[{"page":"1633 - 1643","publication_status":"published","quality_controlled":"1","file":[{"content_type":"application/pdf","file_name":"2018_NatureEcology_Igler.pdf","file_id":"7830","access_level":"open_access","date_created":"2020-05-14T11:28:52Z","file_size":1135973,"date_updated":"2020-07-14T12:47:37Z","checksum":"383a2e2c944a856e2e821ec8e7bf71b6","creator":"dernst","relation":"main_file"}],"publication":"Nature Ecology and Evolution","title":"Evolutionary potential of transcription factors for gene regulatory rewiring","author":[{"first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia","last_name":"Igler","orcid":"0000-0001-7777-546X"},{"first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","last_name":"Lagator"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"}],"date_published":"2018-09-10T00:00:00Z","related_material":{"record":[{"id":"5585","status":"public","relation":"popular_science"},{"status":"public","id":"6371","relation":"dissertation_contains"}]},"article_type":"original","date_updated":"2026-08-31T22:30:42Z","issue":"10","volume":2,"abstract":[{"lang":"eng","text":"Gene regulatory networks evolve through rewiring of individual components—that is, through changes in regulatory connections. However, the mechanistic basis of regulatory rewiring is poorly understood. Using a canonical gene regulatory system, we quantify the properties of transcription factors that determine the evolutionary potential for rewiring of regulatory connections: robustness, tunability and evolvability. In vivo repression measurements of two repressors at mutated operator sites reveal their contrasting evolutionary potential: while robustness and evolvability were positively correlated, both were in trade-off with tunability. Epistatic interactions between adjacent operators alleviated this trade-off. A thermodynamic model explains how the differences in robustness, tunability and evolvability arise from biophysical characteristics of repressor–DNA binding. The model also uncovers that the energy matrix, which describes how mutations affect repressor–DNA binding, encodes crucial information about the evolutionary potential of a repressor. The biophysical determinants of evolutionary potential for regulatory rewiring constitute a mechanistic framework for understanding network evolution."}],"month":"09","isi":1,"oa_version":"Submitted Version","has_accepted_license":"1","type":"journal_article","citation":{"ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Evolutionary potential of transcription factors for gene regulatory rewiring. Nature Ecology and Evolution. 2(10), 1633–1643.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, Nature Ecology and Evolution 2 (2018) 1633–1643.","mla":"Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” <i>Nature Ecology and Evolution</i>, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:<a href=\"https://doi.org/10.1038/s41559-018-0651-y\">10.1038/s41559-018-0651-y</a>.","ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Evolutionary potential of transcription factors for gene regulatory rewiring,” <i>Nature Ecology and Evolution</i>, vol. 2, no. 10. Nature Publishing Group, pp. 1633–1643, 2018.","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” <i>Nature Ecology and Evolution</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41559-018-0651-y\">https://doi.org/10.1038/s41559-018-0651-y</a>.","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Evolutionary potential of transcription factors for gene regulatory rewiring. <i>Nature Ecology and Evolution</i>. 2018;2(10):1633-1643. doi:<a href=\"https://doi.org/10.1038/s41559-018-0651-y\">10.1038/s41559-018-0651-y</a>","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., &#38; Guet, C. C. (2018). Evolutionary potential of transcription factors for gene regulatory rewiring. <i>Nature Ecology and Evolution</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41559-018-0651-y\">https://doi.org/10.1038/s41559-018-0651-y</a>"},"article_processing_charge":"No","_id":"67","status":"public","ec_funded":1,"project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"648440"},{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture","grant_number":"24573"}],"year":"2018","intvolume":"         2","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"JoBo"}],"date_created":"2018-12-11T11:44:27Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","file_date_updated":"2020-07-14T12:47:37Z","oa":1,"external_id":{"isi":["000447947600021"]},"language":[{"iso":"eng"}],"publist_id":"7987","ddc":["570"],"scopus_import":"1","doi":"10.1038/s41559-018-0651-y","publisher":"Nature Publishing Group","day":"10"},{"type":"research_data","doi":"10.15479/AT:ISTA:108","article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","citation":{"ista":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. 2018. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>.","short":"C. Igler, M. Lagator, G. Tkačik, J.P. Bollback, C.C. Guet, (2018).","mla":"Igler, Claudia, et al. <i>Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>.","ieee":"C. Igler, M. Lagator, G. Tkačik, J. P. Bollback, and C. C. Guet, “Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring.” Institute of Science and Technology Austria, 2018.","chicago":"Igler, Claudia, Mato Lagator, Gašper Tkačik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:108\">https://doi.org/10.15479/AT:ISTA:108</a>.","ama":"Igler C, Lagator M, Tkačik G, Bollback JP, Guet CC. Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:108\">10.15479/AT:ISTA:108</a>","apa":"Igler, C., Lagator, M., Tkačik, G., Bollback, J. P., &#38; Guet, C. C. (2018). Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:108\">https://doi.org/10.15479/AT:ISTA:108</a>"},"day":"20","_id":"5585","status":"public","related_material":{"record":[{"relation":"research_paper","id":"67","status":"public"},{"status":"public","id":"6371","relation":"research_paper"}]},"abstract":[{"lang":"eng","text":"Mean repression values and standard error of the mean are given for all operator mutant libraries."}],"month":"07","date_updated":"2026-08-31T22:30:42Z","datarep_id":"108","has_accepted_license":"1","ddc":["576"],"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)"},"title":"Data for the paper Evolutionary potential of transcription factors for gene regulatory rewiring","date_created":"2018-12-12T12:31:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"file_date_updated":"2020-07-14T12:47:07Z","date_published":"2018-07-20T00:00:00Z","author":[{"orcid":"0000-0001-7777-546X","last_name":"Igler","full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia"},{"full_name":"Lagator, Mato","last_name":"Lagator","first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"ec_funded":1,"year":"2018","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"},{"_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440","call_identifier":"H2020"},{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture","grant_number":"24573"}],"file":[{"access_level":"open_access","file_name":"IST-2018-108-v1+1_data_figures.xlsx","file_id":"5611","content_type":"application/vnd.openxmlformats-officedocument.spreadsheetml.sheet","file_size":16507,"date_created":"2018-12-12T13:02:45Z","date_updated":"2020-07-14T12:47:07Z","checksum":"1435781526c77413802adee0d4583cce","creator":"system","relation":"main_file"}]},{"project":[{"call_identifier":"FP7","grant_number":"604102","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425","name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches"},{"name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","call_identifier":"FWF"}],"intvolume":"         8","year":"2017","department":[{"_id":"GaTk"}],"ec_funded":1,"file_date_updated":"2018-12-12T10:16:06Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:50:10Z","external_id":{"isi":["000417241200004"]},"language":[{"iso":"eng"}],"publist_id":"6266","scopus_import":"1","ddc":["571"],"publisher":"Nature Publishing Group","doi":"10.1038/s41467-017-02159-y","day":"06","publication_status":"published","publication":"Nature Communications","file":[{"relation":"main_file","creator":"system","date_updated":"2018-12-12T10:16:06Z","file_size":2872887,"date_created":"2018-12-12T10:16:06Z","access_level":"open_access","file_name":"IST-2018-921-v1+1_s41467-017-02159-y.pdf","file_id":"5191","content_type":"application/pdf"}],"quality_controlled":"1","title":"Multiplexed computations in retinal ganglion cells of a single type","author":[{"first_name":"Stephane","last_name":"Deny","full_name":"Deny, Stephane"},{"first_name":"Ulisse","full_name":"Ferrari, Ulisse","last_name":"Ferrari"},{"first_name":"Emilie","last_name":"Mace","full_name":"Mace, Emilie"},{"first_name":"Pierre","last_name":"Yger","full_name":"Yger, Pierre"},{"last_name":"Caplette","full_name":"Caplette, Romain","first_name":"Romain"},{"full_name":"Picaud, Serge","last_name":"Picaud","first_name":"Serge"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"}],"article_number":"1964","date_published":"2017-12-06T00:00:00Z","issue":"1","pubrep_id":"921","date_updated":"2025-07-10T11:50:05Z","volume":8,"abstract":[{"lang":"eng","text":"In the early visual system, cells of the same type perform the same computation in different places of the visual field. How these cells code together a complex visual scene is unclear. A common assumption is that cells of a single-type extract a single-stimulus feature to form a feature map, but this has rarely been observed directly. Using large-scale recordings in the rat retina, we show that a homogeneous population of fast OFF ganglion cells simultaneously encodes two radically different features of a visual scene. Cells close to a moving object code quasilinearly for its position, while distant cells remain largely invariant to the object's position and, instead, respond nonlinearly to changes in the object's speed. We develop a quantitative model that accounts for this effect and identify a disinhibitory circuit that mediates it. Ganglion cells of a single type thus do not code for one, but two features simultaneously. This richer, flexible neural map might also be present in other sensory systems."