[{"corr_author":"1","ddc":["570"],"scopus_import":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"OA_type":"hybrid","issue":"11","title":"Learning reshapes the hippocampal representation hierarchy","day":"10","type":"journal_article","acknowledgement":"We would like to thank Rebecca Morse for performing the recordings in one of the animals under the supervision of H.S.C.C., Jago Wallenschus for the technical support, especially with maze design, Wiktor Mlynarski for the advice and discussions and Andrea Cumpelik for suggestions during the writing. M.N. was supported by the Howard Hughes Medical Institute. H.S.C.C. received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 665385.","date_created":"2025-03-25T07:38:35Z","doi":"10.1073/pnas.2417025122","status":"public","has_accepted_license":"1","date_published":"2025-03-10T00:00:00Z","citation":{"ama":"Chiossi HSC, Nardin M, Tkačik G, Csicsvari JL. Learning reshapes the hippocampal representation hierarchy. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(11). doi:<a href=\"https://doi.org/10.1073/pnas.2417025122\">10.1073/pnas.2417025122</a>","chicago":"Chiossi, Heloisa S. C., Michele Nardin, Gašper Tkačik, and Jozsef L Csicsvari. “Learning Reshapes the Hippocampal Representation Hierarchy.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2417025122\">https://doi.org/10.1073/pnas.2417025122</a>.","ieee":"H. S. C. Chiossi, M. Nardin, G. Tkačik, and J. L. Csicsvari, “Learning reshapes the hippocampal representation hierarchy,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 11. National Academy of Sciences, 2025.","mla":"Chiossi, Heloisa S. C., et al. “Learning Reshapes the Hippocampal Representation Hierarchy.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 11, e2417025122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2417025122\">10.1073/pnas.2417025122</a>.","apa":"Chiossi, H. S. C., Nardin, M., Tkačik, G., &#38; Csicsvari, J. L. (2025). Learning reshapes the hippocampal representation hierarchy. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2417025122\">https://doi.org/10.1073/pnas.2417025122</a>","ista":"Chiossi HSC, Nardin M, Tkačik G, Csicsvari JL. 2025. Learning reshapes the hippocampal representation hierarchy. Proceedings of the National Academy of Sciences. 122(11), e2417025122.","short":"H.S.C. Chiossi, M. Nardin, G. Tkačik, J.L. Csicsvari, Proceedings of the National Academy of Sciences 122 (2025)."},"tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"intvolume":"       122","article_number":"e2417025122","month":"03","pmid":1,"language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","OA_place":"publisher","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences","file_date_updated":"2025-03-25T07:49:04Z","date_updated":"2026-05-06T13:12:01Z","publication_status":"published","APC_amount":"3317,75 EUR","volume":122,"year":"2025","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"file":[{"success":1,"creator":"dernst","checksum":"1217207c254553154faa065964990988","date_created":"2025-03-25T07:49:04Z","access_level":"open_access","date_updated":"2025-03-25T07:49:04Z","file_size":1553502,"relation":"main_file","content_type":"application/pdf","file_id":"19454","file_name":"2025_PNAS_Chiossi.pdf"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"18991"}],"link":[{"relation":"software","url":"https://github.com/hchiossi/hpc-hierarchy"}]},"oa":1,"article_type":"original","oa_version":"Published Version","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"}],"_id":"19453","ec_funded":1,"department":[{"_id":"GaTk"},{"_id":"JoCs"}],"abstract":[{"lang":"eng","text":"A key feature of biological and artificial neural networks is the progressive refinement of their neural representations with experience. In neuroscience, this fact has inspired several recent studies in sensory and motor systems. However, less is known about how higher associational cortical areas, such as the hippocampus, modify representations throughout the learning of complex tasks. Here, we focus on associative learning, a process that requires forming a connection between the representations of different variables for appropriate behavioral response. We trained rats in a space-context associative task and monitored hippocampal neural activity throughout the entire learning period, over several days. This allowed us to assess changes in the representations of context, movement direction, and position, as well as their relationship to behavior. We identified a hierarchical representational structure in the encoding of these three task variables that was preserved throughout learning. Nevertheless, we also observed changes at the lower levels of the hierarchy where context was encoded. These changes were local in neural activity space and restricted to physical positions where context identification was necessary for correct decision-making, supporting better context decoding and contextual code compression. Our results demonstrate that the hippocampal code not only accommodates hierarchical relationships between different variables but also enables efficient learning through minimal changes in neural activity space. Beyond the hippocampus, our work reveals a representation learning mechanism that might be implemented in other biological and artificial networks performing similar tasks."}],"author":[{"orcid":"0009-0004-2973-278X","full_name":"Chiossi, Heloisa","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87","first_name":"Heloisa","last_name":"Chiossi"},{"id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","last_name":"Nardin","first_name":"Michele"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","first_name":"Gašper"},{"first_name":"Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["001459499500001"],"pmid":["40063792"]}},{"month":"03","pmid":1,"publisher":"National Academy of Sciences","OA_place":"publisher","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","publication":"Proceedings of the National Academy of Sciences","citation":{"mla":"Muroya Lei, Stefanie, et al. “Hardware-Optimal Quantum Algorithms.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 12, e2419273122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2419273122\">10.1073/pnas.2419273122</a>.","ieee":"S. Muroya Lei, K. Chatterjee, and T. A. Henzinger, “Hardware-optimal quantum algorithms,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 12. National Academy of Sciences, 2025.","chicago":"Muroya Lei, Stefanie, Krishnendu Chatterjee, and Thomas A Henzinger. “Hardware-Optimal Quantum Algorithms.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2419273122\">https://doi.org/10.1073/pnas.2419273122</a>.","ama":"Muroya Lei S, Chatterjee K, Henzinger TA. Hardware-optimal quantum algorithms. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(12). doi:<a href=\"https://doi.org/10.1073/pnas.2419273122\">10.1073/pnas.2419273122</a>","short":"S. Muroya Lei, K. Chatterjee, T.A. Henzinger, Proceedings of the National Academy of Sciences 122 (2025).","ista":"Muroya Lei S, Chatterjee K, Henzinger TA. 2025. Hardware-optimal quantum algorithms. Proceedings of the National Academy of Sciences. 122(12), e2419273122.","apa":"Muroya Lei, S., Chatterjee, K., &#38; Henzinger, T. A. (2025). Hardware-optimal quantum algorithms. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2419273122\">https://doi.org/10.1073/pnas.2419273122</a>"},"date_published":"2025-03-25T00:00:00Z","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"intvolume":"       122","article_number":"e2419273122","type":"journal_article","day":"25","acknowledgement":"We thank the reviewers. In particular, they inspired us to analyze the reset and state-preparation problems, to compute optimal qubit mappings, and to apply our method to a quantum error correction scheme that includes both bitflip and phaseflip corrections. We also thank Raimundo Saona and Marek Chalupa for their time spent in insightful discussions. This research was partially supported by the European Research Council CoG 863818 (ForM-SMArt) grant.","doi":"10.1073/pnas.2419273122","date_created":"2025-04-06T22:01:32Z","has_accepted_license":"1","status":"public","scopus_import":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"ddc":["000"],"corr_author":"1","title":"Hardware-optimal quantum algorithms","issue":"12","OA_type":"hybrid","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"Quantum hardware is inherently fragile and noisy. We find that the accuracy of traditional quantum error correction algorithms can be improved depending on the hardware. Given different hardware specifications, we automatically synthesize hardware-optimal algorithms for parity correction, qubit resetting, and GHZ (Greenberger–Horne–Zeilinger) state preparation. Using stochastic techniques from computer science, our method presents a computational tool to compute exact accuracy guarantees and synthesize optimal algorithms that are often different from traditional ones. We also show that improvements can be gained with respect to the Qiskit transpiler as we compute the hardware-optimal qubit mapping for the GHZ state-preparation problem."}],"external_id":{"pmid":["40106357"],"isi":["001459435600001"]},"author":[{"id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","full_name":"Muroya Lei, Stefanie","last_name":"Muroya Lei","first_name":"Stefanie"},{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"}],"oa":1,"article_type":"original","oa_version":"Published Version","ec_funded":1,"_id":"19499","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"publication_status":"published","year":"2025","volume":122,"isi":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"link":[{"relation":"software","url":"https://github.com/smml1996/algorithm_synthesis"},{"relation":"press_release","description":"News on ISTA website","url":"https://ista.ac.at/en/news/hardware-optimal-quantum-algorithms/"}]},"file":[{"checksum":"83501b8a65ee5fdd3f5604fc28eddc22","date_created":"2025-04-07T11:42:22Z","success":1,"creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"19524","date_updated":"2025-04-07T11:42:22Z","file_size":6805668,"file_name":"2025_PNAS_Muroya.pdf"}],"file_date_updated":"2025-04-07T11:42:22Z","date_updated":"2026-04-28T13:41:14Z"},{"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"scopus_import":"1","corr_author":"1","ddc":["570"],"title":"Pulsatile basal gene expression as a fitness determinant in bacteria","issue":"15","OA_type":"hybrid","acknowledgement":"K.J. thanks B. Wu, I. Tomanek, K. Tomasek for detailed discussions on the manuscript, all other members from the Guet laboratory for valuable feedback, R. Chait, & Imaging and Optics Facility, Institute of Science and Technology Austria for helping with microscopy, Dr. Sudha Rao and Dr. Raja Mugasimangalam, Genotypic Technology India for allowing time off to address the revisions. K.J. acknowledges Institute of Science and Technology fellowship IC1006FELL02, R.H. was supported in part by Chan Zuckerberg Initiative and Donor Advised-Fund grant 2020-225401 (https://doi.org/10.37921/120055ratwvi), O.O.B. acknowledges Fonds Zur Förderung der Wissenschaftlichen Forschung (FWF) Grant ESP253-B, R.R. acknowledges FWF Grant 10.55776/ESP219, C.C.G. acknowledges FWF I5127-B.","type":"journal_article","day":"15","status":"public","has_accepted_license":"1","date_created":"2025-04-27T22:02:13Z","doi":"10.1073/pnas.2413709122","citation":{"mla":"Jain, Kirti, et al. “Pulsatile Basal Gene Expression as a Fitness Determinant in Bacteria.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 15, e2413709122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2413709122\">10.1073/pnas.2413709122</a>.","ama":"Jain K, Hauschild R, Bochkareva O, Römhild R, Tkačik G, Guet CC. Pulsatile basal gene expression as a fitness determinant in bacteria. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(15). doi:<a href=\"https://doi.org/10.1073/pnas.2413709122\">10.1073/pnas.2413709122</a>","chicago":"Jain, Kirti, Robert Hauschild, Olga Bochkareva, Roderich Römhild, Gašper Tkačik, and Calin C Guet. “Pulsatile Basal Gene Expression as a Fitness Determinant in Bacteria.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2413709122\">https://doi.org/10.1073/pnas.2413709122</a>.","ieee":"K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, and C. C. Guet, “Pulsatile basal gene expression as a fitness determinant in bacteria,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 15. National Academy of Sciences, 2025.","short":"K. Jain, R. Hauschild, O. Bochkareva, R. Römhild, G. Tkačik, C.C. Guet, Proceedings of the National Academy of Sciences 122 (2025).","apa":"Jain, K., Hauschild, R., Bochkareva, O., Römhild, R., Tkačik, G., &#38; Guet, C. C. (2025). Pulsatile basal gene expression as a fitness determinant in bacteria. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2413709122\">https://doi.org/10.1073/pnas.2413709122</a>","ista":"Jain K, Hauschild R, Bochkareva O, Römhild R, Tkačik G, Guet CC. 2025. Pulsatile basal gene expression as a fitness determinant in bacteria. Proceedings of the National Academy of Sciences. 122(15), e2413709122."