[{"day":"20","oa":1,"title":"Synthetic discrete tomography problems","keyword":["discrete tomography"],"department":[{"_id":"VlKo"}],"doi":"10.15479/AT:ISTA:46","date_published":"2016-09-20T00:00:00Z","publisher":"Institute of Science and Technology Austria","_id":"5557","status":"public","ddc":["006"],"file_date_updated":"2020-07-14T12:47:02Z","datarep_id":"46","author":[{"first_name":"Paul","full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda"}],"month":"09","article_processing_charge":"No","date_updated":"2024-02-21T13:50:21Z","file":[{"creator":"system","access_level":"open_access","content_type":"application/zip","relation":"main_file","file_id":"5645","date_created":"2018-12-12T13:05:19Z","file_size":36058401,"date_updated":"2020-07-14T12:47:02Z","file_name":"IST-2016-46-v1+1_discrete_tomography_synthetic.zip","checksum":"aa5a16a0dc888da7186fb8fc45e88439"}],"license":"https://creativecommons.org/publicdomain/zero/1.0/","abstract":[{"lang":"eng","text":"Small synthetic discrete tomography problems.\r\nSizes are 32x32, 64z64 and 256x256.\r\nProjection angles are 2, 4, and 6.\r\nNumber of labels are 3 and 5."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"research_data","has_accepted_license":"1","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"year":"2016","oa_version":"Published Version","citation":{"short":"P. Swoboda, (2016).","ieee":"P. Swoboda, “Synthetic discrete tomography problems.” Institute of Science and Technology Austria, 2016.","ista":"Swoboda P. 2016. Synthetic discrete tomography problems, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>.","chicago":"Swoboda, Paul. “Synthetic Discrete Tomography Problems.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:46\">https://doi.org/10.15479/AT:ISTA:46</a>.","ama":"Swoboda P. Synthetic discrete tomography problems. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>","mla":"Swoboda, Paul. <i>Synthetic Discrete Tomography Problems</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>.","apa":"Swoboda, P. (2016). Synthetic discrete tomography problems. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:46\">https://doi.org/10.15479/AT:ISTA:46</a>"},"contributor":[{"last_name":"Kuske","first_name":"Jan","contributor_type":"data_collector"}],"date_created":"2018-12-12T12:31:31Z"},{"oa":1,"title":"Tracking, Correcting and Absorbing Water Surface Waves","day":"23","department":[{"_id":"ChWo"}],"_id":"5558","publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:48","date_published":"2016-09-23T00:00:00Z","publist_id":"6238","file_date_updated":"2020-07-14T12:47:02Z","related_material":{"record":[{"relation":"other","id":"1122","status":"public"}]},"ddc":["004"],"status":"public","pubrep_id":"640","month":"09","author":[{"first_name":"Morten","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","last_name":"Bojsen-Hansen","full_name":"Bojsen-Hansen, Morten","orcid":"0000-0002-4417-3224"}],"datarep_id":"48","abstract":[{"text":"PhD thesis LaTeX source code","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2024-02-21T13:50:48Z","file":[{"file_name":"IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2","date_updated":"2020-07-14T12:47:02Z","checksum":"5b1b256ad796fbddb4b7729f5e45e444","file_size":55237885,"date_created":"2018-12-12T13:02:18Z","content_type":"application/x-bzip2","access_level":"open_access","creator":"system","file_id":"5589","relation":"main_file"}],"has_accepted_license":"1","type":"research_data","citation":{"ista":"Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>.","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:48\">https://doi.org/10.15479/AT:ISTA:48</a>.","short":"M. Bojsen-Hansen, (2016).","ieee":"M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016.","mla":"Bojsen-Hansen, Morten. <i>Tracking, Correcting and Absorbing Water Surface Waves</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>.","apa":"Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:48\">https://doi.org/10.15479/AT:ISTA:48</a>","ama":"Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>"},"oa_version":"Published Version","date_created":"2018-12-12T12:31:31Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2016"},{"department":[{"_id":"CaGu"}],"page":"770-782","title":"Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria","publication_status":"published","file_date_updated":"2020-07-14T12:47:10Z","ddc":["576"],"publisher":"Oxford University Press","_id":"5749","article_processing_charge":"No","file":[{"checksum":"47d9010690b6c5c17f2ac830cc63ac5c","date_updated":"2020-07-14T12:47:10Z","file_name":"2016_MolBiolEvol_Wielgoss.pdf","date_created":"2018-12-18T13:21:45Z","file_size":634037,"relation":"main_file","file_id":"5750","creator":"dernst","access_level":"open_access","content_type":"application/pdf"}],"date_updated":"2023-09-05T13:46:05Z","abstract":[{"text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","pmid":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"author":[{"last_name":"Wielgoss","full_name":"Wielgoss, Sébastien","first_name":"Sébastien"},{"first_name":"Tobias","last_name":"Bergmiller","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346"},{"first_name":"Anna M.","last_name":"Bischofberger","full_name":"Bischofberger, Anna M."},{"full_name":"Hall, Alex R.","last_name":"Hall","first_name":"Alex R."