[{"title":"Supplementary appendix","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-08-10T07:05:10Z","date_published":"2017-06-01T00:00:00Z","author":[{"full_name":"Chalk, Matthew J","last_name":"Chalk","orcid":"0000-0001-7782-4436","first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Paul","full_name":"Masset, Paul","last_name":"Masset"},{"full_name":"Gutkin, Boris","last_name":"Gutkin","first_name":"Boris"},{"last_name":"Denève","full_name":"Denève, Sophie","first_name":"Sophie"}],"year":"2017","department":[{"_id":"GaTk"}],"type":"research_data_reference","doi":"10.1371/journal.pcbi.1005582.s001","publisher":"Public Library of Science","article_processing_charge":"No","citation":{"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>","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>","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>.","short":"M.J. Chalk, P. Masset, B. Gutkin, S. Denève, (2017).","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>.","ieee":"M. J. Chalk, P. Masset, B. Gutkin, and S. Denève, “Supplementary appendix.” Public Library of Science, 2017."},"status":"public","_id":"9855","day":"01","related_material":{"record":[{"status":"public","id":"680","relation":"used_in_publication"}]},"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."}],"month":"06","date_updated":"2025-09-10T14:20:48Z","oa_version":"Published Version"},{"date_created":"2018-12-11T11:49:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"file_date_updated":"2020-07-14T12:48:19Z","language":[{"iso":"eng"}],"external_id":{"isi":["000400560700001"]},"ec_funded":1,"department":[{"_id":"GaTk"},{"_id":"JoCs"}],"intvolume":"         8","year":"2017","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"doi":"10.1038/ncomms15140","publisher":"Nature Publishing Group","day":"04","publist_id":"6406","ddc":["005","571"],"scopus_import":"1","title":"Subsampling scaling","article_number":"15140","date_published":"2017-05-04T00:00:00Z","author":[{"id":"35AF8020-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Levina (Martius)","full_name":"Levina (Martius), Anna"},{"first_name":"Viola","last_name":"Priesemann","full_name":"Priesemann, Viola"}],"publication_status":"published","quality_controlled":"1","file":[{"relation":"main_file","checksum":"9880212f8c4c53404c7c6fbf9023c53a","creator":"system","date_updated":"2020-07-14T12:48:19Z","date_created":"2018-12-12T10:15:05Z","file_size":746224,"access_level":"open_access","file_name":"IST-2017-819-v1+1_2017_Levina_SubsamplingScaling.pdf","content_type":"application/pdf","file_id":"5122"}],"publication":"Nature Communications","type":"journal_article","publication_identifier":{"issn":["2041-1723"]},"article_processing_charge":"Yes (in subscription journal)","citation":{"ista":"Levina (Martius) A, Priesemann V. 2017. Subsampling scaling. Nature Communications. 8, 15140.","short":"A. Levina (Martius), V. Priesemann, Nature Communications 8 (2017).","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>.","ieee":"A. Levina (Martius) and V. Priesemann, “Subsampling scaling,” <i>Nature Communications</i>, vol. 8. Nature Publishing Group, 2017.","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>.","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>","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>"},"status":"public","_id":"993","volume":8,"month":"05","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."}],"date_updated":"2025-07-10T12:02:06Z","pubrep_id":"819","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"}},{"publist_id":"6826","scopus_import":"1","publisher":"IOP Publishing","arxiv":1,"doi":"10.1088/1742-5468/aa85c3","day":"26","intvolume":"      2017","department":[{"_id":"GaTk"}],"year":"2017","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"ec_funded":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.06303"}],"oa":1,"das_tickbox":"1","date_created":"2018-12-11T11:48:41Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"external_id":{"arxiv":["1705.06303"],"isi":["000411842900001"]},"abstract":[{"text":"The resolution of a linear system with positive integer variables is a basic yet difficult computational problem with many applications. We consider sparse uncorrelated random systems parametrised by the density c and the ratio α=N/M between number of variables N and number of constraints M. By means of ensemble calculations we show that the space of feasible solutions endows a Van-Der-Waals phase diagram in the plane (c, α). We give numerical evidence that the associated computational problems become more difficult across the critical point and in particular in the coexistence region.","lang":"eng"}],"month":"09","volume":2017,"date_updated":"2026-07-07T13:11:04Z","issue":"9","oa_version":"Submitted Version","isi":1,"article_processing_charge":"No","citation":{"ama":"Colabrese S, De Martino D, Leuzzi L, Marinari E. Phase transitions in integer linear problems. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. 2017;2017(9). doi:<a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">10.1088/1742-5468/aa85c3</a>","apa":"Colabrese, S., De Martino, D., Leuzzi, L., &#38; Marinari, E. (2017). Phase transitions in integer linear problems. <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">https://doi.org/10.1088/1742-5468/aa85c3</a>","ista":"Colabrese S, De Martino D, Leuzzi L, Marinari E. 2017. Phase transitions in integer linear problems. Journal of Statistical Mechanics: Theory and Experiment. 2017(9), 093404.","short":"S. Colabrese, D. De Martino, L. Leuzzi, E. Marinari, Journal of Statistical Mechanics: Theory and Experiment 2017 (2017).","mla":"Colabrese, Simona, et al. “Phase Transitions in Integer Linear Problems.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2017, no. 9, 093404, IOP Publishing, 2017, doi:<a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">10.1088/1742-5468/aa85c3</a>.","chicago":"Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari. “Phase Transitions in Integer Linear Problems.” <i>Journal of Statistical Mechanics: Theory and Experiment</i>. IOP Publishing, 2017. <a href=\"https://doi.org/10.1088/1742-5468/aa85c3\">https://doi.org/10.1088/1742-5468/aa85c3</a>.","ieee":"S. Colabrese, D. De Martino, L. Leuzzi, and E. Marinari, “Phase transitions in integer linear problems,” <i>Journal of Statistical Mechanics: Theory and Experiment</i>, vol. 2017, no. 9. IOP Publishing, 2017."