},"date_published":"2025-04-15T00:00:00Z","intvolume":"       122","article_number":"e2413709122","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"National Academy of Sciences","OA_place":"publisher","language":[{"iso":"eng"}],"month":"04","pmid":1,"publication":"Proceedings of the National Academy of Sciences","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","file_date_updated":"2025-06-24T07:27:43Z","date_updated":"2026-05-20T08:33:08Z","year":"2025","volume":122,"APC_amount":"5949 EUR","publication_status":"published","related_material":{"record":[{"id":"19294","relation":"research_data","status":"public"}],"link":[{"url":"https://ista.ac.at/en/news/clockwork-just-for-antibiotic-resistance/","description":"News on ISTA website","relation":"press_release"}]},"file":[{"file_name":"2025_PNAS_Jain.pdf","date_updated":"2025-06-24T07:27:43Z","file_size":2949523,"content_type":"application/pdf","file_id":"19888","relation":"main_file","access_level":"open_access","creator":"dernst","success":1,"date_created":"2025-06-24T07:27:43Z","checksum":"115a687f40009660eb4b38b4f6559d41"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","oa":1,"project":[{"_id":"c08e9ad1-5a5b-11eb-8a69-9d1cf3b07473","grant_number":"CZI01","name":"Tools for automation and feedback microscopy"},{"grant_number":"E219","_id":"bd6f94d1-d553-11ed-ba76-ae9f07250f74","name":"Non-canonical antibiotic interactions"},{"grant_number":"I05127","_id":"34e076d6-11ca-11ed-8bc3-aec76c41a181","name":"Evolutionary analysis of gene regulation"}],"_id":"19626","oa_version":"Published Version","department":[{"_id":"CaGu"},{"_id":"Bio"},{"_id":"FyKo"},{"_id":"GaTk"}],"external_id":{"pmid":["40193613"],"isi":["001471235200001"]},"author":[{"id":"330F0278-F248-11E8-B48F-1D18A9856A87","full_name":"Jain, Kirti","orcid":"0000-0002-3809-0449","last_name":"Jain","first_name":"Kirti"},{"first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bochkareva","first_name":"Olga","id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639"},{"last_name":"Römhild","first_name":"Roderich","id":"68E56E44-62B0-11EA-B963-444F3DDC885E","orcid":"0000-0001-9480-5261","full_name":"Römhild, Roderich"},{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C"}],"acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"Active regulation of gene expression, orchestrated by complex interactions of activators and repressors at promoters, controls the fate of organisms. In contrast, basal expression at uninduced promoters is considered to be a dynamically inert mode of nonfunctional “promoter leakiness,” merely a byproduct of transcriptional regulation. Here, we investigate the basal expression mode of the mar operon, the main regulator of intrinsic multiple antibiotic resistance in Escherichia coli, and link its dynamic properties to the noncanonical, yet highly conserved start codon of marR across Enterobacteriaceae. Real-time, single-cell measurements across tens of generations reveal that basal expression consists of rare stochastic gene expression pulses, which maximize variability in wildtype and, surprisingly, transiently accelerate cellular elongation rates. Competition experiments show that basal expression confers fitness advantages to wildtype across several transitions between exponential and stationary growth by shortening lag times. The dynamically rich basal expression of the mar operon has likely been evolutionarily maintained for its role in growth homeostasis of Enterobacteria within the gut environment, thereby allowing other ancillary gene regulatory roles to evolve, e.g., control of costly-to-induce multidrug efflux pumps. Understanding the complex selection forces governing genetic systems involved in intrinsic multidrug resistance is crucial for effective public health measures."}]},{"publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","OA_place":"publisher","month":"04","pmid":1,"article_number":"e2423072122","intvolume":"       122","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_published":"2025-04-15T00:00:00Z","citation":{"ista":"Bombari S, Mondelli M. 2025. Privacy for free in the overparameterized regime. Proceedings of the National Academy of Sciences. 122(15), e2423072122.","apa":"Bombari, S., &#38; Mondelli, M. (2025). Privacy for free in the overparameterized regime. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2423072122\">https://doi.org/10.1073/pnas.2423072122</a>","short":"S. Bombari, M. Mondelli, Proceedings of the National Academy of Sciences 122 (2025).","ieee":"S. Bombari and M. Mondelli, “Privacy for free in the overparameterized regime,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 15. National Academy of Sciences, 2025.","chicago":"Bombari, Simone, and Marco Mondelli. “Privacy for Free in the Overparameterized Regime.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2423072122\">https://doi.org/10.1073/pnas.2423072122</a>.","ama":"Bombari S, Mondelli M. Privacy for free in the overparameterized regime. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(15). doi:<a href=\"https://doi.org/10.1073/pnas.2423072122\">10.1073/pnas.2423072122</a>","mla":"Bombari, Simone, and Marco Mondelli. “Privacy for Free in the Overparameterized Regime.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 15, e2423072122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2423072122\">10.1073/pnas.2423072122</a>."},"has_accepted_license":"1","status":"public","arxiv":1,"doi":"10.1073/pnas.2423072122","date_created":"2025-04-27T22:02:13Z","acknowledgement":"This research was funded in whole, or in part, by the Austrian Science Fund (FWF) Grant number COE 12. 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 authors were also supported by the 2019 Lopez-Loreta prize, and Simone Bombari was supported by a Google PhD fellowship. We thank Diyuan Wu, Edwige Cyffers, Francesco Pedrotti, Inbar Seroussi, Nikita P. Kalinin, Pietro Pelliconi, Roodabeh Safavi, Yizhe Zhu, and Zhichao Wang for helpful discussions.","day":"15","type":"journal_article","OA_type":"hybrid","issue":"15","title":"Privacy for free in the overparameterized regime","ddc":["000"],"corr_author":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"scopus_import":"1","author":[{"last_name":"Bombari","first_name":"Simone","id":"ca726dda-de17-11ea-bc14-f9da834f63aa","full_name":"Bombari, Simone"},{"last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"}],"external_id":{"pmid":["40215275"],"arxiv":["2410.14787"],"isi":["001471214000001"]},"abstract":[{"lang":"eng","text":"Differentially private gradient descent (DP-GD) is a popular algorithm to train deep learning models with provable guarantees on the privacy of the training data. In the last decade, the problem of understanding its performance cost with respect to standard GD has received remarkable attention from the research community, which formally derived upper bounds on the excess population risk  RP  in different learning settings. However, existing bounds typically degrade with over-parameterization, i.e., as the number of parameters  p  gets larger than the number of training samples  n  -- a regime which is ubiquitous in current deep-learning practice. As a result, the lack of theoretical insights leaves practitioners without clear guidance, leading some to reduce the effective number of trainable parameters to improve performance, while others use larger models to achieve better results through scale. In this work, we show that in the popular random features model with quadratic loss, for any sufficiently large  p , privacy can be obtained for free, i.e.,  |RP|=o(1) , not only when the privacy parameter  ε  has constant order, but also in the strongly private setting  ε=o(1) . This challenges the common wisdom that over-parameterization inherently hinders performance in private learning."}],"department":[{"_id":"MaMo"}],"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"_id":"92099302-16d5-11f0-9cad-f9a785f54fbd","name":"Trustworthy Deep Learning Theory: Private Over-Parameterized Models and Robust LLMs"}],"_id":"19627","oa_version":"Published Version","article_type":"original","oa":1,"file":[{"checksum":"1ac6f78e368d35a0cafb4d2d9bd63443","date_created":"2025-05-05T07:27:54Z","success":1,"creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"19648","file_size":2328320,"date_updated":"2025-05-05T07:27:54Z","file_name":"2025_PNAS_Bombari.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"APC_amount":"2754,32 EUR","year":"2025","volume":122,"publication_status":"published","date_updated":"2026-05-20T08:23:19Z","file_date_updated":"2025-05-05T07:27:54Z"},{"ec_funded":1,"_id":"19965","project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"}],"oa_version":"Published Version","article_type":"original","oa":1,"external_id":{"pmid":["40523172"],"isi":["001522351900001"]},"author":[{"full_name":"Mcavoy, Alex","first_name":"Alex","last_name":"Mcavoy"},{"full_name":"Sehwag, Udari Madhushani","last_name":"Sehwag","first_name":"Udari Madhushani"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian"},{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Barfuss, Wolfram","first_name":"Wolfram","last_name":"Barfuss"},{"first_name":"Qi","last_name":"Su","full_name":"Su, Qi"},{"full_name":"Leonard, Naomi Ehrich","first_name":"Naomi Ehrich","last_name":"Leonard"},{"first_name":"Joshua B.","last_name":"Plotkin","full_name":"Plotkin, Joshua B."}],"abstract":[{"lang":"eng","text":"Multiagent learning is challenging when agents face mixed-motivation interactions, where conflicts of interest arise as agents independently try to optimize their respective outcomes. Recent advancements in evolutionary game theory have identified a class of “zero-determinant” strategies, which confer an agent with significant unilateral control over outcomes in repeated games. Building on these insights, we present a comprehensive generalization of zero-determinant strategies to stochastic games, encompassing dynamic environments. We propose an algorithm that allows an agent to discover strategies enforcing predetermined linear (or approximately linear) payoff relationships. Of particular interest is the relationship in which both payoffs are equal, which serves as a proxy for fairness in symmetric games. We demonstrate that an agent can discover strategies enforcing such relationships through experience alone, without coordinating with an opponent. In finding and using such a strategy, an agent (“enforcer”) can incentivize optimal and equitable outcomes, circumventing potential exploitation. In particular, from the opponent’s viewpoint, the enforcer transforms a mixed-motivation problem into a cooperative problem, paving the way for more collaboration and fairness in multiagent systems."}],"department":[{"_id":"KrCh"}],"date_updated":"2025-09-30T13:47:14Z","file_date_updated":"2025-07-08T05:52:26Z","file":[{"content_type":"application/pdf","file_id":"19972","relation":"main_file","date_updated":"2025-07-08T05:52:26Z","file_size":29525932,"file_name":"2025_PNAS_McAvoy.pdf","date_created":"2025-07-08T05:52:26Z","checksum":"3b35befd959a3e37aa9080a64a6afaf3","creator":"dernst","success":1,"access_level":"open_access"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"year":"2025","volume":122,"publication_status":"published","article_number":"e2319927121","intvolume":"       122","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"citation":{"ista":"Mcavoy A, Sehwag UM, Hilbe C, Chatterjee K, Barfuss W, Su Q, Leonard NE, Plotkin JB. 2025. Unilateral incentive alignment in two-agent stochastic games. Proceedings of the National Academy of Sciences. 122(25), e2319927121.","apa":"Mcavoy, A., Sehwag, U. M., Hilbe, C., Chatterjee, K., Barfuss, W., Su, Q., … Plotkin, J. B. (2025). Unilateral incentive alignment in two-agent stochastic games. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2319927121\">https://doi.org/10.1073/pnas.2319927121</a>","short":"A. Mcavoy, U.M. Sehwag, C. Hilbe, K. Chatterjee, W. Barfuss, Q. Su, N.E. Leonard, J.B. Plotkin, Proceedings of the National Academy of Sciences 122 (2025).","chicago":"Mcavoy, Alex, Udari Madhushani Sehwag, Christian Hilbe, Krishnendu Chatterjee, Wolfram Barfuss, Qi Su, Naomi Ehrich Leonard, and Joshua B. Plotkin. “Unilateral Incentive Alignment in Two-Agent Stochastic Games.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2319927121\">https://doi.org/10.1073/pnas.2319927121</a>.","ieee":"A. Mcavoy <i>et al.</i>, “Unilateral incentive alignment in two-agent stochastic games,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 25. National Academy of Sciences, 2025.","ama":"Mcavoy A, Sehwag UM, Hilbe C, et al. Unilateral incentive alignment in two-agent stochastic games. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(25). doi:<a href=\"https://doi.org/10.1073/pnas.2319927121\">10.1073/pnas.2319927121</a>","mla":"Mcavoy, Alex, et al. “Unilateral Incentive Alignment in Two-Agent Stochastic Games.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 25, e2319927121, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2319927121\">10.1073/pnas.2319927121</a>."