}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"scopus_import":"1","issue":"3","year":"2016","volume":33,"has_accepted_license":"1","external_id":{"pmid":["26609077"]},"day":"01","oa":1,"status":"public","related_material":{"record":[{"status":"public","relation":"research_data","id":"9719"}]},"date_published":"2016-03-01T00:00:00Z","doi":"10.1093/molbev/msv270","intvolume":"        33","quality_controlled":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","acknowledgement":"The authors thank three anonymous reviewers and the editor for helpful comments on the manuscript, as well as Dominique Schneider for feedback on an earlier draft, Jenna Gallie for lytic λ and Julien Capelle for T5 and T6. This work was supported by the Swiss National Science Foundation (PZ00P3_148255 to A.H.) and an EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development (FP7-PEOPLE-2012-IEF-331824 to S.W.).","pubrep_id":"587","month":"03","publication":"Molecular Biology and Evolution","citation":{"chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>.","ista":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2016. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. Molecular Biology and Evolution. 33(3), 770–782.","short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology and Evolution 33 (2016) 770–782.","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria,” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3. Oxford University Press, pp. 770–782, 2016.","mla":"Wielgoss, Sébastien, et al. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3, Oxford University Press, 2016, pp. 770–82, doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>.","apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &#38; Hall, A. R. (2016). Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>","ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. 2016;33(3):770-782. doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>"},"oa_version":"Published Version","date_created":"2018-12-18T13:18:10Z","type":"journal_article"},{"page":"1098 - 1107","title":"An orthogonal permease–inducer–repressor feedback loop shows bistability","day":"05","department":[{"_id":"CaGu"}],"_id":"1008","intvolume":"         5","publist_id":"6390","doi":"10.1021/acssynbio.6b00013","date_published":"2016-05-05T00:00:00Z","publisher":"American Chemical Society","publication_status":"published","status":"public","author":[{"first_name":"Robert","last_name":"Gnügge","full_name":"Gnügge, Robert"},{"full_name":"Dharmarajan, Lekshmi","last_name":"Dharmarajan","first_name":"Lekshmi"},{"full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","last_name":"Lang","first_name":"Moritz"},{"full_name":"Stelling, Jörg","last_name":"Stelling","first_name":"Jörg"}],"month":"05","language":[{"iso":"eng"}],"acknowledgement":"We thank Julio Polaina (Instituto de Agroqu ı ́ mica y Tecnolog ı ́ a de Alimentos, C.S.I.C., Paterna, Spain) for the gift of plasmid pMR4, Gregor W. Schmidt for provision of and support with the micro fl uidic device, Markus Du ̈ rr for the cell tracking R script, and Lukas Widmer for the script for MEIGO using “ parfor ” in MATLAB. We acknowledge the members of the Stelling group for discussions, comments, and support.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Feedback loops in biological networks, among others, enable differentiation and cell cycle progression, and increase robustness in signal transduction. In natural networks, feedback loops are often complex and intertwined, making it challenging to identify which loops are mainly responsible for an observed behavior. However, minimal synthetic replicas could allow for such identification. Here, we engineered a synthetic permease-inducer-repressor system in Saccharomyces cerevisiae to analyze if a transport-mediated positive feedback loop could be a core mechanism for the switch-like behavior in the regulation of metabolic gene networks such as the S. cerevisiae GAL system or the Escherichia coli lac operon. We characterized the synthetic circuit using deterministic and stochastic mathematical models. Similar to its natural counterparts, our synthetic system shows bistable and hysteretic behavior, and the inducer concentration range for bistability as well as the switching rates between the two stable states depend on the repressor concentration. Our results indicate that a generic permease–inducer–repressor circuit with a single feedback loop is sufficient to explain the experimentally observed bistable behavior of the natural systems. We anticipate that the approach of reimplementing natural systems with orthogonal parts to identify crucial network components is applicable to other natural systems such as signaling pathways."}],"quality_controlled":"1","date_updated":"2021-01-12T06:47:37Z","volume":5,"type":"journal_article","date_created":"2018-12-11T11:49:40Z","oa_version":"None","citation":{"apa":"Gnügge, R., Dharmarajan, L., Lang, M., &#38; Stelling, J. (2016). An orthogonal permease–inducer–repressor feedback loop shows bistability. <i>ACS Synthetic Biology</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssynbio.6b00013\">https://doi.org/10.1021/acssynbio.6b00013</a>","mla":"Gnügge, Robert, et al. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” <i>ACS Synthetic Biology</i>, vol. 5, no. 10, American Chemical Society, 2016, pp. 1098–107, doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00013\">10.1021/acssynbio.6b00013</a>.","ama":"Gnügge R, Dharmarajan L, Lang M, Stelling J. An orthogonal permease–inducer–repressor feedback loop shows bistability. <i>ACS Synthetic Biology</i>. 