[{"publication_identifier":{"issn":["1084-9521"]},"month":"12","project":[{"call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"quality_controlled":"1","isi":1,"external_id":{"pmid":["36470715"],"isi":["001053522200001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.semcdb.2022.11.005","license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"file_date_updated":"2024-01-08T10:16:04Z","department":[{"_id":"EdHa"}],"publisher":"Elsevier","publication_status":"published","pmid":1,"acknowledgement":"This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.).\r\nB. C-M wants to acknowledge the support of the field of excellence Complexity of Life, in Basic Research and Innovation of the University of Graz.","year":"2023","volume":"150-151","date_created":"2023-01-12T12:09:47Z","date_updated":"2024-01-16T13:22:32Z","author":[{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643","first_name":"Bernat","last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"}],"keyword":["Cell Biology","Developmental Biology"],"scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"02","page":"58-65","article_type":"review","citation":{"chicago":"Corominas-Murtra, Bernat, and Edouard B Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology. Elsevier, 2023. https://doi.org/10.1016/j.semcdb.2022.11.005.","mla":"Corominas-Murtra, Bernat, and Edouard B. Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology, vol. 150–151, Elsevier, 2023, pp. 58–65, doi:10.1016/j.semcdb.2022.11.005.","short":"B. Corominas-Murtra, E.B. Hannezo, Seminars in Cell & Developmental Biology 150–151 (2023) 58–65.","ista":"Corominas-Murtra B, Hannezo EB. 2023. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. 150–151, 58–65.","ieee":"B. Corominas-Murtra and E. B. Hannezo, “Modelling the dynamics of mammalian gut homeostasis,” Seminars in Cell & Developmental Biology, vol. 150–151. Elsevier, pp. 58–65, 2023.","apa":"Corominas-Murtra, B., & Hannezo, E. B. (2023). Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. Elsevier. https://doi.org/10.1016/j.semcdb.2022.11.005","ama":"Corominas-Murtra B, Hannezo EB. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. 2023;150-151:58-65. doi:10.1016/j.semcdb.2022.11.005"},"publication":"Seminars in Cell & Developmental Biology","date_published":"2023-12-02T00:00:00Z","type":"journal_article","abstract":[{"text":"Homeostatic balance in the intestinal epithelium relies on a fast cellular turnover, which is coordinated by an intricate interplay between biochemical signalling, mechanical forces and organ geometry. We review recent modelling approaches that have been developed to understand different facets of this remarkable homeostatic equilibrium. Existing models offer different, albeit complementary, perspectives on the problem. First, biomechanical models aim to explain the local and global mechanical stresses driving cell renewal as well as tissue shape maintenance. Second, compartmental models provide insights into the conditions necessary to keep a constant flow of cells with well-defined ratios of cell types, and how perturbations can lead to an unbalance of relative compartment sizes. A third family of models address, at the cellular level, the nature and regulation of stem fate choices that are necessary to fuel cellular turnover. We also review how these different approaches are starting to be integrated together across scales, to provide quantitative predictions and new conceptual frameworks to think about the dynamics of cell renewal in complex tissues.","lang":"eng"}],"title":"Modelling the dynamics of mammalian gut homeostasis","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12162","file":[{"file_name":"2023_SeminarsCellDevBiology_CorominasMurtra.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1343750,"creator":"dernst","relation":"main_file","file_id":"14741","date_created":"2024-01-08T10:16:04Z","date_updated":"2024-01-08T10:16:04Z","checksum":"c619887cf130f4649bf3035417186004","success":1}],"oa_version":"Published Version"},{"scopus_import":"1","keyword":["Multidisciplinary"],"article_processing_charge":"No","day":"13","citation":{"chicago":"Azkanaz, Maria, Bernat Corominas-Murtra, Saskia I. J. Ellenbroek, Lotte Bruens, Anna T. Webb, Dimitrios Laskaris, Koen C. Oost, et al. “Retrograde Movements Determine Effective Stem Cell Numbers in the Intestine.” Nature. Springer Nature, 2022. https://doi.org/10.1038/s41586-022-04962-0.","mla":"Azkanaz, Maria, et al. “Retrograde Movements Determine Effective Stem Cell Numbers in the Intestine.” Nature, vol. 607, no. 7919, Springer Nature, 2022, pp. 548–54, doi:10.1038/s41586-022-04962-0.","short":"M. Azkanaz, B. Corominas-Murtra, S.I.J. Ellenbroek, L. Bruens, A.T. Webb, D. Laskaris, K.C. Oost, S.J.A. Lafirenze, K. Annusver, H.A. Messal, S. Iqbal, D.J. Flanagan, D.J. Huels, F. Rojas-Rodríguez, M. Vizoso, M. Kasper, O.J. Sansom, H.J. Snippert, P. Liberali, B.D. Simons, P. Katajisto, E.B. Hannezo, J. van Rheenen, Nature 607 (2022) 548–554.","ista":"Azkanaz M, Corominas-Murtra B, Ellenbroek SIJ, Bruens L, Webb AT, Laskaris D, Oost KC, Lafirenze SJA, Annusver K, Messal HA, Iqbal S, Flanagan DJ, Huels DJ, Rojas-Rodríguez F, Vizoso M, Kasper M, Sansom OJ, Snippert HJ, Liberali P, Simons BD, Katajisto P, Hannezo EB, van Rheenen J. 2022. Retrograde movements determine effective stem cell numbers in the intestine. Nature. 