[{"isi":1,"issue":"4","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"19763"}]},"article_type":"original","page":"567-580","type":"journal_article","has_accepted_license":"1","project":[{"_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579","name":"Mechanisms of tissue size regulation in spinal cord development"},{"grant_number":"F7802","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"},{"_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","grant_number":"SC19-011","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"article_processing_charge":"Yes (via OA deal)","doi":"10.1016/j.devcel.2024.10.024","_id":"18807","day":"24","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1016/j.devcel.2024.10.024","oa_version":"Published Version","citation":{"apa":"Rus, S., Brückner, D., Minchington, T., Greunz, M., Merrin, J., Hannezo, E. B., & Kicheva, A. (2025). Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2024.10.024","ieee":"S. Rus et al., “Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling,” Developmental Cell, vol. 60, no. 4. Cell Press, pp. 567–580, 2025.","mla":"Rus, Stefanie, et al. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” Developmental Cell, vol. 60, no. 4, Cell Press, 2025, pp. 567–80, doi:10.1016/j.devcel.2024.10.024.","short":"S. Rus, D. Brückner, T. Minchington, M. Greunz, J. Merrin, E.B. Hannezo, A. Kicheva, Developmental Cell 60 (2025) 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. Developmental Cell. 2025;60(4):567-580. doi:10.1016/j.devcel.2024.10.024","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.","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.” Developmental Cell. Cell Press, 2025. https://doi.org/10.1016/j.devcel.2024.10.024."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["001434279000001"],"pmid":["39603235"]},"publication_status":"published","publication_identifier":{"issn":["1534-5807"]},"title":"Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling","publisher":"Cell Press","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"corr_author":"1","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"}],"file_date_updated":"2025-04-16T10:54:07Z","oa":1,"author":[{"id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","first_name":"Stefanie","orcid":"0000-0001-8703-1093","full_name":"Rus, Stefanie","last_name":"Rus"},{"full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","orcid":"0000-0001-7205-2975","last_name":"Brückner"},{"full_name":"Minchington, Thomas","first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","last_name":"Minchington"},{"last_name":"Greunz","first_name":"Martina","id":"48A59534-F248-11E8-B48F-1D18A9856A87","full_name":"Greunz, Martina"},{"orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","full_name":"Merrin, Jack","last_name":"Merrin"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"last_name":"Kicheva","orcid":"0000-0003-4509-4998","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","full_name":"Kicheva, Anna"}],"intvolume":" 60","scopus_import":"1","pmid":1,"OA_type":"hybrid","ddc":["570"],"quality_controlled":"1","status":"public","researchdata_availability":"yes","volume":60,"year":"2025","publication":"Developmental Cell","das_tickbox":"1","date_updated":"2026-10-21T22:31:33Z","file":[{"checksum":"bb58db4a908a1f4aabe4004706154541","success":1,"file_name":"2025_DevelopmentalCell_Lehr.pdf","date_created":"2025-04-16T10:54:07Z","creator":"dernst","access_level":"open_access","date_updated":"2025-04-16T10:54:07Z","file_size":6994499,"file_id":"19584","relation":"main_file","content_type":"application/pdf"}],"date_created":"2025-01-09T11:25:47Z","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).","department":[{"_id":"AnKi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"date_published":"2025-02-24T00:00:00Z","dataavailabilitystatement":"RNA-seq data has been deposited at GEO and are publicly available as of the date of publication. Accession numbers are listed in the key resources table. Code for the quantification of fluorescence intensity (FI) profiles in differentiated cells on stencils, as well as for model simulations, is available on GitHub (https://github.com/dbrueckner/NeuralTubeColonies, https://doi.org/10.5281/zenodo.13335390","OA_place":"publisher","supplementarymaterial":"yes","month":"02"},{"department":[{"_id":"EdHa"}],"acknowledgement":"This study was partially funded by Science and Engineering Research Board, Department of Science and Technology, Government of India to Vishwesha Guttal.","date_created":"2025-08-05T06:49:59Z","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7137151","open_access":"1"}],"date_updated":"2025-09-30T14:14:42Z","citation":{"ieee":"A. Nabeel et al., “PyDaddy: A Python Package for Discovering SDEs from Time Series Data.” Zenodo, 2024.","mla":"Nabeel, Arshed, et al. PyDaddy: A Python Package for Discovering SDEs from Time Series Data. Zenodo, 2024, doi:10.5281/ZENODO.7137151.","short":"A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, M. Danny Raj, V. Guttal, (2024).","ama":"Nabeel A, Karichannavar A, Palathingal S, et al. PyDaddy: A Python Package for Discovering SDEs from Time Series Data. 2024. doi:10.5281/ZENODO.7137151","apa":"Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Danny Raj, M., & Guttal, V. (2024). PyDaddy: A Python Package for Discovering SDEs from Time Series Data. Zenodo. https://doi.org/10.5281/ZENODO.7137151","ista":"Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Danny Raj M, Guttal V. 2024. PyDaddy: A Python Package for Discovering SDEs from Time Series Data, Zenodo, 10.5281/ZENODO.7137151.","chicago":"Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar, David Brückner, Masila Danny Raj, and Vishwesha Guttal. “PyDaddy: A Python Package for Discovering SDEs from Time Series Data.” Zenodo, 2024. https://doi.org/10.5281/ZENODO.7137151."},"title":"PyDaddy: A Python Package for Discovering SDEs from Time Series Data","month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2024-09-18T00:00:00Z","author":[{"first_name":"Arshed","full_name":"Nabeel, Arshed","last_name":"Nabeel"},{"last_name":"Karichannavar","full_name":"Karichannavar, Ashwin","first_name":"Ashwin"},{"last_name":"Palathingal","full_name":"Palathingal, Shuaib","first_name":"Shuaib"},{"full_name":"Jhawar, Jitesh","first_name":"Jitesh","last_name":"Jhawar"},{"full_name":"Brückner, David","orcid":"0000-0001-7205-2975","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner"},{"last_name":"Danny Raj","first_name":"Masila","full_name":"Danny Raj, Masila"},{"last_name":"Guttal","full_name":"Guttal, Vishwesha","first_name":"Vishwesha"}],"has_accepted_license":"1","oa":1,"type":"research_data_reference","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"PyDaddy is an open source package which is a key contribution of the manuscript Nabeel et al, arXiv:2205.02645. The basic scientific premise for this package is to discover the nature of stochasticity in ecological time series datasets. It is well known that the stochasticity can affect the dynamics of ecological systems in counter-intuitive ways. Without understanding the equations (typically, in the form of stochastic differential equations or SDEs, in short) that govern the dynamics of populations or ecosystems, it's challenging to determine the impact of randomness on real datasets. In this manuscript and accompanying package, we introduce a methodology for discovering equations (SDEs) that transforms time series data of state variables into stochastic differential equations. This approach merges traditional stochastic calculus with modern equation-discovery techniques. We showcase the generality of our method through various applications and discuss its limitations and potential pitfalls, offering diagnostic measures to address these challenges."}],"related_material":{"record":[{"id":"20056","relation":"used_for_analysis_in","status":"public"}]},"publisher":"Zenodo","fulldoi":"https://doi.org/10.5281/ZENODO.7137151","oa_version":"Published Version","_id":"20121","year":"2024","day":"18","doi":"10.5281/ZENODO.7137151","ddc":["570"],"status":"public","article_processing_charge":"No"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"publication_status":"published","external_id":{"isi":["001154500400001"],"pmid":["38134934"]},"title":"Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts","citation":{"apa":"Arslan, F. N., Hannezo, E. B., Merrin, J., Loose, M., & Heisenberg, C.-P. J. (2024). Adhesion-induced cortical flows pattern E-cadherin-mediated cell contacts. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2023.11.067","short":"F.N. Arslan, E.B. Hannezo, J. Merrin, M. Loose, C.-P.J. Heisenberg, Current Biology 34 (2024) 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. Current Biology. 2024;34(1):171-182.e8. doi:10.1016/j.cub.2023.11.067","mla":"Arslan, Feyza N., et al. “Adhesion-Induced Cortical Flows Pattern E-Cadherin-Mediated Cell Contacts.” Current Biology, vol. 34, no. 1, Elsevier, 2024, p. 171–182.e8, doi:10.1016/j.cub.2023.11.067.","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,” Current Biology, vol. 34, no. 1. Elsevier, p. 171–182.e8, 2024.","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.” Current Biology. Elsevier, 2024. https://doi.org/10.1016/j.cub.2023.11.067.","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."},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"article_processing_charge":"Yes (via OA deal)","doi":"10.1016/j.cub.2023.11.067","fulldoi":"https://doi.org/10.1016/j.cub.2023.11.067","language":[{"iso":"eng"}],"oa_version":"Published Version","day":"08","_id":"14795","issue":"1","isi":1,"page":"171-182.e8","article_type":"original","project":[{"_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742573","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"has_accepted_license":"1","type":"journal_article","date_published":"2024-01-08T00:00:00Z","dataavailabilitystatement":"All original microscopy data any additional information reported in this paper is available from the lead contact upon request. All original code is available from the lead contact upon request","supplementarymaterial":"yes","month":"01","date_updated":"2026-10-01T08:33:05Z","das_tickbox":"1","file":[{"access_level":"open_access","date_updated":"2024-01-16T10:53:31Z","creator":"dernst","checksum":"51220b76d72a614208f84bdbfbaf9b72","file_name":"2024_CurrentBiology_Arslan.pdf","success":1,"date_created":"2024-01-16T10:53:31Z","content_type":"application/pdf","relation":"main_file","file_size":5183861,"file_id":"14813"}],"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.","date_created":"2024-01-14T23:00:56Z","ec_funded":1,"department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MaLo"},{"_id":"NanoFab"}],"intvolume":" 34","quality_controlled":"1","ddc":["570"],"status":"public","scopus_import":"1","pmid":1,"researchdata_availability":"upon request","publication":"Current Biology","year":"2024","volume":34,"publisher":"Elsevier","abstract":[{"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.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"corr_author":"1","author":[{"last_name":"Arslan","orcid":"0000-0001-5809-9566","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","first_name":"Feyza N","full_name":"Arslan, Feyza N"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo"},{"full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"},{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg"}],"oa":1,"file_date_updated":"2024-01-16T10:53:31Z"},{"quality_controlled":"1","status":"public","ddc":["530"],"pmid":1,"scopus_import":"1","intvolume":" 87","publication":"Reports on Progress in Physics","year":"2024","volume":87,"researchdata_availability":"not applicable","publisher":"IOP Publishing","author":[{"full_name":"Brückner, David","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","last_name":"Brückner"},{"last_name":"Broedersz","first_name":"Chase P.","full_name":"Broedersz, Chase P."