2016;5(10):1098-1107. doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00013\">10.1021/acssynbio.6b00013</a>","chicago":"Gnügge, Robert, Lekshmi Dharmarajan, Moritz Lang, and Jörg Stelling. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” <i>ACS Synthetic Biology</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acssynbio.6b00013\">https://doi.org/10.1021/acssynbio.6b00013</a>.","ista":"Gnügge R, Dharmarajan L, Lang M, Stelling J. 2016. An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. 5(10), 1098–1107.","short":"R. Gnügge, L. Dharmarajan, M. Lang, J. Stelling, ACS Synthetic Biology 5 (2016) 1098–1107.","ieee":"R. Gnügge, L. Dharmarajan, M. Lang, and J. Stelling, “An orthogonal permease–inducer–repressor feedback loop shows bistability,” <i>ACS Synthetic Biology</i>, vol. 5, no. 10. American Chemical Society, pp. 1098–1107, 2016."},"publication":"ACS Synthetic Biology","year":"2016","issue":"10"},{"tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"scopus_import":"1","year":"2016","volume":58,"has_accepted_license":"1","article_processing_charge":"No","file":[{"date_updated":"2018-12-12T10:16:02Z","file_name":"IST-2017-779-v1+1_LIPIcs-MFCS-2016-25.pdf","date_created":"2018-12-12T10:16:02Z","file_size":632786,"creator":"system","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5187"}],"date_updated":"2025-06-02T08:53:50Z","abstract":[{"lang":"eng","text":"Games on graphs provide the appropriate framework to study several central problems in computer science, such as verification and synthesis of reactive systems. One of the most basic objectives for games on graphs is the liveness (or Büchi) objective that given a target set of vertices requires that some vertex in the target set is visited infinitely often. We study generalized Büchi objectives (i.e., conjunction of liveness objectives), and implications between two generalized Büchi objectives (known as GR(1) objectives), that arise in numerous applications in computer-aided verification. We present improved algorithms and conditional super-linear lower bounds based on widely believed assumptions about the complexity of (A1) combinatorial Boolean matrix multiplication and (A2) CNF-SAT. We consider graph games with n vertices, m edges, and generalized Büchi objectives with k conjunctions. First, we present an algorithm with running time O(k*n^2), improving the previously known O(k*n*m) and O(k^2*n^2) worst-case bounds. Our algorithm is optimal for dense graphs under (A1). Second, we show that the basic algorithm for the problem is optimal for sparse graphs when the target sets have constant size under (A2). Finally, we consider GR(1) objectives, with k_1 conjunctions in the antecedent and k_2 conjunctions in the consequent, and present an O(k_1 k_2 n^{2.5})-time algorithm, improving the previously known O(k_1*k_2*n*m)-time algorithm for m &gt; n^{1.5}. "}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Wolfgang","full_name":"Dvorák, Wolfgang","last_name":"Dvorák"},{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530"},{"first_name":"Veronika","full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer"}],"conference":{"end_date":"2016-08-26","name":"MFCS: Mathematical Foundations of Computer Science (SG)","start_date":"2016-08-22","location":"Krakow, Poland"},"ddc":["000","004","006"],"file_date_updated":"2018-12-12T10:16:02Z","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publist_id":"6317","ec_funded":1,"_id":"1068","alternative_title":["LIPIcs"],"department":[{"_id":"KrCh"}],"project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"title":"Conditionally optimal algorithms for generalized Büchi Games","oa_version":"Published Version","citation":{"short":"K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ieee":"K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Conditionally optimal algorithms for generalized Büchi Games,” presented at the MFCS: Mathematical Foundations of Computer Science (SG), Krakow, Poland, 2016, vol. 58.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Conditionally Optimal Algorithms for Generalized Büchi Games,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">https://doi.org/10.4230/LIPIcs.MFCS.2016.25</a>.","ista":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2016. Conditionally optimal algorithms for generalized Büchi Games. MFCS: Mathematical Foundations of Computer Science (SG), LIPIcs, vol. 58, 25.","ama":"Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Conditionally optimal algorithms for generalized Büchi Games. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">10.4230/LIPIcs.MFCS.2016.25</a>","mla":"Chatterjee, Krishnendu, et al. <i>Conditionally Optimal Algorithms for Generalized Büchi Games</i>. Vol. 58, 25, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">10.4230/LIPIcs.MFCS.2016.25</a>.