[{"publication":"Proceedings of the National Academy of Sciences of the United States of America","ddc":["570"],"status":"public","month":"10","corr_author":"1","issue":"44","language":[{"iso":"eng"}],"OA_type":"hybrid","intvolume":"       121","pmid":1,"abstract":[{"text":"As their statistical power grows, genome-wide association studies (GWAS) have identified an increasing number of loci underlying quantitative traits of interest. These loci are scattered throughout the genome and are individually responsible only for small fractions of the total heritable trait variance. The recently proposed omnigenic model provides a conceptual framework to explain these observations by postulating that numerous distant loci contribute to each complex trait via effect propagation through intracellular regulatory networks. We formalize this conceptual framework by proposing the “quantitative omnigenic model” (QOM), a statistical model that combines prior knowledge of the regulatory network topology with genomic data. By applying our model to gene expression traits in yeast, we demonstrate that QOM achieves similar gene expression prediction performance to traditional GWAS with hundreds of times less parameters, while simultaneously extracting candidate causal and quantitative chains of effect propagation through the regulatory network for every individual gene. We estimate the fraction of heritable trait variance in cis- and in trans-, break the latter down by effect propagation order, assess the trans- variance not attributable to transcriptional regulation, and show that QOM correctly accounts for the low-dimensional structure of gene expression covariance. We furthermore demonstrate the relevance of QOM for systems biology, by employing it as a statistical test for the quality of regulatory network reconstructions, and linking it to the propagation of nontranscriptional (including environmental) effects.","lang":"eng"}],"date_created":"2024-11-10T23:01:59Z","has_accepted_license":"1","publisher":"National Academy of Sciences","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-10-29T00:00:00Z","article_number":"e2402340121","year":"2024","article_processing_charge":"Yes","publication_status":"published","file":[{"success":1,"file_id":"18536","date_updated":"2024-11-11T09:31:00Z","date_created":"2024-11-11T09:31:00Z","relation":"main_file","checksum":"d930e2ccf9ec900c7d7509a78cfb3564","creator":"dernst","file_name":"2024_PNAS_Ruzickova.pdf","file_size":25529709,"access_level":"open_access","content_type":"application/pdf"}],"type":"journal_article","isi":1,"oa":1,"_id":"18525","quality_controlled":"1","oa_version":"Published Version","APC_amount":"3062,93 EUR","project":[{"name":"Collective behaviour of cells in pancreatic Islets of Langerhans","_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.1073/pnas.2402340121","citation":{"short":"N. Ruzickova, M. Hledik, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","chicago":"Ruzickova, Natalia, Michal Hledik, and Gašper Tkačik. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” <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.2402340121\">https://doi.org/10.1073/pnas.2402340121</a>.","apa":"Ruzickova, N., Hledik, M., &#38; Tkačik, G. (2024). Quantitative omnigenic model discovers interpretable genome-wide associations. <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.2402340121\">https://doi.org/10.1073/pnas.2402340121</a>","ama":"Ruzickova N, Hledik M, Tkačik G. Quantitative omnigenic model discovers interpretable genome-wide associations. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(44). doi:<a href=\"https://doi.org/10.1073/pnas.2402340121\">10.1073/pnas.2402340121</a>","ista":"Ruzickova N, Hledik M, Tkačik G. 2024. Quantitative omnigenic model discovers interpretable genome-wide associations. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2402340121.","ieee":"N. Ruzickova, M. Hledik, and G. Tkačik, “Quantitative omnigenic model discovers interpretable genome-wide associations,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024.","mla":"Ruzickova, Natalia, et al. “Quantitative Omnigenic Model Discovers Interpretable Genome-Wide Associations.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2402340121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2402340121\">10.1073/pnas.2402340121</a>."},"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"scopus_import":"1","volume":121,"date_updated":"2026-08-10T07:47:55Z","title":"Quantitative omnigenic model discovers interpretable genome-wide associations","author":[{"last_name":"Ruzickova","first_name":"Natalia","id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia"},{"last_name":"Hledik","first_name":"Michal","full_name":"Hledik, Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"OA_place":"publisher","external_id":{"pmid":["39441639"],"isi":["001349462600001"]},"file_date_updated":"2024-11-11T09:31:00Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"related_material":{"record":[{"id":"20357","relation":"dissertation_contains","status":"public"}]},"acknowledgement":"N.R.acknowledges the support of the Austrian Academy of Sciences through the Doctoral Fellowship Programme (DOC) of the Austrian Academy of Sciences 26917. M.H. and G.T. were supported in part by the Human Frontiers Science Program Grant RGP0034/2018. We thank Nicholas H. Barton, Fyodor Kondrashov, and Matthew R. Robinson for fruitful discussions.","article_type":"original","day":"29"},{"external_id":{"pmid":["37766992"],"isi":["001082331200001"]},"day":"20","article_type":"original","acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411, and from the Austrian Science Fund (FWF) under the Lise Meitner fellowship No. PT1013M03318. IA acknowledges financial support from the MIUR PRIN 2017WZFTZP.","publication_identifier":{"eissn":["2589-0042"]},"file_date_updated":"2023-10-09T07:23:46Z","title":"Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture","date_updated":"2025-04-14T07:44:00Z","author":[{"full_name":"Scarpetta, Silvia","first_name":"Silvia","last_name":"Scarpetta"},{"first_name":"Niccolò","last_name":"Morrisi","full_name":"Morrisi, Niccolò"},{"full_name":"Mutti, Carlotta","last_name":"Mutti","first_name":"Carlotta"},{"first_name":"Nicoletta","last_name":"Azzi","full_name":"Azzi, Nicoletta"},{"full_name":"Trippi, Irene","first_name":"Irene","last_name":"Trippi"},{"full_name":"Ciliento, Rosario","last_name":"Ciliento","first_name":"Rosario"},{"first_name":"Ilenia","last_name":"Apicella","full_name":"Apicella, Ilenia"},{"full_name":"Messuti, Giovanni","first_name":"Giovanni","last_name":"Messuti"},{"first_name":"Marianna","last_name":"Angiolelli","full_name":"Angiolelli, Marianna"},{"first_name":"Fabrizio","last_name":"Lombardi","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"first_name":"Liborio","last_name":"Parrino","full_name":"Parrino, Liborio"},{"full_name":"Vaudano, Anna Elisabetta","last_name":"Vaudano","first_name":"Anna Elisabetta"}],"doi":"10.1016/j.isci.2023.107840","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Scarpetta, Silvia, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” <i>IScience</i>, vol. 26, no. 10, Elsevier, 2023, p. 107840, doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107840\">10.1016/j.isci.2023.107840</a>.","ieee":"S. Scarpetta <i>et al.</i>, “Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture,” <i>iScience</i>, vol. 26, no. 10. Elsevier, p. 107840, 2023.","ista":"Scarpetta S, Morrisi N, Mutti C, Azzi N, Trippi I, Ciliento R, Apicella I, Messuti G, Angiolelli M, Lombardi F, Parrino L, Vaudano AE. 2023. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. iScience. 26(10), 107840.","ama":"Scarpetta S, Morrisi N, Mutti C, et al. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. <i>iScience</i>. 2023;26(10):107840. doi:<a href=\"https://doi.org/10.1016/j.isci.2023.107840\">10.1016/j.isci.2023.107840</a>","apa":"Scarpetta, S., Morrisi, N., Mutti, C., Azzi, N., Trippi, I., Ciliento, R., … Vaudano, A. E. (2023). Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2023.107840\">https://doi.org/10.1016/j.isci.2023.107840</a>","chicago":"Scarpetta, Silvia, Niccolò Morrisi, Carlotta Mutti, Nicoletta Azzi, Irene Trippi, Rosario Ciliento, Ilenia Apicella, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” <i>IScience</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.isci.2023.107840\">https://doi.org/10.1016/j.isci.2023.107840</a>.","short":"S. Scarpetta, N. Morrisi, C. Mutti, N. Azzi, I. Trippi, R. Ciliento, I. Apicella, G. Messuti, M. Angiolelli, F. Lombardi, L. Parrino, A.E. Vaudano, IScience 26 (2023) 107840."},"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67"}],"volume":26,"department":[{"_id":"GaTk"}],"scopus_import":"1","oa_version":"Published Version","quality_controlled":"1","_id":"12487","oa":1,"ec_funded":1,"type":"journal_article","isi":1,"page":"107840","date_published":"2023-10-20T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2023-10-09T07:23:46Z","file_id":"14412","success":1,"content_type":"application/pdf","access_level":"open_access","file_size":4872708,"creator":"dernst","file_name":"2023_iScience_Scarpetta.pdf","checksum":"f499836af172ecc9865de4bb41fa99d1","relation":"main_file","date_created":"2023-10-09T07:23:46Z"}],"publication_status":"published","article_processing_charge":"Yes","year":"2023","intvolume":"        26","language":[{"iso":"eng"}],"publisher":"Elsevier","has_accepted_license":"1","pmid":1,"date_created":"2023-02-02T10:50:17Z","abstract":[{"text":"Sleep plays a key role in preserving brain function, keeping the brain network in a state that ensures optimal computational capabilities. Empirical evidence indicates that such a state is consistent with criticality, where scale-free neuronal avalanches emerge. However, the relationship between sleep, emergent avalanches, and criticality remains poorly understood. Here we fully characterize the critical behavior of avalanches during sleep, and study their relationship with the sleep macro- and micro-architecture, in particular the cyclic alternating pattern (CAP). We show that avalanche size and duration distributions exhibit robust power laws with exponents approximately equal to −3/2 e −2, respectively. Importantly, we find that sizes scale as a power law of the durations, and that all critical exponents for neuronal avalanches obey robust scaling relations, which are consistent with the mean-field directed percolation universality class. Our analysis demonstrates that avalanche dynamics depends on the position within the NREM-REM cycles, with the avalanche density increasing in the descending phases and decreasing in the ascending phases of sleep cycles. Moreover, we show that, within NREM sleep, avalanche occurrence correlates with CAP activation phases, particularly A1, which are the expression of slow wave sleep propensity and have been proposed to be beneficial for cognitive processes. The results suggest that neuronal avalanches, and thus tuning to criticality, actively contribute to sleep development and play a role in preserving network function. Such findings, alongside characterization of the universality class for avalanches, open new avenues to the investigation of functional role of criticality during sleep with potential clinical application.