[{"file":[{"relation":"main_file","embargo":"2024-06-01","file_id":"14674","checksum":"e2503c8f84be1050e28f64320f1d5bd2","date_created":"2023-12-11T11:30:37Z","date_updated":"2023-12-11T11:30:37Z","access_level":"closed","embargo_to":"open_access","file_name":"2023_JourNeuroscience_Nardin.pdf","file_size":2280632,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","ddc":["570"],"status":"public","intvolume":" 43","_id":"14656","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain."}],"issue":"48","type":"journal_article","date_published":"2023-11-29T00:00:00Z","article_type":"original","page":"8140-8156","publication":"The Journal of Neuroscience","citation":{"ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 2023;43(48):8140-8156. doi:10.1523/JNEUROSCI.0194-23.2023","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156.","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” The Journal of Neuroscience, vol. 43, no. 48. Society of Neuroscience, pp. 8140–8156, 2023.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. Society of Neuroscience. https://doi.org/10.1523/JNEUROSCI.0194-23.2023","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience, vol. 43, no. 48, Society of Neuroscience, 2023, pp. 8140–56, doi:10.1523/JNEUROSCI.0194-23.2023.","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” The Journal of Neuroscience. Society of Neuroscience, 2023. https://doi.org/10.1523/JNEUROSCI.0194-23.2023."},"day":"29","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","scopus_import":"1","date_updated":"2023-12-11T11:37:20Z","date_created":"2023-12-10T23:00:58Z","volume":43,"author":[{"first_name":"Michele","last_name":"Nardin","id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele"},{"full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","last_name":"Savin","full_name":"Savin, Cristina"}],"publication_status":"published","department":[{"_id":"JoCs"},{"_id":"GaTk"}],"publisher":"Society of Neuroscience","year":"2023","acknowledgement":"M.N. was supported by the European Union Horizon 2020 Grant 665385. J.C. was supported by the European Research Council Consolidator Grant 281511. G.T. was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported by an Institute of Science and Technology fellow award and by the National Science Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella, Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi, Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.","pmid":1,"file_date_updated":"2023-12-11T11:30:37Z","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1523/JNEUROSCI.0194-23.2023","quality_controlled":"1","project":[{"name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7","_id":"257A4776-B435-11E9-9278-68D0E5697425","grant_number":"281511"},{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1523/JNEUROSCI.0194-23.2023"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["37758476"]},"oa":1,"month":"11","publication_identifier":{"eissn":["1529-2401"]}},{"article_processing_charge":"Yes","has_accepted_license":"1","day":"20","scopus_import":"1","date_published":"2023-10-20T00:00:00Z","page":"107840","article_type":"original","citation":{"chicago":"Scarpetta, Silvia, Niccolò Morrisi, Carlotta Mutti, Nicoletta Azzi, Irene Trippi, Rosario Ciliento, Ilenia Apicella, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” IScience. Elsevier, 2023. https://doi.org/10.1016/j.isci.2023.107840.","short":"S. Scarpetta, N. Morrisi, C. Mutti, N. Azzi, I. Trippi, R. Ciliento, I. Apicella, G. Messuti, M. Angiolelli, F. Lombardi, L. Parrino, A.E. Vaudano, IScience 26 (2023) 107840.","mla":"Scarpetta, Silvia, et al. “Criticality of Neuronal Avalanches in Human Sleep and Their Relationship with Sleep Macro- and Micro-Architecture.” IScience, vol. 26, no. 10, Elsevier, 2023, p. 107840, doi:10.1016/j.isci.2023.107840.","apa":"Scarpetta, S., Morrisi, N., Mutti, C., Azzi, N., Trippi, I., Ciliento, R., … Vaudano, A. E. (2023). Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. IScience. Elsevier. https://doi.org/10.1016/j.isci.2023.107840","ieee":"S. Scarpetta et al., “Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture,” iScience, vol. 26, no. 10. Elsevier, p. 107840, 2023.","ista":"Scarpetta S, Morrisi N, Mutti C, Azzi N, Trippi I, Ciliento R, Apicella I, Messuti G, Angiolelli M, Lombardi F, Parrino L, Vaudano AE. 2023. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. iScience. 26(10), 107840.","ama":"Scarpetta S, Morrisi N, Mutti C, et al. Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture. iScience. 2023;26(10):107840. doi:10.1016/j.isci.2023.107840"},"publication":"iScience","issue":"10","abstract":[{"lang":"eng","text":"Sleep plays a key role in preserving brain function, keeping the brain network in a state that ensures optimal computational capabilities. Empirical evidence indicates that such a state is consistent with criticality, where scale-free neuronal avalanches emerge. However, the relationship between sleep, emergent avalanches, and criticality remains poorly understood. Here we fully characterize the critical behavior of avalanches during sleep, and study their relationship with the sleep macro- and micro-architecture, in particular the cyclic alternating pattern (CAP). We show that avalanche size and duration distributions exhibit robust power laws with exponents approximately equal to −3/2 e −2, respectively. Importantly, we find that sizes scale as a power law of the durations, and that all critical exponents for neuronal avalanches obey robust scaling relations, which are consistent with the mean-field directed percolation universality class. Our analysis