[{"OA_type":"hybrid","day":"20","fulldoi":"https://doi.org/10.1016/j.cell.2026.06.009","article_type":"original","publication_status":"published","date_published":"2026-08-20T00:00:00Z","file_date_updated":"2026-10-01T08:34:11Z","scopus_import":"1","das_tickbox":"1","OA_place":"publisher","tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"type":"journal_article","ec_funded":1,"author":[{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","last_name":"Schwayer","first_name":"Cornelia","orcid":"0000-0001-5130-2226","full_name":"Schwayer, Cornelia"},{"last_name":"Barbiero","first_name":"Silvia","full_name":"Barbiero, Silvia"},{"full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","orcid":"0000-0001-7205-2975","first_name":"David"},{"full_name":"Oost, Koen C.","last_name":"Oost","first_name":"Koen C."},{"first_name":"Clara","last_name":"Baader","full_name":"Baader, Clara"},{"full_name":"Repina, Nicole A.","last_name":"Repina","first_name":"Nicole A."},{"first_name":"Jinse","last_name":"Kim","full_name":"Kim, Jinse"},{"first_name":"Oscar E.","last_name":"Diaz","full_name":"Diaz, Oscar E."},{"full_name":"Uccelli, Isa","last_name":"Uccelli","first_name":"Isa"},{"full_name":"Capolupo, Laura","last_name":"Capolupo","first_name":"Laura"},{"full_name":"Meylan, Ludivine Challet","first_name":"Ludivine Challet","last_name":"Meylan"},{"full_name":"Kalck, Veronique","last_name":"Kalck","first_name":"Veronique"},{"first_name":"Franziska","last_name":"Moos","full_name":"Moos, Franziska"},{"first_name":"Simon","last_name":"Suppinger","full_name":"Suppinger, Simon"},{"last_name":"Yang","first_name":"Qiutan","full_name":"Yang, Qiutan"},{"full_name":"Schnabl, Jakob","last_name":"Schnabl","first_name":"Jakob"},{"last_name":"Kilik","first_name":"Umut","full_name":"Kilik, Umut"},{"first_name":"Matthieu","last_name":"Bourdon","full_name":"Bourdon, Matthieu"},{"full_name":"Camp, J. Gray","first_name":"J. Gray","last_name":"Camp"},{"full_name":"Stockinger, Brigitta","first_name":"Brigitta","last_name":"Stockinger"},{"last_name":"Ferrari","first_name":"Alessandra","full_name":"Ferrari, Alessandra"},{"last_name":"Bühler","first_name":"Marc","full_name":"Bühler, Marc"},{"last_name":"Stadler","first_name":"Michael B.","full_name":"Stadler, Michael B."},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"last_name":"Liberali","first_name":"Prisca","full_name":"Liberali, Prisca"}],"month":"08","date_created":"2026-09-17T11:06:12Z","citation":{"chicago":"Schwayer, Cornelia, Silvia Barbiero, David Brückner, Koen C. Oost, Clara Baader, Nicole A. Repina, Jinse Kim, et al. “Multiscale Integration of Tissue and Chromatin Context Converts Cell Heterogeneity into Stable Intestinal Patterning.” <i>Cell</i>. Cell Press, 2026. <a href=\"https://doi.org/10.1016/j.cell.2026.06.009\">https://doi.org/10.1016/j.cell.2026.06.009</a>.","short":"C. Schwayer, S. Barbiero, D. Brückner, K.C. Oost, C. Baader, N.A. Repina, J. Kim, O.E. Diaz, I. Uccelli, L. Capolupo, L.C. Meylan, V. Kalck, F. Moos, S. Suppinger, Q. Yang, J. Schnabl, U. Kilik, M. Bourdon, J.G. Camp, B. Stockinger, A. Ferrari, M. Bühler, M.B. Stadler, E.B. Hannezo, P. Liberali, Cell 189 (2026) 5266–5282.e17.","mla":"Schwayer, Cornelia, et al. “Multiscale Integration of Tissue and Chromatin Context Converts Cell Heterogeneity into Stable Intestinal Patterning.” <i>Cell</i>, vol. 189, no. 17, Cell Press, 2026, p. 5266–5282.e17, doi:<a href=\"https://doi.org/10.1016/j.cell.2026.06.009\">10.1016/j.cell.2026.06.009</a>.","apa":"Schwayer, C., Barbiero, S., Brückner, D., Oost, K. C., Baader, C., Repina, N. A., … Liberali, P. (2026). Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2026.06.009\">https://doi.org/10.1016/j.cell.2026.06.009</a>","ista":"Schwayer C, Barbiero S, Brückner D, Oost KC, Baader C, Repina NA, Kim J, Diaz OE, Uccelli I, Capolupo L, Meylan LC, Kalck V, Moos F, Suppinger S, Yang Q, Schnabl J, Kilik U, Bourdon M, Camp JG, Stockinger B, Ferrari A, Bühler M, Stadler MB, Hannezo EB, Liberali P. 2026. Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning. Cell. 189(17), 5266–5282.e17.","ama":"Schwayer C, Barbiero S, Brückner D, et al. Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning. <i>Cell</i>. 2026;189(17):5266-5282.e17. doi:<a href=\"https://doi.org/10.1016/j.cell.2026.06.009\">10.1016/j.cell.2026.06.009</a>","ieee":"C. Schwayer <i>et al.</i>, “Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning,” <i>Cell</i>, vol. 189, no. 17. Cell Press, p. 5266–5282.e17, 2026."},"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"doi":"10.1016/j.cell.2026.06.009","title":"Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning","publication":"Cell","license":"https://creativecommons.org/licenses/by-nc/4.0/","issue":"17","pmid":1,"quality_controlled":"1","project":[{"grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"},{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"23014","checksum":"3ff0f4f8be0e79940ba11b18af318ae3","file_name":"2026_Cell_Schwayer.pdf","success":1,"file_size":15536364,"creator":"dernst","date_created":"2026-10-01T08:34:11Z","date_updated":"2026-10-01T08:34:11Z"}],"corr_author":"1","abstract":[{"lang":"eng","text":"Tissue regeneration requires de novo patterning, which has been proposed to be facilitated by cellular heterogeneity. Yet how such heterogeneities are integrated with the mechanochemical state of the tissue and stabilized at the chromatin level into stable, spatially organized fates remains poorly understood. Using in vivo mouse intestinal regeneration models and organoids, we identify a critical density regime that produces a permissive window for heterogeneity in the mechanosensor Yes-associated protein 1 (YAP1). We show that YAP1 heterogeneity is coupled to lineage-biased chromatin accessibility and is decoded through FOXA1, which integrates the permissive chromatin state to Delta-Notch supracellular feedback and lineage commitment. This circuit generates fate bistability and preserves a memory of transient YAP1 activity, thereby maintaining spatial patterning as tissues return to homeostasis after injury. Together, our findings establish a multiscale framework in which tissue-scale mechanics tune single-cell competence and, through FOXA1-mediated bistability, convert transient heterogeneity into stable and self-organized tissue architecture."}],"dataavailabilitystatement":"All sequencing data have been deposited at the Gene Expression Omnibus (GEO) under accession number GEO: GSE283662.\r\nAnalysis of imaging and sequencing data was developed in the Liberali lab and is available at https://github.com/LiberaliLab/symmetry-breaking-2026. Detailed information on the packages used is provided in the STAR Methods section.