[{"doi":"10.1103/fdcf-dkws","article_number":"017001","language":[{"iso":"eng"}],"abstract":[{"text":"Developmental patterning comprises processes that range from purely instructed, where external signals specify cell fates, to fully self-organized, where spatial patterns emerge autonomously through cellular interactions. We propose that both extremes—as well as the continuum of intermediate cases—can be conceptualized as information-processing systems, whose operation can be described using “Marr's three levels of analysis”: the computational problem being solved, the algorithms employed, and their molecular implementation. At the first level, we argue that normative theories, such as information-theoretic optimization principles, provide a formalization of the computational problem. At the second level, we show how simplified information-processing architectures provide a framework for developmental algorithms, which are formalized mathematically using dynamical systems theory. At the third level, the implementation of developmental algorithms is described by mechanistic biophysical and gene regulatory network models.","lang":"eng"}],"OA_place":"publisher","_id":"21282","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"author":[{"orcid":"0000-0001-7205-2975","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","last_name":"Brückner"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-02-24T07:00:16Z","arxiv":1,"fulldoi":"https://doi.org/10.1103/fdcf-dkws","publisher":"American Physical Society","oa_version":"Published Version","day":"23","volume":4,"oa":1,"external_id":{"arxiv":["2510.24536"]},"month":"01","date_published":"2026-01-23T00:00:00Z","acknowledgement":"We thank Edouard Hannezo, Anna Kicheva, Fridtjof Brauns, and all members of the Brückner and Tkačik groups for feedback and inspiring discussions. This work was supported in part by European Research Council ERC-2023-SyG “Dynatrans” Grant No. 101118866 (G.T.). This work was conducted while visiting the Okinawa Institute of Science and Technology (OIST) through the Theoretical Sciences Visiting Program (TSVP); at the 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; and at Lucullus, Vienna.","department":[{"_id":"GaTk"}],"DOAJ_listed":"1","ddc":["570"],"title":"Marr's three levels for embryonic development: Information, dynamical systems, gene networks","file_date_updated":"2026-02-24T06:57:44Z","corr_author":"1","article_type":"original","year":"2026","article_processing_charge":"Yes","date_created":"2026-02-17T08:29:10Z","publication_status":"published","publication_identifier":{"eissn":["2835-8279"]},"file":[{"file_size":1147994,"date_updated":"2026-02-24T06:57:44Z","content_type":"application/pdf","date_created":"2026-02-24T06:57:44Z","access_level":"open_access","relation":"main_file","file_name":"2026_PRXLife_Brueckner.pdf","checksum":"99ef02dd741c4536eeefd12d409d5269","file_id":"21352","success":1,"creator":"dernst"}],"has_accepted_license":"1","intvolume":"         4","OA_type":"gold","publication":"PRX Life","quality_controlled":"1","project":[{"grant_number":"101118866","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9"}],"type":"journal_article","PlanS_conform":"1","status":"public","citation":{"mla":"Brückner, David, and Gašper Tkačik. “Marr’s Three Levels for Embryonic Development: Information, Dynamical Systems, Gene Networks.” <i>PRX Life</i>, vol. 4, 017001, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/fdcf-dkws\">10.1103/fdcf-dkws</a>.","ista":"Brückner D, Tkačik G. 2026. Marr’s three levels for embryonic development: Information, dynamical systems, gene networks. PRX Life. 4, 017001.","ieee":"D. Brückner and G. Tkačik, “Marr’s three levels for embryonic development: Information, dynamical systems, gene networks,” <i>PRX Life</i>, vol. 4. American Physical Society, 2026.","ama":"Brückner D, Tkačik G. Marr’s three levels for embryonic development: Information, dynamical systems, gene networks. <i>PRX Life</i>. 2026;4. doi:<a href=\"https://doi.org/10.1103/fdcf-dkws\">10.1103/fdcf-dkws</a>","apa":"Brückner, D., &#38; Tkačik, G. (2026). Marr’s three levels for embryonic development: Information, dynamical systems, gene networks. <i>PRX Life</i>. American Physical Society. <a href=\"https://doi.org/10.1103/fdcf-dkws\">https://doi.org/10.1103/fdcf-dkws</a>","short":"D. Brückner, G. Tkačik, PRX Life 4 (2026).","chicago":"Brückner, David, and Gašper Tkačik. “Marr’s Three Levels for Embryonic Development: Information, Dynamical Systems, Gene Networks.” <i>PRX Life</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/fdcf-dkws\">https://doi.org/10.1103/fdcf-dkws</a>."}},{"volume":137,"oa":1,"dataavailabilitystatement":"Code to evaluate PI, to run algorithmic implementations of ALP and RLP decoding, and to\r\nperform simulations is publicly available at https://github.com/alex-chenyi-zhang/nonlocdec_pici.","publisher":"American Physical Society","fulldoi":"https://doi.org/10.1103/mbjk-v4ym","das_tickbox":"1","day":"15","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"22326","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"author":[{"first_name":"Chen Y","id":"81b43fb8-c9d5-11ef-bf68-ade532a1f204","full_name":"Zhang, Chen Y","last_name":"Zhang"},{"last_name":"Mateu Hoyos","first_name":"Pablo","full_name":"Mateu Hoyos, Pablo","id":"50b236c7-50c1-11ef-bb9a-a2375694f8b5"},{"first_name":"David","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","last_name":"Brückner"},{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"}],"date_updated":"2026-07-16T09:58:04Z","supplementarymaterial":"no","doi":"10.1103/mbjk-v4ym","OA_place":"publisher","language":[{"iso":"eng"}],"article_number":"038401","abstract":[{"lang":"eng","text":"In many developmental systems, cells differentiate into a tissue by reading out morphogen concentration fields, a process fundamentally limited by noise. How much can the precision of this process be improved by nonlocal information, e.g., via cell-cell communication? Using a Bayes-optimal framework, we show that positional inference depends crucially on morphogen spatial correlations and on the \"structural prior\" that encodes the geometry of the cellular lattice performing the readout, thereby determining what a cell can reliably assume about the position of its neighbors when interpreting nonlocal morphogen signals. We derive upper bounds on positional information gain due to nonlocal readout and identify signal processing algorithms that approximate optimal positional inference, as well as simple chemical reaction schemes which implement such algorithms. Our theory suggests that correlational information can be exploited to significantly enhance developmental precision."}],"researchdata_availability":"no","PlanS_conform":"1","type":"journal_article","citation":{"apa":"Zhang, C. Y., Mateu Hoyos, P., Brückner, D., &#38; Tkačik, G. (2026). Nonlocal decoding of positional and correlational information during development. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/mbjk-v4ym\">https://doi.org/10.1103/mbjk-v4ym</a>","ama":"Zhang CY, Mateu Hoyos P, Brückner D, Tkačik G. Nonlocal decoding of positional and correlational information during development. <i>Physical Review Letters</i>. 2026;137. doi:<a href=\"https://doi.org/10.1103/mbjk-v4ym\">10.1103/mbjk-v4ym</a>","ieee":"C. Y. Zhang, P. Mateu Hoyos, D. Brückner, and G. Tkačik, “Nonlocal decoding of positional and correlational information during development,” <i>Physical Review Letters</i>, vol. 137. American Physical Society, 2026.","ista":"Zhang CY, Mateu Hoyos P, Brückner D, Tkačik G. 2026. Nonlocal decoding of positional and correlational information during development. Physical Review Letters. 