</jats:p><jats:sec><jats:title>Significance statement</jats:title><jats:p>We fully characterize the critical behavior of neuronal avalanches during sleep, and show that avalanches follow precise scaling laws that are consistent with the mean-field directed percolation universality class. The analysis provides first evidence of a functional relationship between avalanche occurrence, slow-wave sleep dynamics, sleep stage transitions and occurrence of CAP phase A during NREM sleep. Because CAP is considered one of the major guardians of NREM sleep that allows the brain to dynamically react to external perturbation and contributes to the cognitive consolidation processes occurring in sleep, our observations suggest that neuronal avalanches at criticality are associated with flexible response to external inputs and to cognitive processes, a key assumption of the critical brain hypothesis.","lang":"eng"}],"ddc":["570"],"status":"public","month":"10","publication":"iScience","issue":"10"},{"acknowledged_ssus":[{"_id":"LifeSc"}],"month":"06","ddc":["570"],"corr_author":"1","status":"public","publication":"Nature Communications","publisher":"Springer Nature","pmid":1,"has_accepted_license":"1","date_created":"2023-06-11T22:00:40Z","abstract":[{"text":"Cooperative disease defense emerges as group-level collective behavior, yet how group members make the underlying individual decisions is poorly understood. Using garden ants and fungal pathogens as an experimental model, we derive the rules governing individual ant grooming choices and show how they produce colony-level hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic modeling reveal that ants increase grooming and preferentially target highly-infectious individuals when perceiving high pathogen load, but transiently suppress grooming after having been groomed by nestmates. Ants thus react to both, the infectivity of others and the social feedback they receive on their own contagiousness. While inferred solely from momentary ant decisions, these behavioral rules quantitatively predict hour-long experimental dynamics, and synergistically combine into efficient colony-wide pathogen removal. Our analyses show that noisy individual decisions based on only local, incomplete, yet dynamically-updated information on pathogen threat and social feedback can lead to potent collective disease defense.","lang":"eng"}],"intvolume":"        14","language":[{"iso":"eng"}],"file":[{"date_updated":"2023-06-13T08:05:46Z","file_id":"13132","success":1,"file_size":2358167,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-06-13T08:05:46Z","file_name":"2023_NatureComm_CasillasPerez.pdf","checksum":"4af0393e3ed47b3fc46e68b81c3c1007","creator":"dernst"}],"article_processing_charge":"Yes","year":"2023","publication_status":"published","article_number":"3232","date_published":"2023-06-03T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"isi":1,"ec_funded":1,"type":"journal_article","oa_version":"Published Version","quality_controlled":"1","_id":"13127","volume":14,"scopus_import":"1","department":[{"_id":"SyCr"},{"_id":"GaTk"}],"doi":"10.1038/s41467-023-38947-y","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38947-y\">https://doi.org/10.1038/s41467-023-38947-y</a>.","short":"B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023).","mla":"Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” <i>Nature Communications</i>, vol. 14, 3232, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38947-y\">10.1038/s41467-023-38947-y</a>.","ieee":"B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ista":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 14, 3232.","ama":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen detection and social feedback shape collective hygiene in ants. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-38947-y\">10.1038/s41467-023-38947-y</a>","apa":"Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., &#38; Cremer, S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene in ants. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38947-y\">https://doi.org/10.1038/s41467-023-38947-y</a>"},"project":[{"name":"Epidemics in ant societies on a chip","grant_number":"771402","call_identifier":"H2020","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"},{"_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012"}],"author":[{"first_name":"Barbara E","last_name":"Casillas Perez","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","full_name":"Casillas Perez, Barbara E"},{"full_name":"Bod'Ová, Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bod'Ová","orcid":"0000-0002-7214-0171","first_name":"Katarína"},{"first_name":"Anna V","last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"},{"orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia"}],"date_updated":"2025-04-14T07:47:53Z","title":"Dynamic pathogen detection and social feedback shape collective hygiene in ants","related_material":{"record":[{"id":"12945","relation":"research_data","status":"public"}]},"file_date_updated":"2023-06-13T08:05:46Z","article_type":"original","acknowledgement":"We thank Mike Bidochka for the fungal strains, the ISTA Social Immunity Team for ant collection, Hanna Leitner for experimental and molecular support, Jennifer Robb and Lukas Lindorfer for microscopy, and the LabSupport Facility at ISTA for general laboratory support. We further thank Victor Mireles, Iain Couzin, Fabian Theis and the Social Immunity Team for continued feedback throughout, and Michael Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg for comments on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","publication_identifier":{"eissn":["2041-1723"]},"day":"03","external_id":{"pmid":["37270641"],"isi":["001002562700005"]}},{"author":[{"first_name":"Manuel","last_name":"Reinhardt","full_name":"Reinhardt, Manuel"},{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"},{"first_name":"Pieter Rein","last_name":"Ten Wolde","full_name":"Ten Wolde, Pieter Rein"}],"date_updated":"2025-09-09T13:18:24Z","title":"Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories","article_type":"original","file_date_updated":"2023-11-13T09:00:19Z","publication_identifier":{"eissn":["2160-3308"]},"acknowledgement":"We thank Bela Mulder, Tom Shimizu, Fotios Avgidis, Peter Bolhuis, and Daan Frenkel for useful discussions and a careful reading of the manuscript, and we thank Age Tjalma for support with obtaining the Gaussian approximation of the chemotaxis system. This work is part of the Dutch Research Council (NWO) and was performed at the research institute AMOLF. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 885065) and was\r\nfinancially supported by NWO through the “Building a Synthetic Cell (BaSyC)” Gravitation Grant (024.003.019).","day":"26","arxiv":1,"external_id":{"arxiv":["2203.03461"],"isi":["001122894200001"]},"_id":"14515","oa_version":"Published Version","quality_controlled":"1","department":[{"_id":"GaTk"}],"scopus_import":"1","volume":13,"doi":"10.1103/PhysRevX.13.041017","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Reinhardt M, Tkačik G, Ten Wolde PR. 2023. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. Physical Review X. 13(4), 041017.","ama":"Reinhardt M, Tkačik G, Ten Wolde PR. Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. <i>Physical Review X</i>. 2023;13(4). doi:<a href=\"https://doi.org/10.1103/PhysRevX.13.041017\">10.1103/PhysRevX.13.041017</a>","apa":"Reinhardt, M., Tkačik, G., &#38; Ten Wolde, P. R. (2023). Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevX.13.041017\">https://doi.org/10.1103/PhysRevX.13.041017</a>","ieee":"M. Reinhardt, G. Tkačik, and P. R. Ten Wolde, “Path weight sampling: Exact Monte Carlo computation of the mutual information between stochastic trajectories,” <i>Physical Review X</i>, vol. 13, no. 4. American Physical Society, 2023.","mla":"Reinhardt, Manuel, et al. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” <i>Physical Review X</i>, vol. 13, no. 4, 041017, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevX.13.041017\">10.1103/PhysRevX.13.041017</a>.","short":"M. Reinhardt, G. Tkačik, P.R. Ten Wolde, Physical Review X 13 (2023).","chicago":"Reinhardt, Manuel, Gašper Tkačik, and Pieter Rein Ten Wolde. “Path Weight Sampling: Exact Monte Carlo Computation of the Mutual Information between Stochastic Trajectories.” <i>Physical Review X</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevX.13.041017\">https://doi.org/10.1103/PhysRevX.13.041017</a>."},"year":"2023","article_processing_charge":"Yes","publication_status":"published","file":[{"success":1,"file_id":"14522","date_updated":"2023-11-13T09:00:19Z","creator":"dernst","checksum":"32574aeebcca7347a4152c611b66b3d5","file_name":"2023_PhysReviewX_Reinhardt.pdf","relation":"main_file","date_created":"2023-11-13T09:00:19Z","content_type":"application/pdf","access_level":"open_access","file_size":1595223}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"041017","date_published":"2023-10-26T00:00:00Z","type":"journal_article","isi":1,"oa":1,"issue":"4","month":"10","ddc":["530"],"status":"public","publication":"Physical Review X","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Most natural and engineered information-processing systems transmit information via signals that vary in time. Computing the information transmission rate or the information encoded in the temporal characteristics of these signals requires the mutual information between the input and output signals as a function of time, i.e., between the input and output trajectories. Yet, this is notoriously difficult because of the high-dimensional nature of the trajectory space, and all existing techniques require approximations. We present an exact Monte Carlo technique called path weight sampling (PWS) that, for the first time, makes it possible to compute the mutual information between input and output trajectories for any stochastic system that is described by a master equation. The principal idea is to use the master equation to evaluate the exact conditional probability of an individual output trajectory for a given input trajectory and average this via Monte Carlo sampling in trajectory space to obtain the mutual information. We present three variants of PWS, which all generate the trajectories using the standard stochastic simulation algorithm. While direct PWS is a brute-force method, Rosenbluth-Rosenbluth PWS exploits the analogy between signal trajectory sampling and polymer sampling, and thermodynamic integration PWS is based on a reversible work calculation in trajectory space. PWS also makes it possible to compute the mutual information between input and output trajectories for systems with hidden internal states as well as systems with feedback from output to input. Applying PWS to the bacterial chemotaxis system, consisting of 182 coupled chemical reactions, demonstrates not only that the scheme is highly efficient but also that the number of receptor clusters is much smaller than hitherto believed, while their size is much larger."