"Published Version","article_type":"original","type":"journal_article","acknowledgement":"The author(s) declare that financial support was received for the research and/or publication of this article. This work was supported by grants from the European Research Council (Starting Independent Research Grant ERC-2007-Stg- 207362-HCPO to EB) and MG was recipient of an IST Interdisciplinary project (IC1022IPC03).\r\nWe acknowledge Jaume F. Martı́nez Garcı́a for phyAphyB mutant seeds. We acknowledge CF Nanobiotechnology of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2018127). We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and Library. We thank Stefan Riegler for the efforts to establish immunodetection method.","date_published":"2025-07-04T00:00:00Z","language":[{"iso":"eng"}],"month":"07","date_updated":"2026-05-20T07:53:03Z","publisher":"Frontiers Media","department":[{"_id":"EdHa"},{"_id":"EvBe"},{"_id":"CaGu"}],"isi":1,"DOAJ_listed":"1","file_date_updated":"2025-07-31T07:28:54Z","oa":1,"status":"public","day":"04","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"gold","ec_funded":1,"citation":{"ama":"Gallemi M, Montesinos López JC, Zarevski N, et al. Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. <i>Frontiers in Plant Science</i>. 2025;16. doi:<a href=\"https://doi.org/10.3389/fpls.2025.1612366\">10.3389/fpls.2025.1612366</a>","ista":"Gallemi M, Montesinos López JC, Zarevski N, Pribyl J, Skládal P, Hannezo EB, Benková E. 2025. Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. Frontiers in Plant Science. 16, 1612366.","ieee":"M. Gallemi <i>et al.</i>, “Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties,” <i>Frontiers in Plant Science</i>, vol. 16. Frontiers Media, 2025.","short":"M. Gallemi, J.C. Montesinos López, N. Zarevski, J. Pribyl, P. Skládal, E.B. Hannezo, E. Benková, Frontiers in Plant Science 16 (2025).","mla":"Gallemi, Marçal, et al. “Dual Role of Pectin Methyl Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.” <i>Frontiers in Plant Science</i>, vol. 16, 1612366, Frontiers Media, 2025, doi:<a href=\"https://doi.org/10.3389/fpls.2025.1612366\">10.3389/fpls.2025.1612366</a>.","apa":"Gallemi, M., Montesinos López, J. C., Zarevski, N., Pribyl, J., Skládal, P., Hannezo, E. B., &#38; Benková, E. (2025). Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties. <i>Frontiers in Plant Science</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fpls.2025.1612366\">https://doi.org/10.3389/fpls.2025.1612366</a>","chicago":"Gallemi, Marçal, Juan C Montesinos López, Nikola Zarevski, Jan Pribyl, Petr Skládal, Edouard B Hannezo, and Eva Benková. “Dual Role of Pectin Methyl Esterase Activity in the Regulation of Plant Cell Wall Biophysical Properties.” <i>Frontiers in Plant Science</i>. Frontiers Media, 2025. <a href=\"https://doi.org/10.3389/fpls.2025.1612366\">https://doi.org/10.3389/fpls.2025.1612366</a>."},"PlanS_conform":"1","project":[{"name":"Hormonal cross-talk in plant organogenesis","call_identifier":"FP7","grant_number":"207362","_id":"253FCA6A-B435-11E9-9278-68D0E5697425"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"}],"pmid":1,"author":[{"last_name":"Gallemi","first_name":"Marçal","orcid":"0000-0003-4675-6893","id":"460C6802-F248-11E8-B48F-1D18A9856A87","full_name":"Gallemi, Marçal"},{"last_name":"Montesinos López","first_name":"Juan C","orcid":"0000-0001-9179-6099","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","full_name":"Montesinos López, Juan C"},{"full_name":"Zarevski, Nikola","id":"18e95355-e05a-11ea-a9c0-8fba1b89e83a","first_name":"Nikola","last_name":"Zarevski"},{"full_name":"Pribyl, Jan","first_name":"Jan","last_name":"Pribyl"},{"full_name":"Skládal, Petr","first_name":"Petr","last_name":"Skládal"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","volume":16,"title":"Dual role of pectin methyl esterase activity in the regulation of plant cell wall biophysical properties","article_processing_charge":"Yes","external_id":{"isi":["001530690900001"],"pmid":["40688689"]},"publication_status":"published","abstract":[{"text":"Introduction: Acid-growth theory has been postulated in the 70s to explain the rapid elongation of plant cells in response to the hormone auxin. More recently, it has been demonstrated that activation of the proton ATPs pump (H+-ATPs) promoting acidification of the apoplast is the principal mechanism by which auxin and other hormones such as brassinosteroids (BR) induce cell elongation. Despite these advances, the impact of this acidification on the mechanical properties of the cell wall remained largely unexplored.\r\n\r\nMethods: Here, we use elongation assays of Arabidopsis thaliana hypocotyls and Atomic Force Microscopy (AFM) to correlate hormone-induced tissue elongation and local changes in cell wall mechanical properties. Furthermore, employing transgenic lines over-expressing Pectin Methyl Esterase (PME), along with calcium chelators, we investigate the effect of pectin modification in hormone-driven cell elongation.\r\n\r\nResults: We demonstrate that acidification of apoplast is necessary and sufficient to induce cell elongation through promoting cell wall softening. Moreover, we show that enhanced PME activity can induce both cell wall softening or stiffening in extracellular calcium dependent-manner and that tight control of PME activity is required for proper hypocotyl elongation.\r\n\r\nDiscussion: Our results confirm a dual role of PME in plant cell elongation. However, further investigation is needed to assess the status of pectin following short- or long-term PME treatments in order to determine if pectin methyl-esterification might promote its degradation as well as the role of PME inhibitors upon PME induction.","lang":"eng"}],"doi":"10.3389/fpls.2025.1612366","publication_identifier":{"eissn":["1664-462X"]},"APC_amount":"3642,79 EUR","publication":"Frontiers in Plant Science","date_created":"2025-07-27T22:01:26Z","year":"2025","article_number":"1612366","has_accepted_license":"1","ddc":["580"],"corr_author":"1","quality_controlled":"1","file":[{"file_id":"20093","checksum":"9e6b8b53ba56d4a24a9bd91cf6d2dc58","relation":"main_file","access_level":"open_access","date_updated":"2025-07-31T07:28:54Z","file_size":3665187,"date_created":"2025-07-31T07:28:54Z","file_name":"2025_FrontiersPlantSc_Gallemi.pdf","content_type":"application/pdf","creator":"dernst","success":1}]},{"doi":"10.1038/s41567-025-02980-z","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"publication":"Nature Physics","year":"2025","date_created":"2025-08-31T22:01:33Z","corr_author":"1","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kalukula, Yohalie","first_name":"Yohalie","last_name":"Kalukula"},{"first_name":"Marine","last_name":"Luciano","full_name":"Luciano, Marine"},{"first_name":"Gleb","last_name":"Simanov","full_name":"Simanov, Gleb"},{"first_name":"Guillaume","last_name":"Charras","full_name":"Charras, Guillaume"},{"first_name":"David","last_name":"Brückner","full_name":"Brückner, David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"full_name":"Gabriele, Sylvain","first_name":"Sylvain","last_name":"Gabriele"}],"volume":21,"title":"The actin cortex acts as a mechanical memory of morphology in confined migrating cells","page":"1451-1461","article_processing_charge":"No","abstract":[{"text":"Cell migration in narrow microenvironments occurs in numerous physiological processes. It involves successive cycles of confinement and release that drive important morphological changes. However, it remains unclear whether migrating cells can retain a memory of their past morphological states that could potentially facilitate their navigation through confined spaces. We demonstrate that local geometry governs a switch between two cell morphologies, thereby facilitating cell passage through long and narrow gaps. We combined cell migration assays on standardized microsystems with biophysical modelling and biochemical perturbations to show that migrating cells have a long-term memory of past confinement events. The morphological cell states correlate across transitions through actin cortex remodelling. These findings indicate that mechanical memory in migrating cells plays an active role in their migratory potential in confined environments.","lang":"eng"}],"external_id":{"isi":["001556019400001"]},"publication_status":"published","day":"01","status":"public","OA_type":"closed access","citation":{"ama":"Kalukula Y, Luciano M, Simanov G, Charras G, Brückner D, Gabriele S. The actin cortex acts as a mechanical memory of morphology in confined migrating cells. <i>Nature Physics</i>. 2025;21:1451-1461. doi:<a href=\"https://doi.org/10.1038/s41567-025-02980-z\">10.1038/s41567-025-02980-z</a>","ista":"Kalukula Y, Luciano M, Simanov G, Charras G, Brückner D, Gabriele S. 2025. The actin cortex acts as a mechanical memory of morphology in confined migrating cells. Nature Physics. 21, 1451–1461.","short":"Y. Kalukula, M. Luciano, G. Simanov, G. Charras, D. Brückner, S. Gabriele, Nature Physics 21 (2025) 1451–1461.","ieee":"Y. Kalukula, M. Luciano, G. Simanov, G. Charras, D. Brückner, and S. Gabriele, “The actin cortex acts as a mechanical memory of morphology in confined migrating cells,” <i>Nature Physics</i>, vol. 21. Springer Nature, pp. 1451–1461, 2025.","mla":"Kalukula, Yohalie, et al. “The Actin Cortex Acts as a Mechanical Memory of Morphology in Confined Migrating Cells.” <i>Nature Physics</i>, vol. 21, Springer Nature, 2025, pp. 1451–61, doi:<a href=\"https://doi.org/10.1038/s41567-025-02980-z\">10.1038/s41567-025-02980-z</a>.","apa":"Kalukula, Y., Luciano, M., Simanov, G., Charras, G., Brückner, D., &#38; Gabriele, S. (2025). The actin cortex acts as a mechanical memory of morphology in confined migrating cells. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-025-02980-z\">https://doi.org/10.1038/s41567-025-02980-z</a>","chicago":"Kalukula, Yohalie, Marine Luciano, Gleb Simanov, Guillaume Charras, David Brückner, and Sylvain Gabriele. “The Actin Cortex Acts as a Mechanical Memory of Morphology in Confined Migrating Cells.” <i>Nature Physics</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41567-025-02980-z\">https://doi.org/10.1038/s41567-025-02980-z</a>."