[{"article_number":"023240","file_date_updated":"2022-07-25T07:47:23Z","license":"https://creativecommons.org/licenses/by/4.0/","funded_apc":"1","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","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"American Physical Society","author":[{"full_name":"Ngampruetikorn, Vudtiwat","first_name":"Vudtiwat","last_name":"Ngampruetikorn"},{"last_name":"Sachdeva","first_name":"Vedant","full_name":"Sachdeva, Vedant"},{"full_name":"Torrence, Johanna","first_name":"Johanna","last_name":"Torrence"},{"full_name":"Humplik, Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Humplik"},{"full_name":"Schwab, David J.","last_name":"Schwab","first_name":"David J."},{"full_name":"Palmer, Stephanie E.","first_name":"Stephanie E.","last_name":"Palmer"}],"date_created":"2022-07-24T22:01:42Z","date_updated":"2022-07-25T07:52:35Z","volume":4,"month":"06","publication_identifier":{"issn":["2643-1564"]},"external_id":{"arxiv":["2106.02349"]},"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","doi":"10.1103/PhysRevResearch.4.023240","language":[{"iso":"eng"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Statistical inference is central to many scientific endeavors, yet how it works remains unresolved. Answering this requires a quantitative understanding of the intrinsic interplay between statistical models, inference methods, and the structure in the data. To this end, we characterize the efficacy of direct coupling analysis (DCA)—a highly successful method for analyzing amino acid sequence data—in inferring pairwise interactions from samples of ferromagnetic Ising models on random graphs. Our approach allows for physically motivated exploration of qualitatively distinct data regimes separated by phase transitions. We show that inference quality depends strongly on the nature of data-generating distributions: optimal accuracy occurs at an intermediate temperature where the detrimental effects from macroscopic order and thermal noise are minimal. Importantly our results indicate that DCA does not always outperform its local-statistics-based predecessors; while DCA excels at low temperatures, it becomes inferior to simple correlation thresholding at virtually all temperatures when data are limited. Our findings offer insights into the regime in which DCA operates so successfully, and more broadly, how inference interacts with the structure in the data."}],"issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11638","ddc":["530"],"status":"public","title":"Inferring couplings in networks across order-disorder phase transitions","intvolume":" 4","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":1379683,"creator":"dernst","access_level":"open_access","file_name":"2022_PhysicalReviewResearch_Ngampruetikorn.pdf","checksum":"ed6fdc2a3a096df785fa5f7b17b716c6","success":1,"date_updated":"2022-07-25T07:47:23Z","date_created":"2022-07-25T07:47:23Z","relation":"main_file","file_id":"11644"}],"scopus_import":"1","day":"24","has_accepted_license":"1","article_processing_charge":"No","publication":"Physical Review Research","citation":{"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","ista":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. 2022. Inferring couplings in networks across order-disorder phase transitions. Physical Review Research. 4(2), 023240.","apa":"Ngampruetikorn, V., Sachdeva, V., Torrence, J., Humplik, J., Schwab, D. J., & 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.","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.","short":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E. Palmer, Physical Review Research 4 (2022).","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."},"article_type":"original","date_published":"2022-06-24T00:00:00Z"},{"type":"journal_article","issue":"9","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"}],"intvolume":" 31","ddc":["570"],"status":"public","title":"Eukaryotic gene regulation at equilibrium, or non?","_id":"12156","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2023-01-24T12:14:10Z","date_created":"2023-01-24T12:14:10Z","success":1,"checksum":"97ef01e0cc60cdc84f45640a0f248fb0","file_id":"12362","relation":"main_file","creator":"dernst","file_size":2214944,"content_type":"application/pdf","file_name":"2022_CurrentBiology_Zoller.pdf","access_level":"open_access"}],"oa_version":"Published Version","keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"01","article_type":"original","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.","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","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."