}],"date_created":"2023-11-12T23:00:55Z","publisher":"American Physical Society","language":[{"iso":"eng"}],"intvolume":"        13"},{"author":[{"first_name":"Simon","last_name":"Rella","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","full_name":"Rella, Simon"},{"first_name":"Y","last_name":"Kulikova","full_name":"Kulikova, Y"},{"id":"87DF77F0-1D9A-11EA-B6AE-CE443DDC885E","full_name":"Minnegalieva, Aygul","first_name":"Aygul","last_name":"Minnegalieva"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor"}],"title":"Complex vaccination strategies prevent the emergence of vaccine resistance","date_updated":"2025-09-08T09:58:11Z","day":"01","file_date_updated":"2024-01-24T11:12:33Z","publication_identifier":{"issn":["1101-1262"],"eissn":["1464-360X"]},"related_material":{"record":[{"status":"public","id":"18307","relation":"used_in_publication"}]},"license":"https://creativecommons.org/licenses/by-nc/4.0/","_id":"14862","oa_version":"Published Version","quality_controlled":"1","department":[{"_id":"GaTk"}],"volume":33,"doi":"10.1093/eurpub/ckad160.597","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"citation":{"short":"S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal of Public Health, Oxford University Press, 2023.","chicago":"Rella, Simon, Y Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” In <i>European Journal of Public Health</i>, Vol. 33. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">https://doi.org/10.1093/eurpub/ckad160.597</a>.","ista":"Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. 2023. Complex vaccination strategies prevent the emergence of vaccine resistance. European Journal of Public Health. vol. 33, ckad160.597.","ama":"Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. Complex vaccination strategies prevent the emergence of vaccine resistance. In: <i>European Journal of Public Health</i>. Vol 33. Oxford University Press; 2023. doi:<a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">10.1093/eurpub/ckad160.597</a>","apa":"Rella, S., Kulikova, Y., Minnegalieva, A., &#38; Kondrashov, F. (2023). Complex vaccination strategies prevent the emergence of vaccine resistance. In <i>European Journal of Public Health</i> (Vol. 33). Oxford University Press. <a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">https://doi.org/10.1093/eurpub/ckad160.597</a>","mla":"Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” <i>European Journal of Public Health</i>, vol. 33, no. Supplement_2, ckad160.597, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/eurpub/ckad160.597\">10.1093/eurpub/ckad160.597</a>.","ieee":"S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination strategies prevent the emergence of vaccine resistance,” in <i>European Journal of Public Health</i>, 2023, vol. 33, no. Supplement_2."},"publication_status":"published","keyword":["Public Health","Environmental and Occupational Health"],"year":"2023","article_processing_charge":"No","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":71057,"checksum":"98706755bb4cc5d553818ade7660a7d2","file_name":"2023_EurJourPublicHealth_Rella.pdf","creator":"dernst","date_created":"2024-01-24T11:12:33Z","relation":"main_file","date_updated":"2024-01-24T11:12:33Z","file_id":"14882","success":1}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-10-01T00:00:00Z","article_number":"ckad160.597","type":"conference_abstract","oa":1,"issue":"Supplement_2","corr_author":"1","ddc":["570"],"month":"10","publication":"European Journal of Public Health","status":"public","date_created":"2024-01-22T12:02:28Z","has_accepted_license":"1","publisher":"Oxford University Press","language":[{"iso":"eng"}],"intvolume":"        33"},{"oa":1,"ec_funded":1,"isi":1,"type":"journal_article","article_number":"113162","date_published":"2023-10-31T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2024-01-30T14:07:08Z","file_id":"14914","success":1,"access_level":"open_access","content_type":"application/pdf","file_size":5599007,"creator":"dernst","file_name":"2023_CellReports_Lombardi.pdf","checksum":"9c71eb2a03aa160415f01ad95f49ceb5","date_created":"2024-01-30T14:07:08Z","relation":"main_file"}],"publication_status":"published","article_processing_charge":"Yes","year":"2023","intvolume":"        42","language":[{"iso":"eng"}],"publisher":"Elsevier","has_accepted_license":"1","date_created":"2023-10-08T22:01:15Z","pmid":1,"abstract":[{"text":"Alpha oscillations are a distinctive feature of the awake resting state of the human brain. However, their functional role in resting-state neuronal dynamics remains poorly understood. Here we show that, during resting wakefulness, alpha oscillations drive an alternation of attenuation and amplification bouts in neural activity. Our analysis indicates that inhibition is activated in pulses that last for a single alpha cycle and gradually suppress neural activity, while excitation is successively enhanced over a few alpha cycles to amplify neural activity. Furthermore, we show that long-term alpha amplitude fluctuations—the “waxing and waning” phenomenon—are an attenuation-amplification mechanism described by a power-law decay of the activity rate in the “waning” phase. Importantly, we do not observe such dynamics during non-rapid eye movement (NREM) sleep with marginal alpha oscillations. The results suggest that alpha oscillations modulate neural activity not only through pulses of inhibition (pulsed inhibition hypothesis) but also by timely enhancement of excitation (or disinhibition).","lang":"eng"}],"status":"public","corr_author":"1","publication":"Cell Reports","ddc":["570"],"month":"10","issue":"10","external_id":{"isi":["001086695500001"],"pmid":["37777965"]},"day":"31","file_date_updated":"2024-01-30T14:07:08Z","related_material":{"record":[{"id":"10821","relation":"earlier_version","status":"public"}]},"acknowledgement":"This research was funded in whole or in part by the Austrian Science Fund (FWF) (grant PT1013M03318 to F.L.). For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 Research and Innovation Program under the Marie Sklodowska-Curie action (grant agreement 754411 to F.L.) and in part by the NextGenerationEU through the grant TAlent in ReSearch@University of Padua – STARS@UNIPD (to F.L.) (project BRAINCIP [brain criticality and information processing]). L.d.A. acknowledges support from the Italian MIUR project PRIN2017WZFTZP and partial support from NEXTGENERATIONEU (NGEU) funded by the Ministry of University and Research (MUR), National Recovery and Resilience Plan (NRRP), and project MNESYS (PE0000006)—a multiscale integrated approach to the study of the nervous system in health and disease (DN. 1553 11.10.2022). O.S. acknowledges support from the Israel Science Foundation, grant 504/17. The work was supported in part by DIRP ZIAMH02797 (to D.P.).","article_type":"original","publication_identifier":{"eissn":["2211-1247"]},"title":"Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state","date_updated":"2026-07-06T12:48:55Z","author":[{"first_name":"Fabrizio","last_name":"Lombardi","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"first_name":"Hans J.","last_name":"Herrmann","full_name":"Herrmann, Hans J."},{"first_name":"Liborio","last_name":"Parrino","full_name":"Parrino, Liborio"},{"first_name":"Dietmar","last_name":"Plenz","full_name":"Plenz, Dietmar"},{"full_name":"Scarpetta, Silvia","last_name":"Scarpetta","first_name":"Silvia"},{"last_name":"Vaudano","first_name":"Anna Elisabetta","full_name":"Vaudano, Anna Elisabetta"},{"full_name":"De Arcangelis, Lucilla","first_name":"Lucilla","last_name":"De Arcangelis"},{"first_name":"Oren","last_name":"Shriki","full_name":"Shriki, Oren"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1016/j.celrep.2023.113162","citation":{"short":"F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. De Arcangelis, O. Shriki, Cell Reports 42 (2023).","chicago":"Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla De Arcangelis, and Oren Shriki. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification of Neural Activity in the Awake Resting State.” <i>Cell Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">https://doi.org/10.1016/j.celrep.2023.113162</a>.","apa":"Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano, A. E., … Shriki, O. (2023). Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">https://doi.org/10.1016/j.celrep.2023.113162</a>","ista":"Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, De Arcangelis L, Shriki O. 2023. Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. Cell Reports. 42(10), 113162.","ama":"Lombardi F, Herrmann HJ, Parrino L, et al. Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. <i>Cell Reports</i>. 2023;42(10). doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">10.1016/j.celrep.2023.113162</a>","mla":"Lombardi, Fabrizio, et al. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification of Neural Activity in the Awake Resting State.” <i>Cell Reports</i>, vol. 42, no. 10, 113162, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">10.1016/j.celrep.2023.113162</a>.","ieee":"F. Lombardi <i>et al.</i>, “Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state,” <i>Cell Reports</i>, vol. 42, no. 10. Elsevier, 2023."},"project":[{"name":"Functional Advantages of Critical Brain Dynamics","grant_number":"M03318","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"volume":42,"scopus_import":"1","department":[{"_id":"GaTk"}],"quality_controlled":"1","oa_version":"Published Version","_id":"14402"},{"_id":"12762","quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"GaTk"},{"_id":"GradSch"}],"scopus_import":"1","volume":3,"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","name":"Functional Advantages of Critical Brain Dynamics","grant_number":"M03318"},{"_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism","grant_number":"P34015"}],"citation":{"ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain,” <i>Nature Computational Science</i>, vol. 3. Springer Nature, pp. 254–263, 2023.","mla":"Lombardi, Fabrizio, et al. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” <i>Nature Computational Science</i>, vol. 3, Springer Nature, 2023, pp. 254–63, doi:<a href=\"https://doi.org/10.1038/s43588-023-00410-9\">10.1038/s43588-023-00410-9</a>.","ista":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. 2023. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. Nature Computational Science. 3, 254–263.","apa":"Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., &#38; De Martino, D. (2023). Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. <i>Nature Computational Science</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s43588-023-00410-9\">https://doi.org/10.1038/s43588-023-00410-9</a>","ama":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain. <i>Nature Computational Science</i>. 2023;3:254-263. doi:<a href=\"https://doi.org/10.1038/s43588-023-00410-9\">10.1038/s43588-023-00410-9</a>","chicago":"Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Statistical Modeling of Adaptive Neural Networks Explains Co-Existence of Avalanches and Oscillations in Resting Human Brain.” <i>Nature Computational Science</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s43588-023-00410-9\">https://doi.org/10.1038/s43588-023-00410-9</a>.","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, Nature Computational Science 3 (2023) 254–263."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s43588-023-00410-9","author":[{"last_name":"Lombardi","orcid":"0000-0003-2623-5249","first_name":"Fabrizio","full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"first_name":"Selver","last_name":"Pepic","full_name":"Pepic, Selver","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425"},{"last_name":"Shriki","first_name":"Oren","full_name":"Shriki, Oren"},{"first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"},{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino","first_name":"Daniele"}],"date_updated":"2026-07-29T06:53:41Z","title":"Statistical modeling of adaptive neural networks explains co-existence of avalanches and oscillations in resting human brain","file_date_updated":"2023-08-16T12:39:57Z","publication_identifier":{"eissn":["2662-8457"]},"article_type":"original","related_material":{"record":[{"relation":"earlier_version","id":"10912","status":"public"}]},"acknowledgement":"This research was funded in whole, or in part, by the Austrian Science Fund (FWF) (grant no. PT1013M03318 to F.L. and no. P34015 to G.T.). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 research and innovation program under the Marie Sklodowska-Curie action (grant agreement No. 754411 to F.L.).","day":"20","arxiv":1,"external_id":{"pmid":["38177880"],"arxiv":["2108.06686"],"isi":["000968161800002"]},"status":"public","month":"03","ddc":["570"],"corr_author":"1","publication":"Nature Computational Science","pmid":1,"has_accepted_license":"1","abstract":[{"text":"Neurons in the brain are wired into adaptive networks that exhibit collective dynamics as diverse as scale-specific oscillations and scale-free neuronal avalanches. Although existing models account for oscillations and avalanches separately, they typically do not explain both phenomena, are too complex to analyze analytically or intractable to infer from data rigorously. Here we propose a feedback-driven Ising-like class of neural networks that captures avalanches and oscillations simultaneously and quantitatively. In the simplest yet fully microscopic model version, we can analytically compute the phase diagram and make direct contact with human brain resting-state activity recordings via tractable inference of the model’s two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor oscillations to collective behaviors of extreme events and neuronal avalanches. Importantly, the inferred parameters indicate that the co-existence of scale-specific (oscillations) and scale-free (avalanches) dynamics occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations.","lang":"eng"}],"date_created":"2023-03-26T22:01:08Z","publisher":"Springer Nature","language":[{"iso":"eng"}],"intvolume":"         3","article_processing_charge":"No","year":"2023","publication_status":"published","file":[{"relation":"main_file","date_created":"2023-08-16T12:39:57Z","file_name":"2023_NatureCompScience_Lombardi.pdf","creator":"dernst","checksum":"7c63b2b2edfd68aaffe96d70ca6a865a","file_size":4474284,"content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"14073","date_updated":"2023-08-16T12:39:57Z"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2023-03-20T00:00:00Z","page":"254-263","type":"journal_article","ec_funded":1,"isi":1,"oa":1},{"day":"29","acknowledgement":"M.N. was supported by the European Union Horizon 2020 Grant 665385. J.C. was supported by the European Research Council Consolidator Grant 281511. G.T. was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported by an Institute of Science and Technology fellow award and by the National Science Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella, Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi, Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"10077"}]},"publication_identifier":{"eissn":["1529-2401"]},"file_date_updated":"2024-06-02T22:30:03Z","article_type":"original","external_id":{"pmid":["37758476"],"isi":["001148071000005"]},"author":[{"first_name":"Michele","orcid":"0000-0001-8849-6570","last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","full_name":"Nardin, Michele"},{"orcid":"0000-0002-5193-4036","last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L"},{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","last_name":"Savin"}],"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","date_updated":"2026-07-06T12:47:25Z","volume":43,"scopus_import":"1","department":[{"_id":"JoCs"},{"_id":"GaTk"}],"doi":"10.1523/JNEUROSCI.0194-23.2023","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156.","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. 2023;43(48):8140-8156. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>, vol. 43, no. 48, Society for Neuroscience, 2023, pp. 8140–56, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>.","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>The Journal of Neuroscience</i>, vol. 43, no. 48. Society for Neuroscience, pp. 8140–8156, 2023.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>. Society for Neuroscience, 2023. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>."},"project":[{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511","call_identifier":"FP7","_id":"257A4776-B435-11E9-9278-68D0E5697425"},{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"oa_version":"Published Version","quality_controlled":"1","_id":"14656","page":"8140-8156","oa":1,"ec_funded":1,"isi":1,"type":"journal_article","file":[{"embargo":"2024-06-01","file_id":"14674","date_updated":"2024-06-02T22:30:03Z","date_created":"2023-12-11T11:30:37Z","relation":"main_file","creator":"dernst","file_name":"2023_JourNeuroscience_Nardin.pdf","checksum":"e2503c8f84be1050e28f64320f1d5bd2","file_size":2280632,"access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","year":"2023","article_processing_charge":"Yes (in subscription journal)","date_published":"2023-11-29T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Society for Neuroscience","has_accepted_license":"1","abstract":[{"text":"Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.","lang":"eng"}],"pmid":1,"date_created":"2023-12-10T23:00:58Z","intvolume":"        43","language":[{"iso":"eng"}],"issue":"48","ddc":["570"],"status":"public","publication":"The Journal of Neuroscience","month":"11"},{"author":[{"last_name":"Ngampruetikorn","first_name":"Vudtiwat","full_name":"Ngampruetikorn, Vudtiwat"},{"last_name":"Sachdeva","first_name":"Vedant","full_name":"Sachdeva, Vedant"},{"full_name":"Torrence, Johanna","first_name":"Johanna","last_name":"Torrence"},{"first_name":"Jan","last_name":"Humplik","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","full_name":"Humplik, Jan"},{"first_name":"David J.","last_name":"Schwab","full_name":"Schwab, David J."},{"full_name":"Palmer, Stephanie E.","first_name":"Stephanie E.","last_name":"Palmer"}],"title":"Inferring couplings in networks across order-disorder phase transitions","date_updated":"2025-03-06T14:09:21Z","day":"24","publication_identifier":{"issn":["2643-1564"]},"acknowledgement":"This work was supported in part by the Alfred P. Sloan Foundation, the Simons Foundation, the National Institutes of Health under Award No. R01EB026943, and the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030).","article_type":"original","file_date_updated":"2022-07-25T07:47:23Z","arxiv":1,"external_id":{"pmid":["37576946"],"arxiv":["2106.02349"]},"_id":"11638","oa_version":"Published Version","quality_controlled":"1","department":[{"_id":"GaTk"}],"scopus_import":"1","volume":4,"doi":"10.1103/PhysRevResearch.4.023240","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Ngampruetikorn, Vudtiwat, Vedant Sachdeva, Johanna Torrence, Jan Humplik, David J. Schwab, and Stephanie E. Palmer. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>.","short":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E. Palmer, Physical Review Research 4 (2022).","ieee":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D. J. Schwab, and S. E. Palmer, “Inferring couplings in networks across order-disorder phase transitions,” <i>Physical Review Research</i>, vol. 4, no. 2. American Physical Society, 2022.","mla":"Ngampruetikorn, Vudtiwat, et al. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>, vol. 4, no. 2, 023240, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>.","ista":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. 2022. Inferring couplings in networks across order-disorder phase transitions. Physical Review Research. 4(2), 023240.","apa":"Ngampruetikorn, V., Sachdeva, V., Torrence, J., Humplik, J., Schwab, D. J., &#38; Palmer, S. E. (2022). Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>","ama":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. 2022;4(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>"},"publication_status":"published","article_processing_charge":"No","year":"2022","file":[{"date_updated":"2022-07-25T07:47:23Z","success":1,"file_id":"11644","file_size":1379683,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2022-07-25T07:47:23Z","checksum":"ed6fdc2a3a096df785fa5f7b17b716c6","file_name":"2022_PhysicalReviewResearch_Ngampruetikorn.pdf","creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-06-24T00:00:00Z","article_number":"023240","type":"journal_article","oa":1,"issue":"2","ddc":["530"],"month":"06","status":"public","publication":"Physical Review Research","pmid":1,"has_accepted_license":"1","abstract":[{"lang":"eng","text":"Statistical inference is central to many scientific endeavors, yet how it works remains unresolved. Answering this requires a quantitative understanding of the intrinsic interplay between statistical models, inference methods, and the structure in the data. To this end, we characterize the efficacy of direct coupling analysis (DCA)—a highly successful method for analyzing amino acid sequence data—in inferring pairwise interactions from samples of ferromagnetic Ising models on random graphs. Our approach allows for physically motivated exploration of qualitatively distinct data regimes separated by phase transitions. We show that inference quality depends strongly on the nature of data-generating distributions: optimal accuracy occurs at an intermediate temperature where the detrimental effects from macroscopic order and thermal noise are minimal. Importantly our results indicate that DCA does not always outperform its local-statistics-based predecessors; while DCA excels at low temperatures, it becomes inferior to simple correlation thresholding at virtually all temperatures when data are limited. Our findings offer insights into the regime in which DCA operates so successfully, and more broadly, how inference interacts with the structure in the data."