},"project":[{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"_id":"20259","scopus_import":"1","article_type":"original","intvolume":"        21","oa_version":"None","type":"journal_article","acknowledgement":"We are grateful to members of S.G.’s laboratory for feedback and suggestions. We thank E. Hannezo, J. O. Rädler, M. Piel, O. du Roure and J. Heuvingh for inspiring discussions. Y.K. and S.G. acknowledge J. B. Braquenier from Nikon Instruments Belux and the Nikon BioImaging Lab in Leiden (the Netherlands) for their support with the Nikon Spatial Array Confocal enhanced-resolution confocal microscopy. We thank D. S. Herrador and M. Balland for their help in improving the microprinting method. D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). Y.K., M.L. and S.G. acknowledge funding from the University of Mons (FEDER Prostem Research Project no. 1510614, Wallonia DG06), the F.R.S.-FNRS (Epiforce Project no. T.0092.21, Cellsqueezer Project no. J.0061.23 and Optopattern Project no. U.NO26.22) and the Interreg projects ANTIRESI and MICROPLAITE, which are financially supported by Interreg France-Wallonie-Vlaanderen (Fonds Européen de Développement Régional). Y.K. and M.L. are financially supported by F.R.S.-FNRS as FRIA Grantee FNRS and Postdoctoral Fellow (Chargé de Recherches), respectively. Y.K. and S.G. acknowledge le Fonds pour la Recherche Médicale dans le Hainaut (FRMH). G.C. was supported by a grant from the Biotechnology and Biological Sciences Research Council (grant no. BB/V007483/1).","month":"09","language":[{"iso":"eng"}],"date_published":"2025-09-01T00:00:00Z","department":[{"_id":"EdHa"}],"publisher":"Springer Nature","date_updated":"2025-12-30T09:34:11Z","isi":1},{"citation":{"apa":"Ucar, M. C., Zane, A., Alanko, J. H., Sixt, M. K., &#38; Hannezo, E. B. (2025). Self-generated chemotaxis of mixed cell populations. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2504064122\">https://doi.org/10.1073/pnas.2504064122</a>","chicago":"Ucar, Mehmet C, Alsberga Zane, Jonna H Alanko, Michael K Sixt, and Edouard B Hannezo. “Self-Generated Chemotaxis of Mixed Cell Populations.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2504064122\">https://doi.org/10.1073/pnas.2504064122</a>.","mla":"Ucar, Mehmet C., et al. “Self-Generated Chemotaxis of Mixed Cell Populations.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 34, e2504064122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2504064122\">10.1073/pnas.2504064122</a>.","ieee":"M. C. Ucar, A. Zane, J. H. Alanko, M. K. Sixt, and E. B. Hannezo, “Self-generated chemotaxis of mixed cell populations,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 34. National Academy of Sciences, 2025.","short":"M.C. Ucar, A. Zane, J.H. Alanko, M.K. Sixt, E.B. Hannezo, Proceedings of the National Academy of Sciences 122 (2025).","ama":"Ucar MC, Zane A, Alanko JH, Sixt MK, Hannezo EB. Self-generated chemotaxis of mixed cell populations. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(34). doi:<a href=\"https://doi.org/10.1073/pnas.2504064122\">10.1073/pnas.2504064122</a>","ista":"Ucar MC, Zane A, Alanko JH, Sixt MK, Hannezo EB. 2025. Self-generated chemotaxis of mixed cell populations. Proceedings of the National Academy of Sciences. 122(34), e2504064122."},"PlanS_conform":"1","project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"status":"public","day":"26","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid","ec_funded":1,"date_published":"2025-08-26T00:00:00Z","month":"08","language":[{"iso":"eng"}],"date_updated":"2026-05-20T08:59:54Z","department":[{"_id":"EdHa"},{"_id":"MiSi"}],"publisher":"National Academy of Sciences","isi":1,"file_date_updated":"2025-09-08T07:23:29Z","oa":1,"scopus_import":"1","_id":"20289","oa_version":"Published Version","intvolume":"       122","article_type":"original","type":"journal_article","acknowledgement":"We thank all members of the M.S. and E.H. groups for stimulating discussions.We thank the Imaging and Optics facility, the Pre-clinical and Lab Support facility of the Institute of Science and Technology Austria for their excellent support and provided resources for the experimental research. In particular, we thank Jack Merrin from the Nanofabrication facility who generated the microfabricated channel used in this study. This work received funding fromt he European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 851288 to E.H.). M.C.U.is funded by a University of Sheffield Strategic Research Fellowship in the Physics of Life and Quantitative Biology.","has_accepted_license":"1","ddc":["570"],"corr_author":"1","file":[{"access_level":"open_access","checksum":"b36abd92673b6d76376fc9434bad52cc","relation":"main_file","date_updated":"2025-09-08T07:23:29Z","file_size":16069140,"file_id":"20307","success":1,"creator":"dernst","date_created":"2025-09-08T07:23:29Z","file_name":"2025_PNAS_Ucar.pdf","content_type":"application/pdf"}],"quality_controlled":"1","doi":"10.1073/pnas.2504064122","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"issue":"34","APC_amount":"5766,07 EUR","publication":"Proceedings of the National Academy of Sciences","date_created":"2025-09-07T22:01:32Z","year":"2025","article_number":"e2504064122","title":"Self-generated chemotaxis of mixed cell populations","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["40838890"],"isi":["001562181600001"]},"publication_status":"published","abstract":[{"text":"Cell and tissue movement in development, cancer invasion, and immune response relies on chemical or mechanical guidance cues. In many systems, this behavior is locally directed by self-generated signaling gradients rather than long-range, prepatterned cues. However, how heterogeneous mixtures of cells interact nonreciprocally and navigate through self-generated gradients remains largely unexplored. Here, we introduce a theoretical framework for the self-organized chemotaxis of heterogeneous cell populations. We find that the relative chemotactic sensitivities of different cell populations control their long-time coupling and comigration dynamics, with boundary conditions such as external cell and attractant reservoirs substantially influencing the migration patterns. Our model predicts an optimal parameter regime that enables robust and colocalized migration. We test our theoretical predictions with in vitro experiments demonstrating the comigration of distinct immune cell populations, and quantitatively reproduce observed migration patterns under wild-type and perturbed conditions. Interestingly, immune cell comigration occurs close to the predicted optimal regime. Finally, we incorporate mechanical interactions into our framework, revealing a nontrivial interplay between chemotactic and mechanical nonreciprocity in driving collective migration. Together, our findings suggest that self-generated chemotaxis is a robust strategy for the navigation of mixed cell populations.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"pmid":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/mehmetcanucar/Self-generated-chemotaxis"}]},"author":[{"first_name":"Mehmet C","last_name":"Ucar","orcid":"0000-0003-0506-4217","id":"50B2A802-6007-11E9-A42B-EB23E6697425","full_name":"Ucar, Mehmet C"},{"first_name":"Alsberga","last_name":"Zane","orcid":"0009-0003-0415-7603","id":"60f7509a-f652-11ea-9d86-b963d6490d7c","full_name":"Zane, Alsberga"},{"first_name":"Jonna H","last_name":"Alanko","full_name":"Alanko, Jonna H","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7698-3061"},{"first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","volume":122},{"type":"dissertation","oa_version":"Published Version","_id":"20393","file_date_updated":"2025-10-02T07:51:21Z","department":[{"_id":"GradSch"},{"_id":"AnKi"},{"_id":"EdHa"}],"publisher":"Institute of Science and Technology Austria","date_updated":"2026-04-14T09:50:52Z","language":[{"iso":"eng"}],"month":"09","date_published":"2025-09-24T00:00:00Z","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"day":"24","status":"public","alternative_title":["ISTA Thesis"],"citation":{"chicago":"Kishi, Kasumi. “Regulation of Notochord and Floor Plate Size during Mouse Development.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20393\">https://doi.org/10.15479/AT-ISTA-20393</a>.","apa":"Kishi, K. (2025). <i>Regulation of notochord and floor plate size during mouse development</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20393\">https://doi.org/10.15479/AT-ISTA-20393</a>","mla":"Kishi, Kasumi. <i>Regulation of Notochord and Floor Plate Size during Mouse Development</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20393\">10.15479/AT-ISTA-20393</a>.","ieee":"K. Kishi, “Regulation of notochord and floor plate size during mouse development,” Institute of Science and Technology Austria, 2025.","short":"K. Kishi, Regulation of Notochord and Floor Plate Size during Mouse Development, Institute of Science and Technology Austria, 2025.","ama":"Kishi K. Regulation of notochord and floor plate size during mouse development. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20393\">10.15479/AT-ISTA-20393</a>","ista":"Kishi K. 2025. Regulation of notochord and floor plate size during mouse development. Institute of Science and Technology Austria."},"OA_place":"publisher","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"first_name":"Kasumi","last_name":"Kishi","id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6060-4795","full_name":"Kishi, Kasumi"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"18481","status":"public"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"publication_status":"published","page":"102","article_processing_charge":"No","title":"Regulation of notochord and floor plate size during mouse development","degree_awarded":"PhD","supervisor":[{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","first_name":"Anna","last_name":"Kicheva"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B"}],"year":"2025","date_created":"2025-09-25T10:08:10Z","doi":"10.15479/AT-ISTA-20393","publication_identifier":{"issn":["2663-337X"]},"file":[{"date_created":"2025-09-30T14:33:17Z","content_type":"application/x-zip-compressed","file_name":"2025-Kishi-Kasumi-Thesis.zip","creator":"kkishi","file_id":"20413","access_level":"closed","relation":"source_file","checksum":"6bb5a7ce318dc3f7bd165f2523e77b89","date_updated":"2025-10-01T11:54:41Z","file_size":41847994},{"file_size":55747072,"embargo_to":"open_access","date_updated":"2025-10-02T07:51:21Z","checksum":"88349b9177e1dcbe1242cd3884b36fdb","relation":"main_file","access_level":"closed","embargo":"2026-09-30","file_id":"20414","creator":"kkishi","content_type":"application/pdf","file_name":"2025-Kishi-Kasumi-Thesis.pdf","date_created":"2025-09-30T14:33:22Z"}],"corr_author":"1","ddc":["570"],"has_accepted_license":"1"},{"publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-025-62882-9","publication":"Nature