607(7919), 548–554.","apa":"Azkanaz, M., Corominas-Murtra, B., Ellenbroek, S. I. J., Bruens, L., Webb, A. T., Laskaris, D., … van Rheenen, J. (2022). Retrograde movements determine effective stem cell numbers in the intestine. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-04962-0","ieee":"M. Azkanaz et al., “Retrograde movements determine effective stem cell numbers in the intestine,” Nature, vol. 607, no. 7919. Springer Nature, pp. 548–554, 2022.","ama":"Azkanaz M, Corominas-Murtra B, Ellenbroek SIJ, et al. Retrograde movements determine effective stem cell numbers in the intestine. Nature. 2022;607(7919):548-554. doi:10.1038/s41586-022-04962-0"},"publication":"Nature","page":"548-554","article_type":"original","date_published":"2022-07-13T00:00:00Z","type":"journal_article","issue":"7919","abstract":[{"text":"The morphology and functionality of the epithelial lining differ along the intestinal tract, but tissue renewal at all sites is driven by stem cells at the base of crypts1,2,3. Whether stem cell numbers and behaviour vary at different sites is unknown. Here we show using intravital microscopy that, despite similarities in the number and distribution of proliferative cells with an Lgr5 signature in mice, small intestinal crypts contain twice as many effective stem cells as large intestinal crypts. We find that, although passively displaced by a conveyor-belt-like upward movement, small intestinal cells positioned away from the crypt base can function as long-term effective stem cells owing to Wnt-dependent retrograde cellular movement. By contrast, the near absence of retrograde movement in the large intestine restricts cell repositioning, leading to a reduction in effective stem cell number. Moreover, after suppression of the retrograde movement in the small intestine, the number of effective stem cells is reduced, and the rate of monoclonal conversion of crypts is accelerated. Together, these results show that the number of effective stem cells is determined by active retrograde movement, revealing a new channel of stem cell regulation that can be experimentally and pharmacologically manipulated.","lang":"eng"}],"_id":"12274","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 607","title":"Retrograde movements determine effective stem cell numbers in the intestine","status":"public","oa_version":"Submitted Version","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"month":"07","main_file_link":[{"url":"https://helda.helsinki.fi/items/94433455-4854-45c0-9de8-7326caea8780","open_access":"1"}],"oa":1,"external_id":{"pmid":["35831497"],"isi":["000824430000004"]},"project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis"}],"quality_controlled":"1","isi":1,"doi":"10.1038/s41586-022-04962-0","language":[{"iso":"eng"}],"ec_funded":1,"pmid":1,"acknowledgement":"We thank the members of the van Rheenen laboratory for reading the manuscript, and the members of the bioimaging, FACS and animal facility of the NKI for experimental support. We acknowledge the staff at the MedH Flow Cytometry core facility, Karolinska Institutet, and LCI facility/Nikon Center of Excellence, Karolinska Institutet. This work was financially supported by the Netherlands Organization of Scientific Research NWO (Veni grant 863.15.011 to S.I.J.E. and Vici grant 09150182110004 to J.v.R.) and the CancerGenomics.nl (Netherlands Organisation for Scientific Research) program (to J.v.R.) the Doctor Josef Steiner Foundation (to J.v.R). B.D.S. acknowledges funding from the Royal Society E.P. Abraham Research Professorship (RP\\R1\\180165) and the Wellcome Trust (098357/Z/12/Z and 219478/Z/19/Z). B.C.