[{"date_published":"2014-11-27T00:00:00Z","intvolume":"         4","month":"11","oa":1,"issue":"24","date_updated":"2023-09-07T11:55:53Z","page":"4589 - 4597","year":"2014","volume":4,"day":"27","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:55:16Z","ddc":["570"],"publication":"Ecology and Evolution","doi":"10.1002/ece3.1289","oa_version":"Published Version","ec_funded":1,"related_material":{"record":[{"id":"1125","relation":"dissertation_contains","status":"public"}]},"publisher":"Wiley-Blackwell","has_accepted_license":"1","author":[{"last_name":"Novak","orcid":"0000-0002-2519-824X","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","full_name":"Novak, Sebastian"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution","file":[{"file_name":"IST-2016-462-v1+1_Novak-2014-Ecology_and_Evolution.pdf","date_created":"2018-12-12T10:12:28Z","date_updated":"2020-07-14T12:45:25Z","file_size":118813,"creator":"system","content_type":"application/pdf","file_id":"4946","access_level":"open_access","relation":"main_file","checksum":"9ab43db1b0fede7bfe560ed77e177b76"}],"publist_id":"5049","department":[{"_id":"NiBa"}],"pubrep_id":"462","language":[{"iso":"eng"}],"scopus_import":1,"abstract":[{"lang":"eng","text":"Understanding the evolution of dispersal is essential for understanding and predicting the dynamics of natural populations. Two main factors are known to influence dispersal evolution: spatio-temporal variation in the environment and relatedness between individuals. However, the relation between these factors is still poorly understood, and they are usually treated separately. In this article, I present a theoretical framework that contains and connects effects of both environmental variation and relatedness, and reproduces and extends their known features. Spatial habitat variation selects for balanced dispersal strategies, whereby the population is kept at an ideal free distribution. Within this class of dispersal strategies, I explain how increased dispersal is promoted by perturbations to the dispersal type frequencies. An explicit formula shows the magnitude of the selective advantage of increased dispersal in terms of the spatial variability in the frequencies of the different dispersal strategies present. These variances are capable of capturing various sources of stochasticity and hence establish a common scale for their effects on the evolution of dispersal. The results furthermore indicate an alternative approach to identifying effects of relatedness on dispersal evolution."}],"file_date_updated":"2020-07-14T12:45:25Z","type":"journal_article","citation":{"short":"S. Novak, Ecology and Evolution 4 (2014) 4589–4597.","ista":"Novak S. 2014. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. Ecology and Evolution. 4(24), 4589–4597.","ieee":"S. Novak, “Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution,” <i>Ecology and Evolution</i>, vol. 4, no. 24. Wiley-Blackwell, pp. 4589–4597, 2014.","ama":"Novak S. Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. <i>Ecology and Evolution</i>. 2014;4(24):4589-4597. doi:<a href=\"https://doi.org/10.1002/ece3.1289\">10.1002/ece3.1289</a>","chicago":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” <i>Ecology and Evolution</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/ece3.1289\">https://doi.org/10.1002/ece3.1289</a>.","apa":"Novak, S. (2014). Habitat heterogeneities versus spatial type frequency variances as driving forces of dispersal evolution. <i>Ecology and Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/ece3.1289\">https://doi.org/10.1002/ece3.1289</a>","mla":"Novak, Sebastian. “Habitat Heterogeneities versus Spatial Type Frequency Variances as Driving Forces of Dispersal Evolution.” <i>Ecology and Evolution</i>, vol. 4, no. 24, Wiley-Blackwell, 2014, pp. 4589–97, doi:<a href=\"https://doi.org/10.1002/ece3.1289\">10.1002/ece3.1289</a>."},"quality_controlled":"1","_id":"2023","publication_status":"published","project":[{"grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}]},{"year":"2014","oa":1,"date_updated":"2021-01-12T06:54:48Z","article_number":"3498","month":"03","intvolume":"         5","date_published":"2014-03-25T00:00:00Z","oa_version":"Submitted Version","doi":"10.1038/ncomms4498","publication":"Nature Communications","day":"25","status":"public","ddc":["570"],"date_created":"2018-12-11T11:55:16Z","volume":5,"pubrep_id":"616","language":[{"iso":"eng"}],"department":[{"_id":"DaSi"}],"publist_id":"5048","file":[{"file_name":"IST-2016-616-v1+1_DaSi_Bifurcation_Postprint.pdf","date_created":"2018-12-12T10:11:11Z","date_updated":"2020-07-14T12:45:25Z","file_id":"4864","content_type":"application/pdf","creator":"system","file_size":4803515,"relation":"main_file","access_level":"open_access","checksum":"614fb6579c86d1f95bdd95eeb9ab01b0"}],"title":"Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole","author":[{"last_name":"Toshima","first_name":"Junko","full_name":"Toshima, Junko"},{"first_name":"Show","last_name":"Nishinoaki","full_name":"Nishinoaki, Show"},{"full_name":"Sato, Yoshifumi","first_name":"Yoshifumi","last_name":"Sato"},{"full_name":"Yamamoto, Wataru","first_name":"Wataru","last_name":"Yamamoto"},{"last_name":"Furukawa","first_name":"Daiki","full_name":"Furukawa, Daiki"},{"full_name":"Siekhaus, Daria E","last_name":"Siekhaus","orcid":"0000-0001-8323-8353","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Akira","last_name":"Sawaguchi","full_name":"Sawaguchi, Akira"},{"full_name":"Toshima, Jiro","first_name":"Jiro","last_name":"Toshima"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Nature Publishing Group","has_accepted_license":"1","publication_status":"published","quality_controlled":"1","_id":"2024","file_date_updated":"2020-07-14T12:45:25Z","type":"journal_article","abstract":[{"lang":"eng","text":"The yeast Rab5 homologue, Vps21p, is known to be involved both in the vacuolar protein sorting (VPS) pathway from the trans-Golgi network to the vacuole, and in the endocytic pathway from the plasma membrane to the vacuole. However, the intracellular location at which these two pathways converge remains unclear. In addition, the endocytic pathway is not completely blocked in yeast cells lacking all Rab5 genes, suggesting the existence of an unidentified route that bypasses the Rab5-dependent endocytic pathway. Here we show that convergence of the endocytic and VPS pathways occurs upstream of the requirement for Vps21p in these pathways. We also identify a previously unidentified endocytic pathway mediated by the AP-3 complex. Importantly, the AP-3-mediated pathway appears mostly intact in Rab5-disrupted cells, and thus works as an alternative route to the vacuole/lysosome. We propose that the endocytic traffic branches into two routes to reach the vacuole: a Rab5-dependent VPS pathway and a Rab5-independent AP-3-mediated pathway."}],"scopus_import":1,"citation":{"mla":"Toshima, Junko, et al. “Bifurcation of the Endocytic Pathway into Rab5-Dependent and -Independent Transport to the Vacuole.” <i>Nature Communications</i>, vol. 5, 3498, Nature Publishing Group, 2014, doi:<a href=\"https://doi.org/10.1038/ncomms4498\">10.1038/ncomms4498</a>.","apa":"Toshima, J., Nishinoaki, S., Sato, Y., Yamamoto, W., Furukawa, D., Siekhaus, D. E., … Toshima, J. (2014). Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms4498\">https://doi.org/10.1038/ncomms4498</a>","chicago":"Toshima, Junko, Show Nishinoaki, Yoshifumi Sato, Wataru Yamamoto, Daiki Furukawa, Daria E Siekhaus, Akira Sawaguchi, and Jiro Toshima. “Bifurcation of the Endocytic Pathway into Rab5-Dependent and -Independent Transport to the Vacuole.” <i>Nature Communications</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/ncomms4498\">https://doi.org/10.1038/ncomms4498</a>.","ama":"Toshima J, Nishinoaki S, Sato Y, et al. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. <i>Nature Communications</i>. 2014;5. doi:<a href=\"https://doi.org/10.1038/ncomms4498\">10.1038/ncomms4498</a>","short":"J. Toshima, S. Nishinoaki, Y. Sato, W. Yamamoto, D. Furukawa, D.E. Siekhaus, A. Sawaguchi, J. Toshima, Nature Communications 5 (2014).","ieee":"J. Toshima <i>et al.</i>, “Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole,” <i>Nature Communications</i>, vol. 5. Nature Publishing Group, 2014.","ista":"Toshima J, Nishinoaki S, Sato Y, Yamamoto W, Furukawa D, Siekhaus DE, Sawaguchi A, Toshima J. 2014. Bifurcation of the endocytic pathway into Rab5-dependent and -independent transport to the vacuole. Nature Communications. 5, 3498."}},{"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"publist_id":"5045","title":"Rabinizer 3: Safraless translation of ltl to small deterministic automata","author":[{"last_name":"Komárková","first_name":"Zuzana","full_name":"Komárková, Zuzana"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","full_name":"Kretinsky, Jan"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","publication_status":"published","project":[{"grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"}],"quality_controlled":"1","editor":[{"first_name":"Franck","last_name":"Cassez","full_name":"Cassez, Franck"},{"first_name":"Jean-François","last_name":"Raskin","full_name":"Raskin, Jean-François"}],"_id":"2026","type":"conference","abstract":[{"lang":"eng","text":"We present a tool for translating LTL formulae into deterministic ω-automata. It is the first tool that covers the whole LTL that does not use Safra’s determinization or any of its variants. This leads to smaller automata. There are several outputs of the tool: firstly, deterministic Rabin automata, which are the standard input for probabilistic model checking, e.g. for the probabilistic model-checker PRISM; secondly, deterministic generalized Rabin automata, which can also be used for probabilistic model checking and are sometimes by orders of magnitude smaller. We also link our tool to PRISM and show that this leads to a significant speed-up of probabilistic LTL model checking, especially with the generalized Rabin automata."}],"citation":{"chicago":"Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Franck Cassez and Jean-François Raskin, 8837:235–41. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">https://doi.org/10.1007/978-3-319-11936-6_17</a>.","short":"Z. Komárková, J. Kretinsky, in:, F. Cassez, J.