},"type":"journal_article","publication_identifier":{"issn":["1742-5468"]},"_id":"823","status":"public","publication_status":"published","publication":"Journal of Statistical Mechanics: Theory and Experiment","quality_controlled":"1","title":"Phase transitions in integer linear problems","article_number":"093404","date_published":"2017-09-26T00:00:00Z","author":[{"first_name":"Simona","full_name":"Colabrese, Simona","last_name":"Colabrese"},{"id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino","full_name":"De Martino, Daniele"},{"full_name":"Leuzzi, Luca","last_name":"Leuzzi","first_name":"Luca"},{"last_name":"Marinari","full_name":"Marinari, Enzo","first_name":"Enzo"}]},{"doi":"10.1103/PhysRevE.96.010401","arxiv":1,"publisher":"American Physical Society","day":"10","publist_id":"6470","scopus_import":"1","date_created":"2018-12-11T11:49:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"das_tickbox":"1","external_id":{"isi":["000405194200002"],"arxiv":["1703.00219"]},"language":[{"iso":"eng"}],"ec_funded":1,"project":[{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"year":"2017","department":[{"_id":"GaTk"}],"intvolume":"        96","main_file_link":[{"url":"https://arxiv.org/abs/1703.00219","open_access":"1"}],"publication_identifier":{"issn":["2470-0045"]},"type":"journal_article","citation":{"short":"D. De Martino, F. Capuani, A. De Martino, Physical Review E 96 (2017).","ista":"De Martino D, Capuani F, De Martino A. 2017. Quantifying the entropic cost of cellular growth control. Physical Review E. 96(1), 010401.","ieee":"D. De Martino, F. Capuani, and A. De Martino, “Quantifying the entropic cost of cellular growth control,” <i>Physical Review E</i>, vol. 96, no. 1. American Physical Society, 2017.","chicago":"De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying the Entropic Cost of Cellular Growth Control.” <i>Physical Review E</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">https://doi.org/10.1103/PhysRevE.96.010401</a>.","mla":"De Martino, Daniele, et al. “Quantifying the Entropic Cost of Cellular Growth Control.” <i>Physical Review E</i>, vol. 96, no. 1, 010401, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">10.1103/PhysRevE.96.010401</a>.","ama":"De Martino D, Capuani F, De Martino A. Quantifying the entropic cost of cellular growth control. <i>Physical Review E</i>. 2017;96(1). doi:<a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">10.1103/PhysRevE.96.010401</a>","apa":"De Martino, D., Capuani, F., &#38; De Martino, A. (2017). Quantifying the entropic cost of cellular growth control. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.96.010401\">https://doi.org/10.1103/PhysRevE.96.010401</a>"},"article_processing_charge":"No","status":"public","_id":"947","date_updated":"2026-08-12T14:29:46Z","issue":"1","abstract":[{"text":"Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models. We link the mean growth rate achieved by a population of cells to the minimal amount of metabolic regulation needed to achieve it through a phase diagram that highlights how growth suppression can be as costly (in regulatory terms) as growth enhancement. Moreover, we provide an interpretation of the inverse temperature β controlling maximum-entropy distributions based on the underlying growth dynamics. Specifically, we show that the asymptotic value of β for a cell population can be expected to depend on (i) the carrying capacity of the environment, (ii) the initial size of the colony, and (iii) the probability distribution from which the inoculum was sampled. Results obtained for E. coli and human cells are found to be remarkably consistent with empirical evidence.","lang":"eng"}],"volume":96,"month":"07","isi":1,"oa_version":"Submitted Version","title":"Quantifying the entropic cost of cellular growth control","author":[{"first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino"},{"last_name":"Capuani","full_name":"Capuani, Fabrizio","first_name":"Fabrizio"},{"first_name":"Andrea","last_name":"De Martino","full_name":"De Martino, Andrea"}],"article_number":"010401","date_published":"2017-07-10T00:00:00Z","publication_status":"published","quality_controlled":"1","publication":"Physical Review E"},{"isi":1,"oa_version":"Submitted Version","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"}],"volume":95,"month":"06","issue":"6","date_updated":"2026-08-12T14:29:35Z","_id":"959","status":"public","article_processing_charge":"No","citation":{"apa":"De Martino, D. (2017). Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">https://doi.org/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</i>. 2017;95(6):062419. doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">10.1103/PhysRevE.95.062419</a>","ieee":"D. De Martino, “Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics,” <i>Physical Review E</i>, vol. 95, no. 6. American Physical Society, p. 062419, 2017.","chicago":"De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.” <i>Physical Review E</i>. American Physical Society, 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</i>, vol. 95, no. 6, American Physical Society, 2017, p. 062419, doi:<a href=\"https://doi.org/10.1103/PhysRevE.95.062419\">10.1103/PhysRevE.95.062419</a>.","short":"D. De Martino, Physical Review E 95 (2017) 062419.","ista":"De Martino D. 2017. Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics. Physical Review E. 95(6), 062419."},"type":"journal_article","publication_identifier":{"issn":["2470-0045"]},"publication":"Physical Review E","quality_controlled":"1","publication_status":"published","page":"062419","date_published":"2017-06-28T00:00:00Z","author":[{"orcid":"0000-0002-5214-4706","last_name":"De Martino","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele"}],"title":"Scales and multimodal flux distributions in stationary metabolic network models via thermodynamics","scopus_import":"1","publist_id":"6446","day":"28","publisher":"American Physical Society","arxiv":1,"doi":"10.1103/PhysRevE.95.062419","main_file_link":[{"url":"https://arxiv.org/abs/1703.00853","open_access":"1"}],"department":[{"_id":"GaTk"}],"intvolume":"        95","year":"2017","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"ec_funded":1,"language":[{"iso":"eng"}],"external_id":{"arxiv":["1703.00853"],"isi":["000404546400004"]},"oa":1,"das_tickbox":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:49:25Z"},{"_id":"735","status":"public","article_processing_charge":"No","citation":{"short":"V. Barone, M. Lang, G. Krens, S. Pradhan, S. Shamipour, K. Sako, M.K. Sikora, C.C. Guet, C.-P.J. Heisenberg, Developmental Cell 43 (2017) 198–211.","ista":"Barone V, Lang M, Krens G, Pradhan S, Shamipour S, Sako K, Sikora MK, Guet CC, Heisenberg C-PJ. 2017. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. Developmental Cell. 43(2), 198–211.","chicago":"Barone, Vanessa, Moritz Lang, Gabriel Krens, Saurabh Pradhan, Shayan Shamipour, Keisuke Sako, Mateusz K Sikora, Calin C Guet, and Carl-Philipp J Heisenberg. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” <i>Developmental Cell</i>. Cell Press, 2017. <a href=\"https://doi.org/10.1016/j.devcel.2017.09.014\">https://doi.org/10.1016/j.devcel.2017.09.014</a>.","ieee":"V. Barone <i>et al.