},"publication":"Current Opinion in Systems Biology","date_published":"2022-09-01T00:00:00Z","article_number":"100435","file_date_updated":"2023-01-24T12:14:10Z","department":[{"_id":"GaTk"}],"publisher":"Elsevier","publication_status":"published","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","volume":31,"date_updated":"2023-02-13T09:20:34Z","date_created":"2023-01-12T12:08:51Z","author":[{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"full_name":"Gregor, Thomas","first_name":"Thomas","last_name":"Gregor"},{"orcid":"1","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"publication_identifier":{"issn":["2452-3100"]},"month":"09","project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"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,"language":[{"iso":"eng"}],"doi":"10.1016/j.coisb.2022.100435"},{"date_published":"2022-01-04T00:00:00Z","publication":"Biophysical Journal","citation":{"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.","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.","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","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","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.","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."},"article_type":"original","page":"P44-60","day":"04","article_processing_charge":"No","has_accepted_license":"1","keyword":["Biophysics"],"oa_version":"Published Version","file":[{"date_updated":"2022-07-29T10:17:10Z","date_created":"2022-07-29T10:17:10Z","success":1,"checksum":"1aa7c3478e0c8256b973b632efd1f6b4","file_id":"11697","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":4475504,"file_name":"2022_BiophysicalJour_Zisis.pdf","access_level":"open_access"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10530","ddc":["570"],"status":"public","title":"Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration","intvolume":" 121","abstract":[{"text":"Cell dispersion from a confined area is fundamental in a number of biological processes,\r\nincluding cancer metastasis. To date, a quantitative understanding of the interplay of single\r\ncell motility, cell proliferation, and intercellular contacts remains elusive. In particular, the role\r\nof E- and N-Cadherin junctions, central components of intercellular contacts, is still\r\ncontroversial. Combining theoretical modeling with in vitro observations, we investigate the\r\ncollective spreading behavior of colonies of human cancer cells (T24). The spreading of these\r\ncolonies is driven by stochastic single-cell migration with frequent transient cell-cell contacts.\r\nWe find that inhibition of E- and N-Cadherin junctions decreases colony spreading and average\r\nspreading velocities, without affecting the strength of correlations in spreading velocities of\r\nneighboring cells. Based on a biophysical simulation model for cell migration, we show that the\r\nbehavioral changes upon disruption of these junctions can be explained by reduced repulsive\r\nexcluded volume interactions between cells. This suggests that in cancer cell migration,\r\ncadherin-based intercellular contacts sharpen cell boundaries leading to repulsive rather than\r\ncohesive interactions between cells, thereby promoting efficient cell spreading during collective\r\nmigration.\r\n","lang":"eng"}],"issue":"1","type":"journal_article","doi":"10.1016/j.bpj.2021.12.006","language":[{"iso":"eng"}],"oa":1,"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"},"external_id":{"isi":["000740815400007"]},"quality_controlled":"1","isi":1,"project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"month":"01","publication_identifier":{"issn":["0006-3495"]},"author":[{"last_name":"Zisis","first_name":"Themistoklis","full_name":"Zisis, Themistoklis"},{"full_name":"Brückner, David","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","first_name":"David"},{"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.","last_name":"Vollmar","first_name":"Angelika M."},{"full_name":"Broedersz, Chase P.","last_name":"Broedersz","first_name":"Chase P."},{"last_name":"Zahler","first_name":"Stefan","full_name":"Zahler, Stefan"}],"date_updated":"2023-08-02T13:34:25Z","date_created":"2021-12-10T09:48:19Z","volume":121,"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"}],"file_date_updated":"2022-07-29T10:17:10Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/"},{"day":"26","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2022-01-26T00:00:00Z","publication":"eLife","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.","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.","short":"M. Lagator, S. Sarikas, M. Steinrueck, D. Toledo-Aparicio, J.P. Bollback, C.C. Guet, G. Tkačik, ELife 11 (2022).","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.","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","ieee":"M. Lagator et al., “Predicting bacterial promoter function and evolution from random sequences,” eLife, vol. 