\r\nAny additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.","language":[{"iso":"eng"}],"oa_version":"Published Version","year":"2026","volume":189,"researchdata_availability":"yes","keyword":["tissue patterning","heterogeneity","mechanics","intestinal regeneration","epigenetic competence","multiscale integration","modeling","organoids","image-based phenotyping","Yap1"],"external_id":{"pmid":["42379166"]},"intvolume":"       189","page":"5266-5282.e17","_id":"22956","article_processing_charge":"Yes (in subscription journal)","date_updated":"2026-10-01T08:42:00Z","status":"public","supplementarymaterial":"yes","publisher":"Cell Press","has_accepted_license":"1","acknowledgement":"We thank the Liberali group, M. Verbeek, and C. Soneson for fruitful discussions; E. Tagliavini for IT support; J. Lüthi for Fractal support; H. Köhler for FACS sorting; T.O. Buchholz for help on cell segmentation; B. Treutlein and A. Xavier da Silveira dos Santos for help with library preparation of single-cell ATAC-seq; M. Garioni for help with mouse salivary organoids; M. Kahnwald for help with human intestinal organoids; M. Lütolf, M. Nikolaev, and O. Mitrofanova for providing material and initial training for microwell experiments; J. Tchorz and V. Orsini for intestinal tissue sections of the YAP1 activator experiment in homeostasis; R. Kageyama for DLL1-Venus-T2A-mCherry mice; J.-F. Spetz for technical assistance; C. Lambert and N. Accart for help with sample preparation; Claudia Flandoli for graphic design of schemes; and Zuzana Nascakova for the graphical abstract. We thank the Foundation Hubrecht Organoid Technology (now Foundation Hubrecht Organoid Biobank, https://www.hubrechtorganoidbiobank.org/) for the duodenal organoid line used in this study (HUB-04-A2-001). We thank C.P. Heisenberg, M. Lütolf, C. Tsiairis, J. Zaugg, G. D’Angelo, L. Giorgetti, S. Arber, and the Liberali group for reading the manuscript. C.S. was supported by the European Molecular Biology Organization (Postdoctoral Fellowship ALTF 660-2020) and the Human Frontier Science Program (HFSP) LT000746/2021-L. D.B.B. was supported by the NOMIS Foundation as a NOMIS fellow, an EMBO Postdoctoral Fellowship (ALTF 343-2022), and the Austrian Academy of Sciences through an APART-MINT Fellowship. B.S. was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK, the UK Medical Research Council, and the Wellcome Trust (FC001159). This work received funding from ERC to E.H. (grant number 851288) and to P.L. (grant number 758617) and from SNSF (310030_208162 and SNSF ERC TMCG-3_223263).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"ddc":["570"]},{"type":"journal_article","month":"04","author":[{"first_name":"Arshed","last_name":"Nabeel","full_name":"Nabeel, Arshed"},{"last_name":"Karichannavar","first_name":"Ashwin","full_name":"Karichannavar, Ashwin"},{"first_name":"Shuaib","last_name":"Palathingal","full_name":"Palathingal, Shuaib"},{"last_name":"Jhawar","first_name":"Jitesh","full_name":"Jhawar, Jitesh"},{"full_name":"Brückner, David","orcid":"0000-0001-7205-2975","first_name":"David","last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"full_name":"Raj M, Danny","last_name":"Raj M","first_name":"Danny"},{"first_name":"Vishwesha","last_name":"Guttal","full_name":"Guttal, Vishwesha"}],"date_created":"2025-07-21T08:37:27Z","fulldoi":"https://doi.org/10.1086/734083","OA_type":"green","day":"01","date_published":"2025-04-01T00:00:00Z","publication_status":"published","article_type":"original","OA_place":"repository","issue":"4","quality_controlled":"1","pmid":1,"arxiv":1,"publication_identifier":{"issn":["0003-0147"],"eissn":["1537-5323"]},"citation":{"chicago":"Nabeel, Arshed, Ashwin Karichannavar, Shuaib Palathingal, Jitesh Jhawar, David Brückner, Danny Raj M, and Vishwesha Guttal. “Discovering Stochastic Dynamical Equations from Ecological Time Series Data.” <i>The American Naturalist</i>. University of Chicago Press, 2025. <a href=\"https://doi.org/10.1086/734083\">https://doi.org/10.1086/734083</a>.","short":"A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, D. Raj M, V. Guttal, The American Naturalist 205 (2025) E100–E117.","mla":"Nabeel, Arshed, et al. “Discovering Stochastic Dynamical Equations from Ecological Time Series Data.” <i>The American Naturalist</i>, vol. 205, no. 4, University of Chicago Press, 2025, pp. E100–17, doi:<a href=\"https://doi.org/10.1086/734083\">10.1086/734083</a>.","ama":"Nabeel A, Karichannavar A, Palathingal S, et al. Discovering stochastic dynamical equations from ecological time series data. <i>The American Naturalist</i>. 2025;205(4):E100-E117. doi:<a href=\"https://doi.org/10.1086/734083\">10.1086/734083</a>","ista":"Nabeel A, Karichannavar A, Palathingal S, Jhawar J, Brückner D, Raj M D, Guttal V. 2025. Discovering stochastic dynamical equations from ecological time series data. The American Naturalist. 205(4), E100–E117.","apa":"Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Raj M, D., &#38; Guttal, V. (2025). Discovering stochastic dynamical equations from ecological time series data. <i>The American Naturalist</i>. University of Chicago Press. <a href=\"https://doi.org/10.1086/734083\">https://doi.org/10.1086/734083</a>","ieee":"A. Nabeel <i>et al.</i>, “Discovering stochastic dynamical equations from ecological time series data,” <i>The American Naturalist</i>, vol. 205, no. 4. University of Chicago Press, pp. E100–E117, 2025."},"doi":"10.1086/734083","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2205.02645"}],"title":"Discovering stochastic dynamical equations from ecological time series data","publication":"The American Naturalist","department":[{"_id":"EdHa"}],"intvolume":"       205","_id":"20056","page":"E100-E117","status":"public","related_material":{"record":[{"status":"public","id":"20121","relation":"software"}]},"date_updated":"2025-09-30T14:14:43Z","article_processing_charge":"No","isi":1,"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"}],"abstract":[{"lang":"eng","text":"Theoretical studies have shown that stochasticity can affect the dynamics of ecosystems in counterintuitive ways. However, without knowing the equations governing the dynamics of populations or ecosystems, it is difficult to ascertain the role of stochasticity in real datasets. Therefore, the inverse problem of inferring the governing stochastic equations from datasets is important. Here, we present an equation discovery methodology that takes time series data of state variables as input and outputs a stochastic differential equation. We achieve this by combining traditional approaches from stochastic calculus with the equation discovery techniques. We demonstrate the generality of the method via several applications. First, we deliberately choose various stochastic models with fundamentally different governing equations, yet they produce nearly identical steady-state distributions. We show that we can recover the correct underlying equations, and thus infer the structure of their stability, accurately from the analysis of time series data alone. We demonstrate our method on two real-world datasets—fish schooling and single-cell migration—that have vastly different spatiotemporal scales and dynamics. We illustrate various limitations and potential pitfalls of the method and how to overcome them via diagnostic measures. Finally, we provide our open-source code via a package named PyDaDDy (Python Library for Data-Driven Dynamics)."