-F. Raskin (Eds.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 235–241.","ista":"Komárková Z, Kretinsky J. 2014. Rabinizer 3: Safraless translation of ltl to small deterministic automata. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 235–241.","ieee":"Z. Komárková and J. Kretinsky, “Rabinizer 3: Safraless translation of ltl to small deterministic automata,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Sydney, Australia, 2014, vol. 8837, pp. 235–241.","ama":"Komárková Z, Kretinsky J. Rabinizer 3: Safraless translation of ltl to small deterministic automata. In: Cassez F, Raskin J-F, eds. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8837. Springer; 2014:235-241. doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">10.1007/978-3-319-11936-6_17</a>","mla":"Komárková, Zuzana, and Jan Kretinsky. “Rabinizer 3: Safraless Translation of Ltl to Small Deterministic Automata.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 235–41, doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">10.1007/978-3-319-11936-6_17</a>.","apa":"Komárková, Z., &#38; Kretinsky, J. (2014). Rabinizer 3: Safraless translation of ltl to small deterministic automata. In F. Cassez &#38; J.-F. Raskin (Eds.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8837, pp. 235–241). Sydney, Australia: Springer. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_17\">https://doi.org/10.1007/978-3-319-11936-6_17</a>"},"year":"2014","conference":{"location":"Sydney, Australia","name":"ATVA: Automated Technology for Verification and Analysis","end_date":"2014-11-07","start_date":"2014-11-03"},"page":"235 - 241","date_updated":"2021-01-12T06:54:49Z","acknowledgement":"Sponsor: P202/12/G061; GACR; Czech Science Foundation\r\n\r\n","intvolume":"      8837","month":"01","alternative_title":["LNCS"],"date_published":"2014-01-01T00:00:00Z","ec_funded":1,"oa_version":"None","doi":"10.1007/978-3-319-11936-6_17","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","status":"public","day":"01","date_created":"2018-12-11T11:55:17Z","volume":8837},{"status":"public","day":"01","date_created":"2018-12-11T11:55:17Z","volume":8837,"ec_funded":1,"oa_version":"Submitted Version","publication":" Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.2967"}],"doi":"10.1007/978-3-319-11936-6_8","oa":1,"date_updated":"2021-01-12T06:54:49Z","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 246967 (VERIWARE), by the EU FP7 project HIERATIC, by the Czech Science Foundation grant No P202/12/P612, by EPSRC project EP/K038575/1.","alternative_title":["LNCS"],"date_published":"2014-11-01T00:00:00Z","month":"11","intvolume":"      8837","year":"2014","conference":{"start_date":"2014-11-03","end_date":"2014-11-07","name":"ALENEX: Algorithm Engineering and Experiments","location":"Sydney, Australia"},"page":"98 - 114","quality_controlled":"1","_id":"2027","editor":[{"last_name":"Cassez","first_name":"Franck","full_name":"Cassez, Franck"},{"full_name":"Raskin, Jean-François","first_name":"Jean-François","last_name":"Raskin"}],"abstract":[{"text":"We present a general framework for applying machine-learning algorithms to the verification of Markov decision processes (MDPs). The primary goal of these techniques is to improve performance by avoiding an exhaustive exploration of the state space. Our framework focuses on probabilistic reachability, which is a core property for verification, and is illustrated through two distinct instantiations. The first assumes that full knowledge of the MDP is available, and performs a heuristic-driven partial exploration of the model, yielding precise lower and upper bounds on the required probability. The second tackles the case where we may only sample the MDP, and yields probabilistic guarantees, again in terms of both the lower and upper bounds, which provides efficient stopping criteria for the approximation. The latter is the first extension of statistical model checking for unbounded properties inMDPs. In contrast with other related techniques, our approach is not restricted to time-bounded (finite-horizon) or discounted properties, nor does it assume any particular properties of the MDP. We also show how our methods extend to LTL objectives. We present experimental results showing the performance of our framework on several examples.","lang":"eng"}],"type":"conference","citation":{"ama":"Brázdil T, Chatterjee K, Chmelik M, et al. Verification of markov decision processes using learning algorithms. In: Cassez F, Raskin J-F, eds. <i> Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8837. Society of Industrial and Applied Mathematics; 2014:98-114. doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_8\">10.1007/978-3-319-11936-6_8</a>","short":"T. Brázdil, K. Chatterjee, M. Chmelik, V. Forejt, J. Kretinsky, M. Kwiatkowska, D. Parker, M. Ujma, in:, F. Cassez, J.-F. Raskin (Eds.),  Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Society of Industrial and Applied Mathematics, 2014, pp. 98–114.","ieee":"T. Brázdil <i>et al.</i>, “Verification of markov decision processes using learning algorithms,” in <i> Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Sydney, Australia, 2014, vol. 8837, pp. 98–114.","ista":"Brázdil T, Chatterjee K, Chmelik M, Forejt V, Kretinsky J, Kwiatkowska M, Parker D, Ujma M. 2014. Verification of markov decision processes using learning algorithms.  Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). ALENEX: Algorithm Engineering and Experiments, LNCS, vol. 8837, 98–114.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Martin Chmelik, Vojtěch Forejt, Jan Kretinsky, Marta Kwiatkowska, David Parker, and Mateusz Ujma. “Verification of Markov Decision Processes Using Learning Algorithms.” In <i> Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Franck Cassez and Jean-François Raskin, 8837:98–114. Society of Industrial and Applied Mathematics, 2014. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_8\">https://doi.org/10.1007/978-3-319-11936-6_8</a>.","apa":"Brázdil, T., Chatterjee, K., Chmelik, M., Forejt, V., Kretinsky, J., Kwiatkowska, M., … Ujma, M. (2014). Verification of markov decision processes using learning algorithms. In F. Cassez &#38; J.-F. Raskin (Eds.), <i> Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8837, pp. 98–114). Sydney, Australia: Society of Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_8\">https://doi.org/10.1007/978-3-319-11936-6_8</a>","mla":"Brázdil, Tomáš, et al. “Verification of Markov Decision Processes Using Learning Algorithms.” <i> Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Society of Industrial and Applied Mathematics, 2014, pp. 98–114, doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_8\">10.1007/978-3-319-11936-6_8</a>."},"publication_status":"published","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"},{"name":"LIGHT-REGULATED LIGAND TRAPS FOR SPATIO-TEMPORAL INHIBITION OF CELL SIGNALING","_id":"26241A12-B435-11E9-9278-68D0E5697425","grant_number":"24696"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"grant_number":"S11402-N23","call_identifier":"FWF","name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"title":"Verification of markov decision processes using learning algorithms","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Brázdil","first_name":"Tomáš","full_name":"Brázdil, Tomáš"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik"},{"last_name":"Forejt","first_name":"Vojtěch","full_name":"Forejt, Vojtěch"},{"full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky","first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marta","last_name":"Kwiatkowska","full_name":"Kwiatkowska, Marta"},{"last_name":"Parker","first_name":"David","full_name":"Parker, David"},{"full_name":"Ujma, Mateusz","last_name":"Ujma","first_name":"Mateusz"}],"publisher":"Society of Industrial and Applied Mathematics","language":[{"iso":"eng"}],"publist_id":"5046","department":[{"_id":"KrCh"},{"_id":"ToHe"}]},{"publication_status":"published","citation":{"ama":"Bodova K, Paydarfar D, Forger D. Characterizing spiking in noisy type II neurons. <i> Journal of Theoretical Biology</i>. 2014;365:40-54. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2014.09.041\">10.1016/j.jtbi.2014.09.041</a>","short":"K. Bodova, D. Paydarfar, D. Forger,  Journal of Theoretical Biology 365 (2014) 40–54.","ista":"Bodova K, Paydarfar D, Forger D. 2014. Characterizing spiking in noisy type II neurons.  Journal of Theoretical Biology. 365, 40–54.","ieee":"K. Bodova, D. Paydarfar, and D. Forger, “Characterizing spiking in noisy type II neurons,” <i> Journal of Theoretical Biology</i>, vol. 365. Academic Press, pp. 40–54, 2014.","chicago":"Bodova, Katarina, David Paydarfar, and Daniel Forger. “Characterizing Spiking in Noisy Type II Neurons.” <i> Journal of Theoretical Biology</i>. Academic Press, 2014. <a href=\"https://doi.org/10.1016/j.jtbi.2014.09.041\">https://doi.org/10.1016/j.jtbi.2014.09.041</a>.","apa":"Bodova, K., Paydarfar, D., &#38; Forger, D. (2014). Characterizing spiking in noisy type II neurons. <i> Journal of Theoretical Biology</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jtbi.2014.09.041\">https://doi.org/10.1016/j.jtbi.2014.09.041</a>","mla":"Bodova, Katarina, et al. “Characterizing Spiking in Noisy Type II Neurons.” <i> Journal of Theoretical Biology</i>, vol. 365, Academic Press, 2014, pp. 40–54, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2014.09.041\">10.1016/j.jtbi.2014.09.041</a>."