demonstrates that avalanche dynamics depends on the position within the NREM-REM cycles, with the avalanche density increasing in the descending phases and decreasing in the ascending phases of sleep cycles. Moreover, we show that, within NREM sleep, avalanche occurrence correlates with CAP activation phases, particularly A1, which are the expression of slow wave sleep propensity and have been proposed to be beneficial for cognitive processes. The results suggest that neuronal avalanches, and thus tuning to criticality, actively contribute to sleep development and play a role in preserving network function. Such findings, alongside characterization of the universality class for avalanches, open new avenues to the investigation of functional role of criticality during sleep with potential clinical application.Significance statementWe fully characterize the critical behavior of neuronal avalanches during sleep, and show that avalanches follow precise scaling laws that are consistent with the mean-field directed percolation universality class. The analysis provides first evidence of a functional relationship between avalanche occurrence, slow-wave sleep dynamics, sleep stage transitions and occurrence of CAP phase A during NREM sleep. Because CAP is considered one of the major guardians of NREM sleep that allows the brain to dynamically react to external perturbation and contributes to the cognitive consolidation processes occurring in sleep, our observations suggest that neuronal avalanches at criticality are associated with flexible response to external inputs and to cognitive processes, a key assumption of the critical brain hypothesis."}],"type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"f499836af172ecc9865de4bb41fa99d1","date_created":"2023-10-09T07:23:46Z","date_updated":"2023-10-09T07:23:46Z","file_id":"14412","relation":"main_file","creator":"dernst","file_size":4872708,"content_type":"application/pdf","access_level":"open_access","file_name":"2023_iScience_Scarpetta.pdf"}],"intvolume":" 26","status":"public","title":"Criticality of neuronal avalanches in human sleep and their relationship with sleep macro- and micro-architecture","ddc":["570"],"_id":"12487","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["2589-0042"]},"month":"10","language":[{"iso":"eng"}],"doi":"10.1016/j.isci.2023.107840","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics"}],"quality_controlled":"1","isi":1,"external_id":{"pmid":["37766992"],"isi":["001082331200001"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"ec_funded":1,"file_date_updated":"2023-10-09T07:23:46Z","volume":26,"date_updated":"2023-12-13T11:11:24Z","date_created":"2023-02-02T10:50:17Z","author":[{"last_name":"Scarpetta","first_name":"Silvia","full_name":"Scarpetta, Silvia"},{"last_name":"Morrisi","first_name":"Niccolò","full_name":"Morrisi, Niccolò"},{"first_name":"Carlotta","last_name":"Mutti","full_name":"Mutti, Carlotta"},{"full_name":"Azzi, Nicoletta","last_name":"Azzi","first_name":"Nicoletta"},{"first_name":"Irene","last_name":"Trippi","full_name":"Trippi, Irene"},{"full_name":"Ciliento, Rosario","last_name":"Ciliento","first_name":"Rosario"},{"last_name":"Apicella","first_name":"Ilenia","full_name":"Apicella, Ilenia"},{"full_name":"Messuti, Giovanni","first_name":"Giovanni","last_name":"Messuti"},{"full_name":"Angiolelli, Marianna","first_name":"Marianna","last_name":"Angiolelli"},{"full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","first_name":"Fabrizio"},{"last_name":"Parrino","first_name":"Liborio","full_name":"Parrino, Liborio"},{"first_name":"Anna Elisabetta","last_name":"Vaudano","full_name":"Vaudano, Anna Elisabetta"}],"publisher":"Elsevier","department":[{"_id":"GaTk"}],"publication_status":"published","pmid":1,"year":"2023","acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411, and from the Austrian Science Fund (FWF) under the Lise Meitner fellowship No. PT1013M03318. IA acknowledges financial support from the MIUR PRIN 2017WZFTZP."},{"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"oa":1,"quality_controlled":"1","doi":"10.1093/eurpub/ckad160.597","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1464-360X"],"issn":["1101-1262"]},"month":"10","year":"2023","publisher":"Oxford University Press","department":[{"_id":"GaTk"}],"publication_status":"published","author":[{"first_name":"Simon","last_name":"Rella","id":"B4765ACA-AA38-11E9-AC9A-0930E6697425","full_name":"Rella, Simon"},{"last_name":"Kulikova","first_name":"Y","full_name":"Kulikova, Y"},{"full_name":"Minnegalieva, Aygul","id":"87DF77F0-1D9A-11EA-B6AE-CE443DDC885E","first_name":"Aygul","last_name":"Minnegalieva"},{"first_name":"Fyodor","last_name":"Kondrashov","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"}],"volume":33,"date_created":"2024-01-22T12:02:28Z","date_updated":"2024-01-24T11:16:09Z","article_number":"ckad160.597","file_date_updated":"2024-01-24T11:12:33Z","citation":{"mla":"Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” European Journal of Public Health, vol. 33, no. Supplement_2, ckad160.597, Oxford University Press, 2023, doi:10.1093/eurpub/ckad160.597.","short":"S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal of Public Health, Oxford University Press, 2023.","chicago":"Rella, Simon, Y Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” In European Journal of Public Health, Vol. 33. Oxford University Press, 2023. https://doi.org/10.1093/eurpub/ckad160.597.","ama":"Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. Complex vaccination strategies prevent the emergence of vaccine resistance. In: European Journal of Public Health. Vol 33. Oxford University Press; 2023. doi:10.1093/eurpub/ckad160.597","ista":"Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. 