}],"oa_version":"Preprint","language":[{"iso":"eng"}],"external_id":{"pmid":["40179429"],"isi":["001433250500001"],"arxiv":["2205.02645"]},"year":"2025","volume":205,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"V.G. acknowledges support from the Science and Engi-neering Research Board, Department of Biotechnology,and the Indo-French Centre for the Promotion of Ad-vanced Research (64T4-1). D.R.M. acknowledges supportfrom a Department of Science and Technology (DST) In-novation in Science Pursuit for Inspired Research (IN-SPIRE) Faculty Award. J.J. acknowledges support froma Humboldt postdoctoral fellowship and the Heidelber-ger Akademie der Wissenschaften, Heidelberg, Germany.D.B.B. acknowledges support from the NOMIS Founda-tion and an European Molecular Biology Organization(EMBO) postdoctoral fellowship (ALTF 343-2022). A.N.and S.P. acknowledge support from Ministry of Educa-tion (MoE) PhD fellowships. We thank Ashrit Mangal-wedhekar, Vivek Jadhav, Shikhara Bhat, Cassandre Aimon,and Harishankar Muppirala for comments on the manu-script and code. We thank Kollegala Sharma for his inputon the Kannada translation of the title and abstract.Data-Driven Model Discovery E115","oa":1,"publisher":"University of Chicago Press"},{"publisher":"Springer Nature","acknowledgement":"We are grateful to members of S.G.’s laboratory for feedback and suggestions. We thank E. Hannezo, J. O. Rädler, M. Piel, O. du Roure and J. Heuvingh for inspiring discussions. Y.K. and S.G. acknowledge J. B. Braquenier from Nikon Instruments Belux and the Nikon BioImaging Lab in Leiden (the Netherlands) for their support with the Nikon Spatial Array Confocal enhanced-resolution confocal microscopy. We thank D. S. Herrador and M. Balland for their help in improving the microprinting method. D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). Y.K., M.L. and S.G. acknowledge funding from the University of Mons (FEDER Prostem Research Project no. 1510614, Wallonia DG06), the F.R.S.-FNRS (Epiforce Project no. T.0092.21, Cellsqueezer Project no. J.0061.23 and Optopattern Project no. U.NO26.22) and the Interreg projects ANTIRESI and MICROPLAITE, which are financially supported by Interreg France-Wallonie-Vlaanderen (Fonds Européen de Développement Régional). Y.K. and M.L. are financially supported by F.R.S.-FNRS as FRIA Grantee FNRS and Postdoctoral Fellow (Chargé de Recherches), respectively. Y.K. and S.G. acknowledge le Fonds pour la Recherche Médicale dans le Hainaut (FRMH). G.C. was supported by a grant from the Biotechnology and Biological Sciences Research Council (grant no. BB/V007483/1).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":21,"year":"2025","external_id":{"isi":["001556019400001"]},"language":[{"iso":"eng"}],"oa_version":"None","abstract":[{"lang":"eng","text":"Cell migration in narrow microenvironments occurs in numerous physiological processes. It involves successive cycles of confinement and release that drive important morphological changes. However, it remains unclear whether migrating cells can retain a memory of their past morphological states that could potentially facilitate their navigation through confined spaces. We demonstrate that local geometry governs a switch between two cell morphologies, thereby facilitating cell passage through long and narrow gaps. We combined cell migration assays on standardized microsystems with biophysical modelling and biochemical perturbations to show that migrating cells have a long-term memory of past confinement events. The morphological cell states correlate across transitions through actin cortex remodelling. These findings indicate that mechanical memory in migrating cells plays an active role in their migratory potential in confined environments."}],"corr_author":"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"}],"isi":1,"article_processing_charge":"No","date_updated":"2025-12-30T09:34:11Z","status":"public","page":"1451-1461","_id":"20259","intvolume":"        21","department":[{"_id":"EdHa"}],"publication":"Nature Physics","title":"The actin cortex acts as a mechanical memory of morphology in confined migrating cells","doi":"10.1038/s41567-025-02980-z","citation":{"ieee":"Y. Kalukula, M. Luciano, G. Simanov, G. Charras, D. Brückner, and S. Gabriele, “The actin cortex acts as a mechanical memory of morphology in confined migrating cells,” <i>Nature Physics</i>, vol. 21. Springer Nature, pp. 1451–1461, 2025.","mla":"Kalukula, Yohalie, et al. “The Actin Cortex Acts as a Mechanical Memory of Morphology in Confined Migrating Cells.” <i>Nature Physics</i>, vol. 21, Springer Nature, 2025, pp. 1451–61, doi:<a href=\"https://doi.org/10.1038/s41567-025-02980-z\">10.1038/s41567-025-02980-z</a>.","ista":"Kalukula Y, Luciano M, Simanov G, Charras G, Brückner D, Gabriele S. 2025. The actin cortex acts as a mechanical memory of morphology in confined migrating cells. Nature Physics. 21, 1451–1461.","ama":"Kalukula Y, Luciano M, Simanov G, Charras G, Brückner D, Gabriele S. The actin cortex acts as a mechanical memory of morphology in confined migrating cells. <i>Nature Physics</i>. 2025;21:1451-1461. doi:<a href=\"https://doi.org/10.1038/s41567-025-02980-z\">10.1038/s41567-025-02980-z</a>","apa":"Kalukula, Y., Luciano, M., Simanov, G., Charras, G., Brückner, D., &#38; Gabriele, S. (2025). The actin cortex acts as a mechanical memory of morphology in confined migrating cells. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-025-02980-z\">https://doi.org/10.1038/s41567-025-02980-z</a>","short":"Y. Kalukula, M. Luciano, G. Simanov, G. Charras, D. Brückner, S. Gabriele, Nature Physics 21 (2025) 1451–1461.","chicago":"Kalukula, Yohalie, Marine Luciano, Gleb Simanov, Guillaume Charras, David Brückner, and Sylvain Gabriele. “The Actin Cortex Acts as a Mechanical Memory of Morphology in Confined Migrating Cells.” <i>Nature Physics</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41567-025-02980-z\">https://doi.org/10.1038/s41567-025-02980-z</a>."