11. eLife Sciences Publications, 2022.","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"},"article_type":"original","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":[{"date_created":"2022-02-07T07:14:09Z","date_updated":"2022-02-07T07:14:09Z","success":1,"checksum":"decdcdf600ff51e9a9703b49ca114170","file_id":"10739","relation":"main_file","creator":"cchlebak","file_size":5604343,"content_type":"application/pdf","file_name":"2022_ELife_Lagator.pdf","access_level":"open_access"}],"oa_version":"Published Version","_id":"10736","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["576"],"status":"public","title":"Predicting bacterial promoter function and evolution from random sequences","intvolume":" 11","month":"01","publication_identifier":{"eissn":["2050-084X"]},"doi":"10.7554/eLife.64543","language":[{"iso":"eng"}],"external_id":{"pmid":["35080492"],"isi":["000751104400001"]},"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":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"file_date_updated":"2022-02-07T07:14:09Z","ec_funded":1,"article_number":"e64543","author":[{"full_name":"Lagator, Mato","first_name":"Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"id":"35F0286E-F248-11E8-B48F-1D18A9856A87","last_name":"Sarikas","first_name":"Srdjan","full_name":"Sarikas, Srdjan"},{"first_name":"Magdalena","last_name":"Steinrueck","full_name":"Steinrueck, Magdalena"},{"full_name":"Toledo-Aparicio, David","first_name":"David","last_name":"Toledo-Aparicio"},{"last_name":"Bollback","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","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"}],"date_updated":"2023-08-02T14:09:02Z","date_created":"2022-02-06T23:01:32Z","volume":11,"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.","year":"2022","pmid":1,"publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"NiBa"}]},{"intvolume":" 20","title":"Efficient coding theory of dynamic attentional modulation","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12332","file":[{"relation":"main_file","file_id":"12337","checksum":"5d7f1111a87e5f2c1bf92f8886738894","success":1,"date_created":"2023-01-23T08:46:40Z","date_updated":"2023-01-23T08:46:40Z","access_level":"open_access","file_name":"2022_PloSBiology_Mlynarski.pdf","file_size":4248838,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","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"}],"page":"e3001889","article_type":"original","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.","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.","short":"W.F. Mlynarski, G. Tkačik, PLoS Biology 20 (2022) e3001889.","ista":"Mlynarski WF, Tkačik G. 2022. Efficient coding theory of dynamic attentional modulation. PLoS Biology. 20(12), e3001889.","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","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","date_published":"2022-12-21T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"21","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publication_status":"published","year":"2022","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.","volume":20,"date_created":"2023-01-22T23:00:55Z","date_updated":"2023-08-03T14:23:49Z","author":[{"last_name":"Mlynarski","first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87","full_name":"Mlynarski, Wiktor F"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"1","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"ec_funded":1,"file_date_updated":"2023-01-23T08:46:40Z","project":[{"grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"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"},"external_id":{"isi":["000925192000001"]},"language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.3001889","publication_identifier":{"eissn":["1545-7885"]},"month":"12"},{"pmid":1,"year":"2022","acknowledgement":"We thank Ksenia Khudiakova, Wiktor Młynarski, Sean Stankowski, and two anonymous reviewers for discussions and comments on the manuscript. G.T. and M.H. acknowledge funding from the Human Frontier Science Program Grant RGP0032/2018. N.B. acknowledges funding from ERC Grant 250152 “Information and Evolution.”","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publication_status":"published","related_material":{"record":[{"id":"15020","relation":"dissertation_contains","status":"public"}]},"author":[{"first_name":"Michal","last_name":"Hledik","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Tkačik, Gašper","orcid":"1","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"}],"volume":119,"date_created":"2022-09-11T22:01:55Z","date_updated":"2024-03-06T14:22:51Z","article_number":"e2123152119","ec_funded":1,"file_date_updated":"2022-09-12T08:08:12Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"pmid":["36037343"],"isi":["000889278400014"]},"project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"}],"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.2123152119","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"08","_id":"12081","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 