</i>, “An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate,” <i>Developmental Cell</i>, vol. 43, no. 2. Cell Press, pp. 198–211, 2017.","mla":"Barone, Vanessa, et al. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.” <i>Developmental Cell</i>, vol. 43, no. 2, Cell Press, 2017, pp. 198–211, doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.09.014\">10.1016/j.devcel.2017.09.014</a>.","ama":"Barone V, Lang M, Krens G, et al. An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. <i>Developmental Cell</i>. 2017;43(2):198-211. doi:<a href=\"https://doi.org/10.1016/j.devcel.2017.09.014\">10.1016/j.devcel.2017.09.014</a>","apa":"Barone, V., Lang, M., Krens, G., Pradhan, S., Shamipour, S., Sako, K., … Heisenberg, C.-P. J. (2017). An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2017.09.014\">https://doi.org/10.1016/j.devcel.2017.09.014</a>"},"type":"journal_article","publication_identifier":{"issn":["1534-5807"]},"isi":1,"oa_version":"None","volume":43,"abstract":[{"text":"Cell-cell contact formation constitutes an essential step in evolution, leading to the differentiation of specialized cell types. However, remarkably little is known about whether and how the interplay between contact formation and fate specification affects development. Here, we identify a positive feedback loop between cell-cell contact duration, morphogen signaling, and mesendoderm cell-fate specification during zebrafish gastrulation. We show that long-lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to respond to Nodal signaling, required for ppl cell-fate specification. We further show that Nodal signaling promotes ppl cell-cell contact duration, generating a positive feedback loop between ppl cell-cell contact duration and cell-fate specification. Finally, by combining mathematical modeling and experimentation, we show that this feedback determines whether anterior axial mesendoderm cells become ppl or, instead, turn into endoderm. Thus, the interdependent activities of cell-cell signaling and contact formation control fate diversification within the developing embryo.","lang":"eng"}],"month":"10","date_updated":"2026-08-31T22:30:20Z","issue":"2","related_material":{"record":[{"id":"961","status":"public","relation":"dissertation_contains"},{"id":"8350","status":"public","relation":"dissertation_contains"}]},"date_published":"2017-10-23T00:00:00Z","author":[{"id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","orcid":"0000-0003-2676-3367","last_name":"Barone","full_name":"Barone, Vanessa"},{"last_name":"Lang","full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","first_name":"Moritz"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens"},{"full_name":"Pradhan, Saurabh","last_name":"Pradhan","first_name":"Saurabh"},{"last_name":"Shamipour","full_name":"Shamipour, Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan"},{"id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","first_name":"Keisuke","last_name":"Sako","orcid":"0000-0002-6453-8075","full_name":"Sako, Keisuke"},{"last_name":"Sikora","full_name":"Sikora, Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"}],"title":"An effective feedback loop between cell-cell contact duration and morphogen signaling determines cell fate","publication":"Developmental Cell","quality_controlled":"1","page":"198 - 211","publication_status":"published","day":"23","publisher":"Cell Press","doi":"10.1016/j.devcel.2017.09.014","scopus_import":"1","publist_id":"6934","corr_author":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000413443700011"]},"date_created":"2018-12-11T11:48:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaHe"},{"_id":"CaGu"},{"_id":"GaTk"}],"intvolume":"        43","year":"2017","project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"},{"name":"Cell segregation in gastrulation: the role of cell fate specification","_id":"252DD2A6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"I2058"}],"ec_funded":1},{"_id":"1082","status":"public","citation":{"ama":"Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems Foundation; 2016:1965-1973.","apa":"Chalk, M. J., Marre, O., &#38; Tkačik, G. (2016). Relevant sparse codes with variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems Foundation.","short":"M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, pp. 1965–1973.","ista":"Chalk MJ, Marre O, Tkačik G. 2016. Relevant sparse codes with variational information bottleneck. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 1965–1973.","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing Systems Foundation, 2016.","mla":"Chalk, Matthew J., et al. <i>Relevant Sparse Codes with Variational Information Bottleneck</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 1965–73."},"article_processing_charge":"No","type":"conference","oa_version":"Preprint","date_updated":"2025-06-03T11:33:51Z","volume":29,"month":"12","abstract":[{"lang":"eng","text":"In many applications, it is desirable to extract only the relevant aspects of data. A principled way to do this is the information bottleneck (IB) method, where one seeks a code that maximises information about a relevance variable, Y, while constraining the information encoded about the original data, X. Unfortunately however, the IB method is computationally demanding when data are high-dimensional and/or non-gaussian. Here we propose an approximate variational scheme for maximising a lower bound on the IB objective, analogous to variational EM. Using this method, we derive an IB algorithm to recover features that are both relevant and sparse. Finally, we demonstrate how kernelised versions of the algorithm can be used to address a broad range of problems with non-linear relation between X and Y."}],"related_material":{"link":[{"url":"https://papers.nips.cc/paper/6101-relevant-sparse-codes-with-variational-information-bottleneck","relation":"other"}]},"author":[{"full_name":"Chalk, Matthew J","last_name":"Chalk","orcid":"0000-0001-7782-4436","first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"}],"date_published":"2016-12-01T00:00:00Z","conference":{"end_date":"2016-12-10","name":"NIPS: Neural Information Processing Systems","location":"Barcelona, Spain","start_date":"2016-12-05"},"title":"Relevant sparse codes with variational information bottleneck","quality_controlled":"1","page":"1965-1973","publication_status":"published","alternative_title":["Advances in Neural Information Processing Systems"],"day":"01","publisher":"Neural Information Processing Systems Foundation","arxiv":1,"scopus_import":"1","publist_id":"6298","external_id":{"arxiv":["1605.07332"]},"language":[{"iso":"eng"}],"oa":1,"date_created":"2018-12-11T11:50:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.07332"}],"year":"2016","department":[{"_id":"GaTk"}],"intvolume":"        29"},{"day":"01","alternative_title":["Advances in Neural Information Processing Systems"],"publisher":"Neural Information Processing Systems Foundation","acknowledgement":"We  thank  Jozsef  Csicsvari  for  kindly  sharing  the  CA1  data.