},"file_date_updated":"2020-07-14T12:45:25Z","type":"journal_article","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"}],"scopus_import":"1","_id":"2028","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"GaTk"}],"publist_id":"5043","language":[{"iso":"eng"}],"pubrep_id":"444","has_accepted_license":"1","publisher":"Academic Press","file":[{"access_level":"open_access","checksum":"a9dbae18d3233b3dab6944fd3f2cd49e","relation":"main_file","content_type":"application/pdf","file_id":"5316","file_size":2679222,"creator":"system","date_created":"2018-12-12T10:17:58Z","date_updated":"2020-07-14T12:45:25Z","file_name":"IST-2016-444-v1+1_1-s2.0-S0022519314005888-main.pdf"}],"author":[{"full_name":"Bodova, Katarina","first_name":"Katarina","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","last_name":"Bodova"},{"last_name":"Paydarfar","first_name":"David","full_name":"Paydarfar, David"},{"full_name":"Forger, Daniel","first_name":"Daniel","last_name":"Forger"}],"title":"Characterizing spiking in noisy type II neurons","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.jtbi.2014.09.041","publication":" Journal of Theoretical Biology","related_material":{"link":[{"url":"https://doi.org/10.1016/j.jtbi.2015.03.013","relation":"erratum"}]},"oa_version":"Published Version","volume":365,"ddc":["570"],"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_created":"2018-12-11T11:55:18Z","day":"12","status":"public","page":"40 - 54","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","year":"2014","intvolume":"       365","month":"10","date_published":"2014-10-12T00:00:00Z","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. ","date_updated":"2022-08-25T14:00:47Z","oa":1},{"publication_status":"published","type":"journal_article","scopus_import":1,"abstract":[{"lang":"eng","text":"Spin-wave theory is a key ingredient in our comprehension of quantum spin systems, and is used successfully for understanding a wide range of magnetic phenomena, including magnon condensation and stability of patterns in dipolar systems. Nevertheless, several decades of research failed to establish the validity of spin-wave theory rigorously, even for the simplest models of quantum spins. A rigorous justification of the method for the three-dimensional quantum Heisenberg ferromagnet at low temperatures is presented here. We derive sharp bounds on its free energy by combining a bosonic formulation of the model introduced by Holstein and Primakoff with probabilistic estimates and operator inequalities."}],"citation":{"mla":"Correggi, Michele, et al. “Validity of Spin-Wave Theory for the Quantum Heisenberg Model.” <i>EPL</i>, vol. 108, no. 2, 20003, IOP Publishing Ltd., 2014, doi:<a href=\"https://doi.org/10.1209/0295-5075/108/20003\">10.1209/0295-5075/108/20003</a>.","apa":"Correggi, M., Giuliani, A., &#38; Seiringer, R. (2014). Validity of spin-wave theory for the quantum Heisenberg model. <i>EPL</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1209/0295-5075/108/20003\">https://doi.org/10.1209/0295-5075/108/20003</a>","chicago":"Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of Spin-Wave Theory for the Quantum Heisenberg Model.” <i>EPL</i>. IOP Publishing Ltd., 2014. <a href=\"https://doi.org/10.1209/0295-5075/108/20003\">https://doi.org/10.1209/0295-5075/108/20003</a>.","short":"M. Correggi, A. Giuliani, R. Seiringer, EPL 108 (2014).","ieee":"M. Correggi, A. Giuliani, and R. Seiringer, “Validity of spin-wave theory for the quantum Heisenberg model,” <i>EPL</i>, vol. 108, no. 2. IOP Publishing Ltd., 2014.","ista":"Correggi M, Giuliani A, Seiringer R. 2014. Validity of spin-wave theory for the quantum Heisenberg model. EPL. 108(2), 20003.","ama":"Correggi M, Giuliani A, Seiringer R. Validity of spin-wave theory for the quantum Heisenberg model. <i>EPL</i>. 2014;108(2). doi:<a href=\"https://doi.org/10.1209/0295-5075/108/20003\">10.1209/0295-5075/108/20003</a>"},"quality_controlled":"1","_id":"2029","department":[{"_id":"RoSe"}],"publist_id":"5044","language":[{"iso":"eng"}],"publisher":"IOP Publishing Ltd.","title":"Validity of spin-wave theory for the quantum Heisenberg model","author":[{"last_name":"Correggi","first_name":"Michele","full_name":"Correggi, Michele"},{"first_name":"Alessandro","last_name":"Giuliani","full_name":"Giuliani, Alessandro"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"http://arxiv.org/abs/1404.4717","open_access":"1"}],"doi":"10.1209/0295-5075/108/20003","publication":"EPL","oa_version":"Submitted Version","volume":108,"status":"public","day":"13","date_created":"2018-12-11T11:55:18Z","year":"2014","article_number":"20003","acknowledgement":"239694; ERC; European Research Council","month":"10","intvolume":"       108","date_published":"2014-10-13T00:00:00Z","issue":"2","oa":1,"date_updated":"2021-01-12T06:54:50Z"},{"abstract":[{"text":"A puzzling property of synaptic transmission, originally established at the neuromuscular junction, is that the time course of transmitter release is independent of the extracellular Ca2+ concentration ([Ca2+]o), whereas the rate of release is highly [Ca2+]o-dependent. Here, we examine the time course of release at inhibitory basket cell-Purkinje cell synapses and show that it is independent of [Ca2+]o. Modeling of Ca2+-dependent transmitter release suggests that the invariant time course of release critically depends on tight coupling between Ca2+ channels and release sensors. Experiments with exogenous Ca2+ chelators reveal that channel-sensor coupling at basket cell-Purkinje cell synapses is very tight, with a mean distance of 10–20 nm. Thus, tight channel-sensor coupling provides a mechanistic explanation for the apparent [Ca2+]o independence of the time course of release.","lang":"eng"}],"scopus_import":1,"type":"journal_article","file_date_updated":"2020-07-14T12:45:26Z","citation":{"ama":"Arai  itaru, Jonas PM. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. <i>eLife</i>. 2014;3. doi:<a href=\"https://doi.org/10.7554/eLife.04057\">10.7554/eLife.04057</a>","short":"itaru Arai, P.M. Jonas, ELife 3 (2014).","ista":"Arai  itaru, Jonas PM. 2014. Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. eLife. 3.","ieee":"itaru Arai and P. M. Jonas, “Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse,” <i>eLife</i>, vol. 3. eLife Sciences Publications, 2014.","chicago":"Arai, itaru, and Peter M Jonas. “Nanodomain Coupling Explains Ca^2+ Independence of Transmitter Release Time Course at a Fast Central Synapse.” <i>ELife</i>. eLife Sciences Publications, 2014. <a href=\"https://doi.org/10.7554/eLife.04057\">https://doi.org/10.7554/eLife.04057</a>.","apa":"Arai,  itaru, &#38; Jonas, P. M. (2014). Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.04057\">https://doi.org/10.7554/eLife.04057</a>","mla":"Arai, itaru, and Peter M. Jonas. “Nanodomain Coupling Explains Ca^2+ Independence of Transmitter Release Time Course at a Fast Central Synapse.” <i>ELife</i>, vol. 3, eLife Sciences Publications, 2014, doi:<a href=\"https://doi.org/10.7554/eLife.04057\">10.7554/eLife.04057</a>."},"quality_controlled":"1","_id":"2031","publication_status":"published","project":[{"_id":"25C26B1E-B435-11E9-9278-68D0E5697425","name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24","call_identifier":"FWF"},{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"268548"}],"publisher":"eLife Sciences Publications","has_accepted_license":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Nanodomain coupling explains Ca^2+ independence of transmitter release time course at a fast central synapse","author":[{"first_name":"Itaru","id":"32A73F6C-F248-11E8-B48F-1D18A9856A87","last_name":"Arai","full_name":"Arai, Itaru"},{"last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M"}],"file":[{"file_name":"IST-2016-421-v1+1_e04057.full.pdf","date_created":"2018-12-12T10:14:41Z","date_updated":"2020-07-14T12:45:26Z","content_type":"application/pdf","file_id":"5094","creator":"system","file_size":2239563,"access_level":"open_access","relation":"main_file","checksum":"c240f915450d4ebe8f95043a2a8c7b1a"}],"department":[{"_id":"PeJo"}],"publist_id":"5041","pubrep_id":"421","language":[{"iso":"eng"}],"volume":3,"status":"public","day":"09","date_created":"2018-12-11T11:55:19Z","ddc":["570"],"publication":"eLife","doi":"10.7554/eLife.04057","ec_funded":1,"oa_version":"Submitted Version","date_published":"2014-12-09T00:00:00Z","intvolume":"         3","month":"12","oa":1,"date_updated":"2021-01-12T06:54:51Z","year":"2014"},{"oa_version":"Published Version","publication":"Molecular and Cellular Oncology","doi":"10.4161/23723548.2014.964045","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"date_created":"2018-12-11T11:55:19Z","ddc":["570"],"status":"public","day":"31","volume":1,"year":"2014","license":"https://creativecommons.org/licenses/by-nc/4.0/","date_updated":"2021-01-12T06:54:51Z","oa":1,"issue":"4","date_published":"2014-12-31T00:00:00Z","month":"12","intvolume":"         1","article_number":"e964045","publication_status":"published","_id":"2032","quality_controlled":"1","citation":{"ama":"Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M. The optogenetic promise for oncology: Episode I. <i>Molecular and Cellular Oncology</i>. 2014;1(4). doi:<a href=\"https://doi.org/10.4161/23723548.2014.964045\">10.4161/23723548.2014.964045</a>","ista":"Inglés Prieto Á, Gschaider-Reichhart E, Schelch K, Janovjak HL, Grusch M. 2014. The optogenetic promise for oncology: Episode I. Molecular and Cellular Oncology. 1(4), e964045.","short":"Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H.L. Janovjak, M. Grusch, Molecular and Cellular Oncology 1 (2014).","ieee":"Á. Inglés Prieto, E. Gschaider-Reichhart, K. Schelch, H. L. Janovjak, and M. Grusch, “The optogenetic promise for oncology: Episode I,” <i>Molecular and Cellular Oncology</i>, vol. 1, no. 4. Taylor &#38; Francis, 2014.","chicago":"Inglés Prieto, Álvaro, Eva Gschaider-Reichhart, Karin Schelch, Harald L Janovjak, and Michael Grusch. “The Optogenetic Promise for Oncology: Episode I.” <i>Molecular and Cellular Oncology</i>. Taylor &#38; Francis, 2014. <a href=\"https://doi.org/10.4161/23723548.2014.964045\">https://doi.org/10.4161/23723548.2014.964045</a>.","apa":"Inglés Prieto, Á., Gschaider-Reichhart, E., Schelch, K., Janovjak, H. L., &#38; Grusch, M. (2014). The optogenetic promise for oncology: Episode I. <i>Molecular and Cellular Oncology</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.4161/23723548.2014.964045\">https://doi.org/10.4161/23723548.2014.964045</a>","mla":"Inglés Prieto, Álvaro, et al. “The Optogenetic Promise for Oncology: Episode I.” <i>Molecular and Cellular Oncology</i>, vol. 1, no. 4, e964045, Taylor &#38; Francis, 2014, doi:<a href=\"https://doi.org/10.4161/23723548.2014.964045\">10.4161/23723548.2014.964045</a>."