137, 038401.","mla":"Zhang, Chen Y., et al. “Nonlocal Decoding of Positional and Correlational Information during Development.” <i>Physical Review Letters</i>, vol. 137, 038401, American Physical Society, 2026, doi:<a href=\"https://doi.org/10.1103/mbjk-v4ym\">10.1103/mbjk-v4ym</a>.","chicago":"Zhang, Chen Y, Pablo Mateu Hoyos, David Brückner, and Gašper Tkačik. “Nonlocal Decoding of Positional and Correlational Information during Development.” <i>Physical Review Letters</i>. American Physical Society, 2026. <a href=\"https://doi.org/10.1103/mbjk-v4ym\">https://doi.org/10.1103/mbjk-v4ym</a>.","short":"C.Y. Zhang, P. Mateu Hoyos, D. Brückner, G. Tkačik, Physical Review Letters 137 (2026)."},"status":"public","OA_type":"hybrid","intvolume":"       137","has_accepted_license":"1","project":[{"name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9","grant_number":"101118866"}],"quality_controlled":"1","publication":"Physical Review Letters","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","file_date_updated":"2026-07-16T09:54:55Z","article_type":"original","corr_author":"1","year":"2026","date_created":"2026-07-14T05:38:28Z","publication_identifier":{"eissn":[" 1079-7114"],"issn":["0031-9007"]},"file":[{"creator":"dernst","success":1,"file_id":"22352","checksum":"28861d31d0f6cf541aaca04faaed1767","file_name":"2026_PhysicalReviewLetters_Zhang.pdf","relation":"main_file","date_created":"2026-07-16T09:54:55Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2026-07-16T09:54:55Z","file_size":2550345}],"publication_status":"published","month":"07","acknowledgement":"This work was supported in part\r\nby European Research Council No. ERC-2023-SyG\r\n“DynaTrans” Grant No. 101118866 (G. T.). We thank\r\nPieter Rein ten Wolde and Vahe Galstyan for stimulating\r\ndiscussions.","department":[{"_id":"GaTk"},{"_id":"EdHa"},{"_id":"GradSch"}],"ddc":["530"],"title":"Nonlocal decoding of positional and correlational information during development","date_published":"2026-07-15T00:00:00Z"},{"volume":3,"oa":1,"external_id":{"arxiv":["2407.17268"]},"publisher":"American Physical Society","fulldoi":"https://doi.org/10.1103/3hhj-rt1n","day":"26","oa_version":"Published Version","_id":"21236","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"author":[{"full_name":"Brandstätter, Tom","first_name":"Tom","last_name":"Brandstätter"},{"first_name":"Emily","full_name":"Brieger, Emily","last_name":"Brieger"},{"last_name":"Brückner","orcid":"0000-0001-7205-2975","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David"},{"first_name":"Georg","full_name":"Ladurner, Georg","last_name":"Ladurner"},{"full_name":"Rädler, Joachim O.","first_name":"Joachim O.","last_name":"Rädler"},{"full_name":"Broedersz, Chase P.","first_name":"Chase P.","last_name":"Broedersz"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"date_updated":"2026-02-17T11:20:20Z","doi":"10.1103/3hhj-rt1n","language":[{"iso":"eng"}],"article_number":"033015","abstract":[{"text":"The migration behavior of colliding cells is critically determined by transient contact interactions. During these interactions, the motility machinery, including the front-rear polarization of the cell, dynamically responds to surface protein-mediated transmission of forces and biochemical signals between cells. While biomolecular details of such contact interactions are increasingly well understood, it remains unclear what biophysical interaction mechanisms govern the cell-level dynamics of colliding cells and how these mechanisms vary across cell types. Here we develop a phenomenological theory based on 14 candidate contact-interaction mechanisms coupling cell position, protrusion, and polarity. Using high-throughput micropattern experiments, we detect which of these phenomenological contact interactions captures the interaction behaviors of cells. We find that various cell types—ranging from mesenchymal to epithelial cells—are accurately captured by a single model with only two interaction mechanisms: polarity-protrusion coupling and polarity-polarity coupling. Remarkably, the qualitatively different interaction behaviors of distinct cells, as well as cells subject to molecular perturbations of surface protein-mediated signaling, can all be quantitatively captured by varying the strength and sign of the polarity-polarity coupling mechanism. Altogether, our data-driven phenomenological theory of cell-cell interactions reveals polarity-polarity coupling as a versatile and general contact-interaction mechanism, which may underlie diverse collective migration behaviors of motile cells.","lang":"eng"}],"OA_place":"publisher","type":"journal_article","PlanS_conform":"1","status":"public","citation":{"mla":"Brandstätter, Tom, et al. “Data-Driven Theory Reveals Protrusion and Polarity Interactions Governing Collision Behavior of Distinct Motile Cells.” <i>PRX Life</i>, vol. 3, no. 3, 033015, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/3hhj-rt1n\">10.1103/3hhj-rt1n</a>.","ista":"Brandstätter T, Brieger E, Brückner D, Ladurner G, Rädler JO, Broedersz CP. 2025. Data-driven theory reveals protrusion and polarity interactions governing collision behavior of distinct motile cells. PRX Life. 3(3), 033015.","ieee":"T. Brandstätter, E. Brieger, D. Brückner, G. Ladurner, J. O. Rädler, and C. P. Broedersz, “Data-driven theory reveals protrusion and polarity interactions governing collision behavior of distinct motile cells,” <i>PRX Life</i>, vol. 3, no. 3. American Physical Society, 2025.","ama":"Brandstätter T, Brieger E, Brückner D, Ladurner G, Rädler JO, Broedersz CP. Data-driven theory reveals protrusion and polarity interactions governing collision behavior of distinct motile cells. <i>PRX Life</i>. 2025;3(3). doi:<a href=\"https://doi.org/10.1103/3hhj-rt1n\">10.1103/3hhj-rt1n</a>","apa":"Brandstätter, T., Brieger, E., Brückner, D., Ladurner, G., Rädler, J. O., &#38; Broedersz, C. P. (2025). Data-driven theory reveals protrusion and polarity interactions governing collision behavior of distinct motile cells. <i>PRX Life</i>. American Physical Society. <a href=\"https://doi.org/10.1103/3hhj-rt1n\">https://doi.org/10.1103/3hhj-rt1n</a>","chicago":"Brandstätter, Tom, Emily Brieger, David Brückner, Georg Ladurner, Joachim O. Rädler, and Chase P. Broedersz. “Data-Driven Theory Reveals Protrusion and Polarity Interactions Governing Collision Behavior of Distinct Motile Cells.” <i>PRX Life</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/3hhj-rt1n\">https://doi.org/10.1103/3hhj-rt1n</a>.","short":"T. Brandstätter, E. Brieger, D. Brückner, G. Ladurner, J.O. Rädler, C.P. Broedersz, PRX Life 3 (2025)."},"has_accepted_license":"1","intvolume":"         3","OA_type":"gold","quality_controlled":"1","publication":"PRX Life","issue":"3","file_date_updated":"2026-02-17T11:18:18Z","article_type":"original","year":"2025","article_processing_charge":"Yes","date_created":"2026-02-16T14:52:02Z","publication_status":"published","file":[{"checksum":"70c067ceef3a8262d9c430e85e3ba9ec","file_id":"21288","success":1,"creator":"dernst","file_size":9366716,"access_level":"open_access","date_created":"2026-02-17T11:18:18Z","content_type":"application/pdf","date_updated":"2026-02-17T11:18:18Z","file_name":"2025_PRXLife_Brandstaetter.pdf","relation":"main_file"}],"publication_identifier":{"eissn":["2835-8279"]},"month":"08","date_published":"2025-08-26T00:00:00Z","DOAJ_listed":"1","acknowledgement":"We thank Johannes Flommersfeld, Bram Hoogland, and Ricard Alert for helpful discussions. We thank Gerlinde Schwake for producing the E-cadherin mRNA. