[{"year":"2017","language":[{"iso":"eng"}],"ddc":["539","576"],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6071"}]},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"pubrep_id":"864","author":[{"id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar","full_name":"Friedlander, Tamar","last_name":"Friedlander"},{"last_name":"Prizak","full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"}],"publication_status":"published","publist_id":"6459","day":"09","license":"https://creativecommons.org/licenses/by/4.0/","date_created":"2018-12-11T11:49:23Z","publication":"Nature Communications","publisher":"Nature Publishing Group","date_updated":"2025-05-28T11:42:50Z","doi":"10.1038/s41467-017-00238-8","article_processing_charge":"Yes (in subscription journal)","article_number":"216","quality_controlled":"1","oa":1,"file":[{"creator":"system","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:14:14Z","file_id":"5064","date_updated":"2020-07-14T12:48:16Z","file_size":998157,"access_level":"open_access","file_name":"IST-2017-864-v1+1_s41467-017-00238-8.pdf","checksum":"29a1b5db458048d3bd5c67e0e2a56818"},{"file_name":"IST-2017-864-v1+2_41467_2017_238_MOESM1_ESM.pdf","access_level":"open_access","checksum":"7b78401e52a576cf3e6bbf8d0abadc17","date_updated":"2020-07-14T12:48:16Z","file_size":9715993,"content_type":"application/pdf","file_id":"5065","date_created":"2018-12-12T10:14:15Z","creator":"system","relation":"main_file"}],"month":"08","volume":8,"date_published":"2017-08-09T00:00:00Z","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"},{"call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","external_id":{"isi":["000407198800005"]},"oa_version":"Published Version","isi":1,"scopus_import":"1","file_date_updated":"2020-07-14T12:48:16Z","issue":"1","publication_identifier":{"issn":["20411723"]},"_id":"955","title":"Evolution of new regulatory functions on biophysically realistic fitness landscapes","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"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","ec_funded":1,"status":"public","has_accepted_license":"1","intvolume":"         8","citation":{"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>.","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>.","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>","short":"T. Friedlander, R. Prizak, N.H. Barton, G. Tkačik, Nature Communications 8 (2017).","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.","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>","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."}},{"isi":1,"scopus_import":"1","issue":"6","publication_identifier":{"issn":["24700045"]},"abstract":[{"text":"In this work it is shown that scale-free tails in metabolic flux distributions inferred in stationary models are an artifact due to reactions involved in thermodynamically unfeasible cycles, unbounded by physical constraints and in principle able to perform work without expenditure of free energy. After implementing thermodynamic constraints by removing such loops, metabolic flux distributions scale meaningfully with the physical limiting factors, acquiring in turn a richer multimodal structure potentially leading to symmetry breaking while optimizing for objective functions.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"959","title":"Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics","ec_funded":1,"status":"public","main_file_link":[{"url":"https://arxiv.org/pdf/1703.00853.pdf","open_access":"1"}],"intvolume":"        95","citation":{"short":"D. De Martino,  Physical Review E Statistical Nonlinear and Soft Matter Physics  95 (2017) 062419.","ieee":"D. De Martino, “Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics,” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 95, no. 6. American Institute of Physics, p. 062419, 2017.","apa":"De Martino, D. (2017). Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">https://doi.org/10.1103/PhysRevE.95.062419</a>","ista":"De Martino D. 2017. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics.  Physical Review E Statistical Nonlinear and Soft Matter Physics . 95(6), 062419.","chicago":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. American Institute of Physics, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">https://doi.org/10.1103/PhysRevE.95.062419</a>.","mla":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>, vol. 95, no. 6, American Institute of Physics, 2017, p. 062419, doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">10.1103/PhysRevE.95.062419</a>.","ama":"De Martino D. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. <i> Physical Review E Statistical Nonlinear and Soft Matter Physics </i>. 2017;95(6):062419. doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">10.1103/PhysRevE.95.062419</a>"},"year":"2017","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"author":[{"last_name":"De Martino","orcid":"0000-0002-5214-4706","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele"}],"page":"062419","date_created":"2018-12-11T11:49:25Z","publist_id":"6446","publication_status":"published","day":"28","article_processing_charge":"No","publication":" Physical Review E Statistical Nonlinear and Soft Matter Physics ","date_updated":"2023-09-22T09:59:01Z","doi":"10.1103/PhysRevE.95.062419","publisher":"American Institute of Physics","month":"06","quality_controlled":"1","oa":1,"volume":95,"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"type":"journal_article","date_published":"2017-06-28T00:00:00Z","external_id":{"isi":["000404546400004"]},"oa_version":"Submitted Version"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.1f1rc"}],"citation":{"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>.","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>","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>.","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).","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."},"oa_version":"Published Version","status":"public","type":"research_data_reference","date_published":"2017-10-18T00:00:00Z","oa":1,"month":"10","_id":"9709","date_updated":"2023-02-21T16:34:41Z","title":"Data from: Error-robust modes of the retinal population code","doi":"10.5061/dryad.1f1rc","publisher":"Dryad","abstract":[{"lang":"eng","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."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","day":"18","date_created":"2021-07-23T11:34:34Z","author":[{"last_name":"Prentice","first_name":"Jason","full_name":"Prentice, Jason"},{"last_name":"Marre","first_name":"Olivier","full_name":"Marre, Olivier"},{"last_name":"Ioffe","first_name":"Mark","full_name":"Ioffe, Mark"},{"last_name":"Loback","first_name":"Adrianna","full_name":"Loback, Adrianna"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"first_name":"Michael","full_name":"Berry, Michael","last_name":"Berry"}],"department":[{"_id":"GaTk"}],"year":"2017","related_material":{"record":[{"id":"1197","status":"public","relation":"used_in_publication"}]}},{"status":"public","date_published":"2017-06-01T00:00:00Z","type":"research_data_reference","citation":{"ista":"Chalk MJ, Masset P, Gutkin B, Denève S. 2017. Supplementary appendix, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005582.s001\">10.1371/journal.pcbi.1005582.s001</a>.","apa":"Chalk, M. J., Masset, P., Gutkin, B., &#38; Denève, S. (2017). Supplementary appendix. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005582.s001\">https://doi.org/10.1371/journal.pcbi.1005582.s001</a>","ieee":"M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Supplementary appendix.” Public Library of Science, 2017.","short":"M.J. Chalk, P. Masset, B. Gutkin, S. Denève, (2017).","ama":"Chalk MJ, Masset P, Gutkin B, Denève S. Supplementary appendix. 2017. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005582.s001\">10.1371/journal.pcbi.1005582.s001</a>","mla":"Chalk, Matthew J., et al. <i>Supplementary Appendix</i>. Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005582.s001\">10.1371/journal.pcbi.1005582.s001</a>.","chicago":"Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Supplementary Appendix.” Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005582.s001\">https://doi.org/10.1371/journal.pcbi.1005582.s001</a>."},"oa_version":"Published Version","_id":"9855","doi":"10.1371/journal.pcbi.1005582.s001","date_updated":"2023-02-23T12:52:17Z","title":"Supplementary appendix","publisher":"Public Library of Science","abstract":[{"lang":"eng","text":"Includes derivation of optimal estimation algorithm, generalisation to non-poisson noise statistics, correlated input noise, and implementation of in a multi-layer neural network."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","month":"06","author":[{"orcid":"0000-0001-7782-4436","last_name":"Chalk","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J","full_name":"Chalk, Matthew J"},{"last_name":"Masset","full_name":"Masset, Paul","first_name":"Paul"},{"full_name":"Gutkin, Boris","first_name":"Boris","last_name":"Gutkin"},{"last_name":"Denève","full_name":"Denève, Sophie","first_name":"Sophie"}],"day":"01","date_created":"2021-08-10T07:05:10Z","year":"2017","related_material":{"record":[{"id":"680","relation":"used_in_publication","status":"public"}]},"department":[{"_id":"GaTk"}]},{"file_date_updated":"2020-07-14T12:48:19Z","isi":1,"scopus_import":"1","publication_identifier":{"issn":["20411723"]},"abstract":[{"lang":"eng","text":"In real-world applications, observations are often constrained to a small fraction of a system. Such spatial subsampling can be caused by the inaccessibility or the sheer size of the system, and cannot be overcome by longer sampling. Spatial subsampling can strongly bias inferences about a system’s aggregated properties. To overcome the bias, we derive analytically a subsampling scaling framework that is applicable to different observables, including distributions of neuronal avalanches, of number of people infected during an epidemic outbreak, and of node degrees. We demonstrate how to infer the correct distributions of the underlying full system, how to apply it to distinguish critical from subcritical systems, and how to disentangle subsampling and finite size effects. Lastly, we apply subsampling scaling to neuronal avalanche models and to recordings from developing neural networks. We show that only mature, but not young networks follow power-law scaling, indicating self-organization to criticality during development."}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"993","title":"Subsampling scaling","has_accepted_license":"1","intvolume":"         8","citation":{"short":"A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017).","ieee":"A. Levina (Martius) and V. Priesemann, “Subsampling scaling,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","apa":"Levina (Martius), A., &#38; Priesemann, V. (2017). Subsampling scaling. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms15140\">https://doi.org/10.1038/ncomms15140</a>","ista":"Levina (Martius) A, Priesemann V. 2017. Subsampling scaling. Nature Communications. 8, 15140.","chicago":"Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” <i>Nature Communications</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/ncomms15140\">https://doi.org/10.1038/ncomms15140</a>.","mla":"Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.” <i>Nature Communications</i>, vol. 8, 15140, Nature Publishing Group, 2017, doi:<a href=\"https://doi.org/10.1038/ncomms15140\">10.1038/ncomms15140</a>.","ama":"Levina (Martius) A, Priesemann V. Subsampling scaling. <i>Nature Communications</i>. 2017;8. doi:<a href=\"https://doi.org/10.1038/ncomms15140\">10.1038/ncomms15140</a>"},"ec_funded":1,"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"GaTk"},{"_id":"JoCs"}],"year":"2017","ddc":["005","571"],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:49:35Z","publist_id":"6406","publication_status":"published","day":"04","pubrep_id":"819","author":[{"last_name":"Levina (Martius)","full_name":"Levina (Martius), Anna","first_name":"Anna","id":"35AF8020-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Priesemann, Viola","first_name":"Viola","last_name":"Priesemann"}],"month":"05","article_number":"15140","oa":1,"quality_controlled":"1","file":[{"file_id":"5122","date_created":"2018-12-12T10:15:05Z","content_type":"application/pdf","creator":"system","relation":"main_file","checksum":"9880212f8c4c53404c7c6fbf9023c53a","file_name":"IST-2017-819-v1+1_2017_Levina_SubsamplingScaling.pdf","access_level":"open_access","file_size":746224,"date_updated":"2020-07-14T12:48:19Z"}],"article_processing_charge":"Yes (in subscription journal)","publication":"Nature Communications","publisher":"Nature Publishing Group","doi":"10.1038/ncomms15140","date_updated":"2023-09-22T09:54:07Z","oa_version":"Published Version","external_id":{"isi":["000400560700001"]},"volume":8,"type":"journal_article","date_published":"2017-05-04T00:00:00Z","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}]},{"external_id":{"isi":["000417241200004"]},"oa_version":"Published Version","date_published":"2017-12-06T00:00:00Z","type":"journal_article","project":[{"name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches","call_identifier":"FP7","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425","grant_number":"604102"},{"name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26"}],"volume":8,"month":"12","quality_controlled":"1","oa":1,"file":[{"content_type":"application/pdf","date_created":"2018-12-12T10:16:06Z","file_id":"5191","relation":"main_file","creator":"system","file_name":"IST-2018-921-v1+1_s41467-017-02159-y.pdf","access_level":"open_access","date_updated":"2018-12-12T10:16:06Z","file_size":2872887}],"article_number":"1964","article_processing_charge":"No","publisher":"Nature Publishing Group","date_updated":"2023-09-20T11:41:19Z","doi":"10.1038/s41467-017-02159-y","publication":"Nature Communications","date_created":"2018-12-11T11:50:10Z","day":"06","publist_id":"6266","publication_status":"published","author":[{"first_name":"Stephane","full_name":"Deny, Stephane","last_name":"Deny"},{"last_name":"Ferrari","first_name":"Ulisse","full_name":"Ferrari, Ulisse"},{"last_name":"Mace","full_name":"Mace, Emilie","first_name":"Emilie"},{"full_name":"Yger, Pierre","first_name":"Pierre","last_name":"Yger"},{"first_name":"Romain","full_name":"Caplette, Romain","last_name":"Caplette"},{"last_name":"Picaud","first_name":"Serge","full_name":"Picaud, Serge"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"}],"pubrep_id":"921","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"GaTk"}],"ddc":["571"],"year":"2017","language":[{"iso":"eng"}],"citation":{"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>.","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>","short":"S. Deny, U. Ferrari, E. Mace, P. Yger, R. Caplette, S. Picaud, G. Tkačik, O. Marre, Nature Communications 8 (2017).","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.","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>","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."},"intvolume":"         8","has_accepted_license":"1","status":"public","ec_funded":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","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."}],"title":"Multiplexed computations in retinal ganglion cells of a single type","_id":"1104","publication_identifier":{"issn":["20411723"]},"issue":"1","file_date_updated":"2018-12-12T10:16:06Z","scopus_import":"1","isi":1},{"_id":"1220","title":"Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency","publisher":"AIAA","date_updated":"2023-02-21T10:17:50Z","doi":"10.2514/6.2016-3764","abstract":[{"lang":"eng","text":"Theoretical and numerical aspects of aerodynamic efficiency of propulsion systems coupled to the boundary layer of a fuselage are studied. We discuss the effects of local flow fields, which are affected both by conservative flow acceleration as well as total pressure losses, on the efficiency of boundary layer immersed propulsion devices. We introduce the concept of a boundary layer retardation turbine that helps reduce skin friction over the fuselage. We numerically investigate efficiency gains offered by boundary layer and wake interacting devices. We discuss the results in terms of a total energy consumption framework and show that efficiency gains of any device depend on all the other elements of the propulsion system."