Communications","APC_amount":"7068 EUR","year":"2025","date_created":"2025-10-05T22:01:34Z","article_number":"8440","has_accepted_license":"1","ddc":["570"],"corr_author":"1","file":[{"success":1,"creator":"dernst","content_type":"application/pdf","file_name":"2025_NatureComm_Sahu.pdf","date_created":"2025-10-13T12:37:04Z","date_updated":"2025-10-13T12:37:04Z","file_size":2816813,"access_level":"open_access","checksum":"d1656576883b23902545328e2d640234","relation":"main_file","file_id":"20464"}],"quality_controlled":"1","acknowledged_ssus":[{"_id":"Bio"}],"pmid":1,"author":[{"first_name":"Preeti","last_name":"Sahu","full_name":"Sahu, Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E"},{"first_name":"Sara","last_name":"Monteiro-Ferreira","full_name":"Monteiro-Ferreira, Sara"},{"last_name":"Canato","first_name":"Sara","full_name":"Canato, Sara"},{"full_name":"Soares, Raquel Maia","first_name":"Raquel Maia","last_name":"Soares"},{"first_name":"Adriana","last_name":"Sánchez-Danés","full_name":"Sánchez-Danés, Adriana"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":16,"OA_place":"publisher","title":"Mechanical control of cell fate decisions in the skin epidermis","article_processing_charge":"Yes","abstract":[{"lang":"eng","text":"Homeostasis relies on a precise balance of fate choices between renewal and differentiation. Although progress has been done to characterize the dynamics of single-cell fate choices, their underlying mechanistic basis often remains unclear. Concentrating on skin epidermis as a paradigm for multilayered tissues with complex fate choices, we develop a 3D vertex-based model with proliferation in the basal layer, showing that mechanical competition for space naturally gives rise to homeostasis and neutral drift dynamics that are seen experimentally. We then explore the effect of introducing mechanical heterogeneities between cellular subpopulations. We uncover that relatively small tension heterogeneities, reflected by distinct morphological changes in single-cell shapes, can be sufficient to heavily tilt cellular dynamics towards exponential growth. We thus derive a master relationship between cell shape and long-term clonal dynamics, which we validated during basal cell carcinoma initiation in mouse epidermis. Altogether, we propose a theoretical framework to link mechanical forces, quantitative cellular morphologies and cellular fate outcomes in complex tissues."}],"publication_status":"published","external_id":{"isi":["001582555200011"],"pmid":["41006218"]},"status":"public","day":"26","ec_funded":1,"OA_type":"gold","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"citation":{"mla":"Sahu, Preeti, et al. “Mechanical Control of Cell Fate Decisions in the Skin Epidermis.” <i>Nature Communications</i>, vol. 16, 8440, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-025-62882-9\">10.1038/s41467-025-62882-9</a>.","apa":"Sahu, P., Monteiro-Ferreira, S., Canato, S., Soares, R. M., Sánchez-Danés, A., &#38; Hannezo, E. B. (2025). Mechanical control of cell fate decisions in the skin epidermis. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-025-62882-9\">https://doi.org/10.1038/s41467-025-62882-9</a>","chicago":"Sahu, Preeti, Sara Monteiro-Ferreira, Sara Canato, Raquel Maia Soares, Adriana Sánchez-Danés, and Edouard B Hannezo. “Mechanical Control of Cell Fate Decisions in the Skin Epidermis.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-025-62882-9\">https://doi.org/10.1038/s41467-025-62882-9</a>.","ista":"Sahu P, Monteiro-Ferreira S, Canato S, Soares RM, Sánchez-Danés A, Hannezo EB. 2025. Mechanical control of cell fate decisions in the skin epidermis. Nature Communications. 16, 8440.","ama":"Sahu P, Monteiro-Ferreira S, Canato S, Soares RM, Sánchez-Danés A, Hannezo EB. Mechanical control of cell fate decisions in the skin epidermis. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-025-62882-9\">10.1038/s41467-025-62882-9</a>","short":"P. Sahu, S. Monteiro-Ferreira, S. Canato, R.M. Soares, A. Sánchez-Danés, E.B. Hannezo, Nature Communications 16 (2025).","ieee":"P. Sahu, S. Monteiro-Ferreira, S. Canato, R. M. Soares, A. Sánchez-Danés, and E. B. Hannezo, “Mechanical control of cell fate decisions in the skin epidermis,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025."},"project":[{"_id":"628f3fb1-2b32-11ec-9570-83ce778803f7","grant_number":"ALTF 522-2021","name":"Biomechanics of stem cell fate determination"},{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"_id":"20424","scopus_import":"1","article_type":"original","oa_version":"Published Version","intvolume":"        16","type":"journal_article","acknowledgement":"We thank Alois Schlögl, Paula Sanematsu, Susana Moreno Flores, Bernat Corominas-Murtra, Stefania Tavano, Gayathri Singharaju, and Hannezo group members for helpful discussions, the Bioimaging facility at ISTA, as well as Matthias Merkel and Lisa Manning for sharing the 3D Voronoi code. We also thank the Champalimaud animal facility, Anna Pezzarossa and the Champalimaud ABBE platform for the help with microscopy and image processing. This work was supported by EMBO (ALTF 522-2021), a Fundação para a Ciência e Tecnologia grant to A.S.D. (PTDC/MED-ONC/5553/2020), as well as the European Research Council (grant 851288 to EH). A.S.D., S.C., and R.M.S. are supported by QuantOCancer Project Horizon European Union’s Horizon 2020 program (grant agreement No 810653).","language":[{"iso":"eng"}],"month":"09","date_published":"2025-09-26T00:00:00Z","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"date_updated":"2026-05-20T08:52:01Z","isi":1,"oa":1,"file_date_updated":"2025-10-13T12:37:04Z","DOAJ_listed":"1"},{"oa_version":"Preprint","intvolume":"        21","article_type":"original","acknowledgement":"We thank all the members of our groups for discussions and support. We thank A. Menéndez, S. Usieto, M. Purciolas and E. Coderch for technical assistance. We thank G. Charras (London Centre for Nanotechnology, UK) and M. Sheetz (Columbia University, USA) for sharing cells used in this work. We thank J. Ivaska (University of Turku, Finland) for sharing integrin α5-GFP DNA plasmid. We thank P. Guillamat for technical advice and A. Labernardie for providing the microfluidic channels. We thank M. Gómez-González for sharing the 2D traction microscopy algorithm. Finally, we thank P. Guillamat, J. Abenza, G. Ceada, L. Faure, E. Dalaka, M. Matejčić, A. Beedle, I. Granero, O. Baguer, A. Albajar and N. Chahare for discussions. This paper was funded by the Generalitat de Catalunya (Grant Nos. AGAUR SGR-2017-01602 to X.T. and 2021 SGR 00523 to R.S. and the CERCA Programme and ICREA Academia awards to P.R.-C.), the Spanish Ministry for Science and Innovation MICCINN/FEDER (Grant Nos. PID2021-128635NB-I00, MCIN/AEI/10.13039/501100011033 and ERDF-EU A way of making Europe to X.T., PID2021-128674OB-I00 and CNS2022-135533 to R.S. and PID2019-110298GB-I00 to P.R.-C.), the European Research Council (Grant Nos. 101097753 to P.R.-C. and Adv-883739 to X.T.), Fundació la Marató de TV3 (Project Award 201903-30-31-32 to X.T.), the European Commission (Grant No. H2020-FETPROACT-01-2016-731957 to P.R.-C. and X.T.) and La Caixa Foundation (Grant No. LCF/PR/HR20/52400004 to P.R.-C. and X.T.). R.S. is a Serra-Hunter fellow. D.B.B. was supported by the NOMIS foundation as a NOMIS fellow, by the European Molecular Biology Organization (Postdoctoral Fellowship ALTF 343-2022) and by the Austrian Academy of Sciences through an APART-MINT Fellowship. I.C.F. acknowledges support from the European Foundation for the Study of Chronic Liver Failure. IBEC is recipient of a Severo Ochoa Award of Excellence from MINECO.","type":"journal_article","scopus_import":"1","_id":"20431","isi":1,"oa":1,"date_published":"2025-10-01T00:00:00Z","language":[{"iso":"eng"}],"month":"10","date_updated":"2026-01-05T14:26:28Z","department":[{"_id":"EdHa"}],"publisher":"Springer Nature","OA_type":"green","status":"public","day":"01","citation":{"ieee":"I. C. Fortunato <i>et al.</i>, “Single-cell migration along and against confined haptotactic gradients,” <i>Nature Physics</i>, vol. 21. Springer Nature, pp. 1638–1647, 2025.","short":"I.C. Fortunato, D. Brückner, S. Grosser, R. Nautiyal, L. Rossetti, M. Bosch-Padrós, J. Trebicka, P. Roca-Cusachs, R. Sunyer, E.B. Hannezo, X. Trepat, Nature Physics 21 (2025) 1638–1647.","ama":"Fortunato IC, Brückner D, Grosser S, et al. Single-cell migration along and against confined haptotactic gradients. <i>Nature Physics</i>. 2025;21:1638-1647. doi:<a href=\"https://doi.org/10.1038/s41567-025-03015-3\">10.1038/s41567-025-03015-3</a>","ista":"Fortunato IC, Brückner D, Grosser S, Nautiyal R, Rossetti L, Bosch-Padrós M, Trebicka J, Roca-Cusachs P, Sunyer R, Hannezo EB, Trepat X. 2025. Single-cell migration along and against confined haptotactic gradients. Nature Physics. 21, 1638–1647.","apa":"Fortunato, I. C., Brückner, D., Grosser, S., Nautiyal, R., Rossetti, L., Bosch-Padrós, M., … Trepat, X. (2025). Single-cell migration along and against confined haptotactic gradients. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-025-03015-3\">https://doi.org/10.1038/s41567-025-03015-3</a>","chicago":"Fortunato, Isabela Corina, David Brückner, Steffen Grosser, Rohit Nautiyal, Leone Rossetti, Miquel Bosch-Padrós, Jonel Trebicka, et al. “Single-Cell Migration along and against Confined Haptotactic Gradients.” <i>Nature Physics</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41567-025-03015-3\">https://doi.org/10.1038/s41567-025-03015-3</a>.","mla":"Fortunato, Isabela Corina, et al. “Single-Cell Migration along and against Confined Haptotactic Gradients.” <i>Nature Physics</i>, vol. 21, Springer Nature, 2025, pp. 1638–47, doi:<a href=\"https://doi.org/10.1038/s41567-025-03015-3\">10.1038/s41567-025-03015-3</a>."