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Project-ID 201269156 - SFB 1032 (Project B01 and B12).","department":[{"_id":"EdHa"}],"ddc":["570"],"title":"Data-driven theory reveals protrusion and polarity interactions governing collision behavior of distinct motile cells"},{"external_id":{"isi":["001456660400001"],"pmid":["38951023"]},"volume":17,"oa_version":"None","day":"01","fulldoi":"https://doi.org/10.1101/cshperspect.a041653","publisher":"Cold Spring Harbor Laboratory Press","date_updated":"2025-12-30T07:08:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18960","author":[{"first_name":"David","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","last_name":"Brückner"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo"}],"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."}],"language":[{"iso":"eng"}],"article_number":"a041653","doi":"10.1101/cshperspect.a041653","ec_funded":1,"citation":{"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.","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>.","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.","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>","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>."},"status":"public","type":"journal_article","isi":1,"scopus_import":"1","issue":"4","quality_controlled":"1","project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"ALTF 343-2022"},{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288"}],"publication":"Cold Spring Harbor Perspectives in Biology","OA_type":"closed access","intvolume":"        17","publication_status":"published","publication_identifier":{"issn":["1943-0264"]},"date_created":"2025-01-29T13:33:47Z","pmid":1,"article_processing_charge":"No","year":"2025","article_type":"original","corr_author":"1","title":"Tissue active matter: Integrating mechanics and signaling into dynamical models","department":[{"_id":"EdHa"}],"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.","date_published":"2025-04-01T00:00:00Z","month":"04"},{"date_updated":"2025-10-22T07:00:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"author":[{"last_name":"Tavano","first_name":"Ste","full_name":"Tavano, Ste","id":"2F162F0C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9970-7804"},{"orcid":"0000-0001-7205-2975","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","last_name":"Brückner"},{"orcid":"0000-0003-1671-393X","full_name":"Tasciyan, Saren","id":"4323B49C-F248-11E8-B48F-1D18A9856A87","first_name":"Saren","last_name":"Tasciyan"},{"last_name":"Tong","first_name":"Xin","id":"50F65CDC-AA30-11E9-A72B-8A12E6697425","full_name":"Tong, Xin"},{"first_name":"Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87","full_name":"Kardos, Roland","last_name":"Kardos"},{"first_name":"Alexandra","orcid":"0000-0001-7659-9142","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra","last_name":"Schauer"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","first_name":"Robert"},{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"_id":"19404","OA_place":"publisher","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","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."}],"article_number":"115387","language":[{"iso":"eng"}],"doi":"10.1016/j.celrep.2025.115387","external_id":{"isi":["001443652700001"],"pmid":["40057955"]},"oa":1,"volume":44,"oa_version":"Published Version","day":"25","publisher":"Elsevier","fulldoi":"https://doi.org/10.1016/j.celrep.2025.115387","publication_identifier":{"eissn":["2211-1247"],"issn":["2639-1856"]},"publication_status":"published","file":[{"checksum":"57e05dd1598c807af0afdb32cec039d3","success":1,"creator":"dernst","file_id":"19413","file_size":9067797,"relation":"main_file","file_name":"2025_CellReports_Tavano.pdf","date_updated":"2025-03-17T10:26:54Z","content_type":"application/pdf","access_level":"open_access","date_created":"2025-03-17T10:26:54Z"}],"pmid":1,"date_created":"2025-03-16T23:01:24Z","article_processing_charge":"Yes","year":"2025","file_date_updated":"2025-03-17T10:26:54Z","article_type":"original","corr_author":"1","ddc":["570"],"title":"BMP-dependent patterning of ectoderm tissue material properties modulates lateral mesendoderm cell migration during early zebrafish gastrulation","department":[{"_id":"CaHe"},{"_id":"EdHa"},{"_id":"MiSi"},{"_id":"Bio"}],"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).","DOAJ_listed":"1","date_published":"2025-03-25T00:00:00Z","month":"03","citation":{"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>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">https://doi.org/10.1016/j.celrep.2025.115387</a>.","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. Elsevier, 2025.","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, Elsevier, 2025, 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>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2025.115387\">https://doi.org/10.1016/j.celrep.2025.115387</a>","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>"},"status":"public","isi":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"type":"journal_article","scopus_import":"1","issue":"3","quality_controlled":"1","publication":"Cell Reports","project":[{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"},{"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"}],"OA_type":"gold","has_accepted_license":"1","intvolume":"        44"},{"article_type":"original","year":"2025","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2205.02645"}],"related_material":{"record":[{"status":"public","relation":"software","id":"20121"}]},"pmid":1,"date_created":"2025-07-21T08:37:27Z","publication_identifier":{"issn":["0003-0147"],"eissn":["1537-5323"]},"publication_status":"published","month":"04","date_published":"2025-04-01T00:00:00Z","department":[{"_id":"EdHa"}],"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","title":"Discovering stochastic dynamical equations from ecological time series data","type":"journal_article","isi":1,"status":"public","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.","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.","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>.","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.","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>","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>"},"intvolume":"       205","OA_type":"green","publication":"The American Naturalist","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"}],"issue":"4","_id":"20056","author":[{"last_name":"Nabeel","first_name":"Arshed","full_name":"Nabeel, Arshed"},{"full_name":"Karichannavar, Ashwin","first_name":"Ashwin","last_name":"Karichannavar"},{"last_name":"Palathingal","full_name":"Palathingal, Shuaib","first_name":"Shuaib"},{"first_name":"Jitesh","full_name":"Jhawar, Jitesh","last_name":"Jhawar"},{"last_name":"Brückner","orcid":"0000-0001-7205-2975","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David"},{"first_name":"Danny","full_name":"Raj M, Danny","last_name":"Raj M"},{"full_name":"Guttal, Vishwesha","first_name":"Vishwesha","last_name":"Guttal"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"date_updated":"2025-09-30T14:14:43Z","doi":"10.1086/734083","language":[{"iso":"eng"}],"abstract":[{"text":"Theoretical studies have shown that stochasticity can affect the dynamics of ecosystems in counterintuitive ways. However, without knowing the equations governing the dynamics of populations or ecosystems, it is difficult to ascertain the role of stochasticity in real datasets. Therefore, the inverse problem of inferring the governing stochastic equations from datasets is important. Here, we present an equation discovery methodology that takes time series data of state variables as input and outputs a stochastic differential equation. We achieve this by combining traditional approaches from stochastic calculus with the equation discovery techniques. We demonstrate the generality of the method via several applications. First, we deliberately choose various stochastic models with fundamentally different governing equations, yet they produce nearly identical steady-state distributions. We show that we can recover the