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","month":"06","status":"public","type":"conference","date_published":"2016-06-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://ntrs.nasa.gov/search.jsp?R=20160010167&amp;hterms=Fuselage+boundary+layer+ingestion+propulsion+applied+thin+haul+commuter+aircraft+optimal+efficiency&amp;qs=N%3D0%26Ntk%3DAll%26Ntt%3DFuselage%2520boundary%2520layer%2520ingestion%2520propulsion%2520applied%2520to%2520a%2520thin%2520haul%2520commuter%2520aircraft%2520for%2520optimal%2520efficiency%26Ntx%3Dmode%2520matchallpartial%26Nm%3D123%7CCollection%7CNASA%2520STI%7C%7C17%7CCollection%7CNACA"}],"citation":{"chicago":"Mikić, Gregor, Alex Stoll, Joe Bevirt, Rok Grah, and Mark Moore. “Fuselage Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for Optimal Efficiency,” 1–19. AIAA, 2016. <a href=\"https://doi.org/10.2514/6.2016-3764\">https://doi.org/10.2514/6.2016-3764</a>.","ama":"Mikić G, Stoll A, Bevirt J, Grah R, Moore M. Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency. In: AIAA; 2016:1-19. doi:<a href=\"https://doi.org/10.2514/6.2016-3764\">10.2514/6.2016-3764</a>","mla":"Mikić, Gregor, et al. <i>Fuselage Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for Optimal Efficiency</i>. AIAA, 2016, pp. 1–19, doi:<a href=\"https://doi.org/10.2514/6.2016-3764\">10.2514/6.2016-3764</a>.","ieee":"G. Mikić, A. Stoll, J. Bevirt, R. Grah, and M. Moore, “Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency,” presented at the AIAA: Aviation Technology, Integration, and Operations Conference, Washington, D.C., USA, 2016, pp. 1–19.","short":"G. Mikić, A. Stoll, J. Bevirt, R. Grah, M. Moore, in:, AIAA, 2016, pp. 1–19.","ista":"Mikić G, Stoll A, Bevirt J, Grah R, Moore M. 2016. Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency. AIAA: Aviation Technology, Integration, and Operations Conference, 1–19.","apa":"Mikić, G., Stoll, A., Bevirt, J., Grah, R., &#38; Moore, M. (2016). Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency (pp. 1–19). Presented at the AIAA: Aviation Technology, Integration, and Operations Conference, Washington, D.C., USA: AIAA. <a href=\"https://doi.org/10.2514/6.2016-3764\">https://doi.org/10.2514/6.2016-3764</a>"},"oa_version":"Preprint","language":[{"iso":"eng"}],"year":"2016","scopus_import":1,"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"page":"1 - 19","conference":{"location":"Washington, D.C., USA","end_date":"2016-06-17","start_date":"2016-06-13","name":"AIAA: Aviation Technology, Integration, and Operations Conference"},"author":[{"full_name":"Mikić, Gregor","first_name":"Gregor","last_name":"Mikić"},{"full_name":"Stoll, Alex","first_name":"Alex","last_name":"Stoll"},{"full_name":"Bevirt, Joe","first_name":"Joe","last_name":"Bevirt"},{"first_name":"Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok","last_name":"Grah","orcid":"0000-0003-2539-3560"},{"last_name":"Moore","full_name":"Moore, Mark","first_name":"Mark"}],"publication_status":"published","publist_id":"6114","day":"01","date_created":"2018-12-11T11:50:47Z"},{"status":"public","citation":{"ieee":"T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic range of transcription factor action by translational regulation,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 93, no. 2. American Institute of Physics, 2016.","short":"T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (2016).","apa":"Sokolowski, T. R., Walczak, A., Bialek, W., &#38; Tkačik, G. (2016). Extending the dynamic range of transcription factor action by translational regulation. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">https://doi.org/10.1103/PhysRevE.93.022404</a>","ista":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404.","chicago":"Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2016. <a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">https://doi.org/10.1103/PhysRevE.93.022404</a>.","mla":"Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 93, no. 2, 022404, American Institute of Physics, 2016, doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">10.1103/PhysRevE.93.022404</a>.","ama":"Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of transcription factor action by translational regulation. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2016;93(2). doi:<a href=\"https://doi.org/10.1103/PhysRevE.93.022404\">10.1103/PhysRevE.93.022404</a>"},"intvolume":"        93","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1507.02562"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule acts as an independent sensor of the input concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression."}],"title":"Extending the dynamic range of transcription factor action by translational regulation","_id":"1242","acknowledgement":"We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions. This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370 from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W. acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561. G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S.","issue":"2","scopus_import":1,"type":"journal_article","date_published":"2016-02-04T00:00:00Z","project":[{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"volume":93,"oa_version":"Preprint","publisher":"American Institute of Physics","date_updated":"2021-01-12T06:49:20Z","doi":"10.1103/PhysRevE.93.022404","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","month":"02","oa":1,"quality_controlled":"1","article_number":"022404","author":[{"last_name":"Sokolowski","orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R","full_name":"Sokolowski, Thomas R"},{"first_name":"Aleksandra","full_name":"Walczak, Aleksandra","last_name":"Walczak"},{"full_name":"Bialek, William","first_name":"William","last_name":"Bialek"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Tkacik, Gasper"}],"date_created":"2018-12-11T11:50:54Z","day":"04","publication_status":"published","publist_id":"6088","language":[{"iso":"eng"}],"year":"2016","department":[{"_id":"GaTk"}]},{"oa_version":"Submitted Version","type":"journal_article","date_published":"2016-02-16T00:00:00Z","volume":113,"month":"02","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","doi":"10.1073/pnas.1419248113","date_updated":"2021-01-12T06:49:21Z","publication":"PNAS","date_created":"2018-12-11T11:50:55Z","day":"16","publication_status":"published","publist_id":"6085","author":[{"last_name":"Recouvreux","first_name":"Pierre","full_name":"Recouvreux, Pierre"},{"orcid":"0000-0002-1287-3779","last_name":"Sokolowski","full_name":"Sokolowski, Thomas R","first_name":"Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Grammoustianou","first_name":"Aristea","full_name":"Grammoustianou, Aristea"},{"first_name":"Pieter","full_name":"Tenwolde, Pieter","last_name":"Tenwolde"},{"last_name":"Dogterom","full_name":"Dogterom, Marileen","first_name":"Marileen"}],"page":"1811 - 1816","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"year":"2016","intvolume":"       113","citation":{"short":"P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom, PNAS 113 (2016) 1811–1816.","ieee":"P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom, “Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells,” <i>PNAS</i>, vol. 113, no. 7. National Academy of Sciences, pp. 1811–1816, 2016.","ista":"Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. 113(7), 1811–1816.","apa":"Recouvreux, P., Sokolowski, T. R., Grammoustianou, A., Tenwolde, P., &#38; Dogterom, M. (2016). Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1419248113\">https://doi.org/10.1073/pnas.1419248113</a>","chicago":"Recouvreux, Pierre, Thomas R Sokolowski, Aristea Grammoustianou, Pieter Tenwolde, and Marileen Dogterom. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” <i>PNAS</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1419248113\">https://doi.org/10.1073/pnas.1419248113</a>.","ama":"Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. <i>PNAS</i>. 2016;113(7):1811-1816. doi:<a href=\"https://doi.org/10.1073/pnas.1419248113\">10.1073/pnas.1419248113</a>","mla":"Recouvreux, Pierre, et al. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” <i>PNAS</i>, vol. 113, no. 7, National Academy of Sciences, 2016, pp. 1811–16, doi:<a href=\"https://doi.org/10.1073/pnas.1419248113\">10.1073/pnas.1419248113</a>."},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/","open_access":"1"}],"status":"public","acknowledgement":"We thank Sophie Martin, Ken Sawin, Stephen Huisman,\r\nand Damian Brunner for strains; Julianne\r\nTeapal, Marcel Janson, Sergio Rincon,\r\nand Phong Tran for technical assistance; Andrew Mugler and Bela Mulder for\r\ndiscussions; and Sander Tans, Phong Tran,\r\nand Anne Paoletti for critical reading\r\nof the manuscript. This work is part of the research program of the\r\n“\r\nStichting\r\nvoor Fundamenteel Onderzoek de Materie,\r\n”\r\nwhich is financially supported by\r\nthe\r\n“\r\nNederlandse organisatie voor Wete\r\nnschappelijk Onderzoek (NWO).\r\n”","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Cell polarity refers to a functional spatial organization of proteins that is crucial for the control of essential cellular processes such as growth and division. To establish polarity, cells rely on elaborate regulation networks that control the distribution of proteins at the cell membrane. In fission yeast cells, a microtubule-dependent network has been identified that polarizes the distribution of signaling proteins that restricts growth to cell ends and targets the cytokinetic machinery to the middle of the cell. Although many molecular components have been shown to play a role in this network, it remains unknown which molecular functionalities are minimally required to establish a polarized protein distribution in this system. Here we show that a membrane-binding protein fragment, which distributes homogeneously in wild-type fission yeast cells, can be made to concentrate at cell ends by attaching it to a cytoplasmic microtubule end-binding protein. This concentration results in a polarized pattern of chimera proteins with a spatial extension that is very reminiscent of natural polarity patterns in fission yeast. However, chimera levels fluctuate in response to microtubule dynamics, and disruption of microtubules leads to disappearance of the pattern. Numerical simulations confirm that the combined functionality of membrane anchoring and microtubule tip affinity is in principle sufficient to create polarized patterns. Our chimera protein may thus represent a simple molecular functionality that is able to polarize the membrane, onto which additional layers of molecular complexity may be built to provide the temporal robustness that is typical of natural polarity patterns."}],"title":"Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells","_id":"1244","issue":"7","scopus_import":1},{"department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"year":"2016","publication_status":"published","publist_id":"6080","day":"10","date_created":"2018-12-11T11:50:56Z","page":"89 - 117","author":[{"full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455"},{"first_name":"William","full_name":"Bialek, William","last_name":"Bialek"}],"oa":1,"quality_controlled":"1","month":"03","publication":"Annual Review of Condensed Matter Physics","doi":"10.1146/annurev-conmatphys-031214-014803","publisher":"Annual Reviews","date_updated":"2021-01-12T06:49:23Z","oa_version":"Preprint","volume":7,"date_published":"2016-03-10T00:00:00Z","type":"journal_article","project":[{"name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26"}],"scopus_import":1,"acknowledgement":"Our work was supported in part by the US\r\nNational Science Foundation (PHY–1305525 and CCF–\r\n0939370), by the Austrian Science Foundation (FWF\r\nP25651), by the Human Frontiers Science Program, and\r\nby the Simons and Swartz Foundations.","_id":"1248","title":"Information processing in living systems","abstract":[{"text":"Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been possible to measure, directly, the flow of information in biological networks, or more generally where information-theoretic ideas have been used to guide the analysis of experiments. Systems of interest range from single molecules (the sequence diversity in families of proteins) to groups of organisms (the distribution of velocities in flocks of birds), and all scales in between. Many of these analyses are motivated by the idea that biological systems may have evolved to optimize the gathering and representation of information, and we review the experimental evidence for this optimization, again across a wide range of scales.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1412.8752"}],"citation":{"ista":"Tkačik G, Bialek W. 2016. Information processing in living systems. Annual Review of Condensed Matter Physics. 7, 89–117.","apa":"Tkačik, G., &#38; Bialek, W. (2016). Information processing in living systems. <i>Annual Review of Condensed Matter Physics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">https://doi.org/10.1146/annurev-conmatphys-031214-014803</a>","ieee":"G. Tkačik and W. Bialek, “Information processing in living systems,” <i>Annual Review of Condensed Matter Physics</i>, vol. 7. Annual Reviews, pp. 89–117, 2016.","short":"G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117.","ama":"Tkačik G, Bialek W. Information processing in living systems. <i>Annual Review of Condensed Matter Physics</i>. 2016;7:89-117. doi:<a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">10.1146/annurev-conmatphys-031214-014803</a>","mla":"Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” <i>Annual Review of Condensed Matter Physics</i>, vol. 7, Annual Reviews, 2016, pp. 89–117, doi:<a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">10.1146/annurev-conmatphys-031214-014803</a>.","chicago":"Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” <i>Annual Review of Condensed Matter Physics</i>. Annual Reviews, 2016. <a href=\"https://doi.org/10.1146/annurev-conmatphys-031214-014803\">https://doi.org/10.1146/annurev-conmatphys-031214-014803</a>."},"intvolume":"         7","status":"public"},{"type":"journal_article","date_published":"2016-06-01T00:00:00Z","volume":27,"oa_version":"Preprint","external_id":{"arxiv":["1505.02963"]},"article_type":"original","doi":"10.1142/S0129183116500674","publisher":"World Scientific Publishing","date_updated":"2021-01-12T06:49:28Z","publication":"International Journal of Modern Physics C","article_processing_charge":"No","oa":1,"quality_controlled":"1","article_number":"1650067","month":"06","author":[{"orcid":"0000-0002-5214-4706","last_name":"De Martino","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele"}],"day":"01","publication_status":"published","publist_id":"6065","arxiv":1,"date_created":"2018-12-11T11:51:00Z","language":[{"iso":"eng"}],"year":"2016","department":[{"_id":"GaTk"}],"status":"public","citation":{"ama":"De Martino D. The dual of the space of interactions in neural network models. <i>International Journal of Modern Physics C</i>. 2016;27(6). doi:<a href=\"https://doi.org/10.1142/S0129183116500674\">10.1142/S0129183116500674</a>","mla":"De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” <i>International Journal of Modern Physics C</i>, vol. 27, no. 6, 1650067, World Scientific Publishing, 2016, doi:<a href=\"https://doi.org/10.1142/S0129183116500674\">10.1142/S0129183116500674</a>.","chicago":"De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” <i>International Journal of Modern Physics C</i>. World Scientific Publishing, 2016. <a href=\"https://doi.org/10.1142/S0129183116500674\">https://doi.org/10.1142/S0129183116500674</a>.","ista":"De Martino D. 2016. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 27(6), 1650067.","apa":"De Martino, D. (2016). The dual of the space of interactions in neural network models. <i>International Journal of Modern Physics C</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129183116500674\">https://doi.org/10.1142/S0129183116500674</a>","ieee":"D. De Martino, “The dual of the space of interactions in neural network models,” <i>International Journal of Modern Physics C</i>, vol. 27, no. 6. World Scientific Publishing, 2016.","short":"D. De Martino, International Journal of Modern Physics C 27 (2016)."