},"date_published":"2025-06-24T00:00:00Z","publication":"Proceedings of the National Academy of Sciences","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","publisher":"National Academy of Sciences","OA_place":"publisher","language":[{"iso":"eng"}],"month":"06","pmid":1,"issue":"25","title":"Unilateral incentive alignment in two-agent stochastic games","OA_type":"hybrid","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"scopus_import":"1","ddc":["000"],"has_accepted_license":"1","status":"public","date_created":"2025-07-06T22:01:23Z","doi":"10.1073/pnas.2319927121","acknowledgement":"We gratefully acknowledge the support from the European Research Council (Starting Grant 850529: E-DIRECT) and the Max Planck Society (C.H.), the European Research Council (Consolidator Grant 863818: ForM-SMArt) (K.C.), the Shanghai Pujiang Program (No. 23PJ1405500) (Q.S.), the Army Research Office (Grant No. W911NF-18-1-0325) (N.E.L.), and the John Templeton Foundation (Grant No. 62281) (J.B.P.).","day":"24","type":"journal_article"},{"acknowledgement":"We thank all members of the M.S. and E.H. groups for stimulating discussions.We thank the Imaging and Optics facility, the Pre-clinical and Lab Support facility of the Institute of Science and Technology Austria for their excellent support and provided resources for the experimental research. In particular, we thank Jack Merrin from the Nanofabrication facility who generated the microfabricated channel used in this study. This work received funding fromt he European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 851288 to E.H.). M.C.U.is funded by a University of Sheffield Strategic Research Fellowship in the Physics of Life and Quantitative Biology.","day":"26","type":"journal_article","has_accepted_license":"1","status":"public","doi":"10.1073/pnas.2504064122","date_created":"2025-09-07T22:01:32Z","scopus_import":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"corr_author":"1","ddc":["570"],"issue":"34","title":"Self-generated chemotaxis of mixed cell populations","OA_type":"hybrid","OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"month":"08","pmid":1,"publication":"Proceedings of the National Academy of Sciences","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","citation":{"mla":"Ucar, Mehmet C., et al. “Self-Generated Chemotaxis of Mixed Cell Populations.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 34, e2504064122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2504064122\">10.1073/pnas.2504064122</a>.","chicago":"Ucar, Mehmet C, Alsberga Zane, Jonna H Alanko, Michael K Sixt, and Edouard B Hannezo. “Self-Generated Chemotaxis of Mixed Cell Populations.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2504064122\">https://doi.org/10.1073/pnas.2504064122</a>.","ieee":"M. C. Ucar, A. Zane, J. H. Alanko, M. K. Sixt, and E. B. Hannezo, “Self-generated chemotaxis of mixed cell populations,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 34. National Academy of Sciences, 2025.","ama":"Ucar MC, Zane A, Alanko JH, Sixt MK, Hannezo EB. Self-generated chemotaxis of mixed cell populations. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(34). doi:<a href=\"https://doi.org/10.1073/pnas.2504064122\">10.1073/pnas.2504064122</a>","short":"M.C. Ucar, A. Zane, J.H. Alanko, M.K. Sixt, E.B. Hannezo, Proceedings of the National Academy of Sciences 122 (2025).","ista":"Ucar MC, Zane A, Alanko JH, Sixt MK, Hannezo EB. 2025. Self-generated chemotaxis of mixed cell populations. Proceedings of the National Academy of Sciences. 122(34), e2504064122.","apa":"Ucar, M. C., Zane, A., Alanko, J. H., Sixt, M. K., &#38; Hannezo, E. B. (2025). Self-generated chemotaxis of mixed cell populations. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2504064122\">https://doi.org/10.1073/pnas.2504064122</a>"},"date_published":"2025-08-26T00:00:00Z","intvolume":"       122","article_number":"e2504064122","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":122,"year":"2025","APC_amount":"5766,07 EUR","publication_status":"published","related_material":{"link":[{"url":"https://github.com/mehmetcanucar/Self-generated-chemotaxis","relation":"software"}]},"file":[{"creator":"dernst","success":1,"date_created":"2025-09-08T07:23:29Z","checksum":"b36abd92673b6d76376fc9434bad52cc","access_level":"open_access","file_size":16069140,"date_updated":"2025-09-08T07:23:29Z","file_id":"20307","content_type":"application/pdf","relation":"main_file","file_name":"2025_PNAS_Ucar.pdf"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-09-08T07:23:29Z","date_updated":"2026-05-20T08:59:54Z","PlanS_conform":"1","department":[{"_id":"EdHa"},{"_id":"MiSi"}],"external_id":{"isi":["001562181600001"],"pmid":["40838890"]},"author":[{"last_name":"Ucar","first_name":"Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C"},{"last_name":"Zane","first_name":"Alsberga","id":"60f7509a-f652-11ea-9d86-b963d6490d7c","full_name":"Zane, Alsberga","orcid":"0009-0003-0415-7603"},{"id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87","full_name":"Alanko, Jonna H","orcid":"0000-0002-7698-3061","last_name":"Alanko","first_name":"Jonna H"},{"last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"Cell and tissue movement in development, cancer invasion, and immune response relies on chemical or mechanical guidance cues. In many systems, this behavior is locally directed by self-generated signaling gradients rather than long-range, prepatterned cues. However, how heterogeneous mixtures of cells interact nonreciprocally and navigate through self-generated gradients remains largely unexplored. Here, we introduce a theoretical framework for the self-organized chemotaxis of heterogeneous cell populations. We find that the relative chemotactic sensitivities of different cell populations control their long-time coupling and comigration dynamics, with boundary conditions such as external cell and attractant reservoirs substantially influencing the migration patterns. Our model predicts an optimal parameter regime that enables robust and colocalized migration. We test our theoretical predictions with in vitro experiments demonstrating the comigration of distinct immune cell populations, and quantitatively reproduce observed migration patterns under wild-type and perturbed conditions. Interestingly, immune cell comigration occurs close to the predicted optimal regime. Finally, we incorporate mechanical interactions into our framework, revealing a nontrivial interplay between chemotactic and mechanical nonreciprocity in driving collective migration. Together, our findings suggest that self-generated chemotaxis is a robust strategy for the navigation of mixed cell populations."}],"article_type":"original","oa":1,"_id":"20289","project":[{"call_identifier":"H2020","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis"}],"ec_funded":1,"oa_version":"Published Version"},{"oa_version":"Published Version","_id":"18849","project":[{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"},{"grant_number":"101118866","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"}],"oa":1,"article_type":"original","abstract":[{"lang":"eng","text":"Many biological systems operate near the physical limits to their performance, suggesting that aspects of their behavior and underlying mechanisms could be derived from optimization principles. However, such principles have often been applied only in simplified models. Here, we explore a detailed mechanistic model of the gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize the information that gene expression levels provide about nuclear positions. This optimization is conducted under realistic constraints, such as limits on the number of available molecules. Remarkably, the optimal networks we derive closely match the architecture and spatial gene expression profiles observed in the real organism. Our framework quantifies the tradeoffs involved in maximizing functional performance and allows for the exploration of alternative network configurations, addressing the question of which features are necessary and which are contingent. Our results suggest that multiple solutions to the optimization problem might exist across closely related organisms, offering insights into the evolution of gene regulatory networks."}],"external_id":{"pmid":["39752518"],"isi":["001392772400001"]},"author":[{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R","last_name":"Sokolowski","first_name":"Thomas R"},{"full_name":"Gregor, Thomas","first_name":"Thomas","last_name":"Gregor"},{"full_name":"Bialek, William","first_name":"William","last_name":"Bialek"},{"last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"department":[{"_id":"GaTk"}],"date_updated":"2026-02-16T12:26:51Z","file_date_updated":"2025-01-20T10:10:04Z","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","date_created":"2025-01-20T10:10:04Z","checksum":"8dbfc7d495413340225ebfae69b0cf9a","creator":"dernst","success":1,"file_name":"2025_PNAS_Sokolowski.pdf","file_id":"18862","content_type":"application/pdf","relation":"main_file","file_size":19073585,"date_updated":"2025-01-20T10:10:04Z"}],"publication_status":"published","year":"2025","volume":122,"tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"intvolume":"       122","article_number":"e2402925121","citation":{"short":"T.R. Sokolowski, T. Gregor, W. Bialek, G. Tkačik, Proceedings of the National Academy of Sciences 122 (2025).","apa":"Sokolowski, T. R., Gregor, T., Bialek, W., &#38; Tkačik, G. (2025). Deriving a genetic regulatory network from an optimization principle. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2402925121\">https://doi.org/10.1073/pnas.2402925121</a>","ista":"Sokolowski TR, Gregor T, Bialek W, Tkačik G. 2025. Deriving a genetic regulatory network from an optimization principle. Proceedings of the National Academy of Sciences. 122(1), e2402925121.","mla":"Sokolowski, Thomas R., et al. “Deriving a Genetic Regulatory Network from an Optimization Principle.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1, e2402925121, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2402925121\">10.1073/pnas.2402925121</a>.","ama":"Sokolowski TR, Gregor T, Bialek W, Tkačik G. Deriving a genetic regulatory network from an optimization principle. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(1). doi:<a href=\"https://doi.org/10.1073/pnas.2402925121\">10.1073/pnas.2402925121</a>","chicago":"Sokolowski, Thomas R, Thomas Gregor, William Bialek, and Gašper Tkačik. “Deriving a Genetic Regulatory Network from an Optimization Principle.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2402925121\">https://doi.org/10.1073/pnas.2402925121</a>.","ieee":"T. R. Sokolowski, T. Gregor, W. Bialek, and G. Tkačik, “Deriving a genetic regulatory network from an optimization principle,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1. National Academy of Sciences, 2025."},"date_published":"2025-01-07T00:00:00Z","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","publication":"Proceedings of the National Academy of Sciences","pmid":1,"month":"01","OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"title":"Deriving a genetic regulatory network from an optimization principle","issue":"1","OA_type":"hybrid","scopus_import":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"corr_author":"1","ddc":["570"],"doi":"10.1073/pnas.2402925121","date_created":"2025-01-19T23:01:50Z","status":"public","has_accepted_license":"1","type":"journal_article","day":"07","acknowledgement":"We thank Nicholas H. Barton for his comments on the manuscript, Benjamin Zoller for helpful discussions, and Aleksandra Walczak and Curtis Callan for early collaborations that shaped this work. Special thanks to Eric F. Wieschaus for many persistently inspiring conversations. This work was supported in part by the Human Frontiers Science Program; the Austrian Science Fund (FWF P28844); by the European Research Council grant DynaTrans (101118866); by U.S. NSF, through the Center for the Physics of Biological Function (PHY–1734030); by NIH Grants R01GM097275, U01DA047730, and U01DK127429; by the John Simon Guggenheim Memorial Foundation; and by the LOEWE priority program “Center for Multiscale Modeling in Life Sciences” (CMMS), sponsored by the Hessian Ministry for Science and Research, Arts and Culture (HMWK)."},{"citation":{"mla":"Perkins, Mindy Liu, et al. “Chromatin Enables Precise and Scalable Gene Regulation with Factors of Limited Specificity.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1, e2411887121, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2411887121\">10.1073/pnas.2411887121</a>.","ieee":"M. L. Perkins, J. Crocker, and G. Tkačik, “Chromatin enables precise and scalable gene regulation with factors of limited specificity,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1. National Academy of Sciences, 2025.","chicago":"Perkins, Mindy Liu, Justin Crocker, and Gašper Tkačik. “Chromatin Enables Precise and Scalable Gene Regulation with Factors of Limited Specificity.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2411887121\">https://doi.org/10.1073/pnas.2411887121</a>.","ama":"Perkins ML, Crocker J, Tkačik G. Chromatin enables precise and scalable gene regulation with factors of limited specificity. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(1). doi:<a href=\"https://doi.org/10.1073/pnas.2411887121\">10.1073/pnas.2411887121</a>","short":"M.L. Perkins, J. Crocker, G. Tkačik, Proceedings of the National Academy of Sciences 122 (2025).","ista":"Perkins ML, Crocker J, Tkačik G. 2025. Chromatin enables precise and scalable gene regulation with factors of limited specificity. Proceedings of the National Academy of Sciences. 122(1), e2411887121.","apa":"Perkins, M. L., Crocker, J., &#38; Tkačik, G. (2025). Chromatin enables precise and scalable gene regulation with factors of limited specificity. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2411887121\">https://doi.org/10.1073/pnas.2411887121</a>"},"date_published":"2025-01-07T00:00:00Z","article_number":"e2411887121","intvolume":"       122","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"month":"01","pmid":1,"publication":"Proceedings of the National Academy of Sciences","quality_controlled":"1","article_processing_charge":"No","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"scopus_import":"1","corr_author":"1","ddc":["570"],"title":"Chromatin enables precise and scalable gene regulation with factors of limited specificity","issue":"1","OA_type":"hybrid","acknowledgement":"M.L.P. was supported by the European Molecular Biology Laboratory (EMBL) Interdisciplinary Postdoc Programme (EIPOD4 fellowships), cofunded by Marie SkÅ‚odowska-Curie Actions (Grant Agreement No. 847543). J.C. and M.L.P. were supported by EMBL Core Funding and Theory@EMBL. This work is supported by European Research Council Grant DynaTrans (101118866) to G.T. We would like to thank the members of the J.C. and G.T. groups, especially Natalia Misunou, Michal Hledík, and Réka Borbély, for helpful feedback and discussion. We also thank EMBL IT Services for the use of high performance computing resources.","day":"07","type":"journal_article","status":"public","has_accepted_license":"1","doi":"10.1073/pnas.2411887121","date_created":"2025-01-19T23:01:51Z","article_type":"original","oa":1,"_id":"18850","project":[{"name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","grant_number":"101118866","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9"}],"oa_version":"Published Version","department":[{"_id":"GaTk"}],"external_id":{"pmid":["39793086"],"isi":["001392765300001"]},"author":[{"full_name":"Perkins, Mindy Liu","last_name":"Perkins","first_name":"Mindy Liu"},{"first_name":"Justin","last_name":"Crocker","full_name":"Crocker, Justin"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik"}],"abstract":[{"lang":"eng","text":"Biophysical constraints limit the specificity with which transcription factors (TFs) can target regulatory DNA. While individual nontarget binding events may be low affinity, the sheer number of such interactions could present a challenge for gene regulation by degrading its precision or possibly leading to an erroneous induction state. Chromatin can prevent nontarget binding by rendering DNA physically inaccessible to TFs, at the cost of energy-consuming remodeling orchestrated by pioneer factors (PFs). Under what conditions and by how much can chromatin reduce regulatory errors on a global scale? We use a theoretical approach to compare two scenarios for gene regulation: one that relies on TF binding to free DNA alone and one that uses a combination of TFs and chromatin-regulating PFs to achieve desired gene expression patterns. We find, first, that chromatin effectively silences groups of genes that should be simultaneously OFF, thereby allowing more accurate graded control of expression for the remaining ON genes. Second, chromatin buffers the deleterious consequences of nontarget binding as the number of OFF genes grows, permitting a substantial expansion in regulatory complexity. Third, chromatin-based regulation productively co-opts nontarget TF binding for ON genes in order to establish a “leaky” baseline expression level, which targeted activator or repressor binding subsequently up- or down-modulates. Thus, on a global scale, using chromatin simultaneously alleviates pressure for high specificity of regulatory interactions and enables an increase in genome size with minimal impact on global expression error."}],"file_date_updated":"2025-01-20T09:38:32Z","date_updated":"2026-05-06T12:43:59Z","volume":122,"year":"2025","APC_amount":"3261,23 EUR","publication_status":"published","related_material":{"link":[{"relation":"software","url":"https://github.com/officerredshirt/network_crosstalk"}]},"file":[{"file_id":"18859","content_type":"application/pdf","relation":"main_file","date_updated":"2025-01-20T09:38:32Z","file_size":30943709,"file_name":"2025_PNAS_Perkins.pdf","date_created":"2025-01-20T09:38:32Z","checksum":"86a8d25a6e282aeb4128f1d0b86ff911","creator":"dernst","success":1,"access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1},{"department":[{"_id":"TiVo"}],"external_id":{"isi":["001422380500004"],"pmid":["39841147"]},"author":[{"full_name":"Naumann, Laura B","id":"81a3b706-8972-11ed-ae7b-8eff728700ca","first_name":"Laura B","last_name":"Naumann"},{"first_name":"Loreen","last_name":"Hertäg","full_name":"Hertäg, Loreen"},{"full_name":"Müller, Jennifer","first_name":"Jennifer","last_name":"Müller"},{"last_name":"Letzkus","first_name":"Johannes J.","full_name":"Letzkus, Johannes J."},{"full_name":"Sprekeler, Henning","last_name":"Sprekeler","first_name":"Henning"}],"abstract":[{"text":"Neuronal processing of external sensory input is shaped by internally generated top–down information. In the neocortex, top–down projections primarily target layer 1, which contains NDNF (neuron-derived neurotrophic factor)-expressing interneurons and the dendrites of pyramidal cells. Here, we investigate the hypothesis that NDNF interneurons shape cortical computations in an unconventional, layer-specific way, by exerting presynaptic inhibition on synapses in layer 1 while leaving synapses in deeper layers unaffected. We first confirm experimentally that in the auditory cortex, synapses from somatostatin-expressing (SOM) onto NDNF neurons are indeed modulated by ambient Gamma-aminobutyric acid (GABA). Shifting to a computational model, we then show that this mechanism introduces a distinct mutual inhibition motif between NDNF interneurons and the synaptic outputs of SOM interneurons. This motif can control inhibition in a layer-specific way and introduces competition between NDNF and SOM interneurons for dendritic inhibition onto pyramidal cells on different timescales. NDNF interneurons can thereby control cortical information flow by redistributing dendritic inhibition from fast to slow timescales and by gating different sources of dendritic inhibition.","lang":"eng"}],"article_type":"original","oa":1,"_id":"19036","oa_version":"Published Version","volume":122,"year":"2025","publication_status":"published","related_material":{"link":[{"relation":"software","url":"https://github.com/LNaumann/NDNF_control_inhibition_Naumann25"}]},"file":[{"file_name":"2025_PNAS_Naumann.pdf","date_updated":"2025-02-17T14:46:18Z","file_size":13726531,"file_id":"19046","content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"dernst","success":1,"date_created":"2025-02-17T14:46:18Z","checksum":"636d5130724e3236ebf4fc658b3945fe"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-02-17T14:46:18Z","date_updated":"2026-02-16T12:28:02Z","OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"pmid":1,"month":"01","publication":"Proceedings of the National Academy of Sciences","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","citation":{"chicago":"Naumann, Laura B, Loreen Hertäg, Jennifer Müller, Johannes J. Letzkus, and Henning Sprekeler. “Layer-Specific Control of Inhibition by NDNF Interneurons.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2408966122\">https://doi.org/10.1073/pnas.2408966122</a>.","ieee":"L. B. Naumann, L. Hertäg, J. Müller, J. J. Letzkus, and H. Sprekeler, “Layer-specific control of inhibition by NDNF interneurons,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 4. National Academy of Sciences, 2025.","ama":"Naumann LB, Hertäg L, Müller J, Letzkus JJ, Sprekeler H. Layer-specific control of inhibition by NDNF interneurons. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(4). doi:<a href=\"https://doi.org/10.1073/pnas.2408966122\">10.1073/pnas.2408966122</a>","mla":"Naumann, Laura B., et al. “Layer-Specific Control of Inhibition by NDNF Interneurons.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 4, e2408966122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2408966122\">10.1073/pnas.2408966122</a>.","apa":"Naumann, L. B., Hertäg, L., Müller, J., Letzkus, J. J., &#38; Sprekeler, H. (2025). Layer-specific control of inhibition by NDNF interneurons. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2408966122\">https://doi.org/10.1073/pnas.2408966122</a>","ista":"Naumann LB, Hertäg L, Müller J, Letzkus JJ, Sprekeler H. 2025. Layer-specific control of inhibition by NDNF interneurons. Proceedings of the National Academy of Sciences. 122(4), e2408966122.","short":"L.B. Naumann, L. Hertäg, J. Müller, J.J. Letzkus, H. Sprekeler, Proceedings of the National Academy of Sciences 122 (2025)."},"date_published":"2025-01-22T00:00:00Z","article_number":"e2408966122","intvolume":"       122","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"acknowledgement":"We thank all members of the Letzkus lab, the Sprekeler lab, and the Vogels lab for discussions, U. Thirimanna for technical assistance, and K. Deisseroth for generously sharing reagents. This work was supported by the German Research Foundation (LE 3804/3-1, LE 3804/4-1, LE 3804/7-1, CRC-TRR 384/1 2024, - 514483642, and 460088091) and the Wellcome Trust Senior Research Fellowship 214316/Z/18/Z.\r\nElectrophysiological recordings, source code for simulations, and data analysis have been deposited in GitHub (https://github.com/LNaumann/NDNF_control_inhibition_Naumann25) (62).","day":"22","type":"journal_article","status":"public","has_accepted_license":"1","doi":"10.1073/pnas.2408966122","date_created":"2025-02-17T09:20:19Z","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"scopus_import":"1","ddc":["570"],"issue":"4","title":"Layer-specific control of inhibition by NDNF interneurons","OA_type":"hybrid"},{"acknowledgement":"This research was funded by Biological Breeding-National Science and Technology Major Project (2023ZD0407201), China Postdoctoral Science Foundation (2024M763575), China Agricultural University Fund (2025RC042), Chinese Universities Scientific Fund (2024RC031), and Austrian Science Fund (FWF; I 6123-B).","type":"journal_article","day":"23","has_accepted_license":"1","status":"public","date_created":"2025-11-12T10:03:20Z","doi":"10.1073/pnas.2512274122","scopus_import":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"ddc":["580"],"issue":"39","title":"Antagonistic SnRK2 and PID kinases' action on auxin transport-mediated root gravitropism","OA_type":"hybrid","OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"month":"09","pmid":1,"publication":"Proceedings of the National Academy of Sciences","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","citation":{"mla":"Sheng, F., et al. “Antagonistic SnRK2 and PID Kinases’ Action on Auxin Transport-Mediated Root Gravitropism.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 39, National Academy of Sciences, 2025, p. e2512274122, doi:<a href=\"https://doi.org/10.1073/pnas.2512274122\">10.1073/pnas.2512274122</a>.","ama":"Sheng F, Gao Y, Wang Y, et al. Antagonistic SnRK2 and PID kinases’ action on auxin transport-mediated root gravitropism. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(39):e2512274122. doi:<a href=\"https://doi.org/10.1073/pnas.2512274122\">10.1073/pnas.2512274122</a>","chicago":"Sheng, F, Y Gao, Y Wang, Y Li, JA Zhang, Z Zhang, X Qin, et al. “Antagonistic SnRK2 and PID Kinases’ Action on Auxin Transport-Mediated Root Gravitropism.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2512274122\">https://doi.org/10.1073/pnas.2512274122</a>.","ieee":"F. Sheng <i>et al.</i>, “Antagonistic SnRK2 and PID kinases’ action on auxin transport-mediated root gravitropism,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 39. National Academy of Sciences, p. e2512274122, 2025.","short":"F. Sheng, Y. Gao, Y. Wang, Y. Li, J. Zhang, Z. Zhang, X. Qin, S. Zhang, W. Song, J. Li, Y. Guo, J. Friml, Z. Gong, Q. Zhang, J. Zhang, Proceedings of the National Academy of Sciences 122 (2025) e2512274122.","apa":"Sheng, F., Gao, Y., Wang, Y., Li, Y., Zhang, J., Zhang, Z., … Zhang, J. (2025). Antagonistic SnRK2 and PID kinases’ action on auxin transport-mediated root gravitropism. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2512274122\">https://doi.org/10.1073/pnas.2512274122</a>","ista":"Sheng F, Gao Y, Wang Y, Li Y, Zhang J, Zhang Z, Qin X, Zhang S, Song W, Li J, Guo Y, Friml J, Gong Z, Zhang Q, Zhang J. 2025. Antagonistic SnRK2 and PID kinases’ action on auxin transport-mediated root gravitropism. Proceedings of the National Academy of Sciences. 122(39), e2512274122."