},"project":[{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"author":[{"full_name":"Fortunato, Isabela Corina","first_name":"Isabela Corina","last_name":"Fortunato"},{"full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","last_name":"Brückner","first_name":"David"},{"last_name":"Grosser","first_name":"Steffen","full_name":"Grosser, Steffen"},{"first_name":"Rohit","last_name":"Nautiyal","full_name":"Nautiyal, Rohit"},{"first_name":"Leone","last_name":"Rossetti","full_name":"Rossetti, Leone"},{"last_name":"Bosch-Padrós","first_name":"Miquel","full_name":"Bosch-Padrós, Miquel"},{"full_name":"Trebicka, Jonel","last_name":"Trebicka","first_name":"Jonel"},{"full_name":"Roca-Cusachs, Pere","first_name":"Pere","last_name":"Roca-Cusachs"},{"first_name":"Raimon","last_name":"Sunyer","full_name":"Sunyer, Raimon"},{"first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"first_name":"Xavier","last_name":"Trepat","full_name":"Trepat, Xavier"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"repository","volume":21,"article_processing_charge":"No","page":"1638-1647","external_id":{"isi":["001581659900001"]},"publication_status":"published","abstract":[{"text":"Haptotaxis is the process of directed cell migration along gradients of extracellular matrix density and is central to morphogenesis, immune responses and cancer invasion. It is commonly assumed that cells respond to these gradients by migrating directionally towards the regions of highest ligand density. In contrast with this view, here we show that cells exposed to micropatterned fibronectin gradients exhibit a wide range of complex trajectories, including directed haptotactic migration up the gradient but also linear oscillations and circles with extended periods of migration down the gradient. To explain this behaviour, we developed a biophysical model of haptotactic cell migration based on a coarse-grained molecular clutch model coupled to persistent stochastic polarity dynamics. Although initial haptotactic migration is explained by the differential friction at the front and back of the cell, the observed complex trajectories over longer timescales arise from the interplay between differential friction, persistence and physical confinement. Overall, our study reveals that confinement and persistence modulate the ability of cells to sense and respond to haptotactic cues and provides a framework for understanding how cells navigate complex environments.","lang":"eng"}],"title":"Single-cell migration along and against confined haptotactic gradients","date_created":"2025-10-05T22:01:36Z","year":"2025","doi":"10.1038/s41567-025-03015-3","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"publication":"Nature Physics","corr_author":"1","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1101/2024.12.02.626413","open_access":"1"}]},{"date_updated":"2026-05-20T08:58:06Z","department":[{"_id":"EdHa"},{"_id":"JePa"}],"arxiv":1,"publisher":"American Physical Society","date_published":"2025-10-31T00:00:00Z","language":[{"iso":"eng"}],"month":"10","DOAJ_listed":"1","file_date_updated":"2025-12-01T07:30:00Z","oa":1,"scopus_import":"1","_id":"20708","acknowledgement":"The authors thank Andela Saric, Christoph Zechner, and Paul Robin for helpful discussions. J. P. acknowledges support by ERC grant (VULCAN, 101086998) and U.S. ARO under Award No. W911NF2310008. Y. I. L. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","type":"journal_article","intvolume":"        15","oa_version":"Published Version","article_type":"original","project":[{"name":"VULCAN: matter, powered from within","_id":"bdac72da-d553-11ed-ba76-eae56e802b74","grant_number":"101086998"},{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"citation":{"apa":"Martinet, Q., Li, Y. I., Aubret, A., Hannezo, E. B., &#38; Palacci, J. A. (2025). Emergent dynamics of active elastic microbeams. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/rjk2-q2wh\">https://doi.org/10.1103/rjk2-q2wh</a>","chicago":"Martinet, Quentin, Yuting I Li, A. Aubret, Edouard B Hannezo, and Jérémie A Palacci. “Emergent Dynamics of Active Elastic Microbeams.” <i>Physical Review X</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/rjk2-q2wh\">https://doi.org/10.1103/rjk2-q2wh</a>.","mla":"Martinet, Quentin, et al. “Emergent Dynamics of Active Elastic Microbeams.” <i>Physical Review X</i>, vol. 15, no. 4, 041017, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/rjk2-q2wh\">10.1103/rjk2-q2wh</a>.","short":"Q. Martinet, Y.I. Li, A. Aubret, E.B. Hannezo, J.A. Palacci, Physical Review X 15 (2025).","ieee":"Q. Martinet, Y. I. Li, A. Aubret, E. B. Hannezo, and J. A. Palacci, “Emergent dynamics of active elastic microbeams,” <i>Physical Review X</i>, vol. 15, no. 4. American Physical Society, 2025.","ama":"Martinet Q, Li YI, Aubret A, Hannezo EB, Palacci JA. Emergent dynamics of active elastic microbeams. <i>Physical Review X</i>. 2025;15(4). doi:<a href=\"https://doi.org/10.1103/rjk2-q2wh\">10.1103/rjk2-q2wh</a>","ista":"Martinet Q, Li YI, Aubret A, Hannezo EB, Palacci JA. 2025. Emergent dynamics of active elastic microbeams. Physical Review X. 15(4), 041017."},"PlanS_conform":"1","status":"public","day":"31","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"gold","ec_funded":1,"title":"Emergent dynamics of active elastic microbeams","external_id":{"arxiv":["2508.20642"]},"publication_status":"published","abstract":[{"text":"In equilibrium, the physical properties of matter are set by the interactions between the constituents. In contrast, the energy input of the individual components controls the behavior of synthetic or living active matter. Great progress has been made in understanding the emergent phenomena in active fluids, though their inability to resist shear forces hinders their practical use. This motivates the exploration of active solids as shape-shifting materials, yet, we lack controlled synthetic systems to devise active solids with unconventional properties. Here we build active elastic beams from dozens of active colloids and unveil complex emergent behaviors such as self-oscillations or persistent rotations. Developing tensile tests at the microscale, we show that the active beams are ultrasoft materials, with large (nonequilibrium) fluctuations. Combining experiments, theory, and stochastic inference, we show that the dynamics of the active beams can be mapped on different phase transitions which are tuned by boundary conditions. More quantitatively, we assess all relevant parameters by independent measurements or first-principles calculations, and find that our theoretical description agrees with the experimental observations. Our results demonstrate that the simple addition of activity to an elastic beam unveils novel physics and can inspire design strategies for active solids and functional microscopic machines.","lang":"eng"}],"article_processing_charge":"Yes","volume":15,"OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Martinet, Quentin","orcid":"0000-0002-2916-6632","id":"b37485a8-d343-11eb-a0e9-df8c484ef8ab","first_name":"Quentin","last_name":"Martinet"},{"id":"ee7a5ca8-8b71-11ed-b662-b3341c05b7eb","full_name":"Li, Yuting I","first_name":"Yuting I","last_name":"Li"},{"last_name":"Aubret","first_name":"A.","full_name":"Aubret, A."},{"orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B"},{"first_name":"Jérémie A","last_name":"Palacci","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A"}],"ddc":["530"],"has_accepted_license":"1","quality_controlled":"1","file":[{"date_created":"2025-12-01T07:30:00Z","file_name":"2025_PhysicalReviewX_Martinet.pdf","content_type":"application/pdf","success":1,"creator":"dernst","file_id":"20714","access_level":"open_access","relation":"main_file","checksum":"bb64ea9f2c400205fd89e9bdd15cc850","file_size":5902259,"date_updated":"2025-12-01T07:30:00Z"}],"corr_author":"1","APC_amount":"4695,11 EUR","publication":"Physical Review X","doi":"10.1103/rjk2-q2wh","publication_identifier":{"eissn":["2160-3308"]},"issue":"4","article_number":"041017","date_created":"2025-11-30T23:02:08Z","year":"2025"},{"project":[{"grant_number":"101071793","_id":"bd91e723-d553-11ed-ba76-fe7eeb2185fd","name":"Pushing from within: Control of cell shape, integrity and motility by cytoskeletal pushing forces"},{"name":"Motile active matter models of migrating cells and chiral filaments","grant_number":"26360","_id":"34d75525-11ca-11ed-8bc3-89b6307fee9d"}],"citation":{"chicago":"Dunajova, Zuzana, Saren Tasciyan, Juraj Majek, Jack Merrin, Erik Sahai, Michael K Sixt, and Edouard B Hannezo. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>.","apa":"Dunajova, Z., Tasciyan, S., Majek, J., Merrin, J., Sahai, E., Sixt, M. K., &#38; Hannezo, E. B. (n.d.). Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.05.20.655037\">https://doi.org/10.1101/2025.05.20.655037</a>","mla":"Dunajova, Zuzana, et al. “Substrate Heterogeneity Promotes Cancer Cell Dissemination through Interface Roughening.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>.","ieee":"Z. Dunajova <i>et al.</i>, “Substrate heterogeneity promotes cancer cell dissemination through interface roughening,” <i>bioRxiv</i>. .","short":"Z. Dunajova, S. Tasciyan, J. Majek, J. Merrin, E. Sahai, M.K. Sixt, E.B. Hannezo, BioRxiv (n.d.).","ama":"Dunajova Z, Tasciyan S, Majek J, et al. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>","ista":"Dunajova Z, Tasciyan S, Majek J, Merrin J, Sahai E, Sixt MK, Hannezo EB. Substrate heterogeneity promotes cancer cell dissemination through interface roughening. bioRxiv, <a href=\"https://doi.org/10.1101/2025.05.20.655037\">10.1101/2025.05.20.655037</a>."},"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","day":"25","oa":1,"department":[{"_id":"GradSch"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"AnSa"}],"date_updated":"2026-07-06T12:38:17Z","language":[{"iso":"eng"}],"month":"09","date_published":"2025-09-25T00:00:00Z","type":"preprint","acknowledgement":"European Research Council, https://ror.org/0472cxd90, 101071793\r\nAustrian Academy of Sciences, 26360","oa_version":"Preprint","_id":"21427","corr_author":"1","ddc":["539","570"],"has_accepted_license":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2025.05.20.655037"}],"year":"2025","date_created":"2026-03-11T08:40:06Z","publication":"bioRxiv","das_tickbox":"1","doi":"10.1101/2025.05.20.655037","abstract":[{"text":"While tumor malignancy has been extensively studied under the prism of genetic and epigenetic heterogeneity, tumor cell states also critically depend on reciprocal interactions with the microenvironment. This raises the hitherto untested possibility that heterogeneity of the untransformed tumor stroma can actively fuel malignant progression. As biological heterogeneity is inherently difficult to control, we adopted a reductionist approach and let tumor cells invade micro-engineered environments harboring obstacles with precision-controlled geometry. We find that not only the presence of obstacles, but more surprisingly their spatial disorder, causes a drastic shift from a collective to a single-cell mode of invasion – comparable in strength to cadherin loss. Combining live-imaging and perturbation experiments with minimal biophysical modeling, we demonstrate that cell detachments result both from local geometrical