[{"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"11644","date_updated":"2022-07-25T07:47:23Z","date_created":"2022-07-25T07:47:23Z","checksum":"ed6fdc2a3a096df785fa5f7b17b716c6","success":1,"file_name":"2022_PhysicalReviewResearch_Ngampruetikorn.pdf","access_level":"open_access","file_size":1379683,"content_type":"application/pdf","creator":"dernst"}],"_id":"11638","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 4","status":"public","ddc":["530"],"title":"Inferring couplings in networks across order-disorder phase transitions","issue":"2","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."}],"type":"journal_article","date_published":"2022-06-24T00:00:00Z","citation":{"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.","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.","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.","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"},"publication":"Physical Review Research","article_type":"original","has_accepted_license":"1","article_processing_charge":"No","day":"24","scopus_import":"1","author":[{"full_name":"Ngampruetikorn, Vudtiwat","first_name":"Vudtiwat","last_name":"Ngampruetikorn"},{"full_name":"Sachdeva, Vedant","first_name":"Vedant","last_name":"Sachdeva"},{"first_name":"Johanna","last_name":"Torrence","full_name":"Torrence, Johanna"},{"id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Humplik","full_name":"Humplik, Jan"},{"first_name":"David J.","last_name":"Schwab","full_name":"Schwab, David J."},{"first_name":"Stephanie E.","last_name":"Palmer","full_name":"Palmer, Stephanie E."}],"volume":4,"date_updated":"2022-07-25T07:52:35Z","date_created":"2022-07-24T22:01:42Z","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","publisher":"American Physical Society","department":[{"_id":"GaTk"}],"publication_status":"published","file_date_updated":"2022-07-25T07:47:23Z","license":"https://creativecommons.org/licenses/by/4.0/","funded_apc":"1","article_number":"023240","doi":"10.1103/PhysRevResearch.4.023240","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"},"oa":1,"external_id":{"arxiv":["2106.02349"]},"quality_controlled":"1","publication_identifier":{"issn":["2643-1564"]},"month":"06"},{"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,"project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1016/j.coisb.2022.100435","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2452-3100"]},"month":"09","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","department":[{"_id":"GaTk"}],"publisher":"Elsevier","publication_status":"published","author":[{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"1","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"volume":31,"date_created":"2023-01-12T12:08:51Z","date_updated":"2023-02-13T09:20:34Z","article_number":"100435","file_date_updated":"2023-01-24T12:14:10Z","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","article_type":"original","date_published":"2022-09-01T00:00:00Z","scopus_import":"1","keyword":["Applied Mathematics","Computer Science Applications","Drug Discovery","General Biochemistry","Genetics and Molecular Biology","Modeling and Simulation"],"article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","day":"01","_id":"12156","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 31","ddc":["570"],"status":"public","title":"Eukaryotic gene regulation at equilibrium, or non?","file":[{"access_level":"open_access","file_name":"2022_CurrentBiology_Zoller.pdf","creator":"dernst","content_type":"application/pdf","file_size":2214944,"file_id":"12362","relation":"main_file","success":1,"checksum":"97ef01e0cc60cdc84f45640a0f248fb0","date_updated":"2023-01-24T12:14:10Z","date_created":"2023-01-24T12:14:10Z"}],"oa_version":"Published Version","type":"journal_article","issue":"9","abstract":[{"lang":"eng","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."}]},{"file_date_updated":"2022-07-29T10:17:10Z","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","author":[{"full_name":"Zisis, Themistoklis","first_name":"Themistoklis","last_name":"Zisis"},{"full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d","orcid":"0000-0001-7205-2975","first_name":"David","last_name":"Brückner"},{"first_name":"Tom","last_name":"Brandstätter","full_name":"Brandstätter, Tom"},{"full_name":"Siow, Wei Xiong","first_name":"Wei Xiong","last_name":"Siow"},{"full_name":"d’Alessandro, Joseph","first_name":"Joseph","last_name":"d’Alessandro"},{"full_name":"Vollmar, Angelika M.","first_name":"Angelika M.","last_name":"Vollmar"},{"full_name":"Broedersz, Chase P.","first_name":"Chase P.","last_name":"Broedersz"},{"full_name":"Zahler, Stefan","first_name":"Stefan","last_name":"Zahler"}],"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","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"publisher":"Elsevier","month":"01","publication_identifier":{"issn":["0006-3495"]},"doi":"10.1016/j.bpj.2021.12.006","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"},"oa":1,"external_id":{"isi":["000740815400007"]},"isi":1,"quality_controlled":"1","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"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","type":"journal_article","oa_version":"Published Version","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","content_type":"application/pdf","file_size":4475504,"creator":"dernst"}],"_id":"10530","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration","status":"public","ddc":["570"],"intvolume":" 121","day":"04","article_processing_charge":"No","has_accepted_license":"1","keyword":["Biophysics"],"date_published":"2022-01-04T00:00:00Z","publication":"Biophysical Journal","citation":{"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.","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","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."