119","status":"public","title":"Accumulation and maintenance of information in evolution","ddc":["570"],"oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":2165752,"creator":"dernst","access_level":"open_access","file_name":"2022_PNAS_Hledik.pdf","checksum":"6dec51f6567da9039982a571508a8e4d","success":1,"date_updated":"2022-09-12T08:08:12Z","date_created":"2022-09-12T08:08:12Z","relation":"main_file","file_id":"12091"}],"type":"journal_article","issue":"36","abstract":[{"lang":"eng","text":"Selection accumulates information in the genome—it guides stochastically evolving populations toward states (genotype frequencies) that would be unlikely under neutrality. This can be quantified as the Kullback–Leibler (KL) divergence between the actual distribution of genotype frequencies and the corresponding neutral distribution. First, we show that this population-level information sets an upper bound on the information at the level of genotype and phenotype, limiting how precisely they can be specified by selection. Next, we study how the accumulation and maintenance of information is limited by the cost of selection, measured as the genetic load or the relative fitness variance, both of which we connect to the control-theoretic KL cost of control. The information accumulation rate is upper bounded by the population size times the cost of selection. This bound is very general, and applies across models (Wright–Fisher, Moran, diffusion) and to arbitrary forms of selection, mutation, and recombination. Finally, the cost of maintaining information depends on how it is encoded: Specifying a single allele out of two is expensive, but one bit encoded among many weakly specified loci (as in a polygenic trait) is cheap."}],"citation":{"mla":"Hledik, Michal, et al. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences, vol. 119, no. 36, e2123152119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2123152119.","short":"M. Hledik, N.H. Barton, G. Tkačik, Proceedings of the National Academy of Sciences 119 (2022).","chicago":"Hledik, Michal, Nicholas H Barton, and Gašper Tkačik. “Accumulation and Maintenance of Information in Evolution.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2123152119.","ama":"Hledik M, Barton NH, Tkačik G. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 2022;119(36). doi:10.1073/pnas.2123152119","ista":"Hledik M, Barton NH, Tkačik G. 2022. Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. 119(36), e2123152119.","apa":"Hledik, M., Barton, N. H., & Tkačik, G. (2022). Accumulation and maintenance of information in evolution. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2123152119","ieee":"M. Hledik, N. H. Barton, and G. Tkačik, “Accumulation and maintenance of information in evolution,” Proceedings of the National Academy of Sciences, vol. 119, no. 36. Proceedings of the National Academy of Sciences, 2022."},"publication":"Proceedings of the National Academy of Sciences","article_type":"original","date_published":"2022-08-29T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"29"},{"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"PLoS Computational Biology","citation":{"mla":"Bodova, Katarina, et al. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational Biology, vol. 17, no. 12, e1009661, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1009661.","short":"K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).","chicago":"Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” PLoS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1009661.","ama":"Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 2021;17(12). doi:10.1371/journal.pcbi.1009661","ista":"Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 17(12), e1009661.","apa":"Bodova, K., Szep, E., & Barton, N. H. (2021). Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1009661","ieee":"K. Bodova, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate approximation of structured population dynamics,” PLoS Computational Biology, vol. 17, no. 12. Public Library of Science, 2021."