[{"department":[{"_id":"NiBa"}],"year":"2016","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1199"}]},"month":"09","citation":{"ama":"Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>","short":"N.H. Barton, (2016).","ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016.","chicago":"Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>.","ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, <a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","mla":"Barton, Nicholas H. <i>Data from: How Does Epistasis Influence the Response to Selection?</i> Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","apa":"Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>"},"date_published":"2016-09-23T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"status":"public","date_updated":"2025-05-28T11:57:03Z","_id":"9710","type":"research_data_reference","date_created":"2021-07-23T11:45:47Z","author":[{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"doi":"10.5061/dryad.s5s7r","article_processing_charge":"No","day":"23","oa_version":"Published Version","publisher":"Dryad","title":"Data from: How does epistasis influence the response to selection?","main_file_link":[{"url":"https://doi.org/10.5061/dryad.s5s7r","open_access":"1"}],"abstract":[{"text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects.","lang":"eng"}]},{"department":[{"_id":"SyCr"}],"related_material":{"record":[{"id":"1855","status":"public","relation":"used_in_publication"}]},"month":"01","year":"2016","date_published":"2016-01-22T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Mcmahon, Dino, et al. <i>Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>.","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., &#38; Paxton, R. (2016). Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. Dryad. <a href=\"https://doi.org/10.5061/dryad.4b565\">https://doi.org/10.5061/dryad.4b565</a>","chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.4b565\">https://doi.org/10.5061/dryad.4b565</a>.","ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2016. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees, Dryad, <a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>.","short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016).","ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees.” Dryad, 2016.","ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>"},"status":"public","oa":1,"type":"research_data_reference","date_created":"2021-07-26T09:14:19Z","date_updated":"2023-02-23T10:17:25Z","_id":"9720","oa_version":"Published Version","title":"Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees","publisher":"Dryad","doi":"10.5061/dryad.4b565","author":[{"last_name":"Mcmahon","full_name":"Mcmahon, Dino","first_name":"Dino"},{"last_name":"Fürst","full_name":"Fürst, Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","orcid":"0000-0002-3712-925X"},{"first_name":"Jesicca","last_name":"Caspar","full_name":"Caspar, Jesicca"},{"first_name":"Panagiotis","last_name":"Theodorou","full_name":"Theodorou, Panagiotis"},{"full_name":"Brown, Mark","last_name":"Brown","first_name":"Mark"},{"full_name":"Paxton, Robert","last_name":"Paxton","first_name":"Robert"}],"day":"22","article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.5061/dryad.4b565","open_access":"1"}],"abstract":[{"text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline.","lang":"eng"}]},{"year":"2016","related_material":{"record":[{"id":"1158","status":"public","relation":"used_in_publication"}]},"month":"12","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"status":"public","citation":{"ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Simulation study to test the robustness of ABC in face of recent times of divergence.” Public Library of Science, 2016.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation study to test the robustness of ABC in face of recent times of divergence. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>","mla":"Roux, Camille, et al. <i>Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation study to test the robustness of ABC in face of recent times of divergence, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.1371/journal.pbio.2000234.s016","author":[{"first_name":"Camille","full_name":"Roux, Camille","last_name":"Roux"},{"first_name":"Christelle","orcid":"0000-0001-8441-5075","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"full_name":"Romiguier, Jonathan","last_name":"Romiguier","first_name":"Jonathan"},{"first_name":"Youann","full_name":"Anciaux, Youann","last_name":"Anciaux"},{"first_name":"Nicolas","last_name":"Galtier","full_name":"Galtier, Nicolas"},{"first_name":"Nicolas","full_name":"Bierne, Nicolas","last_name":"Bierne"}],"day":"27","article_processing_charge":"No","title":"Simulation study to test the robustness of ABC in face of recent times of divergence","publisher":"Public Library of Science","oa_version":"Published Version","date_updated":"2023-02-21T16:21:20Z","_id":"9862","type":"research_data_reference","date_created":"2021-08-10T08:20:17Z"},{"doi":"10.1371/journal.pbio.2000234.s017","author":[{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"last_name":"Fraisse","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","orcid":"0000-0001-8441-5075"},{"last_name":"Romiguier","full_name":"Romiguier, Jonathan","first_name":"Jonathan"},{"full_name":"Anciaux, Youann","last_name":"Anciaux","first_name":"Youann"},{"full_name":"Galtier, Nicolas","last_name":"Galtier","first_name":"Nicolas"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}],"day":"27","article_processing_charge":"No","publisher":"Public Library of Science","title":"Accessions of surveyed individuals, geographic locations and summary statistics","oa_version":"Published Version","date_updated":"2023-02-21T16:21:20Z","_id":"9863","type":"research_data_reference","date_created":"2021-08-10T08:22:52Z","status":"public","citation":{"ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Accessions of surveyed individuals, geographic locations and summary statistics.” Public Library of Science, 2016.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>","mla":"Roux, Camille, et al. <i>Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions of surveyed individuals, geographic locations and summary statistics, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","year":"2016","month":"12","related_material":{"record":[{"id":"1158","status":"public","relation":"used_in_publication"}]},"department":[{"_id":"BeVi"},{"_id":"NiBa"}]},{"status":"public","oa":1,"date_published":"2016-12-14T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016.","short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>","mla":"Fernandes Redondo, Rodrigo A., et al. <i>Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family</i>. The Royal Society, 2016, doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>."