},"article_type":"original","page":"P44-60"},{"type":"journal_article","abstract":[{"text":"Predicting function from sequence is a central problem of biology. Currently, this is possible only locally in a narrow mutational neighborhood around a wildtype sequence rather than globally from any sequence. Using random mutant libraries, we developed a biophysical model that accounts for multiple features of σ70 binding bacterial promoters to predict constitutive gene expression levels from any sequence. We experimentally and theoretically estimated that 10–20% of random sequences lead to expression and ~80% of non-expressing sequences are one mutation away from a functional promoter. The potential for generating expression from random sequences is so pervasive that selection acts against σ70-RNA polymerase binding sites even within inter-genic, promoter-containing regions. This pervasiveness of σ70-binding sites implies that emergence of promoters is not the limiting step in gene regulatory evolution. Ultimately, the inclusion of novel features of promoter function into a mechanistic model enabled not only more accurate predictions of gene expression levels, but also identified that promoters evolve more rapidly than previously thought.","lang":"eng"}],"status":"public","title":"Predicting bacterial promoter function and evolution from random sequences","ddc":["576"],"intvolume":" 11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"10736","oa_version":"Published Version","file":[{"creator":"cchlebak","content_type":"application/pdf","file_size":5604343,"access_level":"open_access","file_name":"2022_ELife_Lagator.pdf","success":1,"checksum":"decdcdf600ff51e9a9703b49ca114170","date_updated":"2022-02-07T07:14:09Z","date_created":"2022-02-07T07:14:09Z","file_id":"10739","relation":"main_file"}],"scopus_import":"1","day":"26","has_accepted_license":"1","article_processing_charge":"No","article_type":"original","publication":"eLife","citation":{"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.","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","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."},"date_published":"2022-01-26T00:00:00Z","article_number":"e64543","file_date_updated":"2022-02-07T07:14:09Z","ec_funded":1,"publication_status":"published","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"NiBa"}],"publisher":"eLife Sciences Publications","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.","pmid":1,"date_updated":"2023-08-02T14:09:02Z","date_created":"2022-02-06T23:01:32Z","volume":11,"author":[{"first_name":"Mato","last_name":"Lagator","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato"},{"full_name":"Sarikas, Srdjan","first_name":"Srdjan","last_name":"Sarikas","id":"35F0286E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Magdalena","last_name":"Steinrueck","full_name":"Steinrueck, Magdalena"},{"full_name":"Toledo-Aparicio, David","last_name":"Toledo-Aparicio","first_name":"David"},{"orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P","full_name":"Bollback, Jonathan P"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"}],"month":"01","publication_identifier":{"eissn":["2050-084X"]},"isi":1,"quality_controlled":"1","project":[{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"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":["000751104400001"],"pmid":["35080492"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.7554/eLife.64543"},{"date_published":"2022-12-21T00:00:00Z","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.","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","article_processing_charge":"No","has_accepted_license":"1","day":"21","scopus_import":"1","oa_version":"Published Version","file":[{"checksum":"5d7f1111a87e5f2c1bf92f8886738894","success":1,"date_created":"2023-01-23T08:46:40Z","date_updated":"2023-01-23T08:46:40Z","relation":"main_file","file_id":"12337","content_type":"application/pdf","file_size":4248838,"creator":"dernst","access_level":"open_access","file_name":"2022_PloSBiology_Mlynarski.pdf"}],"intvolume":" 20","title":"Efficient coding theory of dynamic attentional modulation","ddc":["570"],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12332","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","language":[{"iso":"eng"}],"doi":"10.1371/journal.pbio.3001889","project":[{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"external_id":{"isi":["000925192000001"]},"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,"publication_identifier":{"eissn":["1545-7885"]},"month":"12","volume":20,"date_created":"2023-01-22T23:00:55Z","date_updated":"2023-08-03T14:23:49Z","author":[{"first_name":"Wiktor F","last_name":"Mlynarski","id":"358A453A-F248-11E8-B48F-1D18A9856A87","full_name":"Mlynarski, Wiktor F"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"1","first_name":"Gašper","last_name":"Tkačik"}],"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.","ec_funded":1,"file_date_updated":"2023-01-23T08:46:40Z"},{"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Proceedings of the National Academy of Sciences","publication_status":"published","pmid":1,"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.”","year":"2022","volume":119,"date_updated":"2024-03-06T14:22:51Z","date_created":"2022-09-11T22:01:55Z","related_material":{"record":[{"id":"15020","relation":"dissertation_contains","status":"public"}]},"author":[{"id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","first_name":"Michal","full_name":"Hledik, Michal"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"1","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper"}],"article_number":"e2123152119","ec_funded":1,"file_date_updated":"2022-09-12T08:08:12Z","project":[{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"}],"isi":1,"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":{"pmid":["36037343"],"isi":["000889278400014"]},"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2123152119","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"month":"08","intvolume":" 119","ddc":["570"],"status":"public","title":"Accumulation and maintenance of information in evolution","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12081","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"2022_PNAS_Hledik.pdf","content_type":"application/pdf","file_size":2165752,"creator":"dernst","relation":"main_file","file_id":"12091","checksum":"6dec51f6567da9039982a571508a8e4d","success":1,"date_created":"2022-09-12T08:08:12Z","date_updated":"2022-09-12T08:08:12Z"}],"type":"journal_article","issue":"36","abstract":[{"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.","lang":"eng"}],"article_type":"original","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","date_published":"2022-08-29T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"29"},{"day":"01","article_processing_charge":"No","has_accepted_license":"1","scopus_import":"1","date_published":"2021-12-01T00:00:00Z","publication":"PLoS Computational Biology","citation":{"short":"K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).","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.","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","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.","ista":"Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 17(12), e1009661."},"article_type":"original","abstract":[{"lang":"eng","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."