2023. Complex vaccination strategies prevent the emergence of vaccine resistance. European Journal of Public Health. vol. 33, ckad160.597.","ieee":"S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination strategies prevent the emergence of vaccine resistance,” in European Journal of Public Health, 2023, vol. 33, no. Supplement_2.","apa":"Rella, S., Kulikova, Y., Minnegalieva, A., & Kondrashov, F. (2023). Complex vaccination strategies prevent the emergence of vaccine resistance. In European Journal of Public Health (Vol. 33). Oxford University Press. https://doi.org/10.1093/eurpub/ckad160.597"},"publication":"European Journal of Public Health","date_published":"2023-10-01T00:00:00Z","keyword":["Public Health","Environmental and Occupational Health"],"article_processing_charge":"No","has_accepted_license":"1","day":"01","_id":"14862","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 33","title":"Complex vaccination strategies prevent the emergence of vaccine resistance","status":"public","ddc":["570"],"file":[{"file_name":"2023_EurJourPublicHealth_Rella.pdf","access_level":"open_access","creator":"dernst","file_size":71057,"content_type":"application/pdf","file_id":"14882","relation":"main_file","date_created":"2024-01-24T11:12:33Z","date_updated":"2024-01-24T11:12:33Z","success":1,"checksum":"98706755bb4cc5d553818ade7660a7d2"}],"oa_version":"Published Version","type":"conference_abstract","issue":"Supplement_2"},{"abstract":[{"text":"Alpha oscillations are a distinctive feature of the awake resting state of the human brain. However, their functional role in resting-state neuronal dynamics remains poorly understood. Here we show that, during resting wakefulness, alpha oscillations drive an alternation of attenuation and amplification bouts in neural activity. Our analysis indicates that inhibition is activated in pulses that last for a single alpha cycle and gradually suppress neural activity, while excitation is successively enhanced over a few alpha cycles to amplify neural activity. Furthermore, we show that long-term alpha amplitude fluctuations—the “waxing and waning” phenomenon—are an attenuation-amplification mechanism described by a power-law decay of the activity rate in the “waning” phase. Importantly, we do not observe such dynamics during non-rapid eye movement (NREM) sleep with marginal alpha oscillations. The results suggest that alpha oscillations modulate neural activity not only through pulses of inhibition (pulsed inhibition hypothesis) but also by timely enhancement of excitation (or disinhibition).","lang":"eng"}],"issue":"10","type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2023_CellReports_Lombardi.pdf","access_level":"open_access","content_type":"application/pdf","file_size":5599007,"creator":"dernst","relation":"main_file","file_id":"14914","date_updated":"2024-01-30T14:07:08Z","date_created":"2024-01-30T14:07:08Z","checksum":"9c71eb2a03aa160415f01ad95f49ceb5","success":1}],"_id":"14402","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["570"],"title":"Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state","intvolume":" 42","day":"31","article_processing_charge":"Yes","has_accepted_license":"1","scopus_import":"1","date_published":"2023-10-31T00:00:00Z","publication":"Cell Reports","citation":{"short":"F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. De Arcangelis, O. Shriki, Cell Reports 42 (2023).","mla":"Lombardi, Fabrizio, et al. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification of Neural Activity in the Awake Resting State.” Cell Reports, vol. 42, no. 10, 113162, Elsevier, 2023, doi:10.1016/j.celrep.2023.113162.","chicago":"Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla De Arcangelis, and Oren Shriki. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification of Neural Activity in the Awake Resting State.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.113162.","ama":"Lombardi F, Herrmann HJ, Parrino L, et al. Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. Cell Reports. 2023;42(10). doi:10.1016/j.celrep.2023.113162","ieee":"F. Lombardi et al., “Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state,” Cell Reports, vol. 42, no. 10. Elsevier, 2023.","apa":"Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano, A. E., … Shriki, O. (2023). Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.113162","ista":"Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, De Arcangelis L, Shriki O. 2023. Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. Cell Reports. 42(10), 113162."},"article_type":"original","file_date_updated":"2024-01-30T14:07:08Z","ec_funded":1,"article_number":"113162","author":[{"full_name":"Lombardi, Fabrizio","first_name":"Fabrizio","last_name":"Lombardi","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249"},{"first_name":"Hans J.","last_name":"Herrmann","full_name":"Herrmann, Hans J."