-M. acknowledges the support of the field of excellence ‘Complexity of life in basic research and innovation’ of the University of Graz. O.J.S. and their laboratory acknowledge CRUK core funding to the CRUK Beatson Institute (A17196 and A31287) and CRUK core funding to the Sansom laboratory (A21139). P.K. and their laboratory are supported by grants from the Swedish Research Council (2018-03078), Cancerfonden (190634), Academy of Finland Centre of Excellence (266869, 304591 and 320185) and the Jane and Aatos Erkko Foundation. P.L. has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 758617). E.H. acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 851288).","year":"2022","publisher":"Springer Nature","department":[{"_id":"EdHa"}],"publication_status":"published","related_material":{"link":[{"relation":"software","url":"https://github.com/JaccovanRheenenLab/Retrograde_movement_Azkanaz_Nature_2022"}]},"author":[{"full_name":"Azkanaz, Maria","last_name":"Azkanaz","first_name":"Maria"},{"orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","first_name":"Bernat","full_name":"Corominas-Murtra, Bernat"},{"full_name":"Ellenbroek, Saskia I. J.","first_name":"Saskia I. J.","last_name":"Ellenbroek"},{"first_name":"Lotte","last_name":"Bruens","full_name":"Bruens, Lotte"},{"full_name":"Webb, Anna T.","first_name":"Anna T.","last_name":"Webb"},{"full_name":"Laskaris, Dimitrios","first_name":"Dimitrios","last_name":"Laskaris"},{"first_name":"Koen C.","last_name":"Oost","full_name":"Oost, Koen C."},{"full_name":"Lafirenze, Simona J. A.","last_name":"Lafirenze","first_name":"Simona J. A."},{"full_name":"Annusver, Karl","last_name":"Annusver","first_name":"Karl"},{"first_name":"Hendrik A.","last_name":"Messal","full_name":"Messal, Hendrik A."},{"first_name":"Sharif","last_name":"Iqbal","full_name":"Iqbal, Sharif"},{"first_name":"Dustin J.","last_name":"Flanagan","full_name":"Flanagan, Dustin J."},{"last_name":"Huels","first_name":"David J.","full_name":"Huels, David J."},{"full_name":"Rojas-Rodríguez, Felipe","first_name":"Felipe","last_name":"Rojas-Rodríguez"},{"first_name":"Miguel","last_name":"Vizoso","full_name":"Vizoso, Miguel"},{"last_name":"Kasper","first_name":"Maria","full_name":"Kasper, Maria"},{"last_name":"Sansom","first_name":"Owen J.","full_name":"Sansom, Owen J."},{"last_name":"Snippert","first_name":"Hugo J.","full_name":"Snippert, Hugo J."},{"full_name":"Liberali, Prisca","first_name":"Prisca","last_name":"Liberali"},{"full_name":"Simons, Benjamin D.","first_name":"Benjamin D.","last_name":"Simons"},{"first_name":"Pekka","last_name":"Katajisto","full_name":"Katajisto, Pekka"},{"full_name":"Hannezo, Edouard B","first_name":"Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561"},{"full_name":"van Rheenen, Jacco","last_name":"van Rheenen","first_name":"Jacco"}],"volume":607,"date_created":"2023-01-16T10:01:29Z","date_updated":"2023-10-03T11:16:30Z"},{"isi":1,"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"},{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E","grant_number":"851288"},{"name":"Tissue material properties in embryonic development","call_identifier":"FWF","_id":"2693FD8C-B435-11E9-9278-68D0E5697425","grant_number":"V00736"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"isi":["000636734000022"],"pmid":["33730596"]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.cell.2021.02.017","month":"04","publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"publication_status":"published","department":[{"_id":"CaHe"},{"_id":"EdHa"}],"publisher":"Elsevier","year":"2021","acknowledgement":"We thank Carl Goodrich and the members of the Heisenberg and Hannezo groups, in particular Reka Korei, for help, technical advice, and discussions; and the Bioimaging and zebrafish facilities of the IST Austria for continuous support. This work was supported by the Elise Richter Program of Austrian Science Fund (FWF) to N.I.P. ( V 736-B26 ) and the European Union (European Research Council Advanced Grant 742573 to C.-P.H. and European Research Council Starting Grant 851288 to E.H.).","pmid":1,"date_created":"2021-04-11T22:01:14Z","date_updated":"2023-08-07T14:33:59Z","volume":184,"author":[{"id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8451-1195","first_name":"Nicoletta","last_name":"Petridou","full_name":"Petridou, Nicoletta"},{"full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra","first_name":"Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/embryonic-tissue-undergoes-phase-transition/","relation":"press_release","description":"News on IST Homepage"}]},"file_date_updated":"2021-06-08T10:04:10Z","ec_funded":1,"article_type":"original","page":"1914-1928.e19","publication":"Cell","citation":{"mla":"Petridou, Nicoletta, et al. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” Cell, vol. 184, no. 7, Elsevier, 2021, p. 1914–1928.e19, doi:10.1016/j.cell.2021.02.017.","short":"N. Petridou, B. Corominas-Murtra, C.-P.J. Heisenberg, E.B. Hannezo, Cell 184 (2021) 1914–1928.e19.","chicago":"Petridou, Nicoletta, Bernat Corominas-Murtra, Carl-Philipp J Heisenberg, and Edouard B Hannezo. “Rigidity Percolation Uncovers a Structural Basis for Embryonic Tissue Phase Transitions.” Cell. Elsevier, 2021. https://doi.org/10.1016/j.cell.2021.02.017.","ama":"Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. 