\r\nThis work was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no. 291734.","scopus_import":"1","publist_id":"6265","language":[{"iso":"eng"}],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:50:10Z","oa":1,"main_file_link":[{"url":"http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods","open_access":"1"}],"ec_funded":1,"year":"2016","intvolume":"        29","department":[{"_id":"GaTk"}],"project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"status":"public","_id":"1105","type":"conference","article_processing_charge":"No","citation":{"chicago":"Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information Processing Systems Foundation, 2016.","ieee":"C. Savin and G. Tkačik, “Estimating nonlinear neural response functions using GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.","mla":"Savin, Cristina, and Gašper Tkačik. <i>Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 3610–18.","short":"C. Savin, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, pp. 3610–3618.","ista":"Savin C, Tkačik G. 2016. Estimating nonlinear neural response functions using GP priors and Kronecker methods. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3610–3618.","apa":"Savin, C., &#38; Tkačik, G. (2016). Estimating nonlinear neural response functions using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information Processing Systems Foundation.","ama":"Savin C, Tkačik G. Estimating nonlinear neural response functions using GP priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems Foundation; 2016:3610-3618."},"oa_version":"None","month":"12","abstract":[{"lang":"eng","text":"Jointly characterizing neural responses in terms of several external variables promises novel insights into circuit function, but remains computationally prohibitive in practice. Here we use gaussian process (GP) priors and exploit recent advances in fast GP inference and learning based on Kronecker methods, to efficiently estimate multidimensional nonlinear tuning functions. Our estimator require considerably less data than traditional methods and further provides principled uncertainty estimates. We apply these tools to hippocampal recordings during open field exploration and use them to characterize the joint dependence of CA1 responses on the position of the animal and several other variables, including the animal\\'s speed, direction of motion, and network oscillations.Our results provide an unprecedentedly detailed quantification of the tuning of hippocampal neurons. The model\\'s generality suggests that our approach can be used to estimate neural response properties in other brain regions."}],"volume":29,"date_updated":"2025-06-03T11:36:49Z","date_published":"2016-12-01T00:00:00Z","author":[{"full_name":"Savin, Cristina","last_name":"Savin","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"}],"title":"Estimating nonlinear neural response functions using GP priors and Kronecker methods","conference":{"name":"NIPS: Neural Information Processing Systems","end_date":"2016-12-10","location":"Barcelona; Spain","start_date":"2016-12-05"},"quality_controlled":"1","publication_status":"published","page":"3610-3618"},{"oa_version":"None","isi":1,"related_material":{"record":[{"status":"public","id":"1658","relation":"earlier_version"}]},"date_updated":"2025-09-23T07:44:57Z","month":"11","volume":149,"abstract":[{"text":"Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space. © 2016 Elsevier Ireland Ltd","lang":"eng"}],"_id":"1148","status":"public","type":"journal_article","citation":{"chicago":"Schilling, Christian, Sergiy Bogomolov, Thomas A Henzinger, Andreas Podelski, and Jakob Ruess. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” <i>Biosystems</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">https://doi.org/10.1016/j.biosystems.2016.07.005</a>.","ieee":"C. Schilling, S. Bogomolov, T. A. Henzinger, A. Podelski, and J. Ruess, “Adaptive moment closure for parameter inference of biochemical reaction networks,” <i>Biosystems</i>, vol. 149. Elsevier, pp. 15–25, 2016.","mla":"Schilling, Christian, et al. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” <i>Biosystems</i>, vol. 149, Elsevier, 2016, pp. 15–25, doi:<a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">10.1016/j.biosystems.2016.07.005</a>.","short":"C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems 149 (2016) 15–25.","ista":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. 2016. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. 149, 15–25.","apa":"Schilling, C., Bogomolov, S., Henzinger, T. A., Podelski, A., &#38; Ruess, J. (2016). Adaptive moment closure for parameter inference of biochemical reaction networks. <i>Biosystems</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">https://doi.org/10.1016/j.biosystems.2016.07.005</a>","ama":"Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. Adaptive moment closure for parameter inference of biochemical reaction networks. <i>Biosystems</i>. 2016;149:15-25. doi:<a href=\"https://doi.org/10.1016/j.biosystems.2016.07.005\">10.1016/j.biosystems.2016.07.005</a>"},"article_processing_charge":"No","quality_controlled":"1","publication":"Biosystems","publication_status":"published","page":"15 - 25","author":[{"first_name":"Christian","last_name":"Schilling","full_name":"Schilling, Christian"},{"last_name":"Bogomolov","orcid":"0000-0002-0686-0365","full_name":"Bogomolov, Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","first_name":"Sergiy"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","last_name":"Podelski","full_name":"Podelski, Andreas"},{"first_name":"Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","full_name":"Ruess, Jakob","last_name":"Ruess","orcid":"0000-0003-1615-3282"}],"date_published":"2016-11-01T00:00:00Z","title":"Adaptive moment closure for parameter inference of biochemical reaction networks","acknowledgement":"This work is based on the CMSB 2015 paper “Adaptive moment closure for parameter inference of biochemical reaction networks” (Bogomolov et al., 2015). The work was partly supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS1), by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award). J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734.","scopus_import":"1","publist_id":"6210","day":"01","doi":"10.1016/j.biosystems.2016.07.005","publisher":"Elsevier","ec_funded":1,"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF","grant_number":"Z211"},{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"year":"2016","intvolume":"       149","department":[{"_id":"ToHe"},{"_id":"GaTk"}],"external_id":{"isi":["000390743600003"]},"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:50:24Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"publication":"Physics of Life Reviews","quality_controlled":"1","department":[{"_id":"GaTk"}],"year":"2016","intvolume":"        17","publication_status":"published","page":"166 - 167","date_published":"2016-07-01T00:00:00Z","author":[{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"language":[{"iso":"eng"}],"external_id":{"isi":["000381544100033"]},"title":"Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&quot; by O. C. Martin et al.","date_created":"2018-12-11T11:50:32Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","isi":1,"oa_version":"None","volume":17,"month":"07","date_updated":"2025-09-22T09:50:37Z","publist_id":"6185","_id":"1171","status":"public","day":"01","article_processing_charge":"No","publisher":"Elsevier","citation":{"apa":"Tkačik, G. (2016). Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al. <i>Physics of Life Reviews</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">https://doi.org/10.1016/j.plrev.2016.06.005</a>","ama":"Tkačik G. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al. <i>Physics of Life Reviews</i>. 2016;17:166-167. doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">10.1016/j.plrev.2016.06.005</a>","mla":"Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on &#38;quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&#38;quot; by O. C. Martin et Al.” <i>Physics of Life Reviews</i>, vol. 17, Elsevier, 2016, pp. 166–67, doi:<a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">10.1016/j.plrev.2016.06.005</a>.","ieee":"G. Tkačik, “Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al.,” <i>Physics of Life Reviews</i>, vol. 17. Elsevier, pp. 166–167, 2016.","chicago":"Tkačik, Gašper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on &#38;quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&#38;quot; by O. C. Martin et Al.” <i>Physics of Life Reviews</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.plrev.2016.06.005\">https://doi.org/10.1016/j.plrev.2016.06.005</a>.","ista":"Tkačik G. 2016. Understanding regulatory networks requires more than computing a multitude of graph statistics: Comment on &#38;quot;Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function&#38;quot; by O. C. Martin et al. Physics of Life Reviews. 17, 166–167.","short":"G. Tkačik, Physics of Life Reviews 17 (2016) 166–167."},"type":"journal_article","doi":"10.1016/j.plrev.2016.06.005"},{"title":"Error-robust modes of the retinal population code","article_number":"e1005855","date_published":"2016-11-17T00:00:00Z","author":[{"first_name":"Jason","full_name":"Prentice, Jason","last_name":"Prentice"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"},{"first_name":"Mark","last_name":"Ioffe","full_name":"Ioffe, Mark"},{"first_name":"Adrianna","last_name":"Loback","full_name":"Loback, Adrianna"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"first_name":"Michael","last_name":"Berry","full_name":"Berry, Michael"}],"publication_status":"published","file":[{"access_level":"open_access","file_id":"5884","content_type":"application/pdf","file_name":"2016_PLOS_Prentice.pdf","date_created":"2019-01-25T10:35:00Z","file_size":4492021,"date_updated":"2020-07-14T12:44:38Z","creator":"kschuh","relation":"main_file","checksum":"47b08cbd4dbf32b25ba161f5f4b262cc"}],"publication":"PLoS Computational Biology","quality_controlled":"1","article_processing_charge":"No","citation":{"ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-robust modes of the retinal population code. <i>PLoS Computational Biology</i>. 2016;12(11). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005148\">10.1371/journal.pcbi.1005148</a>","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., &#38; Berry, M. (2016). Error-robust modes of the retinal population code. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005148\">https://doi.org/10.1371/journal.pcbi.1005148</a>","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational Biology 12 (2016).","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2016. Error-robust modes of the retinal population code. PLoS Computational Biology. 12(11), e1005855.","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust modes of the retinal population code,” <i>PLoS Computational Biology</i>, vol. 12, no. 11. Public Library of Science, 2016.","chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” <i>PLoS Computational Biology</i>. Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pcbi.1005148\">https://doi.org/10.1371/journal.pcbi.1005148</a>.","mla":"Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.” <i>PLoS Computational Biology</i>, vol. 12, no. 11, e1005855, Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005148\">10.1371/journal.pcbi.1005148</a>."},"type":"journal_article","_id":"1197","status":"public","month":"11","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"}],"volume":12,"date_updated":"2025-09-22T09:43:12Z","issue":"11","related_material":{"record":[{"relation":"research_data","id":"9709","status":"public"}]},"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,"oa":1,"file_date_updated":"2020-07-14T12:44:38Z","date_created":"2018-12-11T11:50:40Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"external_id":{"isi":["000391230900008"]},"intvolume":"        12","year":"2016","department":[{"_id":"GaTk"}],"project":[{"name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","call_identifier":"FWF"}],"publisher":"Public Library of Science","doi":"10.1371/journal.pcbi.1005148","day":"17","publist_id":"6153","scopus_import":"1","acknowledgement":"JSP was supported by a C.V. Starr Fellowship from the Starr Foundation (http://www.starrfoundation.org/). GT was supported by Austrian Research Foundation (https://www.fwf.ac.at/en/) grant FWF P25651. MJB received support from National Eye Institute (https://nei.nih.gov/) grant EY 14196 and from the National Science Foundation grant 1504977. The authors thank Cristina Savin and Vicent Botella-Soler for helpful comments on the manuscript.","ddc":["570"]},{"day":"01","publisher":"American Society for Microbiology","doi":"10.1128/JCM.01511-16","scopus_import":"1","acknowledgement":"We are grateful to ABCs for providing strains and the Bacterial Meningitis Laboratory for technical support.","publist_id":"6146","external_id":{"isi":["000389209600026"]},"language":[{"iso":"eng"}],"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:41Z","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121393/","open_access":"1"}],"intvolume":"        54","department":[{"_id":"GaTk"}],"year":"2016","status":"public","_id":"1203","citation":{"short":"F. Hu, L. Rishishwar, A. Sivadas, G. Mitchell, J. King, T. Murphy, J. Gilsdorf, L. Mayer, X. Wang, Journal of Clinical Microbiology 54 (2016) 3010–3017.","ista":"Hu F, Rishishwar L, Sivadas A, Mitchell G, King J, Murphy T, Gilsdorf J, Mayer L, Wang X. 2016. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 54(12), 3010–3017.","chicago":"Hu, Fang, Lavanya Rishishwar, Ambily Sivadas, Gabriel Mitchell, Jordan King, Timothy Murphy, Janet Gilsdorf, Leonard Mayer, and Xin Wang. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” <i>Journal of Clinical Microbiology</i>. American Society for Microbiology, 2016. <a href=\"https://doi.org/10.1128/JCM.01511-16\">https://doi.org/10.1128/JCM.01511-16</a>.","ieee":"F. Hu <i>et al.</i>, “Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination,” <i>Journal of Clinical Microbiology</i>, vol. 54, no. 12. American Society for Microbiology, pp. 3010–3017, 2016.","mla":"Hu, Fang, et al. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” <i>Journal of Clinical Microbiology</i>, vol. 54, no. 12, American Society for Microbiology, 2016, pp. 3010–17, doi:<a href=\"https://doi.org/10.1128/JCM.01511-16\">10.1128/JCM.01511-16</a>.","ama":"Hu F, Rishishwar L, Sivadas A, et al. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. <i>Journal of Clinical Microbiology</i>. 2016;54(12):3010-3017. doi:<a href=\"https://doi.org/10.1128/JCM.01511-16\">10.1128/JCM.01511-16</a>","apa":"Hu, F., Rishishwar, L., Sivadas, A., Mitchell, G., King, J., Murphy, T., … Wang, X. (2016). Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. <i>Journal of Clinical Microbiology</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/JCM.01511-16\">https://doi.org/10.1128/JCM.01511-16</a>"},"article_processing_charge":"No","type":"journal_article","oa_version":"Submitted Version","isi":1,"date_updated":"2025-09-22T09:40:28Z","issue":"12","volume":54,"month":"12","abstract":[{"text":"Haemophilus haemolyticus has been recently discovered to have the potential to cause invasive disease. It is closely related to nontypeable Haemophilus influenzae (NT H. influenzae). NT H. influenzae and H. haemolyticus are often misidentified because none of the existing tests targeting the known phenotypes of H. haemolyticus are able to specifically identify H. haemolyticus. Through comparative genomic analysis of H. haemolyticus and NT H. influenzae, we identified genes unique to H. haemolyticus that can be used as targets for the identification of H. haemolyticus. A real-time PCR targeting purT (encoding phosphoribosylglycinamide formyltransferase 2 in the purine synthesis pathway) was developed and evaluated. The lower limit of detection was 40 genomes/PCR; the sensitivity and specificity in detecting H. haemolyticus were 98.9% and 97%, respectively. To improve the discrimination of H. haemolyticus and NT H. influenzae, a testing scheme combining two targets (H. haemolyticus purT and H. influenzae hpd, encoding protein D lipoprotein) was also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification of H. haemolyticus and 92.8% sensitivity and 100% specificity for the identification of H. influenzae, respectively. The dual-target testing scheme can be used for the diagnosis and surveillance of infection and disease caused by H. haemolyticus and NT H. influenzae.","lang":"eng"}],"author":[{"first_name":"Fang","last_name":"Hu","full_name":"Hu, Fang"},{"first_name":"Lavanya","full_name":"Rishishwar, Lavanya","last_name":"Rishishwar"},{"last_name":"Sivadas","full_name":"Sivadas, Ambily","first_name":"Ambily"},{"full_name":"Mitchell, Gabriel","last_name":"Mitchell","first_name":"Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jordan","last_name":"King","full_name":"King, Jordan"},{"full_name":"Murphy, Timothy","last_name":"Murphy","first_name":"Timothy"},{"full_name":"Gilsdorf, Janet","last_name":"Gilsdorf","first_name":"Janet"},{"full_name":"Mayer, Leonard","last_name":"Mayer","first_name":"Leonard"},{"last_name":"Wang","full_name":"Wang, Xin","first_name":"Xin"}],"date_published":"2016-12-01T00:00:00Z","title":"Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination","publication":"Journal of Clinical Microbiology","quality_controlled":"1","page":"3010 - 3017","publication_status":"published"},{"year":"2016","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"publication_status":"published","quality_controlled":"1","title":"Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:50:45Z","conference":{"end_date":"2016-09-14","name":"IEEE RSJ International Conference on Intelligent Robots and Systems IROS ","location":"Daejeon, Korea","start_date":"2016-09-09"},"language":[{"iso":"eng"}],"date_published":"2016-11-28T00:00:00Z","article_number":"7759138","author":[{"first_name":"Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S","last_name":"Martius"},{"first_name":"Raphael","last_name":"Hostettler","full_name":"Hostettler, Raphael"},{"last_name":"Knoll","full_name":"Knoll, Alois","first_name":"Alois"},{"first_name":"Ralf","last_name":"Der","full_name":"Der, Ralf"}],"publist_id":"6121","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. While very successful with classical robots, these methods run into severe difficulties when applied to soft robots, a new field of robotics with large interest for human-robot interaction. We claim that a novel controller paradigm opens new perspective for this field. This paper applies a recently developed neuro controller with 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 develops to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.","lang":"eng"}],"volume":"2016-November","month":"11","date_updated":"2021-01-12T06:49:08Z","acknowledgement":"RD thanks for the hospitality at the Max-Planck-Institute and for helpful discussions with Nihat Ay and Keyan Zahedi.","oa_version":"None","scopus_import":1,"type":"conference","doi":"10.1109/IROS.2016.7759138","publisher":"IEEE","citation":{"mla":"Martius, Georg S., et al. <i>Compliant Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic Arm</i>. Vol. 2016–November, 7759138, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/IROS.2016.7759138\">10.1109/IROS.2016.7759138</a>.","ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm,” presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea, 2016, vol. 2016–November.","chicago":"Martius, Georg S, Raphael Hostettler, Alois Knoll, and Ralf Der. “Compliant Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic Arm,” Vol. 2016–November. IEEE, 2016. <a href=\"https://doi.org/10.1109/IROS.2016.7759138\">https://doi.org/10.1109/IROS.2016.7759138</a>.","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. IEEE RSJ International Conference on Intelligent Robots and Systems IROS  vol. 2016–November, 7759138.","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, IEEE, 2016.","apa":"Martius, G. S., Hostettler, R., Knoll, A., &#38; Der, R. (2016). Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm (Vol. 2016–November). Presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea: IEEE. <a href=\"https://doi.org/10.1109/IROS.2016.7759138\">https://doi.org/10.1109/IROS.2016.7759138</a>","ama":"Martius GS, Hostettler R, Knoll A, Der R. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. In: Vol 2016-November. IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/IROS.2016.7759138\">10.1109/IROS.2016.7759138</a>"},"_id":"1214","status":"public","day":"28"},{"oa_version":"Preprint","scopus_import":1,"publist_id":"6114","month":"06","abstract":[{"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.","lang":"eng"}],"date_updated":"2023-02-21T10:17:50Z","_id":"1220","status":"public","day":"01","type":"conference","doi":"10.2514/6.2016-3764","publisher":"AIAA","citation":{"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>","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>","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.","short":"G. Mikić, A. Stoll, J. Bevirt, R. Grah, M. Moore, in:, AIAA, 2016, pp. 1–19.","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.","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>."},"quality_controlled":"1","main_file_link":[{"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","open_access":"1"}],"year":"2016","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"page":"1 - 19","publication_status":"published","language":[{"iso":"eng"}],"date_published":"2016-06-01T00:00:00Z","author":[{"first_name":"Gregor","last_name":"Mikić","full_name":"Mikić, Gregor"},{"first_name":"Alex","full_name":"Stoll, Alex","last_name":"Stoll"},{"first_name":"Joe","last_name":"Bevirt","full_name":"Bevirt, Joe"},{"id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","orcid":"0000-0003-2539-3560","last_name":"Grah","full_name":"Grah, Rok"},{"full_name":"Moore, Mark","last_name":"Moore","first_name":"Mark"}],"title":"Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency","date_created":"2018-12-11T11:50:47Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"conference":{"start_date":"2016-06-13","location":"Washington, D.C., USA","name":"AIAA: Aviation Technology, Integration, and Operations Conference","end_date":"2016-06-17"}},{"page":"1811 - 1816","publication_status":"published","publication":"PNAS","quality_controlled":"1","title":"Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells","author":[{"first_name":"Pierre","last_name":"Recouvreux","full_name":"Recouvreux, Pierre"},{"id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R","orcid":"0000-0002-1287-3779","last_name":"Sokolowski","full_name":"Sokolowski, Thomas R"},{"first_name":"Aristea","full_name":"Grammoustianou, Aristea","last_name":"Grammoustianou"},{"first_name":"Pieter","full_name":"Tenwolde, Pieter","last_name":"Tenwolde"},{"first_name":"Marileen","last_name":"Dogterom","full_name":"Dogterom, Marileen"}],"date_published":"2016-02-16T00:00:00Z","date_updated":"2025-09-22T09:15:17Z","issue":"7","abstract":[{"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.","lang":"eng"}],"month":"02","volume":113,"isi":1,"oa_version":"Submitted Version","citation":{"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.","short":"P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom, PNAS 113 (2016) 1811–1816.","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>.","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>.","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.","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>","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>"},"article_processing_charge":"No","type":"journal_article","_id":"1244","status":"public","department":[{"_id":"GaTk"}],"intvolume":"       113","year":"2016","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/","open_access":"1"}],"oa":1,"date_created":"2018-12-11T11:50:55Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["000370220000046"]},"language":[{"iso":"eng"}],"publist_id":"6085","scopus_import":"1","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”","publisher":"National Academy of Sciences","doi":"10.1073/pnas.1419248113","day":"16"},{"day":"10","publisher":"Annual Reviews","doi":"10.1146/annurev-conmatphys-031214-014803","arxiv":1,"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.","publist_id":"6080","external_id":{"isi":["000372188500005"],"arxiv":["1412.8752"]},"language":[{"iso":"eng"}],"oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:56Z","main_file_link":[{"url":"https://arxiv.org/abs/1412.8752","open_access":"1"}],"project":[{"name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","call_identifier":"FWF"}],"year":"2016","department":[{"_id":"GaTk"}],"intvolume":"         7","status":"public","_id":"1248","citation":{"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>","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>","short":"G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117.","ista":"Tkačik G, Bialek W. 2016. Information processing in living systems. Annual Review of Condensed Matter Physics. 7, 89–117.","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>.","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.","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>."},"article_processing_charge":"No","type":"journal_article","oa_version":"Preprint","isi":1,"date_updated":"2025-09-22T09:12:56Z","month":"03","volume":7,"abstract":[{"lang":"eng","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."}],"author":[{"full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bialek, William","last_name":"Bialek","first_name":"William"}],"date_published":"2016-03-10T00:00:00Z","title":"Information processing in living systems","publication":"Annual Review of Condensed Matter Physics","quality_controlled":"1","page":"89 - 117","publication_status":"published"},{"publication":"International Journal of Modern Physics C","quality_controlled":"1","publication_status":"published","date_published":"2016-06-01T00:00:00Z","article_number":"1650067","author":[{"full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","last_name":"De Martino","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"}],"title":"The dual of the space of interactions in neural network models","oa_version":"Preprint","isi":1,"abstract":[{"lang":"eng","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."