}],"oa":1,"file_date_updated":"2024-08-20T11:00:03Z","corr_author":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","image":"/images/cc_by.png","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"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."}],"dataavailabilitystatement":"No new data were created or analysed in this study.","date_published":"2024-04-04T00:00:00Z","month":"04","license":"https://creativecommons.org/licenses/by/3.0/","supplementarymaterial":"no","file":[{"creator":"dernst","date_updated":"2024-08-20T11:00:03Z","access_level":"open_access","success":1,"file_name":"2024_ReportPhysics_Brueckner.pdf","date_created":"2024-08-20T11:00:03Z","checksum":"c5910078230ade20f4dd83592e862a72","content_type":"application/pdf","relation":"main_file","file_id":"17451","file_size":4376898}],"date_updated":"2026-10-01T10:09:41Z","das_tickbox":"1","department":[{"_id":"EdHa"}],"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.","date_created":"2024-04-14T22:01:01Z","article_processing_charge":"Yes (in subscription journal)","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1088/1361-6633/ad36d2","oa_version":"Published Version","day":"04","_id":"15315","doi":"10.1088/1361-6633/ad36d2","article_type":"review","issue":"5","isi":1,"arxiv":1,"has_accepted_license":"1","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"}],"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"056601","title":"Learning dynamical models of single and collective cell migration: a review","publication_status":"published","publication_identifier":{"issn":["0034-4885"],"eissn":["1361-6633"]},"external_id":{"pmid":["38518358"],"arxiv":["2309.00545"],"isi":["001196692400001"]},"citation":{"apa":"Brückner, D., & Broedersz, C. P. (2024). Learning dynamical models of single and collective cell migration: a review. Reports on Progress in Physics. IOP Publishing. https://doi.org/10.1088/1361-6633/ad36d2","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. Reports on Progress in Physics. 2024;87(5). doi:10.1088/1361-6633/ad36d2","ieee":"D. Brückner and C. P. Broedersz, “Learning dynamical models of single and collective cell migration: a review,” Reports on Progress in Physics, vol. 87, no. 5. IOP Publishing, 2024.","mla":"Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of Single and Collective Cell Migration: A Review.” Reports on Progress in Physics, vol. 87, no. 5, 056601, IOP Publishing, 2024, doi:10.1088/1361-6633/ad36d2.","chicago":"Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of Single and Collective Cell Migration: A Review.” Reports on Progress in Physics. IOP Publishing, 2024. https://doi.org/10.1088/1361-6633/ad36d2.","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."}},{"oa":1,"file_date_updated":"2024-02-27T08:12:52Z","author":[{"first_name":"Paul","id":"48c58128-57b0-11ee-9095-dc28fd97fc1d","orcid":"0000-0002-5728-9189","full_name":"Robin, Paul","last_name":"Robin"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"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.","lang":"eng"}],"corr_author":"1","publisher":"AIP Publishing","volume":160,"year":"2024","publication":"Journal of Chemical Physics","researchdata_availability":"not applicable","scopus_import":"1","pmid":1,"ddc":["540"],"quality_controlled":"1","status":"public","intvolume":" 160","department":[{"_id":"EdHa"}],"ec_funded":1,"date_created":"2024-02-25T23:00:55Z","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.","file":[{"creator":"dernst","date_updated":"2024-02-27T08:12:52Z","access_level":"open_access","success":1,"file_name":"2024_JourChemicalPhysics_Robin.pdf","date_created":"2024-02-27T08:12:52Z","checksum":"0a5e0ae70849bce674466fc054390ec0","relation":"main_file","content_type":"application/pdf","file_id":"15034","file_size":5452738}],"das_tickbox":"1","date_updated":"2026-10-01T10:08:50Z","month":"02","supplementarymaterial":"no","dataavailabilitystatement":"Data sharing is not applicable to this article as no new data were created. Data supporting the findings of this study are accessible in the literature, as indicated throughout the article.","date_published":"2024-02-14T00:00:00Z","type":"journal_article","has_accepted_license":"1","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"article_type":"original","isi":1,"arxiv":1,"issue":"6","day":"14","_id":"15024","fulldoi":"https://doi.org/10.1063/5.0188215","language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.1063/5.0188215","article_processing_charge":"Yes (in subscription journal)","citation":{"ama":"Robin P. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 2024;160(6). doi:10.1063/5.0188215","short":"P. Robin, Journal of Chemical Physics 160 (2024).","ieee":"P. Robin, “Correlation-induced viscous dissipation in concentrated electrolytes,” Journal of Chemical Physics, vol. 160, no. 6. AIP Publishing, 2024.","mla":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics, vol. 160, no. 6, 064503, AIP Publishing, 2024, doi:10.1063/5.0188215.","apa":"Robin, P. (2024). Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0188215","chicago":"Robin, Paul. “Correlation-Induced Viscous Dissipation in Concentrated Electrolytes.” Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0188215.","ista":"Robin P. 2024. Correlation-induced viscous dissipation in concentrated electrolytes. Journal of Chemical Physics. 160(6), 064503."},"title":"Correlation-induced viscous dissipation in concentrated electrolytes","external_id":{"arxiv":["2311.11784"],"isi":["001161104900003"],"pmid":["38349632"]},"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"064503"},{"file":[{"file_name":"2024_PhysReviewE_Olmeda.pdf","date_created":"2024-09-11T05:59:36Z","success":1,"checksum":"67fc2cc8eee3155e5c3b7380307d8284","creator":"dernst","date_updated":"2024-09-11T05:59:36Z","access_level":"open_access","file_id":"18053","file_size":445696,"relation":"main_file","content_type":"application/pdf"}],"date_updated":"2026-10-01T10:06:45Z","das_tickbox":"0","department":[{"_id":"EdHa"}],"date_created":"2024-09-08T22:01:12Z","acknowledgement":"We thank F. Piazza, M. Henkel, and F. Jülicher for helpful feedback and the entire Rulands group for fruitful discussions. We thank W. Reik, S. Clark, T. Lohoff, and I. Kafetzopoulos for fruitful discussions about the biological aspects of this work. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Grant No. 950349). This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant No. 101034413.","ec_funded":1,"date_published":"2024-08-01T00:00:00Z","month":"08","supplementarymaterial":"no","publisher":"American Physical Society","author":[{"first_name":"Fabrizio","id":"69dbf5fb-8a76-11ed-866b-fb486d8b5689","full_name":"Olmeda, Fabrizio","last_name":"Olmeda"},{"last_name":"Rulands","first_name":"Steffen","full_name":"Rulands, Steffen"}],"oa":1,"file_date_updated":"2024-09-11T05:59:36Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"text":"Enzyme-substrate kinetics form the basis of many biomolecular processes. The interplay between substrate binding and substrate geometry can give rise to long-range interactions between enzyme binding events. Here we study a general model of enzyme-substrate kinetics with restricted long-range interactions described by an exponent −𝛾. We employ a coherent-state path integral and renormalization group approach to calculate the first moment and two-point correlation function of the enzyme-binding profile. We show that starting from an empty substrate the average occupancy follows a power law with an exponent 1/(1−𝛾) over time. The correlation function decays algebraically with two distinct spatial regimes characterized by exponents −𝛾 on short distances and −(2/3)(2−𝛾) on long distances. The crossover between both regimes scales inversely with the average substrate occupancy. Our work allows associating experimental measurements of bound enzyme locations with their binding kinetics and the spatial conformation of the substrate.","lang":"eng"}],"corr_author":"1","ddc":["530"],"status":"public","quality_controlled":"1","pmid":1,"scopus_import":"1","intvolume":" 110","publication":"Physical Review E","year":"2024","volume":110,"researchdata_availability":"no","citation":{"apa":"Olmeda, F., & Rulands, S. (2024). Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.110.024404","mla":"Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” Physical Review E, vol. 110, no. 2, 024404, American Physical Society, 2024, doi:10.1103/PhysRevE.110.024404.","ieee":"F. Olmeda and S. Rulands, “Field theory of enzyme-substrate systems with restricted long-range interactions,” Physical Review E, vol. 110, no. 2. American Physical Society, 2024.","ama":"Olmeda F, Rulands S. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 2024;110(2). doi:10.1103/PhysRevE.110.024404","short":"F. Olmeda, S. Rulands, Physical Review E 110 (2024).","ista":"Olmeda F, Rulands S. 2024. Field theory of enzyme-substrate systems with restricted long-range interactions. Physical Review E. 110(2), 024404.","chicago":"Olmeda, Fabrizio, and Steffen Rulands. “Field Theory of Enzyme-Substrate Systems with Restricted Long-Range Interactions.” Physical Review E. American Physical Society, 2024. https://doi.org/10.1103/PhysRevE.110.024404."},"article_number":"024404","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Field theory of enzyme-substrate systems with restricted long-range interactions","publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"publication_status":"published","external_id":{"isi":["001299670100004"],"pmid":["39294986"]},"article_type":"original","issue":"2","isi":1,"has_accepted_license":"1","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"type":"journal_article","article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","fulldoi":"https://doi.org/10.1103/PhysRevE.110.024404","language":[{"iso":"eng"}],"_id":"17892","day":"01","doi":"10.1103/PhysRevE.110.024404"},{"citation":{"apa":"Krämer, J. C., Hannezo, E. B., Gompper, G., & Elgeti, J. (2024). Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. SciPost Physics. SciPost Foundation. https://doi.org/10.21468/scipostphys.16.4.097","short":"J.C. Krämer, E.B. Hannezo, G. Gompper, J. Elgeti, SciPost Physics 16 (2024).","ama":"Krämer JC, Hannezo EB, Gompper G, Elgeti J. Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells. SciPost Physics. 2024;16(4). doi:10.21468/scipostphys.16.4.097","mla":"Krämer, Johannes C., et al. “Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” SciPost Physics, vol. 16, no. 4, 097, SciPost Foundation, 2024, doi:10.21468/scipostphys.16.4.097.","ieee":"J. C. Krämer, E. B. Hannezo, G. Gompper, and J. Elgeti, “Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells,” SciPost Physics, vol. 16, no. 4. SciPost Foundation, 2024.","chicago":"Krämer, Johannes C., Edouard B Hannezo, Gerhard Gompper, and Jens Elgeti. “Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” SciPost Physics. SciPost Foundation, 2024. https://doi.org/10.21468/scipostphys.16.4.097.","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."