2021;184(7):1914-1928.e19. doi:10.1016/j.cell.2021.02.017","ista":"Petridou N, Corominas-Murtra B, Heisenberg C-PJ, Hannezo EB. 2021. Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. 184(7), 1914–1928.e19.","apa":"Petridou, N., Corominas-Murtra, B., Heisenberg, C.-P. J., & Hannezo, E. B. (2021). Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions. Cell. Elsevier. https://doi.org/10.1016/j.cell.2021.02.017","ieee":"N. Petridou, B. Corominas-Murtra, C.-P. J. Heisenberg, and E. B. Hannezo, “Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions,” Cell, vol. 184, no. 7. Elsevier, p. 1914–1928.e19, 2021."},"date_published":"2021-04-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","ddc":["570"],"status":"public","title":"Rigidity percolation uncovers a structural basis for embryonic tissue phase transitions","intvolume":" 184","_id":"9316","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"access_level":"open_access","file_name":"2021_Cell_Petridou.pdf","content_type":"application/pdf","file_size":11405875,"creator":"cziletti","relation":"main_file","file_id":"9534","checksum":"1e5295fbd9c2a459173ec45a0e8a7c2e","success":1,"date_updated":"2021-06-08T10:04:10Z","date_created":"2021-06-08T10:04:10Z"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Embryo morphogenesis is impacted by dynamic changes in tissue material properties, which have been proposed to occur via processes akin to phase transitions (PTs). Here, we show that rigidity percolation provides a simple and robust theoretical framework to predict material/structural PTs of embryonic tissues from local cell connectivity. By using percolation theory, combined with directly monitoring dynamic changes in tissue rheology and cell contact mechanics, we demonstrate that the zebrafish blastoderm undergoes a genuine rigidity PT, brought about by a small reduction in adhesion-dependent cell connectivity below a critical value. We quantitatively predict and experimentally verify hallmarks of PTs, including power-law exponents and associated discontinuities of macroscopic observables. Finally, we show that this uniform PT depends on blastoderm cells undergoing meta-synchronous divisions causing random and, consequently, uniform changes in cell connectivity. Collectively, our theoretical and experimental findings reveal the structural basis of material PTs in an organismal context."}],"issue":"7"},{"article_number":"0623","year":"2020","acknowledgement":"AK was supported by Grant No. FQXi-RFP-1622 from the FQXi foundation, and Grant No. CHE-1648973 from the U.S.\r\nNational Science Foundation. AK would like to thank the Santa Fe Institute for supporting this research. The authors\r\nthank Jordi Fortuny, Rudolf Hanel, Joshua Garland, and Blai Vidiella for helpful discussions, as well as the anonymous\r\nreviewers for their insightful suggestions. ","pmid":1,"publication_status":"published","department":[{"_id":"EdHa"}],"publisher":"The Royal Society","author":[{"last_name":"Kolchinsky","first_name":"Artemy","full_name":"Kolchinsky, Artemy"},{"full_name":"Corominas-Murtra, Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","first_name":"Bernat"}],"date_updated":"2023-08-17T14:31:28Z","date_created":"2020-02-02T23:01:03Z","volume":17,"month":"01","publication_identifier":{"eissn":["17425662"]},"oa":1,"external_id":{"arxiv":["1903.10693"],"pmid":["31964273"],"isi":["000538369800002"]},"main_file_link":[{"url":"https://arxiv.org/abs/1903.10693","open_access":"1"}],"quality_controlled":"1","isi":1,"doi":"10.1098/rsif.2019.0623","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"In many real-world systems, information can be transmitted in two qualitatively different ways: by copying or by transformation. Copying occurs when messages are transmitted without modification, e.g. when an offspring receives an unaltered copy of a gene from its parent. Transformation occurs when messages are modified systematically during transmission, e.g. when mutational biases occur during genetic replication. Standard information-theoretic measures do not distinguish these two modes of information transfer, although they may reflect different mechanisms and have different functional consequences. Starting from a few simple axioms, we derive a decomposition of mutual information into the information transmitted by copying versus the information transmitted by transformation. We begin with a decomposition that applies when the source and destination of the channel have the same set of messages and a notion of message identity exists. We then generalize our decomposition to other kinds of channels, which can involve different source and destination sets and broader notions of similarity. In addition, we show that copy information can be interpreted as the minimal work needed by a physical copying process, which is relevant for understanding the physics of replication. We use the proposed decomposition to explore a model of amino acid substitution rates. Our results apply to any system in which the fidelity of copying, rather than simple predictability, is of critical relevance."