constraints and a global integration of spatial disorder over time. We show that different types of microenvironments map onto different universality classes of invasion dynamics - homogeneous substrates follow Kardar–Parisi–Zhang (KPZ) scaling, while disordered ones exhibit exponents consistent with KPZ with quenched disorder (KPZq). Our findings highlight generic physical principles for how the mode of cancer cell invasion depends on environmental heterogeneity, with potential implications to understand tumor evolution in vivo.","lang":"eng"}],"publication_status":"draft","article_processing_charge":"No","title":"Substrate heterogeneity promotes cancer cell dissemination through interface roughening","OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Zuzana","last_name":"Dunajova","full_name":"Dunajova, Zuzana","id":"4B39F286-F248-11E8-B48F-1D18A9856A87"},{"id":"4323B49C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1671-393X","full_name":"Tasciyan, Saren","last_name":"Tasciyan","first_name":"Saren"},{"first_name":"Juraj","last_name":"Majek","id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","full_name":"Majek, Juraj"},{"first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sahai","first_name":"Erik","full_name":"Sahai, Erik"},{"first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo"}],"related_material":{"record":[{"id":"21423","relation":"dissertation_contains","status":"public"},{"status":"public","id":"21439","relation":"research_data"}]}},{"corr_author":"1","file":[{"file_name":"Thesis_PDFA_.pdf","content_type":"application/pdf","date_created":"2025-10-28T13:10:08Z","success":1,"creator":"snaik","file_id":"20567","file_size":6846189,"date_updated":"2025-10-28T13:10:08Z","access_level":"open_access","checksum":"2892f04d4a5c18677871c3e06ac1244a","relation":"main_file"},{"creator":"snaik","date_created":"2025-10-28T13:10:26Z","file_name":"Thesis.zip","content_type":"application/zip","access_level":"open_access","checksum":"15934d4465cd0e9b7c32678da9a33a2f","relation":"source_file","date_updated":"2025-10-28T13:10:26Z","file_size":8839300,"file_id":"20568"}],"has_accepted_license":"1","ddc":["596","597","532"],"year":"2025","date_created":"2025-10-10T14:58:30Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-069-5"]},"doi":"10.15479/AT-ISTA-20441","page":"105","license":"https://creativecommons.org/licenses/by-sa/4.0/","article_processing_charge":"No","abstract":[{"text":"Epithelial spreading plays a pivotal role in the development of organisms especially those\r\nsuch as zebrafish which require the epithelial enveloping layer (EVL) to spread to cover the\r\nsubstantial yolk surface during gastrulation. Epiboly requires the transition of the epithelium\r\nwith cuboidal cells to form a thin, flat squamous epithelial sheet. During this transition, the\r\ncells show tissue-scale mechanosensation with mechanisms such as direct mechanical control\r\nover the axis of cell division.\r\nCytoskeletal intermediate filaments play a crucial role in vertebrate cells, not only facilitating\r\nmechanical stability but also helping facilitate the mechanosensitive response of the cell.\r\nMechanosenstivity displayed by intermediate filaments is due not just to their interesting\r\nphysical properties but also to their interactions with other cytoskeletal elements such as actin\r\nand microtubules. Keratin is the predominant intermediate filament expressed in the EVL.\r\nIt expresses concomitantly with the gastrulation movements of the developing embryo. Our\r\nwork focuses on understanding the role and dynamics of the keratin cytoskeletal network in\r\nmodulating the physical aspects of EVL spreading. We demonstrated with the combination of\r\nphysical characterisation and manipulations of the EVL, utilising a variety of biophysical tools\r\nand microscopy, the mechanistic role of keratin in tissue spreading.\r\nGenerating novel genetic morphants and mutants, we probe the effect that the loss of the\r\nkeratin network has on the physiology of the epithelium and the developing embryo. We\r\nshow that the changing organisation of the keratin network is important for changing EVL\r\nphysical properties as the stress imposed on the EVL increases during epiboly. By modelling\r\nthe epithelium, we study how the mechanical heterogeneity in an epithelium can feed back into\r\na mechanical loop to the maturation of the keratin network and hence affect the mechanics\r\nof the epithelium. However, unlike what would be predicted by the effect of intermediate\r\nfilaments in acting as a security belt and increasing the resistance of the epithelium, we observe\r\nthat loss of keratin leads to a delay in the EVL movement. Using both local aspirations of the\r\nYSL and EVL ablations, we demonstrate the mechanistic facilitation of actin mechanosensation\r\nin a keratin-dependent manner.\r\nFurthermore, using chemical inhibitors of microtubule polymerisation, we provide insight into\r\nthe mechanisms underlying the organisation and distribution of keratin. Interestingly, the\r\nphenotype observed upon this loss of microtubules shows that keratins interact with the nucleus\r\nthrough microtubular interactions. Together with these diverse observations, we describe\r\nthe mechanosensory feedback between resilience and that is critical for uniform and robust\r\nspreading of the epithelium.","lang":"eng"}],"publication_status":"published","degree_awarded":"PhD","title":"Keratins act as global coordinators of tissue spreading through mechanosensitive feedback","supervisor":[{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"last_name":"Naik","first_name":"Suyash","id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8421-5508","full_name":"Naik, Suyash"}],"OA_place":"publisher","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"related_material":{"record":[{"id":"20465","relation":"part_of_dissertation","status":"public"}]},"citation":{"ista":"Naik S. 2025. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. Institute of Science and Technology Austria.","ama":"Naik S. Keratins act as global coordinators of tissue spreading through mechanosensitive feedback. 2025. doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20441\">10.15479/AT-ISTA-20441</a>","ieee":"S. Naik, “Keratins act as global coordinators of tissue spreading through mechanosensitive feedback,” Institute of Science and Technology Austria, 2025.","short":"S. Naik, Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback, Institute of Science and Technology Austria, 2025.","mla":"Naik, Suyash. <i>Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback</i>. Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT-ISTA-20441\">10.15479/AT-ISTA-20441</a>.","chicago":"Naik, Suyash. “Keratins Act as Global Coordinators of Tissue Spreading through Mechanosensitive Feedback.” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT-ISTA-20441\">https://doi.org/10.15479/AT-ISTA-20441</a>.","apa":"Naik, S. (2025). <i>Keratins act as global coordinators of tissue spreading through mechanosensitive feedback</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT-ISTA-20441\">https://doi.org/10.15479/AT-ISTA-20441</a>"},"project":[{"name":"Keratins in epithelial tissue spreading","_id":"8f060199-16d5-11f0-9cad-f3253b266c46","grant_number":"PAT 5044023"},{"name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF","grant_number":"W 1250-B20","_id":"25AA5F24-B435-11E9-9278-68D0E5697425"}],"tmp":{"short":"CC BY-SA (4.0)","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"alternative_title":["ISTA Thesis"],"status":"public","day":"12","oa":1,"file_date_updated":"2025-10-28T13:10:26Z","month":"10","language":[{"iso":"eng"}],"date_published":"2025-10-12T00:00:00Z","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"CaHe"},{"_id":"EdHa"}],"date_updated":"2026-07-06T12:51:41Z","oa_version":"Published Version","type":"dissertation","acknowledgement":"I would also like to thank the LSF and Cryo facility at ISTA, which have been helpful in my\r\nexperiments. I would also like to acknowledge FWF, grant DOI 10.55776/PAT5044023 and JKU Nanocell grant DOI \r\n10.55776/W1250 for providing funding for my PhD research. EMBO and FWF for providing funding for travel grants to attend conferences.","_id":"20441"},{"_id":"20465","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"20441"},{"id":"22608","relation":"later_version","status":"public"}]},"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2C0B105C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8421-5508","full_name":"Naik, Suyash","last_name":"Naik","first_name":"Suyash"},{"last_name":"Keta","first_name":"Yann-Edwin","full_name":"Keta, Yann-Edwin"},{"first_name":"Kornelija","last_name":"Pranjic-Ferscha","full_name":"Pranjic-Ferscha, Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"full_name":"Henkes, Silke","last_name":"Henkes","first_name":"Silke"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"type":"preprint","OA_place":"repository","date_published":"2025-02-17T00:00:00Z","title":"Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties","language":[{"iso":"eng"}],"month":"02","date_updated":"2026-07-29T10:33:31Z","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"article_processing_charge":"No","license":"https://creativecommons.org/licenses/by-nd/4.0/","publication_status":"draft","abstract":[{"text":"For tissues to spread, they must be deformable while maintaining their structural integrity. How these opposing requirements are balanced within spreading tissues is not yet well understood. Here, we show that keratin intermediate filaments function in epithelial spreading by adapting tissue mechanical resilience to the stresses arising in the tissue during the spreading process. By analysing the expansion of the enveloping cell layer (EVL) over the large yolk cell in early zebrafish embryos in vivo, we found that keratin network maturation in EVL cells is promoted by stresses building up within the spreading tissue. Through genetic interference and tissue rheology experiments, complemented by a vertex model with mechanochemical feedback, we demonstrate that stress-induced keratin network maturation in the EVL increases tissue viscosity, which is essential for preventing tissue rupture. Interestingly, keratins are also required in the yolk cell for mechanosensitive actomyosin network contraction and flow, the force-generating processes pulling the EVL. These dual mechanosensitive functions of keratins enable a balance between pulling force production in the yolk cell and the mechanical resilience of the EVL against stresses generated by these pulling forces, thereby ensuring uniform and robust tissue spreading.","lang":"eng"}],"oa":1,"doi":"10.1101/2025.02.14.638262","das_tickbox":"1","publication":"bioRxiv","status":"public","day":"17","date_created":"2025-10-14T07:25:27Z","year":"2025","tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"main_file_link":[{"url":"https://doi.org/10.1101/2025.02.14.638262","open_access":"1"}],"citation":{"ama":"Naik S, Keta Y-E, Pranjic-Ferscha K, Hannezo EB, Henkes S, Heisenberg C-PJ. Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2025.02.14.638262\">10.1101/2025.02.14.638262</a>","ista":"Naik S, Keta Y-E, Pranjic-Ferscha K, Hannezo EB, Henkes S, Heisenberg C-PJ. Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. bioRxiv, <a href=\"https://doi.org/10.1101/2025.02.14.638262\">10.1101/2025.02.14.638262</a>.","short":"S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E.B. Hannezo, S. Henkes, C.-P.J. Heisenberg, BioRxiv (n.d.).","ieee":"S. Naik, Y.-E. Keta, K. Pranjic-Ferscha, E. B. Hannezo, S. Henkes, and C.-P. J. Heisenberg, “Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties,” <i>bioRxiv</i>. .","mla":"Naik, Suyash, et al. “Keratins Coordinate Tissue Spreading by Balancing Spreading Forces with Tissue Material Properties.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2025.02.14.638262\">10.1101/2025.02.14.638262</a>.","chicago":"Naik, Suyash, Yann-Edwin Keta, Kornelija Pranjic-Ferscha, Edouard B Hannezo, Silke Henkes, and Carl-Philipp J Heisenberg. “Keratins Coordinate Tissue Spreading by Balancing Spreading Forces with Tissue Material Properties.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2025.02.14.638262\">https://doi.org/10.1101/2025.02.14.638262</a>.","apa":"Naik, S., Keta, Y.-E., Pranjic-Ferscha, K., Hannezo, E. B., Henkes, S., &#38; Heisenberg, C.-P. J. (n.d.). Keratins coordinate tissue spreading by balancing spreading forces with tissue material properties. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2025.02.14.638262\">https://doi.org/10.1101/2025.02.14.638262</a>"},"corr_author":"1"},{"title":"Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling","publication_status":"published","external_id":{"pmid":["39603235"],"isi":["001434279000001"]},"abstract":[{"text":"Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study bone morphogenetic protein (BMP) signaling dynamics in the mouse neural tube, we developed an embryonic stem cell differentiation system tailored for growing tissues. Differentiating cells form striking self-organized patterns of dorsal neural tube cell types driven by sequential phases of BMP signaling that are observed both in vitro and in vivo. Data-driven biophysical modeling showed that these dynamics result from coupling fast negative feedback with slow positive regulation of signaling by the specification of an endogenous BMP source. Thus, in contrast to relays that propagate morphogen signaling in space, we identify a BMP signaling relay that operates in time. This mechanism allows for a rapid initial concentration-sensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation. Our study provides an experimental and theoretical framework to understand how signaling dynamics are exploited in developing tissues.","lang":"eng"}],"article_processing_charge":"Yes (via OA deal)","page":"567-580","pmid":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19763"}]},"volume":60,"OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8703-1093","full_name":"Rus, Stefanie","last_name":"Rus","first_name":"Stefanie"},{"last_name":"Brückner","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","full_name":"Brückner, David"},{"full_name":"Minchington, Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","last_name":"Minchington","first_name":"Thomas"},{"full_name":"Greunz, Martina","id":"48A59534-F248-11E8-B48F-1D18A9856A87","first_name":"Martina","last_name":"Greunz"},{"last_name":"Merrin","first_name":"Jack","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609"},{"last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B"},{"full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","first_name":"Anna"}],"ddc":["570"],"has_accepted_license":"1","quality_controlled":"1","file":[{"creator":"dernst","success":1,"date_created":"2025-04-16T10:54:07Z","file_name":"2025_DevelopmentalCell_Lehr.pdf","content_type":"application/pdf","relation":"main_file","checksum":"bb58db4a908a1f4aabe4004706154541","access_level":"open_access","date_updated":"2025-04-16T10:54:07Z","file_size":6994499,"file_id":"19584"}],"corr_author":"1","publication":"Developmental Cell","publication_identifier":{"issn":["1534-5807"]},"doi":"10.1016/j.devcel.2024.10.024","issue":"4","date_created":"2025-01-09T11:25:47Z","year":"2025","date_updated":"2026-09-04T22:30:40Z","publisher":"Elsevier","department":[{"_id":"AnKi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"date_published":"2025-02-24T00:00:00Z","month":"02","language":[{"iso":"eng"}],"file_date_updated":"2025-04-16T10:54:07Z","oa":1,"isi":1,"scopus_import":"1","_id":"18807","acknowledgement":"We thank A. Miller and N. Papalopulu for reagents and J. Briscoe for comments on the manuscript. Work in the A.K. lab is supported by ISTA; the European Research Council under Horizon Europe, grant 101044579; and the Austrian Science Fund (FWF), grant https://doi.org/10.55776/F78. S.L. is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022).","type":"journal_article","oa_version":"Published Version","intvolume":"        60","article_type":"original","project":[{"grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","name":"Mechanisms of tissue size regulation in spinal cord development"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F7802"},{"name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube","grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A"}],"citation":{"ieee":"S. Rus <i>et al.</i>, “Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling,” <i>Developmental Cell</i>, vol. 60, no. 4. Elsevier, pp. 567–580, 2025.","short":"S. Rus, D. Brückner, T. Minchington, M. Greunz, J. Merrin, E.B. Hannezo, A. Kicheva, Developmental Cell 60 (2025) 567–580.","ista":"Rus S, Brückner D, Minchington T, Greunz M, Merrin J, Hannezo EB, Kicheva A. 2025. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. 60(4), 567–580.","ama":"Rus S, Brückner D, Minchington T, et al. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. 2025;60(4):567-580. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>","chicago":"Rus, Stefanie, David Brückner, Thomas Minchington, Martina Greunz, Jack Merrin, Edouard B Hannezo, and Anna Kicheva. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>.","apa":"Rus, S., Brückner, D., Minchington, T., Greunz, M., Merrin, J., Hannezo, E. B., &#38; Kicheva, A. (2025). Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>","mla":"Rus, Stefanie, et al. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>, vol. 60, no. 4, Elsevier, 2025, pp. 567–80, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>."},"status":"public","day":"24","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid"},{"author":[{"id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566","full_name":"Arslan, Feyza N","last_name":"Arslan","first_name":"Feyza N"},{"first_name":"Edouard B","last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Merrin","first_name":"Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose","first_name":"Martin"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":34,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"pmid":1,"article_processing_charge":"Yes (via OA deal)","page":"171-182.e8","external_id":{"isi":["001154500400001"],"pmid":["38134934"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Metazoan development relies on the formation and remodeling of cell-cell contacts. Dynamic reorganization of adhesion receptors and the actomyosin cell cortex in space and time plays a central role in cell-cell contact formation and maturation. Nevertheless, how this process is mechanistically achieved when new contacts are formed remains unclear. Here, by building a biomimetic assay composed of progenitor cells adhering to supported lipid bilayers functionalized with E-cadherin ectodomains, we show that cortical F-actin flows, driven by the depletion of myosin-2 at the cell contact center, mediate the dynamic reorganization of adhesion receptors and cell cortex at the contact. E-cadherin-dependent downregulation of the small GTPase RhoA at the forming contact leads to both a depletion of myosin-2 and a decrease of F-actin at the contact center. At the contact rim, in contrast, myosin-2 becomes enriched by the retraction of bleb-like protrusions, resulting in a cortical tension gradient from the contact rim to its center. This tension gradient, in turn, triggers centrifugal F-actin flows, leading to further accumulation of F-actin at the contact rim and the progressive redistribution of E-cadherin from the contact center to the rim. Eventually, this combination of actomyosin downregulation and flows at the contact determines the characteristic molecular organization, with E-cadherin and F-actin accumulating at the contact rim, where they are needed to mechanically link the contractile cortices of the adhering cells."}],"title":"Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts","date_created":"2024-01-14T23:00:56Z","year":"2024","doi":"10.1016/j.cub.2023.11.067","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"issue":"1","publication":"Current Biology","corr_author":"1","quality_controlled":"1","file":[{"file_id":"14813","date_updated":"2024-01-16T10:53:31Z","file_size":5183861,"access_level":"open_access","checksum":"51220b76d72a614208f84bdbfbaf9b72","relation":"main_file","file_name":"2024_CurrentBiology_Arslan.pdf","content_type":"application/pdf","date_created":"2024-01-16T10:53:31Z","success":1,"creator":"dernst"}],"has_accepted_license":"1","ddc":["570"],"intvolume":"        34","oa_version":"Published Version","article_type":"original","type":"journal_article","acknowledgement":"We are grateful to Edwin Munro for their feedback and help with the single particle analysis. We thank members of the Heisenberg and Loose labs for their help and feedback on the manuscript, notably Xin Tong for making the PCS2-mCherry-AHPH plasmid. Finally, we thank the Aquatics and Imaging & Optics facilities of ISTA for their continuous support, especially Yann Cesbron for assistance with the laser cutter. This work was supported by an ERC\r\nAdvanced Grant (MECSPEC) to C.