},"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"quality_controlled":"1","date_published":"2025-09-01T00:00:00Z","article_type":"original","publication_status":"published","scopus_import":"1","day":"01","OA_type":"closed access","fulldoi":"https://doi.org/10.1038/s41567-025-02980-z","date_created":"2025-08-31T22:01:33Z","author":[{"last_name":"Kalukula","first_name":"Yohalie","full_name":"Kalukula, Yohalie"},{"first_name":"Marine","last_name":"Luciano","full_name":"Luciano, Marine"},{"full_name":"Simanov, Gleb","first_name":"Gleb","last_name":"Simanov"},{"last_name":"Charras","first_name":"Guillaume","full_name":"Charras, Guillaume"},{"full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","first_name":"David","orcid":"0000-0001-7205-2975"},{"full_name":"Gabriele, Sylvain","last_name":"Gabriele","first_name":"Sylvain"}],"month":"09","type":"journal_article"},{"publisher":"Springer Nature","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We thank all the members of our groups for discussions and support. We thank A. Menéndez, S. Usieto, M. Purciolas and E. Coderch for technical assistance. We thank G. Charras (London Centre for Nanotechnology, UK) and M. Sheetz (Columbia University, USA) for sharing cells used in this work. We thank J. Ivaska (University of Turku, Finland) for sharing integrin α5-GFP DNA plasmid. We thank P. Guillamat for technical advice and A. Labernardie for providing the microfluidic channels. We thank M. Gómez-González for sharing the 2D traction microscopy algorithm. Finally, we thank P. Guillamat, J. Abenza, G. Ceada, L. Faure, E. Dalaka, M. Matejčić, A. Beedle, I. Granero, O. Baguer, A. Albajar and N. Chahare for discussions. This paper was funded by the Generalitat de Catalunya (Grant Nos. AGAUR SGR-2017-01602 to X.T. and 2021 SGR 00523 to R.S. and the CERCA Programme and ICREA Academia awards to P.R.-C.), the Spanish Ministry for Science and Innovation MICCINN/FEDER (Grant Nos. PID2021-128635NB-I00, MCIN/AEI/10.13039/501100011033 and ERDF-EU A way of making Europe to X.T., PID2021-128674OB-I00 and CNS2022-135533 to R.S. and PID2019-110298GB-I00 to P.R.-C.), the European Research Council (Grant Nos. 101097753 to P.R.-C. and Adv-883739 to X.T.), Fundació la Marató de TV3 (Project Award 201903-30-31-32 to X.T.), the European Commission (Grant No. H2020-FETPROACT-01-2016-731957 to P.R.-C. and X.T.) and La Caixa Foundation (Grant No. LCF/PR/HR20/52400004 to P.R.-C. and X.T.). R.S. is a Serra-Hunter fellow. D.B.B. was supported by the NOMIS foundation as a NOMIS fellow, by the European Molecular Biology Organization (Postdoctoral Fellowship ALTF 343-2022) and by the Austrian Academy of Sciences through an APART-MINT Fellowship. I.C.F. acknowledges support from the European Foundation for the Study of Chronic Liver Failure. IBEC is recipient of a Severo Ochoa Award of Excellence from MINECO.","abstract":[{"lang":"eng","text":"Haptotaxis is the process of directed cell migration along gradients of extracellular matrix density and is central to morphogenesis, immune responses and cancer invasion. It is commonly assumed that cells respond to these gradients by migrating directionally towards the regions of highest ligand density. In contrast with this view, here we show that cells exposed to micropatterned fibronectin gradients exhibit a wide range of complex trajectories, including directed haptotactic migration up the gradient but also linear oscillations and circles with extended periods of migration down the gradient. To explain this behaviour, we developed a biophysical model of haptotactic cell migration based on a coarse-grained molecular clutch model coupled to persistent stochastic polarity dynamics. Although initial haptotactic migration is explained by the differential friction at the front and back of the cell, the observed complex trajectories over longer timescales arise from the interplay between differential friction, persistence and physical confinement. Overall, our study reveals that confinement and persistence modulate the ability of cells to sense and respond to haptotactic cues and provides a framework for understanding how cells navigate complex environments."}],"corr_author":"1","isi":1,"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"}],"external_id":{"isi":["001581659900001"]},"year":"2025","volume":21,"oa_version":"Preprint","language":[{"iso":"eng"}],"intvolume":"        21","department":[{"_id":"EdHa"}],"date_updated":"2026-01-05T14:26:28Z","status":"public","article_processing_charge":"No","_id":"20431","page":"1638-1647","doi":"10.1038/s41567-025-03015-3","citation":{"short":"I.C. Fortunato, D. Brückner, S. Grosser, R. Nautiyal, L. Rossetti, M. Bosch-Padrós, J. Trebicka, P. Roca-Cusachs, R. Sunyer, E.B. Hannezo, X. Trepat, Nature Physics 21 (2025) 1638–1647.","chicago":"Fortunato, Isabela Corina, David Brückner, Steffen Grosser, Rohit Nautiyal, Leone Rossetti, Miquel Bosch-Padrós, Jonel Trebicka, et al. “Single-Cell Migration along and against Confined Haptotactic Gradients.” <i>Nature Physics</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41567-025-03015-3\">https://doi.org/10.1038/s41567-025-03015-3</a>.","ieee":"I. C. Fortunato <i>et al.</i>, “Single-cell migration along and against confined haptotactic gradients,” <i>Nature Physics</i>, vol. 21. Springer Nature, pp. 1638–1647, 2025.","mla":"Fortunato, Isabela Corina, et al. “Single-Cell Migration along and against Confined Haptotactic Gradients.” <i>Nature Physics</i>, vol. 21, Springer Nature, 2025, pp. 1638–47, doi:<a href=\"https://doi.org/10.1038/s41567-025-03015-3\">10.1038/s41567-025-03015-3</a>.","apa":"Fortunato, I. C., Brückner, D., Grosser, S., Nautiyal, R., Rossetti, L., Bosch-Padrós, M., … Trepat, X. (2025). Single-cell migration along and against confined haptotactic gradients. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-025-03015-3\">https://doi.org/10.1038/s41567-025-03015-3</a>","ista":"Fortunato IC, Brückner D, Grosser S, Nautiyal R, Rossetti L, Bosch-Padrós M, Trebicka J, Roca-Cusachs P, Sunyer R, Hannezo EB, Trepat X. 2025. Single-cell migration along and against confined haptotactic gradients. Nature Physics. 21, 1638–1647.","ama":"Fortunato IC, Brückner D, Grosser S, et al. Single-cell migration along and against confined haptotactic gradients. <i>Nature Physics</i>. 2025;21:1638-1647. doi:<a href=\"https://doi.org/10.1038/s41567-025-03015-3\">10.1038/s41567-025-03015-3</a>"},"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"publication":"Nature Physics","title":"Single-cell migration along and against confined haptotactic gradients","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.12.02.626413"}],"quality_controlled":"1","scopus_import":"1","article_type":"original","date_published":"2025-10-01T00:00:00Z","publication_status":"published","fulldoi":"https://doi.org/10.1038/s41567-025-03015-3","OA_type":"green","day":"01","OA_place":"repository","type":"journal_article","date_created":"2025-10-05T22:01:36Z","month":"10","author":[{"full_name":"Fortunato, Isabela Corina","last_name":"Fortunato","first_name":"Isabela Corina"},{"orcid":"0000-0001-7205-2975","first_name":"David","last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David"},{"last_name":"Grosser","first_name":"Steffen","full_name":"Grosser, Steffen"},{"last_name":"Nautiyal","first_name":"Rohit","full_name":"Nautiyal, Rohit"},{"full_name":"Rossetti, Leone","last_name":"Rossetti","first_name":"Leone"},{"full_name":"Bosch-Padrós, Miquel","first_name":"Miquel","last_name":"Bosch-Padrós"},{"full_name":"Trebicka, Jonel","first_name":"Jonel","last_name":"Trebicka"},{"full_name":"Roca-Cusachs, Pere","first_name":"Pere","last_name":"Roca-Cusachs"},{"full_name":"Sunyer, Raimon","last_name":"Sunyer","first_name":"Raimon"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561"},{"full_name":"Trepat, Xavier","first_name":"Xavier","last_name":"Trepat"}]},{"issue":"4","pmid":1,"quality_controlled":"1","citation":{"short":"D. Brückner, E.B. Hannezo, Cold Spring Harbor Perspectives in Biology 17 (2025).","chicago":"Brückner, David, and Edouard B Hannezo. “Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press, 2025. <a href=\"https://doi.org/10.1101/cshperspect.a041653\">https://doi.org/10.1101/cshperspect.a041653</a>.","ieee":"D. Brückner and E. B. Hannezo, “Tissue active matter: Integrating mechanics and signaling into dynamical models,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 17, no. 4. Cold Spring Harbor Laboratory Press, 2025.","mla":"Brückner, David, and Edouard B. Hannezo. “Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 17, no. 4, a041653, Cold Spring Harbor Laboratory Press, 2025, doi:<a href=\"https://doi.org/10.1101/cshperspect.a041653\">10.1101/cshperspect.a041653</a>.","ista":"Brückner D, Hannezo EB. 2025. Tissue active matter: Integrating mechanics and signaling into dynamical models. Cold Spring Harbor Perspectives in Biology. 