}],"issue":"12","type":"journal_article","file":[{"file_id":"11383","relation":"main_file","date_created":"2022-05-16T08:53:11Z","date_updated":"2022-05-16T08:53:11Z","success":1,"checksum":"dcd185d4f7e0acee25edf1d6537f447e","file_name":"2021_PLOsComBio_Bodova.pdf","access_level":"open_access","creator":"dernst","file_size":2299486,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10535","ddc":["570"],"title":"Dynamic maximum entropy provides accurate approximation of structured population dynamics","status":"public","intvolume":" 17","month":"12","publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"doi":"10.1371/journal.pcbi.1009661","acknowledged_ssus":[{"_id":"ScienComp"}],"language":[{"iso":"eng"}],"external_id":{"pmid":["34851948"],"arxiv":["2102.03669"]},"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","file_date_updated":"2022-05-16T08:53:11Z","article_number":"e1009661","author":[{"full_name":"Bod'ová, Katarína","orcid":"0000-0002-7214-0171","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bod'ová","first_name":"Katarína"},{"id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","last_name":"Szep","full_name":"Szep, Eniko"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"}],"date_created":"2021-12-12T23:01:27Z","date_updated":"2022-08-01T10:48:04Z","volume":17,"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,"publication_status":"published","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publisher":"Public Library of Science"},{"main_file_link":[{"url":"https://arxiv.org/abs/2108.06686","open_access":"1"}],"external_id":{"arxiv":["2108.06686"]},"citation":{"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.).","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.","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","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.","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","ieee":"F. Lombardi, S. Pepic, O. Shriki, G. Tkačik, and D. De Martino, “Quantifying the coexistence of neuronal oscillations and avalanches.” arXiv."},"oa":1,"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","name":"Efficient coding with biophysical realism"}],"page":"37","date_published":"2021-08-17T00:00:00Z","doi":"10.48550/ARXIV.2108.06686","language":[{"iso":"eng"}],"article_processing_charge":"No","day":"17","month":"08","year":"2021","_id":"10912","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","department":[{"_id":"GaTk"}],"publisher":"arXiv","publication_status":"submitted","ddc":["570"],"title":"Quantifying the coexistence of neuronal oscillations and avalanches","status":"public","author":[{"full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425","orcid":"0000-0003-2623-5249","first_name":"Fabrizio","last_name":"Lombardi"},{"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"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"},{"first_name":"Daniele","last_name":"De Martino","full_name":"De Martino, Daniele"}],"oa_version":"Preprint","date_created":"2022-03-21T11:41:28Z","date_updated":"2022-03-22T07:53:18Z","type":"preprint","ec_funded":1,"abstract":[{"lang":"eng","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."}]},{"author":[{"last_name":"Kavcic","first_name":"Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"oa_version":"Preprint","date_updated":"2023-05-03T10:54:05Z","date_created":"2021-12-28T06:52:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10579","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.","year":"2021","department":[{"_id":"GaTk"}],"status":"public","publication_status":"submitted","title":"Token-driven totally asymmetric simple exclusion process","ddc":["530"],"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":{"chicago":"Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Process.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2112.13558.","short":"B. Kavcic, G. Tkačik, ArXiv (n.d.).","mla":"Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Process.” ArXiv, 2112.13558, doi:10.48550/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. .","ista":"Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion process. arXiv, 2112.13558.","ama":"Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion process. arXiv. doi:10.48550/arXiv.2112.13558"},"oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/2112.13558","open_access":"1"}],"publication":"arXiv","has_accepted_license":"1","article_processing_charge":"No","month":"12","day":"27"},{"ec_funded":1,"author":[{"full_name":"Lombardi, Fabrizio","last_name":"Lombardi","first_name":"Fabrizio","orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"full_name":"Shriki, Oren","last_name":"Shriki","first_name":"Oren"},{"full_name":"Herrmann, Hans J","first_name":"Hans J","last_name":"Herrmann"},{"last_name":"de Arcangelis","first_name":"Lucilla","full_name":"de Arcangelis, Lucilla"}],"date_updated":"2023-08-04T10:46:29Z","date_created":"2020-02-06T16:09:14Z","volume":461,"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","month":"05","publication_identifier":{"issn":["0925-2312"],"eissn":["1872-8286"]},"doi":"10.1016/j.neucom.2020.05.126","language":[{"iso":"eng"}],"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","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","_id":"7463","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Long-range temporal correlations in the broadband resting state activity of the human brain revealed by neuronal avalanches","intvolume":" 461","day":"13","article_processing_charge":"No","scopus_import":"1","date_published":"2021-05-13T00:00:00Z","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_updated":"2023-08-07T13:57:30Z","date_created":"2021-03-07T23:01:25Z","volume":148,"author":[{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"}],"publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"The Company of Biologists","acknowledgement":"This work was supported in part by the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030), by the National Institutes of Health (R01GM097275) and by the Fonds zur Förderung der wissenschaftlichen Forschung (FWF P28844). Deposited in PMC for release after 12 months.","year":"2021","pmid":1,"article_number":"dev176065","language":[{"iso":"eng"}],"doi":"10.1242/dev.176065","isi":1,"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"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/dev.176065"}],"external_id":{"pmid":["33526425"],"isi":["000613906000007"]},"month":"02","publication_identifier":{"eissn":["1477-9129"]},"oa_version":"Published Version","title":"The many bits of positional information","status":"public","intvolume":" 148","_id":"9226","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"Half a century after Lewis Wolpert's seminal conceptual advance on how cellular fates distribute in space, we provide a brief historical perspective on how the concept of positional information emerged and influenced the field of developmental biology and beyond. We focus on a modern interpretation of this concept in terms of information theory, largely centered on its application to cell specification in the early Drosophila embryo. We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?","lang":"eng"}],"issue":"2","type":"journal_article","date_published":"2021-02-01T00:00:00Z","article_type":"original","publication":"Development","citation":{"ieee":"G. Tkačik and T. Gregor, “The many bits of positional information,” Development, vol. 148, no. 2. The Company of Biologists, 2021.","apa":"Tkačik, G., & Gregor, T. (2021). The many bits of positional information. Development. The Company of Biologists. https://doi.org/10.1242/dev.176065","ista":"Tkačik G, Gregor T. 2021. The many bits of positional information. Development. 