},"scopus_import":1,"abstract":[{"text":"As light-based control of fundamental signaling pathways is becoming a reality, the field of optogenetics is rapidly moving beyond neuroscience. We have recently developed receptor tyrosine kinases that are activated by light and control cell proliferation, epithelial–mesenchymal transition, and angiogenic sprouting—cell behaviors central to cancer progression.","lang":"eng"}],"type":"journal_article","file_date_updated":"2020-07-14T12:45:26Z","language":[{"iso":"eng"}],"department":[{"_id":"HaJa"}],"publist_id":"5040","title":"The optogenetic promise for oncology: Episode I","author":[{"id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro","orcid":"0000-0002-5409-8571","last_name":"Inglés Prieto","full_name":"Inglés Prieto, Álvaro"},{"full_name":"Gschaider-Reichhart, Eva","orcid":"0000-0002-7218-7738","last_name":"Gschaider-Reichhart","first_name":"Eva","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schelch, Karin","first_name":"Karin","last_name":"Schelch"},{"full_name":"Janovjak, Harald L","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","last_name":"Janovjak"},{"full_name":"Grusch, Michael","last_name":"Grusch","first_name":"Michael"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2019-05-16T13:39:11Z","date_updated":"2020-07-14T12:45:26Z","file_name":"2014_Taylor_Alvaro.pdf","access_level":"open_access","checksum":"44e17ad40577ab46eb602e88a8b0b8fd","relation":"main_file","creator":"kschuh","file_size":1765933,"content_type":"application/pdf","file_id":"6464"}],"has_accepted_license":"1","publisher":"Taylor & Francis"},{"year":"2014","language":[{"iso":"eng"}],"publist_id":"5038","department":[{"_id":"ChLa"}],"conference":{"location":"Montreal, Canada","start_date":"2014-12-08","end_date":"2014-12-13","name":"NIPS: Neural Information Processing Systems"},"page":"837-845","title":"Mind the nuisance: Gaussian process classification using privileged noise","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"first_name":"Daniel","last_name":"Hernandez Lobato","full_name":"Hernandez Lobato, Daniel"},{"full_name":"Sharmanska, Viktoriia","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","first_name":"Viktoriia","orcid":"0000-0003-0192-9308","last_name":"Sharmanska"},{"full_name":"Kersting, Kristian","last_name":"Kersting","first_name":"Kristian"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Novi","last_name":"Quadrianto","full_name":"Quadrianto, Novi"}],"issue":"January","date_updated":"2023-02-23T10:25:24Z","publisher":"Neural Information Processing Systems","date_published":"2014-12-08T00:00:00Z","month":"12","intvolume":"         1","oa_version":"Submitted Version","publication":"Advances in Neural Information Processing Systems","main_file_link":[{"open_access":"1","url":"https://papers.nips.cc/paper/5373-mind-the-nuisance-gaussian-process-classification-using-privileged-noise"}],"publication_status":"published","status":"public","quality_controlled":"1","day":"08","date_created":"2018-12-11T11:55:20Z","_id":"2033","scopus_import":1,"abstract":[{"text":"The learning with privileged information setting has recently attracted a lot of attention within the machine learning community, as it allows the integration of additional knowledge into the training process of a classifier, even when this comes in the form of a data modality that is not available at test time. Here, we show that privileged information can naturally be treated as noise in the latent function of a Gaussian process classifier (GPC). That is, in contrast to the standard GPC setting, the latent function is not just a nuisance but a feature: it becomes a natural measure of confidence about the training data by modulating the slope of the GPC probit likelihood function. Extensive experiments on public datasets show that the proposed GPC method using privileged noise, called GPC+, improves over a standard GPC without privileged knowledge, and also over the current state-of-the-art SVM-based method, SVM+. Moreover, we show that advanced neural networks and deep learning methods can be compressed as privileged information.","lang":"eng"}],"type":"conference","volume":1,"citation":{"chicago":"Hernandez Lobato, Daniel, Viktoriia Sharmanska, Kristian Kersting, Christoph Lampert, and Novi Quadrianto. “Mind the Nuisance: Gaussian Process Classification Using Privileged Noise.” In <i>Advances in Neural Information Processing Systems</i>, 1:837–45. Neural Information Processing Systems, 2014.","ama":"Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. Mind the nuisance: Gaussian process classification using privileged noise. In: <i>Advances in Neural Information Processing Systems</i>. Vol 1. Neural Information Processing Systems; 2014:837-845.","ieee":"D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, and N. Quadrianto, “Mind the nuisance: Gaussian process classification using privileged noise,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2014, vol. 1, no. January, pp. 837–845.","ista":"Hernandez Lobato D, Sharmanska V, Kersting K, Lampert C, Quadrianto N. 2014. Mind the nuisance: Gaussian process classification using privileged noise. Advances in Neural Information Processing Systems. NIPS: Neural Information Processing Systems vol. 1, 837–845.","short":"D. Hernandez Lobato, V. Sharmanska, K. Kersting, C. Lampert, N. Quadrianto, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems, 2014, pp. 837–845.","mla":"Hernandez Lobato, Daniel, et al. “Mind the Nuisance: Gaussian Process Classification Using Privileged Noise.” <i>Advances in Neural Information Processing Systems</i>, vol. 1, no. January, Neural Information Processing Systems, 2014, pp. 837–45.","apa":"Hernandez Lobato, D., Sharmanska, V., Kersting, K., Lampert, C., &#38; Quadrianto, N. (2014). Mind the nuisance: Gaussian process classification using privileged noise. In <i>Advances in Neural Information Processing Systems</i> (Vol. 1, pp. 837–845). Montreal, Canada: Neural Information Processing Systems."}},{"publist_id":"5019","department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"publisher":"Royal Society, The","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","full_name":"Lagator, Mato"},{"full_name":"Colegrave, Nick","first_name":"Nick","last_name":"Colegrave"},{"full_name":"Neve, Paul","last_name":"Neve","first_name":"Paul"}],"title":"Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","publication_status":"published","scopus_import":1,"abstract":[{"text":" In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments. ","lang":"eng"}],"type":"journal_article","citation":{"apa":"Lagator, M., Colegrave, N., &#38; Neve, P. (2014). Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rspb.2014.1679\">https://doi.org/10.1098/rspb.2014.1679</a>","mla":"Lagator, Mato, et al. “Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 281, no. 1794, 20141679, Royal Society, The, 2014, doi:<a href=\"https://doi.org/10.1098/rspb.2014.1679\">10.1098/rspb.2014.1679</a>.","ama":"Lagator M, Colegrave N, Neve P. Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2014;281(1794). doi:<a href=\"https://doi.org/10.1098/rspb.2014.1679\">10.1098/rspb.2014.1679</a>","short":"M. Lagator, N. Colegrave, P. Neve, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014).","ista":"Lagator M, Colegrave N, Neve P. 2014. Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Proceedings of the Royal Society of London Series B Biological Sciences. 281(1794), 20141679.","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 281, no. 1794. Royal Society, The, 2014.","chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, The, 2014. <a href=\"https://doi.org/10.1098/rspb.2014.1679\">https://doi.org/10.1098/rspb.2014.1679</a>."},"quality_controlled":"1","_id":"2036","year":"2014","acknowledgement":"The project was supported by Leverhulme Trust.","article_number":"20141679","date_published":"2014-09-17T00:00:00Z","month":"09","intvolume":"       281","oa":1,"issue":"1794","date_updated":"2023-02-23T14:06:44Z","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","doi":"10.1098/rspb.2014.1679","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211454/"}],"oa_version":"Submitted Version","related_material":{"record":[{"relation":"research_data","status":"public","id":"9741"}]},"volume":281,"day":"17","status":"public","date_created":"2018-12-11T11:55:21Z"},{"publication_status":"published","project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11402-N23","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"},{"grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory"},{"call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","_id":"2038","scopus_import":1,"abstract":[{"text":"Recently, there has been an effort to add quantitative objectives to formal verification and synthesis. We introduce and investigate the extension of temporal logics with quantitative atomic assertions. At the heart of quantitative objectives lies the accumulation of values along a computation. It is often the accumulated sum, as with energy objectives, or the accumulated average, as with mean-payoff objectives. We investigate the extension of temporal logics with the prefix-accumulation assertions Sum(v) ≥ c and Avg(v) ≥ c, where v is a numeric (or Boolean) variable of the system, c is a constant rational number, and Sum(v) and Avg(v) denote the accumulated sum and average of the values of v from the beginning of the computation up to the current point in time. We also allow the path-accumulation assertions LimInfAvg(v) ≥ c and LimSupAvg(v) ≥ c, referring to the average value along an entire infinite computation. We study the border of decidability for such quantitative extensions of various temporal logics. In particular, we show that extending the fragment of CTL that has only the EX, EF, AX, and AG temporal modalities with both prefix-accumulation assertions, or extending LTL with both path-accumulation assertions, results in temporal logics whose model-checking problem is decidable. Moreover, the prefix-accumulation assertions may be generalized with &quot;controlled accumulation,&quot; allowing, for example, to specify constraints on the average waiting time between a request and a grant. On the negative side, we show that this branching-time logic is, in a sense, the maximal logic with one or both of the prefix-accumulation assertions that permits a decidable model-checking procedure. Extending a temporal logic that has the EG or EU modalities, such as CTL or LTL, makes the problem undecidable.