},"intvolume":"        27","main_file_link":[{"url":"https://arxiv.org/abs/1505.02963","open_access":"1"}],"title":"The dual of the space of interactions in neural network models","_id":"1260","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"In this work, the Gardner problem of inferring interactions and fields for an Ising neural network from given patterns under a local stability hypothesis is addressed under a dual perspective. By means of duality arguments, an integer linear system is defined whose solution space is the dual of the Gardner space and whose solutions represent mutually unstable patterns. We propose and discuss Monte Carlo methods in order to find and remove unstable patterns and uniformly sample the space of interactions thereafter. We illustrate the problem on a set of real data and perform ensemble calculation that shows how the emergence of phase dominated by unstable patterns can be triggered in a nonlinear discontinuous way.","lang":"eng"}],"issue":"6","scopus_import":1},{"issue":"2016JULY","scopus_import":1,"file_date_updated":"2020-07-14T12:44:42Z","status":"public","citation":{"ista":"Chalk MJ, Gutkin B, Denève S. 2016. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. eLife. 5(2016JULY), e13824.","apa":"Chalk, M. J., Gutkin, B., &#38; Denève, S. (2016). Neural oscillations as a signature of efficient coding in the presence of synaptic delays. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.13824\">https://doi.org/10.7554/eLife.13824</a>","short":"M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016).","ieee":"M. J. Chalk, B. Gutkin, and S. Denève, “Neural oscillations as a signature of efficient coding in the presence of synaptic delays,” <i>eLife</i>, vol. 5, no. 2016JULY. eLife Sciences Publications, 2016.","ama":"Chalk MJ, Gutkin B, Denève S. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. <i>eLife</i>. 2016;5(2016JULY). doi:<a href=\"https://doi.org/10.7554/eLife.13824\">10.7554/eLife.13824</a>","mla":"Chalk, Matthew J., et al. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” <i>ELife</i>, vol. 5, no. 2016JULY, e13824, eLife Sciences Publications, 2016, doi:<a href=\"https://doi.org/10.7554/eLife.13824\">10.7554/eLife.13824</a>.","chicago":"Chalk, Matthew J, Boris Gutkin, and Sophie Denève. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” <i>ELife</i>. eLife Sciences Publications, 2016. <a href=\"https://doi.org/10.7554/eLife.13824\">https://doi.org/10.7554/eLife.13824</a>."},"intvolume":"         5","has_accepted_license":"1","title":"Neural oscillations as a signature of efficient coding in the presence of synaptic delays","_id":"1266","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Cortical networks exhibit ‘global oscillations’, in which neural spike times are entrained to an underlying oscillatory rhythm, but where individual neurons fire irregularly, on only a fraction of cycles. While the network dynamics underlying global oscillations have been well characterised, their function is debated. Here, we show that such global oscillations are a direct consequence of optimal efficient coding in spiking networks with synaptic delays and noise. To avoid firing unnecessary spikes, neurons need to share information about the network state. Ideally, membrane potentials should be strongly correlated and reflect a ‘prediction error’ while the spikes themselves are uncorrelated and occur rarely. We show that the most efficient representation is when: (i) spike times are entrained to a global Gamma rhythm (implying a consistent representation of the error); but (ii) few neurons fire on each cycle (implying high efficiency), while (iii) excitation and inhibition are tightly balanced. This suggests that cortical networks exhibiting such dynamics are tuned to achieve a maximally efficient population code.","lang":"eng"}],"acknowledgement":"Boris Gutkin acknowledges funding by the Russian Academic Excellence Project '5-100’.","author":[{"id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J","full_name":"Chalk, Matthew J","orcid":"0000-0001-7782-4436","last_name":"Chalk"},{"last_name":"Gutkin","first_name":"Boris","full_name":"Gutkin, Boris"},{"first_name":"Sophie","full_name":"Denève, Sophie","last_name":"Denève"}],"pubrep_id":"700","day":"01","publist_id":"6056","publication_status":"published","date_created":"2018-12-11T11:51:02Z","language":[{"iso":"eng"}],"ddc":["571"],"year":"2016","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"GaTk"}],"date_published":"2016-07-01T00:00:00Z","type":"journal_article","volume":5,"oa_version":"Published Version","publisher":"eLife Sciences Publications","date_updated":"2021-01-12T06:49:30Z","doi":"10.7554/eLife.13824","publication":"eLife","quality_controlled":"1","file":[{"checksum":"dc52d967dc76174477bb258d84be2899","access_level":"open_access","file_name":"IST-2016-700-v1+1_e13824-download.pdf","file_size":2819055,"date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:11:20Z","file_id":"4874","content_type":"application/pdf","creator":"system","relation":"main_file"}],"oa":1,"article_number":"e13824","month":"07"},{"file_date_updated":"2020-07-14T12:44:42Z","scopus_import":1,"issue":"9","acknowledgement":"The authors would like to thank Thomas Sokolowski and Filipe Tostevin for helpful discussions. PH and UG were funded by the German Excellence Initiative via the program \"Nanosystems Initiative Munich\" (https://www.nano-initiative-munich.de) and the German Research Foundation via the SFB 1032 \"Nanoagents for Spatiotemporal Control of Molecular and Cellular Reactions\" (http://www.sfb1032.physik.uni-muenchen.de). GT was funded by the Austrian Science Fund (FWF P 28844) (http://www.fwf.ac.at).","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to infer their global position within a tissue or an organism by reading out local gene expression levels. The patterning system is thus said to encode positional information, a concept that was formalized recently in the framework of information theory. Here we introduce a toy model of patterning in one spatial dimension, which can be seen as an extension of Wolpert's paradigmatic &quot;French Flag&quot; model, to patterning by several interacting, spatially coupled genes subject to intrinsic and extrinsic noise. Our model, a variant of an Ising spin system, allows us to systematically explore expression patterns that optimally encode positional information. We find that optimal patterning systems use positional cues, as in the French Flag model, together with gene-gene interactions to generate combinatorial codes for position which we call &quot;Counter&quot; patterns. Counter patterns can also be stabilized against noise and variations in system size or morphogen dosage by longer-range spatial interactions of the type invoked in the Turing model. The simple setup proposed here qualitatively captures many of the experimentally observed properties of biological patterning systems and allows them to be studied in a single, theoretically consistent framework.","lang":"eng"}],"title":"Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information","_id":"1270","intvolume":"        11","citation":{"short":"P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016).","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information,” <i>PLoS One</i>, vol. 11, no. 9. Public Library of Science, 2016.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. 11(9), e0163628.","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628\">https://doi.org/10.1371/journal.pone.0163628</a>","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” <i>PLoS One</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628\">https://doi.org/10.1371/journal.pone.0163628</a>.","ama":"Hillenbrand P, Gerland U, Tkačik G. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. <i>PLoS One</i>. 2016;11(9). doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628\">10.1371/journal.pone.0163628</a>","mla":"Hillenbrand, Patrick, et al. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” <i>PLoS One</i>, vol. 11, no. 9, e0163628, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628\">10.1371/journal.pone.0163628</a>."