}],"date_created":"2022-07-24T22:01:42Z","publisher":"American Physical Society","language":[{"iso":"eng"}],"intvolume":"         4"},{"abstract":[{"lang":"eng","text":"Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap."}],"date_created":"2022-09-11T22:01:55Z","pmid":1,"has_accepted_license":"1","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"intvolume":"       119","issue":"36","ddc":["570"],"publication":"Proceedings of the National Academy of Sciences of the United States of America","corr_author":"1","month":"08","status":"public","type":"journal_article","isi":1,"ec_funded":1,"oa":1,"year":"2022","article_processing_charge":"No","publication_status":"published","file":[{"relation":"main_file","date_created":"2022-09-12T08:08:12Z","creator":"dernst","file_name":"2022_PNAS_Hledik.pdf","checksum":"6dec51f6567da9039982a571508a8e4d","file_size":2165752,"content_type":"application/pdf","access_level":"open_access","file_id":"12091","success":1,"date_updated":"2022-09-12T08:08:12Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-08-29T00:00:00Z","article_number":"e2123152119","scopus_import":"1","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"volume":119,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425"}],"doi":"10.1073/pnas.2123152119","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Hledik, M., Barton, N. H., &#38; Tkačik, G. (2022). Accumulation and maintenance of information in evolution. <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.2123152119\">https://doi.org/10.1073/pnas.2123152119</a>","ista":"Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences of the United States of America. 119(36), e2123152119.","ama":"Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(36). doi:<a href=\"https://doi.org/10.1073/pnas.2123152119\">10.1073/pnas.2123152119</a>","mla":"Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 36, e2123152119, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2123152119\">10.1073/pnas.2123152119</a>.","ieee":"M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 36. National Academy of Sciences, 2022.","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","chicago":"Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2123152119\">https://doi.org/10.1073/pnas.2123152119</a>."},"_id":"12081","oa_version":"Published Version","quality_controlled":"1","related_material":{"record":[{"status":"public","id":"15020","relation":"dissertation_contains"}]},"article_type":"original","acknowledgement":"We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and two anonymous reviewers for discussions and comments on the manuscript. G.T. and M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018. N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"file_date_updated":"2022-09-12T08:08:12Z","day":"29","external_id":{"pmid":["36037343"],"isi":["000889278400014"]},"author":[{"full_name":"Hledik, Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","first_name":"Michal"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"orcid":"1","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"date_updated":"2026-04-07T12:59:24Z","title":"Accumulation and maintenance of information in evolution"},{"oa":1,"type":"journal_article","date_published":"2022-09-01T00:00:00Z","article_number":"100435","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2023-01-24T12:14:10Z","relation":"main_file","creator":"dernst","file_name":"2022_CurrentBiology_Zoller.pdf","checksum":"97ef01e0cc60cdc84f45640a0f248fb0","file_size":2214944,"access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"12362","date_updated":"2023-01-24T12:14:10Z"}],"publication_status":"published","article_processing_charge":"Yes (via OA deal)","year":"2022","keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"intvolume":"        31","language":[{"iso":"eng"}],"publisher":"Elsevier","date_created":"2023-01-12T12:08:51Z","has_accepted_license":"1","pmid":1,"abstract":[{"text":"Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory—theory that prescribes rather than just describes—in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code.","lang":"eng"}],"ddc":["570"],"month":"09","corr_author":"1","status":"public","publication":"Current Opinion in Systems Biology","issue":"9","external_id":{"pmid":["36590072"]},"day":"01","article_type":"original","file_date_updated":"2023-01-24T12:14:10Z","acknowledgement":"This work was supported through the Center for the Physics of Biological Function (PHYe1734030) and by National Institutes of Health Grants R01GM097275 and U01DK127429 (TG). GT acknowledges the support of the Austrian Science Fund grant FWF P28844 and the Human Frontiers Science Program. ","publication_identifier":{"issn":["2452-3100"]},"title":"Eukaryotic gene regulation at equilibrium, or non?","date_updated":"2025-06-11T13:47:43Z","author":[{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"full_name":"Gregor, Thomas","last_name":"Gregor","first_name":"Thomas"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"1","last_name":"Tkačik","first_name":"Gašper"}],"doi":"10.1016/j.coisb.2022.100435","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"mla":"Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9, 100435, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>.","ieee":"B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium, or non?,” <i>Current Opinion in Systems Biology</i>, vol. 31, no. 9. Elsevier, 2022.","apa":"Zoller, B., Gregor, T., &#38; Tkačik, G. (2022). Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>","ama":"Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? <i>Current Opinion in Systems Biology</i>. 2022;31(9). doi:<a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">10.1016/j.coisb.2022.100435</a>","ista":"Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 31(9), 100435.","chicago":"Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” <i>Current Opinion in Systems Biology</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.coisb.2022.100435\">https://doi.org/10.1016/j.coisb.2022.100435</a>.","short":"B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022)."},"project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"volume":31,"scopus_import":"1","department":[{"_id":"GaTk"}],"oa_version":"Published Version","quality_controlled":"1","_id":"12156"},{"project":[{"grant_number":"P34015","name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1371/journal.pbio.3001889","citation":{"mla":"Mlynarski, Wiktor F., and Gašper Tkačik. “Efficient Coding Theory of Dynamic Attentional Modulation.” <i>PLoS Biology</i>, vol. 20, no. 12, Public Library of Science, 2022, p. e3001889, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001889\">10.1371/journal.pbio.3001889</a>.","ieee":"W. F. Mlynarski and G. Tkačik, “Efficient coding theory of dynamic attentional modulation,” <i>PLoS Biology</i>, vol. 20, no. 12. Public Library of Science, p. e3001889, 2022.","ama":"Mlynarski WF, Tkačik G. Efficient coding theory of dynamic attentional modulation. <i>PLoS Biology</i>. 2022;20(12):e3001889. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001889\">10.1371/journal.pbio.3001889</a>","ista":"Mlynarski WF, Tkačik G. 2022. Efficient coding theory of dynamic attentional modulation. PLoS Biology. 20(12), e3001889.","apa":"Mlynarski, W. F., &#38; Tkačik, G. (2022). Efficient coding theory of dynamic attentional modulation. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001889\">https://doi.org/10.1371/journal.pbio.3001889</a>","chicago":"Mlynarski, Wiktor F, and Gašper Tkačik. “Efficient Coding Theory of Dynamic Attentional Modulation.” <i>PLoS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001889\">https://doi.org/10.1371/journal.pbio.3001889</a>.","short":"W.F. Mlynarski, G. Tkačik, PLoS Biology 20 (2022) e3001889."},"department":[{"_id":"GaTk"}],"scopus_import":"1","volume":20,"_id":"12332","quality_controlled":"1","oa_version":"Published Version","external_id":{"isi":["000925192000001"],"pmid":["36542662"]},"day":"21","article_type":"original","acknowledgement":"We thank Robbe Goris for generously providing figures from his work and Ann M. Hermundstad for helpful discussions.\r\nGT & WM were supported by the Austrian Science Fund Standalone Grant P 34015 \"Efficient Coding with Biophysical Realism\" (https://pf.fwf.ac.at/) WM was additionally supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (https://ec.europa.eu/research/mariecurieactions/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","publication_identifier":{"eissn":["1545-7885"]},"file_date_updated":"2023-01-23T08:46:40Z","title":"Efficient coding theory of dynamic attentional modulation","date_updated":"2025-06-11T13:57:01Z","author":[{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","full_name":"Mlynarski, Wiktor F","last_name":"Mlynarski","first_name":"Wiktor F"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","first_name":"Gašper","orcid":"1","last_name":"Tkačik"}],"language":[{"iso":"eng"}],"intvolume":"        20","abstract":[{"text":"Activity of sensory neurons is driven not only by external stimuli but also by feedback signals from higher brain areas. Attention is one particularly important internal signal whose presumed role is to modulate sensory representations such that they only encode information currently relevant to the organism at minimal cost. This hypothesis has, however, not yet been expressed in a normative computational framework. Here, by building on normative principles of probabilistic inference and efficient coding, we developed a model of dynamic population coding in the visual cortex. By continuously adapting the sensory code to changing demands of the perceptual observer, an attention-like modulation emerges. This modulation can dramatically reduce the amount of neural activity without deteriorating the accuracy of task-specific inferences. Our results suggest that a range of seemingly disparate cortical phenomena such as intrinsic gain modulation, attention-related tuning modulation, and response variability could be