},"month":"12","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1077"}]},"year":"2016","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"abstract":[{"lang":"eng","text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.4315652.v1"}],"oa_version":"Published Version","publisher":"The Royal Society","title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","doi":"10.6084/m9.figshare.4315652.v1","author":[{"first_name":"Rodrigo A","orcid":"0000-0002-5837-2793","last_name":"Fernandes Redondo","full_name":"Fernandes Redondo, Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Harold","orcid":"0000-0002-5985-7653","id":"2A181218-F248-11E8-B48F-1D18A9856A87","full_name":"de Vladar, Harold","last_name":"de Vladar"},{"first_name":"Tomasz","last_name":"Włodarski","full_name":"Włodarski, Tomasz"},{"last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612","first_name":"Jonathan P"}],"day":"14","article_processing_charge":"No","type":"research_data_reference","date_created":"2021-08-10T08:29:47Z","date_updated":"2025-05-28T11:57:06Z","_id":"9864"},{"related_material":{"record":[{"id":"1167","status":"public","relation":"used_in_publication"}]},"month":"12","year":"2016","department":[{"_id":"AnKi"}],"status":"public","date_published":"2016-12-09T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"apa":"Zagórski, M. P., Burda, Z., &#38; Wacław, B. (2016). ZIP-archived directory containing all data and computer programs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">https://doi.org/10.1371/journal.pcbi.1005218.s009</a>","mla":"Zagórski, Marcin P., et al. <i>ZIP-Archived Directory Containing All Data and Computer Programs</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>.","ista":"Zagórski MP, Burda Z, Wacław B. 2016. ZIP-archived directory containing all data and computer programs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>.","chicago":"Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “ZIP-Archived Directory Containing All Data and Computer Programs.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">https://doi.org/10.1371/journal.pcbi.1005218.s009</a>.","ieee":"M. P. Zagórski, Z. Burda, and B. Wacław, “ZIP-archived directory containing all data and computer programs.” Public Library of Science, 2016.","short":"M.P. Zagórski, Z. Burda, B. Wacław, (2016).","ama":"Zagórski MP, Burda Z, Wacław B. ZIP-archived directory containing all data and computer programs. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>"},"title":"ZIP-archived directory containing all data and computer programs","oa_version":"Published Version","publisher":"Public Library of Science","author":[{"full_name":"Zagórski, Marcin P","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","last_name":"Zagórski","first_name":"Marcin P","orcid":"0000-0001-7896-7762"},{"first_name":"Zdzisław","last_name":"Burda","full_name":"Burda, Zdzisław"},{"last_name":"Wacław","full_name":"Wacław, Bartłomiej","first_name":"Bartłomiej"}],"doi":"10.1371/journal.pcbi.1005218.s009","day":"09","article_processing_charge":"No","type":"research_data_reference","date_created":"2021-08-10T08:37:20Z","date_updated":"2023-02-21T16:24:29Z","_id":"9866"},{"abstract":[{"text":"In the beginning of our experiment, subjects were asked to read a few pages on their computer screens that would explain the rules of the subsequent game. Here, we provide these instructions, translated from German.","lang":"eng"}],"date_updated":"2023-02-21T16:59:01Z","_id":"9867","type":"research_data_reference","date_created":"2021-08-10T08:42:00Z","doi":"10.1371/journal.pone.0163867.s008","author":[{"last_name":"Hilbe","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","first_name":"Christian"},{"full_name":"Hagel, Kristin","last_name":"Hagel","first_name":"Kristin"},{"first_name":"Manfred","last_name":"Milinski","full_name":"Milinski, Manfred"}],"day":"04","article_processing_charge":"No","title":"Experimental game instructions","publisher":"Public Library of Science","oa_version":"Published Version","citation":{"ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental game instructions, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>.","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Game Instructions.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">https://doi.org/10.1371/journal.pone.0163867.s008</a>.","mla":"Hilbe, Christian, et al. <i>Experimental Game Instructions</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>.","apa":"Hilbe, C., Hagel, K., &#38; Milinski, M. (2016). Experimental game instructions. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">https://doi.org/10.1371/journal.pone.0163867.s008</a>","ama":"Hilbe C, Hagel K, Milinski M. Experimental game instructions. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>","short":"C. Hilbe, K. Hagel, M. Milinski, (2016).","ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental game instructions.” Public Library of Science, 2016."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","department":[{"_id":"KrCh"}],"year":"2016","month":"10","related_material":{"record":[{"id":"1322","status":"public","relation":"used_in_publication"}]}},{"citation":{"ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental data, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>.","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Data.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">https://doi.org/10.1371/journal.pone.0163867.s009</a>.","apa":"Hilbe, C., Hagel, K., &#38; Milinski, M. (2016). Experimental data. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">https://doi.org/10.1371/journal.pone.0163867.s009</a>","mla":"Hilbe, Christian, et al. <i>Experimental Data</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>.","ama":"Hilbe C, Hagel K, Milinski M. Experimental data. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>","ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental data.” Public Library of Science, 2016.","short":"C. Hilbe, K. Hagel, M. Milinski, (2016)."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2016-10-04T00:00:00Z","status":"public","department":[{"_id":"KrCh"}],"year":"2016","related_material":{"record":[{"id":"1322","status":"public","relation":"used_in_publication"}]},"month":"10","abstract":[{"lang":"eng","text":"The raw data file containing the experimental decisions of all our study subjects."}],"_id":"9868","date_updated":"2023-02-21T16:59:01Z","date_created":"2021-08-10T08:45:00Z","type":"research_data_reference","article_processing_charge":"No","day":"04","author":[{"first_name":"Christian","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","last_name":"Hilbe"},{"first_name":"Kristin","last_name":"Hagel","full_name":"Hagel, Kristin"},{"first_name":"Manfred","last_name":"Milinski","full_name":"Milinski, Manfred"}],"doi":"10.1371/journal.pone.0163867.s009","title":"Experimental data","publisher":"Public Library of Science","oa_version":"Published Version"},{"date_updated":"2023-02-21T16:56:40Z","_id":"9869","type":"research_data_reference","date_created":"2021-08-10T08:53:48Z","author":[{"first_name":"Patrick","last_name":"Hillenbrand","full_name":"Hillenbrand, Patrick"},{"first_name":"Ulrich","full_name":"Gerland, Ulrich","last_name":"Gerland"},{"first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik"}],"doi":"10.1371/journal.pone.0163628.s001","article_processing_charge":"No","day":"27","oa_version":"Published Version","title":"Error bound on an estimator of position","publisher":"Public Library of Science","abstract":[{"lang":"eng","text":"A lower bound on the error of a positional estimator with limited positional information is derived."}],"department":[{"_id":"GaTk"}],"year":"2016","related_material":{"record":[{"id":"1270","relation":"used_in_publication","status":"public"}]},"month":"09","citation":{"ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Error bound on an estimator of position, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Error Bound on an Estimator of Position.