},{"first_name":"Liborio","last_name":"Parrino","full_name":"Parrino, Liborio"},{"full_name":"Plenz, Dietmar","first_name":"Dietmar","last_name":"Plenz"},{"full_name":"Scarpetta, Silvia","last_name":"Scarpetta","first_name":"Silvia"},{"full_name":"Vaudano, Anna Elisabetta","first_name":"Anna Elisabetta","last_name":"Vaudano"},{"first_name":"Lucilla","last_name":"De Arcangelis","full_name":"De Arcangelis, Lucilla"},{"full_name":"Shriki, Oren","last_name":"Shriki","first_name":"Oren"}],"date_created":"2023-10-08T22:01:15Z","date_updated":"2024-01-30T14:07:40Z","volume":42,"year":"2023","acknowledgement":"This research was funded in whole or in part by the Austrian Science Fund (FWF) (grant PT1013M03318 to F.L.). For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 Research and Innovation Program under the Marie Sklodowska-Curie action (grant agreement 754411 to F.L.) and in part by the NextGenerationEU through the grant TAlent in ReSearch@University of Padua – STARS@UNIPD (to F.L.) (project BRAINCIP [brain criticality and information processing]). L.d.A. acknowledges support from the Italian MIUR project PRIN2017WZFTZP and partial support from NEXTGENERATIONEU (NGEU) funded by the Ministry of University and Research (MUR), National Recovery and Resilience Plan (NRRP), and project MNESYS (PE0000006)—a multiscale integrated approach to the study of the nervous system in health and disease (DN. 1553 11.10.2022). O.S. acknowledges support from the Israel Science Foundation, grant 504/17. The work was supported in part by DIRP ZIAMH02797 (to D.P.).","pmid":1,"publication_status":"published","publisher":"Elsevier","department":[{"_id":"GaTk"}],"month":"10","publication_identifier":{"eissn":["2211-1247"]},"doi":"10.1016/j.celrep.2023.113162","language":[{"iso":"eng"}],"external_id":{"isi":["001086695500001"],"pmid":["37777965"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67","grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}]},{"date_published":"2022-03-04T00:00:00Z","doi":"10.1101/2022.03.03.482657","language":[{"iso":"eng"}],"publication":"bioRxiv","main_file_link":[{"url":"https://doi.org/10.1101/2022.03.03.482657","open_access":"1"}],"citation":{"ama":"Lombardi F, Herrmann HJ, Parrino L, et al. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. bioRxiv. 2022. doi:10.1101/2022.03.03.482657","apa":"Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano, A. E., … Shriki, O. (2022). Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2022.03.03.482657","ieee":"F. Lombardi et al., “Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades,” bioRxiv. Cold Spring Harbor Laboratory, 2022.","ista":"Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, de Arcangelis L, Shriki O. 2022. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. bioRxiv, 10.1101/2022.03.03.482657.","short":"F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. de Arcangelis, O. Shriki, BioRxiv (2022).","mla":"Lombardi, Fabrizio, et al. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” BioRxiv, Cold Spring Harbor Laboratory, 2022, doi:10.1101/2022.03.03.482657.","chicago":"Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla de Arcangelis, and Oren Shriki. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” BioRxiv. Cold Spring Harbor Laboratory, 2022. https://doi.org/10.1101/2022.03.03.482657."},"oa":1,"page":"25","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"day":"04","month":"03","article_processing_charge":"No","author":[{"full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","first_name":"Fabrizio"},{"last_name":"Herrmann","first_name":"Hans J.","full_name":"Herrmann, Hans J."},{"full_name":"Parrino, Liborio","first_name":"Liborio","last_name":"Parrino"},{"full_name":"Plenz, Dietmar","first_name":"Dietmar","last_name":"Plenz"},{"first_name":"Silvia","last_name":"Scarpetta","full_name":"Scarpetta, Silvia"},{"last_name":"Vaudano","first_name":"Anna Elisabetta","full_name":"Vaudano, Anna Elisabetta"},{"last_name":"de Arcangelis","first_name":"Lucilla","full_name":"de Arcangelis, Lucilla"},{"full_name":"Shriki, Oren","first_name":"Oren","last_name":"Shriki"}],"date_created":"2022-03-04T22:20:59Z","date_updated":"2022-03-07T07:28:34Z","oa_version":"Preprint","year":"2022","_id":"10821","acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. LdA acknowledges the Italian MIUR project PRIN2017WZFTZP for financial support and the project E-PASSION of the program VALERE 2019 funded by the University of Campania, Italy “L. Vanvitelli”. OS acknowledges support from the Israel Science Foundation, Grant No. 504/17. Supported in part by DIRP ZIAMH02797 to DP.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades","status":"public","department":[{"_id":"GaTk"}],"publisher":"Cold Spring Harbor Laboratory","abstract":[{"text":"Rhythmical cortical activity has long been recognized as a pillar in the architecture of brain functions. Yet, the dynamic organization of its underlying neuronal population activity remains elusive. Here we uncover a unique organizational principle regulating collective neural dynamics associated with the alpha rhythm in the awake resting-state. We demonstrate that cascades of neural activity obey attenuation-amplification dynamics (AAD), with a transition from the attenuation regime—within alpha cycles—to the amplification regime—across a few alpha cycles—that correlates with the characteristic frequency of the alpha rhythm. We find that this short-term AAD is part of a large-scale, size-dependent temporal structure of neural cascades that obeys the Omori law: Following large cascades, smaller cascades occur at a rate that decays as a power-law of the time elapsed from such events—a long-term AAD regulating brain activity over the timescale of seconds. We show that such an organization corresponds to the \"waxing and waning\" of the alpha rhythm. Importantly, we observe that short- and long-term AAD are unique to the awake resting-state, being absent during NREM sleep. These results provide a quantitative, dynamical description of the so-far-qualitative notion of the \"waxing and waning\" phenomenon, and suggest the AAD as a key principle governing resting-state dynamics across timescales.","lang":"eng"}],"ec_funded":1,"type":"preprint"},{"type":"journal_article","abstract":[{"text":"Statistical