manifestations of the same underlying principles, which combine efficient sensory coding with optimal probabilistic inference in dynamic environments.","lang":"eng"}],"pmid":1,"date_created":"2023-01-22T23:00:55Z","has_accepted_license":"1","publisher":"Public Library of Science","publication":"PLoS Biology","month":"12","ddc":["570"],"corr_author":"1","status":"public","issue":"12","type":"journal_article","isi":1,"ec_funded":1,"oa":1,"page":"e3001889","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-12-21T00:00:00Z","publication_status":"published","year":"2022","article_processing_charge":"No","file":[{"success":1,"file_id":"12337","date_updated":"2023-01-23T08:46:40Z","date_created":"2023-01-23T08:46:40Z","relation":"main_file","creator":"dernst","checksum":"5d7f1111a87e5f2c1bf92f8886738894","file_name":"2022_PloSBiology_Mlynarski.pdf","file_size":4248838,"access_level":"open_access","content_type":"application/pdf"}]},{"intvolume":"       121","language":[{"iso":"eng"}],"publisher":"Elsevier","pmid":1,"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"}],"date_created":"2021-12-10T09:48:19Z","has_accepted_license":"1","month":"01","publication":"Biophysical Journal","status":"public","ddc":["570"],"issue":"1","oa":1,"isi":1,"type":"journal_article","page":"P44-60","date_published":"2022-01-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"11697","success":1,"date_updated":"2022-07-29T10:17:10Z","relation":"main_file","date_created":"2022-07-29T10:17:10Z","creator":"dernst","file_name":"2022_BiophysicalJour_Zisis.pdf","checksum":"1aa7c3478e0c8256b973b632efd1f6b4","file_size":4475504,"content_type":"application/pdf","access_level":"open_access"}],"publication_status":"published","keyword":["Biophysics"],"article_processing_charge":"No","year":"2022","citation":{"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>.","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.","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>.","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.","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>","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."},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.1016/j.bpj.2021.12.006","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"volume":121,"department":[{"_id":"EdHa"},{"_id":"GaTk"}],"scopus_import":"1","oa_version":"Published Version","quality_controlled":"1","_id":"10530","external_id":{"isi":["000740815400007"],"pmid":["34890578"]},"day":"04","file_date_updated":"2022-07-29T10:17:10Z","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.","article_type":"original","publication_identifier":{"issn":["0006-3495"]},"title":"Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration","date_updated":"2025-06-11T13:59:29Z","author":[{"full_name":"Zisis, Themistoklis","last_name":"Zisis","first_name":"Themistoklis"},{"full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","last_name":"Brückner","orcid":"0000-0001-7205-2975"},{"last_name":"Brandstätter","first_name":"Tom","full_name":"Brandstätter, Tom"},{"last_name":"Siow","first_name":"Wei Xiong","full_name":"Siow, Wei Xiong"},{"first_name":"Joseph","last_name":"d’Alessandro","full_name":"d’Alessandro, Joseph"},{"full_name":"Vollmar, Angelika M.","first_name":"Angelika M.","last_name":"Vollmar"},{"first_name":"Chase P.","last_name":"Broedersz","full_name":"Broedersz, Chase P."},{"full_name":"Zahler, Stefan","first_name":"Stefan","last_name":"Zahler"}]},{"acknowledgement":"We thank Hande Acar, Nicholas H Barton, Rok Grah, Tiago Paixao, Maros Pleska, Anna Staron, and Murat Tugrul for insightful comments and input on the manuscript. This work was supported by: Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant number 216779/Z/19/Z) to ML; IPC Grant from IST Austria to ML and SS; European Research Council Funding Programme 7 (2007–2013, grant agreement number 648440) to JPB.","file_date_updated":"2022-02-07T07:14:09Z","publication_identifier":{"eissn":["2050-084X"]},"article_type":"original","day":"26","external_id":{"isi":["000751104400001"],"pmid":["35080492"]},"author":[{"first_name":"Mato","last_name":"Lagator","full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sarikas","first_name":"Srdjan","id":"35F0286E-F248-11E8-B48F-1D18A9856A87","full_name":"Sarikas, Srdjan"},{"full_name":"Steinrück, Magdalena","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","last_name":"Steinrück","orcid":"0000-0003-1229-9719","first_name":"Magdalena"},{"last_name":"Toledo-Aparicio","first_name":"David","full_name":"Toledo-Aparicio, David"},{"first_name":"Jonathan P","last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","orcid":"0000-0002-6699-1455","first_name":"Gašper"}],"date_updated":"2025-03-31T16:00:23Z","title":"Predicting bacterial promoter function and evolution from random sequences","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"NiBa"}],"scopus_import":"1","volume":11,"project":[{"_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer"}],"citation":{"chicago":"Lagator, Mato, Srdjan Sarikas, Magdalena Steinrück, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.64543\">https://doi.org/10.7554/eLife.64543</a>.","short":"M. Lagator, S. Sarikas, M. Steinrück, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).","mla":"Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” <i>ELife</i>, vol. 11, e64543, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.64543\">10.7554/eLife.64543</a>.","ieee":"M. Lagator <i>et al.</i>, “Predicting bacterial promoter function and evolution from random sequences,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","ama":"Lagator M, Sarikas S, Steinrück M, et al. Predicting bacterial promoter function and evolution from random sequences. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.64543\">10.7554/eLife.64543</a>","apa":"Lagator, M., Sarikas, S., Steinrück, M., Toledo-Aparicio, D., Bollback, J. P., Guet, C. C., &#38; Tkačik, G. (2022). Predicting bacterial promoter function and evolution from random sequences. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.64543\">https://doi.org/10.7554/eLife.64543</a>","ista":"Lagator M, Sarikas S, Steinrück M, Toledo-Aparicio D, Bollback JP, Guet CC, Tkačik G. 2022. Predicting bacterial promoter function and evolution from random sequences. eLife. 11, e64543."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.7554/eLife.64543","_id":"10736","oa_version":"Published Version","quality_controlled":"1","ec_funded":1,"isi":1,"type":"journal_article","oa":1,"year":"2022","article_processing_charge":"No","publication_status":"published","file":[{"relation":"main_file","date_created":"2022-02-07T07:14:09Z","creator":"cchlebak","checksum":"decdcdf600ff51e9a9703b49ca114170","file_name":"2022_ELife_Lagator.pdf","file_size":5604343,"content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"10739","date_updated":"2022-02-07T07:14:09Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e64543","date_published":"2022-01-26T00:00:00Z","abstract":[{"text":"Predicting function from sequence is a central problem of biology. Currently, this is possible only locally in a narrow mutational neighborhood around a wildtype sequence rather than globally from any sequence. Using random mutant libraries, we developed a biophysical model that accounts for multiple features of σ70 binding bacterial promoters to predict constitutive gene expression levels from any sequence. We experimentally and theoretically estimated that 10–20% of random sequences lead to expression and ~80% of non-expressing sequences are one mutation away from a functional promoter. The potential for generating expression from random sequences is so pervasive that selection acts against σ70-RNA polymerase binding sites even within inter-genic, promoter-containing regions. This pervasiveness of σ70-binding sites implies that emergence of promoters is not the limiting step in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter function into a mechanistic model enabled not only more accurate predictions of gene expression levels, but also identified that promoters evolve more rapidly than previously thought.","lang":"eng"}],"pmid":1,"date_created":"2022-02-06T23:01:32Z","has_accepted_license":"1","publisher":"eLife Sciences Publications","language":[{"iso":"eng"}],"intvolume":"        11","publication":"eLife","status":"public","ddc":["576"],"month":"01","corr_author":"1"},{"_id":"10821","main_file_link":[{"url":"https://doi.org/10.1101/2022.03.03.482657","open_access":"1"}],"oa_version":"Preprint","department":[{"_id":"GaTk"}],"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"ista":"Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, de Arcangelis L, Shriki O. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. bioRxiv, <a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>.","apa":"Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano, A. E., … Shriki, O. (n.d.). Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2022.03.03.482657\">https://doi.org/10.1101/2022.03.03.482657</a>","ama":"Lombardi F, Herrmann HJ, Parrino L, et al. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>","ieee":"F. Lombardi <i>et al.</i>, “Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades,” <i>bioRxiv</i>. .","mla":"Lombardi, Fabrizio, et al. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>.","short":"F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. de Arcangelis, O. Shriki, BioRxiv (n.d.).","chicago":"Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla de Arcangelis, and Oren Shriki. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2022.03.03.482657\">https://doi.org/10.1101/2022.03.03.482657</a>."