148(2), dev176065.","ama":"Tkačik G, Gregor T. The many bits of positional information. Development. 2021;148(2). doi:10.1242/dev.176065","chicago":"Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” Development. The Company of Biologists, 2021. https://doi.org/10.1242/dev.176065.","short":"G. Tkačik, T. Gregor, Development 148 (2021).","mla":"Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” Development, vol. 148, no. 2, dev176065, The Company of Biologists, 2021, doi:10.1242/dev.176065."},"day":"01","article_processing_charge":"No","scopus_import":"1"},{"language":[{"iso":"eng"}],"doi":"10.1038/s41593-021-00846-0","quality_controlled":"1","isi":1,"project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"main_file_link":[{"url":"https://doi.org/10.1101/669200 ","open_access":"1"}],"external_id":{"isi":["000652577300003"]},"oa":1,"month":"05","publication_identifier":{"eissn":["1546-1726"],"issn":["1097-6256"]},"date_updated":"2023-08-08T13:51:14Z","date_created":"2021-05-30T22:01:24Z","volume":24,"author":[{"full_name":"Mlynarski, Wiktor F","last_name":"Mlynarski","first_name":"Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hermundstad, Ann M.","first_name":"Ann M.","last_name":"Hermundstad"}],"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"GaTk"}],"year":"2021","acknowledgement":"We thank D. Kastner and T. Münch for generously providing figures from their work. We also thank V. Jayaraman, M. Noorman, T. Ma, and K. Krishnamurthy for useful discussions and feedback on the manuscript. W.F.M. was funded by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie Grant Agreement No. 754411. A.M.H. was supported by the Howard Hughes Medical Institute.","ec_funded":1,"date_published":"2021-05-20T00:00:00Z","article_type":"original","page":"998-1009","publication":"Nature Neuroscience","citation":{"mla":"Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience, vol. 24, Springer Nature, 2021, pp. 998–1009, doi:10.1038/s41593-021-00846-0.","short":"W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.","chicago":"Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00846-0.","ama":"Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0","ista":"Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes. Nature Neuroscience. 24, 998–1009.","ieee":"W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,” Nature Neuroscience, vol. 24. Springer Nature, pp. 998–1009, 2021.","apa":"Mlynarski, W. F., & Hermundstad, A. M. (2021). Efficient and adaptive sensory codes. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-021-00846-0"},"day":"20","article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","title":"Efficient and adaptive sensory codes","status":"public","intvolume":" 24","_id":"9439","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"The ability to adapt to changes in stimulus statistics is a hallmark of sensory systems. Here, we developed a theoretical framework that can account for the dynamics of adaptation from an information processing perspective. We use this framework to optimize and analyze adaptive sensory codes, and we show that codes optimized for stationary environments can suffer from prolonged periods of poor performance when the environment changes. To mitigate the adversarial effects of these environmental changes, sensory systems must navigate tradeoffs between the ability to accurately encode incoming stimuli and the ability to rapidly detect and adapt to changes in the distribution of these stimuli. We derive families of codes that balance these objectives, and we demonstrate their close match to experimentally observed neural dynamics during mean and variance adaptation. Our results provide a unifying perspective on adaptation across a range of sensory systems, environments, and sensory tasks."}],"type":"journal_article"},{"day":"04","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","date_published":"2021-08-04T00:00:00Z","article_type":"original","page":"35545–35560","publication":"ACS Applied Materials and Interfaces","citation":{"apa":"Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.1c09850","ieee":"T. Zisis et al., “Sequential and switchable patterning for studying cellular processes under spatiotemporal control,” ACS Applied Materials and Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.","ista":"Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 13(30), 35545–35560.","ama":"Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850","chicago":"Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850.","short":"T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560.","mla":"Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:10.1021/acsami.1c09850."},"abstract":[{"text":"Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science.","lang":"eng"}],"issue":"30","type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"9833","date_updated":"2021-08-09T09:44:03Z","date_created":"2021-08-09T09:44:03Z","checksum":"b043a91d9f9200e467b970b692687ed3","success":1,"file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf","access_level":"open_access","file_size":7123293,"content_type":"application/pdf","creator":"asandaue"}],"title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","ddc":["620","570"],"status":"public","intvolume":" 13","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9822","month":"08","publication_identifier":{"issn":["19448244"],"eissn":["19448252"]},"language":[{"iso":"eng"}],"doi":"10.1021/acsami.1c09850","isi":1,"quality_controlled":"1","project":[{"name":"Cellular navigation along spatial gradients","call_identifier":"H2020","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"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,"external_id":{"isi":["000683741400026"],"pmid":["34283577"]},"file_date_updated":"2021-08-09T09:44:03Z","ec_funded":1,"date_updated":"2023-08-10T14:22:48Z","date_created":"2021-08-08T22:01:28Z","volume":13,"author":[{"full_name":"Zisis, Themistoklis","first_name":"Themistoklis","last_name":"Zisis"},{"first_name":"Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan"},{"full_name":"Balles, Miriam","last_name":"Balles","first_name":"Miriam"},{"full_name":"Kretschmer, Maibritt","last_name":"Kretschmer","first_name":"Maibritt"},{"full_name":"Nemethova, Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Nemethova"},{"full_name":"Chait, Remy