},"date_published":"2025-09-23T00:00:00Z","intvolume":"       122","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"volume":122,"year":"2025","publication_status":"published","file":[{"access_level":"open_access","date_created":"2025-11-24T13:48:09Z","checksum":"38b723a909bf321d7ee537c9d064aa25","creator":"dernst","success":1,"file_name":"2025_PNAS_Sheng.pdf","content_type":"application/pdf","file_id":"20681","relation":"main_file","date_updated":"2025-11-24T13:48:09Z","file_size":2667764}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2025-11-24T13:48:09Z","date_updated":"2026-02-16T12:32:51Z","PlanS_conform":"1","department":[{"_id":"JiFr"}],"external_id":{"pmid":["40986351"],"isi":["001589177800001"]},"author":[{"first_name":"F","last_name":"Sheng","full_name":"Sheng, F"},{"full_name":"Gao, Y","first_name":"Y","last_name":"Gao"},{"full_name":"Wang, Y","first_name":"Y","last_name":"Wang"},{"last_name":"Li","first_name":"Y","full_name":"Li, Y"},{"last_name":"Zhang","first_name":"JA","full_name":"Zhang, JA"},{"last_name":"Zhang","first_name":"Z","full_name":"Zhang, Z"},{"full_name":"Qin, X","last_name":"Qin","first_name":"X"},{"full_name":"Zhang, S","last_name":"Zhang","first_name":"S"},{"full_name":"Song, W","last_name":"Song","first_name":"W"},{"first_name":"J","last_name":"Li","full_name":"Li, J"},{"last_name":"Guo","first_name":"Y","full_name":"Guo, Y"},{"first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gong","first_name":"Z","full_name":"Gong, Z"},{"full_name":"Zhang, Q","last_name":"Zhang","first_name":"Q"},{"full_name":"Zhang, J","first_name":"J","last_name":"Zhang"}],"abstract":[{"text":"Plants have evolved sophisticated mechanisms to adapt to environmental changes, with root gravitropism playing a pivotal role in nutrient and water acquisition. Our study reveals that SnRK2 kinases (SnRK2.2 and SnRK2.3) are critical regulators of root gravitropism through their direct phosphorylation of the auxin transporter PIN2 at S259. We demonstrate that SnRK2s-mediated phosphorylation modulates both the polar localization and transport activity of PIN2. Importantly, SnRK2s function antagonistically to the AGCVIII kinase PID, which phosphorylates PIN2 at a distinct site (S258), establishing a regulatory balance essential for adaptive root growth. Structural modeling and phosphorylation assays further suggest that SnRK2s-mediated phosphorylation at S259 sterically hinders access of PID to S258, providing a mechanistic basis for their antagonistic relationship. These findings uncover a novel regulatory mechanism, by which plants fine-tune root developmental programs to adapt to environmental stimuli, highlighting the evolutionary significance of multilayered kinase-mediated regulation in plant adaptation.","lang":"eng"}],"page":"e2512274122","article_type":"original","oa":1,"project":[{"name":"Peptide receptors for auxin canalization in Arabidopsis","_id":"bd76d395-d553-11ed-ba76-f678c14f9033","grant_number":"I06123"}],"_id":"20635","oa_version":"Published Version"},{"scopus_import":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"corr_author":"1","ddc":["550"],"issue":"48","title":"Tropics-wide intraseasonal oscillations","OA_type":"hybrid","type":"journal_article","day":"02","acknowledgement":"J.B. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant (grant agreement No. 101034413). S.B. acknowledges funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Project Mesoscale organization of tropical convection, grant agreement No 101098063). D.T. acknowledges funding from the Japan Society for the Promotion of Science (JSPS) (Project JSPS Grants-in-Aid for Scientific Research, grant No. JP24K22893). C.M. gratefully acknowledges funding from the ERC under the European Union’s Horizon 2020 research and innovation program (Project organisation of CLoUdS, and implications for Tropical cyclones and for the Energetics of the tropics, in current and in a waRming climate, grant agreement No. 805041). We thank Martin Singh, Steven Sherwood, Bjorn Stevens, and Lokahith Agasthya for helpful discussions. JSPS Core-to-Core Program, “International Core-to-Core Project on Global Storm Resolving Analysis” (Grant Number: JPJSCCA20220001)","date_created":"2025-12-11T10:41:13Z","doi":"10.1073/pnas.2511549122","has_accepted_license":"1","status":"public","citation":{"apa":"Bao, J., Bony, S., Takasuka, D., &#38; Muller, C. J. (2025). Tropics-wide intraseasonal oscillations. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2511549122\">https://doi.org/10.1073/pnas.2511549122</a>","ista":"Bao J, Bony S, Takasuka D, Muller CJ. 2025. Tropics-wide intraseasonal oscillations. Proceedings of the National Academy of Sciences. 122(48), e2511549122.","short":"J. Bao, S. Bony, D. Takasuka, C.J. Muller, Proceedings of the National Academy of Sciences 122 (2025).","ama":"Bao J, Bony S, Takasuka D, Muller CJ. Tropics-wide intraseasonal oscillations. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(48). doi:<a href=\"https://doi.org/10.1073/pnas.2511549122\">10.1073/pnas.2511549122</a>","chicago":"Bao, Jiawei, Sandrine Bony, Daisuke Takasuka, and Caroline J Muller. “Tropics-Wide Intraseasonal Oscillations.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2511549122\">https://doi.org/10.1073/pnas.2511549122</a>.","ieee":"J. Bao, S. Bony, D. Takasuka, and C. J. Muller, “Tropics-wide intraseasonal oscillations,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 48. National Academy of Sciences, 2025.","mla":"Bao, Jiawei, et al. “Tropics-Wide Intraseasonal Oscillations.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 48, e2511549122, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2511549122\">10.1073/pnas.2511549122</a>."},"date_published":"2025-12-02T00:00:00Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"       122","article_number":"e2511549122","pmid":1,"month":"12","publisher":"National Academy of Sciences","OA_place":"publisher","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","publication":"Proceedings of the National Academy of Sciences","file_date_updated":"2025-12-15T09:17:33Z","date_updated":"2026-05-20T08:11:56Z","publication_status":"published","year":"2025","volume":122,"APC_amount":"5651,35 EUR","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"description":"News on ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/hidden-in-plain-sight/"}]},"file":[{"creator":"dernst","success":1,"date_created":"2025-12-15T09:17:33Z","checksum":"093a8685170e4a1de9176f68ee449493","access_level":"open_access","date_updated":"2025-12-15T09:17:33Z","file_size":30890293,"content_type":"application/pdf","file_id":"20822","relation":"main_file","file_name":"2025_PNAS_Bao.pdf"}],"oa":1,"article_type":"original","oa_version":"Published Version","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"},{"_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041","call_identifier":"H2020","name":"Organization of CLoUdS, and implications of Tropical  cyclones and for the Energetics of the tropics, in current and waRming climate"}],"_id":"20795","ec_funded":1,"department":[{"_id":"CaMu"}],"PlanS_conform":"1","abstract":[{"lang":"eng","text":"The tropical climate variability is characterized by various oscillations across a range of timescales. Oscillations that imprint the tropical mean state are generally attributed to slow processes, such as the seasonal cycle or interannual variability. Here, we identify a pronounced tropics-wide intraseasonal oscillation (TWISO) in satellite observations and reanalyses. This oscillation, with a period of 30 to 60 d, is evident across multiple variables and involves interactions between convection, radiation, surface fluxes, and large-scale circulation. It is primarily manifested as convective perturbations in the tropical Indo-Pacific warm pool accompanied by oscillations in the large-scale tropical overturning circulation. Here, we examine the relationship between TWISO, the Madden–Julian Oscillation (MJO), and the instability of radiative-convective equilibrium. Certain phases of TWISO coincide with specific phases of the MJO, suggesting a potential connection between the two. However, although the MJO can amplify the oscillation amplitude of TWISO, it is not essential for TWISO to occur. Finally, due to its broad manifestation across the tropics, TWISO potentially exerts widespread influence on tropical weather and climate at regional scales."}],"external_id":{"pmid":["41284872"]},"author":[{"last_name":"Bao","first_name":"Jiawei","id":"bb9a7399-fefd-11ed-be3c-ae648fd1d160","full_name":"Bao, Jiawei"},{"last_name":"Bony","first_name":"Sandrine","full_name":"Bony, Sandrine"},{"last_name":"Takasuka","first_name":"Daisuke","full_name":"Takasuka, Daisuke"},{"first_name":"Caroline J","last_name":"Muller","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"}]},{"date_updated":"2025-06-10T11:50:48Z","volume":121,"year":"2024","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","oa":1,"_id":"19809","oa_version":"Published Version","author":[{"last_name":"Sun","first_name":"Fei","full_name":"Sun, Fei"},{"last_name":"Mishra","first_name":"Simli","full_name":"Mishra, Simli"},{"last_name":"Stockert","first_name":"Ulrike","full_name":"Stockert, Ulrike"},{"last_name":"Daou","first_name":"Ramzy","full_name":"Daou, Ramzy"},{"first_name":"Naoki","last_name":"Kikugawa","full_name":"Kikugawa, Naoki"},{"last_name":"Perry","first_name":"Robin S.","full_name":"Perry, Robin S."},{"full_name":"Hassinger, Elena","last_name":"Hassinger","first_name":"Elena"},{"full_name":"Hartnoll, Sean A.","last_name":"Hartnoll","first_name":"Sean A."},{"full_name":"Mackenzie, Andrew P.","first_name":"Andrew P.","last_name":"Mackenzie"},{"first_name":"Veronika","last_name":"Sunko","full_name":"Sunko, Veronika","orcid":"0000-0003-2724-3523","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3"}],"external_id":{"pmid":["39172781"]},"extern":"1","abstract":[{"text":"In many physical situations in which many-body assemblies exist at temperature T, a characteristic quantum-mechanical time scale of approximately h/kbT can be identified in both theory and experiment, leading to speculation that it may be the shortest meaningful time in such circumstances. This behavior can be investigated by probing the scattering rate of electrons in a broad class of materials often referred to as “strongly correlated metals”. It is clear that in some cases only electron–electron scattering can be its cause, while in others it arises from high-temperature scattering of electrons from quantized lattice vibrations, i.e., phonons. In metallic oxides, which are among the most studied materials, analysis of electrical transport does not satisfactorily identify the relevant scattering mechanism at “high” temperatures near room temperature. We therefore employ a contactless optical method to measure thermal diffusivity in two Ru-based layered perovskites, Sr3Ru2O7 and Sr2RuO4, and use the measurements to extract the dimensionless Lorenz ratio. By comparing our results to the literature data on both conventional and unconventional metals, we show how the analysis of high-temperature thermal transport can both give important insight into dominant scattering mechanisms and be offered as a stringent test of theories attempting to explain anomalous scattering.","lang":"eng"}],"scopus_import":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"OA_type":"hybrid","issue":"35","title":"The Lorenz ratio as a guide to scattering contributions to transport in strongly correlated metals","day":"27","type":"journal_article","status":"public","has_accepted_license":"1","date_created":"2025-06-10T09:12:41Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.2318159121"}],"doi":"10.1073/pnas.2318159121","date_published":"2024-08-27T00:00:00Z","citation":{"mla":"Sun, Fei, et al. “The Lorenz Ratio as a Guide to Scattering Contributions to Transport in Strongly Correlated Metals.” <i>Proceedings of the National Academy of Sciences</i>, vol. 121, no. 35, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2318159121\">10.1073/pnas.2318159121</a>.","ama":"Sun F, Mishra S, Stockert U, et al. The Lorenz ratio as a guide to scattering contributions to transport in strongly correlated metals. <i>Proceedings of the National Academy of Sciences</i>. 2024;121(35). doi:<a href=\"https://doi.org/10.1073/pnas.2318159121\">10.1073/pnas.2318159121</a>","chicago":"Sun, Fei, Simli Mishra, Ulrike Stockert, Ramzy Daou, Naoki Kikugawa, Robin S. Perry, Elena Hassinger, Sean A. Hartnoll, Andrew P. Mackenzie, and Veronika Sunko. “The Lorenz Ratio as a Guide to Scattering Contributions to Transport in Strongly Correlated Metals.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2318159121\">https://doi.org/10.1073/pnas.2318159121</a>.","ieee":"F. Sun <i>et al.</i>, “The Lorenz ratio as a guide to scattering contributions to transport in strongly correlated metals,” <i>Proceedings of the National Academy of Sciences</i>, vol. 121, no. 35. National Academy of Sciences, 2024.","short":"F. Sun, S. Mishra, U. Stockert, R. Daou, N. Kikugawa, R.S. Perry, E. Hassinger, S.A. Hartnoll, A.P. Mackenzie, V. Sunko, Proceedings of the National Academy of Sciences 121 (2024).","apa":"Sun, F., Mishra, S., Stockert, U., Daou, R., Kikugawa, N., Perry, R. S., … Sunko, V. (2024). The Lorenz ratio as a guide to scattering contributions to transport in strongly correlated metals. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2318159121\">https://doi.org/10.1073/pnas.2318159121</a>","ista":"Sun F, Mishra S, Stockert U, Daou R, Kikugawa N, Perry RS, Hassinger E, Hartnoll SA, Mackenzie AP, Sunko V. 2024. The Lorenz ratio as a guide to scattering contributions to transport in strongly correlated metals. Proceedings of the National Academy of Sciences. 121(35)."