[{"day":"07","publication":"Journal of Theoretical Biology","language":[{"iso":"eng"}],"publication_status":"published","year":"2014","doi":"10.1016/j.jtbi.2014.06.039","volume":360,"date_published":"2014-11-07T00:00:00Z","date_created":"2018-12-11T11:54:46Z","page":"149 - 162","oa_version":"None","acknowledgement":"J.H. received support from the Zdenek Bakala Foundation and the Mobility Fund of Charles University in Prague.","abstract":[{"text":"In infectious disease epidemiology the basic reproductive ratio, R0, is defined as the average number of new infections caused by a single infected individual in a fully susceptible population. Many models describing competition for hosts between non-interacting pathogen strains in an infinite population lead to the conclusion that selection favors invasion of new strains if and only if they have higher R0 values than the resident. Here we demonstrate that this picture fails in finite populations. Using a simple stochastic SIS model, we show that in general there is no analogous optimization principle. We find that successive invasions may in some cases lead to strains that infect a smaller fraction of the host population, and that mutually invasible pathogen strains exist. In the limit of weak selection we demonstrate that an optimization principle does exist, although it differs from R0 maximization. For strains with very large R0, we derive an expression for this local fitness function and use it to establish a lower bound for the error caused by neglecting stochastic effects. Furthermore, we apply this weak selection limit to investigate the selection dynamics in the presence of a trade-off between the virulence and the transmission rate of a pathogen.","lang":"eng"}],"month":"11","intvolume":" 360","publisher":"Elsevier","scopus_import":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:54:08Z","citation":{"mla":"Humplik, Jan, et al. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology, vol. 360, Elsevier, 2014, pp. 149–62, doi:10.1016/j.jtbi.2014.06.039.","short":"J. Humplik, A. Hill, M. Nowak, Journal of Theoretical Biology 360 (2014) 149–162.","ieee":"J. Humplik, A. Hill, and M. Nowak, “Evolutionary dynamics of infectious diseases in finite populations,” Journal of Theoretical Biology, vol. 360. Elsevier, pp. 149–162, 2014.","apa":"Humplik, J., Hill, A., & Nowak, M. (2014). Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2014.06.039","ama":"Humplik J, Hill A, Nowak M. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 2014;360:149-162. doi:10.1016/j.jtbi.2014.06.039","chicago":"Humplik, Jan, Alison Hill, and Martin Nowak. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology. Elsevier, 2014. https://doi.org/10.1016/j.jtbi.2014.06.039.","ista":"Humplik J, Hill A, Nowak M. 2014. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 360, 149–162."},"title":"Evolutionary dynamics of infectious diseases in finite populations","department":[{"_id":"GaTk"}],"author":[{"id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Humplik","full_name":"Humplik, Jan"},{"first_name":"Alison","full_name":"Hill, Alison","last_name":"Hill"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"publist_id":"5166","_id":"1928","status":"public","type":"journal_article"},{"oa":1,"quality_controlled":"1","publisher":"Frontiers Research Foundation","acknowledgement":"Supported in part by EC MEXT project PLICON and the LOEWE-Program “Neuronal Coordination Research Focus Frankfurt” (NeFF). Jochen Triesch was supported by the Quandt foundation.","date_created":"2018-12-11T11:54:46Z","date_published":"2014-05-28T00:00:00Z","doi":"10.3389/fncom.2014.00057","year":"2014","publication":"Frontiers in Computational Neuroscience","day":"28","article_number":"57","author":[{"full_name":"Savin, Cristina","last_name":"Savin","id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina"},{"first_name":"Jochen","last_name":"Triesch","full_name":"Triesch, Jochen"}],"publist_id":"5163","title":"Emergence of task-dependent representations in working memory circuits","citation":{"chicago":"Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2014. https://doi.org/10.3389/fncom.2014.00057.","ista":"Savin C, Triesch J. 2014. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 8(MAY), 57.","mla":"Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience, vol. 8, no. MAY, 57, Frontiers Research Foundation, 2014, doi:10.3389/fncom.2014.00057.","apa":"Savin, C., & Triesch, J. (2014). Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2014.00057","ama":"Savin C, Triesch J. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 2014;8(MAY). doi:10.3389/fncom.2014.00057","ieee":"C. Savin and J. Triesch, “Emergence of task-dependent representations in working memory circuits,” Frontiers in Computational Neuroscience, vol. 8, no. MAY. Frontiers Research Foundation, 2014.","short":"C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014)."},"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035833/"}],"scopus_import":1,"intvolume":" 8","month":"05","abstract":[{"lang":"eng","text":"A wealth of experimental evidence suggests that working memory circuits preferentially represent information that is behaviorally relevant. Still, we are missing a mechanistic account of how these representations come about. Here we provide a simple explanation for a range of experimental findings, in light of prefrontal circuits adapting to task constraints by reward-dependent learning. In particular, we model a neural network shaped by reward-modulated spike-timing dependent plasticity (r-STDP) and homeostatic plasticity (intrinsic excitability and synaptic scaling). We show that the experimentally-observed neural representations naturally emerge in an initially unstructured circuit as it learns to solve several working memory tasks. These results point to a critical, and previously unappreciated, role for reward-dependent learning in shaping prefrontal cortex activity."