[{"article_processing_charge":"No","day":"01","month":"06","citation":{"chicago":"Symonova, Olga, Christopher Topp, and Herbert Edelsbrunner. “Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0127657.s001.","short":"O. Symonova, C. Topp, H. Edelsbrunner, (2015).","mla":"Symonova, Olga, et al. Root Traits Computed by DynamicRoots for the Maize Root Shown in Fig 2. Public Library of Science, 2015, doi:10.1371/journal.pone.0127657.s001.","apa":"Symonova, O., Topp, C., & Edelsbrunner, H. (2015). Root traits computed by DynamicRoots for the maize root shown in fig 2. Public Library of Science. https://doi.org/10.1371/journal.pone.0127657.s001","ieee":"O. Symonova, C. Topp, and H. Edelsbrunner, “Root traits computed by DynamicRoots for the maize root shown in fig 2.” Public Library of Science, 2015.","ista":"Symonova O, Topp C, Edelsbrunner H. 2015. Root traits computed by DynamicRoots for the maize root shown in fig 2, Public Library of Science, 10.1371/journal.pone.0127657.s001.","ama":"Symonova O, Topp C, Edelsbrunner H. Root traits computed by DynamicRoots for the maize root shown in fig 2. 2015. doi:10.1371/journal.pone.0127657.s001"},"doi":"10.1371/journal.pone.0127657.s001","date_published":"2015-06-01T00:00:00Z","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9737","year":"2015","publisher":"Public Library of Science","department":[{"_id":"MaJö"},{"_id":"HeEd"}],"status":"public","title":"Root traits computed by DynamicRoots for the maize root shown in fig 2","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1793"}]},"author":[{"first_name":"Olga","last_name":"Symonova","id":"3C0C7BC6-F248-11E8-B48F-1D18A9856A87","full_name":"Symonova, Olga"},{"first_name":"Christopher","last_name":"Topp","full_name":"Topp, Christopher"},{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"oa_version":"Published Version","date_created":"2021-07-28T06:20:13Z","date_updated":"2023-02-23T10:14:42Z"},{"citation":{"short":"T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015).","mla":"Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology, vol. 11, no. 3, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.","chicago":"Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.","ama":"Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 2015;11(3). doi:10.1371/journal.pcbi.1004055","ieee":"T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library of Science, 2015.","apa":"Friedlander, T., Mayo, A., Tlusty, T., & Alon, U. (2015). Evolution of bow-tie architectures in biology. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055","ista":"Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3)."},"publication":"PLoS Computational Biology","date_published":"2015-03-23T00:00:00Z","scopus_import":1,"has_accepted_license":"1","article_processing_charge":"No","day":"23","_id":"1827","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","intvolume":" 11","status":"public","ddc":["576"],"title":"Evolution of bow-tie architectures in biology","pubrep_id":"452","oa_version":"Published Version","file":[{"checksum":"b8aa66f450ff8de393014b87ec7d2efb","date_created":"2018-12-12T10:15:39Z","date_updated":"2020-07-14T12:45:17Z","relation":"main_file","file_id":"5161","content_type":"application/pdf","file_size":1811647,"creator":"system","access_level":"open_access","file_name":"IST-2016-452-v1+1_journal.pcbi.1004055.pdf"}],"type":"journal_article","issue":"3","abstract":[{"text":"Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"quality_controlled":"1","doi":"10.1371/journal.pcbi.1004055","language":[{"iso":"eng"}],"month":"03","year":"2015","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publication_status":"published","related_material":{"record":[{"id":"9718","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9773"}]},"author":[{"full_name":"Friedlander, Tamar","first_name":"Tamar","last_name":"Friedlander","id":"36A5845C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mayo, Avraham","last_name":"Mayo","first_name":"Avraham"},{"last_name":"Tlusty","first_name":"Tsvi","full_name":"Tlusty, Tsvi"},{"full_name":"Alon, Uri","last_name":"Alon","first_name":"Uri"}],"volume":11,"date_updated":"2023-02-23T14:07:51Z","date_created":"2018-12-11T11:54:14Z","ec_funded":1,"publist_id":"5278","file_date_updated":"2020-07-14T12:45:17Z","license":"https://creativecommons.org/licenses/by/4.0/"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1371/journal.pone.0126907","language":[{"iso":"eng"}],"month":"05","year":"2015","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","publication_status":"published","related_material":{"record":[{"id":"9715","status":"public","relation":"research_data"},{"id":"9772","relation":"research_data","status":"public"}]},"author":[{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","first_name":"Barbora","last_name":"Trubenova","full_name":"Trubenova, Barbora"},{"first_name":"Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"full_name":"Hager, Reinmar","last_name":"Hager","first_name":"Reinmar"}],"volume":10,"date_updated":"2023-02-23T14:07:48Z","date_created":"2018-12-11T11:54:07Z","publist_id":"5299","file_date_updated":"2020-07-14T12:45:17Z","citation":{"ama":"Trubenova B, Novak S, Hager R. Indirect genetic effects and the dynamics of social interactions. PLoS One. 2015;10(5). doi:10.1371/journal.pone.0126907","ista":"Trubenova B, Novak S, Hager R. 2015. Indirect genetic effects and the dynamics of social interactions. PLoS One. 10(5).","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Indirect genetic effects and the dynamics of social interactions. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907","ieee":"B. Trubenova, S. Novak, and R. Hager, “Indirect genetic effects and the dynamics of social interactions,” PLoS One, vol. 10, no. 5. Public Library of Science, 2015.","mla":"Trubenova, Barbora, et al. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One, vol. 10, no. 5, Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.","short":"B. Trubenova, S. Novak, R. Hager, PLoS One 10 (2015).","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Indirect Genetic Effects and the Dynamics of Social Interactions.” PLoS One. Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907."},"publication":"PLoS One","date_published":"2015-05-18T00:00:00Z","scopus_import":1,"has_accepted_license":"1","day":"18","_id":"1809","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 10","title":"Indirect genetic effects and the dynamics of social interactions","status":"public","ddc":["570","576"],"pubrep_id":"453","file":[{"checksum":"d3a4a58ef4bd3b3e2f32b7fd7af4a743","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:09:07Z","relation":"main_file","file_id":"4730","content_type":"application/pdf","file_size":2748982,"creator":"system","access_level":"open_access","file_name":"IST-2016-453-v1+1_journal.pone.0126907.pdf"}],"oa_version":"Published Version","type":"journal_article","issue":"5","abstract":[{"text":"Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.","lang":"eng"}]},{"type":"research_data_reference","publisher":"Public Library of Science","department":[{"_id":"NiBa"}],"status":"public","title":"Description of the agent based simulations","_id":"9772","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2015","oa_version":"Published Version","date_created":"2021-08-05T12:55:20Z","date_updated":"2023-02-23T10:15:25Z","related_material":{"record":[{"id":"1809","relation":"used_in_publication","status":"public"}]},"author":[{"id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","first_name":"Barbora","last_name":"Trubenova","full_name":"Trubenova, Barbora"},{"first_name":"Sebastian","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","full_name":"Novak, Sebastian"},{"full_name":"Hager, Reinmar","last_name":"Hager","first_name":"Reinmar"}],"article_processing_charge":"No","day":"18","month":"05","citation":{"mla":"Trubenova, Barbora, et al. Description of the Agent Based Simulations. Public Library of Science, 2015, doi:10.1371/journal.pone.0126907.s003.","short":"B. Trubenova, S. Novak, R. Hager, (2015).","chicago":"Trubenova, Barbora, Sebastian Novak, and Reinmar Hager. “Description of the Agent Based Simulations.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pone.0126907.s003.","ama":"Trubenova B, Novak S, Hager R. Description of the agent based simulations. 2015. doi:10.1371/journal.pone.0126907.s003","ista":"Trubenova B, Novak S, Hager R. 2015. Description of the agent based simulations, Public Library of Science, 10.1371/journal.pone.0126907.s003.","ieee":"B. Trubenova, S. Novak, and R. Hager, “Description of the agent based simulations.” Public Library of Science, 2015.","apa":"Trubenova, B., Novak, S., & Hager, R. (2015). Description of the agent based simulations. Public Library of Science. https://doi.org/10.1371/journal.pone.0126907.s003"},"doi":"10.1371/journal.pone.0126907.s003","date_published":"2015-05-18T00:00:00Z"},{"article_processing_charge":"No","month":"03","day":"23","date_published":"2015-03-23T00:00:00Z","doi":"10.1371/journal.pcbi.1004055.s002","citation":{"apa":"Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Evolutionary simulation code. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s002","ieee":"T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015.","ista":"Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science, 10.1371/journal.pcbi.1004055.s002.","ama":"Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015. doi:10.1371/journal.pcbi.1004055.s002","chicago":"Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary Simulation Code.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s002.","short":"T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015).","mla":"Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s002."},"type":"research_data_reference","oa_version":"Published Version","date_created":"2021-08-05T12:58:07Z","date_updated":"2023-02-23T10:16:13Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1827"}]},"author":[{"first_name":"Tamar","last_name":"Friedlander","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar"},{"last_name":"Mayo","first_name":"Avraham E.","full_name":"Mayo, Avraham E."},{"first_name":"Tsvi","last_name":"Tlusty","full_name":"Tlusty, Tsvi"},{"full_name":"Alon, Uri","first_name":"Uri","last_name":"Alon"}],"publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"status":"public","title":"Evolutionary simulation code","_id":"9773","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2015"}]