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"097","title":"Mechanically-driven stem cell separation in tissues caused by proliferating daughter cells","external_id":{"isi":["001202370200001"],"arxiv":["2310.04272"]},"publication_identifier":{"issn":["2542-4653"]},"publication_status":"published","article_type":"original","arxiv":1,"isi":1,"related_material":{"record":[{"status":"public","id":"23022","relation":"research_data"}]},"issue":"4","type":"journal_article","has_accepted_license":"1","article_processing_charge":"No","_id":"17104","day":"08","fulldoi":"https://doi.org/10.21468/scipostphys.16.4.097","language":[{"iso":"eng"}],"oa_version":"Published Version","doi":"10.21468/scipostphys.16.4.097","file":[{"file_id":"17109","file_size":4973291,"content_type":"application/pdf","relation":"main_file","date_created":"2024-06-03T11:18:51Z","file_name":"2024_SciPostPhys_Kraemer.pdf","success":1,"checksum":"6fdeecd21c166db8dedb927ecc2e6025","date_updated":"2024-06-03T11:18:51Z","access_level":"open_access","creator":"dernst"}],"das_tickbox":"1","date_updated":"2026-10-01T09:44:06Z","department":[{"_id":"EdHa"}],"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’.","date_created":"2024-06-03T08:58:44Z","dataavailabilitystatement":"Source code, simulation data, and analysis scripts will be made publicly available on zenodo.org (10.5281/zenodo.8410957) after acceptance of the manuscript.","date_published":"2024-04-08T00:00:00Z","month":"04","supplementarymaterial":"yes","publisher":"SciPost Foundation","oa":1,"file_date_updated":"2024-06-03T11:18:51Z","author":[{"full_name":"Krämer, Johannes C.","first_name":"Johannes C.","last_name":"Krämer"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"last_name":"Gompper","full_name":"Gompper, Gerhard","first_name":"Gerhard"},{"last_name":"Elgeti","first_name":"Jens","full_name":"Elgeti, Jens"}],"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"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"scopus_import":"1","status":"public","ddc":["530"],"quality_controlled":"1","intvolume":" 16","year":"2024","volume":16,"publication":"SciPost Physics","researchdata_availability":"yes"},{"citation":{"ieee":"J. Elgeti and J. Krämer, “Data for Mechanically-driven Stem Cell Separation in Tissues caused by Proliferating Daughter Cells.” Zenodo, 2024.","mla":"Elgeti, Jens, and Johannes Krämer. Data for Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells. Zenodo, 2024, doi:10.5281/zenodo.8410956.","ama":"Elgeti J, Krämer J. Data for Mechanically-driven Stem Cell Separation in Tissues caused by Proliferating Daughter Cells. 2024. doi:10.5281/zenodo.8410956","short":"J. Elgeti, J. Krämer, (2024).","apa":"Elgeti, J., & Krämer, J. (2024). Data for Mechanically-driven Stem Cell Separation in Tissues caused by Proliferating Daughter Cells. Zenodo. https://doi.org/10.5281/zenodo.8410956","ista":"Elgeti J, Krämer J. 2024. Data for Mechanically-driven Stem Cell Separation in Tissues caused by Proliferating Daughter Cells, Zenodo, 10.5281/zenodo.8410956.","chicago":"Elgeti, Jens, and Johannes Krämer. “Data for Mechanically-Driven Stem Cell Separation in Tissues Caused by Proliferating Daughter Cells.” Zenodo, 2024. https://doi.org/10.5281/zenodo.8410956."},"date_updated":"2026-10-01T09:44:07Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8410956"}],"date_created":"2026-10-01T09:44:01Z","department":[{"_id":"EdHa"}],"date_published":"2024-03-25T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","OA_place":"repository","title":"Data for Mechanically-driven Stem Cell Separation in Tissues caused by Proliferating Daughter Cells","month":"03","related_material":{"record":[{"id":"17104","relation":"used_in_publication","status":"public"}]},"publisher":"Zenodo","abstract":[{"text":"Contains animations, data, and source code used for the paper \"Mechanically-driven Stem Cell Separation in Tissues caused by Proliferating Daughter Cells\" by the same authors. \r\n\r\n\r\nThis repository contains all the data and analysis scripts to support the manuscript\r\nThe file structure is as follows:\r\n- \"analysis\" contains all the analysis scripts\r\n- \"gfx\" and \"animations\" the figures and supporting animations\r\n- \"1-SCpair\", \"2-SCtissue\", \"3-BDsimulation\", \"4-tissue-stochdiv\", \"6-inertia-effects\" all the source code and data for the respective models.","lang":"eng"}],"oa":1,"type":"research_data_reference","author":[{"first_name":"Jens","full_name":"Elgeti, Jens","last_name":"Elgeti"},{"last_name":"Krämer","first_name":"Johannes","full_name":"Krämer, Johannes"}],"article_processing_charge":"No","status":"public","ddc":["530"],"OA_type":"green","doi":"10.5281/zenodo.8410956","year":"2024","_id":"23022","day":"25","fulldoi":"https://doi.org/10.5281/zenodo.8410956","oa_version":"None"},{"title":"Information content and optimization of self-organized developmental systems","external_id":{"isi":["001244835000006"],"pmid":["38819997"]},"publication_status":"published","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"e2322326121","citation":{"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.","chicago":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2322326121.","ieee":"D. Brückner and G. Tkačik, “Information content and optimization of self-organized developmental systems,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 23. National Academy of Sciences, 2024.","mla":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 23, e2322326121, National Academy of Sciences, 2024, doi:10.1073/pnas.2322326121.","short":"D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ama":"Brückner D, Tkačik G. Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(23). doi:10.1073/pnas.2322326121","apa":"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. National Academy of Sciences. https://doi.org/10.1073/pnas.2322326121"},"_id":"17123","day":"04","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1073/pnas.2322326121","oa_version":"Published Version","doi":"10.1073/pnas.2322326121","article_processing_charge":"Yes (in subscription journal)","type":"journal_article","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"}],"has_accepted_license":"1","article_type":"original","isi":1,"related_material":{"link":[{"url":"https://github.com/dbrueckner/SelforgInformation","relation":"software"},{"url":"https://ista.ac.at/en/news/the-embryo-assembles-itself/","description":"News on the ISTA website","relation":"press_release"}]},"issue":"23","month":"06","supplementarymaterial":"yes","OA_place":"publisher","dataavailabilitystatement":"There were no data generated as part of this study. Code to perform simulations, evaluate entropy and information quantities, and optimize parameters is available at https://github.com/dbrueckner/SelforgInformation (90).","date_published":"2024-06-04T00:00:00Z","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"date_created":"2024-06-09T22:01:02Z","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.","file":[{"date_updated":"2024-06-10T10:27:37Z","access_level":"open_access","creator":"dernst","file_name":"2024_PNAS_Brueckner.pdf","date_created":"2024-06-10T10:27:37Z","success":1,"checksum":"59797a75db7beb3721ed7a4d14c241f9","relation":"main_file","content_type":"application/pdf","file_id":"17130","file_size":12329234}],"das_tickbox":"1","date_updated":"2026-10-01T11:03:59Z","volume":121,"year":"2024","publication":"Proceedings of the National Academy of Sciences of the United States of America","APC_amount":"2570,79 EUR","researchdata_availability":"not applicable","pmid":1,"scopus_import":"1","ddc":["570"],"status":"public","OA_type":"hybrid","quality_controlled":"1","intvolume":" 121","oa":1,"file_date_updated":"2024-06-10T10:27:37Z","author":[{"last_name":"Brückner","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","full_name":"Brückner, David"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"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"},"corr_author":"1","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."}],"publisher":"National Academy of Sciences"},{"abstract":[{"lang":"eng","text":"In this repository, you will find the R-scripts used to generate the figures, along with the data necessary to make the plots. You will also find the Python-scripts used to compute the pair-wise distance between embryos, to estimate the surface, the volume, the α-parameter, to identify the closest rigid packing and to generate the morphomap. Additionally, you have access to the base model used with Plantseg to predict and label the cells at the 8-cell stage. Note that a more accurate and more specific model was generated for each embryo based on the curation of at least 5 timepoints.\r\n\r\nFigures\r\nThe plots in Figure 1-7 and Figure S1-S7 can be generated with the respective files. The code is written in R and requires RStudio to work out-of-the-box. The R scripts are located in figures/. Figures and supplemental figures are generated with the same file (e.g., Figure 1.R generates all the computed panels of Figure 1 and Figure S1). Data required to generate the plots are located in figures/data/. Note that the code to work with the morphomap and the tracking data is located in local packages figures/fabreges.morphomap and figures/fabreges.tracking. An additional package figures/fabreges.generic contains utility functions.\r\n\r\nPython packages\r\nFor the needs of this study, we developed a series of package for Python located in python-packages/. The packages can be directly imported within your scripts. Along with the packages, you will find 6 scripts used to compute, extract or estimate the data from the source. The folder is organised as follow:\r\n\r\npackage interfaces is located in python-packages/interfaces/ and can be tested by running the scripts to extract the angles an estimate the surface of contact (compute-angles.py and estimate-contacts.py respectively) in folder python-packages,\r\npackage morphomap is located in python-packages/morphomap/ and can be tested by running the script to compute the geometrical distances between embryos, project the data in 2D and compute the volume of the cells (compute-distances.py, process-distances.py and compute-volumes.py respectively) in folder python-packages,\r\npackage splinefit is included in morphomap in python-packages/morphomap/splinefit/, but can function independently,\r\npackage rbb is located in python-packages/rbb/ and can be tested by running the script to identify the closest rigid packing of an embryo at the 8-cell stage (identify-packing.py) in folder python-packages.\r\nWe provide example of segmented data in python-packages/samples/.\r\n\r\nCNN\r\nWe provide a convolutional neural network (CNN) used in our study, located in cnn. Please note that we optimised the CNN further for each dataset by doing manual curation of at least 5 time points and by retraining the network with those ground truth. The CNN were trained using pytorch-3dunet. The CNN can be used with Plantseg. Currently (plantseg v.1.6.0 and pytorch-3dunet v.1.6.0), the output model from pytorch-3dunet must currently be modified to work with plantseg:\r\n\r\n# python\r\nimport torch\r\nfor model in ('best_checkpoint.pytorch', 'last_checkpoint.pytorch'):\r\n state = torch.load(model, map_location='cpu')\r\n state = state['model_state_dict']\r\n torch.save(state, model)\r\n\r\nRequierements\r\nFigures\r\nThe figures were generated with R (v. 4.4.0) and RStudio (v. 2024.04.1+748). The following packages must be installed prior to execution:\r\n\r\nalphashape3d (v. 1.3.2)\r\ndevtools (v. 2.4.5)\r\nggplot2 (v. 3.5.1)\r\nggrepel (v. 0.9.5)\r\nrstudioapi (v. 0.16.0)\r\nTo install all these packages, run the following command in the RStudio console:\r\n\r\n# R\r\ninstall.packages(c(\"alphashape3d@1.3.2\", \"devtools@2.4.5\", \"ggplot2@3.5.1\", \"ggrepel@0.9.5\", \"rstudioapi@0.16\"))\r\n\r\nMore recent version of R, RStudio and the packages may also work (not tested).