P","first_name":"Remy P","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","first_name":"Robert","last_name":"Hauschild","full_name":"Hauschild, Robert"},{"full_name":"Lange, Janina","last_name":"Lange","first_name":"Janina"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"last_name":"Zahler","first_name":"Stefan","full_name":"Zahler, Stefan"}],"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"acknowledgement":"We would like to thank Charlott Leu for the production of our chromium wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim Rädler for his valuable scientific guidance.","year":"2021","pmid":1},{"oa_version":"Preprint","_id":"9828","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Fast and accurate amplitude demodulation of wideband signals","status":"public","intvolume":" 69","abstract":[{"text":"Amplitude demodulation is a classical operation used in signal processing. For a long time, its effective applications in practice have been limited to narrowband signals. In this work, we generalize amplitude demodulation to wideband signals. We pose demodulation as a recovery problem of an oversampled corrupted signal and introduce special iterative schemes belonging to the family of alternating projection algorithms to solve it. Sensibly chosen structural assumptions on the demodulation outputs allow us to reveal the high inferential accuracy of the method over a rich set of relevant signals. This new approach surpasses current state-of-the-art demodulation techniques apt to wideband signals in computational efficiency by up to many orders of magnitude with no sacrifice in quality. Such performance opens the door for applications of the amplitude demodulation procedure in new contexts. In particular, the new method makes online and large-scale offline data processing feasible, including the calculation of modulator-carrier pairs in higher dimensions and poor sampling conditions, independent of the signal bandwidth. We illustrate the utility and specifics of applications of the new method in practice by using natural speech and synthetic signals.","lang":"eng"}],"type":"journal_article","date_published":"2021-06-09T00:00:00Z","publication":"IEEE Transactions on Signal Processing","citation":{"ista":"Gabrielaitis M. 2021. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 69, 4039–4054.","apa":"Gabrielaitis, M. (2021). Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/TSP.2021.3087899","ieee":"M. Gabrielaitis, “Fast and accurate amplitude demodulation of wideband signals,” IEEE Transactions on Signal Processing, vol. 69. Institute of Electrical and Electronics Engineers, pp. 4039–4054, 2021.","ama":"Gabrielaitis M. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 2021;69:4039-4054. doi:10.1109/TSP.2021.3087899","chicago":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/TSP.2021.3087899.","mla":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing, vol. 69, Institute of Electrical and Electronics Engineers, 2021, pp. 4039–54, doi:10.1109/TSP.2021.3087899.","short":"M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054."},"article_type":"original","page":"4039 - 4054","day":"09","article_processing_charge":"No","scopus_import":"1","author":[{"full_name":"Gabrielaitis, Mantas","last_name":"Gabrielaitis","first_name":"Mantas","orcid":"0000-0002-7758-2016","id":"4D5B0CBC-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-08-10T14:19:33Z","date_created":"2021-08-08T22:01:31Z","volume":69,"acknowledgement":"The author thanks his colleagues K. Huszár and G. Tkačik for valuable discussions and comments on the manuscript.","year":"2021","publication_status":"published","department":[{"_id":"GaTk"}],"publisher":"Institute of Electrical and Electronics Engineers","doi":"10.1109/TSP.2021.3087899","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000682123900002"],"arxiv":["2102.04832"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.04832"}],"quality_controlled":"1","isi":1,"month":"06","publication_identifier":{"issn":["1053-587X"],"eissn":["1941-0476"]}},{"ddc":["570"],"status":"public","title":"Inferring the function performed by a recurrent neural network","intvolume":" 16","_id":"9362","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"file_id":"9371","relation":"main_file","date_updated":"2021-05-04T13:22:19Z","date_created":"2021-05-04T13:22:19Z","success":1,"checksum":"c52da133850307d2031f552d998f00e8","file_name":"2021_pone_Chalk.pdf","access_level":"open_access","creator":"kschuh","content_type":"application/pdf","file_size":2768282}],"type":"journal_article","abstract":[{"text":"A central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose an inverse reinforcement learning (RL) framework for inferring the function performed by a neural network from data. We assume that the responses of each neuron in a network are optimised so as to drive the network towards ‘rewarded’ states, that are desirable for performing a given function. We then show how one can use inverse RL to infer the reward function optimised by the network from observing its responses. This inferred reward function can be used to predict how the neural network should adapt its dynamics to perform the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death and/or varying sensory stimulus statistics.","lang":"eng"}],"issue":"4","article_type":"original","publication":"PLoS ONE","citation":{"ama":"Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. PLoS ONE. 2021;16(4). doi:10.1371/journal.pone.0248940","ieee":"M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” PLoS ONE, vol. 16, no. 4. Public Library of Science, 2021.","apa":"Chalk, M. J., Tkačik, G., & Marre, O. (2021). Inferring the function performed by a recurrent neural network. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0248940","ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940.","short":"M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).","mla":"Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:10.1371/journal.pone.0248940.","chicago":"Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0248940."