correct underlying equations, and thus infer the structure of their stability, accurately from the analysis of time series data alone. We demonstrate our method on two real-world datasets—fish schooling and single-cell migration—that have vastly different spatiotemporal scales and dynamics. We illustrate various limitations and potential pitfalls of the method and how to overcome them via diagnostic measures. Finally, we provide our open-source code via a package named PyDaDDy (Python Library for Data-Driven Dynamics).","lang":"eng"}],"OA_place":"repository","volume":205,"page":"E100-E117","oa":1,"external_id":{"isi":["001433250500001"],"arxiv":["2205.02645"],"pmid":["40179429"]},"publisher":"University of Chicago Press","fulldoi":"https://doi.org/10.1086/734083","oa_version":"Preprint","day":"01"},{"date_updated":"2025-12-30T09:34:11Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Kalukula","first_name":"Yohalie","full_name":"Kalukula, Yohalie"},{"first_name":"Marine","full_name":"Luciano, Marine","last_name":"Luciano"},{"full_name":"Simanov, Gleb","first_name":"Gleb","last_name":"Simanov"},{"full_name":"Charras, Guillaume","first_name":"Guillaume","last_name":"Charras"},{"last_name":"Brückner","first_name":"David","orcid":"0000-0001-7205-2975","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"full_name":"Gabriele, Sylvain","first_name":"Sylvain","last_name":"Gabriele"}],"_id":"20259","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."}],"language":[{"iso":"eng"}],"doi":"10.1038/s41567-025-02980-z","external_id":{"isi":["001556019400001"]},"page":"1451-1461","volume":21,"day":"01","oa_version":"None","publisher":"Springer Nature","fulldoi":"https://doi.org/10.1038/s41567-025-02980-z","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"publication_status":"published","date_created":"2025-08-31T22:01:33Z","article_processing_charge":"No","year":"2025","article_type":"original","corr_author":"1","title":"The actin cortex acts as a mechanical memory of morphology in confined migrating cells","department":[{"_id":"EdHa"}],"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).","date_published":"2025-09-01T00:00:00Z","month":"09","citation":{"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.","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>.","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.","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>","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>.","short":"Y. Kalukula, M. Luciano, G. Simanov, G. Charras, D. Brückner, S. Gabriele, Nature Physics 21 (2025) 1451–1461."},"status":"public","type":"journal_article","isi":1,"scopus_import":"1","quality_controlled":"1","publication":"Nature Physics","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"}],"OA_type":"closed access","intvolume":"        21"},{"citation":{"ieee":"I. C. Fortunato <i>et al.</i>, “Single-cell migration along and against confined haptotactic gradients,” <i>Nature Physics</i>, vol. 21. Springer Nature, pp. 1638–1647, 2025.","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>.","ista":"Fortunato IC, Brückner D, Grosser S, Nautiyal R, Rossetti L, Bosch-Padrós M, Trebicka J, Roca-Cusachs P, Sunyer R, Hannezo EB, Trepat X. 2025. Single-cell migration along and against confined haptotactic gradients. Nature Physics. 21, 1638–1647.","apa":"Fortunato, I. C., Brückner, D., Grosser, S., Nautiyal, R., Rossetti, L., Bosch-Padrós, M., … Trepat, X. (2025). Single-cell migration along and against confined haptotactic gradients. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-025-03015-3\">https://doi.org/10.1038/s41567-025-03015-3</a>","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>","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>."},"status":"public","type":"journal_article","isi":1,"scopus_import":"1","quality_controlled":"1","publication":"Nature Physics","project":[{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"OA_type":"green","intvolume":"        21","publication_status":"published","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"date_created":"2025-10-05T22:01:36Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.12.02.626413"}],"article_processing_charge":"No","year":"2025","corr_author":"1","article_type":"original","title":"Single-cell migration along and against confined haptotactic gradients","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.","department":[{"_id":"EdHa"}],"date_published":"2025-10-01T00:00:00Z","month":"10","external_id":{"isi":["001581659900001"]},"oa":1,"page":"1638-1647","volume":21,"day":"01","oa_version":"Preprint","fulldoi":"https://doi.org/10.1038/s41567-025-03015-3","publisher":"Springer Nature","date_updated":"2026-01-05T14:26:28Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Fortunato, Isabela Corina","first_name":"Isabela Corina","last_name":"Fortunato"},{"last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David","orcid":"0000-0001-7205-2975","first_name":"David"},{"first_name":"Steffen","full_name":"Grosser, Steffen","last_name":"Grosser"},{"first_name":"Rohit","full_name":"Nautiyal, Rohit","last_name":"Nautiyal"},{"last_name":"Rossetti","first_name":"Leone","full_name":"Rossetti, Leone"},{"last_name":"Bosch-Padrós","full_name":"Bosch-Padrós, Miquel","first_name":"Miquel"},{"last_name":"Trebicka","full_name":"Trebicka, Jonel","first_name":"Jonel"},{"first_name":"Pere","full_name":"Roca-Cusachs, Pere","last_name":"Roca-Cusachs"},{"last_name":"Sunyer","first_name":"Raimon","full_name":"Sunyer, Raimon"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo"},{"last_name":"Trepat","full_name":"Trepat, Xavier","first_name":"Xavier"}],"_id":"20431","OA_place":"repository","abstract":[{"text":"Haptotaxis is the process of directed cell migration along gradients of extracellular matrix density and is central to morphogenesis, immune responses and cancer invasion. It is commonly assumed that cells respond to these gradients by migrating directionally towards the regions of highest ligand density. In contrast with this view, here we show that cells exposed to micropatterned fibronectin gradients exhibit a wide range of complex trajectories, including directed haptotactic migration up the gradient but also linear oscillations and circles with extended periods of migration down the gradient. To explain this behaviour, we developed a biophysical model of haptotactic cell migration based on a coarse-grained molecular clutch model coupled to persistent stochastic polarity dynamics. Although initial haptotactic migration is explained by the differential friction at the front and back of the cell, the observed complex trajectories over longer timescales arise from the interplay between differential friction, persistence and physical confinement. Overall, our study reveals that confinement and persistence modulate the ability of cells to sense and respond to haptotactic cues and provides a framework for understanding how cells navigate complex environments.","lang":"eng"}],"language":[{"iso":"eng"}],"doi":"10.1038/s41567-025-03015-3"},{"doi":"10.1016/j.devcel.2024.10.024","OA_place":"publisher","language":[{"iso":"eng"}],"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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"_id":"18807","author":[{"orcid":"0000-0001-8703-1093","id":"4D9EC9B6-F248-11E8-B48F-1D18A9856A87","full_name":"Rus, Stefanie","first_name":"Stefanie","last_name":"Rus"},{"last_name":"Brückner","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David","first_name":"David"},{"id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f","full_name":"Minchington, Thomas","first_name":"Thomas","last_name":"Minchington"},{"last_name":"Greunz","id":"48A59534-F248-11E8-B48F-1D18A9856A87","full_name":"Greunz, Martina","first_name":"Martina"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","last_name":"Merrin"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"last_name":"Kicheva","orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"date_updated":"2026-09-09T22:30:38Z","publisher":"Elsevier","fulldoi":"https://doi.org/10.1016/j.devcel.2024.10.024","oa_version":"Published