-P.H.","scopus_import":"1","_id":"14795","isi":1,"file_date_updated":"2024-01-16T10:53:31Z","oa":1,"date_published":"2024-01-08T00:00:00Z","language":[{"iso":"eng"}],"month":"01","date_updated":"2025-09-04T11:39:10Z","publisher":"Elsevier","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"NanoFab"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"day":"08","status":"public","citation":{"mla":"Arslan, Feyza N., et al. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” <i>Current Biology</i>, vol. 34, no. 1, Elsevier, 2024, p. 171–182.e8, doi:<a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">10.1016/j.cub.2023.11.067</a>.","chicago":"Arslan, Feyza N, Edouard B Hannezo, Jack Merrin, Martin Loose, and Carl-Philipp J Heisenberg. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” <i>Current Biology</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">https://doi.org/10.1016/j.cub.2023.11.067</a>.","apa":"Arslan, F. N., Hannezo, E. B., Merrin, J., Loose, M., &#38; Heisenberg, C.-P. J. (2024). Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">https://doi.org/10.1016/j.cub.2023.11.067</a>","ista":"Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. 2024. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. 34(1), 171–182.e8.","ama":"Arslan FN, Hannezo EB, Merrin J, Loose M, Heisenberg C-PJ. Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. <i>Current Biology</i>. 2024;34(1):171-182.e8. doi:<a href=\"https://doi.org/10.1016/j.cub.2023.11.067\">10.1016/j.cub.2023.11.067</a>","short":"F.N. Arslan, E.B. Hannezo, J. Merrin, M. Loose, C.-P.J. Heisenberg, Current Biology 34 (2024) 171–182.e8.","ieee":"F. N. Arslan, E. B. Hannezo, J. Merrin, M. Loose, and C.-P. J. Heisenberg, “Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts,” <i>Current Biology</i>, vol. 34, no. 1. Elsevier, p. 171–182.e8, 2024."},"project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"}]},{"volume":160,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"first_name":"Paul","last_name":"Robin","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","orcid":"0000-0002-5728-9189","full_name":"Robin, Paul"}],"pmid":1,"external_id":{"isi":["001161104900003"],"arxiv":["2311.11784"],"pmid":["38349632"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Electrostatic correlations between ions dissolved in water are known to impact their transport properties in numerous ways, from conductivity to ion selectivity. The effects of these correlations on the solvent itself remain, however, much less clear. In particular, the addition of salt has been consistently reported to affect the solution’s viscosity, but most modeling attempts fail to reproduce experimental data even at moderate salt concentrations. Here, we use an approach based on stochastic density functional theory, which accurately captures charge fluctuations and correlations. We derive a simple analytical expression for the viscosity correction in concentrated electrolytes, by directly linking it to the liquid’s structure factor. Our prediction compares quantitatively to experimental data at all temperatures and all salt concentrations up to the saturation limit. This universal link between the microscopic structure and viscosity allows us to shed light on the nanoscale dynamics of water and ions under highly concentrated and correlated conditions."}],"article_processing_charge":"Yes (in subscription journal)","title":"Correlation-induced viscous dissipation in concentrated electrolytes","article_number":"064503","date_created":"2024-02-25T23:00:55Z","year":"2024","publication":"Journal of Chemical Physics","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"doi":"10.1063/5.0188215","issue":"6","file":[{"file_id":"15034","access_level":"open_access","relation":"main_file","checksum":"0a5e0ae70849bce674466fc054390ec0","date_updated":"2024-02-27T08:12:52Z","file_size":5452738,"date_created":"2024-02-27T08:12:52Z","file_name":"2024_JourChemicalPhysics_Robin.pdf","content_type":"application/pdf","success":1,"creator":"dernst"}],"quality_controlled":"1","corr_author":"1","ddc":["540"],"has_accepted_license":"1","type":"journal_article","acknowledgement":"The author thanks Lydéric Bocquet, Baptiste Coquinot, and Mathieu Lizée for fruitful discussions. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","oa_version":"Published Version","intvolume":"       160","article_type":"original","scopus_import":"1","_id":"15024","file_date_updated":"2024-02-27T08:12:52Z","oa":1,"isi":1,"date_updated":"2025-09-04T12:07:33Z","publisher":"AIP Publishing","department":[{"_id":"EdHa"}],"arxiv":1,"date_published":"2024-02-14T00:00:00Z","month":"02","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"status":"public","day":"14","project":[{"call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"citation":{"ieee":"P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,” <i>Journal of Chemical Physics</i>, vol. 160, no. 6. AIP Publishing, 2024.","short":"P. Robin, Journal of Chemical Physics 160 (2024).","ista":"Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 160(6), 064503.","ama":"Robin P. Correlation-induced viscous dissipation in concentrated electrolytes. <i>Journal of Chemical Physics</i>. 2024;160(6). doi:<a href=\"https://doi.org/10.1063/5.0188215\">10.1063/5.0188215</a>","apa":"Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes. <i>Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0188215\">https://doi.org/10.1063/5.0188215</a>","chicago":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” <i>Journal of Chemical Physics</i>. AIP Publishing, 2024. <a href=\"https://doi.org/10.1063/5.0188215\">https://doi.org/10.1063/5.0188215</a>.","mla":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” <i>Journal of Chemical Physics</i>, vol. 160, no. 6, 064503, AIP Publishing, 2024, doi:<a href=\"https://doi.org/10.1063/5.0188215\">10.1063/5.0188215</a>."}},{"date_created":"2024-04-14T22:01:01Z","year":"2024","article_number":"056601","publication_identifier":{"eissn":["1361-6633"],"issn":["0034-4885"]},"doi":"10.1088/1361-6633/ad36d2","issue":"5","publication":"Reports on Progress in Physics","corr_author":"1","file":[{"relation":"main_file","checksum":"c5910078230ade20f4dd83592e862a72","access_level":"open_access","date_updated":"2024-08-20T11:00:03Z","file_size":4376898,"file_id":"17451","creator":"dernst","success":1,"date_created":"2024-08-20T11:00:03Z","file_name":"2024_ReportPhysics_Brueckner.pdf","content_type":"application/pdf"}],"quality_controlled":"1","has_accepted_license":"1","ddc":["530"],"author":[{"first_name":"David","last_name":"Brückner","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975"},{"last_name":"Broedersz","first_name":"Chase P.","full_name":"Broedersz, Chase P."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":87,"pmid":1,"article_processing_charge":"Yes (in subscription journal)","publication_status":"published","external_id":{"pmid":["38518358"],"arxiv":["2309.00545"],"isi":["001196692400001"]},"abstract":[{"lang":"eng","text":"Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical perspective, a broad variety of models for the underlying physical mechanisms that govern cell motility have been developed. A key challenge in the development of such models is how to connect them to experimental observations, which often exhibit complex stochastic behaviours. In this review, we discuss recent advances in data-driven theoretical approaches that directly connect with experimental data to infer dynamical models of stochastic cell migration. Leveraging advances in nanofabrication, image analysis, and tracking technology, experimental studies now provide unprecedented large datasets on cellular dynamics. In parallel, theoretical efforts have been directed towards integrating such datasets into physical models from the single cell to the tissue scale with the aim of conceptualising the emergent behaviour of cells. We first review how this inference problem has been addressed in both freely migrating and confined cells. Next, we discuss why these dynamics typically take the form of underdamped stochastic equations of motion, and how such equations can be inferred from data. We then review applications of data-driven inference and machine learning approaches to heterogeneity in cell behaviour, subcellular degrees of freedom, and to the collective dynamics of multicellular systems. Across these applications, we emphasise how data-driven methods can be integrated with physical active matter models of migrating cells, and help reveal how underlying molecular mechanisms control cell behaviour. Together, these data-driven approaches are a promising avenue for building physical models of cell migration directly from experimental data, and for providing conceptual links between different length-scales of description."}],"title":"Learning dynamical models of single and collective cell migration: a review","tmp":{"short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"day":"04","status":"public","citation":{"ieee":"D. Brückner and C. P. Broedersz, “Learning dynamical models of single and collective cell migration: a review,” <i>Reports on Progress in Physics</i>, vol. 87, no. 5. IOP Publishing, 2024.","short":"D. Brückner, C.P. Broedersz, Reports on Progress in Physics 87 (2024).","ama":"Brückner D, Broedersz CP. Learning dynamical models of single and collective cell migration: a review. <i>Reports on Progress in Physics</i>. 2024;87(5). doi:<a href=\"https://doi.org/10.1088/1361-6633/ad36d2\">10.1088/1361-6633/ad36d2</a>","ista":"Brückner D, Broedersz CP. 2024. Learning dynamical models of single and collective cell migration: a review. Reports on Progress in Physics. 87(5), 056601.","apa":"Brückner, D., &#38; Broedersz, C. P. (2024). Learning dynamical models of single and collective cell migration: a review. <i>Reports on Progress in Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6633/ad36d2\">https://doi.org/10.1088/1361-6633/ad36d2</a>","chicago":"Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of Single and Collective Cell Migration: A Review.” <i>Reports on Progress in Physics</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.1088/1361-6633/ad36d2\">https://doi.org/10.1088/1361-6633/ad36d2</a>.","mla":"Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of Single and Collective Cell Migration: A Review.” <i>Reports on Progress in Physics</i>, vol. 87, no. 5, 056601, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.1088/1361-6633/ad36d2\">10.1088/1361-6633/ad36d2</a>."