},"date_published":"2021-04-15T00:00:00Z","scopus_import":"1","day":"15","article_processing_charge":"No","has_accepted_license":"1","publication_status":"published","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"year":"2021","acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","pmid":1,"date_updated":"2023-10-18T08:17:42Z","date_created":"2021-05-02T22:01:28Z","volume":16,"author":[{"first_name":"Matthew J","last_name":"Chalk","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"}],"article_number":"e0248940","file_date_updated":"2021-05-04T13:22:19Z","quality_controlled":"1","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000641474900072"],"pmid":["33857170"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0248940","month":"04","publication_identifier":{"eissn":["19326203"]}},{"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":["000608045000010"]},"project":[{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","grant_number":"P27201-B22","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"doi":"10.1371/journal.pcbi.1008529","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1553-7358"]},"month":"01","year":"2021","acknowledgement":"This work was supported in part by Tum stipend of Knafelj foundation (to B.K.), Austrian Science Fund (FWF) standalone grants P 27201-B22 (to T.B.) and P 28844(to G.T.), HFSP program Grant RGP0042/2013 (to T.B.), German Research Foundation (DFG) individual grant BO 3502/2-1 (to T.B.), and German Research Foundation (DFG) Collaborative Research Centre (SFB) 1310 (to T.B.). ","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publication_status":"published","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"7673"},{"status":"public","relation":"research_data","id":"8930"}]},"author":[{"full_name":"Kavcic, Bor","orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","first_name":"Bor"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Tobias","full_name":"Bollenbach, Tobias"}],"volume":17,"date_updated":"2024-02-21T12:41:41Z","date_created":"2021-01-08T07:16:18Z","article_number":"e1008529","file_date_updated":"2021-02-04T12:30:48Z","citation":{"ista":"Kavcic B, Tkačik G, Bollenbach MT. 2021. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 17, e1008529.","apa":"Kavcic, B., Tkačik, G., & Bollenbach, M. T. (2021). Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1008529","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “Minimal biophysical model of combined antibiotic action,” PLOS Computational Biology, vol. 17. Public Library of Science, 2021.","ama":"Kavcic B, Tkačik G, Bollenbach MT. Minimal biophysical model of combined antibiotic action. PLOS Computational Biology. 2021;17. doi:10.1371/journal.pcbi.1008529","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “Minimal Biophysical Model of Combined Antibiotic Action.” PLOS Computational Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pcbi.1008529.","mla":"Kavcic, Bor, et al. “Minimal Biophysical Model of Combined Antibiotic Action.” PLOS Computational Biology, vol. 17, e1008529, Public Library of Science, 2021, doi:10.1371/journal.pcbi.1008529.","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, PLOS Computational Biology 17 (2021)."},"publication":"PLOS Computational Biology","article_type":"original","date_published":"2021-01-07T00:00:00Z","keyword":["Modelling and Simulation","Genetics","Molecular Biology","Antibiotics","Drug interactions"],"article_processing_charge":"Yes","has_accepted_license":"1","day":"07","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"8997","intvolume":" 17","title":"Minimal biophysical model of combined antibiotic action","status":"public","ddc":["570"],"file":[{"relation":"main_file","file_id":"9092","date_created":"2021-02-04T12:30:48Z","date_updated":"2021-02-04T12:30:48Z","checksum":"e29f2b42651bef8e034781de8781ffac","success":1,"file_name":"2021_PlosComBio_Kavcic.pdf","access_level":"open_access","file_size":3690053,"content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}]},{"doi":"10.7554/elife.65993","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":["000631050900001"]},"oa":1,"project":[{"_id":"2517526A-B435-11E9-9278-68D0E5697425","grant_number":"628377","name":"The Systems Biology of Transcriptional Read-Through in Bacteria: from Synthetic Networks to Genomic Studies","call_identifier":"FP7"},{"_id":"268BFA92-B435-11E9-9278-68D0E5697425","grant_number":"I03901","call_identifier":"FWF","name":"CyberCircuits: Cybergenetic circuits to test composability of gene networks"}],"isi":1,"quality_controlled":"1","publication_identifier":{"issn":["2050-084X"]},"month":"03","related_material":{"record":[{"status":"public","relation":"research_data","id":"8951"}]},"author":[{"last_name":"Nagy-Staron","first_name":"Anna A","orcid":"0000-0002-1391-8377","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","full_name":"Nagy-Staron, Anna A"},{"orcid":"0000-0003-3768-877X","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","last_name":"Tomasek","first_name":"Kathrin","full_name":"Tomasek, Kathrin"},{"full_name":"Caruso Carter, Caroline","last_name":"Caruso Carter","first_name":"Caroline"},{"first_name":"Elisabeth","last_name":"Sonnleitner","full_name":"Sonnleitner, Elisabeth"},{"orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","first_name":"Bor","full_name":"Kavcic, Bor"},{"last_name":"Paixão","first_name":"Tiago","full_name":"Paixão, Tiago"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","full_name":"Guet, Calin C"}],"volume":10,"date_updated":"2024-02-21T12:41:57Z","date_created":"2021-03-23T10:11:46Z","acknowledgement":"We thank J Bollback, L Hurst, M Lagator, C Nizak, O Rivoire, M Savageau, G Tkacik, and B Vicozo\r\nfor helpful discussions; A Dolinar and A Greshnova for technical assistance; T Bollenbach for supplying the strain JW0336; C Rusnac, and members of the Guet lab for comments. The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n˚\r\n628377 (ANS) and an Austrian Science Fund (FWF) grant n˚ I 3901-B32 (CCG).","year":"2021","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"publisher":"eLife Sciences Publications","publication_status":"published","ec_funded":1,"file_date_updated":"2021-03-23T10:12:58Z","article_number":"e65993","date_published":"2021-03-08T00:00:00Z","citation":{"short":"A.A. Nagy-Staron, K. Tomasek, C. Caruso Carter, E. Sonnleitner, B. Kavcic, T. Paixão, C.C. Guet, ELife 10 (2021).","mla":"Nagy-Staron, Anna A., et al. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” ELife, vol. 10, e65993, eLife Sciences Publications, 2021, doi:10.7554/elife.65993.","chicago":"Nagy-Staron, Anna A, Kathrin Tomasek, Caroline Caruso Carter, Elisabeth Sonnleitner, Bor Kavcic, Tiago Paixão, and Calin C Guet. “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.65993.","ama":"Nagy-Staron AA, Tomasek K, Caruso Carter C, et al. Local genetic context shapes the function of a gene regulatory network. eLife. 2021;10. doi:10.7554/elife.65993","ieee":"A. A. Nagy-Staron et al., “Local genetic context shapes the function of a gene regulatory network,” eLife, vol. 10. eLife Sciences Publications, 2021.","apa":"Nagy-Staron, A. A., Tomasek, K., Caruso Carter, C., Sonnleitner, E., Kavcic, B., Paixão, T., & Guet, C. C. (2021). Local genetic context shapes the function of a gene regulatory network. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.65993","ista":"Nagy-Staron AA, Tomasek K, Caruso Carter C, Sonnleitner E, Kavcic B, Paixão T, Guet CC. 2021. Local genetic context shapes the function of a gene regulatory network. eLife. 