},"doi":"10.1101/2022.03.03.482657","author":[{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","full_name":"Lombardi, Fabrizio","first_name":"Fabrizio","orcid":"0000-0003-2623-5249","last_name":"Lombardi"},{"full_name":"Herrmann, Hans J.","first_name":"Hans J.","last_name":"Herrmann"},{"full_name":"Parrino, Liborio","last_name":"Parrino","first_name":"Liborio"},{"last_name":"Plenz","first_name":"Dietmar","full_name":"Plenz, Dietmar"},{"full_name":"Scarpetta, Silvia","last_name":"Scarpetta","first_name":"Silvia"},{"full_name":"Vaudano, Anna Elisabetta","first_name":"Anna Elisabetta","last_name":"Vaudano"},{"full_name":"de Arcangelis, Lucilla","first_name":"Lucilla","last_name":"de Arcangelis"},{"full_name":"Shriki, Oren","first_name":"Oren","last_name":"Shriki"}],"date_updated":"2026-07-06T12:48:55Z","title":"Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades","related_material":{"record":[{"id":"14402","relation":"later_version","status":"public"}]},"acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. LdA acknowledges the Italian MIUR project PRIN2017WZFTZP for financial support and the project E-PASSION of the program VALERE 2019 funded by the University of Campania, Italy “L. Vanvitelli”. OS acknowledges support from the Israel Science Foundation, Grant No. 504/17. Supported in part by DIRP ZIAMH02797 to DP.","day":"04","OA_place":"repository","das_tickbox":"1","corr_author":"1","publication":"bioRxiv","status":"public","month":"03","date_created":"2022-03-04T22:20:59Z","abstract":[{"lang":"eng","text":"Rhythmical cortical activity has long been recognized as a pillar in the architecture of brain functions. Yet, the dynamic organization of its underlying neuronal population activity remains elusive. Here we uncover a unique organizational principle regulating collective neural dynamics associated with the alpha rhythm in the awake resting-state. We demonstrate that cascades of neural activity obey attenuation-amplification dynamics (AAD), with a transition from the attenuation regime—within alpha cycles—to the amplification regime—across a few alpha cycles—that correlates with the characteristic frequency of the alpha rhythm. We find that this short-term AAD is part of a large-scale, size-dependent temporal structure of neural cascades that obeys the Omori law: Following large cascades, smaller cascades occur at a rate that decays as a power-law of the time elapsed from such events—a long-term AAD regulating brain activity over the timescale of seconds. We show that such an organization corresponds to the \"waxing and waning\" of the alpha rhythm. Importantly, we observe that short- and long-term AAD are unique to the awake resting-state, being absent during NREM sleep. These results provide a quantitative, dynamical description of the so-far-qualitative notion of the \"waxing and waning\" phenomenon, and suggest the AAD as a key principle governing resting-state dynamics across timescales."}],"language":[{"iso":"eng"}],"year":"2022","article_processing_charge":"No","publication_status":"draft","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-03-04T00:00:00Z","page":"25","type":"preprint","ec_funded":1,"oa":1},{"file":[{"relation":"main_file","date_created":"2022-05-16T08:53:11Z","checksum":"dcd185d4f7e0acee25edf1d6537f447e","creator":"dernst","file_name":"2021_PLOsComBio_Bodova.pdf","file_size":2299486,"content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"11383","date_updated":"2022-05-16T08:53:11Z"}],"publication_status":"published","year":"2021","article_processing_charge":"No","article_number":"e1009661","date_published":"2021-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"type":"journal_article","issue":"12","publication":"PLoS Computational Biology","corr_author":"1","month":"12","ddc":["570"],"status":"public","acknowledged_ssus":[{"_id":"ScienComp"}],"publisher":"Public Library of Science","pmid":1,"date_created":"2021-12-12T23:01:27Z","has_accepted_license":"1","abstract":[{"text":"Realistic models of biological processes typically involve interacting components on multiple scales, driven by changing environment and inherent stochasticity. Such models are often analytically and numerically intractable. We revisit a dynamic maximum entropy method that combines a static maximum entropy with a quasi-stationary approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics, without the need to track microscopic details. Although the method has been previously applied to a few (rather complicated) applications in population genetics, our main goal here is to explain and to better understand how the method works. We demonstrate the usefulness of the method for two widely studied stochastic problems, highlighting its accuracy in capturing important macroscopic quantities even in rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process, the method recovers the exact dynamics whilst for a stochastic island model with migration from other habitats, the approximation retains high macroscopic accuracy under a wide range of scenarios in a dynamic environment.","lang":"eng"}],"intvolume":"        17","language":[{"iso":"eng"}],"author":[{"full_name":"Bod'ová, Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarína","last_name":"Bod'ová","orcid":"0000-0002-7214-0171"},{"first_name":"Eniko","last_name":"Szep","full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"title":"Dynamic maximum entropy provides accurate approximation of structured population dynamics","date_updated":"2024-10-09T21:01:16Z","arxiv":1,"day":"01","file_date_updated":"2022-05-16T08:53:11Z","acknowledgement":"Computational resources for the study were provided by the Institute of Science and Technology, Austria.\r\nKB received funding from the Scientific Grant Agency of the Slovak Republic under the Grants Nos. 1/0755/19 and 1/0521/20.","publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"article_type":"original","external_id":{"arxiv":["2102.03669"],"pmid":["34851948"]},"oa_version":"Published Version","quality_controlled":"1","_id":"10535","volume":17,"scopus_import":"1","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"doi":"10.1371/journal.pcbi.1009661","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Bodova, K., Szep, E., &#38; Barton, N. H. (2021). Dynamic maximum entropy provides accurate approximation of structured population dynamics. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">https://doi.org/10.1371/journal.pcbi.1009661</a>","ista":"Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 17(12), e1009661.","ama":"Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation of structured population dynamics. <i>PLoS Computational Biology</i>. 2021;17(12). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">10.1371/journal.pcbi.1009661</a>","mla":"Bodova, Katarina, et al. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” <i>PLoS Computational Biology</i>, vol. 17, no. 12, e1009661, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">10.1371/journal.pcbi.1009661</a>.","ieee":"K. Bodova, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate approximation of structured population dynamics,” <i>PLoS Computational Biology</i>, vol. 17, no. 12. Public Library of Science, 2021.","short":"K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).","chicago":"Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” <i>PLoS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">https://doi.org/10.1371/journal.pcbi.1009661</a>."}},{"publication_status":"published","year":"2021","keyword":["Genetics and Molecular Biology"],"article_processing_charge":"Yes","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":1390469,"file_name":"elife-65993-v2.pdf","checksum":"3c2f44058c2dd45a5a1027f09d263f8e","creator":"bkavcic","relation":"main_file","date_created":"2021-03-23T10:12:58Z","date_updated":"2021-03-23T10:12:58Z","success":1,"file_id":"9284"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-03-08T00:00:00Z","article_number":"e65993","isi":1,"ec_funded":1,"type":"journal_article","oa":1,"status":"public","month":"03","corr_author":"1","ddc":["570"],"publication":"eLife","has_accepted_license":"1","abstract":[{"text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic GRN to study in Escherichia coli how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one GRN with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Transcriptional read-through is the main molecular mechanism that places one transcriptional unit (TU) within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual TUs, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of GRNs.","lang":"eng"}],"date_created":"2021-03-23T10:11:46Z","pmid":1,"publisher":"eLife Sciences Publications","language":[{"iso":"eng"}],"intvolume":"        10","author":[{"first_name":"Anna A","last_name":"Nagy-Staron","orcid":"0000-0002-1391-8377","full_name":"Nagy-Staron, Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-3768-877X","last_name":"Tomasek","first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","full_name":"Tomasek, Kathrin"},{"full_name":"Caruso Carter, Caroline","last_name":"Caruso Carter","first_name":"Caroline"},{"full_name":"Sonnleitner, Elisabeth","last_name":"Sonnleitner","first_name":"Elisabeth"},{"first_name":"Bor","last_name":"Kavcic","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tiago","last_name":"Paixão","full_name":"Paixão, Tiago"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"title":"Local genetic context shapes the function of a gene regulatory network","date_updated":"2025-06-12T06:36:17Z","day":"08","acknowledgement":"We thank J Bollback, L Hurst, M Lagator, C Nizak, O Rivoire, M Savageau, G Tkacik, and B Vicozo\r\nfor helpful discussions; A Dolinar and A Greshnova for technical assistance; T Bollenbach for supplying the strain JW0336; C Rusnac, and members of the Guet lab for comments. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n˚\r\n628377 (ANS) and an Austrian Science Fund (FWF) grant n˚ I 3901-B32 (CCG).","publication_identifier":{"issn":["2050-084X"]},"related_material":{"record":[{"status":"public","relation":"research_data","id":"8951"}]},"article_type":"original","file_date_updated":"2021-03-23T10:12:58Z","external_id":{"pmid":["33683203"],"isi":["000631050900001"]},"_id":"9283","quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"scopus_import":"1","volume":10,"project":[{"_id":"2517526A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"628377","name":"The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic Networks to Genomic Studies"},{"name":"Cybergenetic circuits to test composability of gene networks","grant_number":"I03901","call_identifier":"FWF","_id":"268BFA92-B435-11E9-9278-68D0E5697425"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.7554/elife.65993","citation":{"apa":"Nagy-Staron, A. A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavcic, B., Paixão, T., &#38; Guet, C. C. (2021). Local genetic context shapes the function of a gene regulatory network. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.65993\">https://doi.org/10.7554/elife.65993</a>","ista":"Nagy-Staron AA, Tomasek K, Caruso Carter C, Sonnleitner E, Kavcic B, Paixão T, Guet CC. 2021. Local genetic context shapes the function of a gene regulatory network. eLife. 10, e65993.","ama":"Nagy-Staron AA, Tomasek K, Caruso Carter C, et al. Local genetic context shapes the function of a gene regulatory network. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.65993\">10.7554/elife.65993</a>","mla":"Nagy-Staron, Anna A., et al. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” <i>ELife</i>, vol. 10, e65993, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.65993\">10.7554/elife.65993</a>.","ieee":"A. A. Nagy-Staron <i>et al.</i>, “Local genetic context shapes the function of a gene regulatory network,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","short":"A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic, T. Paixão, C.C. Guet, ELife 10 (2021).","chicago":"Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.65993\">https://doi.org/10.7554/elife.65993</a>."