},"date_published":"2021-12-01T00:00:00Z","type":"journal_article","abstract":[{"text":"Realistic models of biological processes typically involve interacting components on multiple scales, driven by changing environment and inherent stochasticity. Such models are often analytically and numerically intractable. We revisit a dynamic maximum entropy method that combines a static maximum entropy with a quasi-stationary approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics, without the need to track microscopic details. Although the method has been previously applied to a few (rather complicated) applications in population genetics, our main goal here is to explain and to better understand how the method works. We demonstrate the usefulness of the method for two widely studied stochastic problems, highlighting its accuracy in capturing important macroscopic quantities even in rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process, the method recovers the exact dynamics whilst for a stochastic island model with migration from other habitats, the approximation retains high macroscopic accuracy under a wide range of scenarios in a dynamic environment.","lang":"eng"}],"issue":"12","ddc":["570"],"title":"Dynamic maximum entropy provides accurate approximation of structured population dynamics","status":"public","intvolume":" 17","_id":"10535","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"date_updated":"2022-05-16T08:53:11Z","date_created":"2022-05-16T08:53:11Z","checksum":"dcd185d4f7e0acee25edf1d6537f447e","success":1,"relation":"main_file","file_id":"11383","content_type":"application/pdf","file_size":2299486,"creator":"dernst","file_name":"2021_PLOsComBio_Bodova.pdf","access_level":"open_access"}],"month":"12","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"quality_controlled":"1","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"},"external_id":{"pmid":["34851948"],"arxiv":["2102.03669"]},"acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1009661","article_number":"e1009661","file_date_updated":"2022-05-16T08:53:11Z","publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Public Library of Science","year":"2021","acknowledgement":"Computational resources for the study were provided by the Institute of Science and Technology, Austria.\r\nKB received funding from the Scientific Grant Agency of the Slovak Republic under the Grants Nos. 1/0755/19 and 1/0521/20.","pmid":1,"date_created":"2021-12-12T23:01:27Z","date_updated":"2022-08-01T10:48:04Z","volume":17,"author":[{"full_name":"Bod'ová, Katarína","last_name":"Bod'ová","first_name":"Katarína","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","last_name":"Szep","first_name":"Eniko","full_name":"Szep, Eniko"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}]},{"type":"preprint","abstract":[{"text":"Brain dynamics display collective phenomena as diverse as neuronal oscillations and avalanches. Oscillations are rhythmic, with fluctuations occurring at a characteristic scale, whereas avalanches are scale-free cascades of neural activity. Here we show that such antithetic features can coexist in a very generic class of adaptive neural networks. In the most simple yet fully microscopic model from this class we make direct contact with human brain resting-state activity recordings via tractable inference of the model's two essential parameters. The inferred model quantitatively captures the dynamics over a broad range of scales, from single sensor fluctuations, collective behaviors of nearly-synchronous extreme events on multiple sensors, to neuronal avalanches unfolding over multiple sensors across multiple time-bins. Importantly, the inferred parameters correlate with model-independent signatures of \"closeness to criticality\", suggesting that the coexistence of scale-specific (neural oscillations) and scale-free (neuronal avalanches) dynamics in brain activity occurs close to a non-equilibrium critical point at the onset of self-sustained oscillations.","lang":"eng"}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10912","acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. GT\r\nacknowledges the support of the Austrian Science Fund (FWF) under Stand-Alone Grant\r\nNo. P34015.","year":"2021","ddc":["570"],"publication_status":"submitted","title":"Quantifying the coexistence of neuronal oscillations and avalanches","status":"public","department":[{"_id":"GaTk"}],"publisher":"arXiv","author":[{"full_name":"Lombardi, Fabrizio","first_name":"Fabrizio","last_name":"Lombardi","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249"},{"full_name":"Pepic, Selver","first_name":"Selver","last_name":"Pepic","id":"F93245C4-C3CA-11E9-B4F0-C6F4E5697425"},{"full_name":"Shriki, Oren","last_name":"Shriki","first_name":"Oren"},{"first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"},{"full_name":"De Martino, Daniele","last_name":"De Martino","first_name":"Daniele"}],"date_updated":"2022-03-22T07:53:18Z","date_created":"2022-03-21T11:41:28Z","oa_version":"Preprint","month":"08","day":"17","article_processing_charge":"No","external_id":{"arxiv":["2108.06686"]},"oa":1,"citation":{"ista":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Quantifying the coexistence of neuronal oscillations and avalanches. 