10, e65993."},"publication":"eLife","article_type":"original","article_processing_charge":"Yes","has_accepted_license":"1","day":"08","keyword":["Genetics and Molecular Biology"],"file":[{"relation":"main_file","file_id":"9284","date_updated":"2021-03-23T10:12:58Z","date_created":"2021-03-23T10:12:58Z","checksum":"3c2f44058c2dd45a5a1027f09d263f8e","success":1,"file_name":"elife-65993-v2.pdf","access_level":"open_access","content_type":"application/pdf","file_size":1390469,"creator":"bkavcic"}],"oa_version":"Published Version","_id":"9283","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 10","status":"public","title":"Local genetic context shapes the function of a gene regulatory network","ddc":["570"],"abstract":[{"lang":"eng","text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks (GRNs) remains a major challenge. Here, we use a well-defined synthetic GRN to study in Escherichia coli how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one GRN with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Transcriptional read-through is the main molecular mechanism that places one transcriptional unit (TU) within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual TUs, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of GRNs."}],"type":"journal_article"},{"oa_version":"Preprint","_id":"7553","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":" 109","status":"public","title":"Statistical analysis and optimality of neural systems","issue":"7","abstract":[{"text":"Normative theories and statistical inference provide complementary approaches for the study of biological systems. A normative theory postulates that organisms have adapted to efficiently solve essential tasks, and proceeds to mathematically work out testable consequences of such optimality; parameters that maximize the hypothesized organismal function can be derived ab initio, without reference to experimental data. In contrast, statistical inference focuses on efficient utilization of data to learn model parameters, without reference to any a priori notion of biological function, utility, or fitness. Traditionally, these two approaches were developed independently and applied separately. Here we unify them in a coherent Bayesian framework that embeds a normative theory into a family of maximum-entropy “optimization priors.” This family defines a smooth interpolation between a data-rich inference regime (characteristic of “bottom-up” statistical models), and a data-limited ab inito prediction regime (characteristic of “top-down” normative theory). We demonstrate the applicability of our framework using data from the visual cortex, and argue that the flexibility it affords is essential to address a number of fundamental challenges relating to inference and prediction in complex, high-dimensional biological problems.","lang":"eng"}],"type":"journal_article","date_published":"2021-04-07T00:00:00Z","citation":{"apa":"Mlynarski, W. F., Hledik, M., Sokolowski, T. R., & Tkačik, G. (2021). Statistical analysis and optimality of neural systems. Neuron. Cell Press. https://doi.org/10.1016/j.neuron.2021.01.020","ieee":"W. F. Mlynarski, M. Hledik, T. R. Sokolowski, and G. Tkačik, “Statistical analysis and optimality of neural systems,” Neuron, vol. 109, no. 7. Cell Press, p. 1227–1241.e5, 2021.","ista":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. 2021. Statistical analysis and optimality of neural systems. Neuron. 109(7), 1227–1241.e5.","ama":"Mlynarski WF, Hledik M, Sokolowski TR, Tkačik G. Statistical analysis and optimality of neural systems. Neuron. 2021;109(7):1227-1241.e5. doi:10.1016/j.neuron.2021.01.020","chicago":"Mlynarski, Wiktor F, Michal Hledik, Thomas R Sokolowski, and Gašper Tkačik. “Statistical Analysis and Optimality of Neural Systems.” Neuron. Cell Press, 2021. https://doi.org/10.1016/j.neuron.2021.01.020.","short":"W.F. Mlynarski, M. Hledik, T.R. Sokolowski, G. Tkačik, Neuron 109 (2021) 1227–1241.e5.","mla":"Mlynarski, Wiktor F., et al. “Statistical Analysis and Optimality of Neural Systems.” Neuron, vol. 109, no. 7, Cell Press, 2021, p. 1227–1241.e5, doi:10.1016/j.neuron.2021.01.020."},"publication":"Neuron","page":"1227-1241.e5","article_processing_charge":"No","day":"07","scopus_import":"1","related_material":{"record":[{"id":"15020","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/can-evolution-be-predicted/"}]},"author":[{"full_name":"Mlynarski, Wiktor F","id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F","last_name":"Mlynarski"},{"last_name":"Hledik","first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal"},{"full_name":"Sokolowski, Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1287-3779","first_name":"Thomas R","last_name":"Sokolowski"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper"}],"volume":109,"date_created":"2020-02-28T11:00:12Z","date_updated":"2024-03-06T14:22:51Z","year":"2021","acknowledgement":"The authors thank Dario Ringach for providing the V1 receptive fields and Olivier Marre for providing the retinal receptive fields. W.M. was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 754411. M.H. was funded in part by Human Frontiers Science grant no. HFSP RGP0032/2018.","department":[{"_id":"GaTk"}],"publisher":"Cell Press","publication_status":"published","ec_funded":1,"doi":"10.1016/j.neuron.2021.01.020","language":[{"iso":"eng"}],"oa":1,"external_id":{"isi":["000637809600006"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/848374"}],"project":[{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"}],"quality_controlled":"1","isi":1,"month":"04"},{"month":"09","day":"29","article_processing_charge":"No","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"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","grant_number":"P34015","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6"}],"publication":"bioRxiv","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"},"citation":{"short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, BioRxiv (n.d.).","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2021.09.28.460602.","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2021.09.28.460602.","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. doi:10.1101/2021.09.28.460602","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” bioRxiv. Cold Spring Harbor Laboratory.","apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., & Savin, C. (n.d.). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.09.28.460602","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. bioRxiv, 10.1101/2021.09.28.460602."