inference is central to many scientific endeavors, yet how it works remains unresolved. Answering this requires a quantitative understanding of the intrinsic interplay between statistical models, inference methods, and the structure in the data. To this end, we characterize the efficacy of direct coupling analysis (DCA)—a highly successful method for analyzing amino acid sequence data—in inferring pairwise interactions from samples of ferromagnetic Ising models on random graphs. Our approach allows for physically motivated exploration of qualitatively distinct data regimes separated by phase transitions. We show that inference quality depends strongly on the nature of data-generating distributions: optimal accuracy occurs at an intermediate temperature where the detrimental effects from macroscopic order and thermal noise are minimal. Importantly our results indicate that DCA does not always outperform its local-statistics-based predecessors; while DCA excels at low temperatures, it becomes inferior to simple correlation thresholding at virtually all temperatures when data are limited. Our findings offer insights into the regime in which DCA operates so successfully, and more broadly, how inference interacts with the structure in the data.","lang":"eng"}],"issue":"2","ddc":["530"],"status":"public","title":"Inferring couplings in networks across order-disorder phase transitions","intvolume":" 4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11638","file":[{"success":1,"checksum":"ed6fdc2a3a096df785fa5f7b17b716c6","date_created":"2022-07-25T07:47:23Z","date_updated":"2022-07-25T07:47:23Z","file_id":"11644","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":1379683,"access_level":"open_access","file_name":"2022_PhysicalReviewResearch_Ngampruetikorn.pdf"}],"oa_version":"Published Version","scopus_import":"1","day":"24","article_processing_charge":"No","has_accepted_license":"1","article_type":"original","publication":"Physical Review Research","citation":{"apa":"Ngampruetikorn, V., Sachdeva, V., Torrence, J., Humplik, J., Schwab, D. J., & Palmer, S. E. (2022). Inferring couplings in networks across order-disorder phase transitions. Physical Review Research. American Physical Society. https://doi.org/10.1103/PhysRevResearch.4.023240","ieee":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D. J. Schwab, and S. E. Palmer, “Inferring couplings in networks across order-disorder phase transitions,” Physical Review Research, vol. 4, no. 2. American Physical Society, 2022.","ista":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. 2022. Inferring couplings in networks across order-disorder phase transitions. Physical Review Research. 4(2), 023240.","ama":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. Inferring couplings in networks across order-disorder phase transitions. Physical Review Research. 2022;4(2). doi:10.1103/PhysRevResearch.4.023240","chicago":"Ngampruetikorn, Vudtiwat, Vedant Sachdeva, Johanna Torrence, Jan Humplik, David J. Schwab, and Stephanie E. Palmer. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” Physical Review Research. American Physical Society, 2022. https://doi.org/10.1103/PhysRevResearch.4.023240.","short":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E. Palmer, Physical Review Research 4 (2022).","mla":"Ngampruetikorn, Vudtiwat, et al. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” Physical Review Research, vol. 4, no. 2, 023240, American Physical Society, 2022, doi:10.1103/PhysRevResearch.4.023240."},"date_published":"2022-06-24T00:00:00Z","article_number":"023240","funded_apc":"1","file_date_updated":"2022-07-25T07:47:23Z","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"American Physical Society","acknowledgement":"This work was supported in part by the Alfred P. Sloan Foundation, the Simons Foundation, the National Institutes of Health under Award No. R01EB026943, and the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030).","year":"2022","date_updated":"2022-07-25T07:52:35Z","date_created":"2022-07-24T22:01:42Z","volume":4,"author":[{"full_name":"Ngampruetikorn, Vudtiwat","last_name":"Ngampruetikorn","first_name":"Vudtiwat"},{"last_name":"Sachdeva","first_name":"Vedant","full_name":"Sachdeva, Vedant"},{"full_name":"Torrence, Johanna","last_name":"Torrence","first_name":"Johanna"},{"full_name":"Humplik, Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","last_name":"Humplik","first_name":"Jan"},{"first_name":"David J.","last_name":"Schwab","full_name":"Schwab, David J."},{"full_name":"Palmer, Stephanie E.","last_name":"Palmer","first_name":"Stephanie E."}],"month":"06","publication_identifier":{"issn":["2643-1564"]},"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2106.02349"]},"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevResearch.4.023240"},{"article_number":"100435","file_date_updated":"2023-01-24T12:14:10Z","acknowledgement":"This work was supported through the Center for the Physics of Biological Function (PHYe1734030) and by National Institutes of Health Grants R01GM097275 and U01DK127429 (TG). GT acknowledges the support of the Austrian Science Fund grant FWF P28844 and the Human Frontiers Science Program. ","year":"2022","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Elsevier","author":[{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"1","full_name":"Tkačik, Gašper"}],"date_created":"2023-01-12T12:08:51Z","date_updated":"2023-02-13T09:20:34Z","volume":31,"month":"09","publication_identifier":{"issn":["2452-3100"]},"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"doi":"10.1016/j.coisb.2022.100435","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"text":"Models