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">https://doi.org/10.1371/journal.pone.0163628.s001</a>.","mla":"Hillenbrand, Patrick, et al. <i>Error Bound on an Estimator of Position</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>.","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Error bound on an estimator of position. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">https://doi.org/10.1371/journal.pone.0163628.s001</a>","ama":"Hillenbrand P, Gerland U, Tkačik G. Error bound on an estimator of position. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s001\">10.1371/journal.pone.0163628.s001</a>","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016."},"date_published":"2016-09-27T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public"},{"abstract":[{"lang":"eng","text":"The effect of noise in the input field on an Ising model is approximated. Furthermore, methods to compute positional information in an Ising model by transfer matrices and Monte Carlo sampling are outlined."}],"title":"Computation of positional information in an Ising model","publisher":"Public Library of Science","oa_version":"Published Version","day":"27","article_processing_charge":"No","author":[{"full_name":"Hillenbrand, Patrick","last_name":"Hillenbrand","first_name":"Patrick"},{"first_name":"Ulrich","last_name":"Gerland","full_name":"Gerland, Ulrich"},{"orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.1371/journal.pone.0163628.s002","date_created":"2021-08-10T09:23:45Z","type":"research_data_reference","_id":"9870","date_updated":"2023-02-21T16:56:40Z","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2016-09-27T00:00:00Z","citation":{"ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in an Ising model. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in an Ising model, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in an Ising Model.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">https://doi.org/10.1371/journal.pone.0163628.s002</a>.","mla":"Hillenbrand, Patrick, et al. <i>Computation of Positional Information in an Ising Model</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">10.1371/journal.pone.0163628.s002</a>.","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Computation of positional information in an Ising model. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s002\">https://doi.org/10.1371/journal.pone.0163628.s002</a>"},"month":"09","related_material":{"record":[{"id":"1270","relation":"used_in_publication","status":"public"}]},"year":"2016","department":[{"_id":"GaTk"}]},{"_id":"9871","date_updated":"2023-02-21T16:56:40Z","date_created":"2021-08-10T09:27:35Z","type":"research_data_reference","day":"27","article_processing_charge":"No","author":[{"first_name":"Patrick","full_name":"Hillenbrand, Patrick","last_name":"Hillenbrand"},{"last_name":"Gerland","full_name":"Gerland, Ulrich","first_name":"Ulrich"},{"first_name":"Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"doi":"10.1371/journal.pone.0163628.s003","publisher":"Public Library of Science","title":"Computation of positional information in a discrete morphogen field","oa_version":"Published Version","abstract":[{"text":"The positional information in a discrete morphogen field with Gaussian noise is computed.","lang":"eng"}],"department":[{"_id":"GaTk"}],"year":"2016","month":"09","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1270"}]},"citation":{"ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in a discrete morphogen field. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">10.1371/journal.pone.0163628.s003</a>","apa":"Hillenbrand, P., Gerland, U., &#38; Tkačik, G. (2016). Computation of positional information in a discrete morphogen field. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">https://doi.org/10.1371/journal.pone.0163628.s003</a>","mla":"Hillenbrand, Patrick, et al. <i>Computation of Positional Information in a Discrete Morphogen Field</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">10.1371/journal.pone.0163628.s003</a>.","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in a Discrete Morphogen Field.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">https://doi.org/10.1371/journal.pone.0163628.s003</a>.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in a discrete morphogen field, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163628.s003\">10.1371/journal.pone.0163628.s003</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public"},{"publisher":"Public Library of Science","title":"Quantification of the growth rate reduction as a consequence of age-specific mortality","oa_version":"Published Version","article_processing_charge":"No","day":"19","author":[{"first_name":"Alex","last_name":"Boehm","full_name":"Boehm, Alex"},{"full_name":"Arnoldini, Markus","last_name":"Arnoldini","first_name":"Markus"},{"last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","first_name":"Tobias"},{"last_name":"Röösli","full_name":"Röösli, Thomas","first_name":"Thomas"},{"first_name":"Colette","last_name":"Bigosch","full_name":"Bigosch, Colette"},{"full_name":"Ackermann, Martin","last_name":"Ackermann","first_name":"Martin"}],"doi":"10.1371/journal.pgen.1005974.s015","date_created":"2021-08-10T09:42:34Z","type":"research_data_reference","_id":"9873","date_updated":"2023-02-21T16:50:13Z","status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Boehm, Alex, et al. <i>Quantification of the Growth Rate Reduction as a Consequence of Age-Specific Mortality</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">10.1371/journal.pgen.1005974.s015</a>.","apa":"Boehm, A., Arnoldini, M., Bergmiller, T., Röösli, T., Bigosch, C., &#38; Ackermann, M. (2016). Quantification of the growth rate reduction as a consequence of age-specific mortality. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">https://doi.org/10.1371/journal.pgen.1005974.s015</a>","ista":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. 2016. Quantification of the growth rate reduction as a consequence of age-specific mortality, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">10.1371/journal.pgen.1005974.s015</a>.","chicago":"Boehm, Alex, Markus Arnoldini, Tobias Bergmiller, Thomas Röösli, Colette Bigosch, and Martin Ackermann. “Quantification of the Growth Rate Reduction as a Consequence of Age-Specific Mortality.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">https://doi.org/10.1371/journal.pgen.1005974.s015</a>.","short":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, M. Ackermann, (2016).","ieee":"A. Boehm, M. Arnoldini, T. Bergmiller, T. Röösli, C. Bigosch, and M. Ackermann, “Quantification of the growth rate reduction as a consequence of age-specific mortality.” Public Library of Science, 2016.","ama":"Boehm A, Arnoldini M, Bergmiller T, Röösli T, Bigosch C, Ackermann M. Quantification of the growth rate reduction as a consequence of age-specific mortality. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005974.s015\">10.1371/journal.pgen.1005974.s015</a>"},"month":"04","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1250"}]},"year":"2016","department":[{"_id":"CaGu"}]},{"volume":3,"article_type":"original","date_created":"2022-02-25T11:42:25Z","author":[{"last_name":"Parise","full_name":"Parise, Francesca","first_name":"Francesca"},{"last_name":"Lygeros","full_name":"Lygeros, John","first_name":"John"},{"last_name":"Ruess","full_name":"Ruess, Jakob","id":"4A245D00-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1615-3282","first_name":"Jakob"}],"day":"10","scopus_import":"1","oa_version":"Published Version","title":"Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study","publication_identifier":{"issn":["2296-665X"]},"publication_status":"published","file_date_updated":"2022-02-25T11:55:26Z","has_accepted_license":"1","intvolume":"         3","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"Mathematical models are of fundamental importance in the understanding of complex population dynamics. For instance, they can be used to predict the population evolution starting from different initial conditions or to test how a system responds to external perturbations. For this analysis to be meaningful in real applications, however, it is of paramount importance to choose an appropriate model structure and to infer the model parameters from measured data. While many parameter inference methods are available for models based on deterministic ordinary differential equations, the same does not hold for more detailed individual-based models. Here we consider, in particular, stochastic models in which the time evolution of the species abundances is described by a continuous-time Markov chain. These models are governed by a master equation that is typically difficult to solve. Consequently, traditional inference methods that rely on iterative evaluation of parameter likelihoods are computationally intractable. The aim of this paper is to present recent advances in parameter inference for continuous-time Markov chain models, based on a moment closure approximation of the parameter likelihood, and to investigate how these results can help in understanding, and ultimately controlling, complex systems in ecology. Specifically, we illustrate through an agricultural pest case study how parameters of a stochastic individual-based model can be identified from measured data and how the resulting model can be used to solve an optimal control problem in a stochastic setting. In particular, we show how the matter of determining the optimal combination of two different pest control methods can be formulated as a chance constrained optimization problem where the control action is modeled as a state reset, leading to a hybrid system formulation."}],"department":[{"_id":"ToHe"},{"_id":"GaTk"}],"article_number":"42","file":[{"file_id":"10795","date_created":"2022-02-25T11:55:26Z","file_size":1371201,"creator":"dernst","date_updated":"2022-02-25T11:55:26Z","relation":"main_file","checksum":"26c222487564e1be02a11d688d6f769d","success":1,"file_name":"2015_FrontiersEnvironmScience_Parise.pdf","access_level":"open_access","content_type":"application/pdf"}],"month":"06","citation":{"ama":"Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. <i>Frontiers in Environmental Science</i>. 2015;3. doi:<a href=\"https://doi.org/10.3389/fenvs.2015.00042\">10.3389/fenvs.2015.00042</a>","short":"F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015).","ieee":"F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study,” <i>Frontiers in Environmental Science</i>, vol. 3. Frontiers, 2015.","ista":"Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 3, 42.","chicago":"Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” <i>Frontiers in Environmental Science</i>. Frontiers, 2015. <a href=\"https://doi.org/10.3389/fenvs.2015.00042\">https://doi.org/10.3389/fenvs.2015.00042</a>.","mla":"Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” <i>Frontiers in Environmental Science</i>, vol. 3, 42, Frontiers, 2015, doi:<a href=\"https://doi.org/10.3389/fenvs.2015.00042\">10.3389/fenvs.2015.00042</a>.","apa":"Parise, F., Lygeros, J., &#38; Ruess, J. (2015). Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. <i>Frontiers in Environmental Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fenvs.2015.00042\">https://doi.org/10.3389/fenvs.2015.00042</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"date_updated":"2022-02-25T11:59:23Z","_id":"10794","type":"journal_article","doi":"10.3389/fenvs.2015.00042","article_processing_charge":"No","publisher":"Frontiers","quality_controlled":"1","ddc":["000","570"],"keyword":["General Environmental Science"],"year":"2015","ec_funded":1,"acknowledgement":"The authors would like to acknowledge contributions from Baptiste Mottet who performed preliminary analysis regarding parameter inference for the considered case study in a student project (Mottet, 2014/2015).\r\nThe research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. [291734] and from SystemsX under the project SignalX.","date_published":"2015-06-10T00:00:00Z","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"publication":"Frontiers in Environmental Science","status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","citation":{"apa":"Chatterjee, K., &#38; Ibsen-Jensen, R. (2015). The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i> (Vol. 2015, pp. 1018–1029). San Diego, CA, United States: SIAM. <a href=\"https://doi.org/10.1137/1.9781611973730.69\">https://doi.org/10.1137/1.9781611973730.69</a>","mla":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, vol. 2015, no. 1, SIAM, 2015, pp. 1018–29, doi:<a href=\"https://doi.org/10.1137/1.9781611973730.69\">10.1137/1.9781611973730.69</a>.","chicago":"Chatterjee, Krishnendu, and Rasmus Ibsen-Jensen. “The Value 1 Problem under Finite-Memory Strategies for Concurrent Mean-Payoff Games.” In <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 2015:1018–29. SIAM, 2015. <a href=\"https://doi.org/10.1137/1.9781611973730.69\">https://doi.org/10.1137/1.9781611973730.69</a>.","ista":"Chatterjee K, Ibsen-Jensen R. 2015. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms vol. 2015, 1018–1029.","ieee":"K. Chatterjee and R. Ibsen-Jensen, “The value 1 problem under finite-memory strategies for concurrent mean-payoff games,” in <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>, San Diego, CA, United States, 2015, vol. 2015, no. 1, pp. 1018–1029.","short":"K. Chatterjee, R. Ibsen-Jensen, in:, Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, SIAM, 2015, pp. 1018–1029.","ama":"Chatterjee K, Ibsen-Jensen R. The value 1 problem under finite-memory strategies for concurrent mean-payoff games. In: <i>Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Vol 2015. SIAM; 2015:1018-1029. doi:<a href=\"https://doi.org/10.1137/1.9781611973730.69\">10.1137/1.9781611973730.69</a>"},"language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"arxiv":1,"month":"01","publication_identifier":{"isbn":["978-161197374-7"]},"publication_status":"published","abstract":[{"text":"We consider concurrent mean-payoff games, a very well-studied class of two-player (player 1 vs player 2) zero-sum games on finite-state graphs where every transition is assigned a reward between 0 and 1, and the payoff function is the long-run average of the rewards. The value is the maximal expected payoff that player 1 can guarantee against all strategies of player 2. We consider the computation of the set of states with value 1 under finite-memory strategies for player 1, and our main results for the problem are as follows: (1) we