}],"issue":"162","_id":"7431","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Decomposing information into copying versus transformation","intvolume":" 17","oa_version":"Preprint","scopus_import":"1","day":"29","article_processing_charge":"No","publication":"Journal of the Royal Society Interface","citation":{"short":"A. Kolchinsky, B. Corominas-Murtra, Journal of the Royal Society Interface 17 (2020).","mla":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” Journal of the Royal Society Interface, vol. 17, no. 162, 0623, The Royal Society, 2020, doi:10.1098/rsif.2019.0623.","chicago":"Kolchinsky, Artemy, and Bernat Corominas-Murtra. “Decomposing Information into Copying versus Transformation.” Journal of the Royal Society Interface. The Royal Society, 2020. https://doi.org/10.1098/rsif.2019.0623.","ama":"Kolchinsky A, Corominas-Murtra B. Decomposing information into copying versus transformation. Journal of the Royal Society Interface. 2020;17(162). doi:10.1098/rsif.2019.0623","apa":"Kolchinsky, A., & Corominas-Murtra, B. (2020). Decomposing information into copying versus transformation. Journal of the Royal Society Interface. The Royal Society. https://doi.org/10.1098/rsif.2019.0623","ieee":"A. Kolchinsky and B. Corominas-Murtra, “Decomposing information into copying versus transformation,” Journal of the Royal Society Interface, vol. 17, no. 162. The Royal Society, 2020.","ista":"Kolchinsky A, Corominas-Murtra B. 2020. Decomposing information into copying versus transformation. Journal of the Royal Society Interface. 17(162), 0623."},"article_type":"original","date_published":"2020-01-29T00:00:00Z"},{"language":[{"iso":"eng"}],"doi":"10.1073/pnas.1921205117","quality_controlled":"1","isi":1,"project":[{"name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["32611816"],"isi":["000553292900014"]},"month":"07","publication_identifier":{"eissn":["10916490"]},"date_created":"2020-08-09T22:00:52Z","date_updated":"2023-08-22T08:29:30Z","volume":117,"author":[{"first_name":"Bernat","last_name":"Corominas-Murtra","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat"},{"full_name":"Scheele, Colinda L.G.J.","first_name":"Colinda L.G.J.","last_name":"Scheele"},{"id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","last_name":"Kishi","first_name":"Kasumi","full_name":"Kishi, Kasumi"},{"full_name":"Ellenbroek, Saskia I.J.","first_name":"Saskia I.J.","last_name":"Ellenbroek"},{"last_name":"Simons","first_name":"Benjamin D.","full_name":"Simons, Benjamin D."},{"full_name":"Van Rheenen, Jacco","last_name":"Van Rheenen","first_name":"Jacco"},{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/order-from-noise/","relation":"press_release"}]},"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"EdHa"}],"acknowledgement":"We thank all members of the E.H., B.D.S., and J.v.R. groups for stimulating discussions. This project was supported by\r\nthe European Research Council (648804 to J.v.R. and 851288 to E.H.). It has also received support from the CancerGenomics.nl (Netherlands Organization for Scientific Research) program (J.v.R.) and the Doctor Josef Steiner Foundation (J.v.R). B.D.S. was supported by Royal Society E. P. Abraham Research Professorship RP/R1/180165 and Wellcome Trust Grant 098357/Z/12/Z.","year":"2020","pmid":1,"file_date_updated":"2020-08-10T06:50:28Z","ec_funded":1,"date_published":"2020-07-21T00:00:00Z","article_type":"original","page":"16969-16975","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"ama":"Corominas-Murtra B, Scheele CLGJ, Kishi K, et al. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 2020;117(29):16969-16975. doi:10.1073/pnas.1921205117","apa":"Corominas-Murtra, B., Scheele, C. L. G. J., Kishi, K., Ellenbroek, S. I. J., Simons, B. D., Van Rheenen, J., & Hannezo, E. B. (2020). Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1921205117","ieee":"B. Corominas-Murtra et al., “Stem cell lineage survival as a noisy competition for niche access,” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29. National Academy of Sciences, pp. 16969–16975, 2020.","ista":"Corominas-Murtra B, Scheele CLGJ, Kishi K, Ellenbroek SIJ, Simons BD, Van Rheenen J, Hannezo EB. 2020. Stem cell lineage survival as a noisy competition for niche access. Proceedings of the National Academy of Sciences of the United States of America. 