Version","day":"24","volume":60,"external_id":{"pmid":["39603235"],"isi":["001434279000001"]},"page":"567-580","oa":1,"month":"02","department":[{"_id":"AnKi"},{"_id":"EdHa"},{"_id":"NanoFab"}],"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).","ddc":["570"],"title":"Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling","date_published":"2025-02-24T00:00:00Z","article_processing_charge":"Yes (via OA deal)","article_type":"original","corr_author":"1","file_date_updated":"2025-04-16T10:54:07Z","year":"2025","pmid":1,"date_created":"2025-01-09T11:25:47Z","related_material":{"record":[{"id":"19763","status":"public","relation":"dissertation_contains"}]},"file":[{"checksum":"bb58db4a908a1f4aabe4004706154541","file_id":"19584","creator":"dernst","success":1,"file_size":6994499,"access_level":"open_access","date_created":"2025-04-16T10:54:07Z","content_type":"application/pdf","date_updated":"2025-04-16T10:54:07Z","file_name":"2025_DevelopmentalCell_Lehr.pdf","relation":"main_file"}],"publication_status":"published","publication_identifier":{"issn":["1534-5807"]},"OA_type":"hybrid","intvolume":"        60","has_accepted_license":"1","project":[{"grant_number":"101044579","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","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"},{"grant_number":"SC19-011","_id":"9B9B39FA-BA93-11EA-9121-9846C619BF3A","name":"The regulatory logic of pattern formation in the vertebrate dorsal neural tube"}],"publication":"Developmental Cell","quality_controlled":"1","scopus_import":"1","issue":"4","type":"journal_article","isi":1,"citation":{"chicago":"Rus, Stefanie, David Brückner, Thomas Minchington, Martina Greunz, Jack Merrin, Edouard B Hannezo, and Anna Kicheva. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>.","short":"S. Rus, D. Brückner, T. Minchington, M. Greunz, J. Merrin, E.B. Hannezo, A. Kicheva, Developmental Cell 60 (2025) 567–580.","apa":"Rus, S., Brückner, D., Minchington, T., Greunz, M., Merrin, J., Hannezo, E. B., &#38; Kicheva, A. (2025). Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">https://doi.org/10.1016/j.devcel.2024.10.024</a>","ama":"Rus S, Brückner D, Minchington T, et al. Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling. <i>Developmental Cell</i>. 2025;60(4):567-580. doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>","ieee":"S. Rus <i>et al.</i>, “Self-organized pattern formation in the developing mouse neural tube by a temporal relay of BMP signaling,” <i>Developmental Cell</i>, vol. 60, no. 4. Elsevier, pp. 567–580, 2025.","mla":"Rus, Stefanie, et al. “Self-Organized Pattern Formation in the Developing Mouse Neural Tube by a Temporal Relay of BMP Signaling.” <i>Developmental Cell</i>, vol. 60, no. 4, Elsevier, 2025, pp. 567–80, doi:<a href=\"https://doi.org/10.1016/j.devcel.2024.10.024\">10.1016/j.devcel.2024.10.024</a>.","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."},"status":"public"},{"day":"04","oa_version":"Published Version","publisher":"IOP Publishing","fulldoi":"https://doi.org/10.1088/1361-6633/ad36d2","external_id":{"pmid":["38518358"],"arxiv":["2309.00545"],"isi":["001196692400001"]},"oa":1,"volume":87,"license":"https://creativecommons.org/licenses/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."}],"article_number":"056601","language":[{"iso":"eng"}],"doi":"10.1088/1361-6633/ad36d2","date_updated":"2025-09-04T13:39:07Z","arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","image":"/images/cc_by.png"},"_id":"15315","author":[{"last_name":"Brückner","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","first_name":"David"},{"first_name":"Chase P.","full_name":"Broedersz, Chase P.","last_name":"Broedersz"}],"scopus_import":"1","issue":"5","publication":"Reports on Progress in Physics","quality_controlled":"1","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"}],"has_accepted_license":"1","intvolume":"        87","citation":{"ieee":"D. Brückner and C. P. Broedersz, “Learning dynamical models of single and collective cell migration: a review,” <i>Reports on Progress in Physics</i>, vol. 87, no. 5. IOP Publishing, 2024.","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.","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>.","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>","short":"D. Brückner, C.P. Broedersz, Reports on Progress in Physics 87 (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>."},"status":"public","type":"journal_article","isi":1,"ddc":["530"],"title":"Learning dynamical models of single and collective cell migration: a review","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.","department":[{"_id":"EdHa"}],"date_published":"2024-04-04T00:00:00Z","month":"04","publication_status":"published","publication_identifier":{"issn":["0034-4885"],"eissn":["1361-6633"]},"file":[{"success":1,"creator":"dernst","file_id":"17451","checksum":"c5910078230ade20f4dd83592e862a72","relation":"main_file","file_name":"2024_ReportPhysics_Brueckner.pdf","date_updated":"2024-08-20T11:00:03Z","content_type":"application/pdf","date_created":"2024-08-20T11:00:03Z","access_level":"open_access","file_size":4376898}],"date_created":"2024-04-14T22:01:01Z","pmid":1,"article_processing_charge":"Yes (in subscription journal)","year":"2024","file_date_updated":"2024-08-20T11:00:03Z","article_type":"review","corr_author":"1"},{"intvolume":"       121","has_accepted_license":"1","OA_type":"hybrid","scopus_import":"1","issue":"23","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"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","type":"journal_article","isi":1,"APC_amount":"2570,79 EUR","status":"public","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).","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.","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.","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>","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>"},"month":"06","date_published":"2024-06-04T00:00:00Z","title":"Information content and optimization of self-organized developmental systems","ddc":["570"],"department":[{"_id":"EdHa"},{"_id":"GaTk"}],"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.","year":"2024","corr_author":"1","file_date_updated":"2024-06-10T10:27:37Z","article_type":"original","article_processing_charge":"Yes (in subscription journal)","file":[{"success":1,"creator":"dernst","file_id":"17130","checksum":"59797a75db7beb3721ed7a4d14c241f9","relation":"main_file","file_name":"2024_PNAS_Brueckner.pdf","date_created":"2024-06-10T10:27:37Z","access_level":"open_access","date_updated":"2024-06-10T10:27:37Z","content_type":"application/pdf","file_size":12329234}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","related_material":{"link":[{"relation":"software","url":"https://github.com/dbrueckner/SelforgInformation"},{"relation":"press_release","url":"https://ista.ac.at/en/news/the-embryo-assembles-itself/","description":"News on the ISTA website"}]},"pmid":1,"date_created":"2024-06-09T22:01:02Z","publisher":"National Academy of Sciences","fulldoi":"https://doi.org/10.1073/pnas.2322326121","day":"04","oa_version":"Published Version","volume":121,"oa":1,"external_id":{"pmid":["38819997"],"isi":["001244835000006"]},"doi":"10.1073/pnas.2322326121","abstract":[{"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.","lang":"eng"}],"article_number":"e2322326121","language":[{"iso":"eng"}],"OA_place":"publisher","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"author":[{"last_name":"Brückner","first_name":"David","orcid":"0000-0001-7205-2975","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"_id":"17123","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-08T07:51:01Z"},{"oa_version":"Published Version","day":"18","publisher":"Zenodo","fulldoi":"https://doi.org/10.5281/ZENODO.7137151","has_accepted_license":"1","status":"public","oa":1,"citation":{"apa":"Nabeel, A., Karichannavar, A., Palathingal, S., Jhawar, J., Brückner, D., Danny Raj, M., &#38; Guttal, V. (2024). PyDaddy: A Python Package for Discovering SDEs from Time Series Data. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7137151\">https://doi.org/10.5281/ZENODO.7137151</a>","ama":"Nabeel A, Karichannavar A, Palathingal S, et al. PyDaddy: A Python Package for Discovering SDEs from Time Series Data. 2024. doi:<a href=\"https://doi.org/10.5281/ZENODO.7137151\">10.5281/ZENODO.7137151</a>","ieee":"A. Nabeel <i>et al.</i>, “PyDaddy: A Python Package for Discovering SDEs from Time Series Data.” Zenodo, 2024.","mla":"Nabeel, Arshed, et al. <i>PyDaddy: A Python Package for Discovering SDEs from Time Series Data</i>. Zenodo, 2024, doi:<a href=\"https://doi.org/10.5281/ZENODO.7137151\">10.5281/ZENODO.7137151</a>.","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, <a href=\"https://doi.org/10.5281/ZENODO.7137151\">10.5281/ZENODO.7137151</a>.","short":"A. Nabeel, A. Karichannavar, S. Palathingal, J. Jhawar, D. Brückner, M. Danny Raj, V. Guttal, (2024).","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. <a href=\"https://doi.org/10.5281/ZENODO.7137151\">https://doi.org/10.5281/ZENODO.7137151</a>."},"type":"research_data_reference","date_published":"2024-09-18T00:00:00Z","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."}],"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.","ddc":["570"],"title":"PyDaddy: A Python Package for Discovering SDEs from Time Series Data","month":"09","doi":"10.5281/ZENODO.7137151","related_material":{"record":[{"status":"public","relation":"used_for_analysis_in","id":"20056"}]},"date_created":"2025-08-05T06:49:59Z","date_updated":"2025-09-30T14:14:42Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"_id":"20121","author":[{"last_name":"Nabeel","first_name":"Arshed","full_name":"Nabeel, Arshed"},{"last_name":"Karichannavar","first_name":"Ashwin","full_name":"Karichannavar, Ashwin"},{"full_name":"Palathingal, Shuaib","first_name":"Shuaib","last_name":"Palathingal"},{"last_name":"Jhawar","full_name":"Jhawar, Jitesh","first_name":"Jitesh"},{"last_name":"Brückner","first_name":"David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David"},{"last_name":"Danny Raj","full_name":"Danny Raj, Masila","first_name":"Masila"},{"last_name":"Guttal","first_name":"Vishwesha","full_name":"Guttal, Vishwesha"}],"year":"2024","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.7137151","open_access":"1"}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"status":"public","citation":{"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.","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>.","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.","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>.","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.","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>"},"isi":1,"type":"journal_article","scopus_import":"1","publication":"Nature Physics","quality_controlled":"1","project":[{"name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","call_identifier":"H2020"},{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"intvolume":"        20","OA_type":"green","publication_status":"published","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"related_material":{"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/a-railroad-of-cells/","description":"News on ISTA website"}]},"date_created":"2024-07-16T12:32:17Z","year":"2024","corr_author":"1","article_type":"original","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1101/2022.07.17.500364","open_access":"1"}],"date_published":"2024-09-01T00:00:00Z","title":"Geometry-driven migration efficiency of autonomous epithelial cell clusters","department":[{"_id":"EdHa"}],"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.","month":"09","oa":1,"page":"1492-1500","external_id":{"isi":["001250246200004"]},"volume":20,"day":"01","oa_version":"Preprint","publisher":"Springer Nature","fulldoi":"https://doi.org/10.1038/s41567-024-02532-x","date_updated":"2025-09-08T08:28:31Z","author":[{"last_name":"Vercruysse","full_name":"Vercruysse, Eléonore","first_name":"Eléonore"},{"last_name":"Brückner","first_name":"David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David"},{"full_name":"Gómez-González, Manuel","first_name":"Manuel","last_name":"Gómez-González"},{"last_name":"Remson","first_name":"Alexandre","full_name":"Remson, Alexandre"},{"full_name":"Luciano, Marine","first_name":"Marine","last_name":"Luciano"},{"first_name":"Yohalie","full_name":"Kalukula, Yohalie","last_name":"Kalukula"},{"last_name":"Rossetti","first_name":"Leone","full_name":"Rossetti, Leone"},{"last_name":"Trepat","full_name":"Trepat, Xavier","first_name":"Xavier"},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"full_name":"Gabriele, Sylvain","first_name":"Sylvain","last_name":"Gabriele"}],"_id":"17269","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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"}],"language":[{"iso":"eng"}],"OA_place":"repository","ec_funded":1,"doi":"10.1038/s41567-024-02532-x"},{"has_accepted_license":"1","intvolume":"        14","scopus_import":"1","quality_controlled":"1","publication":"Nature Communications","type":"journal_article","isi":1,"status":"public","citation":{"apa":"Brandstätter, T., Brückner, D., Han, Y. L., Alert, R., Guo, M., &#38; Broedersz, C. P. (2023). Curvature induces active velocity waves in rotating spherical tissues. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-37054-2\">https://doi.org/10.1038/s41467-023-37054-2</a>","ama":"Brandstätter T, Brückner D, Han YL, Alert R, Guo M, Broedersz CP. Curvature induces active velocity waves in rotating spherical tissues. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-37054-2\">10.1038/s41467-023-37054-2</a>","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,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","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.","mla":"Brandstätter, Tom, et al. “Curvature Induces Active Velocity Waves in Rotating Spherical Tissues.” <i>Nature Communications</i>, vol. 14, 1643, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-37054-2\">10.1038/s41467-023-37054-2</a>.","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.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-37054-2\">https://doi.org/10.1038/s41467-023-37054-2</a>.","short":"T. Brandstätter, D. Brückner, Y.L. Han, R. Alert, M. Guo, C.P. Broedersz, Nature Communications 14 (2023)."},"month":"03","date_published":"2023-03-24T00:00:00Z","ddc":["570"],"title":"Curvature induces active velocity waves in rotating spherical tissues","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"}],"year":"2023","file_date_updated":"2023-04-11T06:27:00Z","article_type":"original","article_processing_charge":"No","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","file":[{"content_type":"application/pdf","date_updated":"2023-04-11T06:27:00Z","access_level":"open_access","date_created":"2023-04-11T06:27:00Z","file_name":"2023_NatureComm_Brandstaetter.pdf","relation":"main_file","file_size":4146777,"file_id":"12821","success":1,"creator":"dernst","checksum":"54f06f9eee11d43bab253f3492c983ba"}],"pmid":1,"date_created":"2023-04-09T22:01:00Z","fulldoi":"https://doi.org/10.1038/s41467-023-37054-2","publisher":"Springer Nature","day":"24","oa_version":"Published Version","volume":14,"oa":1,"external_id":{"pmid":["36964141"],"isi":["000959887700008"]},"doi":"10.1038/s41467-023-37054-2","abstract":[{"lang":"eng","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."