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:26Z","type":"journal_article","citation":{"ama":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. Temporal specifications with accumulative values. <i>ACM Transactions on Computational Logic (TOCL)</i>. 2014;15(4). doi:<a href=\"https://doi.org/10.1145/2629686\">10.1145/2629686</a>","ista":"Boker U, Chatterjee K, Henzinger TA, Kupferman O. 2014. Temporal specifications with accumulative values. ACM Transactions on Computational Logic (TOCL). 15(4), 27.","ieee":"U. Boker, K. Chatterjee, T. A. Henzinger, and O. Kupferman, “Temporal specifications with accumulative values,” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 15, no. 4. ACM, 2014.","short":"U. Boker, K. Chatterjee, T.A. Henzinger, O. Kupferman, ACM Transactions on Computational Logic (TOCL) 15 (2014).","chicago":"Boker, Udi, Krishnendu Chatterjee, Thomas A Henzinger, and Orna Kupferman. “Temporal Specifications with Accumulative Values.” <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM, 2014. <a href=\"https://doi.org/10.1145/2629686\">https://doi.org/10.1145/2629686</a>.","apa":"Boker, U., Chatterjee, K., Henzinger, T. A., &#38; Kupferman, O. (2014). Temporal specifications with accumulative values. <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM. <a href=\"https://doi.org/10.1145/2629686\">https://doi.org/10.1145/2629686</a>","mla":"Boker, Udi, et al. “Temporal Specifications with Accumulative Values.” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 15, no. 4, 27, ACM, 2014, doi:<a href=\"https://doi.org/10.1145/2629686\">10.1145/2629686</a>."},"article_type":"original","pubrep_id":"192","language":[{"iso":"eng"}],"publist_id":"5013","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"article_processing_charge":"No","author":[{"full_name":"Boker, Udi","last_name":"Boker","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Temporal specifications with accumulative values","file":[{"content_type":"application/pdf","file_id":"4851","file_size":346184,"creator":"system","checksum":"354c41d37500b56320afce94cf9a99c2","relation":"main_file","access_level":"open_access","file_name":"IST-2014-192-v1+1_AccumulativeValues.pdf","date_created":"2018-12-12T10:10:59Z","date_updated":"2020-07-14T12:45:26Z"}],"publisher":"ACM","has_accepted_license":"1","oa_version":"Submitted Version","ec_funded":1,"related_material":{"record":[{"id":"3356","status":"public","relation":"earlier_version"},{"id":"5385","relation":"earlier_version","status":"public"}]},"publication":"ACM Transactions on Computational Logic (TOCL)","doi":"10.1145/2629686","status":"public","day":"16","ddc":["000","004"],"date_created":"2018-12-11T11:55:21Z","volume":15,"year":"2014","oa":1,"issue":"4","date_updated":"2023-02-23T12:23:54Z","acknowledgement":"The research was supported in part by ERC Starting grant 278410 (QUALITY).","article_number":"27","date_published":"2014-09-16T00:00:00Z","month":"09","intvolume":"        15"},{"citation":{"ama":"Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. The time scale of evolutionary innovation. <i>PLoS Computational Biology</i>. 2014;10(9). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818\">10.1371/journal.pcbi.1003818</a>","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Nowak, “The time scale of evolutionary innovation,” <i>PLoS Computational Biology</i>, vol. 10, no. 9. Public Library of Science, 2014.","ista":"Chatterjee K, Pavlogiannis A, Adlam B, Nowak M. 2014. The time scale of evolutionary innovation. PLoS Computational Biology. 10(9), 7p.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Nowak, PLoS Computational Biology 10 (2014).","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Nowak. “The Time Scale of Evolutionary Innovation.” <i>PLoS Computational Biology</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818\">https://doi.org/10.1371/journal.pcbi.1003818</a>.","apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., &#38; Nowak, M. (2014). The time scale of evolutionary innovation. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818\">https://doi.org/10.1371/journal.pcbi.1003818</a>","mla":"Chatterjee, Krishnendu, et al. “The Time Scale of Evolutionary Innovation.” <i>PLoS Computational Biology</i>, vol. 10, no. 9, 7p, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818\">10.1371/journal.pcbi.1003818</a>."},"abstract":[{"lang":"eng","text":"A fundamental question in biology is the following: what is the time scale that is needed for evolutionary innovations? There are many results that characterize single steps in terms of the fixation time of new mutants arising in populations of certain size and structure. But here we ask a different question, which is concerned with the much longer time scale of evolutionary trajectories: how long does it take for a population exploring a fitness landscape to find target sequences that encode new biological functions? Our key variable is the length, (Formula presented.) of the genetic sequence that undergoes adaptation. In computer science there is a crucial distinction between problems that require algorithms which take polynomial or exponential time. The latter are considered to be intractable. Here we develop a theoretical approach that allows us to estimate the time of evolution as function of (Formula presented.) We show that adaptation on many fitness landscapes takes time that is exponential in (Formula presented.) even if there are broad selection gradients and many targets uniformly distributed in sequence space. These negative results lead us to search for specific mechanisms that allow evolution to work on polynomial time scales. We study a regeneration process and show that it enables evolution to work in polynomial time."}],"scopus_import":1,"file_date_updated":"2020-07-14T12:45:26Z","type":"journal_article","_id":"2039","quality_controlled":"1","project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publication_status":"published","has_accepted_license":"1","publisher":"Public Library of Science","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"},{"full_name":"Adlam, Ben","first_name":"Ben","last_name":"Adlam"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"The time scale of evolutionary innovation","file":[{"checksum":"712d4c5787ddf97809cfc962507f0738","relation":"main_file","access_level":"open_access","file_id":"4890","content_type":"application/pdf","creator":"system","file_size":1399093,"date_updated":"2020-07-14T12:45:26Z","date_created":"2018-12-12T10:11:35Z","file_name":"IST-2016-440-v1+1_journal.pcbi.1003818.pdf"}],"publist_id":"5012","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"pubrep_id":"440","volume":10,"ddc":["510"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:55:22Z","day":"11","status":"public","publication":"PLoS Computational Biology","doi":"10.1371/journal.pcbi.1003818","related_material":{"record":[{"id":"9739","relation":"research_data","status":"public"}]},"ec_funded":1,"oa_version":"Published Version","date_published":"2014-09-11T00:00:00Z","month":"09","intvolume":"        10","article_number":"7p","date_updated":"2023-02-23T14:06:36Z","oa":1,"issue":"9","year":"2014"},{"publication_status":"published","doi":"10.1126/science.1254927","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228193/","open_access":"1"}],"publication":"Science","oa_version":"Submitted Version","citation":{"chicago":"Kicheva, Anna, Mark Tobias Bollenbach, Ana Ribeiro, Helena Pérez Valle, Robin Lovell Badge, Vasso Episkopou, and James Briscoe. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” <i>Science</i>. American Association for the Advancement of Science, 2014. <a href=\"https://doi.org/10.1126/science.1254927\">https://doi.org/10.1126/science.1254927</a>.","short":"A. Kicheva, M.T. Bollenbach, A. Ribeiro, H. Pérez Valle, R. Lovell Badge, V. Episkopou, J. Briscoe, Science 345 (2014).","ista":"Kicheva A, Bollenbach MT, Ribeiro A, Pérez Valle H, Lovell Badge R, Episkopou V, Briscoe J. 2014. Coordination of progenitor specification and growth in mouse and chick spinal cord. Science. 345(6204), 1254927.","ieee":"A. Kicheva <i>et al.</i>, “Coordination of progenitor specification and growth in mouse and chick spinal cord,” <i>Science</i>, vol. 345, no. 6204. American Association for the Advancement of Science, 2014.","ama":"Kicheva A, Bollenbach MT, Ribeiro A, et al. Coordination of progenitor specification and growth in mouse and chick spinal cord. <i>Science</i>. 2014;345(6204). doi:<a href=\"https://doi.org/10.1126/science.1254927\">10.1126/science.1254927</a>","mla":"Kicheva, Anna, et al. “Coordination of Progenitor Specification and Growth in Mouse and Chick Spinal Cord.” <i>Science</i>, vol. 345, no. 6204, 1254927, American Association for the Advancement of Science, 2014, doi:<a href=\"https://doi.org/10.1126/science.1254927\">10.1126/science.1254927</a>.","apa":"Kicheva, A., Bollenbach, M. T., Ribeiro, A., Pérez Valle, H., Lovell Badge, R., Episkopou, V., &#38; Briscoe, J. (2014). Coordination of progenitor specification and growth in mouse and chick spinal cord. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1254927\">https://doi.org/10.1126/science.1254927</a>"},"volume":345,"type":"journal_article","abstract":[{"lang":"eng","text":"Development requires tissue growth as well as cell diversification. To address how these processes are coordinated, we analyzed the development of molecularly distinct domains of neural progenitors in the mouse and chick neural tube. We show that during development, these domains undergo changes in size that do not scale with changes in overall tissue size. Our data show that domain proportions are first established by opposing morphogen gradients and subsequently controlled by domain-specific regulation of differentiation rate but not differences in proliferation rate. Regulation of differentiation rate is key to maintaining domain proportions while accommodating both intra- and interspecies variations in size. Thus, the sequential control of progenitor specification and differentiation elaborates pattern without requiring that signaling gradients grow as tissues expand. "}],"scopus_import":1,"_id":"2040","date_created":"2018-12-11T11:55:22Z","quality_controlled":"1","status":"public","day":"26","publist_id":"5011","department":[{"_id":"ToBo"}],"language":[{"iso":"eng"}],"year":"2014","month":"09","intvolume":"       345","date_published":"2014-09-26T00:00:00Z","article_number":"1254927","publisher":"American Association for the Advancement of Science","date_updated":"2021-01-12T06:54:55Z","issue":"6204","title":"Coordination of progenitor specification and growth in mouse and chick spinal cord","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"author":[{"last_name":"Kicheva","first_name":"Anna","full_name":"Kicheva, Anna"},{"full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Ribeiro, Ana","first_name":"Ana","last_name":"Ribeiro"},{"full_name":"Pérez Valle, Helena","last_name":"Pérez Valle","first_name":"Helena"},{"first_name":"Robin","last_name":"Lovell Badge","full_name":"Lovell Badge, Robin"},{"full_name":"Episkopou, Vasso","first_name":"Vasso","last_name":"Episkopou"},{"full_name":"Briscoe, James","last_name":"Briscoe","first_name":"James"}]},{"oa_version":"Published Version","doi":"10.3389/fncir.2014.00107","publication":"Frontiers in Neural Circuits","status":"public","day":"10","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:55:22Z","ddc":["570"],"volume":8,"year":"2014","oa":1,"date_updated":"2021-01-12T06:54:55Z","article_number":"2p","intvolume":"         8","month":"09","date_published":"2014-09-10T00:00:00Z","publication_status":"published","quality_controlled":"1","_id":"2041","type":"journal_article","file_date_updated":"2020-07-14T12:45:26Z","abstract":[{"lang":"eng","text":"The hippocampus mediates several higher brain functions, such as learning, memory, and spatial coding. The input region of the hippocampus, the dentate gyrus, plays a critical role in these processes. Several lines of evidence suggest that the dentate gyrus acts as a preprocessor of incoming information, preparing it for subsequent processing in CA3. For example, the dentate gyrus converts input from the entorhinal cortex, where cells have multiple spatial fields, into the spatially more specific place cell activity characteristic of the CA3 region. Furthermore, the dentate gyrus is involved in pattern separation, transforming relatively similar input patterns into substantially different output patterns. Finally, the dentate gyrus produces a very sparse coding scheme in which only a very small fraction of neurons are active at any one time."}],"scopus_import":1,"citation":{"apa":"Jonas, P. M., &#38; Lisman, J. (2014). Structure, function and plasticity of hippocampal dentate gyrus microcircuits. <i>Frontiers in Neural Circuits</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fncir.2014.00107\">https://doi.org/10.3389/fncir.2014.00107</a>","mla":"Jonas, Peter M., and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” <i>Frontiers in Neural Circuits</i>, vol. 8, 2p, Frontiers Research Foundation, 2014, doi:<a href=\"https://doi.org/10.3389/fncir.2014.00107\">10.3389/fncir.2014.00107</a>.","ieee":"P. M. Jonas and J. Lisman, “Structure, function and plasticity of hippocampal dentate gyrus microcircuits,” <i>Frontiers in Neural Circuits</i>, vol. 8. Frontiers Research Foundation, 2014.","short":"P.M. Jonas, J. Lisman, Frontiers in Neural Circuits 8 (2014).","ista":"Jonas PM, Lisman J. 2014. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. Frontiers in Neural Circuits. 8, 2p.","ama":"Jonas PM, Lisman J. Structure, function and plasticity of hippocampal dentate gyrus microcircuits. <i>Frontiers in Neural Circuits</i>. 2014;8. doi:<a href=\"https://doi.org/10.3389/fncir.2014.00107\">10.3389/fncir.2014.00107</a>","chicago":"Jonas, Peter M, and John Lisman. “Structure, Function and Plasticity of Hippocampal Dentate Gyrus Microcircuits.” <i>Frontiers in Neural Circuits</i>. Frontiers Research Foundation, 2014. <a href=\"https://doi.org/10.3389/fncir.2014.00107\">https://doi.org/10.3389/fncir.2014.00107</a>."},"pubrep_id":"424","language":[{"iso":"eng"}],"publist_id":"5010","department":[{"_id":"PeJo"}],"file":[{"access_level":"open_access","relation":"main_file","checksum":"3ca57b164045523f876407e9f13a9fb8","file_id":"5294","content_type":"application/pdf","creator":"system","file_size":201110,"date_created":"2018-12-12T10:17:38Z","date_updated":"2020-07-14T12:45:26Z","file_name":"IST-2016-424-v1+1_fncir-08-00107.pdf"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Structure, function and plasticity of hippocampal dentate gyrus microcircuits","author":[{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Jonas, Peter M"},{"full_name":"Lisman, John","first_name":"John","last_name":"Lisman"}],"publisher":"Frontiers Research Foundation","has_accepted_license":"1"},{"doi":"10.1186/1471-2164-15-663","publication":"BMC Genomics","oa_version":"Published Version","volume":15,"status":"public","day":"08","tmp":{"short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"ddc":["570"],"date_created":"2018-12-11T11:55:23Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","year":"2014","article_number":"663","intvolume":"        15","month":"08","date_published":"2014-08-08T00:00:00Z","issue":"1","oa":1,"date_updated":"2021-01-12T06:54:56Z","publication_status":"published","type":"journal_article","file_date_updated":"2020-07-14T12:45:26Z","scopus_import":1,"abstract":[{"lang":"eng","text":"Background: CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. The system also requires protospacer associated motifs (PAMs), short motifs close to the target sequence that are required for interference in CRISPR types I and II. Here, we investigate whether PAMs are depleted in phage genomes due to selection pressure to escape recognition.Results: To this end, we analyzed two data sets. Phages infecting all bacterial hosts were analyzed first, followed by a detailed analysis of phages infecting the genus Streptococcus, where PAMs are best understood. We use two different measures of motif underrepresentation that control for codon bias and the frequency of submotifs. We compare phages infecting species with a particular CRISPR type to those infecting species without that type. Since only known PAMs were investigated, the analysis is restricted to CRISPR types I-C and I-E and in Streptococcus to types I-C and II. We found evidence for PAM depletion in Streptococcus phages infecting hosts with CRISPR type I-C, in Vibrio phages infecting hosts with CRISPR type I-E and in Streptococcus thermopilus phages infecting hosts with type II-A, known as CRISPR3.Conclusions: The observed motif depletion in phages with hosts having CRISPR can be attributed to selection rather than to mutational bias, as mutational bias should affect the phages of all hosts. This observation implies that the CRISPR system has been efficient in the groups discussed here."}],"citation":{"chicago":"Kupczok, Anne, and Jonathan P Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” <i>BMC Genomics</i>. BioMed Central, 2014. <a href=\"https://doi.org/10.1186/1471-2164-15-663\">https://doi.org/10.1186/1471-2164-15-663</a>.","ista":"Kupczok A, Bollback JP. 2014. Motif depletion in bacteriophages infecting hosts with CRISPR systems. BMC Genomics. 15(1), 663.","ieee":"A. Kupczok and J. P. Bollback, “Motif depletion in bacteriophages infecting hosts with CRISPR systems,” <i>BMC Genomics</i>, vol. 15, no. 1. BioMed Central, 2014.","short":"A. Kupczok, J.P. Bollback, BMC Genomics 15 (2014).","ama":"Kupczok A, Bollback JP. Motif depletion in bacteriophages infecting hosts with CRISPR systems. <i>BMC Genomics</i>. 2014;15(1). doi:<a href=\"https://doi.org/10.1186/1471-2164-15-663\">10.1186/1471-2164-15-663</a>","mla":"Kupczok, Anne, and Jonathan P. Bollback. “Motif Depletion in Bacteriophages Infecting Hosts with CRISPR Systems.” <i>BMC Genomics</i>, vol. 15, no. 1, 663, BioMed Central, 2014, doi:<a href=\"https://doi.org/10.1186/1471-2164-15-663\">10.1186/1471-2164-15-663</a>.","apa":"Kupczok, A., &#38; Bollback, J. P. (2014). Motif depletion in bacteriophages infecting hosts with CRISPR systems. <i>BMC Genomics</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2164-15-663\">https://doi.org/10.1186/1471-2164-15-663</a>"},"quality_controlled":"1","_id":"2042","publist_id":"5009","department":[{"_id":"JoBo"}],"pubrep_id":"396","language":[{"iso":"eng"}],"publisher":"BioMed Central","has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:45:26Z","date_created":"2018-12-12T10:11:24Z","file_name":"IST-2015-396-v1+1_1471-2164-15-663.pdf","relation":"main_file","checksum":"3f6d2776b90a842a28359cc957d3d04b","access_level":"open_access","file_id":"4878","content_type":"application/pdf","file_size":1489769,"creator":"system"}],"title":"Motif depletion in bacteriophages infecting hosts with CRISPR systems","author":[{"last_name":"Kupczok","first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Kupczok, Anne"},{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Submitted Version","ec_funded":1,"main_file_link":[{"url":"http://arxiv.org/abs/1310.0710","open_access":"1"}],"doi":"10.1137/1.9781611973198.4","publication":"Proceedings of the Workshop on Algorithm Engineering and Experiments","day":"01","status":"public","date_created":"2018-12-11T11:55:23Z","year":"2014","conference":{"location":"Portland, USA","start_date":"2014-01-05","end_date":"2014-01-05","name":"ALENEX: Algorithm Engineering and Experiments"},"page":"31 - 38","oa":1,"date_updated":"2021-01-12T06:54:56Z","month":"01","date_published":"2014-01-01T00:00:00Z","publication_status":"published","project":[{"grant_number":"318493","call_identifier":"FP7","name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","editor":[{"first_name":"Catherine","last_name":" McGeoch","full_name":" McGeoch, Catherine"},{"full_name":"Meyer, Ulrich","first_name":"Ulrich","last_name":"Meyer"}],"_id":"2043","type":"conference","abstract":[{"text":"Persistent homology is a popular and powerful tool for capturing topological features of data. Advances in algorithms for computing persistent homology have reduced the computation time drastically – as long as the algorithm does not exhaust the available memory. Following up on a recently presented parallel method for persistence computation on shared memory systems [1], we demonstrate that a simple adaption of the standard reduction algorithm leads to a variant for distributed systems. Our algorithmic design ensures that the data is distributed over the nodes without redundancy; this permits the computation of much larger instances than on a single machine. Moreover, we observe that the parallelism at least compensates for the overhead caused by communication between nodes, and often even speeds up the computation compared to sequential and even parallel shared memory algorithms. In our experiments, we were able to compute the persistent homology of filtrations with more than a billion (109) elements within seconds on a cluster with 32 nodes using less than 6GB of memory per node.","lang":"eng"}],"scopus_import":1,"citation":{"mla":"Bauer, Ulrich, et al. “Distributed Computation of Persistent Homology.” <i>Proceedings of the Workshop on Algorithm Engineering and Experiments</i>, edited by Catherine  McGeoch and Ulrich Meyer, Society of Industrial and Applied Mathematics, 2014, pp. 31–38, doi:<a href=\"https://doi.org/10.1137/1.9781611973198.4\">10.1137/1.9781611973198.4</a>.","apa":"Bauer, U., Kerber, M., &#38; Reininghaus, J. (2014). Distributed computation of persistent homology. In C.  