present a polynomial-time algorithm; (2) we show that whenever there is a finite-memory strategy, there is a stationary strategy that does not need memory at all; and (3) we present an optimal bound (which is double exponential) on the patience of stationary strategies (where patience of a distribution is the inverse of the smallest positive probability and represents a complexity measure of a stationary strategy).","lang":"eng"}],"intvolume":"      2015","date_created":"2022-02-25T12:18:43Z","volume":2015,"oa_version":"Preprint","title":"The value 1 problem under finite-memory strategies for concurrent mean-payoff games","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","first_name":"Rasmus"}],"day":"01","scopus_import":"1","acknowledgement":"The research was partly supported by FWF Grant No P 23499-N23, FWF NFN Grant\r\nNo S11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","date_published":"2015-01-01T00:00:00Z","conference":{"location":"San Diego, CA, United States","name":"SODA: Symposium on Discrete Algorithms","end_date":"2015-01-06","start_date":"2015-01-04"},"ec_funded":1,"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publication":"Proceedings of the Twenty-Sixth Annual ACM-SIAM Symposium on Discrete Algorithms","status":"public","external_id":{"arxiv":["1409.6690"]},"year":"2015","quality_controlled":"1","page":"1018-1029","type":"conference","date_updated":"2022-02-25T12:33:32Z","_id":"10796","publisher":"SIAM","doi":"10.1137/1.9781611973730.69","article_processing_charge":"No"},{"month":"12","external_id":{"pmid":["26306635"]},"year":"2015","publist_id":"6851","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"status":"public","publication":"Glycobiology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2015-12-01T00:00:00Z","citation":{"ieee":"J. Engel, P. S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, and F. Routier, “Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis,” <i>Glycobiology</i>, vol. 25, no. 12. Oxford University Press, pp. 1423–1430, 2015.","short":"J. Engel, P.S. Schmalhorst, A. Kruger, C. Muller, F. Buettner, F. Routier, Glycobiology 25 (2015) 1423–1430.","ama":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. <i>Glycobiology</i>. 2015;25(12):1423-1430. doi:<a href=\"https://doi.org/10.1093/glycob/cwv059\">10.1093/glycob/cwv059</a>","apa":"Engel, J., Schmalhorst, P. S., Kruger, A., Muller, C., Buettner, F., &#38; Routier, F. (2015). Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. <i>Glycobiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/glycob/cwv059\">https://doi.org/10.1093/glycob/cwv059</a>","mla":"Engel, Jakob, et al. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” <i>Glycobiology</i>, vol. 25, no. 12, Oxford University Press, 2015, pp. 1423–30, doi:<a href=\"https://doi.org/10.1093/glycob/cwv059\">10.1093/glycob/cwv059</a>.","ista":"Engel J, Schmalhorst PS, Kruger A, Muller C, Buettner F, Routier F. 2015. Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis. Glycobiology. 25(12), 1423–1430.","chicago":"Engel, Jakob, Philipp S Schmalhorst, Anke Kruger, Christina Muller, Falk Buettner, and Françoise Routier. “Characterization of an N-Acetylglucosaminyltransferase Involved in Aspergillus Fumigatus Zwitterionic Glycoinositolphosphoceramide Biosynthesis.” <i>Glycobiology</i>. Oxford University Press, 2015. <a href=\"https://doi.org/10.1093/glycob/cwv059\">https://doi.org/10.1093/glycob/cwv059</a>."},"issue":"12","pmid":1,"publisher":"Oxford University Press","title":"Characterization of an N-acetylglucosaminyltransferase involved in Aspergillus fumigatus zwitterionic glycoinositolphosphoceramide biosynthesis","oa_version":"None","scopus_import":1,"day":"01","doi":"10.1093/glycob/cwv059","author":[{"first_name":"Jakob","last_name":"Engel","full_name":"Engel, Jakob"},{"first_name":"Philipp S","orcid":"0000-0002-5795-0133","last_name":"Schmalhorst","full_name":"Schmalhorst, Philipp S","id":"309D50DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kruger","full_name":"Kruger, Anke","first_name":"Anke"},{"last_name":"Muller","full_name":"Muller, Christina","first_name":"Christina"},{"full_name":"Buettner, Falk","last_name":"Buettner","first_name":"Falk"},{"first_name":"Françoise","full_name":"Routier, Françoise","last_name":"Routier"}],"date_created":"2018-12-11T11:48:35Z","type":"journal_article","_id":"802","volume":25,"date_updated":"2021-01-12T08:16:33Z","intvolume":"        25","abstract":[{"lang":"eng","text":"Glycoinositolphosphoceramides (GIPCs) are complex sphingolipids present at the plasma membrane of various eukaryotes with the important exception of mammals. In fungi, these glycosphingolipids commonly contain an alpha-mannose residue (Man) linked at position 2 of the inositol. However, several pathogenic fungi additionally synthesize zwitterionic GIPCs carrying an alpha-glucosamine residue (GlcN) at this position. In the human pathogen Aspergillus fumigatus, the GlcNalpha1,2IPC core (where IPC is inositolphosphoceramide) is elongated to Manalpha1,3Manalpha1,6GlcNalpha1,2IPC, which is the most abundant GIPC synthesized by this fungus. In this study, we identified an A. fumigatus N-acetylglucosaminyltransferase, named GntA, and demonstrate its involvement in the initiation of zwitterionic GIPC biosynthesis. Targeted deletion of the gene encoding GntA in A. fumigatus resulted in complete absence of zwitterionic GIPC; a phenotype that could be reverted by episomal expression of GntA in the mutant. The N-acetylhexosaminyltransferase activity of GntA was substantiated by production of N-acetylhexosamine-IPC in the yeast Saccharomyces cerevisiae upon GntA expression. Using an in vitro assay, GntA was furthermore shown to use UDP-N-acetylglucosamine as donor substrate to generate a glycolipid product resistant to saponification and to digestion by phosphatidylinositol-phospholipase C as expected for GlcNAcalpha1,2IPC. Finally, as the enzymes involved in mannosylation of IPC, GntA was localized to the Golgi apparatus, the site of IPC synthesis."}],"page":"1423 - 1430","quality_controlled":"1","publication_status":"published"},{"month":"11","related_material":{"record":[{"id":"9308","status":"public","relation":"later_version"},{"relation":"later_version","status":"public","id":"10220"},{"id":"8156","status":"public","relation":"dissertation_contains"}]},"arxiv":1,"external_id":{"arxiv":["1511.03501"]},"year":"2015","article_number":"1511.03501","department":[{"_id":"UlWa"}],"publication":"arXiv","language":[{"iso":"eng"}],"status":"public","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2015-11-15T00:00:00Z","acknowledgement":"We would like to thank A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful discussions.","citation":{"chicago":"Avvakumov, Sergey, Isaac Mabillard, A. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” <i>ArXiv</i>, n.d.","ista":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. arXiv, 1511.03501.","apa":"Avvakumov, S., Mabillard, I., Skopenkov, A., &#38; Wagner, U. (n.d.). Eliminating higher-multiplicity intersections, III. Codimension 2. <i>arXiv</i>.","mla":"Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections, III. Codimension 2.” <i>ArXiv</i>, 1511.03501.","ama":"Avvakumov S, Mabillard I, Skopenkov A, Wagner U. Eliminating higher-multiplicity intersections, III. Codimension 2. <i>arXiv</i>.","ieee":"S. Avvakumov, I. Mabillard, A. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections, III. Codimension 2,” <i>arXiv</i>. .","short":"S. Avvakumov, I. Mabillard, A. Skopenkov, U. Wagner, ArXiv (n.d.)."},"title":"Eliminating higher-multiplicity intersections, III. Codimension 2","oa_version":"Preprint","article_processing_charge":"No","day":"15","author":[{"last_name":"Avvakumov","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","full_name":"Avvakumov, Sergey","first_name":"Sergey"},{"last_name":"Mabillard","id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","full_name":"Mabillard, Isaac","first_name":"Isaac"},{"first_name":"A.","full_name":"Skopenkov, A.","last_name":"Skopenkov"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568","first_name":"Uli"}],"date_created":"2020-07-30T10:45:19Z","type":"preprint","_id":"8183","date_updated":"2023-09-07T13:12:17Z","abstract":[{"text":"We study conditions under which a finite simplicial complex $K$ can be mapped to $\\mathbb R^d$ without higher-multiplicity intersections. An almost $r$-embedding is a map $f: K\\to \\mathbb R^d$ such that the images of any $r$\r\npairwise disjoint simplices of $K$ do not have a common point. We show that if $r$ is not a prime power and $d\\geq 2r+1$, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost $r$-embedding of\r\nthe $(d+1)(r-1)$-simplex in $\\mathbb R^d$. This improves on previous constructions of counterexamples (for $d\\geq 3r$) based on a series of papers by M. \\\"Ozaydin, M. Gromov, P. Blagojevi\\'c, F. Frick, G. Ziegler, and the second and fourth present authors. The counterexamples are obtained by proving the following algebraic criterion in codimension 2: If $r\\ge3$ and if $K$ is a finite $2(r-1)$-complex then there exists an almost $r$-embedding $K\\to \\mathbb R^{2r}$ if and only if there exists a general position PL map $f:K\\to \\mathbb R^{2r}$ such that the algebraic intersection number of the $f$-images of any $r$ pairwise disjoint simplices of $K$ is zero. This result can be restated in terms of cohomological obstructions or equivariant maps, and extends an analogous codimension 3 criterion by the second and fourth authors. As another application we classify ornaments $f:S^3 \\sqcup S^3\\sqcup S^3\\to \\mathbb R^5$ up to ornament\r\nconcordance. It follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for $r=2$ is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample.","lang":"eng"}],"publication_status":"submitted","main_file_link":[{"url":"https://arxiv.org/abs/1511.03501","open_access":"1"}]},{"oa":1,"pubrep_id":"470","language":[{"iso":"eng"}],"issue":"3","citation":{"apa":"Hammer, M., Krueger Burg, D., Tuffy, L., Cooper, B., Taschenberger, H., Goswami, S., … Brose, N. (2015). Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">https://doi.org/10.1016/j.celrep.2015.09.011</a>","mla":"Hammer, Matthieu, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” <i>Cell Reports</i>, vol. 13, no. 3, Cell Press, 2015, pp. 516–23, doi:<a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">10.1016/j.celrep.2015.09.011</a>.","ista":"Hammer M, Krueger Burg D, Tuffy L, Cooper B, Taschenberger H, Goswami S, Ehrenreich H, Jonas PM, Varoqueaux F, Rhee J, Brose N. 2015. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 13(3), 516–523.","chicago":"Hammer, Matthieu, Dilja Krueger Burg, Liam Tuffy, Benjamin Cooper, Holger Taschenberger, Sarit Goswami, Hannelore Ehrenreich, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” <i>Cell Reports</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">https://doi.org/10.1016/j.celrep.2015.09.011</a>.","ieee":"M. Hammer <i>et al.</i>, “Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism,” <i>Cell Reports</i>, vol. 13, no. 3. Cell Press, pp. 516–523, 2015.","short":"M. Hammer, D. Krueger Burg, L. Tuffy, B. Cooper, H. Taschenberger, S. Goswami, H. Ehrenreich, P.M. Jonas, F. Varoqueaux, J. Rhee, N. Brose, Cell Reports 13 (2015) 516–523.","ama":"Hammer M, Krueger Burg D, Tuffy L, et al. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. <i>Cell Reports</i>. 2015;13(3):516-523. doi:<a href=\"https://doi.org/10.1016/j.celrep.2015.09.011\">10.1016/j.celrep.2015.09.011</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","department":[{"_id":"PeJo"}],"file":[{"file_name":"IST-2016-470-v1+1_1-s2.0-S2211124715010220-main.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"44d30fbb543774b076b4938bd36af9d7","date_created":"2018-12-12T10:13:23Z","file_size":2314406,"creator":"system","date_updated":"2020-07-14T12:45:07Z","file_id":"5005"}],"has_accepted_license":"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        13","abstract":[{"lang":"eng","text":"Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are among the most common genetic abnormalities associated with autism spectrum disorders, but little is known about the function of Neuroligin-4 and the consequences of its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout mice, focusing on the hippocampus as a model brain region with a critical role in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects of the protein composition and function of GABAergic synapses in the hippocampal CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced perturbations of γ-oscillatory network activity, which has been implicated in cognitive function and is altered in multiple psychiatric and neurodevelopmental disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent GABAergic synapses may contribute to autism phenotypes and indicate new strategies for therapeutic approaches."}],"publication_status":"published","file_date_updated":"2020-07-14T12:45:07Z","author":[{"last_name":"Hammer","full_name":"Hammer, Matthieu","first_name":"Matthieu"},{"last_name":"Krueger Burg","full_name":"Krueger Burg, Dilja","first_name":"Dilja"},{"last_name":"Tuffy","full_name":"Tuffy, Liam","first_name":"Liam"},{"first_name":"Benjamin","last_name":"Cooper","full_name":"Cooper, Benjamin"},{"full_name":"Taschenberger, Holger","last_name":"Taschenberger","first_name":"Holger"},{"last_name":"Goswami","id":"3A578F32-F248-11E8-B48F-1D18A9856A87","full_name":"Goswami, Sarit","first_name":"Sarit"},{"first_name":"Hannelore","full_name":"Ehrenreich, Hannelore","last_name":"Ehrenreich"},{"orcid":"0000-0001-5001-4804","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M"},{"first_name":"Frederique","full_name":"Varoqueaux, Frederique","last_name":"Varoqueaux"},{"first_name":"Jeong","last_name":"Rhee","full_name":"Rhee, Jeong"},{"last_name":"Brose","full_name":"Brose, Nils","first_name":"Nils"}],"scopus_import":1,"day":"20","oa_version":"Published Version","title":"Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism","volume":13,"date_created":"2018-12-11T11:53:02Z","status":"public","publication":"Cell Reports","acknowledgement":"This work was supported by the Max Planck Society (N.B. and H.E.), the European Commission (EU-AIMS FP7-115300, N.B. and H.E.; Marie Curie IRG, D.K.-B.), the German Research Foundation (CNMPB, N.B., H.E., and F.V.), the Alexander von Humboldt-Foundation (D.K.-B.), and the Austrian Fond zur Förderung der Wissenschaftlichen Forschung (P 24909-B24, P.J.). M.H. was a student of the doctoral program Molecular Physiology of the Brain. Dr. J.