}],"month":"12","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","isi":1,"has_accepted_license":"1","citation":{"ieee":"S. Deny <i>et al.</i>, “Multiplexed computations in retinal ganglion cells of a single type,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","chicago":"Deny, Stephane, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette, Serge Picaud, Gašper Tkačik, and Olivier Marre. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-02159-y\">https://doi.org/10.1038/s41467-017-02159-y</a>.","mla":"Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” <i>Nature Communications</i>, vol. 8, no. 1, 1964, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-02159-y\">10.1038/s41467-017-02159-y</a>.","short":"S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik, O. Marre, Nature Communications 8 (2017).","ista":"Deny S, Ferrari U, Mace E, Yger P, Caplette R, Picaud S, Tkačik G, Marre O. 2017. Multiplexed computations in retinal ganglion cells of a single type. Nature Communications. 8(1), 1964.","apa":"Deny, S., Ferrari, U., Mace, E., Yger, P., Caplette, R., Picaud, S., … Marre, O. (2017). Multiplexed computations in retinal ganglion cells of a single type. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-02159-y\">https://doi.org/10.1038/s41467-017-02159-y</a>","ama":"Deny S, Ferrari U, Mace E, et al. Multiplexed computations in retinal ganglion cells of a single type. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-02159-y\">10.1038/s41467-017-02159-y</a>"},"article_processing_charge":"No","publication_identifier":{"issn":["2041-1723"]},"type":"journal_article","status":"public","_id":"1104"},{"scopus_import":"1","publist_id":"7266","alternative_title":["Rapid Communications"],"day":"21","arxiv":1,"doi":"10.1103/PhysRevE.96.060401","publisher":"American Physical Society","main_file_link":[{"url":"https://arxiv.org/abs/1707.00320","open_access":"1"}],"ec_funded":1,"intvolume":"        96","year":"2017","department":[{"_id":"GaTk"}],"project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"language":[{"iso":"eng"}],"external_id":{"arxiv":["1707.00320"],"isi":["000418574400001"]},"corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:47:06Z","oa":1,"oa_version":"Submitted Version","isi":1,"volume":96,"month":"12","abstract":[{"lang":"eng","text":"In this work maximum entropy distributions in the space of steady states of metabolic networks are considered upon constraining the first and second moments of the growth rate. Coexistence of fast and slow phenotypes, with bimodal flux distributions, emerges upon considering control on the average growth (optimization) and its fluctuations (heterogeneity). This is applied to the carbon catabolic core of Escherichia coli where it quantifies the metabolic activity of slow growing phenotypes and it provides a quantitative map with metabolic fluxes, opening the possibility to detect coexistence from flux data. A preliminary analysis on data for E. coli cultures in standard conditions shows degeneracy for the inferred parameters that extend in the coexistence region."}],"issue":"6","date_updated":"2025-09-18T09:41:11Z","status":"public","_id":"548","type":"journal_article","publication_identifier":{"issn":["2470-0045"]},"article_processing_charge":"No","citation":{"ista":"De Martino D. 2017. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. Physical Review E. 96(6), 060401.","short":"D. De Martino, Physical Review E 96 (2017).","mla":"De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” <i>Physical Review E</i>, vol. 96, no. 6, 060401, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">10.1103/PhysRevE.96.060401</a>.","chicago":"De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.” <i>Physical Review E</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">https://doi.org/10.1103/PhysRevE.96.060401</a>.","ieee":"D. De Martino, “Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes,” <i>Physical Review E</i>, vol. 96, no. 6. American Physical Society, 2017.","ama":"De Martino D. Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. <i>Physical Review E</i>. 2017;96(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">10.1103/PhysRevE.96.060401</a>","apa":"De Martino, D. (2017). Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.96.060401\">https://doi.org/10.1103/PhysRevE.96.060401</a>"},"quality_controlled":"1","publication":"Physical Review E","publication_status":"published","article_number":"060401","date_published":"2017-12-21T00:00:00Z","author":[{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino","full_name":"De Martino, Daniele"}],"title":"Maximum entropy modeling of metabolic networks by constraining growth-rate moments predicts coexistence of phenotypes"},{"oa_version":"Published Version","has_accepted_license":"1","datarep_id":"53","ddc":["571"],"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)"},"related_material":{"record":[{"relation":"research_paper","status":"public","id":"665"}]},"keyword":["single cell microscopy","mother machine microfluidic device","AcrAB-TolC pump","multi-drug efflux","Escherichia coli"],"date_updated":"2025-09-11T07:05:03Z","abstract":[{"text":"This repository contains the data collected for the manuscript \"Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity\".\r\nThe data is compressed into a single archive. Within the archive, different folders correspond to figures of the main text and the SI of the related publication.\r\nData is saved as plain text, with each folder containing a separate readme file describing the format. Typically, the data is from fluorescence microscopy measurements of single cells growing in a microfluidic \"mother machine\" device, and consists of relevant values (primarily arbitrary unit or normalized fluorescence measurements, and division times / growth rates) after raw microscopy images have been processed, segmented, and their features extracted, as described in the methods section of the related publication.","lang":"eng"}],"month":"03","status":"public","_id":"5560","day":"10","doi":"10.15479/AT:ISTA:53","type":"research_data","citation":{"mla":"Bergmiller, Tobias, et al. <i>Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:53\">10.15479/AT:ISTA:53</a>.","chicago":"Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:53\">https://doi.org/10.15479/AT:ISTA:53</a>.","ieee":"T. Bergmiller <i>et al.</i>, “Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity.” Institute of Science and Technology Austria, 2017.","ista":"Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik G, Guet CC. 2017. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:53\">10.15479/AT:ISTA:53</a>.","short":"T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, (2017).","apa":"Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:53\">https://doi.org/10.15479/AT:ISTA:53</a>","ama":"Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:53\">10.15479/AT:ISTA:53</a>"},"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","file":[{"creator":"system","relation":"main_file","checksum":"d77859af757ac8025c50c7b12b52eaf3","date_updated":"2020-07-14T12:47:03Z","file_size":6773204,"date_created":"2018-12-12T13:02:38Z","content_type":"application/zip","file_id":"5603","file_name":"IST-2017-53-v1+1_Data_MDE.zip","access_level":"open_access"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"year":"2017","author":[{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller"},{"first_name":"Anna M","id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87","full_name":"Andersson, Anna M","orcid":"0000-0003-2912-6769","last_name":"Andersson"},{"id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin","last_name":"Tomasek","orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin"},{"first_name":"Enrique","full_name":"Balleza, Enrique","last_name":"Balleza"},{"last_name":"Kiviet","full_name":"Kiviet, Daniel","first_name":"Daniel"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"}],"date_published":"2017-03-10T00:00:00Z","date_created":"2018-12-12T12:31:32Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Biased partitioning of the multi-drug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity","file_date_updated":"2020-07-14T12:47:03Z","oa":1},{"keyword":["multi-electrode recording","retinal ganglion cells"],"related_material":{"record":[{"relation":"used_in_publication","id":"2257","status":"public"}]},"month":"02","abstract":[{"text":"This data was collected as part of the study [1]. It consists of preprocessed multi-electrode array recording from 160 salamander retinal ganglion cells responding to 297 repeats of a 19 s natural movie. The data is available in two formats: (1) a .mat file containing an array with dimensions “number of repeats” x “number of neurons” x “time in a repeat”; (2) a zipped .txt file containing the same data represented as an array with dimensions “number of neurons” x “number of samples”, where the number of samples is equal to the product of the number of repeats and timebins within a repeat. The time dimension is divided into 20 ms time windows, and the array is binary indicating whether a given cell elicited at least one spike in a given time window during a particular repeat. See the reference below for details regarding collection and preprocessing:\r\n\r\n[1] Tkačik G, Marre O, Amodei D, Schneidman E, Bialek W, Berry MJ II. Searching for Collective Behavior in a Large Network of Sensory Neurons. PLoS Comput Biol. 2014;10(1):e1003408.","lang":"eng"}],"date_updated":"2025-09-29T11:14:05Z","datarep_id":"61","ddc":["570"],"has_accepted_license":"1","oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","short":"CC0 (1.0)"},"type":"research_data","doi":"10.15479/AT:ISTA:61","publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","citation":{"ieee":"O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, and M. Berry, “Multi-electrode array recording from salamander retinal ganglion cells.” Institute of Science and Technology Austria, 2017.","chicago":"Marre, Olivier, Gašper Tkačik, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:61\">https://doi.org/10.15479/AT:ISTA:61</a>.","mla":"Marre, Olivier, et al. <i>Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:61\">10.15479/AT:ISTA:61</a>.","short":"O. Marre, G. Tkačik, D. Amodei, E. Schneidman, W. Bialek, M. Berry, (2017).","ista":"Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. 