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M. H., &#38; Loitzenbauer, V. (2016). Conditionally optimal algorithms for generalized Büchi Games (Vol. 58). Presented at the MFCS: Mathematical Foundations of Computer Science (SG), Krakow, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">https://doi.org/10.4230/LIPIcs.MFCS.2016.25</a>"},"date_created":"2018-12-11T11:49:58Z","type":"conference","quality_controlled":"1","license":"https://creativecommons.org/licenses/by/3.0/","acknowledgement":"K. C., M. H., and W. D. are partially supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Start grant (279307","pubrep_id":"779","month":"08","status":"public","doi":"10.4230/LIPIcs.MFCS.2016.25","date_published":"2016-08-01T00:00:00Z","intvolume":"        58","article_number":"25","day":"01","oa":1},{"date_updated":"2021-01-12T06:48:03Z","file":[{"file_id":"5213","relation":"main_file","access_level":"open_access","content_type":"application/pdf","creator":"system","file_size":521415,"date_created":"2018-12-12T10:16:26Z","file_name":"IST-2017-778-v1+1_LIPIcs-ICALP-2016-100.pdf","date_updated":"2018-12-12T10:16:26Z"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The Continuous Skolem Problem asks whether a real-valued function satisfying a linear differen-\r\ntial equation has a zero in a given interval of real numbers. This is a fundamental reachability\r\nproblem for continuous linear dynamical systems, such as linear hybrid automata and continuous-\r\ntime Markov chains. Decidability of the problem is currently open – indeed decidability is open\r\neven for the sub-problem in which a zero is sought in a bounded interval. In this paper we show\r\ndecidability of the bounded problem subject to Schanuel’s Conjecture, a unifying conjecture in\r\ntranscendental number theory. We furthermore analyse the unbounded problem in terms of the\r\nfrequencies of the differential equation, that is, the imaginary parts of the characteristic roots.\r\nWe show that the unbounded problem can be reduced to the bounded problem if there is at most\r\none rationally linearly independent frequency, or if there are two rationally linearly independent\r\nfrequencies and all characteristic roots are simple. We complete the picture by showing that de-\r\ncidability of the unbounded problem in the case of two (or more) rationally linearly independent\r\nfrequencies would entail a major new effectiveness result in Diophantine approximation, namely\r\ncomputability of the Diophantine-approximation types of all real algebraic numbers.","lang":"eng"}],"language":[{"iso":"eng"}],"author":[{"last_name":"Chonev","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Chonev, Ventsislav K","first_name":"Ventsislav K"},{"first_name":"Joël","last_name":"Ouaknine","full_name":"Ouaknine, Joël"},{"first_name":"James","full_name":"Worrell, James","last_name":"Worrell"}],"conference":{"location":"Rome, Italy","start_date":"2016-07-12","name":"ICALP: Automata, Languages and Programming","end_date":"2016-07-15"},"year":"2016","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":1,"volume":55,"has_accepted_license":"1","department":[{"_id":"KrCh"}],"alternative_title":["LIPIcs"],"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"}],"title":"On the skolem problem for continuous linear dynamical systems","ddc":["004","006"],"publication_status":"published","file_date_updated":"2018-12-12T10:16:26Z","publist_id":"6314","publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik","_id":"1069","ec_funded":1,"quality_controlled":"1","acknowledgement":"Ventsislav Chonev is supported by Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307:  Graph Games), and ERC Advanced Grant (267989: QUAREM).","pubrep_id":"778","month":"08","date_created":"2018-12-11T11:49:59Z","oa_version":"Published Version","citation":{"apa":"Chonev, V. K., Ouaknine, J., &#38; Worrell, J. (2016). On the skolem problem for continuous linear dynamical systems (Vol. 55). Presented at the ICALP: Automata, Languages and Programming, Rome, Italy: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">https://doi.org/10.4230/LIPIcs.ICALP.2016.100</a>","mla":"Chonev, Ventsislav K., et al. <i>On the Skolem Problem for Continuous Linear Dynamical Systems</i>. Vol. 55, 100, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">10.4230/LIPIcs.ICALP.2016.100</a>.","ama":"Chonev VK, Ouaknine J, Worrell J. On the skolem problem for continuous linear dynamical systems. In: Vol 55. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">10.4230/LIPIcs.ICALP.2016.100</a>","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Skolem Problem for Continuous Linear Dynamical Systems,” Vol. 55. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">https://doi.org/10.4230/LIPIcs.ICALP.2016.100</a>.","ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On the skolem problem for continuous linear dynamical systems. ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 100.","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On the skolem problem for continuous linear dynamical systems,” presented at the ICALP: Automata, Languages and Programming, Rome, Italy, 2016, vol. 55.","short":"V.K. Chonev, J. Ouaknine, J. Worrell, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016."},"type":"conference","day":"01","oa":1,"status":"public","intvolume":"        55","doi":"10.4230/LIPIcs.ICALP.2016.100","date_published":"2016-08-01T00:00:00Z","article_number":"100"},{"citation":{"ieee":"K. Chatterjee and L. Doyen, “Computation tree logic for synchronization properties,” presented at the ICALP: Automata, Languages and Programming, Rome, Italy, 2016, vol. 55.","short":"K. Chatterjee, L. Doyen, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016.","ista":"Chatterjee K, Doyen L. 2016. Computation tree logic for synchronization properties. ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 98.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Computation Tree Logic for Synchronization Properties,” Vol. 55. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">https://doi.org/10.4230/LIPIcs.ICALP.2016.98</a>.","ama":"Chatterjee K, Doyen L. Computation tree logic for synchronization properties. In: Vol 55. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">10.4230/LIPIcs.ICALP.2016.98</a>","mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Computation Tree Logic for Synchronization Properties</i>. Vol. 55, 98, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">10.4230/LIPIcs.ICALP.2016.98</a>.","apa":"Chatterjee, K., &#38; Doyen, L. (2016). Computation tree logic for synchronization properties (Vol. 55). Presented at the ICALP: Automata, Languages and Programming, Rome, Italy: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">https://doi.org/10.4230/LIPIcs.ICALP.2016.98</a>"},"oa_version":"Published Version","date_created":"2018-12-11T11:49:59Z","type":"conference","quality_controlled":"1","acknowledgement":"This research was partially supported by Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003, and European project Cassting (FP7-601148).\r\n\r\nWe thank Stefan Göller and anonymous reviewers for their insightful\r\ncomments and suggestions.\r\n","month":"01","pubrep_id":"812","status":"public","date_published":"2016-01-01T00:00:00Z","doi":"10.4230/LIPIcs.ICALP.2016.98","intvolume":"        55","article_number":"98","day":"01","oa":1,"scopus_import":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2016","volume":55,"has_accepted_license":"1","date_updated":"2021-01-12T06:48:03Z","file":[{"date_updated":"2018-12-12T10:08:52Z","file_name":"IST-2017-812-v1+1_LIPIcs-ICALP-2016-98.pdf","date_created":"2018-12-12T10:08:52Z","file_size":546133,"creator":"system","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"4714"}],"abstract":[{"text":"We present a logic that extends CTL (Computation Tree Logic) with operators that express synchronization properties. A property is synchronized in a system if it holds in all paths of a certain length. The new logic is obtained by using the same path quantifiers and temporal operators as in CTL, but allowing a different order of the quantifiers. This small syntactic variation induces a logic that can express non-regular properties for which known extensions of MSO with equality of path length are undecidable. We show that our variant of CTL is decidable and that the model-checking problem is in Delta_3^P = P^{NP^NP}, and is DP-hard. We analogously consider quantifier exchange in extensions of CTL, and we present operators defined using basic operators of CTL* that express the occurrence of infinitely many synchronization points. We show that the model-checking problem remains in Delta_3^P. The distinguishing power of CTL and of our new logic coincide if the Next operator is allowed in the logics, thus the classical bisimulation quotient can be used for state-space reduction before model checking. ","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"conference":{"location":"Rome, Italy","name":"ICALP: Automata, Languages and Programming","start_date":"2016-07-12","end_date":"2016-07-15"},"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"}],"file_date_updated":"2018-12-12T10:08:52Z","ddc":["005"],"publication_status":"published","publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik","publist_id":"6313","ec_funded":1,"_id":"1070","alternative_title":["LIPIcs"],"department":[{"_id":"KrCh"}],"project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"}],"title":"Computation tree logic for synchronization properties"},{"ec_funded":1,"_id":"1071","publisher":"Schloss Dagstuhl- Leibniz-Zentrum fur Informatik","publist_id":"6312","file_date_updated":"2018-12-12T10:14:31Z","publication_status":"published","ddc":["004","006"],"title":"Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"alternative_title":["LIPIcs"],"department":[{"_id":"KrCh"}],"has_accepted_license":"1","volume":57,"scopus_import":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"year":"2016","conference":{"start_date":"2016-08-22","name":"ESA: European Symposium on Algorithms","location":"Aarhus, Denmark","end_date":"2016-08-24"},"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389"},{"orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas"}],"language":[{"iso":"eng"}],"abstract":[{"text":"We consider data-structures for answering reachability and distance queries on constant-treewidth graphs with n nodes, on the standard RAM computational model with wordsize W=Theta(log n). Our first contribution is a data-structure that after O(n) preprocessing time, allows (1) pair reachability queries in O(1) time; and (2) single-source reachability queries in O(n/log n) time. This is (asymptotically) optimal and is faster than DFS/BFS when answering more than a constant number of single-source queries. The data-structure uses at all times O(n) space. Our second contribution is a space-time tradeoff data-structure for distance queries. For any epsilon in [1/2,1], we provide a data-structure with polynomial preprocessing time that allows pair queries in O(n^{1-\\epsilon} alpha(n)) time, where alpha is the inverse of the Ackermann function, and at all times uses O(n^epsilon) space. The input graph G is not considered in the space complexity. ","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","file":[{"access_level":"open_access","content_type":"application/pdf","creator":"system","file_id":"5084","relation":"main_file","file_size":579225,"date_created":"2018-12-12T10:14:31Z","file_name":"IST-2017-777-v1+1_LIPIcs-ESA-2016-28.pdf","date_updated":"2018-12-12T10:14:31Z"}],"date_updated":"2023-09-07T12:01:58Z","article_number":"28","date_published":"2016-08-01T00:00:00Z","doi":"10.4230/LIPIcs.ESA.2016.28","intvolume":"        57","related_material":{"record":[{"id":"821","relation":"dissertation_contains","status":"public"}]},"status":"public","oa":1,"day":"01","type":"conference","citation":{"ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs,” presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark, 2016, vol. 57.