of transcriptional regulation that assume equilibrium binding of transcription factors have been less successful at predicting gene expression from sequence in eukaryotes than in bacteria. This could be due to the non-equilibrium nature of eukaryotic regulation. Unfortunately, the space of possible non-equilibrium mechanisms is vast and predominantly uninteresting. The key question is therefore how this space can be navigated efficiently, to focus on mechanisms and models that are biologically relevant. In this review, we advocate for the normative role of theory—theory that prescribes rather than just describes—in providing such a focus. Theory should expand its remit beyond inferring mechanistic models from data, towards identifying non-equilibrium gene regulatory schemes that may have been evolutionarily selected, despite their energy consumption, because they are precise, reliable, fast, or otherwise outperform regulation at equilibrium. We illustrate our reasoning by toy examples for which we provide simulation code.","lang":"eng"}],"issue":"9","_id":"12156","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"title":"Eukaryotic gene regulation at equilibrium, or non?","status":"public","intvolume":" 31","file":[{"checksum":"97ef01e0cc60cdc84f45640a0f248fb0","success":1,"date_updated":"2023-01-24T12:14:10Z","date_created":"2023-01-24T12:14:10Z","relation":"main_file","file_id":"12362","content_type":"application/pdf","file_size":2214944,"creator":"dernst","access_level":"open_access","file_name":"2022_CurrentBiology_Zoller.pdf"}],"oa_version":"Published Version","scopus_import":"1","keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"day":"01","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","publication":"Current Opinion in Systems Biology","citation":{"mla":"Zoller, Benjamin, et al. “Eukaryotic Gene Regulation at Equilibrium, or Non?” Current Opinion in Systems Biology, vol. 31, no. 9, 100435, Elsevier, 2022, doi:10.1016/j.coisb.2022.100435.","short":"B. Zoller, T. Gregor, G. Tkačik, Current Opinion in Systems Biology 31 (2022).","chicago":"Zoller, Benjamin, Thomas Gregor, and Gašper Tkačik. “Eukaryotic Gene Regulation at Equilibrium, or Non?” Current Opinion in Systems Biology. Elsevier, 2022. https://doi.org/10.1016/j.coisb.2022.100435.","ama":"Zoller B, Gregor T, Tkačik G. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 2022;31(9). doi:10.1016/j.coisb.2022.100435","ista":"Zoller B, Gregor T, Tkačik G. 2022. Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. 31(9), 100435.","ieee":"B. Zoller, T. Gregor, and G. Tkačik, “Eukaryotic gene regulation at equilibrium, or non?,” Current Opinion in Systems Biology, vol. 31, no. 9. Elsevier, 2022.","apa":"Zoller, B., Gregor, T., & Tkačik, G. (2022). Eukaryotic gene regulation at equilibrium, or non? Current Opinion in Systems Biology. Elsevier. https://doi.org/10.1016/j.coisb.2022.100435"},"article_type":"original","date_published":"2022-09-01T00:00:00Z"},{"keyword":["Biophysics"],"day":"04","article_processing_charge":"No","has_accepted_license":"1","publication":"Biophysical Journal","citation":{"chicago":"Zisis, Themistoklis, David Brückner, Tom Brandstätter, Wei Xiong Siow, Joseph d’Alessandro, Angelika M. Vollmar, Chase P. Broedersz, and Stefan Zahler. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” Biophysical Journal. Elsevier, 2022. https://doi.org/10.1016/j.bpj.2021.12.006.","short":"T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M. Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) P44-60.","mla":"Zisis, Themistoklis, et al. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” Biophysical Journal, vol. 121, no. 1, Elsevier, 2022, pp. P44-60, doi:10.1016/j.bpj.2021.12.006.","ieee":"T. Zisis et al., “Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration,” Biophysical Journal, vol. 121, no. 1. Elsevier, pp. P44-60, 2022.","apa":"Zisis, T., Brückner, D., Brandstätter, T., Siow, W. X., d’Alessandro, J., Vollmar, A. M., … Zahler, S. (2022). Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2021.12.006","ista":"Zisis T, Brückner D, Brandstätter T, Siow WX, d’Alessandro J, Vollmar AM, Broedersz CP, Zahler S. 2022. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. 121(1), P44-60.","ama":"Zisis T, Brückner D, Brandstätter T, et al. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. 2022;121(1):P44-60. doi:10.1016/j.bpj.2021.12.006"},"article_type":"original","page":"P44-60","date_published":"2022-01-04T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Cell dispersion from a confined area is fundamental in a number of biological processes,\r\nincluding cancer metastasis. To date, a quantitative understanding of the interplay of single\r\ncell motility, cell proliferation, and intercellular contacts remains elusive. In particular, the role\r\nof E- and N-Cadherin junctions, central components of intercellular contacts, is still\r\ncontroversial. Combining theoretical modeling with in vitro observations, we investigate the\r\ncollective spreading behavior of colonies of human cancer cells (T24). The spreading of these\r\ncolonies is driven by stochastic single-cell migration with frequent transient cell-cell contacts.\r\nWe find that inhibition of E- and N-Cadherin junctions decreases colony spreading and average\r\nspreading velocities, without affecting the strength of correlations in spreading velocities of\r\nneighboring cells. Based on a biophysical simulation model for cell migration, we show that the\r\nbehavioral changes upon disruption of these junctions can be explained by reduced repulsive\r\nexcluded volume interactions between cells. This suggests that in cancer cell migration,\r\ncadherin-based intercellular contacts sharpen cell boundaries leading to repulsive rather than\r\ncohesive interactions between cells, thereby promoting efficient cell spreading during collective\r\nmigration.