},"project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"oa_version":"Published Version","intvolume":"        87","article_type":"review","type":"journal_article","acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft (German Research Foundation)—Project-ID 201269156—SFB 1032 (Project B12). D B B was supported by an NOMIS Fellowship and an EMBO Fellowship (ALTF 343-2022). We thank Joachim Rädler, Alexandra Fink, Erwin Frey, Pierre Ronceray, Ricard Alert, Edouard Hannezo, Henrik Flyvbjerg, Ulrich Schwarz, Joshua Shaevitz, Greg Stephens, Andrea Cavagna, Grzegorz Gradziuk, Fridtjof Brauns, Nikolas Claussen, Tom Brandstätter, Johannes Flommersfeld, Christoph Schreiber, Nicolas Arlt, Matthew Schmitt, Joris Messelink, Federico Gnesotto, Federica Mura, Bram Hoogland, Manon Wigbers, Isabella Graf, Jessica Lober, and many others for inspiring discussions. We also thank Claudia Flandoli for the artwork in figures 1, 5, 8 and 9.","scopus_import":"1","_id":"15315","isi":1,"file_date_updated":"2024-08-20T11:00:03Z","oa":1,"date_published":"2024-04-04T00:00:00Z","language":[{"iso":"eng"}],"month":"04","date_updated":"2025-09-04T13:39:07Z","department":[{"_id":"EdHa"}],"arxiv":1,"publisher":"IOP Publishing"},{"_id":"17104","scopus_import":"1","type":"journal_article","acknowledgement":"JE and JK gratefully acknowledge financial support from the Initiative and Networking Fund (IVF) via the grant number ERC-RA-004. Simulations were performed with computing resources granted by RWTH Aachen University under project ‘rwth0475’.","article_type":"original","intvolume":"        16","oa_version":"Published Version","publisher":"SciPost Foundation","arxiv":1,"department":[{"_id":"EdHa"}],"date_updated":"2025-09-08T07:45:40Z","month":"04","language":[{"iso":"eng"}],"date_published":"2024-04-08T00:00:00Z","oa":1,"file_date_updated":"2024-06-03T11:18:51Z","isi":1,"day":"08","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"ieee":"J. C. Krämer, E. B. Hannezo, G. Gompper, and J. Elgeti, “Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells,” <i>SciPost Physics</i>, vol. 16, no. 4. SciPost Foundation, 2024.","short":"J.C. Krämer, E.B. Hannezo, G. Gompper, J. Elgeti, SciPost Physics 16 (2024).","ista":"Krämer JC, Hannezo EB, Gompper G, Elgeti J. 2024. Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. SciPost Physics. 16(4), 097.","ama":"Krämer JC, Hannezo EB, Gompper G, Elgeti J. Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. <i>SciPost Physics</i>. 2024;16(4). doi:<a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">10.21468/scipostphys.16.4.097</a>","chicago":"Krämer, Johannes C., Edouard B Hannezo, Gerhard Gompper, and Jens Elgeti. “Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” <i>SciPost Physics</i>. SciPost Foundation, 2024. <a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">https://doi.org/10.21468/scipostphys.16.4.097</a>.","apa":"Krämer, J. C., Hannezo, E. B., Gompper, G., &#38; Elgeti, J. (2024). Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">https://doi.org/10.21468/scipostphys.16.4.097</a>","mla":"Krämer, Johannes C., et al. “Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” <i>SciPost Physics</i>, vol. 16, no. 4, 097, SciPost Foundation, 2024, doi:<a href=\"https://doi.org/10.21468/scipostphys.16.4.097\">10.21468/scipostphys.16.4.097</a>."},"volume":16,"author":[{"first_name":"Johannes C.","last_name":"Krämer","full_name":"Krämer, Johannes C."},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo"},{"first_name":"Gerhard","last_name":"Gompper","full_name":"Gompper, Gerhard"},{"full_name":"Elgeti, Jens","first_name":"Jens","last_name":"Elgeti"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells","abstract":[{"text":"The homeostasis of epithelial tissue relies on a balance between the self-renewal of stem cell populations, cellular differentiation, and loss. Although this balance needs to be tightly regulated to avoid pathologies, such as tumor growth, the regulatory mechanisms, both cell-intrinsic and collective, which ensure tissue steady-state are still poorly understood. Here, we develop a computational model that incorporates basic assumptions of stem cell renewal into distinct populations and mechanical interactions between cells. We find that the model generates unexpected dynamic features: stem cells repel each other in the bulk tissue and are thus found rather isolated, as in a number of in vivo contexts. By mapping the system onto a gas of passive Brownian particles with effective repulsive interactions, that arise from the generated flows of differentiated cells, we show that we can quantitatively describe such stem cell distribution in tissues. The interaction potential between a pair of stem cells decays exponentially with a characteristic length that spans several cell sizes, corresponding to the volume of cells generated per stem cell division. Our findings may help understanding the dynamics of normal and cancerous epithelial tissues.","lang":"eng"}],"external_id":{"isi":["001202370200001"],"arxiv":["2310.04272"]},"publication_status":"published","article_processing_charge":"No","publication":"SciPost Physics","issue":"4","publication_identifier":{"issn":["2542-4653"]},"doi":"10.21468/scipostphys.16.4.097","article_number":"097","year":"2024","date_created":"2024-06-03T08:58:44Z","ddc":["530"],"has_accepted_license":"1","file":[{"file_size":4973291,"date_updated":"2024-06-03T11:18:51Z","access_level":"open_access","relation":"main_file","checksum":"6fdeecd21c166db8dedb927ecc2e6025","file_id":"17109","success":1,"creator":"dernst","file_name":"2024_SciPostPhys_Kraemer.pdf","content_type":"application/pdf","date_created":"2024-06-03T11:18:51Z"}],"quality_controlled":"1"},{"OA_type":"hybrid","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","day":"04","citation":{"mla":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 23, e2322326121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2322326121\">10.1073/pnas.2322326121</a>.","chicago":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2322326121\">https://doi.org/10.1073/pnas.2322326121</a>.","apa":"Brückner, D., &#38; Tkačik, G. (2024). Information content and optimization of self-organized developmental systems. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2322326121\">https://doi.org/10.1073/pnas.2322326121</a>","ista":"Brückner D, Tkačik G. 2024. Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America. 121(23), e2322326121.","ama":"Brückner D, Tkačik G. Information content and optimization of self-organized developmental systems. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(23). doi:<a href=\"https://doi.org/10.1073/pnas.2322326121\">10.1073/pnas.2322326121</a>","ieee":"D. Brückner and G. Tkačik, “Information content and optimization of self-organized developmental systems,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 23. National Academy of Sciences, 2024.","short":"D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024)."},"project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"article_type":"original","intvolume":"       121","oa_version":"Published Version","type":"journal_article","acknowledgement":"We thank Wiktor Młynarski, Juraj Majek, Michal Hledík, Fridtjof Brauns, Nikolas Claussen, Benjamin Zoller, Erwin Frey, Thomas Gregor, and Edouard Hannezo for inspiring discussions. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 343-2022). This research was performed in part at the Aspen Center for Physics, which is supported by NSF Grant No. PHY-1607611, and Kavli Institute for Theoretical Physics (KITP) Santa Barbara, supported by NSF Grant No. PHY-1748958 and the Gordon and Betty Moore Foundation Grant No. 2919.02.","_id":"17123","scopus_import":"1","isi":1,"oa":1,"file_date_updated":"2024-06-10T10:27:37Z","language":[{"iso":"eng"}],"month":"06","date_published":"2024-06-04T00:00:00Z","publisher":"National Academy of Sciences","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"date_updated":"2025-09-08T07:51:01Z","year":"2024","date_created":"2024-06-09T22:01:02Z","article_number":"e2322326121","issue":"23","doi":"10.1073/pnas.2322326121","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication":"Proceedings of the National Academy of Sciences of the United States of America","APC_amount":"2570,79 EUR","corr_author":"1","quality_controlled":"1","file":[{"date_updated":"2024-06-10T10:27:37Z","file_size":12329234,"access_level":"open_access","checksum":"59797a75db7beb3721ed7a4d14c241f9","relation":"main_file","file_id":"17130","success":1,"creator":"dernst","file_name":"2024_PNAS_Brueckner.pdf","content_type":"application/pdf","date_created":"2024-06-10T10:27:37Z"}],"has_accepted_license":"1","ddc":["570"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Brückner","first_name":"David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David"},{"last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"volume":121,"OA_place":"publisher","related_material":{"link":[{"relation":"software","url":"https://github.com/dbrueckner/SelforgInformation"},{"description":"News on the ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/the-embryo-assembles-itself/"}]},"pmid":1,"article_processing_charge":"Yes (in subscription journal)","abstract":[{"lang":"eng","text":"A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and even harnessing intrinsic and extrinsic fluctuations. While the relevant molecular processes are increasingly well understood, we lack a principled framework to quantify the performance of such stochastic self-organizing systems. To that end, we introduce an information-theoretic measure for self-organized fate specification during embryonic development. We show that the proposed measure assesses the total information content of fate patterns and decomposes it into interpretable contributions corresponding to the positional and correlational information. By optimizing the proposed measure, our framework provides a normative theory for developmental circuits, which we demonstrate on lateral inhibition, cell type proportioning, and reaction–diffusion models of self-organization. This paves a way toward a classification of developmental systems based on a common information-theoretic language, thereby organizing the zoo of implicated chemical and mechanical signaling processes."}],"external_id":{"isi":["001244835000006"],"pmid":["38819997"]},"publication_status":"published","title":"Information content and optimization of self-organized developmental systems"}]