\r\n\r\nPython packages\r\nPython 3.12.3 was used to analyse the data. The scripts may work with more recent version of Python and with Python 3.8 or earlier (not tested). To run the code, you must first install the following packages:\r\n\r\nnumpy (v. 1.26.4)\r\nimageio (v. 2.34.1)\r\nscipy (v. 1.13.1)\r\nscikit-image (v. 0.23.2)\r\nscikit-learn (v. 1.5.0)\r\nAlternatively, you can create a conda environment:\r\n\r\n# Shell script\r\nconda create -y --name fabreges2024 python=3.12.3\r\nconda activate fabreges2024\r\npython -m pip install numpy==1.26.4 imageio==2.34.1 scipy==1.13.1 scikit-image==0.23.2 scikit-learn==1.5.0\r\n\r\nMore recent version of the dependencies may work (not tested).\r\n\r\nUsage\r\nFigures\r\nOpen one of the figure script in RStudio and run the entire code. You may have to create a folder output in figures/ if it does not exist.\r\n\r\nThe code has local dependencies that will be installed on your computer when encountering them for the first time. They start with fabreges.* and are necessary to generate the figures.\r\n\r\nPython packages (example)\r\nCompute angles\r\n# Shell script\r\n# Compute a summary (mean, median, s.d.) of the angles in embryo C1 at time 40\r\npython compute-angles.py -s -r 15 -R 20 samples/C1_t040.tif.gz output/C1_t040_angles.csv\r\n# Compute a detailed list of angle values\r\npython compute-angles.py -r 15 -R 20 samples/C1_t041.tif.gz output/C1_t041_angles.csv\r\n\r\nCompute distances\r\n# Shell script\r\n# Compute the distance between two embryos\r\npython compute-distances.py -c 5 -s 5 samples/C1_t040.tif.gz samples/C1_t041.tif.gz output/distances.csv\r\n# Append another distance measurement\r\npython compute-distances.py -a -c 5 -s 5 samples/C1_t040.tif.gz samples/C1_t042.tif.gz output/distances.csv\r\n\r\nCompute volumes\r\n# Shell script\r\n# Compute the volume in isotropic data\r\npython compute-volumes.py -r 0.416 0.416 0.416 samples/C1_t040.tif.gz output/volumes.csv\r\n\r\nEstimate contacts\r\n# Shell script\r\n# Estimate the contacts and the free surface area\r\npython estimate-contacts.py -r 0.416 0.416 0.416 samples/C1_t040.tif.gz output/contacts.csv\r\n\r\nIdentify the closest rigid packing\r\n# Shell script\r\n# Assuming the file `output/contacts.csv` exists and contains the output\r\n# from command `estimate-contacts.py`.\r\n# Identify the closest rigid packings\r\npython identify-packing.py output/contacts.csv output/backbones.csv\r\n\r\nGenerate the seeds for Surface Evolver\r\n# Shell script\r\n# Assuming the file `output/contacts.csv` exists and contains the output\r\n# from command `estimate-contacts.py`, and the file `output/volumes.csv`\r\n# exists and contains the output from command `compute-volumes.py`\r\n# Generate the seeds for Surface Evolver using automatic thresholding\r\n# Automatic threshold will determine the highest cell-cell contact threshold\r\n# that preserves rigidity of the embryo (or 0 if not rigid)\r\npython generate-seed.py output/contacts.csv output/volumes.csv output/seed.fe\r\n# Generate the seeds for Surface Evolver with custom threshold\r\npython generate-seed.py --threshold 0.1 output/contacts.csv output/volumes.csv output/seed.fe\r\n\r\nProject in 2D and generate a distance matrix\r\n# Shell script\r\n# Assuming the folder `foo` only contains one or more CSV\r\n# from command `compute-distances.py`.\r\n\r\n# Compute the tSNE 2D projection\r\npython process-distances.py -D2 -t output/tsne_2d.csv foo/\r\n\r\n# Compute the tSNE 3D projection\r\npython process-distances.py -D3 -t output/tsne_2d.csv foo/\r\n\r\n# Generate the distance matrix\r\npython process-distances.py -m output/dismat.csv foo/"}],"author":[{"full_name":"Corominas-Murtra, Bernat","first_name":"Bernat","last_name":"Corominas-Murtra"},{"last_name":" Moghe","first_name":"Prachiti","full_name":" Moghe, Prachiti"},{"last_name":"Kickuth","full_name":"Kickuth, Alison","first_name":"Alison"},{"last_name":"Ichikawa","full_name":"Ichikawa, Takafumi","first_name":"Takafumi"},{"last_name":"Iwatani","first_name":"Chizuru","full_name":"Iwatani, Chizuru"},{"last_name":"Tsukiyama","first_name":"Tomoyuki","full_name":"Tsukiyama, Tomoyuki"},{"first_name":"Nathalie","full_name":"Daniel, Nathalie","last_name":"Daniel"},{"full_name":"Gering, Julie","first_name":"Julie","last_name":"Gering"},{"first_name":"Anniek","full_name":"Stokkermans, Anniek","last_name":"Stokkermans"},{"full_name":"Wolny, Adrian","first_name":"Adrian","last_name":"Wolny"},{"first_name":"Anna","full_name":"Kreshuk, Anna","last_name":"Kreshuk"},{"first_name":"Véronique","full_name":"Duranthon, Véronique","last_name":"Duranthon"},{"full_name":"Uhlmann, Virginie","first_name":"Virginie","last_name":"Uhlmann"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard","first_name":"Edouard"},{"full_name":"Hiiragi, Takashi","first_name":"Takashi","last_name":"Hiiragi"}],"type":"research_data_reference","oa":1,"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"relation":"used_in_publication","id":"18446","status":"public"}]},"doi":"10.5281/zenodo.12819780","oa_version":"None","fulldoi":"https://doi.org/10.5281/zenodo.12819780","_id":"23023","year":"2024","day":"25","contributor":[{"first_name":"Dimitri","last_name":"Fabrèges","contributor_type":"contact_person"}],"article_processing_charge":"No","status":"public","OA_type":"green","date_created":"2026-10-01T10:54:27Z","department":[{"_id":"EdHa"}],"date_updated":"2026-10-01T10:54:33Z","citation":{"chicago":"Corominas-Murtra, Bernat, Prachiti Moghe, Alison Kickuth, Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, Nathalie Daniel, et al. “Data and Software from: Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” Institute of Science and Technology Austria, 2024. https://doi.org/10.5281/zenodo.12819780.","ista":"Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C, Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon V, Uhlmann V, Hannezo E, Hiiragi T. 2024. Data and software from: Temporal variability and cell mechanics control robustness in mammalian embryogenesis, Institute of Science and Technology Austria, 10.5281/zenodo.12819780.","short":"B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani, T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon, V. Uhlmann, E. Hannezo, T. Hiiragi, (2024).","ama":"Corominas-Murtra B, Moghe P, Kickuth A, et al. Data and software from: Temporal variability and cell mechanics control robustness in mammalian embryogenesis. 2024. doi:10.5281/zenodo.12819780","mla":"Corominas-Murtra, Bernat, et al. Data and Software from: Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis. Institute of Science and Technology Austria, 2024, doi:10.5281/zenodo.12819780.","ieee":"B. Corominas-Murtra et al., “Data and software from: Temporal variability and cell mechanics control robustness in mammalian embryogenesis.” Institute of Science and Technology Austria, 2024.","apa":"Corominas-Murtra, B., Moghe, P., Kickuth, A., Ichikawa, T., Iwatani, C., Tsukiyama, T., … Hiiragi, T. (2024). Data and software from: Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Institute of Science and Technology Austria. https://doi.org/10.5281/zenodo.12819780"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.12819780"}],"OA_place":"repository","month":"07","title":"Data and software from: Temporal variability and cell mechanics control robustness in mammalian embryogenesis","date_published":"2024-07-25T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"title":"Geometry-driven migration efficiency of autonomous epithelial cell clusters","publication_status":"published","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"external_id":{"isi":["001250246200004"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.07.17.500364"}],"citation":{"ista":"Vercruysse E, Brückner D, Gómez-González M, Remson A, Luciano M, Kalukula Y, Rossetti L, Trepat X, Hannezo EB, Gabriele S. 2024. Geometry-driven migration efficiency of autonomous epithelial cell clusters. Nature Physics. 20, 1492–1500.","chicago":"Vercruysse, Eléonore, David Brückner, Manuel Gómez-González, Alexandre Remson, Marine Luciano, Yohalie Kalukula, Leone Rossetti, Xavier Trepat, Edouard B Hannezo, and Sylvain Gabriele. “Geometry-Driven Migration Efficiency of Autonomous Epithelial Cell Clusters.” Nature Physics. Springer Nature, 2024. https://doi.org/10.1038/s41567-024-02532-x.","apa":"Vercruysse, E., Brückner, D., Gómez-González, M., Remson, A., Luciano, M., Kalukula, Y., … Gabriele, S. (2024). Geometry-driven migration efficiency of autonomous epithelial cell clusters. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-024-02532-x","mla":"Vercruysse, Eléonore, et al. “Geometry-Driven Migration Efficiency of Autonomous Epithelial Cell Clusters.” Nature Physics, vol. 20, Springer Nature, 2024, pp. 1492–500, doi:10.1038/s41567-024-02532-x.","ieee":"E. Vercruysse et al., “Geometry-driven migration efficiency of autonomous epithelial cell clusters,” Nature Physics, vol. 20. Springer Nature, pp. 1492–1500, 2024.","short":"E. Vercruysse, D. Brückner, M. Gómez-González, A. Remson, M. Luciano, Y. Kalukula, L. Rossetti, X. Trepat, E.B. Hannezo, S. Gabriele, Nature Physics 20 (2024) 1492–1500.","ama":"Vercruysse E, Brückner D, Gómez-González M, et al. Geometry-driven migration efficiency of autonomous epithelial cell clusters. Nature Physics. 2024;20:1492-1500. doi:10.1038/s41567-024-02532-x"},"oa_version":"Preprint","fulldoi":"https://doi.org/10.1038/s41567-024-02532-x","language":[{"iso":"eng"}],"_id":"17269","day":"01","doi":"10.1038/s41567-024-02532-x","article_processing_charge":"No","project":[{"name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"},{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"ALTF 343-2022"}],"type":"journal_article","page":"1492-1500","article_type":"original","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/a-railroad-of-cells/","description":"News on ISTA website"}]},"isi":1,"month":"09","OA_place":"repository","supplementarymaterial":"yes","dataavailabilitystatement":"All data are available from the corresponding authors upon request. Source data are provided with this paper.","date_published":"2024-09-01T00:00:00Z","department":[{"_id":"EdHa"}],"date_created":"2024-07-16T12:32:17Z","acknowledgement":"M.L., E.V. and S.G. acknowledge funding from the European Regional Development Fund (ERDF) Prostem Research Project (No. 1510614, Wallonia DG06), the Epiforce Project of the National Fund for Scientific Research, Belgium (FRS-FNRS; Project No. T.0092.21), the Cellsqueezer Project of FRS-FNRS (Project No. J.0061.23), the Optopattern Project of FRS-FNRS (Project no. U.NO26.22) and the Interreg MAT(T)ISSE project, which is financially supported by Interreg France-Wallonie-Vlaanderen, ERDF). A.R. and M.L. are financially supported by FRS-FNRS as a research fellow (Aspirant FNRS) and Postdoctoral Researcher (Chargée de Recherches FNRS), respectively. E.V. and Y.K. are financially supported by FRS-FNRS through grants from the Fund for Research Training in Industry and Agriculture (FRIA). This project was supported by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No. 851288 to E.H.) and Marie Skłodowska-Curie Actions (Grant Agreement No. 797621 to M.G.-G.). D.B.B. was supported by the NOMIS foundation as a NOMIS fellow and by the European Molecular Biology Organization (Postdoctoral Fellowship ALTF 343-2022) and performed this work in part at the Aspen Center for Physics, which is supported by the National Science Foundation (Grant No. PHY-1607611). X.T. and M.G.