17(4), a041653.","ama":"Brückner D, Hannezo EB. Tissue active matter: Integrating mechanics and signaling into dynamical models. <i>Cold Spring Harbor Perspectives in Biology</i>. 2025;17(4). doi:<a href=\"https://doi.org/10.1101/cshperspect.a041653\">10.1101/cshperspect.a041653</a>","apa":"Brückner, D., &#38; Hannezo, E. B. (2025). Tissue active matter: Integrating mechanics and signaling into dynamical models. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/cshperspect.a041653\">https://doi.org/10.1101/cshperspect.a041653</a>"},"publication_identifier":{"issn":["1943-0264"]},"doi":"10.1101/cshperspect.a041653","title":"Tissue active matter: Integrating mechanics and signaling into dynamical models","publication":"Cold Spring Harbor Perspectives in Biology","type":"journal_article","ec_funded":1,"author":[{"full_name":"Brückner, David","orcid":"0000-0001-7205-2975","first_name":"David","last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","last_name":"Hannezo"}],"article_number":"a041653","month":"04","date_created":"2025-01-29T13:33:47Z","OA_type":"closed access","day":"01","fulldoi":"https://doi.org/10.1101/cshperspect.a041653","date_published":"2025-04-01T00:00:00Z","publication_status":"published","article_type":"original","scopus_import":"1","das_tickbox":"0","acknowledgement":"We thank Fridtjof Brauns, Anna Kicheva, and Carl-Philipp Heisenberg for a critical reading of the manuscript and Claudia Flandoli for the artwork in the figures. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). This work received funding from the European Research Council (ERC) under the European Union\\u2019s Horizon 2020 Research and Innovation Programme Grant Agreement no. 851288.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Cold Spring Harbor Laboratory Press","supplementarymaterial":"no","department":[{"_id":"EdHa"}],"intvolume":"        17","_id":"18960","article_processing_charge":"No","date_updated":"2026-10-01T11:03:02Z","status":"public","isi":1,"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"},{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"abstract":[{"lang":"eng","text":"The importance of physical forces in the morphogenesis, homeostatic function, and pathological dysfunction of multicellular tissues is being increasingly characterized, both theoretically and experimentally. Analogies between biological systems and inert materials such as foams, gels, and liquid crystals have provided striking insights into the core design principles underlying multicellular organization. However, these connections can seem surprising given that a key feature of multicellular systems is their ability to constantly consume energy, providing an active origin for the forces that they produce. Key emerging questions are, therefore, to understand whether and how this activity grants tissues novel properties that do not have counterparts in classical materials, as well as their consequences for biological function. Here, we review recent discoveries at the intersection of active matter and tissue biology, with an emphasis on how modeling and experiments can be combined to understand the dynamics of multicellular systems. These approaches suggest that a number of key biological tissue-scale phenomena, such as morphogenetic shape changes, collective migration, or fate decisions, share unifying design principles that can be described by physical models of tissue active matter."}],"corr_author":"1","language":[{"iso":"eng"}],"oa_version":"None","volume":17,"researchdata_availability":"no","year":"2025","external_id":{"pmid":["38951023"],"isi":["001456660400001"]}},{"acknowledgement":"We are grateful to the colleagues who contributed to this work with discussions, technical advice, and feedback on the manuscript: Irene Steccari, David Labrousse Arias and the other members of the Heisenberg lab, Nicole Amberg, Florian Pauler, Nicoletta Petridou, Elena Scarpa, and Edouard Hannezo. We also thank the Imaging and Optics Facility, the Life Science Facility, and the Scientific Computing Unit at ISTA for support. The Next Generation Sequencing Facility at Vienna BioCenter Core Facilities performed the RNA-seq for animal and lateral ectoderm. D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). S. Tavano was supported by an EMBO Postdoctoral Fellowship (ALTF 1159-2018).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"oa":1,"has_accepted_license":"1","publisher":"Cell Press","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"Bio"}],"intvolume":"        44","_id":"19404","article_processing_charge":"Yes","status":"public","date_updated":"2026-10-20T08:20:45Z","project":[{"grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"},{"grant_number":"ALTF 1159-2018","name":"Mechanosensation in cell migration: the role of friction forces in cell polarization and directed migration","_id":"269CD5C4-B435-11E9-9278-68D0E5697425"}],"isi":1,"file":[{"relation":"main_file","access_level":"open_access","checksum":"57e05dd1598c807af0afdb32cec039d3","file_id":"19413","content_type":"application/pdf","success":1,"file_size":9067797,"file_name":"2025_CellReports_Tavano.pdf","date_created":"2025-03-17T10:26:54Z","date_updated":"2025-03-17T10:26:54Z","creator":"dernst"}],"abstract":[{"lang":"eng","text":"Cell migration is a fundamental process during embryonic development. Most studies in vivo have focused on the migration of cells using the extracellular matrix (ECM) as their substrate for migration. In contrast, much less is known about how cells migrate on other cells, as found in early embryos when the ECM has not yet formed. Here, we show that lateral mesendoderm (LME) cells in the early zebrafish gastrula use the ectoderm as their substrate for migration. We show that the lateral ectoderm is permissive for the animal-pole-directed migration of LME cells, while the ectoderm at the animal pole halts it. These differences in permissiveness depend on the lateral ectoderm being more cohesive than the animal ectoderm, a property controlled by bone morphogenetic protein (BMP) signaling within the ectoderm. Collectively, these findings identify ectoderm tissue cohesion as one critical factor in regulating LME migration during zebrafish gastrulation."