}],"month":"06","volume":27,"issue":"6","date_updated":"2025-09-22T09:01:25Z","article_type":"original","status":"public","_id":"1260","article_processing_charge":"No","citation":{"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>.","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.","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.","short":"D. De Martino, International Journal of Modern Physics C 27 (2016).","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>","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>"},"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1505.02963"}],"year":"2016","department":[{"_id":"GaTk"}],"intvolume":"        27","corr_author":"1","language":[{"iso":"eng"}],"external_id":{"arxiv":["1505.02963"],"isi":["000377674800010"]},"oa":1,"date_created":"2018-12-11T11:51:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","publist_id":"6065","day":"01","publisher":"World Scientific Publishing","arxiv":1,"doi":"10.1142/S0129183116500674"},{"scopus_import":"1","acknowledgement":"Boris Gutkin acknowledges funding by the Russian Academic Excellence Project '5-100’.","ddc":["571"],"publist_id":"6056","day":"01","publisher":"eLife Sciences Publications","doi":"10.7554/eLife.13824","intvolume":"         5","department":[{"_id":"GaTk"}],"year":"2016","corr_author":"1","external_id":{"isi":["000380855400001"]},"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:44:42Z","oa":1,"date_created":"2018-12-11T11:51:02Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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","date_updated":"2025-09-22T08:49:58Z","pubrep_id":"700","issue":"2016JULY","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"}],"month":"07","volume":5,"_id":"1266","status":"public","citation":{"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>.","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.","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.","short":"M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016).","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>","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>"},"article_processing_charge":"No","type":"journal_article","file":[{"file_id":"4874","access_level":"open_access","file_name":"IST-2016-700-v1+1_e13824-download.pdf","content_type":"application/pdf","date_created":"2018-12-12T10:11:20Z","file_size":2819055,"date_updated":"2020-07-14T12:44:42Z","creator":"system","checksum":"dc52d967dc76174477bb258d84be2899","relation":"main_file"}],"publication":"eLife","quality_controlled":"1","publication_status":"published","author":[{"last_name":"Chalk","orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J"},{"full_name":"Gutkin, Boris","last_name":"Gutkin","first_name":"Boris"},{"first_name":"Sophie","full_name":"Denève, Sophie","last_name":"Denève"}],"article_number":"e13824","date_published":"2016-07-01T00:00:00Z","title":"Neural oscillations as a signature of efficient coding in the presence of synaptic delays"},{"date_created":"2018-12-11T11:51:03Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","file_date_updated":"2020-07-14T12:44:42Z","oa":1,"external_id":{"isi":["000384169900025"]},"language":[{"iso":"eng"}],"corr_author":"1","project":[{"name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","call_identifier":"FWF"}],"department":[{"_id":"GaTk"}],"intvolume":"        11","year":"2016","doi":"10.1371/journal.pone.0163628","publisher":"Public Library of Science","day":"27","publist_id":"6050","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).","ddc":["571"],"scopus_import":"1","title":"Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information","author":[{"full_name":"Hillenbrand, Patrick","last_name":"Hillenbrand","first_name":"Patrick"},{"last_name":"Gerland","full_name":"Gerland, Ulrich","first_name":"Ulrich"},{"first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"date_published":"2016-09-27T00:00:00Z","article_number":"e0163628","publication_status":"published","quality_controlled":"1","publication":"PLoS One","file":[{"access_level":"open_access","content_type":"application/pdf","file_name":"IST-2016-696-v1+1_journal.pone.0163628.PDF","file_id":"4837","date_created":"2018-12-12T10:10:47Z","file_size":4950415,"date_updated":"2020-07-14T12:44:42Z","relation":"main_file","checksum":"3d0d55d373096a033bd9cf79288c8586","creator":"system"}],"type":"journal_article","citation":{"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>","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>.","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.","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>.","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.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016)."},"article_processing_charge":"No","_id":"1270","status":"public","related_material":{"record":[{"relation":"research_data","id":"9869","status":"public"},{"status":"public","id":"9870","relation":"research_data"},{"id":"9871","status":"public","relation":"research_data"}]},"pubrep_id":"696","date_updated":"2025-09-22T08:46:15Z","issue":"9","month":"09","volume":11,"abstract":[{"lang":"eng","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."}],"isi":1,"oa_version":"Published Version","has_accepted_license":"1","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"}},{"publisher":"Nature Publishing Group","doi":"10.1038/nchembio.2176","day":"01","publist_id":"6026","scopus_import":"1","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","oa":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:51:10Z","external_id":{"isi":["000386798800008"]},"language":[{"iso":"eng"}],"year":"2016","intvolume":"        12","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/"}],"citation":{"short":"L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature Chemical Biology 12 (2016) 902–904.","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.","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>.","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.","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>.","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>","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>"},"article_processing_charge":"No","type":"journal_article","_id":"1290","status":"public","issue":"11","date_updated":"2025-09-22T08:30:48Z","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."}],"month":"11","volume":12,"oa_version":"Preprint","isi":1,"title":"Compounds that select against the tetracycline-resistance efflux pump","author":[{"full_name":"Stone, Laura","last_name":"Stone","first_name":"Laura"},{"full_name":"Baym, Michael","last_name":"Baym","first_name":"Michael"},{"last_name":"Lieberman","full_name":"Lieberman, Tami","first_name":"Tami"},{"orcid":"0000-0003-0876-3187","last_name":"Chait","full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P"},{"first_name":"Jon","last_name":"Clardy","full_name":"Clardy, Jon"},{"full_name":"Kishony, Roy","last_name":"Kishony","first_name":"Roy"}],"date_published":"2016-11-01T00:00:00Z","publication_status":"published","page":"902 - 904","publication":"Nature Chemical Biology","quality_controlled":"1"}]