}],"article_number":"1643","language":[{"iso":"eng"}],"author":[{"first_name":"Tom","full_name":"Brandstätter, Tom","last_name":"Brandstätter"},{"last_name":"Brückner","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","first_name":"David"},{"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"},{"full_name":"Broedersz, Chase P.","first_name":"Chase P.","last_name":"Broedersz"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"_id":"12818","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-01T14:05:30Z"},{"date_published":"2023-06-29T00:00:00Z","title":"Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome","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.","month":"06","publication_status":"published","publication_identifier":{"eissn":["1095-9203"]},"date_created":"2023-07-23T22:01:12Z","year":"2023","article_type":"original","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.adf5568"}],"article_processing_charge":"No","issue":"6652","scopus_import":"1","project":[{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"publication":"Science","quality_controlled":"1","intvolume":"       380","status":"public","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.","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>","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>","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>."},"type":"journal_article","isi":1,"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."}],"language":[{"iso":"eng"}],"doi":"10.1126/science.adf5568","date_updated":"2025-04-14T08:55:54Z","author":[{"last_name":"Brückner","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David","first_name":"David"},{"last_name":"Chen","full_name":"Chen, Hongtao","first_name":"Hongtao"},{"last_name":"Barinov","full_name":"Barinov, Lev","first_name":"Lev"},{"full_name":"Zoller, Benjamin","first_name":"Benjamin","last_name":"Zoller"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"}],"_id":"13261","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"29","oa_version":"Preprint","publisher":"American Association for the Advancement of Science","fulldoi":"https://doi.org/10.1126/science.adf5568","oa":1,"page":"1357-1362","external_id":{"isi":["001106405600028"]},"volume":380},{"date_updated":"2025-09-09T14:22:02Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"orcid":"0000-0001-5130-2226","full_name":"Schwayer, Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia","last_name":"Schwayer"},{"last_name":"Brückner","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David","orcid":"0000-0001-7205-2975","first_name":"David"}],"_id":"14827","keyword":["Cell Biology"],"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."}],"article_number":"jcs.261515","language":[{"iso":"eng"}],"doi":"10.1242/jcs.261515","external_id":{"isi":["001165394900011"],"pmid":["38149871"]},"volume":136,"oa_version":"None","day":"27","fulldoi":"https://doi.org/10.1242/jcs.261515","publisher":"The Company of Biologists","publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"publication_status":"published","date_created":"2024-01-17T12:46:55Z","pmid":1,"article_processing_charge":"No","year":"2023","corr_author":"1","article_type":"original","title":"Connecting theory and experiment in cell and tissue mechanics","department":[{"_id":"EdHa"},{"_id":"CaHe"}],"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).","date_published":"2023-12-27T00:00:00Z","month":"12","citation":{"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>.","short":"C. Schwayer, D. Brückner, Journal of Cell Science 136 (2023).","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>","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>","ista":"Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. 136(24), jcs. 261515.","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>.","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."},"status":"public","type":"journal_article","isi":1,"issue":"24","scopus_import":"1","publication":"Journal of Cell Science","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"}],"intvolume":"       136"},{"arxiv":1,"date_updated":"2023-08-04T10:25:49Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"_id":"12277","author":[{"last_name":"Brückner","first_name":"David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David"},{"first_name":"Matthew","full_name":"Schmitt, Matthew","last_name":"Schmitt"},{"first_name":"Alexandra","full_name":"Fink, Alexandra","last_name":"Fink"},{"last_name":"Ladurner","first_name":"Georg","full_name":"Ladurner, Georg"},{"last_name":"Flommersfeld","first_name":"Johannes","full_name":"Flommersfeld, Johannes"},{"last_name":"Arlt","full_name":"Arlt, Nicolas","first_name":"Nicolas"},{"last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","first_name":"Edouard B"},{"full_name":"Rädler, Joachim O.","first_name":"Joachim O.","last_name":"Rädler"},{"last_name":"Broedersz","first_name":"Chase P.","full_name":"Broedersz, Chase P."}],"keyword":["General Physics and Astronomy"],"abstract":[{"lang":"eng","text":"Cell migration in confining physiological environments relies on the concerted dynamics of several cellular components, including protrusions, adhesions with the environment, and the cell nucleus. However, it remains poorly understood how the dynamic interplay of these components and the cell polarity determine the emergent migration behavior at the cellular scale. Here, we combine data-driven inference with a mechanistic bottom-up approach to develop a model for protrusion and polarity dynamics in confined cell migration, revealing how the cellular dynamics adapt to confining geometries. Specifically, we use experimental data of joint protrusion-nucleus migration trajectories of cells on confining micropatterns to systematically determine a mechanistic model linking the stochastic dynamics of cell polarity, protrusions, and nucleus. This model indicates that the cellular dynamics adapt to confining constrictions through a switch in the polarity dynamics from a negative to a positive self-reinforcing feedback loop. Our model further reveals how this feedback loop leads to stereotypical cycles of protrusion-nucleus dynamics that drive the migration of the cell through constrictions. These cycles are disrupted upon perturbation of cytoskeletal components, indicating that the positive feedback is controlled by cellular migration mechanisms. Our data-driven theoretical approach therefore identifies polarity feedback adaptation as a key mechanism in confined cell migration."