},"main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2021.09.28.460602"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1101/2021.09.28.460602","date_published":"2021-09-29T00:00:00Z","type":"preprint","abstract":[{"text":"Although much is known about how single neurons in the hippocampus represent an animal’s position, how cell-cell interactions contribute to spatial coding remains poorly understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured cell-to-cell interactions whose statistics depend on familiar vs. novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the signal-to-noise ratio of their spatial inputs. Moreover, the topology of the interactions facilitates linear decodability, making the information easy to read out by downstream circuits. These findings suggest that the efficient coding hypothesis is not applicable only to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.","lang":"eng"}],"ec_funded":1,"title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience","publication_status":"submitted","status":"public","department":[{"_id":"GradSch"},{"_id":"JoCs"},{"_id":"GaTk"}],"publisher":"Cold Spring Harbor Laboratory","_id":"10077","acknowledgement":"We thank Peter Baracskay, Karola Kaefer and Hugo Malagon-Vina for the acquisition of the data. We thank Federico Stella for comments on an earlier version of the manuscript. MN was supported by European Union Horizon 2020 grant 665385, JC was supported by European Research Council consolidator grant 281511, GT was supported by the Austrian Science Fund (FWF) grant P34015, CS was supported by an IST fellow grant, National Institute of Mental Health Award 1R01MH125571-01, by the National Science Foundation under NSF Award No. 1922658 and a Google faculty award.","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2021","date_created":"2021-10-04T06:23:34Z","date_updated":"2024-03-28T23:30:16Z","oa_version":"Preprint","author":[{"id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","first_name":"Michele","last_name":"Nardin","full_name":"Nardin, Michele"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","first_name":"Cristina","full_name":"Savin, Cristina"}],"related_material":{"record":[{"id":"11932","status":"public","relation":"dissertation_contains"}]}},{"oa_version":"Published Version","file":[{"relation":"main_file","file_id":"8144","date_updated":"2020-07-22T06:17:11Z","date_created":"2020-07-22T06:17:11Z","success":1,"file_name":"2020_EPJWebConf_Lombardi.pdf","access_level":"open_access","file_size":2197543,"content_type":"application/pdf","creator":"dernst"}],"_id":"8105","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 230","status":"public","ddc":["530"],"title":"Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality","abstract":[{"text":"Physical and biological systems often exhibit intermittent dynamics with bursts or avalanches (active states) characterized by power-law size and duration distributions. These emergent features are typical of systems at the critical point of continuous phase transitions, and have led to the hypothesis that such systems may self-organize at criticality, i.e. without any fine tuning of parameters. Since the introduction of the Bak-Tang-Wiesenfeld (BTW) model, the paradigm of self-organized criticality (SOC) has been very fruitful for the analysis of emergent collective behaviors in a number of systems, including the brain. Although considerable effort has been devoted in identifying and modeling scaling features of burst and avalanche statistics, dynamical aspects related to the temporal organization of bursts remain often poorly understood or controversial. Of crucial importance to understand the mechanisms responsible for emergent behaviors is the relationship between active and quiet periods, and the nature of the correlations. Here we investigate the dynamics of active (θ-bursts) and quiet states (δ-bursts) in brain activity during the sleep-wake cycle. We show the duality of power-law (θ, active phase) and exponential-like (δ, quiescent phase) duration distributions, typical of SOC, jointly emerge with power-law temporal correlations and anti-correlated coupling between active and quiet states. Importantly, we demonstrate that such temporal organization shares important similarities with earthquake dynamics, and propose that specific power-law correlations and coupling between active and quiet states are distinctive characteristics of a class of systems with self-organization at criticality.","lang":"eng"}],"type":"journal_article","date_published":"2020-03-11T00:00:00Z","citation":{"ieee":"F. Lombardi, J. W. J. L. Wang, X. Zhang, and P. C. Ivanov, “Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality,” EPJ Web of Conferences, vol. 230. EDP Sciences, 2020.","apa":"Lombardi, F., Wang, J. W. J. L., Zhang, X., & Ivanov, P. C. (2020). Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality. EPJ Web of Conferences. EDP Sciences. https://doi.org/10.1051/epjconf/202023000005","ista":"Lombardi F, Wang JWJL, Zhang X, Ivanov PC. 2020. Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality. EPJ Web of Conferences. 230, 00005.","ama":"Lombardi F, Wang JWJL, Zhang X, Ivanov PC. Power-law correlations and coupling of active and quiet states underlie a class of complex systems with self-organization at criticality. EPJ Web of Conferences. 2020;230. doi:10.1051/epjconf/202023000005","chicago":"Lombardi, Fabrizio, Jilin W.J.L. Wang, Xiyun Zhang, and Plamen Ch Ivanov. “Power-Law Correlations and Coupling of Active and Quiet States Underlie a Class of Complex Systems with Self-Organization at Criticality.” EPJ Web of Conferences. EDP Sciences, 2020. https://doi.org/10.1051/epjconf/202023000005.","short":"F. Lombardi, J.W.J.L. Wang, X. Zhang, P.C. Ivanov, EPJ Web of Conferences 230 (2020).","mla":"Lombardi, Fabrizio, et al. “Power-Law Correlations and Coupling of Active and Quiet States Underlie a Class of Complex Systems with Self-Organization at Criticality.” EPJ Web of Conferences, vol. 230, 00005, EDP Sciences, 2020, doi:10.1051/epjconf/202023000005."},"publication":"EPJ Web of Conferences","article_type":"original","article_processing_charge":"No","has_accepted_license":"1","day":"11","author":[{"orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425","last_name":"Lombardi","first_name":"Fabrizio","full_name":"Lombardi, Fabrizio"},{"full_name":"Wang, Jilin W.J.L.","first_name":"Jilin W.J.L.","last_name":"Wang"},{"full_name":"Zhang, Xiyun","first_name":"Xiyun","last_name":"Zhang"},{"last_name":"Ivanov","first_name":"Plamen Ch","full_name":"Ivanov, Plamen Ch"}],"volume":230,"date_updated":"2021-01-12T08:16:55Z","date_created":"2020-07-12T16:20:33Z","year":"2020","department":[{"_id":"GaTk"}],"publisher":"EDP Sciences","publication_status":"published","file_date_updated":"2020-07-22T06:17:11Z","article_number":"00005","doi":"10.1051/epjconf/202023000005","language":[{"iso":"eng"}],"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","publication_identifier":{"issn":["2100-014X"]},"month":"03"}]