McGeoch &#38; U. Meyer (Eds.), <i>Proceedings of the Workshop on Algorithm Engineering and Experiments</i> (pp. 31–38). Portland, USA: Society of Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611973198.4\">https://doi.org/10.1137/1.9781611973198.4</a>","chicago":"Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Distributed Computation of Persistent Homology.” In <i>Proceedings of the Workshop on Algorithm Engineering and Experiments</i>, edited by Catherine  McGeoch and Ulrich Meyer, 31–38. Society of Industrial and Applied Mathematics, 2014. <a href=\"https://doi.org/10.1137/1.9781611973198.4\">https://doi.org/10.1137/1.9781611973198.4</a>.","ama":"Bauer U, Kerber M, Reininghaus J. Distributed computation of persistent homology. In:  McGeoch C, Meyer U, eds. <i>Proceedings of the Workshop on Algorithm Engineering and Experiments</i>. Society of Industrial and Applied Mathematics; 2014:31-38. doi:<a href=\"https://doi.org/10.1137/1.9781611973198.4\">10.1137/1.9781611973198.4</a>","ista":"Bauer U, Kerber M, Reininghaus J. 2014. Distributed computation of persistent homology. Proceedings of the Workshop on Algorithm Engineering and Experiments. ALENEX: Algorithm Engineering and Experiments, 31–38.","ieee":"U. Bauer, M. Kerber, and J. Reininghaus, “Distributed computation of persistent homology,” in <i>Proceedings of the Workshop on Algorithm Engineering and Experiments</i>, Portland, USA, 2014, pp. 31–38.","short":"U. Bauer, M. Kerber, J. Reininghaus, in:, C.  McGeoch, U. Meyer (Eds.), Proceedings of the Workshop on Algorithm Engineering and Experiments, Society of Industrial and Applied Mathematics, 2014, pp. 31–38."},"language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"publist_id":"5008","title":"Distributed computation of persistent homology","author":[{"full_name":"Bauer, Ulrich","last_name":"Bauer","orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich"},{"full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","last_name":"Kerber","first_name":"Michael"},{"first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus","full_name":"Reininghaus, Jan"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Society of Industrial and Applied Mathematics"},{"project":[{"name":"Topological Complex Systems","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"318493"}],"publication_status":"published","citation":{"chicago":"Bauer, Ulrich, Michael Kerber, and Jan Reininghaus. “Clear and Compress: Computing Persistent Homology in Chunks.” In <i>Topological Methods in Data Analysis and Visualization III</i>, edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 103–17. Mathematics and Visualization. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-04099-8_7\">https://doi.org/10.1007/978-3-319-04099-8_7</a>.","ama":"Bauer U, Kerber M, Reininghaus J. Clear and Compress: Computing Persistent Homology in Chunks. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. <i>Topological Methods in Data Analysis and Visualization III</i>. Mathematics and Visualization. Springer; 2014:103-117. doi:<a href=\"https://doi.org/10.1007/978-3-319-04099-8_7\">10.1007/978-3-319-04099-8_7</a>","ista":"Bauer U, Kerber M, Reininghaus J. 2014.Clear and Compress: Computing Persistent Homology in Chunks. In: Topological Methods in Data Analysis and Visualization III. , 103–117.","short":"U. Bauer, M. Kerber, J. Reininghaus, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III, Springer, 2014, pp. 103–117.","ieee":"U. Bauer, M. Kerber, and J. Reininghaus, “Clear and Compress: Computing Persistent Homology in Chunks,” in <i>Topological Methods in Data Analysis and Visualization III</i>, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Springer, 2014, pp. 103–117.","mla":"Bauer, Ulrich, et al. “Clear and Compress: Computing Persistent Homology in Chunks.” <i>Topological Methods in Data Analysis and Visualization III</i>, edited by Peer-Timo Bremer et al., Springer, 2014, pp. 103–17, doi:<a href=\"https://doi.org/10.1007/978-3-319-04099-8_7\">10.1007/978-3-319-04099-8_7</a>.","apa":"Bauer, U., Kerber, M., &#38; Reininghaus, J. (2014). Clear and Compress: Computing Persistent Homology in Chunks. In P.-T. Bremer, I. Hotz, V. Pascucci, &#38; R. Peikert (Eds.), <i>Topological Methods in Data Analysis and Visualization III</i> (pp. 103–117). Springer. <a href=\"https://doi.org/10.1007/978-3-319-04099-8_7\">https://doi.org/10.1007/978-3-319-04099-8_7</a>"},"scopus_import":1,"abstract":[{"lang":"eng","text":"We present a parallel algorithm for computing the persistent homology of a filtered chain complex. Our approach differs from the commonly used reduction algorithm by first computing persistence pairs within local chunks, then simplifying the unpaired columns, and finally applying standard reduction on the simplified matrix. The approach generalizes a technique by Günther et al., which uses discrete Morse Theory to compute persistence; we derive the same worst-case complexity bound in a more general context. The algorithm employs several practical optimization techniques, which are of independent interest. Our sequential implementation of the algorithm is competitive with state-of-the-art methods, and we further improve the performance through parallel computation."}],"type":"book_chapter","_id":"2044","editor":[{"first_name":"Peer-Timo","last_name":"Bremer","full_name":"Bremer, Peer-Timo"},{"last_name":"Hotz","first_name":"Ingrid","full_name":"Hotz, Ingrid"},{"full_name":"Pascucci, Valerio","last_name":"Pascucci","first_name":"Valerio"},{"last_name":"Peikert","first_name":"Ronald","full_name":"Peikert, Ronald"}],"quality_controlled":"1","department":[{"_id":"HeEd"}],"publist_id":"5007","language":[{"iso":"eng"}],"publisher":"Springer","title":"Clear and Compress: Computing Persistent Homology in Chunks","author":[{"full_name":"Bauer, Ulrich","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich","orcid":"0000-0002-9683-0724","last_name":"Bauer"},{"full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","last_name":"Kerber","first_name":"Michael"},{"full_name":"Reininghaus, Jan","last_name":"Reininghaus","id":"4505473A-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publication":"Topological Methods in Data Analysis and Visualization III","doi":"10.1007/978-3-319-04099-8_7","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1303.0477"}],"oa_version":"Submitted Version","ec_funded":1,"date_created":"2018-12-11T11:55:23Z","day":"19","status":"public","page":"103 - 117","series_title":"Mathematics and Visualization","year":"2014","date_published":"2014-03-19T00:00:00Z","month":"03","date_updated":"2021-01-12T06:54:56Z","oa":1},{"date_updated":"2021-01-12T06:54:57Z","oa":1,"month":"01","intvolume":"      8383","alternative_title":["LNCS"],"date_published":"2014-01-01T00:00:00Z","acknowledgement":"The second author was supported by EPSRC grant EP/H043454/1.","year":"2014","page":"329 - 344","conference":{"location":"Buenos Aires, Argentina","name":"PKC: Public Key Crypography","end_date":"2014-03-28","start_date":"2014-03-26"},"date_created":"2018-12-11T11:55:24Z","status":"public","day":"01","volume":8383,"ec_funded":1,"oa_version":"Submitted Version","doi":"10.1007/978-3-642-54631-0_19","main_file_link":[{"url":"https://eprint.iacr.org/2012/543","open_access":"1"}],"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Enhanced chosen-ciphertext security and applications","author":[{"last_name":"Dachman Soled","first_name":"Dana","full_name":"Dachman Soled, Dana"},{"full_name":"Fuchsbauer, Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","first_name":"Georg","last_name":"Fuchsbauer"},{"last_name":"Mohassel","first_name":"Payman","full_name":"Mohassel, Payman"},{"first_name":"Adam","last_name":"O’Neill","full_name":"O’Neill, Adam"}],"publisher":"Springer","language":[{"iso":"eng"}],"department":[{"_id":"KrPi"}],"publist_id":"5006","editor":[{"first_name":"Hugo","last_name":"Krawczyk","full_name":"Krawczyk, Hugo"}],"_id":"2045","quality_controlled":"1","citation":{"mla":"Dachman Soled, Dana, et al. “Enhanced Chosen-Ciphertext Security and Applications.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 329–44, doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_19\">10.1007/978-3-642-54631-0_19</a>.","apa":"Dachman Soled, D., Fuchsbauer, G., Mohassel, P., &#38; O’Neill, A. (2014). Enhanced chosen-ciphertext security and applications. In H. Krawczyk (Ed.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8383, pp. 329–344). Buenos Aires, Argentina: Springer. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_19\">https://doi.org/10.1007/978-3-642-54631-0_19</a>","chicago":"Dachman Soled, Dana, Georg Fuchsbauer, Payman Mohassel, and Adam O’Neill. “Enhanced Chosen-Ciphertext Security and Applications.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Hugo Krawczyk, 8383:329–44. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_19\">https://doi.org/10.1007/978-3-642-54631-0_19</a>.","ama":"Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. Enhanced chosen-ciphertext security and applications. In: Krawczyk H, ed. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8383. Springer; 2014:329-344. doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_19\">10.1007/978-3-642-54631-0_19</a>","ista":"Dachman Soled D, Fuchsbauer G, Mohassel P, O’Neill A. 2014. Enhanced chosen-ciphertext security and applications. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 329–344.","short":"D. Dachman Soled, G. Fuchsbauer, P. Mohassel, A. O’Neill, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 329–344.","ieee":"D. Dachman Soled, G. Fuchsbauer, P. Mohassel, and A. O’Neill, “Enhanced chosen-ciphertext security and applications,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Buenos Aires, Argentina, 2014, vol. 8383, pp. 329–344."},"type":"conference","scopus_import":1,"abstract":[{"text":"We introduce and study a new notion of enhanced chosen-ciphertext security (ECCA) for public-key encryption. Loosely speaking, in the ECCA security experiment, the decryption oracle provided to the adversary is augmented to return not only the output of the decryption algorithm on a queried ciphertext but also of a randomness-recovery algorithm associated to the scheme. Our results mainly concern the case where the randomness-recovery algorithm is efficient. We provide constructions of ECCA-secure encryption from adaptive trapdoor functions as defined by Kiltz et al. (EUROCRYPT 2010), resulting in ECCA encryption from standard number-theoretic assumptions. We then give two applications of ECCA-secure encryption: (1) We use it as a unifying concept in showing equivalence of adaptive trapdoor functions and tag-based adaptive trapdoor functions, resolving an open question of Kiltz et al. (2) We show that ECCA-secure encryption can be used to securely realize an approach to public-key encryption with non-interactive opening (PKENO) originally suggested by Damgård and Thorbek (EUROCRYPT 2007), resulting in new and practical PKENO schemes quite different from those in prior work. Our results demonstrate that ECCA security is of both practical and theoretical interest.","lang":"eng"}],"project":[{"_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7","grant_number":"259668"}],"publication_status":"published"},{"main_file_link":[{"url":"https://eprint.iacr.org/2013/413","open_access":"1"}],"doi":"10.1007/978-3-642-54631-0_30","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","ec_funded":1,"oa_version":"Submitted Version","volume":8383,"date_created":"2018-12-11T11:55:24Z","status":"public","day":"01","page":"520 - 537","conference":{"location":"Buenos Aires, Argentina","end_date":"2014-05-28","start_date":"2014-05-26","name":"PKC: Public Key Crypography"},"year":"2014","intvolume":"      8383","month":"01","alternative_title":["LNCS"],"date_published":"2014-01-01T00:00:00Z","acknowledgement":"Part of his work was done while at Bristol University, supported by EPSRC grant EP/H043454/1.","date_updated":"2021-01-12T06:54:57Z","oa":1,"project":[{"name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7"}],"publication_status":"published","citation":{"apa":"Bellare, M., &#38; Fuchsbauer, G. (2014). Policy-based signatures. In H. Krawczyk (Ed.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8383, pp. 520–537). Buenos Aires, Argentina: Springer. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_30\">https://doi.org/10.1007/978-3-642-54631-0_30</a>","mla":"Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Hugo Krawczyk, vol. 8383, Springer, 2014, pp. 520–37, doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_30\">10.1007/978-3-642-54631-0_30</a>.","ista":"Bellare M, Fuchsbauer G. 2014. Policy-based signatures. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PKC: Public Key Crypography, LNCS, vol. 8383, 520–537.","ieee":"M. Bellare and G. Fuchsbauer, “Policy-based signatures,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Buenos Aires, Argentina, 2014, vol. 8383, pp. 520–537.","short":"M. Bellare, G. Fuchsbauer, in:, H. Krawczyk (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 520–537.","ama":"Bellare M, Fuchsbauer G. Policy-based signatures. In: Krawczyk H, ed. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8383. Springer; 2014:520-537. doi:<a href=\"https://doi.org/10.1007/978-3-642-54631-0_30\">10.1007/978-3-642-54631-0_30</a>","chicago":"Bellare, Mihir, and Georg Fuchsbauer. “Policy-Based Signatures.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Hugo Krawczyk, 8383:520–37. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54631-0_30\">https://doi.org/10.1007/978-3-642-54631-0_30</a>."},"type":"conference","abstract":[{"lang":"eng","text":"We introduce policy-based signatures (PBS), where a signer can only sign messages conforming to some authority-specified policy. The main requirements are unforgeability and privacy, the latter meaning that signatures not reveal the policy. PBS offers value along two fronts: (1) On the practical side, they allow a corporation to control what messages its employees can sign under the corporate key. (2) On the theoretical side, they unify existing work, capturing other forms of signatures as special cases or allowing them to be easily built. Our work focuses on definitions of PBS, proofs that this challenging primitive is realizable for arbitrary policies, efficient constructions for specific policies, and a few representative applications."}],"scopus_import":1,"editor":[{"full_name":"Krawczyk, Hugo","last_name":"Krawczyk","first_name":"Hugo"}],"_id":"2046","quality_controlled":"1","department":[{"_id":"KrPi"}],"publist_id":"5005","language":[{"iso":"eng"}],"publisher":"Springer","title":"Policy-based signatures","author":[{"first_name":"Mihir","last_name":"Bellare","full_name":"Bellare, Mihir"},{"last_name":"Fuchsbauer","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"project":[{"grant_number":"11-NSF-1070","_id":"25636330-B435-11E9-9278-68D0E5697425","name":"ROOTS Genome-wide Analysis of Root Traits"}],"publication_status":"published","citation":{"chicago":"Yu, Fei, Michal Rybar, Caroline Uhler, and Stephen Fienberg. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Josep Domingo Ferrer, 8744:170–84. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-11257-2_14\">https://doi.org/10.1007/978-3-319-11257-2_14</a>.","ama":"Yu F, Rybar M, Uhler C, Fienberg S. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In: Domingo Ferrer J, ed. <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 8744. Springer; 2014:170-184. doi:<a href=\"https://doi.org/10.1007/978-3-319-11257-2_14\">10.1007/978-3-319-11257-2_14</a>","ieee":"F. Yu, M. Rybar, C. Uhler, and S. Fienberg, “Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Ibiza, Spain, 2014, vol. 8744, pp. 170–184.","ista":"Yu F, Rybar M, Uhler C, Fienberg S. 2014. Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). PSD: Privacy in Statistical Databases, LNCS, vol. 8744, 170–184.","short":"F. Yu, M. Rybar, C. Uhler, S. Fienberg, in:, J. Domingo Ferrer (Ed.), Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer, 2014, pp. 170–184.","mla":"Yu, Fei, et al. “Differentially-Private Logistic Regression for Detecting Multiple-SNP Association in GWAS Databases.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, edited by Josep Domingo Ferrer, vol. 8744, Springer, 2014, pp. 170–84, doi:<a href=\"https://doi.org/10.1007/978-3-319-11257-2_14\">10.1007/978-3-319-11257-2_14</a>.","apa":"Yu, F., Rybar, M., Uhler, C., &#38; Fienberg, S. (2014). Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases. In J. Domingo Ferrer (Ed.), <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 8744, pp. 170–184). Ibiza, Spain: Springer. <a href=\"https://doi.org/10.1007/978-3-319-11257-2_14\">https://doi.org/10.1007/978-3-319-11257-2_14</a>"},"scopus_import":1,"abstract":[{"text":"Following the publication of an attack on genome-wide association studies (GWAS) data proposed by Homer et al., considerable attention has been given to developing methods for releasing GWAS data in a privacy-preserving way. Here, we develop an end-to-end differentially private method for solving regression problems with convex penalty functions and selecting the penalty parameters by cross-validation. In particular, we focus on penalized logistic regression with elastic-net regularization, a method widely used to in GWAS analyses to identify disease-causing genes. We show how a differentially private procedure for penalized logistic regression with elastic-net regularization can be applied to the analysis of GWAS data and evaluate our method’s performance.","lang":"eng"}],"arxiv":1,"type":"conference","_id":"2047","editor":[{"full_name":"Domingo Ferrer, Josep","first_name":"Josep","last_name":"Domingo Ferrer"}],"quality_controlled":"1","department":[{"_id":"KrPi"},{"_id":"CaUh"}],"publist_id":"5004","language":[{"iso":"eng"}],"publisher":"Springer","author":[{"full_name":"Yu, Fei","last_name":"Yu","first_name":"Fei"},{"first_name":"Michal","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","last_name":"Rybar","full_name":"Rybar, Michal"},{"last_name":"Uhler","orcid":"0000-0002-7008-0216","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","full_name":"Uhler, Caroline"},{"full_name":"Fienberg, Stephen","first_name":"Stephen","last_name":"Fienberg"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Differentially-private logistic regression for detecting multiple-SNP association in GWAS databases","publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","doi":"10.1007/978-3-319-11257-2_14","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1407.8067"}],"oa_version":"Submitted Version","volume":8744,"date_created":"2018-12-11T11:55:24Z","status":"public","day":"01","page":"170 - 184","external_id":{"arxiv":["1407.8067"]},"conference":{"name":"PSD: Privacy in Statistical Databases","end_date":"2014-09-19","start_date":"2014-09-17","location":"Ibiza, Spain"},"year":"2014","date_published":"2014-01-01T00:00:00Z","alternative_title":["LNCS"],"month":"01","intvolume":"      8744","acknowledgement":"This research was partially supported by BCS- 0941518 to the Department of Statistics at Carnegie Mellon University.","date_updated":"2021-01-12T06:54:57Z","oa":1}]