}},{"department":[{"_id":"GaTk"}],"scopus_import":"1","volume":16,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1371/journal.pone.0248940","citation":{"ieee":"M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” <i>PLoS ONE</i>, vol. 16, no. 4. Public Library of Science, 2021.","mla":"Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” <i>PLoS ONE</i>, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0248940\">10.1371/journal.pone.0248940</a>.","apa":"Chalk, M. J., Tkačik, G., &#38; Marre, O. (2021). Inferring the function performed by a recurrent neural network. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0248940\">https://doi.org/10.1371/journal.pone.0248940</a>","ama":"Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. <i>PLoS ONE</i>. 2021;16(4). doi:<a href=\"https://doi.org/10.1371/journal.pone.0248940\">10.1371/journal.pone.0248940</a>","ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940.","chicago":"Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0248940\">https://doi.org/10.1371/journal.pone.0248940</a>.","short":"M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021)."},"_id":"9362","quality_controlled":"1","oa_version":"Published Version","publication_identifier":{"eissn":["1932-6203"]},"file_date_updated":"2021-05-04T13:22:19Z","acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","article_type":"original","day":"15","external_id":{"pmid":["33857170"],"isi":["000641474900072"]},"author":[{"first_name":"Matthew J","orcid":"0000-0001-7782-4436","last_name":"Chalk","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","full_name":"Chalk, Matthew J"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"}],"date_updated":"2026-04-02T13:58:56Z","title":"Inferring the function performed by a recurrent neural network","date_created":"2021-05-02T22:01:28Z","has_accepted_license":"1","pmid":1,"abstract":[{"lang":"eng","text":"A central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose an inverse reinforcement learning (RL) framework for inferring the function performed by a neural network from data. We assume that the responses of each neuron in a network are optimised so as to drive the network towards ‘rewarded’ states, that are desirable for performing a given function. We then show how one can use inverse RL to infer the reward function optimised by the network from observing its responses. This inferred reward function can be used to predict how the neural network should adapt its dynamics to perform the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death and/or varying sensory stimulus statistics."}],"publisher":"Public Library of Science","language":[{"iso":"eng"}],"intvolume":"        16","issue":"4","status":"public","month":"04","ddc":["570"],"publication":"PLoS ONE","type":"journal_article","isi":1,"oa":1,"article_processing_charge":"No","year":"2021","publication_status":"published","file":[{"date_created":"2021-05-04T13:22:19Z","relation":"main_file","checksum":"c52da133850307d2031f552d998f00e8","creator":"kschuh","file_name":"2021_pone_Chalk.pdf","file_size":2768282,"access_level":"open_access","content_type":"application/pdf","success":1,"file_id":"9371","date_updated":"2021-05-04T13:22:19Z"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2021-04-15T00:00:00Z","article_number":"e0248940"},{"external_id":{"isi":["000652577300003"],"pmid":["34017131"]},"day":"20","acknowledgement":"We thank D. Kastner and T. Münch for generously providing figures from their work. We also thank V. Jayaraman, M. Noorman, T. Ma, and K. Krishnamurthy for useful discussions and feedback on the manuscript. W.F.M. was funded by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie Grant Agreement No. 754411. A.M.H. was supported by the Howard Hughes Medical Institute.","publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"article_type":"original","title":"Efficient and adaptive sensory codes","date_updated":"2025-06-12T06:41:38Z","author":[{"first_name":"Wiktor F","last_name":"Mlynarski","full_name":"Mlynarski, Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hermundstad, Ann M.","first_name":"Ann M.","last_name":"Hermundstad"}],"doi":"10.1038/s41593-021-00846-0","citation":{"ama":"Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. <i>Nature Neuroscience</i>. 2021;24:998-1009. doi:<a href=\"https://doi.org/10.1038/s41593-021-00846-0\">10.1038/s41593-021-00846-0</a>","apa":"Mlynarski, W. F., &#38; Hermundstad, A. M. (2021). Efficient and adaptive sensory codes. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-021-00846-0\">https://doi.org/10.1038/s41593-021-00846-0</a>","ista":"Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes. Nature Neuroscience. 24, 998–1009.","ieee":"W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,” <i>Nature Neuroscience</i>, vol. 24. Springer Nature, pp. 998–1009, 2021.","mla":"Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” <i>Nature Neuroscience</i>, vol. 24, Springer Nature, 2021, pp. 998–1009, doi:<a href=\"https://doi.org/10.1038/s41593-021-00846-0\">10.1038/s41593-021-00846-0</a>.","short":"W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.","chicago":"Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” <i>Nature Neuroscience</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41593-021-00846-0\">https://doi.org/10.1038/s41593-021-00846-0</a>."},"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"volume":24,"department":[{"_id":"GaTk"}],"scopus_import":"1","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.1101/669200 ","open_access":"1"}],"_id":"9439","oa":1,"isi":1,"ec_funded":1,"type":"journal_article","page":"998-1009","date_published":"2021-05-20T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2021","article_processing_charge":"No","intvolume":"        24","language":[{"iso":"eng"}],"publisher":"Springer Nature","abstract":[{"text":"The ability to adapt to changes in stimulus statistics is a hallmark of sensory systems. Here, we developed a theoretical framework that can account for the dynamics of adaptation from an information processing perspective. We use this framework to optimize and analyze adaptive sensory codes, and we show that codes optimized for stationary environments can suffer from prolonged periods of poor performance when the environment changes. To mitigate the adversarial effects of these environmental changes, sensory systems must navigate tradeoffs between the ability to accurately encode incoming stimuli and the ability to rapidly detect and adapt to changes in the distribution of these stimuli. We derive families of codes that balance these objectives, and we demonstrate their close match to experimentally observed neural dynamics during mean and variance adaptation. Our results provide a unifying perspective on adaptation across a range of sensory systems, environments, and sensory tasks.","lang":"eng"}],"date_created":"2021-05-30T22:01:24Z","pmid":1,"status":"public","publication":"Nature Neuroscience","month":"05"},{"scopus_import":"1","department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"volume":13,"project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"724373","name":"Cellular Navigation Along Spatial Gradients"}],"citation":{"apa":"Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. <i>ACS Applied Materials and Interfaces</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsami.1c09850\">https://doi.org/10.1021/acsami.1c09850</a>","ista":"Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 13(30), 35545–35560.","ama":"Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. <i>ACS Applied Materials and Interfaces</i>. 2021;13(30):35545–35560. doi:<a href=\"https://doi.org/10.1021/acsami.1c09850\">10.1021/acsami.1c09850</a>","ieee":"T. Zisis <i>et al.</i>, “Sequential and switchable patterning for studying cellular processes under spatiotemporal control,” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.","mla":"Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:<a href=\"https://doi.org/10.1021/acsami.1c09850\">10.1021/acsami.1c09850</a>.","short":"T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560.","chicago":"Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” <i>ACS Applied Materials and Interfaces</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsami.1c09850\">https://doi.org/10.1021/acsami.1c09850</a>."},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"doi":"10.1021/acsami.1c09850","_id":"9822","oa_version":"Published Version","quality_controlled":"1","day":"04","acknowledgement":"We would like to thank Charlott Leu for the production of our chromium wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim Rädler for his valuable scientific guidance.","article_type":"original","publication_identifier":{"issn":["1944-8244"],"eissn":["1944-8252"]},"file_date_updated":"2021-08-09T09:44:03Z","external_id":{"isi":["000683741400026"],"pmid":["34283577"]},"author":[{"first_name":"Themistoklis","last_name":"Zisis","full_name":"Zisis, Themistoklis"},{"full_name":"Schwarz, Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Jan"},{"first_name":"Miriam","last_name":"Balles","full_name":"Balles, Miriam"},{"full_name":"Kretschmer, Maibritt","last_name":"Kretschmer","first_name":"Maibritt"},{"full_name":"Nemethova, Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Nemethova"},{"id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","last_name":"Chait","first_name":"Remy P"},{"last_name":"Hauschild","orcid":"0000-0001-9843-3522","first_name":"Robert","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lange","first_name":"Janina","full_name":"Lange, Janina"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C"},{"orcid":"0000-0002-4561-241X","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Zahler, Stefan","last_name":"Zahler","first_name":"Stefan"}],"title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","date_updated":"2025-07-10T12:02:02Z","date_created":"2021-08-08T22:01:28Z","pmid":1,"abstract":[{"text":"Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science.","lang":"eng"}],"has_accepted_license":"1","publisher":"American Chemical Society","language":[{"iso":"eng"}],"intvolume":"        13","issue":"30","ddc":["620","570"],"publication":"ACS Applied Materials and Interfaces","corr_author":"1","month":"08","status":"public","page":"35545–35560","type":"journal_article","isi":1,"ec_funded":1,"oa":1,"publication_status":"published","article_processing_charge":"Yes (in subscription journal)","year":"2021","file":[{"content_type":"application/pdf","access_level":"open_access","file_size":7123293,"creator":"asandaue","file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf","checksum":"b043a91d9f9200e467b970b692687ed3","relation":"main_file","date_created":"2021-08-09T09:44:03Z","date_updated":"2021-08-09T09:44:03Z","file_id":"9833","success":1}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-08-04T00:00:00Z"}]