},"intvolume":"       121","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"National Academy of Sciences","month":"08","pmid":1,"publication":"Proceedings of the National Academy of Sciences","article_processing_charge":"No","quality_controlled":"1"},{"publication":"Proceedings of the National Academy of Sciences of the United States of America","article_processing_charge":"Yes","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","OA_place":"publisher","pmid":1,"month":"10","intvolume":"       121","article_number":"e2402340121","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"date_published":"2024-10-29T00:00:00Z","citation":{"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>.","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>","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.","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>.","short":"N. Ruzickova, M. Hledik, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","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.","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>"},"has_accepted_license":"1","status":"public","doi":"10.1073/pnas.2402340121","date_created":"2024-11-10T23:01:59Z","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.","type":"journal_article","day":"29","OA_type":"hybrid","issue":"44","title":"Quantitative omnigenic model discovers interpretable genome-wide associations","ddc":["570"],"corr_author":"1","scopus_import":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"author":[{"id":"D2761128-D73D-11E9-A1BF-BA0DE6697425","full_name":"Ruzickova, Natalia","last_name":"Ruzickova","first_name":"Natalia"},{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal","last_name":"Hledik","first_name":"Michal"},{"last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"external_id":{"isi":["001349462600001"],"pmid":["39441639"]},"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"}],"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"_id":"18525","project":[{"name":"Collective behaviour of cells in pancreatic Islets of Langerhans","_id":"7bec9174-9f16-11ee-852c-ded9fe5f810e"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"}],"oa_version":"Published Version","article_type":"original","oa":1,"file":[{"date_created":"2024-11-11T09:31:00Z","checksum":"d930e2ccf9ec900c7d7509a78cfb3564","creator":"dernst","success":1,"access_level":"open_access","content_type":"application/pdf","file_id":"18536","relation":"main_file","file_size":25529709,"date_updated":"2024-11-11T09:31:00Z","file_name":"2024_PNAS_Ruzickova.pdf"}],"related_material":{"record":[{"id":"20357","status":"public","relation":"dissertation_contains"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"APC_amount":"3062,93 EUR","year":"2024","volume":121,"publication_status":"published","date_updated":"2026-04-07T12:02:39Z","file_date_updated":"2024-11-11T09:31:00Z"},{"file_date_updated":"2024-11-11T09:35:15Z","date_updated":"2025-09-08T14:38:35Z","publication_status":"published","year":"2024","volume":121,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"file":[{"checksum":"21c82d2ab58ff99b2bd0489797be42e5","date_created":"2024-11-11T09:35:15Z","success":1,"creator":"dernst","access_level":"open_access","relation":"main_file","file_id":"18538","content_type":"application/pdf","file_size":5268074,"date_updated":"2024-11-11T09:35:15Z","file_name":"2024_PNAS_Weiner.pdf"}],"oa":1,"article_type":"original","oa_version":"Published Version","_id":"18526","ec_funded":1,"project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"department":[{"_id":"AnSa"}],"abstract":[{"lang":"eng","text":"Multivesicular endosomes (MVEs) sequester membrane proteins destined for degradation within intralumenal vesicles (ILVs), a process mediated by the membrane-remodeling action of Endosomal Sorting Complex Required for Transport (ESCRT) proteins. In Arabidopsis, endosomal membrane constriction and scission are uncoupled, resulting in the formation of extensive concatenated ILV networks and enhancing cargo sequestration efficiency. Here, we used a combination of electron tomography, computer simulations, and mathematical modeling to address the questions of when concatenated ILV networks evolved in plants and what drives their formation. Through morphometric analyses of tomographic reconstructions of endosomes across yeast, algae, and various land plants, we have found that ILV concatenation is widespread within plant species, but only prevalent in seed plants, especially in flowering plants. Multiple budding sites that require the formation of pores in the limiting membrane were only identified in hornworts and seed plants, suggesting that this mechanism has evolved independently in both plant lineages. To identify the conditions under which these multiple budding sites can arise, we used particle-based molecular dynamics simulations and found that changes in ESCRT filament properties, such as filament curvature and membrane binding energy, can generate the membrane shapes observed in multiple budding sites. To understand the relationship between membrane budding activity and ILV network topology, we performed computational simulations and identified a set of membrane remodeling parameters that can recapitulate our tomographic datasets."}],"external_id":{"pmid":["39441629"],"isi":["001349500800007"]},"author":[{"last_name":"Weiner","first_name":"Ethan","full_name":"Weiner, Ethan"},{"full_name":"Berryman, Elizabeth","first_name":"Elizabeth","last_name":"Berryman"},{"first_name":"Felix F","last_name":"Frey","orcid":"0000-0001-8501-6017","full_name":"Frey, Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3"},{"first_name":"Ariadna González","last_name":"Solís","full_name":"Solís, Ariadna González"},{"full_name":"Leier, André","first_name":"André","last_name":"Leier"},{"full_name":"Lago, Tatiana Marquez","last_name":"Lago","first_name":"Tatiana Marquez"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela"},{"last_name":"Otegui","first_name":"Marisa S.","full_name":"Otegui, Marisa S."}],"scopus_import":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"ddc":["570"],"title":"Endosomal membrane budding patterns in plants","issue":"44","OA_type":"hybrid","type":"journal_article","day":"29","acknowledgement":"We would like to thank Janice Pennington for her support with electron tomography data collection, Dr. Ingrid Jordon-Thaden, director of the Botany Garden and Greenhouse of University of Wisconsin Madison, for her invaluable assistance collecting plant materials, Dr. Marie Trest for providing Chara specimens, and Dr. Nicholas Keuler for his advice on statistical analyses. We thank Charlie Hamilton for exploring the initial computational model. This work was supported by grant NSF MCB 2114603 and NIH 1S10OD026769-01 to M.S.O. F.F acknowledges support as a NOMIS Fellow from the NOMIS Foundation. A.Š. acknowledges ERC Starting Grant “NEPA” 802960.","date_created":"2024-11-10T23:01:59Z","doi":"10.1073/pnas.2409407121","has_accepted_license":"1","status":"public","citation":{"ista":"Weiner E, Berryman E, Frey FF, Solís AG, Leier A, Lago TM, Šarić A, Otegui MS. 2024. Endosomal membrane budding patterns in plants. Proceedings of the National Academy of Sciences of the United States of America. 121(44), e2409407121.","apa":"Weiner, E., Berryman, E., Frey, F. F., Solís, A. G., Leier, A., Lago, T. M., … Otegui, M. S. (2024). Endosomal membrane budding patterns in plants. <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.2409407121\">https://doi.org/10.1073/pnas.2409407121</a>","short":"E. Weiner, E. Berryman, F.F. Frey, A.G. Solís, A. Leier, T.M. Lago, A. Šarić, M.S. Otegui, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","chicago":"Weiner, Ethan, Elizabeth Berryman, Felix F Frey, Ariadna González Solís, André Leier, Tatiana Marquez Lago, Anđela Šarić, and Marisa S. Otegui. “Endosomal Membrane Budding Patterns in Plants.” <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.2409407121\">https://doi.org/10.1073/pnas.2409407121</a>.","ieee":"E. Weiner <i>et al.</i>, “Endosomal membrane budding patterns in plants,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44. National Academy of Sciences, 2024.","ama":"Weiner E, Berryman E, Frey FF, et al. Endosomal membrane budding patterns in plants. <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.2409407121\">10.1073/pnas.2409407121</a>","mla":"Weiner, Ethan, et al. “Endosomal Membrane Budding Patterns in Plants.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 44, e2409407121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2409407121\">10.1073/pnas.2409407121</a>."},"date_published":"2024-10-29T00:00:00Z","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"intvolume":"       121","article_number":"e2409407121","pmid":1,"month":"10","OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","publication":"Proceedings of the National Academy of Sciences of the United States of America"},{"date_updated":"2026-04-07T11:49:11Z","file_date_updated":"2025-01-02T12:14:15Z","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","related_material":{"record":[{"id":"20138","status":"public","relation":"dissertation_contains"}]},"file":[{"checksum":"0115e9090b478e0644308c6dab58605b","date_created":"2025-01-02T12:14:15Z","success":1,"creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"18721","date_updated":"2025-01-02T12:14:15Z","file_size":2491151,"file_name":"2024_PNAS_Svoboda.pdf"}],"publication_status":"published","year":"2024","volume":121,"APC_amount":"3143,76 EUR","oa_version":"Published Version","_id":"18703","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"ec_funded":1,"oa":1,"article_type":"original","abstract":[{"lang":"eng","text":"Spatial games provide a simple and elegant mathematical model to study the evolution of cooperation in networks. In spatial games, individuals reside in vertices, adopt simple strategies, and interact with neighbors to receive a payoff. Depending on their own and neighbors’ payoffs, individuals can change their strategy. The payoff is determined by the Prisoners’ Dilemma, a classical matrix game, where players cooperate or defect. While cooperation is the desired behavior, defection provides a higher payoff for a selfish individual. There are many theoretical and empirical studies related to the role of the network in the evolution of cooperation. However, the fundamental question of whether there exist networks that for low initial cooperation rate ensure a high chance of fixation, i.e., cooperation spreads across the whole population, has remained elusive for spatial games with strong selection. In this work, we answer this fundamental question in the affirmative by presenting network structures that ensure high fixation probability for cooperators in the strong selection regime. Besides, our structures have many desirable properties: (a) they ensure the spread of cooperation even for a low initial density of cooperation and high temptation of defection, (b) they have constant degrees, and (c) the number of steps, until cooperation spreads, is at most quadratic in the size of the network."}],"external_id":{"pmid":["39642209"],"isi":["001379596100014"]},"author":[{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","last_name":"Svoboda","first_name":"Jakub"},{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"department":[{"_id":"KrCh"}],"issue":"50","title":"Density amplifiers of cooperation for spatial games","OA_type":"hybrid","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"scopus_import":"1","corr_author":"1","ddc":["000"],"doi":"10.1073/pnas.2405605121","date_created":"2024-12-22T23:01:47Z","status":"public","has_accepted_license":"1","type":"journal_article","day":"10","acknowledgement":"J.S. and K.C. were supported by the European Research Council CoG 863818 (ForM-SMArt) and Austrian Science Fund 10.55776/COE12.","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"intvolume":"       121","article_number":"e2405605121","citation":{"ieee":"J. Svoboda and K. Chatterjee, “Density amplifiers of cooperation for spatial games,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 50. National Academy of Sciences, 2024.","chicago":"Svoboda, Jakub, and Krishnendu Chatterjee. “Density Amplifiers of Cooperation for Spatial Games.” <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.2405605121\">https://doi.org/10.1073/pnas.2405605121</a>.","ama":"Svoboda J, Chatterjee K. Density amplifiers of cooperation for spatial games. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(50). doi:<a href=\"https://doi.org/10.1073/pnas.2405605121\">10.1073/pnas.2405605121</a>","mla":"Svoboda, Jakub, and Krishnendu Chatterjee. “Density Amplifiers of Cooperation for Spatial Games.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 50, e2405605121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2405605121\">10.1073/pnas.2405605121</a>.","ista":"Svoboda J, Chatterjee K. 2024. Density amplifiers of cooperation for spatial games. Proceedings of the National Academy of Sciences of the United States of America. 121(50), e2405605121.","apa":"Svoboda, J., &#38; Chatterjee, K. (2024). Density amplifiers of cooperation for spatial games. <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.2405605121\">https://doi.org/10.1073/pnas.2405605121</a>","short":"J. Svoboda, K. Chatterjee, Proceedings of the National Academy of Sciences of the United States of America 121 (2024)."},"date_published":"2024-12-10T00:00:00Z","quality_controlled":"1","article_processing_charge":"Yes","publication":"Proceedings of the National Academy of Sciences of the United States of America","month":"12","pmid":1,"OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}]},{"pmid":1,"month":"02","OA_place":"publisher","publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"ista":"Springstein BL, Paulo JA, Park H, Henry K, Fleming E, Feder Z, Harper JW, Hochschild A. 2024. Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. Proceedings of the National Academy of Sciences of the United States of America. 121(6), e2317453121.","apa":"Springstein, B. L., Paulo, J. A., Park, H., Henry, K., Fleming, E., Feder, Z., … Hochschild, A. (2024). Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. <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.2317453121\">https://doi.org/10.1073/pnas.2317453121</a>","short":"B.L. Springstein, J.A. Paulo, H. Park, K. Henry, E. Fleming, Z. Feder, J.W. Harper, A. Hochschild, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ieee":"B. L. Springstein <i>et al.</i>, “Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 6. National Academy of Sciences, 2024.","chicago":"Springstein, Benjamin L, Joao A. Paulo, Hankum Park, Kemardo Henry, Eleanor Fleming, Zoë Feder, J. Wade Harper, and Ann Hochschild. “Systematic Analysis of Nonprogrammed Frameshift Suppression in E.Coli via Translational Tiling Proteomics.” <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.2317453121\">https://doi.org/10.1073/pnas.2317453121</a>.","ama":"Springstein BL, Paulo JA, Park H, et al. Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(6). doi:<a href=\"https://doi.org/10.1073/pnas.2317453121\">10.1073/pnas.2317453121</a>","mla":"Springstein, Benjamin L., et al. “Systematic Analysis of Nonprogrammed Frameshift Suppression in E.Coli via Translational Tiling Proteomics.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 6, e2317453121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2317453121\">10.1073/pnas.2317453121</a>."},"date_published":"2024-02-06T00:00:00Z","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"article_number":"e2317453121","intvolume":"       121","type":"journal_article","day":"06","acknowledgement":"We thank S. L. Dove for valuable discussion and comments on the manuscript and R. Hellmiss for artwork. This work was supported by NIH grants GM136247 to A.H., AG011085 to J.W.H., and GM132129 to J.A.P.","date_created":"2025-01-29T08:39:27Z","doi":"10.1073/pnas.2317453121","has_accepted_license":"1","status":"public","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"scopus_import":"1","ddc":["570"],"title":"Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics","issue":"6","OA_type":"hybrid","department":[{"_id":"MaLo"}],"abstract":[{"text":"The synthesis of proteins as encoded in the genome depends critically on translational fidelity. Nevertheless, errors inevitably occur, and those that result in reading frame shifts are particularly consequential because the resulting polypeptides are typically nonfunctional. Despite the generally maladaptive impact of such errors, the proper decoding of certain mRNAs, including many viral mRNAs, depends on a process known as programmed ribosomal frameshifting. The fact that these programmed events, commonly involving a shift to the –1 frame, occur at specific evolutionarily optimized “slippery” sites has facilitated mechanistic investigation. By contrast, less is known about the scope and nature of error (i.e., nonprogrammed) frameshifting. Here, we examine error frameshifting by monitoring spontaneous frameshift events that suppress the effects of single base pair deletions affecting two unrelated test proteins. To map the precise sites of frameshifting, we developed a targeted mass spectrometry–based method called “translational tiling proteomics” for interrogating the full set of possible –1 slippage events that could produce the observed frameshift suppression. Surprisingly, such events occur at many sites along the transcripts, involving up to one half of the available codons. Only a subset of these resembled canonical “slippery” sites, implicating alternative mechanisms potentially involving noncognate mispairing events. Additionally, the aggregate frequency of these events (ranging from 1 to 10% in our test cases) was higher than we might have anticipated. Our findings point to an unexpected degree of mechanistic diversity among ribosomal frameshifting events and suggest that frameshifted products may contribute more significantly to the proteome than generally assumed.","lang":"eng"}],"external_id":{"pmid":["38289956"]},"author":[{"full_name":"Springstein, Benjamin L","orcid":"0000-0002-3461-5391","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","first_name":"Benjamin L","last_name":"Springstein"},{"full_name":"Paulo, Joao A.","first_name":"Joao A.","last_name":"Paulo"},{"full_name":"Park, Hankum","first_name":"Hankum","last_name":"Park"},{"first_name":"Kemardo","last_name":"Henry","full_name":"Henry, Kemardo"},{"last_name":"Fleming","first_name":"Eleanor","full_name":"Fleming, Eleanor"},{"full_name":"Feder, Zoë","last_name":"Feder","first_name":"Zoë"},{"full_name":"Harper, J. Wade","last_name":"Harper","first_name":"J. Wade"},{"full_name":"Hochschild, Ann","last_name":"Hochschild","first_name":"Ann"}],"oa":1,"article_type":"original","oa_version":"Published Version","_id":"18938","publication_status":"published","year":"2024","volume":121,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"5bd62c7cb4287e3706a1d45d6ef61fd1","date_created":"2025-01-29T08:43:16Z","success":1,"creator":"dernst","access_level":"open_access","relation":"main_file","file_id":"18939","content_type":"application/pdf","file_size":720902,"date_updated":"2025-01-29T08:43:16Z","file_name":"2024_PNAS_Springstein.pdf"}],"file_date_updated":"2025-01-29T08:43:16Z","date_updated":"2025-05-14T11:02:52Z"},{"_id":"14478","project":[{"name":"Epidemics in ant societies on a chip","call_identifier":"H2020","grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"oa_version":"Published Version","article_type":"original","oa":1,"author":[{"full_name":"Habig, Michael","last_name":"Habig","first_name":"Michael"},{"full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse"},{"last_name":"Müller","first_name":"Judith","full_name":"Müller, Judith"},{"last_name":"Stukenbrock","first_name":"Eva H.","full_name":"Stukenbrock, Eva H."},{"full_name":"Leitner, Hanna","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","first_name":"Hanna","last_name":"Leitner"},{"first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["001207630200005"],"pmid":["38442176"]},"abstract":[{"lang":"eng","text":"Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungus<jats:italic>Metarhizium robertsii</jats:italic>during experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome – but no other – was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment between<jats:italic>M. robertsii</jats:italic>and another congeneric insect pathogen,<jats:italic>M. guizhouense</jats:italic>. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange.</jats:p><jats:sec><jats:title>Significance Statement</jats:title><jats:p>The enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens."}],"department":[{"_id":"SyCr"}],"date_updated":"2025-08-05T13:30:51Z","file_date_updated":"2024-03-19T09:02:57Z","file":[{"file_id":"15124","content_type":"application/pdf","relation":"main_file","file_size":5750361,"date_updated":"2024-03-19T09:02:57Z","file_name":"2024_PNAS_Habig.pdf","date_created":"2024-03-19T09:02:57Z","checksum":"f5e871db617b682edc71fcd08670dc81","creator":"dernst","success":1,"access_level":"open_access"}],"isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","APC_amount":"3040,36 EUR","year":"2024","volume":121,"publication_status":"published","article_number":"e2316284121","intvolume":"       121","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"date_published":"2024-03-12T00:00:00Z","citation":{"short":"M. Habig, A.V. Grasse, J. Müller, E.H. Stukenbrock, H. Leitner, S. Cremer, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. 2024. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2316284121.","apa":"Habig, M., Grasse, A. V., Müller, J., Stukenbrock, E. H., Leitner, H., &#38; Cremer, S. (2024). Frequent horizontal chromosome transfer between asexual fungal insect pathogens. <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.2316284121\">https://doi.org/10.1073/pnas.2316284121</a>","mla":"Habig, Michael, et al. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 11, e2316284121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2316284121\">10.1073/pnas.2316284121</a>.","ieee":"M. Habig, A. V. Grasse, J. Müller, E. H. Stukenbrock, H. Leitner, and S. Cremer, “Frequent horizontal chromosome transfer between asexual fungal insect pathogens,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 11. National Academy of Sciences, 2024.","chicago":"Habig, Michael, Anna V Grasse, Judith Müller, Eva H. Stukenbrock, Hanna Leitner, and Sylvia Cremer. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” <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.2316284121\">https://doi.org/10.1073/pnas.2316284121</a>.","ama":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(11). doi:<a href=\"https://doi.org/10.1073/pnas.2316284121\">10.1073/pnas.2316284121</a>"},"publication":"Proceedings of the National Academy of Sciences of the United States of America","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","OA_place":"publisher","month":"03","pmid":1,"OA_type":"hybrid","issue":"11","title":"Frequent horizontal chromosome transfer between asexual fungal insect pathogens","corr_author":"1","ddc":["570"],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"scopus_import":"1","status":"public","has_accepted_license":"1","doi":"10.1073/pnas.2316284121","date_created":"2023-10-31T13:30:00Z","acknowledgement":"We thank Bernhardt Steinwender, Jorgen Eilenberg, and Nicolai V. Meyling for the fungal strains. We further thank Chengshu Wang for providing the short sequencing reads for M. guizhouense ARESF977 he used for his published genome assembly, and Kristian Ullrich for help in the bioinformatics analysis for methylation pattern in Nanopore reads, and the VBC and the Max Planck Society for the use of their sequencing centers. We thank Barbara Milutinović and Hinrich Schulenburg for discussion, and Tal Dagan and Jens Rolff for comments on a previous version of the manuscript. Fig. 1A was created with BioRender.com. This study received funding by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP) to S.C. and by the German Research Foundation (DFG grant HA9263/1-1) to M.H.","day":"12","type":"journal_article"},{"date_published":"2024-03-05T00:00:00Z","citation":{"ista":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. 2024. Efficiency and resilience of cooperation in asymmetric social dilemmas. Proceedings of the National Academy of Sciences of the United States of America. 121(10), e2315558121.","apa":"Hübner, V., Staab, M., Hilbe, C., Chatterjee, K., &#38; Kleshnina, M. (2024). Efficiency and resilience of cooperation in asymmetric social dilemmas. <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.2315558121\">https://doi.org/10.1073/pnas.2315558121</a>","short":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, M. Kleshnina, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ama":"Hübner V, Staab M, Hilbe C, Chatterjee K, Kleshnina M. Efficiency and resilience of cooperation in asymmetric social dilemmas. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(10). doi:<a href=\"https://doi.org/10.1073/pnas.2315558121\">10.1073/pnas.2315558121</a>","chicago":"Hübner, Valentin, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” <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.2315558121\">https://doi.org/10.1073/pnas.2315558121</a>.","ieee":"V. Hübner, M. Staab, C. Hilbe, K. Chatterjee, and M. Kleshnina, “Efficiency and resilience of cooperation in asymmetric social dilemmas,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 10. National Academy of Sciences, 2024.","mla":"Hübner, Valentin, et al. “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 10, e2315558121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2315558121\">10.1073/pnas.2315558121</a>."