2017. Multi-electrode array recording from salamander retinal ganglion cells, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:61\">10.15479/AT:ISTA:61</a>.","apa":"Marre, O., Tkačik, G., Amodei, D., Schneidman, E., Bialek, W., &#38; Berry, M. (2017). Multi-electrode array recording from salamander retinal ganglion cells. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:61\">https://doi.org/10.15479/AT:ISTA:61</a>","ama":"Marre O, Tkačik G, Amodei D, Schneidman E, Bialek W, Berry M. Multi-electrode array recording from salamander retinal ganglion cells. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:61\">10.15479/AT:ISTA:61</a>"},"day":"27","_id":"5562","status":"public","year":"2017","department":[{"_id":"GaTk"}],"file":[{"file_size":1336936,"date_created":"2018-12-12T13:03:04Z","file_id":"5622","access_level":"open_access","file_name":"IST-2017-61-v1+1_bint_fishmovie32_100.mat","content_type":"application/octet-stream","creator":"system","checksum":"e620eff260646f57b479a69492c8b765","relation":"main_file","date_updated":"2020-07-14T12:47:03Z"},{"date_updated":"2020-07-14T12:47:03Z","checksum":"de83f9b81ea0aae3cddfc3ed982e0759","relation":"main_file","creator":"system","access_level":"open_access","file_id":"5623","content_type":"application/zip","file_name":"IST-2017-61-v1+2_bint_fishmovie32_100.zip","date_created":"2018-12-12T13:03:05Z","file_size":1897543}],"title":"Multi-electrode array recording from salamander retinal ganglion cells","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T12:31:33Z","oa":1,"file_date_updated":"2020-07-14T12:47:03Z","date_published":"2017-02-27T00:00:00Z","author":[{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"first_name":"Dario","last_name":"Amodei","full_name":"Amodei, Dario"},{"first_name":"Elad","full_name":"Schneidman, Elad","last_name":"Schneidman"},{"first_name":"William","full_name":"Bialek, William","last_name":"Bialek"},{"first_name":"Michael","last_name":"Berry","full_name":"Berry, Michael"}]},{"abstract":[{"lang":"eng","text":"Bacteria in groups vary individually, and interact with other bacteria and the environment to produce population-level patterns of gene expression. Investigating such behavior in detail requires measuring and controlling populations at the single-cell level alongside precisely specified interactions and environmental characteristics. Here we present an automated, programmable platform that combines image-based gene expression and growth measurements with on-line optogenetic expression control for hundreds of individual Escherichia coli cells over days, in a dynamically adjustable environment. This integrated platform broadly enables experiments that bridge individual and population behaviors. We demonstrate: (i) population structuring by independent closed-loop control of gene expression in many individual cells, (ii) cell-cell variation control during antibiotic perturbation, (iii) hybrid bio-digital circuits in single cells, and freely specifiable digital communication between individual bacteria. These examples showcase the potential for real-time integration of theoretical models with measurement and control of many individual cells to investigate and engineer microbial population behavior."}],"month":"12","volume":8,"date_updated":"2025-09-11T07:34:12Z","issue":"1","pubrep_id":"911","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","oa_version":"Published Version","isi":1,"article_processing_charge":"Yes (in subscription journal)","citation":{"short":"R.P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, C.C. Guet, Nature Communications 8 (2017).","ista":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. 2017. Shaping bacterial population behavior through computer interfaced control of individual cells. Nature Communications. 8(1), 1535.","chicago":"Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gašper Tkačik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-01683-1\">https://doi.org/10.1038/s41467-017-01683-1</a>.","ieee":"R. P. Chait, J. Ruess, T. Bergmiller, G. Tkačik, and C. C. Guet, “Shaping bacterial population behavior through computer interfaced control of individual cells,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","mla":"Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” <i>Nature Communications</i>, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-01683-1\">10.1038/s41467-017-01683-1</a>.","ama":"Chait RP, Ruess J, Bergmiller T, Tkačik G, Guet CC. Shaping bacterial population behavior through computer interfaced control of individual cells. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-01683-1\">10.1038/s41467-017-01683-1</a>","apa":"Chait, R. P., Ruess, J., Bergmiller, T., Tkačik, G., &#38; Guet, C. C. (2017). Shaping bacterial population behavior through computer interfaced control of individual cells. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-01683-1\">https://doi.org/10.1038/s41467-017-01683-1</a>"},"type":"journal_article","publication_identifier":{"issn":["2041-1723"]},"status":"public","_id":"613","publication_status":"published","publication":"Nature Communications","file":[{"date_updated":"2020-07-14T12:47:20Z","checksum":"44bb5d0229926c23a9955d9fe0f9723f","creator":"system","relation":"main_file","file_name":"IST-2017-911-v1+1_s41467-017-01683-1.pdf","access_level":"open_access","file_id":"5190","content_type":"application/pdf","file_size":1951699,"date_created":"2018-12-12T10:16:05Z"}],"quality_controlled":"1","title":"Shaping bacterial population behavior through computer interfaced control of individual cells","article_number":"1535","date_published":"2017-12-01T00:00:00Z","author":[{"first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","last_name":"Chait"},{"last_name":"Ruess","orcid":"0000-0003-1615-3282","full_name":"Ruess, Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","first_name":"Jakob"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7191","scopus_import":"1","acknowledgement":"We are grateful to M. Lang, H. Janovjak, M. Khammash, A. Milias-Argeitis, M. Rullan, G. Batt, A. Bosma-Moody, Aryan, S. Leibler, and members of the Guet and Tkačik groups for helpful discussion, comments, and suggestions. We thank A. Moglich, T. Mathes, J. Tabor, and S. Schmidl for kind gifts of strains, and R. Hauschild, B. Knep, M. Lang, T. Asenov, E. Papusheva, T. Menner, T. Adletzberger, and J. Merrin for technical assistance. 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 no. [291734]. (to R.C. and J.R.), Austrian Science Fund grant FWF P28844 (to G.T.), and internal IST Austria Interdisciplinary Project Support. J.R. acknowledges support from the Agence Nationale de la Recherche (ANR) under Grant Nos. ANR-16-CE33-0018 (MEMIP), ANR-16-CE12-0025 (COGEX) and ANR-10-BINF-06-01 (ICEBERG).","ddc":["576","579"],"publisher":"Nature Publishing Group","doi":"10.1038/s41467-017-01683-1","day":"01","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"intvolume":"         8","year":"2017","project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"}],"ec_funded":1,"oa":1,"file_date_updated":"2020-07-14T12:47:20Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:47:30Z","corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000415323000008"]}},{"date_published":"2017-06-01T00:00:00Z","author":[{"first_name":"Abraham","full_name":"Martin Del Campo Sanchez, Abraham","last_name":"Martin Del Campo Sanchez"},{"first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","full_name":"Cepeda Humerez, Sarah A","last_name":"Cepeda Humerez"},{"first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","full_name":"Uhler, Caroline","last_name":"Uhler","orcid":"0000-0002-7008-0216"}],"title":"Exact goodness-of-fit testing for the Ising model","publication":"Scandinavian Journal of Statistics","quality_controlled":"1","publication_status":"published","page":"285 - 306","_id":"2016","status":"public","article_processing_charge":"No","citation":{"ieee":"A. Martin Del Campo Sanchez, S. A. Cepeda Humerez, and C. Uhler, “Exact goodness-of-fit testing for the Ising model,” <i>Scandinavian Journal of Statistics</i>, vol. 44, no. 2. Wiley-Blackwell, pp. 285–306, 2017.","chicago":"Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.” <i>Scandinavian Journal of Statistics</i>. Wiley-Blackwell, 2017. <a href=\"https://doi.org/10.1111/sjos.12251\">https://doi.org/10.1111/sjos.12251</a>.","mla":"Martin Del Campo Sanchez, Abraham, et al. “Exact Goodness-of-Fit Testing for the Ising Model.” <i>Scandinavian Journal of Statistics</i>, vol. 44, no. 2, Wiley-Blackwell, 2017, pp. 285–306, doi:<a href=\"https://doi.org/10.1111/sjos.12251\">10.1111/sjos.12251</a>.","short":"A. Martin Del Campo Sanchez, S.A. Cepeda Humerez, C. Uhler, Scandinavian Journal of Statistics 44 (2017) 285–306.","ista":"Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. 2017. Exact goodness-of-fit testing for the Ising model. Scandinavian Journal of Statistics. 44(2), 285–306.","apa":"Martin Del Campo Sanchez, A., Cepeda Humerez, S. A., &#38; Uhler, C. (2017). Exact goodness-of-fit testing for the Ising model. <i>Scandinavian Journal of Statistics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/sjos.12251\">https://doi.org/10.1111/sjos.12251</a>","ama":"Martin Del Campo Sanchez A, Cepeda Humerez SA, Uhler C. Exact goodness-of-fit testing for the Ising model. <i>Scandinavian Journal of Statistics</i>. 