-M. Fritschy generously provided the GABAARγ2 antibody. We thank F. Benseler, I. Thanhäuser, D. Schwerdtfeger, A. Ronnenberg, and D. Winkler for valuable advice and excellent technical support. We are grateful to the staff at the animal facility of the Max Planck Institute of Experimental Medicine for mouse husbandry.","date_published":"2015-10-20T00:00:00Z","year":"2015","publist_id":"5551","page":"516 - 523","ddc":["570"],"quality_controlled":"1","doi":"10.1016/j.celrep.2015.09.011","publisher":"Cell Press","date_updated":"2021-01-12T06:52:01Z","_id":"1615","type":"journal_article"},{"language":[{"iso":"eng"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Veldkamp C, Kiermaier E, Gabel Eissens S, et al. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. <i>Biochemistry</i>. 2015;54(27):4163-4166. doi:<a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">10.1021/acs.biochem.5b00560</a>","short":"C. Veldkamp, E. Kiermaier, S. Gabel Eissens, M. Gillitzer, D. Lippner, F. Disilvio, C. Mueller, P. Wantuch, G. Chaffee, M. Famiglietti, D. Zgoba, A. Bailey, Y. Bah, S. Engebretson, D. Graupner, E. Lackner, V. Larosa, T. Medeiros, M. Olson, A. Phillips, H. Pyles, A. Richard, S. Schoeller, B. Touzeau, L. Williams, M.K. Sixt, F. Peterson, Biochemistry 54 (2015) 4163–4166.","ieee":"C. Veldkamp <i>et al.</i>, “Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites,” <i>Biochemistry</i>, vol. 54, no. 27. American Chemical Society, pp. 4163–4166, 2015.","ista":"Veldkamp C, Kiermaier E, Gabel Eissens S, Gillitzer M, Lippner D, Disilvio F, Mueller C, Wantuch P, Chaffee G, Famiglietti M, Zgoba D, Bailey A, Bah Y, Engebretson S, Graupner D, Lackner E, Larosa V, Medeiros T, Olson M, Phillips A, Pyles H, Richard A, Schoeller S, Touzeau B, Williams L, Sixt MK, Peterson F. 2015. Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. Biochemistry. 54(27), 4163–4166.","chicago":"Veldkamp, Christopher, Eva Kiermaier, Skylar Gabel Eissens, Miranda Gillitzer, David Lippner, Frank Disilvio, Casey Mueller, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” <i>Biochemistry</i>. American Chemical Society, 2015. <a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">https://doi.org/10.1021/acs.biochem.5b00560</a>.","mla":"Veldkamp, Christopher, et al. “Solution Structure of CCL19 and Identification of Overlapping CCR7 and PSGL-1 Binding Sites.” <i>Biochemistry</i>, vol. 54, no. 27, American Chemical Society, 2015, pp. 4163–66, doi:<a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">10.1021/acs.biochem.5b00560</a>.","apa":"Veldkamp, C., Kiermaier, E., Gabel Eissens, S., Gillitzer, M., Lippner, D., Disilvio, F., … Peterson, F. (2015). Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites. <i>Biochemistry</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.biochem.5b00560\">https://doi.org/10.1021/acs.biochem.5b00560</a>"},"issue":"27","month":"06","department":[{"_id":"MiSi"}],"abstract":[{"lang":"eng","text":"CCL19 and CCL21 are chemokines involved in the trafficking of immune cells, particularly within the lymphatic system, through activation of CCR7. Concurrent expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19 and binding is competitive. Implications for the mechanism of PSGL-1's enhancement of resting T-cell recruitment are discussed."}],"intvolume":"        54","publication_status":"published","title":"Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites","oa_version":"Submitted Version","day":"26","scopus_import":"1","author":[{"full_name":"Veldkamp, Christopher","last_name":"Veldkamp","first_name":"Christopher"},{"first_name":"Eva","orcid":"0000-0001-6165-5738","last_name":"Kiermaier","id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","full_name":"Kiermaier, Eva"},{"first_name":"Skylar","last_name":"Gabel Eissens","full_name":"Gabel Eissens, Skylar"},{"full_name":"Gillitzer, Miranda","last_name":"Gillitzer","first_name":"Miranda"},{"first_name":"David","last_name":"Lippner","full_name":"Lippner, David"},{"first_name":"Frank","full_name":"Disilvio, Frank","last_name":"Disilvio"},{"last_name":"Mueller","full_name":"Mueller, Casey","first_name":"Casey"},{"full_name":"Wantuch, Paeton","last_name":"Wantuch","first_name":"Paeton"},{"first_name":"Gary","full_name":"Chaffee, Gary","last_name":"Chaffee"},{"full_name":"Famiglietti, Michael","last_name":"Famiglietti","first_name":"Michael"},{"first_name":"Danielle","full_name":"Zgoba, Danielle","last_name":"Zgoba"},{"last_name":"Bailey","full_name":"Bailey, Asha","first_name":"Asha"},{"full_name":"Bah, Yaya","last_name":"Bah","first_name":"Yaya"},{"first_name":"Samantha","last_name":"Engebretson","full_name":"Engebretson, Samantha"},{"last_name":"Graupner","full_name":"Graupner, David","first_name":"David"},{"first_name":"Emily","last_name":"Lackner","full_name":"Lackner, Emily"},{"first_name":"Vincent","full_name":"Larosa, Vincent","last_name":"Larosa"},{"first_name":"Tysha","full_name":"Medeiros, Tysha","last_name":"Medeiros"},{"full_name":"Olson, Michael","last_name":"Olson","first_name":"Michael"},{"first_name":"Andrew","last_name":"Phillips","full_name":"Phillips, Andrew"},{"first_name":"Harley","last_name":"Pyles","full_name":"Pyles, Harley"},{"last_name":"Richard","full_name":"Richard, Amanda","first_name":"Amanda"},{"full_name":"Schoeller, Scott","last_name":"Schoeller","first_name":"Scott"},{"full_name":"Touzeau, Boris","last_name":"Touzeau","first_name":"Boris"},{"first_name":"Larry","last_name":"Williams","full_name":"Williams, Larry"},{"first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K"},{"full_name":"Peterson, Francis","last_name":"Peterson","first_name":"Francis"}],"date_created":"2018-12-11T11:53:03Z","volume":54,"status":"public","publication":"Biochemistry","project":[{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556"}],"date_published":"2015-06-26T00:00:00Z","ec_funded":1,"pmid":1,"external_id":{"pmid":["26115234"]},"year":"2015","publist_id":"5548","page":"4163 - 4166","quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4809050/","open_access":"1"}],"publisher":"American Chemical Society","article_processing_charge":"No","doi":"10.1021/acs.biochem.5b00560","type":"journal_article","_id":"1618","date_updated":"2023-03-30T11:32:57Z"},{"department":[{"_id":"ToBo"}],"file":[{"relation":"main_file","checksum":"0e82e3279f50b15c6c170c042627802b","file_name":"IST-2016-468-v1+1_journal.pbio.1002299.pdf","content_type":"application/pdf","access_level":"open_access","file_id":"4723","date_created":"2018-12-12T10:09:00Z","file_size":1387760,"date_updated":"2020-07-14T12:45:07Z","creator":"system"}],"article_number":"e1002299","month":"11","citation":{"ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 13(11), e1002299.","chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” <i>PLoS Biology</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pbio.1002299\">https://doi.org/10.1371/journal.pbio.1002299</a>.","mla":"Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” <i>PLoS Biology</i>, vol. 13, no. 11, e1002299, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299\">10.1371/journal.pbio.1002299</a>.","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak, E., &#38; Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary dynamics leading to drug resistance. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002299\">https://doi.org/10.1371/journal.pbio.1002299</a>","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of evolutionary dynamics leading to drug resistance. <i>PLoS Biology</i>. 2015;13(11). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299\">10.1371/journal.pbio.1002299</a>","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak, M.T. Bollenbach, PLoS Biology 13 (2015).","ieee":"G. Chevereau <i>et al.</i>, “Quantifying the determinants of evolutionary dynamics leading to drug resistance,” <i>PLoS Biology</i>, vol. 13, no. 11. Public Library of Science, 2015."},"issue":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"pubrep_id":"468","language":[{"iso":"eng"}],"volume":13,"date_created":"2018-12-11T11:53:04Z","scopus_import":1,"day":"18","author":[{"first_name":"Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","full_name":"Chevereau, Guillaume","last_name":"Chevereau"},{"full_name":"Dravecka, Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","last_name":"Dravecka","first_name":"Marta","orcid":"0000-0002-2519-8004"},{"first_name":"Tugce","last_name":"Batur","full_name":"Batur, Tugce"},{"first_name":"Aysegul","full_name":"Guvenek, Aysegul","last_name":"Guvenek"},{"last_name":"Ayhan","full_name":"Ayhan, Dilay","first_name":"Dilay"},{"last_name":"Toprak","full_name":"Toprak, Erdal","first_name":"Erdal"},{"last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X"}],"title":"Quantifying the determinants of evolutionary dynamics leading to drug resistance","oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:07Z","publication_status":"published","has_accepted_license":"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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the “morbidostat”, a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations—an almost paradoxical behavior since this drug causes DNA damage and increases the mutation rate. Overall, we identified novel quantitative characteristics of the evolutionary landscape that provide the conceptual foundation for predicting the dynamics of drug resistance evolution.","lang":"eng"}],"intvolume":"        13","publist_id":"5547","year":"2015","related_material":{"record":[{"status":"public","relation":"research_data","id":"9711"},{"id":"9765","status":"public","relation":"research_data"},{"id":"6263","relation":"dissertation_contains","status":"public"}]},"ec_funded":1,"date_published":"2015-11-18T00:00:00Z","publication":"PLoS Biology","status":"public","project":[{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013"},{"_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22"},{"call_identifier":"FP7","grant_number":"303507","name":"Optimality principles in responses to antibiotics","_id":"25E83C2C-B435-11E9-9278-68D0E5697425"}],"_id":"1619","date_updated":"2024-03-25T23:30:14Z","type":"journal_article","doi":"10.1371/journal.pbio.1002299","publisher":"Public Library of Science","quality_controlled":"1","ddc":["570"]},{"_id":"1623","date_updated":"2021-01-12T06:52:04Z","type":"journal_article","doi":"10.1186/s13068-015-0380-2","publisher":"BioMed Central","quality_controlled":"1","ddc":["570"],"publist_id":"5537","year":"2015","date_published":"2015-11-25T00:00:00Z","publication":"Biotechnology for Biofuels","status":"public","volume":8,"date_created":"2018-12-11T11:53:05Z","day":"25","scopus_import":1,"author":[{"first_name":"Petter","last_name":"Hammar","full_name":"Hammar, Petter"},{"first_name":"Andreas","orcid":"0000-0001-8619-2223","full_name":"Angermayr, Andreas","id":"4677C796-F248-11E8-B48F-1D18A9856A87","last_name":"Angermayr"},{"full_name":"Sjostrom, Staffan","last_name":"Sjostrom","first_name":"Staffan"},{"first_name":"Josefin","full_name":"Van Der Meer, Josefin","last_name":"Van Der Meer"},{"first_name":"Klaas","full_name":"Hellingwerf, Klaas","last_name":"Hellingwerf"},{"first_name":"Elton","full_name":"Hudson, Elton","last_name":"Hudson"},{"last_name":"Joensson","full_name":"Joensson, Hakaan","first_name":"Hakaan"}],"oa_version":"Published Version","title":"Single-cell screening of photosynthetic growth and lactate production by cyanobacteria","file_date_updated":"2020-07-14T12:45:07Z","publication_status":"published","has_accepted_license":"1","intvolume":"         8","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","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Background\r\nPhotosynthetic cyanobacteria are attractive for a range of biotechnological applications including biofuel production. However, due to slow growth, screening of mutant libraries using microtiter plates is not feasible.\r\nResults\r\nWe present a method for high-throughput, single-cell analysis and sorting of genetically engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic device is used to encapsulate single cells in picoliter droplets, assay the droplets for l-lactate production, and sort strains with high productivity. We demonstrate the separation of low- and high-producing reference strains, as well as enrichment of a more productive l-lactate-synthesizing population after UV-induced mutagenesis. The droplet platform also revealed population heterogeneity in photosynthetic growth and lactate production, as well as the presence of metabolically stalled cells.\r\nConclusions\r\nThe workflow will facilitate metabolic engineering and directed evolution studies and will be useful in studies of cyanobacteria biochemistry and physiology.\r\n","lang":"eng"}],"department":[{"_id":"ToBo"}],"file":[{"file_id":"4796","file_size":2914089,"date_created":"2018-12-12T10:10:11Z","creator":"system","date_updated":"2020-07-14T12:45:07Z","relation":"main_file","checksum":"172b0b6f4eb2e5c22b7cec1d57dc0107","file_name":"IST-2016-467-v1+1_s13068-015-0380-2.pdf","access_level":"open_access","content_type":"application/pdf"}],"article_number":"193","month":"11","citation":{"ieee":"P. Hammar <i>et al.</i>, “Single-cell screening of photosynthetic growth and lactate production by cyanobacteria,” <i>Biotechnology for Biofuels</i>, vol. 8, no. 1. BioMed Central, 2015.","short":"P. Hammar, A. Angermayr, S. Sjostrom, J. Van Der Meer, K. Hellingwerf, E. Hudson, H. Joensson, Biotechnology for Biofuels 8 (2015).","ama":"Hammar P, Angermayr A, Sjostrom S, et al. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. <i>Biotechnology for Biofuels</i>. 2015;8(1). doi:<a href=\"https://doi.org/10.1186/s13068-015-0380-2\">10.1186/s13068-015-0380-2</a>","apa":"Hammar, P., Angermayr, A., Sjostrom, S., Van Der Meer, J., Hellingwerf, K., Hudson, E., &#38; Joensson, H. (2015). Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. <i>Biotechnology for Biofuels</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13068-015-0380-2\">https://doi.org/10.1186/s13068-015-0380-2</a>","mla":"Hammar, Petter, et al. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” <i>Biotechnology for Biofuels</i>, vol. 8, no. 1, 193, BioMed Central, 2015, doi:<a href=\"https://doi.org/10.1186/s13068-015-0380-2\">10.1186/s13068-015-0380-2</a>.","chicago":"Hammar, Petter, Andreas Angermayr, Staffan Sjostrom, Josefin Van Der Meer, Klaas Hellingwerf, Elton Hudson, and Hakaan Joensson. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” <i>Biotechnology for Biofuels</i>. BioMed Central, 2015. <a href=\"https://doi.org/10.1186/s13068-015-0380-2\">https://doi.org/10.1186/s13068-015-0380-2</a>.","ista":"Hammar P, Angermayr A, Sjostrom S, Van Der Meer J, Hellingwerf K, Hudson E, Joensson H. 2015. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. 8(1), 193."},"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"pubrep_id":"467"}]