117(29), 16969–16975.","short":"B. Corominas-Murtra, C.L.G.J. Scheele, K. Kishi, S.I.J. Ellenbroek, B.D. Simons, J. Van Rheenen, E.B. Hannezo, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 16969–16975.","mla":"Corominas-Murtra, Bernat, et al. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America, vol. 117, no. 29, National Academy of Sciences, 2020, pp. 16969–75, doi:10.1073/pnas.1921205117.","chicago":"Corominas-Murtra, Bernat, Colinda L.G.J. Scheele, Kasumi Kishi, Saskia I.J. Ellenbroek, Benjamin D. Simons, Jacco Van Rheenen, and Edouard B Hannezo. “Stem Cell Lineage Survival as a Noisy Competition for Niche Access.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1921205117."},"day":"21","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2020_PNAS_Corominas.pdf","content_type":"application/pdf","file_size":1111604,"creator":"dernst","relation":"main_file","file_id":"8223","success":1,"date_created":"2020-08-10T06:50:28Z","date_updated":"2020-08-10T06:50:28Z"}],"status":"public","ddc":["570"],"title":"Stem cell lineage survival as a noisy competition for niche access","intvolume":" 117","_id":"8220","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Understanding to what extent stem cell potential is a cell-intrinsic property or an emergent behavior coming from global tissue dynamics and geometry is a key outstanding question of systems and stem cell biology. Here, we propose a theory of stem cell dynamics as a stochastic competition for access to a spatially localized niche, giving rise to a stochastic conveyor-belt model. Cell divisions produce a steady cellular stream which advects cells away from the niche, while random rearrangements enable cells away from the niche to be favorably repositioned. Importantly, even when assuming that all cells in a tissue are molecularly equivalent, we predict a common (“universal”) functional dependence of the long-term clonal survival probability on distance from the niche, as well as the emergence of a well-defined number of functional stem cells, dependent only on the rate of random movements vs. mitosis-driven advection. We test the predictions of this theory on datasets of pubertal mammary gland tips and embryonic kidney tips, as well as homeostatic intestinal crypts. Importantly, we find good agreement for the predicted functional dependency of the competition as a function of position, and thus functional stem cell number in each organ. This argues for a key role of positional fluctuations in dictating stem cell number and dynamics, and we discuss the applicability of this theory to other settings.","lang":"eng"}],"issue":"29","type":"journal_article"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000464125500001"]},"oa":1,"quality_controlled":"1","isi":1,"doi":"10.3390/life9010009","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["20751729"]},"month":"01","year":"2019","publisher":"MDPI","department":[{"_id":"EdHa"}],"publication_status":"published","author":[{"id":"43BE2298-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9806-5643","first_name":"Bernat","last_name":"Corominas-Murtra","full_name":"Corominas-Murtra, Bernat"}],"volume":9,"date_updated":"2023-08-24T14:43:41Z","date_created":"2019-02-10T22:59:15Z","article_number":"9","file_date_updated":"2020-07-14T12:47:13Z","citation":{"mla":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life, vol. 9, no. 1, 9, MDPI, 2019, doi:10.3390/life9010009.","short":"B. Corominas-Murtra, Life 9 (2019).","chicago":"Corominas-Murtra, Bernat. “Thermodynamics of Duplication Thresholds in Synthetic Protocell Systems.” Life. MDPI, 2019. https://doi.org/10.3390/life9010009.","ama":"Corominas-Murtra B. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 2019;9(1). doi:10.3390/life9010009","ista":"Corominas-Murtra B. 2019. Thermodynamics of duplication thresholds in synthetic protocell systems. Life. 9(1), 9.","ieee":"B. Corominas-Murtra, “Thermodynamics of duplication thresholds in synthetic protocell systems,” Life, vol. 9, no. 1. MDPI, 2019.","apa":"Corominas-Murtra, B. (2019). Thermodynamics of duplication thresholds in synthetic protocell systems. Life. MDPI. https://doi.org/10.3390/life9010009"},"publication":"Life","date_published":"2019-01-15T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"15","_id":"5944","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 9","status":"public","title":"Thermodynamics of duplication thresholds in synthetic protocell systems","ddc":["570"],"file":[{"relation":"main_file","file_id":"5951","date_created":"2019-02-11T10:45:27Z","date_updated":"2020-07-14T12:47:13Z","checksum":"7d2322cd96ace41959909b66702d5cf4","file_name":"2019_Life_Corominas.pdf","access_level":"open_access","content_type":"application/pdf","file_size":963454,"creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"text":"Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence. In