}],"corr_author":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","volume":44,"year":"2025","external_id":{"pmid":["40057955"],"isi":["001443652700001"]},"issue":"3","pmid":1,"quality_controlled":"1","publication_identifier":{"eissn":["2211-1247"],"issn":["2639-1856"]},"citation":{"ieee":"S. Tavano <i>et al.</i>, “BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation,” <i>Cell Reports</i>, vol. 44, no. 3. Cell Press, 2025.","ama":"Tavano S, Brückner D, Tasciyan S, et al. BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. <i>Cell Reports</i>. 2025;44(3). doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">10.1016/j.celrep.2025.115387</a>","ista":"Tavano S, Brückner D, Tasciyan S, Tong X, Kardos R, Schauer A, Hauschild R, Heisenberg C-PJ. 2025. BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. Cell Reports. 44(3), 115387.","apa":"Tavano, S., Brückner, D., Tasciyan, S., Tong, X., Kardos, R., Schauer, A., … Heisenberg, C.-P. J. (2025). BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">https://doi.org/10.1016/j.celrep.2025.115387</a>","mla":"Tavano, Ste, et al. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.” <i>Cell Reports</i>, vol. 44, no. 3, 115387, Cell Press, 2025, doi:<a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">10.1016/j.celrep.2025.115387</a>.","short":"S. Tavano, D. Brückner, S. Tasciyan, X. Tong, R. Kardos, A. Schauer, R. Hauschild, C.-P.J. Heisenberg, Cell Reports 44 (2025).","chicago":"Tavano, Ste, David Brückner, Saren Tasciyan, Xin Tong, Roland Kardos, Alexandra Schauer, Robert Hauschild, and Carl-Philipp J Heisenberg. “BMP-Dependent Patterning of Ectoderm Tissue Material Properties Modulates Lateral Mesendoderm Cell Migration during Early Zebrafish Gastrulation.” <i>Cell Reports</i>. Cell Press, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">https://doi.org/10.1016/j.celrep.2025.115387</a>."},"doi":"10.1016/j.celrep.2025.115387","title":"BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication":"Cell Reports","DOAJ_listed":"1","type":"journal_article","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"author":[{"last_name":"Tavano","id":"2F162F0C-F248-11E8-B48F-1D18A9856A87","first_name":"Ste","orcid":"0000-0001-9970-7804","full_name":"Tavano, Ste"},{"full_name":"Brückner, David","orcid":"0000-0001-7205-2975","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner"},{"full_name":"Tasciyan, Saren","orcid":"0000-0003-1671-393X","first_name":"Saren","last_name":"Tasciyan","id":"4323B49C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tong","id":"50F65CDC-AA30-11E9-A72B-8A12E6697425","first_name":"Xin","full_name":"Tong, Xin"},{"first_name":"Roland","last_name":"Kardos","id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland"},{"id":"30A536BA-F248-11E8-B48F-1D18A9856A87","last_name":"Schauer","orcid":"0000-0001-7659-9142","first_name":"Alexandra","full_name":"Schauer, Alexandra"},{"full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J"}],"month":"03","article_number":"115387","date_created":"2025-03-16T23:01:24Z","day":"25","OA_type":"gold","fulldoi":"https://doi.org/10.1016/j.celrep.2025.115387","date_published":"2025-03-25T00:00:00Z","article_type":"original","publication_status":"published","file_date_updated":"2025-03-17T10:26:54Z","scopus_import":"1","OA_place":"publisher"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png"},"type":"journal_article","date_created":"2024-04-14T22:01:01Z","author":[{"full_name":"Brückner, David","last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","orcid":"0000-0001-7205-2975"},{"last_name":"Broedersz","first_name":"Chase P.","full_name":"Broedersz, Chase P."}],"article_number":"056601","month":"04","date_published":"2024-04-04T00:00:00Z","file_date_updated":"2024-08-20T11:00:03Z","publication_status":"published","article_type":"review","scopus_import":"1","day":"04","fulldoi":"https://doi.org/10.1088/1361-6633/ad36d2","das_tickbox":"1","pmid":1,"quality_controlled":"1","issue":"5","doi":"10.1088/1361-6633/ad36d2","citation":{"mla":"Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of Single and Collective Cell Migration: A Review.” <i>Reports on Progress in Physics</i>, vol. 87, no. 5, 056601, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.1088/1361-6633/ad36d2\">10.1088/1361-6633/ad36d2</a>.","ista":"Brückner D, Broedersz CP. 2024. Learning dynamical models of single and collective cell migration: a review. Reports on Progress in Physics. 87(5), 056601.","apa":"Brückner, D., &#38; Broedersz, C. P. (2024). Learning dynamical models of single and collective cell migration: a review. <i>Reports on Progress in Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6633/ad36d2\">https://doi.org/10.1088/1361-6633/ad36d2</a>","ama":"Brückner D, Broedersz CP. Learning dynamical models of single and collective cell migration: a review. <i>Reports on Progress in Physics</i>. 2024;87(5). doi:<a href=\"https://doi.org/10.1088/1361-6633/ad36d2\">10.1088/1361-6633/ad36d2</a>","ieee":"D. Brückner and C. P. Broedersz, “Learning dynamical models of single and collective cell migration: a review,” <i>Reports on Progress in Physics</i>, vol. 87, no. 5. IOP Publishing, 2024.","chicago":"Brückner, David, and Chase P. Broedersz. “Learning Dynamical Models of Single and Collective Cell Migration: A Review.” <i>Reports on Progress in Physics</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.1088/1361-6633/ad36d2\">https://doi.org/10.1088/1361-6633/ad36d2</a>.","short":"D. Brückner, C.P. Broedersz, Reports on Progress in Physics 87 (2024)."},"publication_identifier":{"issn":["0034-4885"],"eissn":["1361-6633"]},"arxiv":1,"publication":"Reports on Progress in Physics","license":"https://creativecommons.org/licenses/by/3.0/","title":"Learning dynamical models of single and collective cell migration: a review","intvolume":"        87","department":[{"_id":"EdHa"}],"article_processing_charge":"Yes (in subscription journal)","date_updated":"2026-10-01T10:09:41Z","status":"public","_id":"15315","file":[{"creator":"dernst","date_updated":"2024-08-20T11:00:03Z","date_created":"2024-08-20T11:00:03Z","file_name":"2024_ReportPhysics_Brueckner.pdf","file_size":4376898,"success":1,"content_type":"application/pdf","file_id":"17451","checksum":"c5910078230ade20f4dd83592e862a72","access_level":"open_access","relation":"main_file"}],"abstract":[{"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.","lang":"eng"}],"dataavailabilitystatement":"No new data were created or analysed in this study.","corr_author":"1","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"}],"isi":1,"year":"2024","researchdata_availability":"not applicable","volume":87,"external_id":{"isi":["001196692400001"],"arxiv":["2309.00545"],"pmid":["38518358"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","ddc":["530"],"oa":1,"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.