-G. acknowledge support from the Government of Catalonia (Grant No. AGAUR SGR-2017-01602 and a CERCA Programme), the Spanish Ministry for Science and Innovation and ERDF (Grant No. PGC2018-099645-B-I00), the European Research Council (Grant No. Adv-883739), Fundació la Marató de TV3 (201903-30-31-32), the European Commission (Grant No. H2020-FETPROACT-01-2016-731957), La Caixa Foundation and the Biomedical Research Center Consortium in Red (Grant No. CB15/00153) at the Carlos III Health Institute, Ministry of Science and Innovation. IBEC is recipient of a Severo Ochoa Award of Excellence from the Spanish Ministry of Economy, Trade and Business.","ec_funded":1,"date_updated":"2026-10-01T11:02:43Z","das_tickbox":"1","publication":"Nature Physics","volume":20,"year":"2024","researchdata_availability":"yes","status":"public","quality_controlled":"1","OA_type":"green","scopus_import":"1","intvolume":" 20","author":[{"last_name":"Vercruysse","first_name":"Eléonore","full_name":"Vercruysse, Eléonore"},{"orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","full_name":"Brückner, David","last_name":"Brückner"},{"full_name":"Gómez-González, Manuel","first_name":"Manuel","last_name":"Gómez-González"},{"first_name":"Alexandre","full_name":"Remson, Alexandre","last_name":"Remson"},{"last_name":"Luciano","full_name":"Luciano, Marine","first_name":"Marine"},{"last_name":"Kalukula","full_name":"Kalukula, Yohalie","first_name":"Yohalie"},{"last_name":"Rossetti","full_name":"Rossetti, Leone","first_name":"Leone"},{"first_name":"Xavier","full_name":"Trepat, Xavier","last_name":"Trepat"},{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"full_name":"Gabriele, Sylvain","first_name":"Sylvain","last_name":"Gabriele"}],"oa":1,"abstract":[{"text":"The directed migration of epithelial cell collectives through coordinated movements plays a crucial role in various physiological processes and is increasingly understood at the level of large confluent monolayers. However, numerous processes rely on the migration of small groups of polarized epithelial clusters in complex environments, and their responses to external geometries remain poorly understood. To address this, we cultivate primary epithelial keratocyte tissues on adhesive microstripes to create autonomous epithelial clusters with well-defined geometries. We show that their migration efficiency is strongly influenced by the contact geometry and the orientation of cell–cell contacts with respect to the direction of migration. A combination of velocity and polarity alignment with contact regulation of locomotion in an active matter model captures quantitatively the experimental data. Furthermore, we predict that this combination of rules enables efficient navigation in complex geometries, which we confirm experimentally. Altogether, our findings provide a conceptual framework for extracting the interaction rules of active systems from their interaction with physical boundaries, as well as design principles for collective navigation in complex microenvironments.","lang":"eng"}],"corr_author":"1","publisher":"Springer Nature"},{"title":"Temporal variability and cell mechanics control robustness in mammalian embryogenesis","publication_identifier":{"eissn":["1095-9203"]},"publication_status":"published","external_id":{"pmid":["39388574"],"isi":["001422132300018"]},"article_number":"eadh1145","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","main_file_link":[{"open_access":"1","url":"https://hal.inrae.fr/hal-04447081v1/file/2023.01.24.525420.full.pdf"}],"citation":{"apa":"Fabrèges, D., Corominas-Murtra, B., Moghe, P., Kickuth, A., Ichikawa, T., Iwatani, C., … Hiiragi, T. (2024). Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. AAAS. https://doi.org/10.1126/science.adh1145","ama":"Fabrèges D, Corominas-Murtra B, Moghe P, et al. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. 2024;386(6718). doi:10.1126/science.adh1145","short":"D. Fabrèges, B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani, T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon, V. Uhlman, E.B. Hannezo, T. Hiiragi, Science 386 (2024).","mla":"Fabrèges, Dimitri, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” Science, vol. 386, no. 6718, eadh1145, AAAS, 2024, doi:10.1126/science.adh1145.","ieee":"D. Fabrèges et al., “Temporal variability and cell mechanics control robustness in mammalian embryogenesis,” Science, vol. 386, no. 6718. AAAS, 2024.","chicago":"Fabrèges, Dimitri, Bernat Corominas-Murtra, Prachiti Moghe, Alison Kickuth, Takafumi Ichikawa, Chizuru Iwatani, Tomoyuki Tsukiyama, et al. “Temporal Variability and Cell Mechanics Control Robustness in Mammalian Embryogenesis.” Science. AAAS, 2024. https://doi.org/10.1126/science.adh1145.","ista":"Fabrèges D, Corominas-Murtra B, Moghe P, Kickuth A, Ichikawa T, Iwatani C, Tsukiyama T, Daniel N, Gering J, Stokkermans A, Wolny A, Kreshuk A, Duranthon V, Uhlman V, Hannezo EB, Hiiragi T. 2024. Temporal variability and cell mechanics control robustness in mammalian embryogenesis. Science. 386(6718), eadh1145."},"oa_version":"Submitted Version","fulldoi":"https://doi.org/10.1126/science.adh1145","language":[{"iso":"eng"}],"day":"11","_id":"18446","doi":"10.1126/science.adh1145","article_processing_charge":"No","type":"journal_article","article_type":"original","issue":"6718","related_material":{"record":[{"status":"public","id":"23023","relation":"research_data"}]},"isi":1,"month":"10","supplementarymaterial":"yes","OA_place":"repository","dataavailabilitystatement":"All original code and data reported in this paper is publicly available as of the date of publication on Zenodo (124).\r\n124\r\nD. Fabrèges, B. Corominas-Murtra, P. Moghe, A. Kickuth, T. Ichikawa, C. Iwatani, T. Tsukiyama, N. Daniel, J. Gering, A. Stokkermans, A. Wolny, A. Kreshuk, V. Duranthon, V. Uhlmann, E. Hannezo, T. Hiiragi, Temporal variability and cell mechanics control robustness in mammalian embryogenesis, version 1.0, Zenodo (2024); https://doi.org/10.5281/ZENODO.12819781.","date_published":"2024-10-11T00:00:00Z","department":[{"_id":"EdHa"}],"acknowledgement":"We are grateful to the members of the Hiiragi laboratory for discussions and comments on the manuscript: R. Bloehs, S. Friese, S. Hozeifi, L. Pérez, and W. Schwarzer for their technical support; V. Janssen for establishing the PAB protocol; members of the Tsukiyama group for the animal care with monkeys, in particular H. Tsuchiya and M. Nakaya; Unité Commune d’Expérimentation Animale (UCEA, Jouy-en-Josas, France) for the animal care with rabbits; the EMBL electronic and mechanical workshops and the EMBL animal facility for their support; We thank Luxendo for the close collaboration in developing the light-sheet microscopy for mammalian embryos.\r\nFunding: This work was funded by the following: EMBL Interdisciplinary Postdoc Program (EIPOD) under Marie Sklodowska Curie Actions COFUND III RTD (to D.F.); JSPS Overseas Research Fellowship (to T.I.); Field of excellence “Complexity of life in basic research and innovation” of the University of Graz (to B.C.M.); European Research Council, ERC Advanced Grant “SelforganisingEmbryo”, grant agreement 742732; ERC Advanced Grant “COORDINATION” grant agreement 101055287 (to T.H.); Stichting LSH-TKI, grant LSHM21020 (to T.H.) JSPS KAKENHI grants JP21H05038 and JP22H05166 (to T.H.)","date_created":"2024-10-20T22:02:06Z","date_updated":"2026-10-01T10:54:32Z","das_tickbox":"1","publication":"Science","volume":386,"year":"2024","researchdata_availability":"yes","OA_type":"green","status":"public","quality_controlled":"1","scopus_import":"1","pmid":1,"intvolume":" 386","author":[{"first_name":"Dimitri","full_name":"Fabrèges, Dimitri","last_name":"Fabrèges"},{"last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643","first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","full_name":"Corominas-Murtra, Bernat"},{"last_name":"Moghe","first_name":"Prachiti","full_name":"Moghe, Prachiti"},{"last_name":"Kickuth","first_name":"Alison","full_name":"Kickuth, Alison"},{"full_name":"Ichikawa, Takafumi","first_name":"Takafumi","last_name":"Ichikawa"},{"full_name":"Iwatani, Chizuru","first_name":"Chizuru","last_name":"Iwatani"},{"last_name":"Tsukiyama","first_name":"Tomoyuki","full_name":"Tsukiyama, Tomoyuki"},{"first_name":"Nathalie","full_name":"Daniel, Nathalie","last_name":"Daniel"},{"full_name":"Gering, Julie","first_name":"Julie","last_name":"Gering"},{"last_name":"Stokkermans","first_name":"Anniek","full_name":"Stokkermans, Anniek"},{"full_name":"Wolny, Adrian","first_name":"Adrian","last_name":"Wolny"},{"last_name":"Kreshuk","first_name":"Anna","full_name":"Kreshuk, Anna"},{"last_name":"Duranthon","full_name":"Duranthon, Véronique","first_name":"Véronique"},{"last_name":"Uhlman","full_name":"Uhlman, Virginie","first_name":"Virginie"},{"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":"Takashi","full_name":"Hiiragi, Takashi","last_name":"Hiiragi"}],"oa":1,"corr_author":"1","abstract":[{"lang":"eng","text":"How living systems achieve precision in form and function despite their intrinsic stochasticity is a fundamental yet ongoing question in biology. We generated morphomaps of preimplantation embryogenesis in mouse, rabbit, and monkey embryos, and these morphomaps revealed that although blastomere divisions desynchronized passively, 8-cell embryos converged toward robust three-dimensional shapes. Using topological analysis and genetic perturbations, we found that embryos progressively changed their cellular connectivity to a preferred topology, which could be predicted by a physical model in which actomyosin contractility and noise facilitate topological transitions, lowering surface energy. This mechanism favored regular embryo packing and promoted a higher number of inner cells in the 16-cell embryo. Synchronized division reduced embryo packing and generated substantially more misallocated cells and fewer inner-cell–mass cells. These findings suggest that stochasticity in division timing contributes to robust patterning."}],"publisher":"AAAS"},{"isi":1,"page":"58-65","article_type":"review","has_accepted_license":"1","project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"}],"type":"journal_article","article_processing_charge":"Yes (via OA deal)","doi":"10.1016/j.semcdb.2022.11.005","fulldoi":"https://doi.org/10.1016/j.semcdb.2022.11.005","oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"12162","keyword":["Cell Biology","Developmental Biology"],"day":"02","citation":{"chicago":"Corominas-Murtra, Bernat, and Edouard B Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology. Elsevier, 2023. https://doi.org/10.1016/j.semcdb.2022.11.005.","ista":"Corominas-Murtra B, Hannezo EB. 2023. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. 150–151, 58–65.","apa":"Corominas-Murtra, B., & Hannezo, E. B. (2023). Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. Elsevier. https://doi.org/10.1016/j.semcdb.2022.11.005","ama":"Corominas-Murtra B, Hannezo EB. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. 2023;150-151:58-65. doi:10.1016/j.semcdb.2022.11.005","short":"B. Corominas-Murtra, E.B. Hannezo, Seminars in Cell & Developmental Biology 150–151 (2023) 58–65.","ieee":"B. Corominas-Murtra and E. B. Hannezo, “Modelling the dynamics of mammalian gut homeostasis,” Seminars in Cell & Developmental Biology, vol. 150–151. Elsevier, pp. 58–65, 2023.","mla":"Corominas-Murtra, Bernat, and Edouard B. Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology, vol. 150–151, Elsevier, 2023, pp. 58–65, doi:10.1016/j.semcdb.2022.11.005."