this paper an abstract—yet realistic—synthetic system made of small synthetic protocell aggregates is studied in detail. A fundamental relation between free energy and entropic gradients is derived for a general, non-equilibrium scenario, setting the thermodynamic conditions for the occurrence and prevalence of duplication phenomena. This relation sets explicitly how the energy gradients invested in creating and maintaining structural—and eventually, functional—elements of the system must always compensate the entropic gradients, whose contributions come from changes in the translational, configurational, and macrostate entropies, as well as from dissipation due to irreversible transitions. Work/energy relations are also derived, defining lower bounds on the energy required for the duplication event to take place. A specific example including real ternary emulsions is provided in order to grasp the orders of magnitude involved in the problem. It is found that the minimal work invested over the system to trigger a duplication event is around ~ 10−13J , which results, in the case of duplication of all the vesicles contained in a liter of emulsion, in an amount of energy around ~ 1kJ . Without aiming to describe a truly biological process of duplication, this theoretical contribution seeks to explicitly define and identify the key actors that participate in it.","lang":"eng"}]},{"article_number":"20180395","department":[{"_id":"EdHa"}],"publisher":"Royal Society Publishing","publication_status":"published","year":"2018","volume":15,"date_created":"2019-01-20T22:59:19Z","date_updated":"2023-09-19T10:40:38Z","author":[{"full_name":"Corominas-Murtra, Bernat","last_name":"Corominas-Murtra","first_name":"Bernat","orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Seoane, Luís F.","last_name":"Seoane","first_name":"Luís F."},{"full_name":"Solé, Ricard","last_name":"Solé","first_name":"Ricard"}],"publication_identifier":{"issn":["17425689"]},"month":"12","quality_controlled":"1","isi":1,"oa":1,"external_id":{"arxiv":["1612.01605"],"isi":["000456783800002"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.01605"}],"language":[{"iso":"eng"}],"doi":"10.1098/rsif.2018.0395","type":"journal_article","issue":"149","abstract":[{"text":"A major problem for evolutionary theory is understanding the so-called open-ended nature of evolutionary change, from its definition to its origins. Open-ended evolution (OEE) refers to the unbounded increase in complexity that seems to characterize evolution on multiple scales. This property seems to be a characteristic feature of biological and technological evolution and is strongly tied to the generative potential associated with combinatorics, which allows the system to grow and expand their available state spaces. Interestingly, many complex systems presumably displaying OEE, from language to proteins, share a common statistical property: the presence of Zipf's Law. Given an inventory of basic items (such as words or protein domains) required to build more complex structures (sentences or proteins) Zipf's Law tells us that most of these elements are rare whereas a few of them are extremely common. Using algorithmic information theory, in this paper we provide a fundamental definition for open-endedness, which can be understood as postulates. Its statistical counterpart, based on standard Shannon information theory, has the structure of a variational problem which is shown to lead to Zipf's Law as the expected consequence of an evolutionary process displaying OEE. We further explore the problem of information conservation through an OEE process and we conclude that statistical information (standard Shannon information) is not conserved, resulting in the paradoxical situation in which the increase of information content has the effect of erasing itself. We prove that this paradox is solved if we consider non-statistical forms of information. This last result implies that standard information theory may not be a suitable theoretical framework to explore the persistence and increase of the information content in OEE systems.","lang":"eng"}],"intvolume":" 15","status":"public","title":"Zipf's Law, unbounded complexity and open-ended evolution","_id":"5860","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","scopus_import":"1","article_processing_charge":"No","day":"12","citation":{"ieee":"B. Corominas-Murtra, L. F. Seoane, and R. Solé, “Zipf’s Law, unbounded complexity and open-ended evolution,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018.","apa":"Corominas-Murtra, B., Seoane, L. F., & Solé, R. (2018). Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0395","ista":"Corominas-Murtra B, Seoane LF, Solé R. 2018. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 15(149), 20180395.","ama":"Corominas-Murtra B, Seoane LF, Solé R. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0395","chicago":"Corominas-Murtra, Bernat, Luís F. Seoane, and Ricard Solé. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0395.","short":"B. Corominas-Murtra, L.F. Seoane, R. Solé, Journal of the Royal Society Interface 15 (2018).","mla":"Corominas-Murtra, Bernat, et al. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180395, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0395."},"publication":"Journal of the Royal Society Interface","date_published":"2018-12-12T00:00:00Z"},{"publisher":"The Royal Society","department":[{"_id":"EdHa"}],"publication_status":"published","pmid":1,"year":"2018","acknowledgement":"This work was supported by the James McDonnell Foundation (B.C-M., S.V. and R.S.)","volume":5,"date_updated":"2023-10-18T06:41:12Z","date_created":"2019-01-20T22:59:18Z","author":[{"orcid":"0000-0001-9806-5643","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","first_name":"Bernat","full_name":"Corominas-Murtra, Bernat"},{"first_name":"Martí Sànchez","last_name":"Fibla","full_name":"Fibla, Martí Sànchez"},{"last_name":"Valverde","first_name":"Sergi","full_name":"Valverde, Sergi"},{"last_name":"Solé","first_name":"Ricard","full_name":"Solé, Ricard"}],"article_number":"181286","file_date_updated":"2020-07-14T12:47:13Z","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000456566500027"],"pmid":["30662738"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1098/rsos.181286","publication_identifier":{"issn":["2054-5703"]},"month":"12","intvolume":" 5","title":"Chromatic transitions in the emergence of syntax networks","ddc":["570"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5859","file":[{"checksum":"9664d4417f6b792242e31eea77ce9501","date_updated":"2020-07-14T12:47:13Z","date_created":"2019-02-05T14:38:09Z","relation":"main_file","file_id":"5924","content_type":"application/pdf","file_size":646732,"creator":"dernst","access_level":"open_access","file_name":"2018_RoyalSocOS_Corominas.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"12","abstract":[{"text":"The emergence of syntax during childhood is a remarkable example of how complex correlations unfold in nonlinear ways through development. In particular, rapid transitions seem to occur as children reach the age of two, which seems to separate a two-word, tree-like network of syntactic relations among words from the scale-free graphs associated with the adult, complex grammar. Here, we explore the evolution of syntax networks through language acquisition using the chromatic number, which captures the transition and provides a natural link to standard theories on syntactic structures. The data analysis is compared to a null model of network growth dynamics which is shown to display non-trivial and sensible differences. At a more general level, we observe that the chromatic classes define independent regions of the graph, and thus, can be interpreted as the footprints of incompatibility relations, somewhat as opposed to modularity considerations.","lang":"eng"}],"article_type":"original","citation":{"chicago":"Corominas-Murtra, Bernat, Martí Sànchez Fibla, Sergi Valverde, and Ricard Solé. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science. The Royal Society, 2018. https://doi.org/10.1098/rsos.181286.","mla":"Corominas-Murtra, Bernat, et al. “Chromatic Transitions in the Emergence of Syntax Networks.” Royal Society Open Science, vol. 5, no. 12, 181286, The Royal Society, 2018, doi:10.1098/rsos.181286.","short":"B. Corominas-Murtra, M.S. Fibla, S. Valverde, R. Solé, Royal Society Open Science 5 (2018).","ista":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. 2018. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 5(12), 181286.","apa":"Corominas-Murtra, B., Fibla, M. S., Valverde, S., & Solé, R. (2018). Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. The Royal Society. https://doi.org/10.1098/rsos.181286","ieee":"B. Corominas-Murtra, M. S. Fibla, S. Valverde, and R. Solé, “Chromatic transitions in the emergence of syntax networks,” Royal Society Open Science, vol. 5, no. 12. The Royal Society, 2018.","ama":"Corominas-Murtra B, Fibla MS, Valverde S, Solé R. Chromatic transitions in the emergence of syntax networks. Royal Society Open Science. 2018;5(12). doi:10.1098/rsos.181286"},"publication":"Royal Society Open Science","date_published":"2018-12-12T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"12"}]