2017;44(2):285-306. doi:<a href=\"https://doi.org/10.1111/sjos.12251\">10.1111/sjos.12251</a>"},"type":"journal_article","publication_identifier":{"issn":["03036898"]},"oa_version":"Preprint","isi":1,"month":"06","abstract":[{"lang":"eng","text":"The Ising model is one of the simplest and most famous models of interacting systems. It was originally proposed to model ferromagnetic interactions in statistical physics and is now widely used to model spatial processes in many areas such as ecology, sociology, and genetics, usually without testing its goodness-of-fit. Here, we propose an exact goodness-of-fit test for the finite-lattice Ising model. The theory of Markov bases has been developed in algebraic statistics for exact goodness-of-fit testing using a Monte Carlo approach. However, this beautiful theory has fallen short of its promise for applications, because finding a Markov basis is usually computationally intractable. We develop a Monte Carlo method for exact goodness-of-fit testing for the Ising model which avoids computing a Markov basis and also leads to a better connectivity of the Markov chain and hence to a faster convergence. We show how this method can be applied to analyze the spatial organization of receptors on the cell membrane."}],"volume":44,"date_updated":"2026-04-08T13:55:45Z","issue":"2","related_material":{"record":[{"id":"6473","status":"public","relation":"part_of_dissertation"}]},"language":[{"iso":"eng"}],"external_id":{"isi":["000400985000001"],"arxiv":["1410.1242"]},"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:55:13Z","main_file_link":[{"url":"http://arxiv.org/abs/1410.1242","open_access":"1"}],"intvolume":"        44","year":"2017","department":[{"_id":"GaTk"}],"day":"01","publisher":"Wiley-Blackwell","arxiv":1,"doi":"10.1111/sjos.12251","scopus_import":"1","publist_id":"5060"},{"abstract":[{"lang":"eng","text":"A nonlinear system possesses an invariance with respect to a set of transformations if its output dynamics remain invariant when transforming the input, and adjusting the initial condition accordingly. Most research has focused on invariances with respect to time-independent pointwise transformations like translational-invariance (u(t) -&gt; u(t) + p, p in R) or scale-invariance (u(t) -&gt; pu(t), p in R&gt;0). In this article, we introduce the concept of s0-invariances with respect to continuous input transformations exponentially growing/decaying over time. We show that s0-invariant systems not only encompass linear time-invariant (LTI) systems with transfer functions having an irreducible zero at s0 in R, but also that the input/output relationship of nonlinear s0-invariant systems possesses properties well known from their linear counterparts. Furthermore, we extend the concept of s0-invariances to second- and higher-order s0-invariances, corresponding to invariances with respect to transformations of the time-derivatives of the input, and encompassing LTI systems with zeros of multiplicity two or higher. Finally, we show that nth-order 0-invariant systems realize – under mild conditions – nth-order nonlinear differential operators: when excited by an input of a characteristic functional form, the system’s output converges to a constant value only depending on the nth (nonlinear) derivative of the input."}],"month":"06","volume":"81C","pubrep_id":"813","date_updated":"2025-04-15T06:50:01Z","has_accepted_license":"1","isi":1,"oa_version":"Published Version","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"type":"journal_article","publication_identifier":{"issn":["0005-1098"]},"article_processing_charge":"Yes (in subscription journal)","citation":{"apa":"Lang, M., &#38; Sontag, E. (2017). Zeros of nonlinear systems with input invariances. <i>Automatica</i>. International Federation of Automatic Control. <a href=\"https://doi.org/10.1016/j.automatica.2017.03.030\">https://doi.org/10.1016/j.automatica.2017.03.030</a>","ama":"Lang M, Sontag E. Zeros of nonlinear systems with input invariances. <i>Automatica</i>. 2017;81C:46-55. doi:<a href=\"https://doi.org/10.1016/j.automatica.2017.03.030\">10.1016/j.automatica.2017.03.030</a>","mla":"Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.” <i>Automatica</i>, vol. 81C, International Federation of Automatic Control, 2017, pp. 46–55, doi:<a href=\"https://doi.org/10.1016/j.automatica.2017.03.030\">10.1016/j.automatica.2017.03.030</a>.","chicago":"Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.” <i>Automatica</i>. International Federation of Automatic Control, 2017. <a href=\"https://doi.org/10.1016/j.automatica.2017.03.030\">https://doi.org/10.1016/j.automatica.2017.03.030</a>.","ieee":"M. Lang and E. Sontag, “Zeros of nonlinear systems with input invariances,” <i>Automatica</i>, vol. 81C. International Federation of Automatic Control, pp. 46–55, 2017.","ista":"Lang M, Sontag E. 2017. Zeros of nonlinear systems with input invariances. Automatica. 81C, 46–55.","short":"M. Lang, E. Sontag, Automatica 81C (2017) 46–55."},"status":"public","_id":"1007","publication_status":"published","page":"46 - 55","quality_controlled":"1","file":[{"date_updated":"2018-12-12T10:11:29Z","creator":"system","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-813-v1+1_ZerosOfNonlinearSystems.pdf","file_id":"4884","file_size":1401954,"date_created":"2018-12-12T10:11:29Z"}],"publication":"Automatica","title":"Zeros of nonlinear systems with input invariances","date_published":"2017-06-01T00:00:00Z","author":[{"id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz","last_name":"Lang","full_name":"Lang, Moritz"},{"first_name":"Eduardo","full_name":"Sontag, Eduardo","last_name":"Sontag"}],"publist_id":"6391","ddc":["000"],"scopus_import":"1","doi":"10.1016/j.automatica.2017.03.030","publisher":"International Federation of Automatic Control","day":"01","ec_funded":1,"year":"2017","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:49:39Z","oa":1,"file_date_updated":"2018-12-12T10:11:29Z","language":[{"iso":"eng"}],"external_id":{"isi":["000403513900006"]}},{"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568706/","open_access":"1"}],"intvolume":"       356","department":[{"_id":"AnKi"},{"_id":"GaTk"}],"year":"2017","project":[{"grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"},{"name":"Coordination of Patterning And Growth In the Spinal Cord","_id":"B6FC0238-B512-11E9-945C-1524E6697425","call_identifier":"H2020","grant_number":"680037"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"name":"Developing High-Throughput Bioassays for Human Cancers in Zebrafish","_id":"2524F500-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"201439"}],"ec_funded":1,"corr_author":"1","language":[{"iso":"eng"}],"external_id":{"pmid":["28663499"],"isi":["000404351500036"]},"oa":1,"date_created":"2018-12-11T11:49:20Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","publist_id":"6474","day":"30","publisher":"American Association for the Advancement of Science","doi":"10.1126/science.aam5887","publication":"Science","quality_controlled":"1","pmid":1,"publication_status":"published","page":"1379 - 1383","date_published":"2017-06-30T00:00:00Z","author":[{"full_name":"Zagórski, Marcin P","orcid":"0000-0001-7896-7762","last_name":"Zagórski","first_name":"Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yoji","full_name":"Tabata, Yoji","last_name":"Tabata"},{"first_name":"Nathalie","last_name":"Brandenberg","full_name":"Brandenberg, Nathalie"},{"last_name":"Lutolf","full_name":"Lutolf, Matthias","first_name":"Matthias"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper"},{"first_name":"Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Tobias"},{"full_name":"Briscoe, James","last_name":"Briscoe","first_name":"James"},{"orcid":"0000-0003-4509-4998","last_name":"Kicheva","full_name":"Kicheva, Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"title":"Decoding of position in the developing neural tube from antiparallel morphogen gradients","oa_version":"Submitted Version","isi":1,"abstract":[{"lang":"eng","text":"Like many developing tissues, the vertebrate neural tube is patterned by antiparallel morphogen gradients. To understand how these inputs are interpreted, we measured morphogen signaling and target gene expression in mouse embryos and chick ex vivo assays. From these data, we derived and validated a characteristic decoding map that relates morphogen input to the positional identity of neural progenitors. Analysis of the observed responses indicates that the underlying interpretation strategy minimizes patterning errors in response to the joint input of noisy opposing gradients. We reverse-engineered a transcriptional network that provides a mechanistic basis for the observed cell fate decisions and accounts for the precision and dynamics of pattern formation. Together, our data link opposing gradient dynamics in a growing tissue to precise pattern formation."}],"volume":356,"month":"06","date_updated":"2025-07-10T12:01:45Z","issue":"6345","status":"public","_id":"943","article_processing_charge":"No","citation":{"apa":"Zagórski, M. P., Tabata, Y., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, T., … Kicheva, A. (2017). Decoding of position in the developing neural tube from antiparallel morphogen gradients. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aam5887\">https://doi.org/10.1126/science.aam5887</a>","ama":"Zagórski MP, Tabata Y, Brandenberg N, et al. Decoding of position in the developing neural tube from antiparallel morphogen gradients. <i>Science</i>. 2017;356(6345):1379-1383. doi:<a href=\"https://doi.org/10.1126/science.aam5887\">10.1126/science.aam5887</a>","chicago":"Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aam5887\">https://doi.org/10.1126/science.aam5887</a>.","ieee":"M. P. Zagórski <i>et al.