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publication_identifier":{"issn":["1084-9521"]},"external_id":{"pmid":["36470715"],"isi":["001053522200001"]},"title":"Modelling the dynamics of mammalian gut homeostasis","publisher":"Elsevier","corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Homeostatic balance in the intestinal epithelium relies on a fast cellular turnover, which is coordinated by an intricate interplay between biochemical signalling, mechanical forces and organ geometry. We review recent modelling approaches that have been developed to understand different facets of this remarkable homeostatic equilibrium. Existing models offer different, albeit complementary, perspectives on the problem. First, biomechanical models aim to explain the local and global mechanical stresses driving cell renewal as well as tissue shape maintenance. Second, compartmental models provide insights into the conditions necessary to keep a constant flow of cells with well-defined ratios of cell types, and how perturbations can lead to an unbalance of relative compartment sizes. A third family of models address, at the cellular level, the nature and regulation of stem fate choices that are necessary to fuel cellular turnover. We also review how these different approaches are starting to be integrated together across scales, to provide quantitative predictions and new conceptual frameworks to think about the dynamics of cell renewal in complex tissues."}],"author":[{"last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"file_date_updated":"2024-01-08T10:16:04Z","oa":1,"ddc":["570"],"status":"public","quality_controlled":"1","scopus_import":"1","pmid":1,"publication":"Seminars in Cell & Developmental Biology","year":"2023","volume":"150-151","date_updated":"2025-04-14T07:52:27Z","file":[{"file_id":"14741","file_size":1343750,"content_type":"application/pdf","relation":"main_file","success":1,"date_created":"2024-01-08T10:16:04Z","file_name":"2023_SeminarsCellDevBiology_CorominasMurtra.pdf","checksum":"c619887cf130f4649bf3035417186004","date_updated":"2024-01-08T10:16:04Z","access_level":"open_access","creator":"dernst"}],"date_created":"2023-01-12T12:09:47Z","acknowledgement":"This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.).\r\nB. C-M wants to acknowledge the support of the field of excellence Complexity of Life, in Basic Research and Innovation of the University of Graz.","ec_funded":1,"department":[{"_id":"EdHa"}],"date_published":"2023-12-02T00:00:00Z","month":"12"},{"citation":{"ama":"Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Margadant C, ed. Cell Migration in Three Dimensions. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:10.1007/978-1-0716-2887-4_12","short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205.","ieee":"E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland,” in Cell Migration in Three Dimensions, vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205.","mla":"Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” Cell Migration in Three Dimensions, edited by Coert Margadant, vol. 2608, Springer Nature, 2023, pp. 183–205, doi:10.1007/978-1-0716-2887-4_12.","apa":"Hannezo, E. B., & Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.), Cell Migration in Three Dimensions (Vol. 2608, pp. 183–205). Springer Nature. https://doi.org/10.1007/978-1-0716-2887-4_12","chicago":"Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” In Cell Migration in Three Dimensions, edited by Coert Margadant, 2608:183–205. MIMB. Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-2887-4_12.","ista":"Hannezo EB, Scheele CLGJ. 2023.A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Cell Migration in Three Dimensions. Methods in Molecular Biology, vol. 2608, 183–205."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","publication_identifier":{"isbn":["9781071628867"],"eisbn":["9781071628874"],"eissn":["1940-6029"]},"publication_status":"published","external_id":{"pmid":["36653709"]},"page":"183-205","has_accepted_license":"1","type":"book_chapter","article_processing_charge":"No","fulldoi":"https://doi.org/10.1007/978-1-0716-2887-4_12","language":[{"iso":"eng"}],"oa_version":"Published Version","day":"19","_id":"12428","doi":"10.1007/978-1-0716-2887-4_12","file":[{"date_updated":"2023-02-03T10:56:39Z","access_level":"open_access","creator":"dernst","date_created":"2023-02-03T10:56:39Z","file_name":"2023_MIMB_Hannezo.pdf","success":1,"checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","relation":"main_file","content_type":"application/pdf","file_id":"12500","file_size":826598}],"date_updated":"2024-10-09T21:04:04Z","editor":[{"last_name":"Margadant","first_name":"Coert","full_name":"Margadant, Coert"}],"department":[{"_id":"EdHa"}],"date_created":"2023-01-29T23:00:58Z","date_published":"2023-01-19T00:00:00Z","month":"01","series_title":"MIMB","alternative_title":["Methods in Molecular Biology"],"publisher":"Springer Nature","author":[{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"first_name":"Colinda L.G.J.","full_name":"Scheele, Colinda L.G.J.","last_name":"Scheele"}],"file_date_updated":"2023-02-03T10:56:39Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"corr_author":"1","abstract":[{"lang":"eng","text":"The mammary gland consists of a bilayered epithelial structure with an extensively branched morphology. The majority of this epithelial tree is laid down during puberty, during which actively proliferating terminal end buds repeatedly elongate and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist of a basal and luminal cell layer with a multitude of identified sub-lineages within both layers. The understanding of how these different cell lineages are cooperatively driving branching morphogenesis is a problem of crossing multiple scales, as this requires information on the macroscopic branched structure of the gland, as well as data on single-cell dynamics driving the morphogenic program. Here we describe a method to combine genetic lineage tracing with whole-gland branching analysis. Quantitative data on the global organ structure can be used to derive a model for mammary gland branching morphogenesis and provide a backbone on which the dynamics of individual cell lineages can be simulated and compared to lineage-tracing approaches. Eventually, these quantitative models and experiments allow to understand the couplings between the macroscopic shape of the mammary gland and the underlying single-cell dynamics driving branching morphogenesis."}],"ddc":["570"],"status":"public","quality_controlled":"1","pmid":1,"scopus_import":"1","intvolume":" 2608","publication":"Cell Migration in Three Dimensions","volume":2608,"year":"2023"},{"article_processing_charge":"No","_id":"12710","day":"29","oa_version":"Published Version","fulldoi":"https://doi.org/10.1002/adma.202206110","language":[{"iso":"eng"}],"doi":"10.1002/adma.202206110","article_type":"review","isi":1,"issue":"13","type":"journal_article","has_accepted_license":"1","article_number":"2206110","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Curvature in biological systems: Its quantification, emergence, and implications across the scales","external_id":{"isi":["000941068900001"],"pmid":["36461812"]},"publication_identifier":{"eissn":["1521-4095"],"issn":["0935-9648"]},"publication_status":"published","citation":{"chicago":"Schamberger, Barbara, Ricardo Ziege, Karine Anselme, Martine Ben Amar, Michał Bykowski, André P.G. Castro, Amaia Cipitria, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” Advanced Materials. Wiley, 2023. https://doi.org/10.1002/adma.202206110.","ista":"Schamberger B, Ziege R, Anselme K, Ben Amar M, Bykowski M, Castro APG, Cipitria A, Coles RA, Dimova R, Eder M, Ehrig S, Escudero LM, Evans ME, Fernandes PR, Fratzl P, Geris L, Gierlinger N, Hannezo EB, Iglič A, Kirkensgaard JJK, Kollmannsberger P, Kowalewska Ł, Kurniawan NA, Papantoniou I, Pieuchot L, Pires THV, Renner LD, Sageman-Furnas AO, Schröder-Turk GE, Sengupta A, Sharma VR, Tagua A, Tomba C, Trepat X, Waters SL, Yeo EF, Roschger A, Bidan CM, Dunlop JWC. 2023. Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. 35(13), 2206110.","ama":"Schamberger B, Ziege R, Anselme K, et al. Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. 2023;35(13). doi:10.1002/adma.202206110","short":"B. Schamberger, R. Ziege, K. Anselme, M. Ben Amar, M. Bykowski, A.P.G. Castro, A. Cipitria, R.A. Coles, R. Dimova, M. Eder, S. Ehrig, L.M. Escudero, M.E. Evans, P.R. Fernandes, P. Fratzl, L. Geris, N. Gierlinger, E.B. Hannezo, A. Iglič, J.J.K. Kirkensgaard, P. Kollmannsberger, Ł. Kowalewska, N.A. Kurniawan, I. Papantoniou, L. Pieuchot, T.H.V. Pires, L.D. Renner, A.O. Sageman-Furnas, G.E. Schröder-Turk, A. Sengupta, V.R. Sharma, A. Tagua, C. Tomba, X. Trepat, S.L. Waters, E.F. Yeo, A. Roschger, C.M. Bidan, J.W.C. Dunlop, Advanced Materials 35 (2023).","ieee":"B. Schamberger et al., “Curvature in biological systems: Its quantification, emergence, and implications across the scales,” Advanced Materials, vol. 35, no. 13. Wiley, 2023.","mla":"Schamberger, Barbara, et al. “Curvature in Biological Systems: Its Quantification, Emergence, and Implications across the Scales.” Advanced Materials, vol. 35, no. 13, 2206110, Wiley, 2023, doi:10.1002/adma.202206110.","apa":"Schamberger, B., Ziege, R., Anselme, K., Ben Amar, M., Bykowski, M., Castro, A. P. G., … Dunlop, J. W. C. (2023). Curvature in biological systems: Its quantification, emergence, and implications across the scales. Advanced Materials. Wiley. https://doi.org/10.1002/adma.202206110"},"pmid":1,"scopus_import":"1","ddc":["570"],"status":"public","quality_controlled":"1","intvolume":" 35","year":"2023","volume":35,"publication":"Advanced Materials","publisher":"Wiley","oa":1,"file_date_updated":"2023-09-26T10:51:56Z","author":[{"last_name":"Schamberger","first_name":"Barbara","full_name":"Schamberger, Barbara"},{"first_name":"Ricardo","full_name":"Ziege, Ricardo","last_name":"Ziege"},{"last_name":"Anselme","full_name":"Anselme, Karine","first_name":"Karine"},{"last_name":"Ben Amar","first_name":"Martine","full_name":"Ben Amar, Martine"},{"first_name":"Michał","full_name":"Bykowski, Michał","last_name":"Bykowski"},{"last_name":"Castro","first_name":"André P.G.","full_name":"Castro, André P.G."},{"first_name":"Amaia","full_name":"Cipitria, Amaia","last_name":"Cipitria"},{"first_name":"Rhoslyn A.","full_name":"Coles, Rhoslyn A.","last_name":"Coles"},{"last_name":"Dimova","full_name":"Dimova, Rumiana","first_name":"Rumiana"},{"full_name":"Eder, Michaela","first_name":"Michaela","last_name":"Eder"},{"full_name":"Ehrig, Sebastian","first_name":"Sebastian","last_name":"Ehrig"},{"last_name":"Escudero","first_name":"Luis M.","full_name":"Escudero, Luis M."},{"last_name":"Evans","first_name":"Myfanwy E.","full_name":"Evans, Myfanwy E."},{"full_name":"Fernandes, Paulo R.","first_name":"Paulo R.","last_name":"Fernandes"},{"full_name":"Fratzl, Peter","first_name":"Peter","last_name":"Fratzl"},{"first_name":"Liesbet","full_name":"Geris, Liesbet","last_name":"Geris"},{"last_name":"Gierlinger","full_name":"Gierlinger, Notburga","first_name":"Notburga"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"last_name":"Iglič","full_name":"Iglič, Aleš","first_name":"Aleš"},{"full_name":"Kirkensgaard, Jacob J.K.","first_name":"Jacob J.K.","last_name":"Kirkensgaard"},{"first_name":"Philip","full_name":"Kollmannsberger, Philip","last_name":"Kollmannsberger"},{"last_name":"Kowalewska","full_name":"Kowalewska, Łucja","first_name":"Łucja"},{"last_name":"Kurniawan","first_name":"Nicholas A.","full_name":"Kurniawan, Nicholas A."},{"full_name":"Papantoniou, Ioannis","first_name":"Ioannis","last_name":"Papantoniou"},{"last_name":"Pieuchot","full_name":"Pieuchot, Laurent","first_name":"Laurent"},{"full_name":"Pires, Tiago H.V.","first_name":"Tiago H.V.","last_name":"Pires"},{"last_name":"Renner","first_name":"Lars D.","full_name":"Renner, Lars D."