},"has_accepted_license":"1","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"GaTk"}],"related_material":{"record":[{"id":"9869","status":"public","relation":"research_data"},{"id":"9870","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9871"}]},"year":"2016","ddc":["571"],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:51:03Z","day":"27","publication_status":"published","publist_id":"6050","author":[{"full_name":"Hillenbrand, Patrick","first_name":"Patrick","last_name":"Hillenbrand"},{"first_name":"Ulrich","full_name":"Gerland, Ulrich","last_name":"Gerland"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"}],"pubrep_id":"696","month":"09","oa":1,"quality_controlled":"1","file":[{"date_updated":"2020-07-14T12:44:42Z","file_size":4950415,"file_name":"IST-2016-696-v1+1_journal.pone.0163628.PDF","access_level":"open_access","checksum":"3d0d55d373096a033bd9cf79288c8586","creator":"system","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:10:47Z","file_id":"4837"}],"article_number":"e0163628","date_updated":"2023-02-23T14:11:37Z","doi":"10.1371/journal.pone.0163628","publisher":"Public Library of Science","publication":"PLoS One","oa_version":"Published Version","date_published":"2016-09-27T00:00:00Z","project":[{"name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"type":"journal_article","volume":11},{"scopus_import":1,"issue":"11","acknowledgement":"This work was supported in part by National Institute of Allergy and Infectious Diseases grant U54 AI057159, US National Institutes of Health grants R01 GM081617 (to R.K.) and GM086258 (to J.C.), European Research Council FP7 ERC grant 281891 (to R.K.) and a National Science Foundation Graduate Fellowship (to L.K.S.).\r\n","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We developed a competition-based screening strategy to identify compounds that invert the selective advantage of antibiotic resistance. Using our assay, we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram. Treating a tetracycline-resistant population with β-thujaplicin selects for loss of the resistance gene, enabling an effective second-phase treatment with doxycycline."}],"title":"Compounds that select against the tetracycline-resistance efflux pump","_id":"1290","citation":{"ista":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 12(11), 902–904.","apa":"Stone, L., Baym, M., Lieberman, T., Chait, R. P., Clardy, J., &#38; Kishony, R. (2016). Compounds that select against the tetracycline-resistance efflux pump. <i>Nature Chemical Biology</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nchembio.2176\">https://doi.org/10.1038/nchembio.2176</a>","ieee":"L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds that select against the tetracycline-resistance efflux pump,” <i>Nature Chemical Biology</i>, vol. 12, no. 11. Nature Publishing Group, pp. 902–904, 2016.","short":"L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature Chemical Biology 12 (2016) 902–904.","ama":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. Compounds that select against the tetracycline-resistance efflux pump. <i>Nature Chemical Biology</i>. 2016;12(11):902-904. doi:<a href=\"https://doi.org/10.1038/nchembio.2176\">10.1038/nchembio.2176</a>","mla":"Stone, Laura, et al. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” <i>Nature Chemical Biology</i>, vol. 12, no. 11, Nature Publishing Group, 2016, pp. 902–04, doi:<a href=\"https://doi.org/10.1038/nchembio.2176\">10.1038/nchembio.2176</a>.","chicago":"Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” <i>Nature Chemical Biology</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/nchembio.2176\">https://doi.org/10.1038/nchembio.2176</a>."},"intvolume":"        12","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/"}],"status":"public","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"year":"2016","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:51:10Z","day":"01","publication_status":"published","publist_id":"6026","author":[{"first_name":"Laura","full_name":"Stone, Laura","last_name":"Stone"},{"full_name":"Baym, Michael","first_name":"Michael","last_name":"Baym"},{"full_name":"Lieberman, Tami","first_name":"Tami","last_name":"Lieberman"},{"first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P","orcid":"0000-0003-0876-3187","last_name":"Chait"},{"first_name":"Jon","full_name":"Clardy, Jon","last_name":"Clardy"},{"last_name":"Kishony","full_name":"Kishony, Roy","first_name":"Roy"}],"page":"902 - 904","month":"11","oa":1,"quality_controlled":"1","doi":"10.1038/nchembio.2176","date_updated":"2021-01-12T06:49:39Z","publisher":"Nature Publishing Group","publication":"Nature Chemical Biology","oa_version":"Preprint","type":"journal_article","date_published":"2016-11-01T00:00:00Z","volume":12},{"oa_version":"Preprint","volume":"2016-July","date_published":"2016-07-28T00:00:00Z","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"type":"conference","article_number":"7526722","quality_controlled":"1","file":[{"date_updated":"2020-07-14T12:44:43Z","file_size":539166,"access_level":"local","file_name":"IST-2017-810-v1+1_root.pdf","checksum":"7219432b43defc62a0d45f48d4ce6a19","creator":"system","relation":"main_file","content_type":"application/pdf","file_id":"5203","date_created":"2018-12-12T10:16:17Z"}],"month":"07","date_updated":"2021-01-12T06:49:51Z","doi":"10.1109/ACC.2016.7526722","publisher":"IEEE","publist_id":"5950","publication_status":"published","day":"28","date_created":"2018-12-11T11:51:21Z","conference":{"start_date":"2016-07-06","name":"ACC: American Control Conference","location":"Boston, MA, USA","end_date":"2016-07-08"},"pubrep_id":"810","author":[{"last_name":"Lang","full_name":"Lang, Moritz","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sontag","first_name":"Eduardo","full_name":"Sontag, Eduardo"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"year":"2016","ddc":["003","621"],"language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"ieee":"M. Lang and E. Sontag, “Scale-invariant systems realize nonlinear differential operators,” presented at the ACC: American Control Conference, Boston, MA, USA, 2016, vol. 2016–July.","short":"M. Lang, E. Sontag, in:, IEEE, 2016.","apa":"Lang, M., &#38; Sontag, E. (2016). Scale-invariant systems realize nonlinear differential operators (Vol. 2016–July). Presented at the ACC: American Control Conference, Boston, MA, USA: IEEE. <a href=\"https://doi.org/10.1109/ACC.2016.7526722\">https://doi.org/10.1109/ACC.2016.7526722</a>","ista":"Lang M, Sontag E. 2016. Scale-invariant systems realize nonlinear differential operators. ACC: American Control Conference vol. 2016–July, 7526722.","chicago":"Lang, Moritz, and Eduardo Sontag. “Scale-Invariant Systems Realize Nonlinear Differential Operators,” Vol. 2016–July. IEEE, 2016. <a href=\"https://doi.org/10.1109/ACC.2016.7526722\">https://doi.org/10.1109/ACC.2016.7526722</a>.","mla":"Lang, Moritz, and Eduardo Sontag. <i>Scale-Invariant Systems Realize Nonlinear Differential Operators</i>. Vol. 2016–July, 7526722, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/ACC.2016.7526722\">10.1109/ACC.2016.7526722</a>.","ama":"Lang M, Sontag E. Scale-invariant systems realize nonlinear differential operators. In: Vol 2016-July. IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/ACC.2016.7526722\">10.1109/ACC.2016.7526722</a>"},"ec_funded":1,"status":"public","acknowledgement":"The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734]. Work supported in part by grants AFOSR FA9550-14-1-0060 and NIH 1R01GM100473.","_id":"1320","title":"Scale-invariant systems realize nonlinear differential operators","abstract":[{"lang":"eng","text":"In recent years, several biomolecular systems have been shown to be scale-invariant (SI), i.e. to show the same output dynamics when exposed to geometrically scaled input signals (u → pu, p &gt; 0) after pre-adaptation to accordingly scaled constant inputs. In this article, we show that SI systems-as well as systems invariant with respect to other input transformations-can realize nonlinear differential operators: when excited by inputs obeying functional forms characteristic for a given class of invariant systems, the systems' outputs converge to constant values directly quantifying the speed of the input."