</i>, “Decoding of position in the developing neural tube from antiparallel morphogen gradients,” <i>Science</i>, vol. 356, no. 6345. American Association for the Advancement of Science, pp. 1379–1383, 2017.","mla":"Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” <i>Science</i>, vol. 356, no. 6345, American Association for the Advancement of Science, 2017, pp. 1379–83, doi:<a href=\"https://doi.org/10.1126/science.aam5887\">10.1126/science.aam5887</a>.","short":"M.P. Zagórski, Y. Tabata, N. Brandenberg, M. Lutolf, G. Tkačik, T. Bollenbach, J. Briscoe, A. Kicheva, Science 356 (2017) 1379–1383.","ista":"Zagórski MP, Tabata Y, Brandenberg N, Lutolf M, Tkačik G, Bollenbach T, Briscoe J, Kicheva A. 2017. Decoding of position in the developing neural tube from antiparallel morphogen gradients. Science. 356(6345), 1379–1383."},"type":"journal_article","publication_identifier":{"issn":["0036-8075"]}},{"month":"08","abstract":[{"text":"Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.","lang":"eng"}],"volume":8,"issue":"1","pubrep_id":"864","date_updated":"2026-04-08T13:54:24Z","related_material":{"record":[{"status":"public","id":"6071","relation":"dissertation_contains"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","oa_version":"Published Version","isi":1,"article_processing_charge":"Yes (in subscription journal)","citation":{"ista":"Friedlander T, Prizak R, Barton NH, Tkačik G. 2017. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nature Communications. 8(1), 216.","short":"T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).","mla":"Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” <i>Nature Communications</i>, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/s41467-017-00238-8\">10.1038/s41467-017-00238-8</a>.","chicago":"Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gašper Tkačik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/s41467-017-00238-8\">https://doi.org/10.1038/s41467-017-00238-8</a>.","ieee":"T. Friedlander, R. Prizak, N. H. Barton, and G. Tkačik, “Evolution of new regulatory functions on biophysically realistic fitness landscapes,” <i>Nature Communications</i>, vol. 8, no. 1. Nature Publishing Group, 2017.","ama":"Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. <i>Nature Communications</i>. 2017;8(1). doi:<a href=\"https://doi.org/10.1038/s41467-017-00238-8\">10.1038/s41467-017-00238-8</a>","apa":"Friedlander, T., Prizak, R., Barton, N. H., &#38; Tkačik, G. (2017). Evolution of new regulatory functions on biophysically realistic fitness landscapes. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-017-00238-8\">https://doi.org/10.1038/s41467-017-00238-8</a>"},"type":"journal_article","publication_identifier":{"issn":["2041-1723"]},"_id":"955","status":"public","publication_status":"published","publication":"Nature Communications","file":[{"date_updated":"2020-07-14T12:48:16Z","checksum":"29a1b5db458048d3bd5c67e0e2a56818","creator":"system","relation":"main_file","file_name":"IST-2017-864-v1+1_s41467-017-00238-8.pdf","file_id":"5064","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:14:14Z","file_size":998157},{"relation":"main_file","creator":"system","checksum":"7b78401e52a576cf3e6bbf8d0abadc17","date_updated":"2020-07-14T12:48:16Z","file_size":9715993,"date_created":"2018-12-12T10:14:15Z","file_id":"5065","content_type":"application/pdf","access_level":"open_access","file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf"}],"quality_controlled":"1","title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","article_number":"216","date_published":"2017-08-09T00:00:00Z","author":[{"last_name":"Friedlander","full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar"},{"first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","full_name":"Prizak, Roshan","last_name":"Prizak"},{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"publist_id":"6459","scopus_import":"1","ddc":["539","576"],"publisher":"Nature Publishing Group","doi":"10.1038/s41467-017-00238-8","day":"09","department":[{"_id":"GaTk"},{"_id":"NiBa"}],"intvolume":"         8","year":"2017","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7"},{"grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"}],"ec_funded":1,"oa":1,"file_date_updated":"2020-07-14T12:48:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:49:23Z","corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000407198800005"]}},{"type":"research_data_reference","doi":"10.5061/dryad.1f1rc","publisher":"Dryad","article_processing_charge":"No","citation":{"ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:<a href=\"https://doi.org/10.5061/dryad.1f1rc\">10.5061/dryad.1f1rc</a>","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., &#38; Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. <a href=\"https://doi.org/10.5061/dryad.1f1rc\">https://doi.org/10.5061/dryad.1f1rc</a>","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad, <a href=\"https://doi.org/10.5061/dryad.1f1rc\">10.5061/dryad.1f1rc</a>.","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).","mla":"Prentice, Jason, et al. <i>Data from: Error-Robust Modes of the Retinal Population Code</i>. Dryad, 2017, doi:<a href=\"https://doi.org/10.5061/dryad.1f1rc\">10.5061/dryad.1f1rc</a>.","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.","chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. <a href=\"https://doi.org/10.5061/dryad.1f1rc\">https://doi.org/10.5061/dryad.1f1rc</a>."},"day":"18","_id":"9709","status":"public","related_material":{"record":[{"status":"public","id":"1197","relation":"used_in_publication"}]},"abstract":[{"text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina.","lang":"eng"}],"month":"10","date_updated":"2025-09-22T09:43:12Z","oa_version":"Published Version","title":"Data from: Error-robust modes of the retinal population code","date_created":"2021-07-23T11:34:34Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"date_published":"2017-10-18T00:00:00Z","author":[{"first_name":"Jason","full_name":"Prentice, Jason","last_name":"Prentice"},{"first_name":"Olivier","last_name":"Marre","full_name":"Marre, Olivier"},{"first_name":"Mark","full_name":"Ioffe, Mark","last_name":"Ioffe"},{"last_name":"Loback","full_name":"Loback, Adrianna","first_name":"Adrianna"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","full_name":"Tkačik, Gašper"},{"first_name":"Michael","last_name":"Berry","full_name":"Berry, Michael"}],"department":[{"_id":"GaTk"}],"year":"2017","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.1f1rc"}]},{"citation":{"ama":"Der R, Martius GS. Dynamical self consistency leads to behavioral development and emergent social interactions in robots. In: IEEE; 2017. doi:<a href=\"https://doi.org/10.1109/DEVLRN.2016.7846789\">10.1109/DEVLRN.2016.7846789</a>","apa":"Der, R., &#38; Martius, G. S. (2017). Dynamical self consistency leads to behavioral development and emergent social interactions in robots. Presented at the ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , Cergy-Pontoise, France: IEEE. <a href=\"https://doi.org/10.1109/DEVLRN.2016.7846789\">https://doi.org/10.1109/DEVLRN.2016.7846789</a>","ista":"Der R, Martius GS. 2017. Dynamical self consistency leads to behavioral development and emergent social interactions in robots. ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , 7846789.","short":"R. Der, G.S. Martius, in:, IEEE, 2017.","mla":"Der, Ralf, and Georg S. Martius. <i>Dynamical Self Consistency Leads to Behavioral Development and Emergent Social Interactions in Robots</i>. 7846789, IEEE, 2017, doi:<a href=\"https://doi.org/10.1109/DEVLRN.2016.7846789\">10.1109/DEVLRN.2016.7846789</a>.","ieee":"R. Der and G. S. Martius, “Dynamical self consistency leads to behavioral development and emergent social interactions in robots,” presented at the ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics , Cergy-Pontoise, France, 2017.","chicago":"Der, Ralf, and Georg S Martius. “Dynamical Self Consistency Leads to Behavioral Development and Emergent Social Interactions in Robots.” IEEE, 2017. <a href=\"https://doi.org/10.1109/DEVLRN.2016.7846789\">https://doi.org/10.1109/DEVLRN.2016.7846789</a>."},"publisher":"IEEE","doi":"10.1109/DEVLRN.2016.7846789","publication_identifier":{"isbn":["978-150905069-7"]},"type":"conference","_id":"652","day":"07","status":"public","date_updated":"2021-01-12T08:07:51Z","month":"02","abstract":[{"lang":"eng","text":"We present an approach that enables robots to self-organize their sensorimotor behavior from scratch without providing specific information about neither the robot nor its environment. This is achieved by a simple neural control law that increases the consistency between external sensor dynamics and internal neural dynamics of the utterly simple controller. In this way, the embodiment and the agent-environment coupling are the only source of individual development. We show how an anthropomorphic tendon driven arm-shoulder system develops different behaviors depending on that coupling. For instance: Given a bottle half-filled with water, the arm starts to shake it, driven by the physical response of the water. When attaching a brush, the arm can be manipulated into wiping a table, and when connected to a revolvable wheel it finds out how to rotate it. Thus, the robot may be said to discover the affordances of the world. When allowing two (simulated) humanoid robots to interact physically, they engage into a joint behavior development leading to, for instance, spontaneous cooperation. More social effects are observed if the robots can visually perceive each other. Although, as an observer, it is tempting to attribute an apparent intentionality, there is nothing of the kind put in. As a conclusion, we argue that emergent behavior may be much less rooted in explicit intentions, internal motivations, or specific reward systems than is commonly believed."