}],"oa_version":"Submitted Version","volume":8,"issue":"MAY","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"1931","department":[{"_id":"GaTk"}],"date_updated":"2021-01-12T06:54:09Z"},{"language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:45:25Z","file_size":2679222,"date_created":"2018-12-12T10:17:58Z","file_name":"IST-2016-444-v1+1_1-s2.0-S0022519314005888-main.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"a9dbae18d3233b3dab6944fd3f2cd49e","file_id":"5316"}],"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","volume":365,"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1016/j.jtbi.2015.03.013"}]},"oa_version":"Published Version","abstract":[{"text":"Understanding the dynamics of noisy neurons remains an important challenge in neuroscience. Here, we describe a simple probabilistic model that accurately describes the firing behavior in a large class (type II) of neurons. To demonstrate the usefulness of this model, we show how it accurately predicts the interspike interval (ISI) distributions, bursting patterns and mean firing rates found by: (1) simulations of the classic Hodgkin-Huxley model with channel noise, (2) experimental data from squid giant axon with a noisy input current and (3) experimental data on noisy firing from a neuron within the suprachiasmatic nucleus (SCN). This simple model has 6 parameters, however, in some cases, two of these parameters are coupled and only 5 parameters account for much of the known behavior. From these parameters, many properties of spiking can be found through simple calculation. Thus, we show how the complex effects of noise can be understood through a simple and general probabilistic model.","lang":"eng"}],"intvolume":" 365","month":"10","scopus_import":"1","ddc":["570"],"date_updated":"2022-08-25T14:00:47Z","file_date_updated":"2020-07-14T12:45:25Z","department":[{"_id":"GaTk"}],"_id":"2028","pubrep_id":"444","status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","publication":" Journal of Theoretical Biology","day":"12","year":"2014","has_accepted_license":"1","date_created":"2018-12-11T11:55:18Z","doi":"10.1016/j.jtbi.2014.09.041","date_published":"2014-10-12T00:00:00Z","page":"40 - 54","acknowledgement":"This work is supported by AFOSR grant FA 9550-11-1-0165, program grant RPG 24/2012 from the Human Frontiers of Science (DBF) and travel support from the European Commission Marie Curie International Reintegration Grant PIRG04-GA-2008-239429 (KB). DP was supported by NIHR01 GM104987 and the Wyss Institute of Biologically Inspired Engineering. ","oa":1,"publisher":"Academic Press","quality_controlled":"1","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"K. Bodova, D. Paydarfar, and D. Forger, “Characterizing spiking in noisy type II neurons,” Journal of Theoretical Biology, vol. 365. Academic Press, pp. 40–54, 2014.","short":"K. Bodova, D. Paydarfar, D. Forger, Journal of Theoretical Biology 365 (2014) 40–54.","ama":"Bodova K, Paydarfar D, Forger D. Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. 2014;365:40-54. doi:10.1016/j.jtbi.2014.09.041","apa":"Bodova, K., Paydarfar, D., & Forger, D. (2014). Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. Academic Press. https://doi.org/10.1016/j.jtbi.2014.09.041","mla":"Bodova, Katarina, et al. “Characterizing Spiking in Noisy Type II Neurons.” Journal of Theoretical Biology, vol. 365, Academic Press, 2014, pp. 40–54, doi:10.1016/j.jtbi.2014.09.041.","ista":"Bodova K, Paydarfar D, Forger D. 2014. Characterizing spiking in noisy type II neurons. Journal of Theoretical Biology. 365, 40–54.","chicago":"Bodova, Katarina, David Paydarfar, and Daniel Forger. “Characterizing Spiking in Noisy Type II Neurons.” Journal of Theoretical Biology. Academic Press, 2014. https://doi.org/10.1016/j.jtbi.2014.09.041."},"title":"Characterizing spiking in noisy type II neurons","article_processing_charge":"No","publist_id":"5043","author":[{"orcid":"0000-0002-7214-0171","full_name":"Bodova, Katarina","last_name":"Bodova","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina"},{"full_name":"Paydarfar, David","last_name":"Paydarfar","first_name":"David"},{"full_name":"Forger, Daniel","last_name":"Forger","first_name":"Daniel"}]},{"article_number":"062809","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"citation":{"mla":"Botella Soler, Vicente, and Paul Glendinning. “Hierarchy and Polysynchrony in an Adaptive Network .” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 6, 062809, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.062809.","ieee":"V. Botella Soler and P. Glendinning, “Hierarchy and polysynchrony in an adaptive network ,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 6. American Institute of Physics, 2014.","short":"V. Botella Soler, P. Glendinning, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","apa":"Botella Soler, V., & Glendinning, P. (2014). Hierarchy and polysynchrony in an adaptive network . Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.062809","ama":"Botella Soler V, Glendinning P. Hierarchy and polysynchrony in an adaptive network . Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(6). doi:10.1103/PhysRevE.89.062809","chicago":"Botella Soler, Vicente, and Paul Glendinning. “Hierarchy and Polysynchrony in an Adaptive Network .” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.062809.","ista":"Botella Soler V, Glendinning P. 2014. Hierarchy and polysynchrony in an adaptive network . Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(6), 062809."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publist_id":"4798","author":[{"id":"421234E8-F248-11E8-B48F-1D18A9856A87","first_name":"Vicente","orcid":"0000-0002-8790-1914","full_name":"Botella Soler, Vicente","last_name":"Botella Soler"},{"full_name":"Glendinning, Paul","last_name":"Glendinning","first_name":"Paul"}],"title":"Hierarchy and polysynchrony in an adaptive network ","acknowledgement":"V.B.S. is partially supported by contract MEC (Grant No. AYA2010-22111-C03-02).\r\n","oa":1,"publisher":"American Institute of Physics","quality_controlled":"1","year":"2014","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","day":"16","date_created":"2018-12-11T11:56:11Z","date_published":"2014-06-16T00:00:00Z","doi":"10.1103/PhysRevE.89.062809","_id":"2183","type":"journal_article","status":"public","date_updated":"2022-08-25T14:04:45Z","department":[{"_id":"GaTk"}],"abstract":[{"text":"We describe a simple adaptive network of coupled chaotic maps. The network reaches a stationary state (frozen topology) for all values of the coupling parameter, although the dynamics of the maps at the nodes of the network can be nontrivial. The structure of the network shows interesting hierarchical properties and in certain parameter regions the dynamics is polysynchronous: Nodes can be divided in differently synchronized classes but, contrary to cluster synchronization, nodes in the same class need not be connected to each other. These complicated synchrony patterns have been conjectured to play roles in systems biology and circuits. The adaptive system we study describes ways whereby this behavior can evolve from undifferentiated nodes.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1403.3209"}],"scopus_import":"1","intvolume":" 89","month":"06","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":89,"issue":"6"},{"year":"2014","day":"04","publication":"Biophysical Journal","page":"1194 - 1204","doi":"10.1016/j.bpj.2014.01.014","date_published":"2014-03-04T00:00:00Z","date_created":"2018-12-11T11:56:28Z","quality_controlled":"1","publisher":"Biophysical Society","oa":1,"citation":{"ista":"Rieckh G, Tkačik G. 2014. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 106(5), 1194–1204.","chicago":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” Biophysical Journal. Biophysical Society, 2014. https://doi.org/10.1016/j.bpj.2014.01.014.","ieee":"G. Rieckh and G. Tkačik, “Noise and information transmission in promoters with multiple internal states,” Biophysical Journal, vol. 106, no. 5. Biophysical Society, pp. 1194–1204, 2014.","short":"G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204.","ama":"Rieckh G, Tkačik G. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 2014;106(5):1194-1204. doi:10.1016/j.bpj.2014.01.014","apa":"Rieckh, G., & Tkačik, G. (2014). Noise and information transmission in promoters with multiple internal states. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2014.01.014","mla":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” Biophysical Journal, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:10.1016/j.bpj.2014.01.014."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4730","author":[{"id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Rieckh","full_name":"Rieckh, Georg"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"external_id":{"pmid":["24606943"]},"title":"Noise and information transmission in promoters with multiple internal states","publication_identifier":{"issn":["00063495"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":106,"issue":"5","abstract":[{"text":"Based on the measurements of noise in gene expression performed during the past decade, it has become customary to think of gene regulation in terms of a two-state model, where the promoter of a gene can stochastically switch between an ON and an OFF state. As experiments are becoming increasingly precise and the deviations from the two-state model start to be observable, we ask about the experimental signatures of complex multistate promoters, as well as the functional consequences of this additional complexity. In detail, we i), extend the calculations for noise in gene expression to promoters described by state transition diagrams with multiple states, ii), systematically compute the experimentally accessible noise characteristics for these complex promoters, and iii), use information theory to evaluate the channel capacities of complex promoter architectures and compare them with the baseline provided by the two-state model. We find that adding internal states to the promoter generically decreases channel capacity, except in certain cases, three of which (cooperativity, dual-role regulation, promoter cycling) we analyze in detail.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026790/"}],"month":"03","intvolume":" 106","date_updated":"2021-01-12T06:56:10Z","department":[{"_id":"GaTk"}],"_id":"2231","type":"journal_article","status":"public"}]