\r\n"}],"issue":"1","_id":"10530","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","title":"Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration","intvolume":" 121","file":[{"relation":"main_file","file_id":"11697","date_created":"2022-07-29T10:17:10Z","date_updated":"2022-07-29T10:17:10Z","checksum":"1aa7c3478e0c8256b973b632efd1f6b4","success":1,"file_name":"2022_BiophysicalJour_Zisis.pdf","access_level":"open_access","file_size":4475504,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","month":"01","publication_identifier":{"issn":["0006-3495"]},"external_id":{"isi":["000740815400007"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"isi":1,"quality_controlled":"1","project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"doi":"10.1016/j.bpj.2021.12.006","language":[{"iso":"eng"}],"file_date_updated":"2022-07-29T10:17:10Z","acknowledgement":"Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 201269156 - SFB 1032 (Projects B8 and B12). D.B.B. is supported in part by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and by the Joachim Herz Stiftung.","year":"2022","publication_status":"published","publisher":"Elsevier","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"author":[{"full_name":"Zisis, Themistoklis","last_name":"Zisis","first_name":"Themistoklis"},{"full_name":"Brückner, David","last_name":"Brückner","first_name":"David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"full_name":"Brandstätter, Tom","last_name":"Brandstätter","first_name":"Tom"},{"full_name":"Siow, Wei Xiong","first_name":"Wei Xiong","last_name":"Siow"},{"full_name":"d’Alessandro, Joseph","last_name":"d’Alessandro","first_name":"Joseph"},{"full_name":"Vollmar, Angelika M.","first_name":"Angelika M.","last_name":"Vollmar"},{"full_name":"Broedersz, Chase P.","last_name":"Broedersz","first_name":"Chase P."},{"first_name":"Stefan","last_name":"Zahler","full_name":"Zahler, Stefan"}],"date_updated":"2023-08-02T13:34:25Z","date_created":"2021-12-10T09:48:19Z","volume":121},{"ec_funded":1,"file_date_updated":"2022-02-07T07:14:09Z","article_number":"e64543","volume":11,"date_created":"2022-02-06T23:01:32Z","date_updated":"2023-08-02T14:09:02Z","author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","last_name":"Lagator"},{"id":"35F0286E-F248-11E8-B48F-1D18A9856A87","first_name":"Srdjan","last_name":"Sarikas","full_name":"Sarikas, Srdjan"},{"full_name":"Steinrueck, Magdalena","first_name":"Magdalena","last_name":"Steinrueck"},{"first_name":"David","last_name":"Toledo-Aparicio","full_name":"Toledo-Aparicio, David"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P"},{"last_name":"Guet","first_name":"Calin C","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","publication_status":"published","pmid":1,"year":"2022","acknowledgement":"We thank Hande Acar, Nicholas H Barton, Rok Grah, Tiago Paixao, Maros Pleska, Anna Staron, and Murat Tugrul for insightful comments and input on the manuscript. This work was supported by: Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant number 216779/Z/19/Z) to ML; IPC Grant from IST Austria to ML and SS; European Research Council Funding Programme 7 (2007–2013, grant agreement number 648440) to JPB.","publication_identifier":{"eissn":["2050-084X"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.7554/eLife.64543","project":[{"call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","_id":"2578D616-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000751104400001"],"pmid":["35080492"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"abstract":[{"lang":"eng","text":"Predicting function from sequence is a central problem of biology. Currently, this is possible only locally in a narrow mutational neighborhood around a wildtype sequence rather than globally from any sequence. Using random mutant libraries, we developed a biophysical model that accounts for multiple features of σ70 binding bacterial promoters to predict constitutive gene expression levels from any sequence. We experimentally and theoretically estimated that 10–20% of random sequences lead to expression and ~80% of non-expressing sequences are one mutation away from a functional promoter. The potential for generating expression from random sequences is so pervasive that selection acts against σ70-RNA polymerase binding sites even within inter-genic, promoter-containing regions. This pervasiveness of σ70-binding sites implies that emergence of promoters is not the limiting step in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter function into a mechanistic model enabled not only more accurate predictions of gene expression levels, but also identified that promoters evolve more rapidly than previously thought."}],"type":"journal_article","file":[{"file_id":"10739","relation":"main_file","success":1,"checksum":"decdcdf600ff51e9a9703b49ca114170","date_updated":"2022-02-07T07:14:09Z","date_created":"2022-02-07T07:14:09Z","access_level":"open_access","file_name":"2022_ELife_Lagator.pdf","creator":"cchlebak","content_type":"application/pdf","file_size":5604343}],"oa_version":"Published Version","intvolume":" 11","title":"Predicting bacterial promoter function and evolution from random sequences","status":"public","ddc":["576"],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10736","article_processing_charge":"No","has_accepted_license":"1","day":"26","scopus_import":"1","date_published":"2022-01-26T00:00:00Z","article_type":"original","citation":{"chicago":"Lagator, Mato, Srdjan Sarikas, Magdalena Steinrueck, David Toledo-Aparicio, Jonathan P Bollback, Calin C Guet, and Gašper Tkačik. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife. eLife Sciences Publications, 2022. https://doi.org/10.7554/eLife.64543.","short":"M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).","mla":"Lagator, Mato, et al. “Predicting Bacterial Promoter Function and Evolution from Random Sequences.” ELife, vol. 11, e64543, eLife Sciences Publications, 2022, doi:10.7554/eLife.64543.","ieee":"M. Lagator et al., “Predicting bacterial promoter function and evolution from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.","apa":"Lagator, M., Sarikas, S., Steinrueck, M., Toledo-Aparicio, D., Bollback, J. P., Guet, C. C., & Tkačik, G. (2022). Predicting bacterial promoter function and evolution from random sequences. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.64543","ista":"Lagator M, Sarikas S, Steinrueck M, Toledo-Aparicio D, Bollback JP, Guet CC, Tkačik G. 2022. Predicting bacterial promoter function and evolution from random sequences. eLife. 11, e64543.","ama":"Lagator M, Sarikas S, Steinrueck M, et al. Predicting bacterial promoter function and evolution from random sequences. eLife. 2022;11. doi:10.7554/eLife.64543"},"publication":"eLife"},{"doi":"10.1371/journal.pbio.3001889","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000925192000001"]},"oa":1,"project":[{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"isi":1,"quality_controlled":"1","publication_identifier":{"eissn":["1545-7885"]},"month":"12","author":[{"first_name":"Wiktor F","last_name":"Mlynarski","id":"358A453A-F248-11E8-B48F-1D18A9856A87","full_name":"Mlynarski, Wiktor F"},{"orcid":"1","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"volume":20,"date_created":"2023-01-22T23:00:55Z","date_updated":"2023-08-03T14:23:49Z","acknowledgement":"We thank Robbe Goris for generously providing figures from his work and Ann M. Hermundstad for helpful discussions.\r\nGT & WM were supported by the Austrian Science Fund Standalone Grant P 34015 \"Efficient Coding with Biophysical Realism\" (https://pf.fwf.ac.at/) WM was additionally supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (https://ec.europa.eu/research/mariecurieactions/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","year":"2022","department":[{"_id":"GaTk"}],"publisher":"Public Library of Science","publication_status":"published","ec_funded":1,"file_date_updated":"2023-01-23T08:46:40Z","date_published":"2022-12-21T00:00:00Z","citation":{"chicago":"Mlynarski, Wiktor F, and Gašper Tkačik. “Efficient Coding Theory of Dynamic Attentional Modulation.” PLoS Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pbio.3001889.","short":"W.F. Mlynarski, G. Tkačik, PLoS Biology 20 (2022) e3001889.","mla":"Mlynarski, Wiktor F., and Gašper Tkačik. “Efficient Coding Theory of Dynamic Attentional Modulation.” PLoS Biology, vol. 20, no. 12, Public Library of Science, 2022, p. e3001889, doi:10.1371/journal.pbio.3001889.","ieee":"W. F. Mlynarski and G. Tkačik, “Efficient coding theory of dynamic attentional modulation,” PLoS Biology, vol. 20, no. 12. Public Library of Science, p. e3001889, 2022.","apa":"Mlynarski, W. F., & Tkačik, G. (2022). Efficient coding theory of dynamic attentional modulation. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3001889","ista":"Mlynarski WF, Tkačik G. 2022. Efficient coding theory of dynamic attentional modulation. PLoS Biology. 20(12), e3001889.","ama":"Mlynarski WF, Tkačik G. Efficient coding theory of dynamic attentional modulation. PLoS Biology. 2022;20(12):e3001889. doi:10.1371/journal.pbio.3001889"},"publication":"PLoS Biology","page":"e3001889","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"21","scopus_import":"1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":4248838,"creator":"dernst","file_name":"2022_PloSBiology_Mlynarski.pdf","access_level":"open_access","date_updated":"2023-01-23T08:46:40Z","date_created":"2023-01-23T08:46:40Z","checksum":"5d7f1111a87e5f2c1bf92f8886738894","success":1,"relation":"main_file","file_id":"12337"}],"_id":"12332","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 20","title":"Efficient coding theory of dynamic attentional modulation","ddc":["570"],"status":"public","issue":"12","abstract":[{"text":"Activity of sensory neurons is driven not only by external stimuli but also by feedback signals from higher brain areas. Attention is one particularly important internal signal whose presumed role is to modulate sensory representations such that they only encode information currently relevant to the organism at minimal cost. This hypothesis has, however, not yet been expressed in a normative computational framework. Here, by building on normative principles of probabilistic inference and efficient coding, we developed a model of dynamic population coding in the visual cortex. By continuously adapting the sensory code to changing demands of the perceptual observer, an attention-like modulation emerges. This modulation can dramatically reduce the amount of neural activity without deteriorating the accuracy of task-specific inferences. Our results suggest that a range of seemingly disparate cortical phenomena such as intrinsic gain modulation, attention-related tuning modulation, and response variability could be manifestations of the same underlying principles, which combine efficient sensory coding with optimal probabilistic inference in dynamic environments.","lang":"eng"}],"type":"journal_article"}]