}],"publist_id":"7100","scopus_import":1,"oa_version":"None","conference":{"start_date":"2016-09-19","location":"Cergy-Pontoise, France","end_date":"2016-09-22","name":"ICDL EpiRob: International Conference on Development and Learning and Epigenetic Robotics "},"date_created":"2018-12-11T11:47:43Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Dynamical self consistency leads to behavioral development and emergent social interactions in robots","author":[{"first_name":"Ralf","last_name":"Der","full_name":"Der, Ralf"},{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","last_name":"Martius","full_name":"Martius, Georg S"}],"article_number":"7846789","date_published":"2017-02-07T00:00:00Z","language":[{"iso":"eng"}],"publication_status":"published","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"year":"2017","quality_controlled":"1"},{"title":"Self organized behavior generation for musculoskeletal robots","author":[{"first_name":"Ralf","last_name":"Der","full_name":"Der, Ralf"},{"first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S","last_name":"Martius"}],"date_published":"2017-03-16T00:00:00Z","article_number":"00008","publication_status":"published","file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-903-v1+1_fnbot-11-00008.pdf","file_id":"5371","file_size":8439566,"date_created":"2018-12-12T10:18:49Z","date_updated":"2020-07-14T12:47:33Z","creator":"system","checksum":"b1bc43f96d1df3313c03032c2a46388d","relation":"main_file"}],"publication":"Frontiers in Neurorobotics","quality_controlled":"1","citation":{"apa":"Der, R., &#38; Martius, G. S. (2017). Self organized behavior generation for musculoskeletal robots. <i>Frontiers in Neurorobotics</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fnbot.2017.00008\">https://doi.org/10.3389/fnbot.2017.00008</a>","ama":"Der R, Martius GS. Self organized behavior generation for musculoskeletal robots. <i>Frontiers in Neurorobotics</i>. 2017;11(MAR). doi:<a href=\"https://doi.org/10.3389/fnbot.2017.00008\">10.3389/fnbot.2017.00008</a>","mla":"Der, Ralf, and Georg S. Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” <i>Frontiers in Neurorobotics</i>, vol. 11, no. MAR, 00008, Frontiers Research Foundation, 2017, doi:<a href=\"https://doi.org/10.3389/fnbot.2017.00008\">10.3389/fnbot.2017.00008</a>.","ieee":"R. Der and G. S. Martius, “Self organized behavior generation for musculoskeletal robots,” <i>Frontiers in Neurorobotics</i>, vol. 11, no. MAR. Frontiers Research Foundation, 2017.","chicago":"Der, Ralf, and Georg S Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.” <i>Frontiers in Neurorobotics</i>. Frontiers Research Foundation, 2017. <a href=\"https://doi.org/10.3389/fnbot.2017.00008\">https://doi.org/10.3389/fnbot.2017.00008</a>.","ista":"Der R, Martius GS. 2017. Self organized behavior generation for musculoskeletal robots. Frontiers in Neurorobotics. 11(MAR), 00008.","short":"R. Der, G.S. Martius, Frontiers in Neurorobotics 11 (2017)."},"article_processing_charge":"Yes","publication_identifier":{"issn":["1662-5218"]},"type":"journal_article","status":"public","_id":"658","issue":"MAR","pubrep_id":"903","date_updated":"2025-09-11T07:10:33Z","month":"03","volume":11,"abstract":[{"lang":"eng","text":"With the accelerated development of robot technologies, control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of specific objectives for the task at hand. While very successful in many applications, self-organized control schemes seem to be favored in large complex systems with unknown dynamics or which are difficult to model. Reasons are the expected scalability, robustness, and resilience of self-organizing systems. The paper presents a self-learning neurocontroller based on extrinsic differential plasticity introduced recently, applying it to an anthropomorphic musculoskeletal robot arm with attached objects of unknown physical dynamics. The central finding of the paper is the following effect: by the mere feedback through the internal dynamics of the object, the robot is learning to relate each of the objects with a very specific sensorimotor pattern. Specifically, an attached pendulum pilots the arm into a circular motion, a half-filled bottle produces axis oriented shaking behavior, a wheel is getting rotated, and wiping patterns emerge automatically in a table-plus-brush setting. By these object-specific dynamical patterns, the robot may be said to recognize the object's identity, or in other words, it discovers dynamical affordances of objects. Furthermore, when including hand coordinates obtained from a camera, a dedicated hand-eye coordination self-organizes spontaneously. These phenomena are discussed from a specific dynamical system perspective. Central is the dedicated working regime at the border to instability with its potentially infinite reservoir of (limit cycle) attractors &quot;waiting&quot; to be excited. Besides converging toward one of these attractors, variate behavior is also arising from a self-induced attractor morphing driven by the learning rule. We claim that experimental investigations with this anthropomorphic, self-learning robot not only generate interesting and potentially useful behaviors, but may also help to better understand what subjective human muscle feelings are, how they can be rooted in sensorimotor patterns, and how these concepts may feed back on robotics."}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","isi":1,"has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:33Z","oa":1,"date_created":"2018-12-11T11:47:45Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","external_id":{"isi":["000396303400001"]},"language":[{"iso":"eng"}],"project":[{"name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7"}],"department":[{"_id":"ChLa"},{"_id":"GaTk"}],"year":"2017","intvolume":"        11","ec_funded":1,"publisher":"Frontiers Research Foundation","doi":"10.3389/fnbot.2017.00008","day":"16","publist_id":"7078","scopus_import":"1","ddc":["006"]},{"status":"public","_id":"665","type":"journal_article","publication_identifier":{"issn":["0036-8075"]},"article_processing_charge":"No","citation":{"ama":"Bergmiller T, Andersson AM, Tomasek K, et al. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. <i>Science</i>. 2017;356(6335):311-315. doi:<a href=\"https://doi.org/10.1126/science.aaf4762\">10.1126/science.aaf4762</a>","apa":"Bergmiller, T., Andersson, A. M., Tomasek, K., Balleza, E., Kiviet, D., Hauschild, R., … Guet, C. C. (2017). Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aaf4762\">https://doi.org/10.1126/science.aaf4762</a>","ista":"Bergmiller T, Andersson AM, Tomasek K, Balleza E, Kiviet D, Hauschild R, Tkačik G, Guet CC. 2017. Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity. Science. 356(6335), 311–315.","short":"T. Bergmiller, A.M. Andersson, K. Tomasek, E. Balleza, D. Kiviet, R. Hauschild, G. Tkačik, C.C. Guet, Science 356 (2017) 311–315.","mla":"Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” <i>Science</i>, vol. 356, no. 6335, American Association for the Advancement of Science, 2017, pp. 311–15, doi:<a href=\"https://doi.org/10.1126/science.aaf4762\">10.1126/science.aaf4762</a>.","ieee":"T. Bergmiller <i>et al.</i>, “Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity,” <i>Science</i>, vol. 356, no. 6335. American Association for the Advancement of Science, pp. 311–315, 2017.","chicago":"Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gašper Tkačik, and Calin C Guet. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” <i>Science</i>. American Association for the Advancement of Science, 2017. <a href=\"https://doi.org/10.1126/science.aaf4762\">https://doi.org/10.1126/science.aaf4762</a>."},"oa_version":"None","isi":1,"article_type":"original","related_material":{"record":[{"relation":"popular_science","id":"5560","status":"public"}]},"month":"04","abstract":[{"lang":"eng","text":"The molecular mechanisms underlying phenotypic variation in isogenic bacterial populations remain poorly understood.We report that AcrAB-TolC, the main multidrug efflux pump of Escherichia coli, exhibits a strong partitioning bias for old cell poles by a segregation mechanism that is mediated by ternary AcrAB-TolC complex formation. Mother cells inheriting old poles are phenotypically distinct and display increased drug efflux activity relative to daughters. Consequently, we find systematic and long-lived growth differences between mother and daughter cells in the presence of subinhibitory drug concentrations. A simple model for biased partitioning predicts a population structure of long-lived and highly heterogeneous phenotypes. This straightforward mechanism of generating sustained growth rate differences at subinhibitory antibiotic concentrations has implications for understanding the emergence of multidrug resistance in bacteria."}],"volume":356,"issue":"6335","date_updated":"2025-09-11T07:05:04Z","date_published":"2017-04-21T00:00:00Z","author":[{"full_name":"Bergmiller, Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anna M","id":"2B8A40DA-F248-11E8-B48F-1D18A9856A87","full_name":"Andersson, Anna M","orcid":"0000-0003-2912-6769","last_name":"Andersson"},{"orcid":"0000-0003-3768-877X","last_name":"Tomasek","full_name":"Tomasek, Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87","first_name":"Kathrin"},{"last_name":"Balleza","full_name":"Balleza, Enrique","first_name":"Enrique"},{"last_name":"Kiviet","full_name":"Kiviet, Daniel","first_name":"Daniel"},{"first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C"}],"title":"Biased partitioning of the multidrug efflux pump AcrAB TolC underlies long lived phenotypic heterogeneity","quality_controlled":"1","publication":"Science","publication_status":"published","page":"311 - 315","day":"21","doi":"10.1126/science.aaf4762","publisher":"American Association for the Advancement of Science","scopus_import":"1","publist_id":"7064","language":[{"iso":"eng"}],"external_id":{"isi":["000399540100060"]},"corr_author":"1","date_created":"2018-12-11T11:47:48Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"Bio"}],"intvolume":"       356","year":"2017","project":[{"grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation"}]},{"doi":"10.1016/j.cels.2017.03.001","publisher":"Cell Press","day":"26","publist_id":"7061","ddc":["576","610"],"scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:47:48Z","file_date_updated":"2020-07-14T12:47:35Z","oa":1,"external_id":{"isi":["000402747300005"]},"language":[{"iso":"eng"}],"corr_author":"1","ec_funded":1,"project":[{"grant_number":"303507","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth"}],"department":[{"_id":"ToBo"},{"_id":"GaTk"}],"intvolume":"         4","year":"2017","publication_identifier":{"issn":["2405-4712"]},"type":"journal_article","citation":{"ama":"Mitosch K, Rieckh G, Bollenbach MT. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. <i>Cell Systems</i>. 2017;4(4):393-403. doi:<a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">10.1016/j.cels.2017.03.001</a>","apa":"Mitosch, K., Rieckh, G., &#38; Bollenbach, M. T. (2017). Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. <i>Cell Systems</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">https://doi.org/10.1016/j.cels.2017.03.001</a>","short":"K. Mitosch, G. Rieckh, M.T. Bollenbach, Cell Systems 4 (2017) 393–403.","ista":"Mitosch K, Rieckh G, Bollenbach MT. 2017. Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment. Cell Systems. 4(4), 393–403.","ieee":"K. Mitosch, G. Rieckh, and M. T. Bollenbach, “Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment,” <i>Cell Systems</i>, vol. 4, no. 4. Cell Press, pp. 393–403, 2017.","chicago":"Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” <i>Cell Systems</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">https://doi.org/10.1016/j.cels.2017.03.001</a>.","mla":"Mitosch, Karin, et al. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.” <i>Cell Systems</i>, vol. 4, no. 4, Cell Press, 2017, pp. 393–403, doi:<a href=\"https://doi.org/10.1016/j.cels.2017.03.001\">10.1016/j.cels.2017.03.001</a>."},"article_processing_charge":"Yes (in subscription journal)","_id":"666","status":"public","related_material":{"record":[{"id":"818","status":"public","relation":"dissertation_contains"}]},"pubrep_id":"901","issue":"4","date_updated":"2026-04-08T14:21:56Z","month":"04","abstract":[{"lang":"eng","text":"Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to “cross-protect” bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid. Combining microfluidics with time-lapse imaging to monitor survival and acid stress response in single cells revealed that the noisy expression of the acid resistance operon gadBC correlates with single-cell survival. Cells with higher gadBC expression following trimethoprim maintain higher intracellular pH and survive the acid stress longer. The seemingly random single-cell survival under acid stress can therefore be predicted from gadBC expression and rationalized in terms of GadB/C molecular function. Overall, we provide a roadmap for identifying the molecular mechanisms of single-cell cross-protection between antibiotics and other stressors."}],"volume":4,"isi":1,"oa_version":"Published Version","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"title":"Noisy response to antibiotic stress predicts subsequent single cell survival in an acidic environment","author":[{"id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin","last_name":"Mitosch","full_name":"Mitosch, Karin"},{"first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","full_name":"Rieckh, Georg","last_name":"Rieckh"},{"last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"}],"date_published":"2017-04-26T00:00:00Z","publication_status":"published","page":"393 - 403","quality_controlled":"1","file":[{"date_updated":"2020-07-14T12:47:35Z","checksum":"04ff20011c3d9a601c514aa999a5fe1a","creator":"system","relation":"main_file","file_name":"IST-2017-901-v1+1_1-s2.0-S2405471217300868-main.pdf","file_id":"5041","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:13:54Z","file_size":2438660}],"publication":"Cell Systems"},{"publication_status":"published","publication":"PLoS Computational Biology","file":[{"content_type":"application/pdf","file_name":"IST-2017-898-v1+1_journal.pcbi.1005582.pdf","file_id":"4645","access_level":"open_access","date_created":"2018-12-12T10:07:47Z","file_size":14555676,"date_updated":"2020-07-14T12:47:40Z","relation":"main_file","creator":"system","checksum":"796a1026076af6f4405a47d985bc7b68"}],"quality_controlled":"1","title":"Sensory noise predicts divisive reshaping of receptive fields","author":[{"full_name":"Chalk, Matthew J","orcid":"0000-0001-7782-4436","last_name":"Chalk","first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Paul","last_name":"Masset","full_name":"Masset, Paul"},{"first_name":"Boris","full_name":"Gutkin, Boris","last_name":"Gutkin"},{"full_name":"Denève, Sophie","last_name":"Denève","first_name":"Sophie"}],"article_number":"e1005582","date_published":"2017-06-01T00:00:00Z","date_updated":"2025-09-10T14:20:48Z","issue":"6","pubrep_id":"898","month":"06","volume":13,"abstract":[{"text":"In order to respond reliably to specific features of their environment, sensory neurons need to integrate multiple incoming noisy signals. Crucially, they also need to compete for the interpretation of those signals with other neurons representing similar features. The form that this competition should take depends critically on the noise corrupting these signals. In this study we show that for the type of noise commonly observed in sensory systems, whose variance scales with the mean signal, sensory neurons should selectively divide their input signals by their predictions, suppressing ambiguous cues while amplifying others. Any change in the stimulus context alters which inputs are suppressed, leading to a deep dynamic reshaping of neural receptive fields going far beyond simple surround suppression. Paradoxically, these highly variable receptive fields go alongside and are in fact required for an invariant representation of external sensory features. In addition to offering a normative account of context-dependent changes in sensory responses, perceptual inference in the presence of signal-dependent noise accounts for ubiquitous features of sensory neurons such as divisive normalization, gain control and contrast dependent temporal dynamics.","lang":"eng"}],"related_material":{"record":[{"id":"9855","status":"public","relation":"research_data"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"oa_version":"Published Version","isi":1,"has_accepted_license":"1","citation":{"apa":"Chalk, M. J., Masset, P., Gutkin, B., &#38; Denève, S. (2017). Sensory noise predicts divisive reshaping of receptive fields. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005582\">https://doi.org/10.1371/journal.pcbi.1005582</a>","ama":"Chalk MJ, Masset P, Gutkin B, Denève S. Sensory noise predicts divisive reshaping of receptive fields. <i>PLoS Computational Biology</i>. 2017;13(6). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005582\">10.1371/journal.pcbi.1005582</a>","chicago":"Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Sensory Noise Predicts Divisive Reshaping of Receptive Fields.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005582\">https://doi.org/10.1371/journal.pcbi.1005582</a>.","ieee":"M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Sensory noise predicts divisive reshaping of receptive fields,” <i>PLoS Computational Biology</i>, vol. 13, no. 6. Public Library of Science, 2017.","mla":"Chalk, Matthew J., et al. “Sensory Noise Predicts Divisive Reshaping of Receptive Fields.” <i>PLoS Computational Biology</i>, vol. 13, no. 6, e1005582, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005582\">10.1371/journal.pcbi.1005582</a>.","short":"M.J. Chalk, P. Masset, B. Gutkin, S. Denève, PLoS Computational Biology 13 (2017).","ista":"Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Sensory noise predicts divisive reshaping of receptive fields. PLoS Computational Biology. 13(6), e1005582."},"article_processing_charge":"No","publication_identifier":{"issn":["1553-734X"]},"type":"journal_article","_id":"680","status":"public","year":"2017","department":[{"_id":"GaTk"}],"intvolume":"        13","file_date_updated":"2020-07-14T12:47:40Z","oa":1,"date_created":"2018-12-11T11:47:53Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","external_id":{"isi":["000404565400034"]},"language":[{"iso":"eng"}],"publist_id":"7035","scopus_import":"1","ddc":["571"],"publisher":"Public Library of Science","doi":"10.1371/journal.pcbi.1005582","day":"01"},{"scopus_import":"1","ddc":["530","571"],"publist_id":"6960","day":"19","publisher":"Public Library of Science","doi":"10.1371/journal.pcbi.1005763","year":"2017","department":[{"_id":"GaTk"}],"intvolume":"        13","project":[{"name":"Information processing and computation in fish groups","_id":"255008E4-B435-11E9-9278-68D0E5697425","grant_number":"RGP0065/2012"},{"grant_number":"P 25651-N26","call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000411981000042"]},"oa":1,"file_date_updated":"2020-07-14T12:47:53Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:48:08Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","isi":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Advances in multi-unit recordings pave the way for statistical modeling of activity patterns in large neural populations. Recent studies have shown that the summed activity of all neurons strongly shapes the population response. A separate recent finding has been that neural populations also exhibit criticality, an anomalously large dynamic range for the probabilities of different population activity patterns. Motivated by these two observations, we introduce a class of probabilistic models which takes into account the prior knowledge that the neural population could be globally coupled and close to critical. These models consist of an energy function which parametrizes interactions between small groups of neurons, and an arbitrary positive, strictly increasing, and twice differentiable function which maps the energy of a population pattern to its probability. We show that: 1) augmenting a pairwise Ising model with a nonlinearity yields an accurate description of the activity of retinal ganglion cells which outperforms previous models based on the summed activity of neurons; 2) prior knowledge that the population is critical translates to prior expectations about the shape of the nonlinearity; 3) the nonlinearity admits an interpretation in terms of a continuous latent variable globally coupling the system whose distribution we can infer from data. Our method is independent of the underlying system’s state space; hence, it can be applied to other systems such as natural scenes or amino acid sequences of proteins which are also known to exhibit criticality."