},{"full_name":"Sageman-Furnas, Andrew O.","first_name":"Andrew O.","last_name":"Sageman-Furnas"},{"last_name":"Schröder-Turk","first_name":"Gerd E.","full_name":"Schröder-Turk, Gerd E."},{"full_name":"Sengupta, Anupam","first_name":"Anupam","last_name":"Sengupta"},{"last_name":"Sharma","first_name":"Vikas R.","full_name":"Sharma, Vikas R."},{"first_name":"Antonio","full_name":"Tagua, Antonio","last_name":"Tagua"},{"last_name":"Tomba","full_name":"Tomba, Caterina","first_name":"Caterina"},{"first_name":"Xavier","full_name":"Trepat, Xavier","last_name":"Trepat"},{"full_name":"Waters, Sarah L.","first_name":"Sarah L.","last_name":"Waters"},{"last_name":"Yeo","first_name":"Edwina F.","full_name":"Yeo, Edwina F."},{"last_name":"Roschger","full_name":"Roschger, Andreas","first_name":"Andreas"},{"first_name":"Cécile M.","full_name":"Bidan, Cécile M.","last_name":"Bidan"},{"full_name":"Dunlop, John W.C.","first_name":"John W.C.","last_name":"Dunlop"}],"abstract":[{"text":"Surface curvature both emerges from, and influences the behavior of, living objects at length scales ranging from cell membranes to single cells to tissues and organs. The relevance of surface curvature in biology is supported by numerous experimental and theoretical investigations in recent years. In this review, first, a brief introduction to the key ideas of surface curvature in the context of biological systems is given and the challenges that arise when measuring surface curvature are discussed. Giving an overview of the emergence of curvature in biological systems, its significance at different length scales becomes apparent. On the other hand, summarizing current findings also shows that both single cells and entire cell sheets, tissues or organisms respond to curvature by modulating their shape and their migration behavior. Finally, the interplay between the distribution of morphogens or micro-organisms and the emergence of curvature across length scales is addressed with examples demonstrating these key mechanistic principles of morphogenesis. Overall, this review highlights that curved interfaces are not merely a passive by-product of the chemical, biological, and mechanical processes but that curvature acts also as a signal that co-determines these processes.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"date_published":"2023-03-29T00:00:00Z","month":"03","file":[{"checksum":"5c04d68130e97a0ecd1ca27fbc15a246","success":1,"date_created":"2023-09-26T10:51:56Z","file_name":"2023_AdvancedMaterials_Schamberger.pdf","creator":"dernst","access_level":"open_access","date_updated":"2023-09-26T10:51:56Z","file_size":2898063,"file_id":"14373","content_type":"application/pdf","relation":"main_file"}],"date_updated":"2023-09-26T10:56:46Z","department":[{"_id":"EdHa"}],"acknowledgement":"B.S. and A.R. contributed equally to this work. A.P.G.C. and P.R.F. acknowledge the funding from Fundação para a Ciência e Tecnologia (Portugal), through IDMEC, under LAETA project UIDB/50022/2020. T.H.V.P. acknowledges the funding from Fundação para a Ciência e Tecnologia (Portugal), through Ph.D. Grant 2020.04417.BD. A.S. acknowledges that this work was partially supported by the ATTRACT Investigator Grant (no. A17/MS/11572821/MBRACE, to A.S.) from the Luxembourg National Research Fund. The author thanks Gerardo Ceada for his help in the graphical representations. N.A.K. acknowledges support from the European Research Council (grant 851960) and the Gravitation Program “Materials Driven Regeneration,” funded by the Netherlands Organization for Scientific Research (024.003.013). M.B.A. acknowledges support from the French National Research Agency (grant ANR-201-8-CE1-3-0008 for the project “Epimorph”). G.E.S.T. acknowledges funding by the Australian Research Council through project DP200102593. A.C. acknowledges the funding from the Deutsche Forschungsgemeinschaft (DFG) Emmy Noether Grant CI 203/-2 1, the Spanish Ministry of Science and Innovation (PID2021-123013O-BI00) and the IKERBASQUE Basque Foundation for Science.","date_created":"2023-03-05T23:01:06Z"},{"intvolume":" 14","scopus_import":"1","pmid":1,"status":"public","ddc":["570"],"quality_controlled":"1","volume":14,"year":"2023","publication":"Nature Communications","publisher":"Springer Nature","abstract":[{"text":"The multicellular organization of diverse systems, including embryos, intestines, and tumors relies on coordinated cell migration in curved environments. In these settings, cells establish supracellular patterns of motion, including collective rotation and invasion. While such collective modes have been studied extensively in flat systems, the consequences of geometrical and topological constraints on collective migration in curved systems are largely unknown. Here, we discover a collective mode of cell migration in rotating spherical tissues manifesting as a propagating single-wavelength velocity wave. This wave is accompanied by an apparently incompressible supracellular flow pattern featuring topological defects as dictated by the spherical topology. Using a minimal active particle model, we reveal that this collective mode arises from the effect of curvature on the active flocking behavior of a cell layer confined to a spherical surface. Our results thus identify curvature-induced velocity waves as a mode of collective cell migration, impacting the dynamical organization of 3D curved tissues.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"file_date_updated":"2023-04-11T06:27:00Z","oa":1,"author":[{"last_name":"Brandstätter","first_name":"Tom","full_name":"Brandstätter, Tom"},{"full_name":"Brückner, David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","last_name":"Brückner"},{"last_name":"Han","first_name":"Yu Long","full_name":"Han, Yu Long"},{"first_name":"Ricard","full_name":"Alert, Ricard","last_name":"Alert"},{"last_name":"Guo","first_name":"Ming","full_name":"Guo, Ming"},{"first_name":"Chase P.","full_name":"Broedersz, Chase P.","last_name":"Broedersz"}],"date_published":"2023-03-24T00:00:00Z","month":"03","date_updated":"2023-08-01T14:05:30Z","file":[{"creator":"dernst","access_level":"open_access","date_updated":"2023-04-11T06:27:00Z","checksum":"54f06f9eee11d43bab253f3492c983ba","date_created":"2023-04-11T06:27:00Z","file_name":"2023_NatureComm_Brandstaetter.pdf","success":1,"relation":"main_file","content_type":"application/pdf","file_size":4146777,"file_id":"12821"}],"date_created":"2023-04-09T22:01:00Z","acknowledgement":"We thank H. Abbaszadeh, M.J. Bowick, G. Gradziuk, M.C. Marchetti, and S. Shankar for their helpful discussions. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12). D.B.B. is a NOMIS fellow supported by the NOMIS foundation and was in part supported by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and Joachim Herz Stiftung. R.A. acknowledges support from the Human Frontier Science Program (LT000475/2018-C) and from the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030). M.G. acknowledges support from NIH R01GM140108 and Alfred Sloan Foundation. Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Project-ID 201269156-SFB 1032 (Project B12).Open Access funding enabled and organized by Projekt DEAL.","department":[{"_id":"EdHa"}],"article_processing_charge":"No","doi":"10.1038/s41467-023-37054-2","_id":"12818","day":"24","fulldoi":"https://doi.org/10.1038/s41467-023-37054-2","language":[{"iso":"eng"}],"oa_version":"Published Version","isi":1,"article_type":"original","type":"journal_article","has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"1643","external_id":{"isi":["000959887700008"],"pmid":["36964141"]},"publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","title":"Curvature induces active velocity waves in rotating spherical tissues","citation":{"chicago":"Brandstätter, Tom, David Brückner, Yu Long Han, Ricard Alert, Ming Guo, and Chase P. Broedersz. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” Nature Communications. Springer Nature, 2023. https://doi.org/10.1038/s41467-023-37054-2.","ista":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. 2023. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 14, 1643.","apa":"Brandstätter, T., Brückner, D., Han, Y. L., Alert, R., Guo, M., & Broedersz, C. P. (2023). Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-023-37054-2","ama":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. Curvature induces active velocity waves in rotating spherical tissues. Nature Communications. 2023;14. doi:10.1038/s41467-023-37054-2","short":"T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz, Nature Communications 14 (2023).","ieee":"T. Brandstätter, D. Brückner, Y. L. Han, R. Alert, M. Guo, and C. P. Broedersz, “Curvature induces active velocity waves in rotating spherical tissues,” Nature Communications, vol. 14. Springer Nature, 2023.","mla":"Brandstätter, Tom, et al. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” Nature Communications, vol. 14, 1643, Springer Nature, 2023, doi:10.1038/s41467-023-37054-2."}},{"month":"06","date_published":"2023-06-29T00:00:00Z","department":[{"_id":"EdHa"}],"acknowledgement":"This work was supported in part by the U.S. National Science Foundation, the Center for the Physics of Biological Function (grant PHY-1734030), and the National Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B. was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship (ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.","date_created":"2023-07-23T22:01:12Z","date_updated":"2025-04-14T08:55:54Z","year":"2023","volume":380,"publication":"Science","scopus_import":"1","quality_controlled":"1","status":"public","intvolume":" 380","oa":1,"author":[{"last_name":"Brückner","full_name":"Brückner, David","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975"},{"first_name":"Hongtao","full_name":"Chen, Hongtao","last_name":"Chen"},{"full_name":"Barinov, Lev","first_name":"Lev","last_name":"Barinov"},{"last_name":"Zoller","first_name":"Benjamin","full_name":"Zoller, Benjamin"},{"last_name":"Gregor","full_name":"Gregor, Thomas","first_name":"Thomas"}],"abstract":[{"lang":"eng","text":"Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression."}],"publisher":"American Association for the Advancement of Science","title":"Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome","external_id":{"isi":["001106405600028"]},"publication_identifier":{"eissn":["1095-9203"]},"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1126/science.adf5568","open_access":"1"}],"citation":{"ista":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 380(6652), 1357–1362.","chicago":"Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” Science. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/science.adf5568.","mla":"Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” Science, vol. 380, no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62, doi:10.1126/science.adf5568.","ieee":"D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,” Science, vol. 380, no. 6652. American Association for the Advancement of Science, pp. 1357–1362, 2023.","ama":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 2023;380(6652):1357-1362. doi:10.1126/science.adf5568","short":"D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023) 1357–1362.","apa":"Brückner, D., Chen, H., Barinov, L., Zoller, B., & Gregor, T. (2023). Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.adf5568"},"day":"29","_id":"13261","oa_version":"Preprint","fulldoi":"https://doi.org/10.1126/science.adf5568","language":[{"iso":"eng"}],"doi":"10.1126/science.adf5568","article_processing_charge":"No","type":"journal_article","project":[{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"ALTF 343-2022"}],"article_type":"original","page":"1357-1362","isi":1,"issue":"6652"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["001037346400005"]},"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"publication_status":"published","title":"Unconventional colloidal aggregation in chiral bacterial baths","citation":{"chicago":"Grober, Daniel, Ivan Palaia, Mehmet C Ucar, Edouard B Hannezo, Anđela Šarić, and Jérémie A Palacci. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02136-x.","ista":"Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. 2023. Unconventional colloidal aggregation in chiral bacterial baths. Nature Physics. 19, 1680–1688.","apa":"Grober, D., Palaia, I., Ucar, M. C., Hannezo, E. B., Šarić, A., & Palacci, J. A. (2023). Unconventional colloidal aggregation in chiral bacterial baths. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02136-x","short":"D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature Physics 19 (2023) 1680–1688.","ama":"Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. Unconventional colloidal aggregation in chiral bacterial baths. Nature Physics. 2023;19:1680-1688. doi:10.1038/s41567-023-02136-x","ieee":"D. Grober, I. Palaia, M. C. Ucar, E. B. Hannezo, A. Šarić, and J. A. Palacci, “Unconventional colloidal aggregation in chiral bacterial baths,” Nature Physics, vol. 19. Springer Nature, pp. 1680–1688, 2023.","mla":"Grober, Daniel, et al. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1680–88, doi:10.1038/s41567-023-02136-x."},"article_processing_charge":"Yes","doi":"10.1038/s41567-023-02136-x","_id":"13971","day":"01","language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1038/s41567-023-02136-x","oa_version":"Published Version","isi":1,"article_type":"original","page":"1680-1688","type":"journal_article","has_accepted_license":"1","project":[{"call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"},{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"date_published":"2023-11-01T00:00:00Z","month":"11","date_updated":"2025-04-14T07:43:56Z","file":[{"date_updated":"2024-01-30T12:26:08Z","access_level":"open_access","creator":"dernst","file_name":"2023_NaturePhysics_Grober.pdf","date_created":"2024-01-30T12:26:08Z","success":1,"checksum":"7e282c2ebc0ac82125a04f6b4742d4c1","content_type":"application/pdf","relation":"main_file","file_id":"14906","file_size":6365607}],"ec_funded":1,"date_created":"2023-08-06T22:01:11Z","acknowledgement":"D.G. and J.P. thank E. Krasnopeeva, C. Guet, G. Guessous and T. Hwa for providing the E. coli strains. This material is based upon work supported by the US Department of Energy under award DE-SC0019769. I.P. acknowledges funding by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 101034413. A.Š. acknowledges funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant No. 802960). M.C.U. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 754411.","department":[{"_id":"EdHa"},{"_id":"AnSa"},{"_id":"JePa"}],"intvolume":" 19","scopus_import":"1","status":"public","quality_controlled":"1","ddc":["530"],"year":"2023","volume":19,"publication":"Nature Physics","publisher":"Springer Nature","corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"When in equilibrium, thermal forces agitate molecules, which then diffuse, collide and bind to form materials. However, the space of accessible structures in which micron-scale particles can be organized by thermal forces is limited, owing to the slow dynamics and metastable states. Active agents in a passive fluid generate forces and flows, forming a bath with active fluctuations. Two unanswered questions are whether those active agents can drive the assembly of passive components into unconventional states and which material properties they will exhibit. Here we show that passive, sticky beads immersed in a bath of swimming Escherichia coli bacteria aggregate into unconventional clusters and gels that are controlled by the activity of the bath. We observe a slow but persistent rotation of the aggregates that originates in the chirality of the E. coli flagella and directs aggregation into structures that are not accessible thermally. We elucidate the aggregation mechanism with a numerical model of spinning, sticky beads and reproduce quantitatively the experimental results. We show that internal activity controls the phase diagram and the structure of the aggregates. Overall, our results highlight the promising role of active baths in designing the structural and mechanical properties of materials with unconventional phases."}],"oa":1,"file_date_updated":"2024-01-30T12:26:08Z","author":[{"full_name":"Grober, Daniel","id":"abdfc56f-34fb-11ee-bd33-fd766fce5a99","first_name":"Daniel","last_name":"Grober"},{"last_name":"Palaia","full_name":"Palaia, Ivan","first_name":"Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","orcid":" 0000-0002-8843-9485 "},{"last_name":"Ucar","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"last_name":"Palacci","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","orcid":"0000-0002-7253-9465"}]},{"file":[{"access_level":"open_access","date_updated":"2023-09-15T06:30:50Z","creator":"dernst","checksum":"f881d98c89eb9f1aa136d7b781511553","date_created":"2023-09-15T06:30:50Z","success":1,"file_name":"2023_PRXLife_Boocock.pdf","relation":"main_file","content_type":"application/pdf","file_size":2559520,"file_id":"14335"}],"date_updated":"2025-04-14T07:52:27Z","department":[{"_id":"EdHa"}],"acknowledgement":"We thank all members of the Hannezo group for discussions and suggestions, as well as Sound Wai Phow for technical assistance. This work received funding from the European Research Council under the EU Horizon 2020 research and innovation program Grant Agreement No. 851288 (E.H.), JSPS KAKENHI Grant No. 21H05290, and the Ministry of Education under the Research Centres of Excellence program through the MBI at NUS.","date_created":"2023-09-06T08:30:59Z","ec_funded":1,"date_published":"2023-07-20T00:00:00Z","month":"07","publisher":"American Physical Society","author":[{"last_name":"Boocock","orcid":"0000-0002-1585-2631","id":"453AF628-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel R","full_name":"Boocock, Daniel R"},{"last_name":"Hirashima","full_name":"Hirashima, Tsuyoshi","first_name":"Tsuyoshi"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"file_date_updated":"2023-09-15T06:30:50Z","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"corr_author":"1","abstract":[{"lang":"eng","text":"Living tissues are characterized by an intrinsically mechanochemical interplay of active physical forces and complex biochemical signaling pathways. Either feature alone can give rise to complex emergent phenomena, for example, mechanically driven glassy dynamics and rigidity transitions, or chemically driven reaction-diffusion instabilities. An important question is how to quantitatively assess the contribution of these different cues to the large-scale dynamics of biological materials. We address this in Madin-Darby canine kidney (MDCK) monolayers, considering both mechanochemical feedback between extracellular signal-regulated kinase (ERK) signaling activity and cellular density as well as a mechanically active tissue rheology via a self-propelled vertex model. We show that the relative strength of active migration forces to mechanochemical couplings controls a transition from a uniform active glass to periodic spatiotemporal waves. We parametrize the model from published experimental data sets on MDCK monolayers and use it to make new predictions on the correlation functions of cellular dynamics and the dynamics of topological defects associated with the oscillatory phase of cells. Interestingly, MDCK monolayers are best described by an intermediary parameter region in which both mechanochemical couplings and noisy active propulsion have a strong influence on the dynamics. Finally, we study how tissue rheology and ERK waves produce feedback on one another and uncover a mechanism via which tissue fluidity can be controlled by mechanochemical waves at both the local and global levels."}],"status":"public","quality_controlled":"1","ddc":["570"],"intvolume":" 1","publication":"PRX Life","volume":1,"year":"2023","citation":{"mla":"Boocock, Daniel R., et al. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” PRX Life, vol. 1, no. 1, 013001, American Physical Society, 2023, doi:10.1103/prxlife.1.013001.","ieee":"D. R. Boocock, T. Hirashima, and E. B. Hannezo, “Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers,” PRX Life, vol. 1, no. 1. American Physical Society, 2023.","ama":"Boocock DR, Hirashima T, Hannezo EB. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 2023;1(1). doi:10.1103/prxlife.1.013001","short":"D.R. Boocock, T. Hirashima, E.B. Hannezo, PRX Life 1 (2023).","apa":"Boocock, D. R., Hirashima, T., & Hannezo, E. B. (2023). Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. American Physical Society. https://doi.org/10.1103/prxlife.1.013001","ista":"Boocock DR, Hirashima T, Hannezo EB. 2023. Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers. PRX Life. 1(1), 013001.","chicago":"Boocock, Daniel R, Tsuyoshi Hirashima, and Edouard B Hannezo. “Interplay between Mechanochemical Patterning and Glassy Dynamics in Cellular Monolayers.” PRX Life. American Physical Society, 2023. https://doi.org/10.1103/prxlife.1.013001."},"article_number":"013001","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Interplay between mechanochemical patterning and glassy dynamics in cellular monolayers","publication_status":"published","publication_identifier":{"issn":["2835-8279"]},"article_type":"original","issue":"1","project":[{"call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","name":"Design Principles of Branching Morphogenesis"}],"has_accepted_license":"1","type":"journal_article","article_processing_charge":"Yes","fulldoi":"https://doi.org/10.1103/prxlife.1.013001","language":[{"iso":"eng"}],"oa_version":"Published Version","_id":"14277","day":"20","doi":"10.1103/prxlife.1.013001"},{"article_processing_charge":"No","status":"public","ddc":["570"],"doi":"10.5281/ZENODO.8133960","oa_version":"Published Version","fulldoi":"https://doi.org/10.5281/ZENODO.8133960","day":"11","_id":"14279","year":"2023","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"14274"}]},"publisher":"Zenodo","corr_author":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"The zip file includes source data used in the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript.\r\nA sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt."}],"has_accepted_license":"1","author":[{"first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","last_name":"Ucar"}],"type":"research_data_reference","oa":1,"date_published":"2023-07-11T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"07","title":"Source data for the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\"","date_updated":"2026-06-18T17:34:48Z","citation":{"ama":"Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” 2023. doi:10.5281/ZENODO.8133960","short":"M.C. Ucar, (2023).","mla":"Ucar, Mehmet C. Source Data for the Manuscript “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Zenodo, 2023, doi:10.5281/ZENODO.8133960.","ieee":"M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023.","apa":"Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. https://doi.org/10.5281/ZENODO.8133960","chicago":"Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133960.","ista":"Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, 10.5281/ZENODO.8133960."},"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.8133960","open_access":"1"}],"date_created":"2023-09-06T08:39:25Z","department":[{"_id":"EdHa"}]}]