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:44:43Z","scopus_import":1},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"ddc":["570","579"],"year":"2016","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:51:25Z","publist_id":"5936","publication_status":"published","day":"20","pubrep_id":"662","author":[{"orcid":"0000-0003-0876-3187","last_name":"Chait","full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P"},{"last_name":"Palmer","full_name":"Palmer, Adam","first_name":"Adam"},{"full_name":"Yelin, Idan","first_name":"Idan","last_name":"Yelin"},{"last_name":"Kishony","full_name":"Kishony, Roy","first_name":"Roy"}],"month":"01","article_number":"10333","quality_controlled":"1","oa":1,"file":[{"creator":"system","relation":"main_file","file_id":"5039","date_created":"2018-12-12T10:13:52Z","content_type":"application/pdf","file_size":1844107,"date_updated":"2020-07-14T12:44:44Z","checksum":"ef147bcbb8bd37e9079cf3ce06f5815d","access_level":"open_access","file_name":"IST-2016-662-v1+1_ncomms10333.pdf"}],"publication":"Nature Communications","doi":"10.1038/ncomms10333","publisher":"Nature Publishing Group","date_updated":"2021-01-12T06:49:57Z","oa_version":"Published Version","volume":7,"date_published":"2016-01-20T00:00:00Z","type":"journal_article","file_date_updated":"2020-07-14T12:44:44Z","scopus_import":1,"acknowledgement":"This work was partially supported by US National Institutes of Health grant R01-GM081617, Israeli Centers of Research Excellence I-CORE Program ISF Grant No. 152/11, and the European Research Council FP7 ERC Grant 281891.","abstract":[{"text":"Antibiotic-sensitive and -resistant bacteria coexist in natural environments with low, if detectable, antibiotic concentrations. Except possibly around localized antibiotic sources, where resistance can provide a strong advantage, bacterial fitness is dominated by stresses unaffected by resistance to the antibiotic. How do such mixed and heterogeneous conditions influence the selective advantage or disadvantage of antibiotic resistance? Here we find that sub-inhibitory levels of tetracyclines potentiate selection for or against tetracycline resistance around localized sources of almost any toxin or stress. Furthermore, certain stresses generate alternating rings of selection for and against resistance around a localized source of the antibiotic. In these conditions, localized antibiotic sources, even at high strengths, can actually produce a net selection against resistance to the antibiotic. Our results show that interactions between the effects of an antibiotic and other stresses in inhomogeneous environments can generate pervasive, complex patterns of selection both for and against antibiotic resistance.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1332","title":"Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments","has_accepted_license":"1","intvolume":"         7","citation":{"ieee":"R. P. Chait, A. Palmer, I. Yelin, and R. Kishony, “Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","short":"R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (2016).","ista":"Chait RP, Palmer A, Yelin I, Kishony R. 2016. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 7, 10333.","apa":"Chait, R. P., Palmer, A., Yelin, I., &#38; Kishony, R. (2016). Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms10333\">https://doi.org/10.1038/ncomms10333</a>","chicago":"Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms10333\">https://doi.org/10.1038/ncomms10333</a>.","ama":"Chait RP, Palmer A, Yelin I, Kishony R. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms10333\">10.1038/ncomms10333</a>","mla":"Chait, Remy P., et al. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” <i>Nature Communications</i>, vol. 7, 10333, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms10333\">10.1038/ncomms10333</a>."},"status":"public"},{"quality_controlled":"1","oa":1,"file":[{"relation":"main_file","creator":"cziletti","content_type":"application/pdf","file_id":"8096","date_created":"2020-07-06T12:59:09Z","date_updated":"2020-07-14T12:48:09Z","file_size":678670,"file_name":"2016_ProcALIFE_Martius.pdf","access_level":"open_access","checksum":"cff63e7a4b8ac466ba51a9c84153a940"}],"month":"09","publication":"Proceedings of the Artificial Life Conference 2016","publisher":"MIT Press","doi":"10.7551/978-0-262-33936-0-ch029","date_updated":"2021-01-12T08:16:53Z","article_processing_charge":"No","oa_version":"Published Version","volume":28,"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"type":"conference","date_published":"2016-09-01T00:00:00Z","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2016","language":[{"iso":"eng"}],"ddc":["610"],"publication_status":"published","day":"01","date_created":"2020-07-05T22:00:47Z","page":"142-143","conference":{"end_date":"2016-07-08","location":"Cancun, Mexico","name":"ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems","start_date":"2016-07-04"},"author":[{"last_name":"Martius","first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S"},{"last_name":"Hostettler","full_name":"Hostettler, Rafael","first_name":"Rafael"},{"last_name":"Knoll","first_name":"Alois","full_name":"Knoll, Alois"},{"last_name":"Der","full_name":"Der, Ralf","first_name":"Ralf"}],"_id":"8094","title":"Self-organized control of an tendon driven arm by differential extrinsic plasticity","abstract":[{"text":"With the accelerated development of robot technologies, optimal 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 the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.","lang":"eng"}],"user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","has_accepted_license":"1","intvolume":"        28","citation":{"ama":"Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon driven arm by differential extrinsic plasticity. In: <i>Proceedings of the Artificial Life Conference 2016</i>. Vol 28. MIT Press; 2016:142-143. doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>","mla":"Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” <i>Proceedings of the Artificial Life Conference 2016</i>, vol. 28, MIT Press, 2016, pp. 142–43, doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>.","chicago":"Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In <i>Proceedings of the Artificial Life Conference 2016</i>, 28:142–43. MIT Press, 2016. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>.","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. Proceedings of the Artificial Life Conference 2016. ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.","apa":"Martius, G. S., Hostettler, R., Knoll, A., &#38; Der, R. (2016). Self-organized control of an tendon driven arm by differential extrinsic plasticity. In <i>Proceedings of the Artificial Life Conference 2016</i> (Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial Life Conference 2016, MIT Press, 2016, pp. 142–143.","ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in <i>Proceedings of the Artificial Life Conference 2016</i>, Cancun, Mexico, 2016, vol. 28, pp. 142–143."},"ec_funded":1,"status":"public","file_date_updated":"2020-07-14T12:48:09Z","scopus_import":1,"publication_identifier":{"isbn":["9780262339360"]}},{"month":"01","oa":1,"quality_controlled":"1","article_number":"016003","doi":"10.1088/1478-3975/13/1/016003","publisher":"IOP Publishing Ltd.","date_updated":"2021-01-12T06:51:04Z","publication":"Physical Biology","oa_version":"Preprint","date_published":"2016-01-29T00:00:00Z","type":"journal_article","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"volume":13,"department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"year":"2016","date_created":"2018-12-11T11:52:18Z","day":"29","publist_id":"5702","publication_status":"published","author":[{"orcid":"0000-0002-5214-4706","last_name":"De Martino","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. Coli in stationary growth conditions from which we infer the metabolites turnover times. However the latter are inferred from net fluxes, and we argue that this approximation is not valid for enzymes working nearby thermodynamic equilibrium. We recalculate turnover times from total fluxes by performing an energy balance analysis of the network and recurring to the fluctuation theorem. We find in many cases values one of order of magnitude lower, implying a faster picture of intermediate metabolism."