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2016. Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs. ESA: European Symposium on Algorithms, LIPIcs, vol. 57, 28.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant Treewidth Graphs,” Vol. 57. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">https://doi.org/10.4230/LIPIcs.ESA.2016.28</a>.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs. In: Vol 57. Schloss Dagstuhl- Leibniz-Zentrum fur Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">10.4230/LIPIcs.ESA.2016.28</a>","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2016). Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs (Vol. 57). Presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">https://doi.org/10.4230/LIPIcs.ESA.2016.28</a>","mla":"Chatterjee, Krishnendu, et al. <i>Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant Treewidth Graphs</i>. Vol. 57, 28, Schloss Dagstuhl- Leibniz-Zentrum fur Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">10.4230/LIPIcs.ESA.2016.28</a>."},"oa_version":"Published Version","date_created":"2018-12-11T11:49:59Z","pubrep_id":"777","month":"08","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE) and ERC Start grant (279307: Graph Games).","quality_controlled":"1"},{"date_published":"2016-07-19T00:00:00Z","doi":"10.1038/celldisc.2016.18","intvolume":"         2","article_number":"16018","status":"public","day":"19","oa":1,"type":"journal_article","publication":"Cell Discovery","citation":{"apa":"Łangowski, Ł., Wabnik, K. T., Li, H., Vanneste, S., Naramoto, S., Tanaka, H., &#38; Friml, J. (2016). Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. <i>Cell Discovery</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/celldisc.2016.18\">https://doi.org/10.1038/celldisc.2016.18</a>","mla":"Łangowski, Łukasz, et al. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” <i>Cell Discovery</i>, vol. 2, 16018, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/celldisc.2016.18\">10.1038/celldisc.2016.18</a>.","ama":"Łangowski Ł, Wabnik KT, Li H, et al. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. <i>Cell Discovery</i>. 2016;2. doi:<a href=\"https://doi.org/10.1038/celldisc.2016.18\">10.1038/celldisc.2016.18</a>","ista":"Łangowski Ł, Wabnik KT, Li H, Vanneste S, Naramoto S, Tanaka H, Friml J. 2016. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. 2, 16018.","chicago":"Łangowski, Łukasz, Krzysztof T Wabnik, Hongjiang Li, Steffen Vanneste, Satoshi Naramoto, Hirokazu Tanaka, and Jiří Friml. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” <i>Cell Discovery</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/celldisc.2016.18\">https://doi.org/10.1038/celldisc.2016.18</a>.","short":"Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J. Friml, Cell Discovery 2 (2016).","ieee":"Ł. Łangowski <i>et al.</i>, “Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells,” <i>Cell Discovery</i>, vol. 2. Nature Publishing Group, 2016."},"oa_version":"Published Version","date_created":"2018-12-11T11:50:02Z","pubrep_id":"757","month":"07","quality_controlled":"1","acknowledgement":"We thank Bonnie Bartel, Jenny Russinova and Niko Geldner\r\nfor sharing published material, Martine de Cock and Annick\r\nBleys for help in preparing the manuscript. This work was\r\nsupported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP); Czech Science Foundation\r\nGAČR (GA13-40637S); project CEITEC—Central European\r\nInstitute of Technology (CZ.1.05/1.1.00/02.0068). SV is a\r\npostdoctoral fellow of the Research Foundation-Flanders.\r\nSN is a Project Assistant Professor supported by the Japanese\r\nSociety for the Promotion of Science (JSPS; 30612022 to SN),\r\nthe NC-CARP project of the Ministry of Education, Culture,\r\nSports, Science and Technology in Japan to SN.","publisher":"Nature Publishing Group","publist_id":"6299","ec_funded":1,"_id":"1081","ddc":["580"],"file_date_updated":"2018-12-12T10:13:33Z","publication_status":"published","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"title":"Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"volume":2,"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"scopus_import":1,"year":"2016","language":[{"iso":"eng"}],"author":[{"full_name":"Łangowski, Łukasz","last_name":"Łangowski","first_name":"Łukasz"},{"first_name":"Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","full_name":"Wabnik, Krzysztof T","last_name":"Wabnik","orcid":"0000-0001-7263-0560"},{"first_name":"Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Hongjiang","last_name":"Li","orcid":"0000-0001-5039-9660"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"first_name":"Satoshi","full_name":"Naramoto, Satoshi","last_name":"Naramoto"},{"first_name":"Hirokazu","last_name":"Tanaka","full_name":"Tanaka, Hirokazu"},{"first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"file":[{"file_name":"IST-2017-757-v1+1_celldisc201618.pdf","date_updated":"2018-12-12T10:13:33Z","file_id":"5017","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"system","file_size":5261671,"date_created":"2018-12-12T10:13:33Z"}],"date_updated":"2021-01-12T06:48:08Z","abstract":[{"lang":"eng","text":"The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"month":"03","acknowledgement":"The authors are thankful to Drs. Roger Abaecherli, Nikus Kjell, Paul Kligfield, Jay Mason, Patrice Nony, Vito Starc, Anders Thurin and the late Galen Wagner for their in depth review and constructive comments.","quality_controlled":"1","type":"conference","citation":{"ama":"Rubel P, Pani D, Schlögl A, et al. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In: <i>2016 Computing in Cardiology Conference</i>. Vol 43. Computing in Cardiology; 2016:309-312. doi:<a href=\"https://doi.org/10.22489/cinc.2016.090-500\">10.22489/cinc.2016.090-500</a>","apa":"Rubel, P., Pani, D., Schlögl, A., Fayn, J., Badilini, F., Macfarlane, P., &#38; Varri, A. (2016). SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. In <i>2016 Computing in Cardiology Conference</i> (Vol. 43, pp. 309–312). Vancouver, Canada: Computing in Cardiology. <a href=\"https://doi.org/10.22489/cinc.2016.090-500\">https://doi.org/10.22489/cinc.2016.090-500</a>","mla":"Rubel, Paul, et al. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” <i>2016 Computing in Cardiology Conference</i>, vol. 43, Computing in Cardiology, 2016, pp. 309–12, doi:<a href=\"https://doi.org/10.22489/cinc.2016.090-500\">10.22489/cinc.2016.090-500</a>.","short":"P. Rubel, D. Pani, A. Schlögl, J. Fayn, F. Badilini, P. Macfarlane, A. Varri, in:, 2016 Computing in Cardiology Conference, Computing in Cardiology, 2016, pp. 309–312.","ieee":"P. Rubel <i>et al.</i>, “SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography,” in <i>2016 Computing in Cardiology Conference</i>, Vancouver, Canada, 2016, vol. 43, pp. 309–312.","chicago":"Rubel, Paul, Danilo Pani, Alois Schlögl, Jocelyne Fayn, Fabio Badilini, Peter Macfarlane, and Alpo Varri. “SCP-ECG V3.0: An Enhanced Standard Communication Protocol for Computer-Assisted Electrocardiography.” In <i>2016 Computing in Cardiology Conference</i>, 43:309–12. Computing in Cardiology, 2016. <a href=\"https://doi.org/10.22489/cinc.2016.090-500\">https://doi.org/10.22489/cinc.2016.090-500</a>.","ista":"Rubel P, Pani D, Schlögl A, Fayn J, Badilini F, Macfarlane P, Varri A. 2016. SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography. 2016 Computing in Cardiology Conference. CinC: Computing in Cardiology vol. 43, 309–312."},"oa_version":"Published Version","date_created":"2022-03-03T10:43:10Z","publication":"2016 Computing in Cardiology Conference","oa":1,"main_file_link":[{"url":"https://doi.org/10.22489/cinc.2016.090-500","open_access":"1"}],"day":"01","date_published":"2016-03-01T00:00:00Z","doi":"10.22489/cinc.2016.090-500","intvolume":"        43","status":"public","publication_identifier":{"issn":["2325-887X"]},"conference":{"start_date":"2016-09-11","name":"CinC: Computing in Cardiology","location":"Vancouver, Canada","end_date":"2016-09-14"},"author":[{"first_name":"Paul","last_name":"Rubel","full_name":"Rubel, Paul"},{"first_name":"Danilo","full_name":"Pani, Danilo","last_name":"Pani"},{"first_name":"Alois","full_name":"Schlögl, Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100"},{"last_name":"Fayn","full_name":"Fayn, Jocelyne","first_name":"Jocelyne"},{"first_name":"Fabio","last_name":"Badilini","full_name":"Badilini, Fabio"},{"full_name":"Macfarlane, Peter","last_name":"Macfarlane","first_name":"Peter"},{"first_name":"Alpo","full_name":"Varri, Alpo","last_name":"Varri"}],"language":[{"iso":"eng"}],"abstract":[{"text":"The main goal of the SCP-ECG standard is to address ECG data and related metadata structuring, semantics and syntax, with the objective of facilitating interoperability and thus supporting and promoting the exchange of the relevant information for unary and serial ECG diagnosis. Starting with version V3.0, the standard now also provides support for the storage of continuous, long-term ECG recordings and affords a repository for selected ECG sequences and the related metadata to accommodate stress tests, drug trials and protocol-based ECG recordings. The global and per-lead measurements sections have been extended and three new sections have been introduced for storing beat-by-beat and/or spike-by-spike measurements\r\nand annotations. The used terminology and the provided measurements and annotations have been harmonized with the ISO/IEEE 11073-10102 Annotated ECG standard. Emphasis has also been put on harmonizing the Universal Statement Codes with the CDISC and the categorized AHA statement codes and similarly the drug and implanted devices codes with the ATC and NASPE/BPEG codes. ","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","date_updated":"2022-03-04T07:34:45Z","volume":43,"scopus_import":"1","year":"2016","page":"309-312","title":"SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography","department":[{"_id":"CampIT"}],"_id":"10810","publisher":"Computing in Cardiology","publication_status":"published"},{"volume":29,"year":"2016","scopus_import":1,"conference":{"end_date":"2016-12-10","start_date":"2016-12-05","location":"Barcelona, Spaine","name":"NIPS: Neural Information Processing Systems"},"author":[{"full_name":"Monk, Travis","last_name":"Monk","first_name":"Travis"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","full_name":"Savin, Cristina","first_name":"Cristina"},{"full_name":"Lücke, Jörg","last_name":"Lücke","first_name":"Jörg"}],"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Experience