}],"volume":13,"month":"09","pubrep_id":"884","issue":"9","date_updated":"2025-09-10T10:58:42Z","_id":"720","status":"public","article_processing_charge":"Yes","citation":{"mla":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” <i>PLoS Computational Biology</i>, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">10.1371/journal.pcbi.1005763</a>.","chicago":"Humplik, Jan, and Gašper Tkačik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">https://doi.org/10.1371/journal.pcbi.1005763</a>.","ieee":"J. Humplik and G. Tkačik, “Probabilistic models for neural populations that naturally capture global coupling and criticality,” <i>PLoS Computational Biology</i>, vol. 13, no. 9. Public Library of Science, 2017.","ista":"Humplik J, Tkačik G. 2017. Probabilistic models for neural populations that naturally capture global coupling and criticality. PLoS Computational Biology. 13(9), e1005763.","short":"J. Humplik, G. Tkačik, PLoS Computational Biology 13 (2017).","apa":"Humplik, J., &#38; Tkačik, G. (2017). Probabilistic models for neural populations that naturally capture global coupling and criticality. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">https://doi.org/10.1371/journal.pcbi.1005763</a>","ama":"Humplik J, Tkačik G. Probabilistic models for neural populations that naturally capture global coupling and criticality. <i>PLoS Computational Biology</i>. 2017;13(9). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005763\">10.1371/journal.pcbi.1005763</a>"},"type":"journal_article","publication_identifier":{"issn":["1553-734X"]},"file":[{"file_size":14167050,"date_created":"2018-12-12T10:18:30Z","access_level":"open_access","file_id":"5352","file_name":"IST-2017-884-v1+1_journal.pcbi.1005763.pdf","content_type":"application/pdf","relation":"main_file","creator":"system","checksum":"81107096c19771c36ddbe6f0282a3acb","date_updated":"2020-07-14T12:47:53Z"}],"publication":"PLoS Computational Biology","quality_controlled":"1","publication_status":"published","date_published":"2017-09-19T00:00:00Z","article_number":"e1005763","author":[{"id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Humplik","full_name":"Humplik, Jan"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"title":"Probabilistic models for neural populations that naturally capture global coupling and criticality"},{"status":"public","_id":"725","article_processing_charge":"No","citation":{"ista":"Harpaz R, Tkačik G, Schneidman E. 2017. Discrete modes of social information processing predict individual behavior of fish in a group. PNAS. 114(38), 10149–10154.","short":"R. Harpaz, G. Tkačik, E. Schneidman, PNAS 114 (2017) 10149–10154.","mla":"Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” <i>PNAS</i>, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:<a href=\"https://doi.org/10.1073/pnas.1703817114\">10.1073/pnas.1703817114</a>.","chicago":"Harpaz, Roy, Gašper Tkačik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1703817114\">https://doi.org/10.1073/pnas.1703817114</a>.","ieee":"R. Harpaz, G. Tkačik, and E. Schneidman, “Discrete modes of social information processing predict individual behavior of fish in a group,” <i>PNAS</i>, vol. 114, no. 38. National Academy of Sciences, pp. 10149–10154, 2017.","ama":"Harpaz R, Tkačik G, Schneidman E. Discrete modes of social information processing predict individual behavior of fish in a group. <i>PNAS</i>. 2017;114(38):10149-10154. doi:<a href=\"https://doi.org/10.1073/pnas.1703817114\">10.1073/pnas.1703817114</a>","apa":"Harpaz, R., Tkačik, G., &#38; Schneidman, E. (2017). Discrete modes of social information processing predict individual behavior of fish in a group. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1703817114\">https://doi.org/10.1073/pnas.1703817114</a>"},"type":"journal_article","publication_identifier":{"issn":["0027-8424"]},"oa_version":"Submitted Version","isi":1,"volume":114,"month":"09","abstract":[{"lang":"eng","text":"Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here, we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. We show that fish alternate between an “active” mode, in which they are sensitive to the swimming patterns of conspecifics, and a “passive” mode, where they ignore them. Using a model that accounts for these two modes explicitly, we predict behaviors of individual fish with high accuracy, outperforming previous approaches that assumed a single continuous computation by individuals and simple metric or topological weighing of neighbors’ behavior. At the group level, switching between active and passive modes is uncorrelated among fish, but correlated directional swimming behavior still emerges. Our quantitative approach for studying complex, multi-modal individual behavior jointly with emergent group behavior is readily extensible to additional behavioral modes and their neural correlates as well as to other species."}],"date_updated":"2025-09-10T10:53:06Z","issue":"38","date_published":"2017-09-19T00:00:00Z","author":[{"first_name":"Roy","last_name":"Harpaz","full_name":"Harpaz, Roy"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"last_name":"Schneidman","full_name":"Schneidman, Elad","first_name":"Elad"}],"title":"Discrete modes of social information processing predict individual behavior of fish in a group","publication":"PNAS","quality_controlled":"1","pmid":1,"publication_status":"published","page":"10149 - 10154","day":"19","publisher":"National Academy of Sciences","doi":"10.1073/pnas.1703817114","scopus_import":"1","publist_id":"6953","language":[{"iso":"eng"}],"external_id":{"isi":["000411157100063"],"pmid":["28874581"]},"oa":1,"date_created":"2018-12-11T11:48:10Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5617265/","open_access":"1"}],"intvolume":"       114","department":[{"_id":"GaTk"}],"year":"2017"},{"publication_status":"published","page":"120 - 126","publication":"Current Opinion in Neurobiology","quality_controlled":"1","title":"Maximum entropy models as a tool for building precise neural controls","author":[{"full_name":"Savin, Cristina","last_name":"Savin","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"date_published":"2017-10-01T00:00:00Z","date_updated":"2026-04-16T10:04:15Z","volume":46,"month":"10","abstract":[{"lang":"eng","text":"Neural responses are highly structured, with population activity restricted to a small subset of the astronomical range of possible activity patterns. Characterizing these statistical regularities is important for understanding circuit computation, but challenging in practice. Here we review recent approaches based on the maximum entropy principle used for quantifying collective behavior in neural activity. We highlight recent models that capture population-level statistics of neural data, yielding insights into the organization of the neural code and its biological substrate. Furthermore, the MaxEnt framework provides a general recipe for constructing surrogate ensembles that preserve aspects of the data, but are otherwise maximally unstructured. This idea can be used to generate a hierarchy of controls against which rigorous statistical tests are possible."}],"oa_version":"None","isi":1,"citation":{"apa":"Savin, C., &#38; Tkačik, G. (2017). Maximum entropy models as a tool for building precise neural controls. <i>Current Opinion in Neurobiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.conb.2017.08.001\">https://doi.org/10.1016/j.conb.2017.08.001</a>","ama":"Savin C, Tkačik G. Maximum entropy models as a tool for building precise neural controls. <i>Current Opinion in Neurobiology</i>. 2017;46:120-126. doi:<a href=\"https://doi.org/10.1016/j.conb.2017.08.001\">10.1016/j.conb.2017.08.001</a>","mla":"Savin, Cristina, and Gašper Tkačik. “Maximum Entropy Models as a Tool for Building Precise Neural Controls.” <i>Current Opinion in Neurobiology</i>, vol. 46, Elsevier, 2017, pp. 120–26, doi:<a href=\"https://doi.org/10.1016/j.conb.2017.08.001\">10.1016/j.conb.2017.08.001</a>.","chicago":"Savin, Cristina, and Gašper Tkačik. “Maximum Entropy Models as a Tool for Building Precise Neural Controls.” <i>Current Opinion in Neurobiology</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.conb.2017.08.001\">https://doi.org/10.1016/j.conb.2017.08.001</a>.","ieee":"C. Savin and G. Tkačik, “Maximum entropy models as a tool for building precise neural controls,” <i>Current Opinion in Neurobiology</i>, vol. 46. Elsevier, pp. 120–126, 2017.","ista":"Savin C, Tkačik G. 2017. Maximum entropy models as a tool for building precise neural controls. Current Opinion in Neurobiology. 46, 120–126.","short":"C. Savin, G. Tkačik, Current Opinion in Neurobiology 46 (2017) 120–126."},"article_processing_charge":"No","publication_identifier":{"issn":["0959-4388"]},"type":"journal_article","_id":"730","status":"public","project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"GaTk"}],"intvolume":"        46","year":"2017","ec_funded":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_created":"2018-12-11T11:48:11Z","external_id":{"isi":["000416196400016"]},"language":[{"iso":"eng"}],"publist_id":"6943","scopus_import":"1","publisher":"Elsevier","doi":"10.1016/j.conb.2017.08.001","day":"01"}]