}],"title":"Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis","_id":"1485","intvolume":"        13","citation":{"ista":"De Martino D. 2016. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. 13(1), 016003.","apa":"De Martino, D. (2016). Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. <i>Physical Biology</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">https://doi.org/10.1088/1478-3975/13/1/016003</a>","short":"D. De Martino, Physical Biology 13 (2016).","ieee":"D. De Martino, “Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis,” <i>Physical Biology</i>, vol. 13, no. 1. IOP Publishing Ltd., 2016.","ama":"De Martino D. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. <i>Physical Biology</i>. 2016;13(1). doi:<a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">10.1088/1478-3975/13/1/016003</a>","mla":"De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” <i>Physical Biology</i>, vol. 13, no. 1, 016003, IOP Publishing Ltd., 2016, doi:<a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">10.1088/1478-3975/13/1/016003</a>.","chicago":"De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” <i>Physical Biology</i>. IOP Publishing Ltd., 2016. <a href=\"https://doi.org/10.1088/1478-3975/13/1/016003\">https://doi.org/10.1088/1478-3975/13/1/016003</a>."},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1505.04613"}],"status":"public","ec_funded":1,"scopus_import":1,"issue":"1"},{"type":"journal_article","date_published":"2016-09-09T00:00:00Z","volume":353,"status":"public","oa_version":"Preprint","citation":{"short":"M. Baym, T. Lieberman, E. Kelsic, R.P. Chait, R. Gross, I. Yelin, R. Kishony, Science 353 (2016) 1147–1151.","ieee":"M. Baym <i>et al.</i>, “Spatiotemporal microbial evolution on antibiotic landscapes,” <i>Science</i>, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1147–1151, 2016.","apa":"Baym, M., Lieberman, T., Kelsic, E., Chait, R. P., Gross, R., Yelin, I., &#38; Kishony, R. (2016). Spatiotemporal microbial evolution on antibiotic landscapes. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.aag0822\">https://doi.org/10.1126/science.aag0822</a>","ista":"Baym M, Lieberman T, Kelsic E, Chait RP, Gross R, Yelin I, Kishony R. 2016. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 353(6304), 1147–1151.","chicago":"Baym, Michael, Tami Lieberman, Eric Kelsic, Remy P Chait, Rotem Gross, Idan Yelin, and Roy Kishony. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” <i>Science</i>. American Association for the Advancement of Science, 2016. <a href=\"https://doi.org/10.1126/science.aag0822\">https://doi.org/10.1126/science.aag0822</a>.","mla":"Baym, Michael, et al. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” <i>Science</i>, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1147–51, doi:<a href=\"https://doi.org/10.1126/science.aag0822\">10.1126/science.aag0822</a>.","ama":"Baym M, Lieberman T, Kelsic E, et al. Spatiotemporal microbial evolution on antibiotic landscapes. <i>Science</i>. 2016;353(6304):1147-1151. doi:<a href=\"https://doi.org/10.1126/science.aag0822\">10.1126/science.aag0822</a>"},"intvolume":"       353","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534434/","open_access":"1"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"A key aspect of bacterial survival is the ability to evolve while migrating across spatially varying environmental challenges. Laboratory experiments, however, often study evolution in well-mixed systems. Here, we introduce an experimental device, the microbial evolution and growth arena (MEGA)-plate, in which bacteria spread and evolved on a large antibiotic landscape (120 × 60 centimeters) that allowed visual observation of mutation and selection in a migrating bacterial front.While resistance increased consistently, multiple coexisting lineages diversified both phenotypically and genotypically. Analyzing mutants at and behind the propagating front,we found that evolution is not always led by the most resistant mutants; highly resistant mutants may be trapped behindmore sensitive lineages.TheMEGA-plate provides a versatile platformfor studying microbial adaption and directly visualizing evolutionary dynamics."}],"title":"Spatiotemporal microbial evolution on antibiotic landscapes","publisher":"American Association for the Advancement of Science","date_updated":"2021-01-12T06:50:01Z","doi":"10.1126/science.aag0822","publication":"Science","_id":"1342","month":"09","oa":1,"quality_controlled":"1","issue":"6304","author":[{"last_name":"Baym","full_name":"Baym, Michael","first_name":"Michael"},{"last_name":"Lieberman","full_name":"Lieberman, Tami","first_name":"Tami"},{"last_name":"Kelsic","full_name":"Kelsic, Eric","first_name":"Eric"},{"first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","full_name":"Chait, Remy P","last_name":"Chait","orcid":"0000-0003-0876-3187"},{"full_name":"Gross, Rotem","first_name":"Rotem","last_name":"Gross"},{"last_name":"Yelin","full_name":"Yelin, Idan","first_name":"Idan"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"}],"page":"1147 - 1151","date_created":"2018-12-11T11:51:29Z","day":"09","publist_id":"5911","publication_status":"published","scopus_import":1,"language":[{"iso":"eng"}],"year":"2016","department":[{"_id":"CaGu"},{"_id":"GaTk"}]},{"publisher":"Nature Publishing Group","date_updated":"2023-09-07T12:53:49Z","doi":"10.1038/ncomms12307","publication":"Nature Communications","month":"08","oa":1,"file":[{"creator":"system","relation":"main_file","date_created":"2018-12-12T10:12:01Z","file_id":"4919","content_type":"application/pdf","file_size":861805,"date_updated":"2020-07-14T12:44:46Z","checksum":"fe3f3a1526d180b29fe691ab11435b78","access_level":"open_access","file_name":"IST-2016-627-v1+1_ncomms12307.pdf"},{"date_created":"2018-12-12T10:12:02Z","file_id":"4920","content_type":"application/pdf","creator":"system","relation":"main_file","checksum":"164864a1a675f3ad80e9917c27aba07f","access_level":"open_access","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","file_size":1084703,"date_updated":"2020-07-14T12:44:46Z"}],"quality_controlled":"1","article_number":"12307","date_published":"2016-08-04T00:00:00Z","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","volume":7,"oa_version":"Published Version","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6071"}]},"ddc":["576"],"year":"2016","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"author":[{"full_name":"Friedlander, Tamar","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","first_name":"Tamar","last_name":"Friedlander"},{"last_name":"Prizak","full_name":"Prizak, Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","first_name":"Roshan"},{"last_name":"Guet","orcid":"0000-0001-6220-2052","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"pubrep_id":"627","date_created":"2018-12-11T11:51:34Z","day":"04","publication_status":"published","publist_id":"5887","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements.","lang":"eng"}],"title":"Intrinsic limits to gene regulation by global crosstalk","_id":"1358","status":"public","ec_funded":1,"citation":{"ama":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>","mla":"Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>, vol. 7, 12307, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms12307\">10.1038/ncomms12307</a>.","chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>.","ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.","apa":"Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., &#38; Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms12307\">https://doi.org/10.1038/ncomms12307</a>","ieee":"T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016)."},"intvolume":"         7","has_accepted_license":"1","scopus_import":1,"file_date_updated":"2020-07-14T12:44:46Z"}]