}],"language":[{"iso":"eng"}],"article_number":"031041","doi":"10.1103/physrevx.12.031041","external_id":{"arxiv":["2106.01014"],"isi":["000861534700001"]},"oa":1,"volume":12,"day":"20","oa_version":"Published Version","publisher":"American Physical Society","fulldoi":"https://doi.org/10.1103/physrevx.12.031041","publication_status":"published","publication_identifier":{"issn":["2160-3308"]},"file":[{"date_updated":"2023-01-30T11:07:27Z","content_type":"application/pdf","date_created":"2023-01-30T11:07:27Z","access_level":"open_access","relation":"main_file","file_name":"2022_PhysicalReviewX_Brueckner.pdf","file_size":4686804,"file_id":"12458","success":1,"creator":"dernst","checksum":"40a8fbc3663bf07b37cb80020974d40d"}],"date_created":"2023-01-16T10:02:06Z","article_processing_charge":"No","year":"2022","article_type":"original","file_date_updated":"2023-01-30T11:07:27Z","ddc":["530","570"],"title":"Geometry adaptation of protrusion and polarity dynamics in confined cell migration","acknowledgement":"We thank Grzegorz Gradziuk, StevenRiedijk, Janni Harju, and M. R. Schnucki for helpful discussions, and Andriy Goychuk for advice on the image segmentation. This project\r\nwas funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), Project No. 201269156—SFB 1032 (Projects B01 and B12). D. B. B. is supported by the NOMIS Foundation and in part by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM), as well as by the Joachim Herz Stiftung.","department":[{"_id":"EdHa"}],"date_published":"2022-09-20T00:00:00Z","month":"09","citation":{"chicago":"Brückner, David, Matthew Schmitt, Alexandra Fink, Georg Ladurner, Johannes Flommersfeld, Nicolas Arlt, Edouard B Hannezo, Joachim O. Rädler, and Chase P. Broedersz. “Geometry Adaptation of Protrusion and Polarity Dynamics in Confined Cell Migration.” <i>Physical Review X</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevx.12.031041\">https://doi.org/10.1103/physrevx.12.031041</a>.","short":"D. Brückner, M. Schmitt, A. Fink, G. Ladurner, J. Flommersfeld, N. Arlt, E.B. Hannezo, J.O. Rädler, C.P. Broedersz, Physical Review X 12 (2022).","ama":"Brückner D, Schmitt M, Fink A, et al. Geometry adaptation of protrusion and polarity dynamics in confined cell migration. <i>Physical Review X</i>. 2022;12(3). doi:<a href=\"https://doi.org/10.1103/physrevx.12.031041\">10.1103/physrevx.12.031041</a>","apa":"Brückner, D., Schmitt, M., Fink, A., Ladurner, G., Flommersfeld, J., Arlt, N., … Broedersz, C. P. (2022). Geometry adaptation of protrusion and polarity dynamics in confined cell migration. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevx.12.031041\">https://doi.org/10.1103/physrevx.12.031041</a>","ista":"Brückner D, Schmitt M, Fink A, Ladurner G, Flommersfeld J, Arlt N, Hannezo EB, Rädler JO, Broedersz CP. 2022. Geometry adaptation of protrusion and polarity dynamics in confined cell migration. Physical Review X. 12(3), 031041.","mla":"Brückner, David, et al. “Geometry Adaptation of Protrusion and Polarity Dynamics in Confined Cell Migration.” <i>Physical Review X</i>, vol. 12, no. 3, 031041, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevx.12.031041\">10.1103/physrevx.12.031041</a>.","ieee":"D. Brückner <i>et al.</i>, “Geometry adaptation of protrusion and polarity dynamics in confined cell migration,” <i>Physical Review X</i>, vol. 12, no. 3. American Physical Society, 2022."},"status":"public","type":"journal_article","isi":1,"scopus_import":"1","issue":"3","quality_controlled":"1","publication":"Physical Review X","has_accepted_license":"1","intvolume":"        12"},{"volume":121,"external_id":{"isi":["000740815400007"],"pmid":["34890578"]},"page":"P44-60","oa":1,"publisher":"Elsevier","fulldoi":"https://doi.org/10.1016/j.bpj.2021.12.006","day":"04","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10530","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)"},"author":[{"last_name":"Zisis","first_name":"Themistoklis","full_name":"Zisis, Themistoklis"},{"full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","first_name":"David","last_name":"Brückner"},{"last_name":"Brandstätter","first_name":"Tom","full_name":"Brandstätter, Tom"},{"first_name":"Wei Xiong","full_name":"Siow, Wei Xiong","last_name":"Siow"},{"last_name":"d’Alessandro","first_name":"Joseph","full_name":"d’Alessandro, Joseph"},{"last_name":"Vollmar","full_name":"Vollmar, Angelika M.","first_name":"Angelika M."},{"first_name":"Chase P.","full_name":"Broedersz, Chase P.","last_name":"Broedersz"},{"last_name":"Zahler","first_name":"Stefan","full_name":"Zahler, Stefan"}],"date_updated":"2025-06-11T13:59:29Z","doi":"10.1016/j.bpj.2021.12.006","keyword":["Biophysics"],"language":[{"iso":"eng"}],"abstract":[{"text":"Cell dispersion from a confined area is fundamental in a number of biological processes,\r\nincluding cancer metastasis. To date, a quantitative understanding of the interplay of single\r\ncell motility, cell proliferation, and intercellular contacts remains elusive. In particular, the role\r\nof E- and N-Cadherin junctions, central components of intercellular contacts, is still\r\ncontroversial. Combining theoretical modeling with in vitro observations, we investigate the\r\ncollective spreading behavior of colonies of human cancer cells (T24). The spreading of these\r\ncolonies is driven by stochastic single-cell migration with frequent transient cell-cell contacts.\r\nWe find that inhibition of E- and N-Cadherin junctions decreases colony spreading and average\r\nspreading velocities, without affecting the strength of correlations in spreading velocities of\r\nneighboring cells. Based on a biophysical simulation model for cell migration, we show that the\r\nbehavioral changes upon disruption of these junctions can be explained by reduced repulsive\r\nexcluded volume interactions between cells. This suggests that in cancer cell migration,\r\ncadherin-based intercellular contacts sharpen cell boundaries leading to repulsive rather than\r\ncohesive interactions between cells, thereby promoting efficient cell spreading during collective\r\nmigration.\r\n","lang":"eng"}],"type":"journal_article","isi":1,"citation":{"apa":"Zisis, T., Brückner, D., Brandstätter, T., Siow, W. X., d’Alessandro, J., Vollmar, A. M., … Zahler, S. (2022). Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">https://doi.org/10.1016/j.bpj.2021.12.006</a>","ama":"Zisis T, Brückner D, Brandstätter T, et al. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. <i>Biophysical Journal</i>. 2022;121(1):P44-60. doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">10.1016/j.bpj.2021.12.006</a>","ieee":"T. Zisis <i>et al.</i>, “Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration,” <i>Biophysical Journal</i>, vol. 121, no. 1. Elsevier, pp. P44-60, 2022.","mla":"Zisis, Themistoklis, et al. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” <i>Biophysical Journal</i>, vol. 121, no. 1, Elsevier, 2022, pp. P44-60, doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">10.1016/j.bpj.2021.12.006</a>.","ista":"Zisis T, Brückner D, Brandstätter T, Siow WX, d’Alessandro J, Vollmar AM, Broedersz CP, Zahler S. 2022. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. 121(1), P44-60.","short":"T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M. Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) P44-60.","chicago":"Zisis, Themistoklis, David Brückner, Tom Brandstätter, Wei Xiong Siow, Joseph d’Alessandro, Angelika M. Vollmar, Chase P. Broedersz, and Stefan Zahler. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” <i>Biophysical Journal</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">https://doi.org/10.1016/j.bpj.2021.12.006</a>."},"status":"public","has_accepted_license":"1","intvolume":"       121","quality_controlled":"1","publication":"Biophysical Journal","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"scopus_import":"1","issue":"1","article_processing_charge":"No","article_type":"original","file_date_updated":"2022-07-29T10:17:10Z","year":"2022","date_created":"2021-12-10T09:48:19Z","pmid":1,"publication_status":"published","file":[{"checksum":"1aa7c3478e0c8256b973b632efd1f6b4","file_id":"11697","creator":"dernst","success":1,"file_size":4475504,"content_type":"application/pdf","date_updated":"2022-07-29T10:17:10Z","date_created":"2022-07-29T10:17:10Z","access_level":"open_access","relation":"main_file","file_name":"2022_BiophysicalJour_Zisis.pdf"}],"publication_identifier":{"issn":["0006-3495"]},"month":"01","acknowledgement":"Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 201269156 - SFB 1032 (Projects B8 and B12). D.B.B. is supported in part by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and by the Joachim Herz Stiftung.","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"title":"Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration","ddc":["570"],"date_published":"2022-01-04T00:00:00Z"}]