},"article_number":"e2315558121","intvolume":"       121","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"language":[{"iso":"eng"}],"OA_place":"publisher","publisher":"National Academy of Sciences","pmid":1,"month":"03","publication":"Proceedings of the National Academy of Sciences of the United States of America","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","corr_author":"1","ddc":["000"],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"scopus_import":"1","OA_type":"hybrid","title":"Efficiency and resilience of cooperation in asymmetric social dilemmas","issue":"10","acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.) and the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir Programme, ANR-17-EURE-0010) (to M.K.).","type":"journal_article","day":"05","has_accepted_license":"1","status":"public","date_created":"2024-03-05T09:18:49Z","doi":"10.1073/pnas.2315558121","article_type":"original","oa":1,"_id":"15083","ec_funded":1,"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"oa_version":"Published Version","department":[{"_id":"KrCh"}],"author":[{"last_name":"Hübner","first_name":"Valentin","id":"2c8aa207-dc7d-11ea-9b2f-f22972ecd910","full_name":"Hübner, Valentin","orcid":"0009-0001-5009-4987"},{"full_name":"Staab, Manuel","first_name":"Manuel","last_name":"Staab"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe","first_name":"Christian"},{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria","last_name":"Kleshnina","full_name":"Kleshnina, Maria"}],"external_id":{"pmid":["38408249"],"isi":["001207786500004"]},"abstract":[{"text":"Direct reciprocity is a powerful mechanism for cooperation in social dilemmas. The very logic of reciprocity, however, seems to require that individuals are symmetric, and that everyone has the same means to influence each others’ payoffs. Yet in many applications, individuals are asymmetric. Herein, we study the effect of asymmetry in linear public good games. Individuals may differ in their endowments (their ability to contribute to a public good) and in their productivities (how effective their contributions are). Given the individuals’ productivities, we ask which allocation of endowments is optimal for cooperation. To this end, we consider two notions of optimality. The first notion focuses on the resilience of cooperation. The respective endowment distribution ensures that full cooperation is feasible even under the most adverse conditions. The second notion focuses on efficiency. The corresponding endowment distribution maximizes group welfare. Using analytical methods, we fully characterize these two endowment distributions. This analysis reveals that both optimality notions favor some endowment inequality: More productive players ought to get higher endowments. Yet the two notions disagree on how unequal endowments are supposed to be. A focus on resilience results in less inequality. With additional simulations, we show that the optimal endowment allocation needs to account for both the resilience and the efficiency of cooperation.","lang":"eng"}],"file_date_updated":"2024-03-12T13:12:22Z","date_updated":"2026-04-07T12:30:56Z","APC_amount":"3041,76 EUR","year":"2024","volume":121,"publication_status":"published","file":[{"file_name":"2024_PNAS_Huebner.pdf","date_updated":"2024-03-12T13:12:22Z","file_size":2203220,"relation":"main_file","content_type":"application/pdf","file_id":"15109","access_level":"open_access","success":1,"creator":"dernst","checksum":"068520e3efd4d008bb9177e8aedb7d22","date_created":"2024-03-12T13:12:22Z"}],"related_material":{"link":[{"url":"https://ista.ac.at/en/news/what-math-tells-us-about-social-dilemmas/","description":"News on ISTA Website","relation":"press_release"}],"record":[{"id":"15108","status":"public","relation":"research_data"},{"status":"public","relation":"dissertation_contains","id":"19903"}]},"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"article_type":"original","oa":1,"_id":"15116","oa_version":"Published Version","department":[{"_id":"AnSa"}],"external_id":{"pmid":["38451946"],"isi":["001206387400001"]},"author":[{"full_name":"Giubertoni, Giulia","first_name":"Giulia","last_name":"Giubertoni"},{"full_name":"Feng, Liru","last_name":"Feng","first_name":"Liru"},{"full_name":"Klein, Kevin","last_name":"Klein","first_name":"Kevin"},{"full_name":"Giannetti, Guido","first_name":"Guido","last_name":"Giannetti"},{"full_name":"Rutten, Luco","first_name":"Luco","last_name":"Rutten"},{"first_name":"Yeji","last_name":"Choi","full_name":"Choi, Yeji"},{"full_name":"Van Der Net, Anouk","first_name":"Anouk","last_name":"Van Der Net"},{"full_name":"Castro-Linares, Gerard","first_name":"Gerard","last_name":"Castro-Linares"},{"first_name":"Federico","last_name":"Caporaletti","full_name":"Caporaletti, Federico"},{"last_name":"Micha","first_name":"Dimitra","full_name":"Micha, Dimitra"},{"last_name":"Hunger","first_name":"Johannes","full_name":"Hunger, Johannes"},{"last_name":"Deblais","first_name":"Antoine","full_name":"Deblais, Antoine"},{"full_name":"Bonn, Daniel","first_name":"Daniel","last_name":"Bonn"},{"first_name":"Nico","last_name":"Sommerdijk","full_name":"Sommerdijk, Nico"},{"last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Ilie, Ioana M.","first_name":"Ioana M.","last_name":"Ilie"},{"last_name":"Koenderink","first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H."},{"full_name":"Woutersen, Sander","last_name":"Woutersen","first_name":"Sander"}],"abstract":[{"text":"Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water–collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H2O/D2O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H2O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D2O is less hydrated than in H2O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen–water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.","lang":"eng"}],"file_date_updated":"2024-03-19T10:22:42Z","date_updated":"2025-09-04T13:03:56Z","year":"2024","volume":121,"publication_status":"published","related_material":{"record":[{"id":"15126","relation":"research_data","status":"public"}]},"file":[{"access_level":"open_access","creator":"dernst","success":1,"date_created":"2024-03-19T10:22:42Z","checksum":"a3f7fdc29dd9f0a38952ab4e322b3a05","file_name":"2024_PNAS_Giubertoni.pdf","file_size":12952586,"date_updated":"2024-03-19T10:22:42Z","file_id":"15125","content_type":"application/pdf","relation":"main_file"}],"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ieee":"G. Giubertoni <i>et al.</i>, “Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 11. National Academy of Sciences, 2024.","chicago":"Giubertoni, Giulia, Liru Feng, Kevin Klein, Guido Giannetti, Luco Rutten, Yeji Choi, Anouk Van Der Net, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” <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.2313162121\">https://doi.org/10.1073/pnas.2313162121</a>.","ama":"Giubertoni G, Feng L, Klein K, et al. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(11). doi:<a href=\"https://doi.org/10.1073/pnas.2313162121\">10.1073/pnas.2313162121</a>","mla":"Giubertoni, Giulia, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 11, e2313162121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2313162121\">10.1073/pnas.2313162121</a>.","apa":"Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., … Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. <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.2313162121\">https://doi.org/10.1073/pnas.2313162121</a>","ista":"Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, Van Der Net A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. 2024. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2313162121.","short":"G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van Der Net, G. Castro-Linares, F. Caporaletti, D. Micha, J. Hunger, A. Deblais, D. Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S. Woutersen, Proceedings of the National Academy of Sciences of the United States of America 121 (2024)."},"date_published":"2024-03-12T00:00:00Z","intvolume":"       121","article_number":"e2313162121","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"National Academy of Sciences","language":[{"iso":"eng"}],"pmid":1,"month":"03","publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"ddc":["550"],"issue":"11","title":"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration","acknowledgement":"We thank Dr. Steven Roeters (Aarhus University), Dr. Federica Burla, and Prof. Dr. Mischa Bonn (Institute for Polymer Research, Mainz, Germany) for the useful discussions. We thank Dr. Wim Roeterdink and Michiel Hilberts for technical support. G.H.K. acknowledges financial support by the “BaSyC Building a Synthetic Cell” Gravitation grant (024.003.019) of The Netherlands Ministry of Education, Culture and Science (OCW) and The Netherlands Organization for Scientific Research and from NWO grant OCENW.GROOT.2019.022. This work has received support from the National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT, under Grant No. 2022K1A3A1A04062969. This publication is part of the project (with Project Number VI.Veni.212.240) of the research programme NWO Talent Programme Veni 2021, which is financed by the Dutch Research Council (NWO). I.M.I. acknowledges support from the Sectorplan Bèta & Techniek of the Dutch Government and the Dementia Research - Synapsis Foundation Switzerland. A.Š. and K.K. acknowledge support from Royal Society and European Research Council Starting Grant. G. Giubertoni kindly thanks to the Care4Bones community and the Collagen Café community for reminding that we do not own the knowledge we create, but it is, rather, a collective resource intended for the advancement of human progress.","day":"12","type":"journal_article","status":"public","has_accepted_license":"1","doi":"10.1073/pnas.2313162121","date_created":"2024-03-17T23:00:57Z"},{"publisher":"National Academy of Sciences","OA_place":"publisher","language":[{"iso":"eng"}],"pmid":1,"month":"06","publication":"Proceedings of the National Academy of Sciences of the United States of America","quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","citation":{"short":"D. Brückner, G. Tkačik, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Brückner D, Tkačik G. 2024. Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences of the United States of America. 121(23), e2322326121.","apa":"Brückner, D., &#38; Tkačik, G. (2024). Information content and optimization of self-organized developmental systems. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2322326121\">https://doi.org/10.1073/pnas.2322326121</a>","mla":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 23, e2322326121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2322326121\">10.1073/pnas.2322326121</a>.","ama":"Brückner D, Tkačik G. Information content and optimization of self-organized developmental systems. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(23). doi:<a href=\"https://doi.org/10.1073/pnas.2322326121\">10.1073/pnas.2322326121</a>","chicago":"Brückner, David, and Gašper Tkačik. “Information Content and Optimization of Self-Organized Developmental Systems.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2322326121\">https://doi.org/10.1073/pnas.2322326121</a>.","ieee":"D. Brückner and G. Tkačik, “Information content and optimization of self-organized developmental systems,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 23. National Academy of Sciences, 2024."},"date_published":"2024-06-04T00:00:00Z","article_number":"e2322326121","intvolume":"       121","tmp":{"short":"CC BY-NC-ND (4.0)","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)","image":"/images/cc_by_nc_nd.png"},"acknowledgement":"We thank Wiktor Młynarski, Juraj Majek, Michal Hledík, Fridtjof Brauns, Nikolas Claussen, Benjamin Zoller, Erwin Frey, Thomas Gregor, and Edouard Hannezo for inspiring discussions. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 343-2022). This research was performed in part at the Aspen Center for Physics, which is supported by NSF Grant No. PHY-1607611, and Kavli Institute for Theoretical Physics (KITP) Santa Barbara, supported by NSF Grant No. PHY-1748958 and the Gordon and Betty Moore Foundation Grant No. 2919.02.","day":"04","type":"journal_article","has_accepted_license":"1","status":"public","date_created":"2024-06-09T22:01:02Z","doi":"10.1073/pnas.2322326121","scopus_import":"1","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"ddc":["570"],"corr_author":"1","issue":"23","title":"Information content and optimization of self-organized developmental systems","OA_type":"hybrid","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"external_id":{"isi":["001244835000006"],"pmid":["38819997"]},"author":[{"full_name":"Brückner, David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David","last_name":"Brückner"},{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and even harnessing intrinsic and extrinsic fluctuations. While the relevant molecular processes are increasingly well understood, we lack a principled framework to quantify the performance of such stochastic self-organizing systems. To that end, we introduce an information-theoretic measure for self-organized fate specification during embryonic development. We show that the proposed measure assesses the total information content of fate patterns and decomposes it into interpretable contributions corresponding to the positional and correlational information. By optimizing the proposed measure, our framework provides a normative theory for developmental circuits, which we demonstrate on lateral inhibition, cell type proportioning, and reaction–diffusion models of self-organization. This paves a way toward a classification of developmental systems based on a common information-theoretic language, thereby organizing the zoo of implicated chemical and mechanical signaling processes.","lang":"eng"}],"article_type":"original","oa":1,"project":[{"name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b"}],"_id":"17123","oa_version":"Published Version","volume":121,"year":"2024","APC_amount":"2570,79 EUR","publication_status":"published","related_material":{"link":[{"url":"https://github.com/dbrueckner/SelforgInformation","relation":"software"},{"description":"News on the ISTA website","relation":"press_release","url":"https://ista.ac.at/en/news/the-embryo-assembles-itself/"}]},"file":[{"access_level":"open_access","date_created":"2024-06-10T10:27:37Z","checksum":"59797a75db7beb3721ed7a4d14c241f9","creator":"dernst","success":1,"file_name":"2024_PNAS_Brueckner.pdf","file_id":"17130","content_type":"application/pdf","relation":"main_file","file_size":12329234,"date_updated":"2024-06-10T10:27:37Z"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"file_date_updated":"2024-06-10T10:27:37Z","date_updated":"2025-09-08T07:51:01Z"}]