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"IOP Publishing","has_accepted_license":"1","supplementarymaterial":"no"},{"project":[{"grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"isi":1,"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."}],"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).","file":[{"file_name":"2024_PNAS_Brueckner.pdf","file_size":12329234,"success":1,"creator":"dernst","date_updated":"2024-06-10T10:27:37Z","date_created":"2024-06-10T10:27:37Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"17130","checksum":"59797a75db7beb3721ed7a4d14c241f9"}],"oa_version":"Published Version","language":[{"iso":"eng"}],"external_id":{"isi":["001244835000006"],"pmid":["38819997"]},"year":"2024","volume":121,"researchdata_availability":"not applicable","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"intvolume":"       121","_id":"17123","date_updated":"2026-10-01T11:03:59Z","related_material":{"link":[{"url":"https://github.com/dbrueckner/SelforgInformation","relation":"software"},{"relation":"press_release","url":"https://ista.ac.at/en/news/the-embryo-assembles-itself/","description":"News on the ISTA website"}]},"status":"public","article_processing_charge":"Yes (in subscription journal)","supplementarymaterial":"yes","publisher":"National Academy of Sciences","has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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.","oa":1,"ddc":["570"],"fulldoi":"https://doi.org/10.1073/pnas.2322326121","day":"04","OA_type":"hybrid","scopus_import":"1","article_type":"original","publication_status":"published","date_published":"2024-06-04T00:00:00Z","file_date_updated":"2024-06-10T10:27:37Z","das_tickbox":"1","OA_place":"publisher","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"type":"journal_article","article_number":"e2322326121","month":"06","author":[{"full_name":"Brückner, David","last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","orcid":"0000-0001-7205-2975"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2024-06-09T22:01:02Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"citation":{"chicago":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2322326121\">https://doi.org/10.1073/pnas.2322326121</a>.","short":"D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","mla":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 23, e2322326121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2322326121\">10.1073/pnas.2322326121</a>.","apa":"Brückner, D., &#38; Tkačik, G. (2024). Information content and optimization of self-organized developmental systems. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2322326121\">https://doi.org/10.1073/pnas.2322326121</a>","ista":"Brückner D, Tkačik G. 2024. Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America. 121(23), e2322326121.","ama":"Brückner D, Tkačik G. Information content and optimization of self-organized developmental systems. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(23). doi:<a href=\"https://doi.org/10.1073/pnas.2322326121\">10.1073/pnas.2322326121</a>","ieee":"D. Brückner and G. Tkačik, “Information content and optimization of self-organized developmental systems,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 23. National Academy of Sciences, 2024."},"doi":"10.1073/pnas.2322326121","title":"Information content and optimization of self-organized developmental systems","APC_amount":"2570,79 EUR","publication":"Proceedings of the National Academy of Sciences of the United States of America","issue":"23","quality_controlled":"1","pmid":1},{"publication":"Nature Physics","title":"Geometry-driven migration efficiency of autonomous epithelial cell clusters","main_file_link":[{"url":"https://doi.org/10.1101/2022.07.17.500364","open_access":"1"}],"doi":"10.1038/s41567-024-02532-x","citation":{"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.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-024-02532-x\">https://doi.org/10.1038/s41567-024-02532-x</a>.","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.","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. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02532-x\">https://doi.org/10.1038/s41567-024-02532-x</a>","ama":"Vercruysse E, Brückner D, Gómez-González M, et al. Geometry-driven migration efficiency of autonomous epithelial cell clusters. <i>Nature Physics</i>. 2024;20:1492-1500. doi:<a href=\"https://doi.org/10.1038/s41567-024-02532-x\">10.1038/s41567-024-02532-x</a>","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.","mla":"Vercruysse, Eléonore, et al. “Geometry-Driven Migration Efficiency of Autonomous Epithelial Cell Clusters.” <i>Nature Physics</i>, vol. 20, Springer Nature, 2024, pp. 1492–500, doi:<a href=\"https://doi.org/10.1038/s41567-024-02532-x\">10.1038/s41567-024-02532-x</a>.","ieee":"E. Vercruysse <i>et al.</i>, “Geometry-driven migration efficiency of autonomous epithelial cell clusters,” <i>Nature Physics</i>, vol. 20. Springer Nature, pp. 1492–1500, 2024."},"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"quality_controlled":"1","OA_place":"repository","das_tickbox":"1","publication_status":"published","article_type":"original","date_published":"2024-09-01T00:00:00Z","scopus_import":"1","day":"01","OA_type":"green","fulldoi":"https://doi.org/10.1038/s41567-024-02532-x","date_created":"2024-07-16T12:32:17Z","author":[{"last_name":"Vercruysse","first_name":"Eléonore","full_name":"Vercruysse, Eléonore"},{"orcid":"0000-0001-7205-2975","first_name":"David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","full_name":"Brückner, David"},{"last_name":"Gómez-González","first_name":"Manuel","full_name":"Gómez-González, Manuel"},{"first_name":"Alexandre","last_name":"Remson","full_name":"Remson, Alexandre"},{"full_name":"Luciano, Marine","first_name":"Marine","last_name":"Luciano"},{"first_name":"Yohalie","last_name":"Kalukula","full_name":"Kalukula, Yohalie"},{"full_name":"Rossetti, Leone","first_name":"Leone","last_name":"Rossetti"},{"first_name":"Xavier","last_name":"Trepat","full_name":"Trepat, Xavier"},{"orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"full_name":"Gabriele, Sylvain","first_name":"Sylvain","last_name":"Gabriele"}],"month":"09","ec_funded":1,"type":"journal_article","publisher":"Springer Nature","supplementarymaterial":"yes","oa":1,"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.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","year":"2024","volume":20,"researchdata_availability":"yes","external_id":{"isi":["001250246200004"]},"language":[{"iso":"eng"}],"oa_version":"Preprint","dataavailabilitystatement":"All data are available from the corresponding authors upon request. Source data are provided with this paper.","corr_author":"1","abstract":[{"lang":"eng","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."