10.48550/ARXIV.2108.06686.","ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Quantifying the coexistence of neuronal oscillations and avalanches.” arXiv.","apa":"Lombardi, F., Pepic, S., Shriki, O., Tkačik, G., & De Martino, D. (n.d.). Quantifying the coexistence of neuronal oscillations and avalanches. arXiv. https://doi.org/10.48550/ARXIV.2108.06686","ama":"Lombardi F, Pepic S, Shriki O, Tkačik G, De Martino D. Quantifying the coexistence of neuronal oscillations and avalanches. doi:10.48550/ARXIV.2108.06686","chicago":"Lombardi, Fabrizio, Selver Pepic, Oren Shriki, Gašper Tkačik, and Daniele De Martino. “Quantifying the Coexistence of Neuronal Oscillations and Avalanches.” arXiv, n.d. https://doi.org/10.48550/ARXIV.2108.06686.","mla":"Lombardi, Fabrizio, et al. Quantifying the Coexistence of Neuronal Oscillations and Avalanches. arXiv, doi:10.48550/ARXIV.2108.06686.","short":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, D. De Martino, (n.d.)."},"main_file_link":[{"url":"https://arxiv.org/abs/2108.06686","open_access":"1"}],"page":"37","project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"}],"doi":"10.48550/ARXIV.2108.06686","date_published":"2021-08-17T00:00:00Z","language":[{"iso":"eng"}]},{"author":[{"last_name":"Kavcic","first_name":"Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"oa_version":"Preprint","date_created":"2021-12-28T06:52:09Z","date_updated":"2023-05-03T10:54:05Z","acknowledgement":"B.K. thanks Stefano Elefante, Simon Rella, and Michal Hledík for their help with the usage of the cluster. B.K. additionally thanks Călin Guet and his group for help and advice. We thank M. Hennessey-Wesen for constructive comments on the manuscript. We thank Ankita Gupta (Indian Institute of Technology) for spotting a typographical error in Eq. (49) in the preprint version of this paper.","_id":"10579","year":"2021","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"}],"publication_status":"submitted","ddc":["530"],"status":"public","title":"Token-driven totally asymmetric simple exclusion process","abstract":[{"text":"We consider a totally asymmetric simple exclusion process (TASEP) consisting of particles on a lattice that require binding by a \"token\" to move. Using a combination of theory and simulations, we address the following questions: (i) How token binding kinetics affects the current-density relation; (ii) How the current-density relation depends on the scarcity of tokens; (iii) How tokens propagate the effects of the locally-imposed disorder (such a slow site) over the entire lattice; (iv) How a shared pool of tokens couples concurrent TASEPs running on multiple lattices; (v) How our results translate to TASEPs with open boundaries that exchange particles with the reservoir. Since real particle motion (including in systems that inspired the standard TASEP model, e.g., protein synthesis or movement of molecular motors) is often catalyzed, regulated, actuated, or otherwise mediated, the token-driven TASEP dynamics analyzed in this paper should allow for a better understanding of real systems and enable a closer match between TASEP theory and experimental observations.","lang":"eng"}],"type":"preprint","article_number":"2112.13558","doi":"10.48550/arXiv.2112.13558","date_published":"2021-12-27T00:00:00Z","language":[{"iso":"eng"}],"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"},"external_id":{"arxiv":["2112.13558"]},"citation":{"ama":"Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion process. arXiv. doi:10.48550/arXiv.2112.13558","ista":"Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion process. arXiv, 2112.13558.","apa":"Kavcic, B., & Tkačik, G. (n.d.). Token-driven totally asymmetric simple exclusion process. arXiv. https://doi.org/10.48550/arXiv.2112.13558","ieee":"B. Kavcic and G. Tkačik, “Token-driven totally asymmetric simple exclusion process,” arXiv. .","mla":"Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Process.” ArXiv, 2112.13558, doi:10.48550/arXiv.2112.13558.","short":"B. Kavcic, G. Tkačik, ArXiv (n.d.).","chicago":"Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Process.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2112.13558."},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2112.13558"}],"oa":1,"publication":"arXiv","article_processing_charge":"No","has_accepted_license":"1","day":"27","month":"12"},{"scopus_import":"1","day":"13","article_processing_charge":"No","publication":"Neurocomputing","citation":{"chicago":"Lombardi, Fabrizio, Oren Shriki, Hans J Herrmann, and Lucilla de Arcangelis. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” Neurocomputing. Elsevier, 2021. https://doi.org/10.1016/j.neucom.2020.05.126.","short":"F. Lombardi, O. Shriki, H.J. Herrmann, L. de Arcangelis, Neurocomputing 461 (2021) 657–666.","mla":"Lombardi, Fabrizio, et al. “Long-Range Temporal Correlations in the Broadband Resting State Activity of the Human Brain Revealed by Neuronal Avalanches.” Neurocomputing, vol. 461, Elsevier, 2021, pp. 657–66, doi:10.1016/j.neucom.2020.05.126.","ieee":"F. Lombardi, O. Shriki, H. J. Herrmann, and L. de Arcangelis, “Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches,” Neurocomputing, vol. 461. Elsevier, pp. 657–666, 2021.","apa":"Lombardi, F., Shriki, O., Herrmann, H. J., & de Arcangelis, L. (2021). Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. Neurocomputing. Elsevier. https://doi.org/10.1016/j.neucom.2020.05.126","ista":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. 2021. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. Neurocomputing. 461, 657–666.","ama":"Lombardi F, Shriki O, Herrmann HJ, de Arcangelis L. Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches. Neurocomputing. 2021;461:657-666. doi:10.1016/j.neucom.2020.05.126"},"article_type":"original","page":"657-666","date_published":"2021-05-13T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Resting-state brain activity is characterized by the presence of neuronal avalanches showing absence of characteristic size. Such evidence has been interpreted in the context of criticality and associated with the normal functioning of the brain. A distinctive attribute of systems at criticality is the presence of long-range correlations. Thus, to verify the hypothesis that the brain operates close to a critical point and consequently assess deviations from criticality for diagnostic purposes, it is of primary importance to robustly and reliably characterize correlations in resting-state brain activity. Recent works focused on the analysis of narrow-band electroencephalography (EEG) and magnetoencephalography (MEG) signal amplitude envelope, showing evidence of long-range temporal correlations (LRTC) in neural oscillations. However, brain activity is a broadband phenomenon, and a significant piece of information useful to precisely discriminate between normal (critical) and pathological behavior (non-critical), may be encoded in the broadband spatio-temporal cortical dynamics. Here we propose to characterize the temporal correlations in the broadband brain activity through the lens of neuronal avalanches. To this end, we consider resting-state EEG and long-term MEG recordings, extract the corresponding neuronal avalanche sequences, and study their temporal correlations. We demonstrate that the broadband resting-state brain activity consistently exhibits long-range power-law correlations in both EEG and MEG recordings, with similar values of the scaling exponents. Importantly, although we observe that the avalanche size distribution depends on scale parameters, scaling exponents characterizing long-range correlations are quite robust. In particular, they are independent of the temporal binning (scale of analysis), indicating that our analysis captures intrinsic characteristics of the underlying dynamics. Because neuronal avalanches constitute a fundamental feature of neural systems with universal characteristics, the proposed approach may serve as a general, systems- and experiment-independent procedure to infer the existence of underlying long-range correlations in extended neural systems, and identify pathological behaviors in the complex spatio-temporal interplay of cortical rhythms."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"7463","title":"Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches","status":"public","intvolume":" 461","oa_version":"Preprint","month":"05","publication_identifier":{"issn":["0925-2312"],"eissn":["1872-8286"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.02.03.930966"}],"oa":1,"external_id":{"isi":["000704086300015"]},"quality_controlled":"1","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"doi":"10.1016/j.neucom.2020.05.126","language":[{"iso":"eng"}],"ec_funded":1,"acknowledgement":"LdA would like to acknowledge the financial support from MIUR-PRIN2017 WZFTZP and VALERE:VAnviteLli pEr la RicErca 2019. FL acknowledges support from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 754411. HJH would like to thank the Agencies CAPES and FUNCAP for financial support.","year":"2021","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Elsevier","author":[{"last_name":"Lombardi","first_name":"Fabrizio","orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425","full_name":"Lombardi, Fabrizio"},{"last_name":"Shriki","first_name":"Oren","full_name":"Shriki, Oren"},{"full_name":"Herrmann, Hans J","last_name":"Herrmann","first_name":"Hans J"},{"full_name":"de Arcangelis, Lucilla","first_name":"Lucilla","last_name":"de Arcangelis"}],"date_updated":"2023-08-04T10:46:29Z","date_created":"2020-02-06T16:09:14Z","volume":461}]