}],"isi":1,"project":[{"grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"ALTF 343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"article_processing_charge":"No","related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/a-railroad-of-cells/","description":"News on ISTA website"}]},"status":"public","date_updated":"2026-10-01T11:02:43Z","page":"1492-1500","_id":"17269","intvolume":"        20","department":[{"_id":"EdHa"}]},{"quality_controlled":"1","issue":"6652","doi":"10.1126/science.adf5568","citation":{"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,” <i>Science</i>, vol. 380, no. 6652. American Association for the Advancement of Science, pp. 1357–1362, 2023.","mla":"Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>, vol. 380, no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62, doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>.","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.","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. <i>Science</i>. 2023;380(6652):1357-1362. doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>","apa":"Brückner, D., Chen, H., Barinov, L., Zoller, B., &#38; Gregor, T. (2023). Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>","short":"D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023) 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.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>."},"publication_identifier":{"eissn":["1095-9203"]},"publication":"Science","title":"Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.adf5568"}],"type":"journal_article","date_created":"2023-07-23T22:01:12Z","month":"06","author":[{"full_name":"Brückner, David","first_name":"David","orcid":"0000-0001-7205-2975","last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"full_name":"Chen, Hongtao","last_name":"Chen","first_name":"Hongtao"},{"last_name":"Barinov","first_name":"Lev","full_name":"Barinov, Lev"},{"first_name":"Benjamin","last_name":"Zoller","full_name":"Zoller, Benjamin"},{"full_name":"Gregor, Thomas","first_name":"Thomas","last_name":"Gregor"}],"scopus_import":"1","date_published":"2023-06-29T00:00:00Z","publication_status":"published","article_type":"original","fulldoi":"https://doi.org/10.1126/science.adf5568","day":"29","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","publisher":"American Association for the Advancement of Science","intvolume":"       380","department":[{"_id":"EdHa"}],"status":"public","date_updated":"2025-04-14T08:55:54Z","article_processing_charge":"No","_id":"13261","page":"1357-1362","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."}],"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"}],"isi":1,"external_id":{"isi":["001106405600028"]},"year":"2023","volume":380,"oa_version":"Preprint","language":[{"iso":"eng"}]},{"scopus_import":"1","publication_status":"published","date_published":"2023-12-27T00:00:00Z","article_type":"original","fulldoi":"https://doi.org/10.1242/jcs.261515","day":"27","date_created":"2024-01-17T12:46:55Z","month":"12","article_number":"jcs.261515","author":[{"full_name":"Schwayer, Cornelia","first_name":"Cornelia","orcid":"0000-0001-5130-2226","last_name":"Schwayer","id":"3436488C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","first_name":"David","full_name":"Brückner, David"}],"type":"journal_article","publication":"Journal of Cell Science","title":"Connecting theory and experiment in cell and tissue mechanics","doi":"10.1242/jcs.261515","publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"citation":{"ieee":"C. Schwayer and D. Brückner, “Connecting theory and experiment in cell and tissue mechanics,” <i>Journal of Cell Science</i>, vol. 136, no. 24. The Company of Biologists, 2023.","ista":"Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. 136(24), jcs. 261515.","apa":"Schwayer, C., &#38; Brückner, D. (2023). Connecting theory and experiment in cell and tissue mechanics. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261515\">https://doi.org/10.1242/jcs.261515</a>","ama":"Schwayer C, Brückner D. Connecting theory and experiment in cell and tissue mechanics. <i>Journal of Cell Science</i>. 2023;136(24). doi:<a href=\"https://doi.org/10.1242/jcs.261515\">10.1242/jcs.261515</a>","mla":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” <i>Journal of Cell Science</i>, vol. 136, no. 24, jcs. 261515, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.261515\">10.1242/jcs.261515</a>.","short":"C. Schwayer, D. Brückner, Journal of Cell Science 136 (2023).","chicago":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.261515\">https://doi.org/10.1242/jcs.261515</a>."},"quality_controlled":"1","pmid":1,"issue":"24","keyword":["Cell Biology"],"external_id":{"isi":["001165394900011"],"pmid":["38149871"]},"volume":136,"year":"2023","oa_version":"None","language":[{"iso":"eng"}],"corr_author":"1","abstract":[{"lang":"eng","text":"Understanding complex living systems, which are fundamentally constrained by physical phenomena, requires combining experimental data with theoretical physical and mathematical models. To develop such models, collaborations between experimental cell biologists and theoreticians are increasingly important but these two groups often face challenges achieving mutual understanding. To help navigate these challenges, this Perspective discusses different modelling approaches, including bottom-up hypothesis-driven and top-down data-driven models, and highlights their strengths and applications. Using cell mechanics as an example, we explore the integration of specific physical models with experimental data from the molecular, cellular and tissue level up to multiscale input. We also emphasize the importance of constraining model complexity and outline strategies for crosstalk between experimental design and model development. Furthermore, we highlight how physical models can provide conceptual insights and produce unifying and generalizable frameworks for biological phenomena. Overall, this Perspective aims to promote fruitful collaborations that advance our understanding of complex biological systems."}],"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"}],"isi":1,"status":"public","date_updated":"2025-09-09T14:22:02Z","article_processing_charge":"No","_id":"14827","intvolume":"       136","department":[{"_id":"EdHa"},{"_id":"CaHe"}],"publisher":"The Company of Biologists","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We thank Prisca Liberali and Edouard Hannezo for many inspiring discussions; Mehmet Can Uçar, Nicoletta I Petridou and Qiutan Yang for a critical reading of the manuscript, and Claudia Flandoli for the artwork in Figs 2 and 3. We would also like to thank The Company of Biologists for the opportunity to attend the 2023 workshop on Collective Cell Migration, and all workshop participants for discussions.\r\nC.S. was supported by a European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 660-2020) and Human Frontier Science Program (HFSP) Postdoctoral fellowship (LT000746/2021-L). D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022)."}]