constantly shapes neural circuits through a variety of plasticity mechanisms. While the functional roles of some plasticity mechanisms are well-understood, it remains unclear how changes in neural excitability contribute to learning. Here, we develop a normative interpretation of intrinsic plasticity (IP) as a key component of unsupervised learning. We introduce a novel generative mixture model that accounts for the class-specific statistics of stimulus intensities, and we derive a neural circuit that learns the input classes and their intensities. We will analytically show that inference and learning for our generative model can be achieved by a neural circuit with intensity-sensitive neurons equipped with a specific form of IP. Numerical experiments verify our analytical derivations and show robust behavior for artificial and natural stimuli. Our results link IP to non-trivial input statistics, in particular the statistics of stimulus intensities for classes to which a neuron is sensitive. More generally, our work paves the way toward new classification algorithms that are robust to intensity variations."}],"date_updated":"2021-01-12T08:22:08Z","_id":"948","ec_funded":1,"publist_id":"6469","publisher":"Neural Information Processing Systems","publication_status":"published","page":"4285 - 4293","title":"Neurons equipped with intrinsic plasticity learn stimulus intensity statistics","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"department":[{"_id":"GaTk"}],"alternative_title":["Advances in Neural Information Processing Systems"],"type":"conference","date_created":"2018-12-11T11:49:21Z","oa_version":"None","citation":{"chicago":"Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems, 2016.","ista":"Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 4285–4293.","ieee":"T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.","short":"T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems, 2016, pp. 4285–4293.","mla":"Monk, Travis, et al. <i>Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics</i>. Vol. 29, Neural Information Processing Systems, 2016, pp. 4285–93.","apa":"Monk, T., Savin, C., &#38; Lücke, J. (2016). Neurons equipped with intrinsic plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural Information Processing Systems.","ama":"Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems; 2016:4285-4293."},"month":"01","acknowledgement":"DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and  LU 1196/5-1 (JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement no. 291734 (CS)","quality_controlled":"1","intvolume":"        29","date_published":"2016-01-01T00:00:00Z","status":"public","day":"01","main_file_link":[{"url":"https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics"}]},{"date_published":"2016-05-06T00:00:00Z","publisher":"Dryad","doi":"10.5061/dryad.cq7t1","_id":"9704","status":"public","related_material":{"record":[{"id":"1262","relation":"used_in_publication","status":"public"}]},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.cq7t1","open_access":"1"}],"day":"06","oa":1,"title":"Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss","department":[{"_id":"SyCr"}],"type":"research_data_reference","year":"2016","date_created":"2021-07-23T08:30:38Z","citation":{"ieee":"D. Mcmahon <i>et al.</i>, “Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss.” Dryad, 2016.","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, (2016).","ista":"Mcmahon D, Natsopoulou M, Doublet V, Fürst M, Weging S, Brown M, Gogol Döring A, Paxton R. 2016. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss, Dryad, <a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>.","chicago":"Mcmahon, Dino, Myrsini Natsopoulou, Vincent Doublet, Matthias Fürst, Silvio Weging, Mark Brown, Andreas Gogol Döring, and Robert Paxton. “Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>.","ama":"Mcmahon D, Natsopoulou M, Doublet V, et al. Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>","apa":"Mcmahon, D., Natsopoulou, M., Doublet, V., Fürst, M., Weging, S., Brown, M., … Paxton, R. (2016). Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss. Dryad. <a href=\"https://doi.org/10.5061/dryad.cq7t1\">https://doi.org/10.5061/dryad.cq7t1</a>","mla":"Mcmahon, Dino, et al. <i>Data from: Elevated Virulence of an Emerging Viral Genotype as a Driver of Honeybee Loss</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.cq7t1\">10.5061/dryad.cq7t1</a>."},"oa_version":"Published Version","month":"05","author":[{"first_name":"Dino","last_name":"Mcmahon","full_name":"Mcmahon, Dino"},{"first_name":"Myrsini","last_name":"Natsopoulou","full_name":"Natsopoulou, Myrsini"},{"first_name":"Vincent","full_name":"Doublet, Vincent","last_name":"Doublet"},{"orcid":"0000-0002-3712-925X","id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias","last_name":"Fürst","first_name":"Matthias"},{"first_name":"Silvio","last_name":"Weging","full_name":"Weging, Silvio"},{"last_name":"Brown","full_name":"Brown, Mark","first_name":"Mark"},{"first_name":"Andreas","full_name":"Gogol Döring, Andreas","last_name":"Gogol Döring"},{"first_name":"Robert","full_name":"Paxton, Robert","last_name":"Paxton"}],"date_updated":"2023-02-21T16:54:31Z","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"Emerging infectious diseases (EIDs) have contributed significantly to the current biodiversity crisis, leading to widespread epidemics and population loss. Owing to genetic variation in pathogen virulence, a complete understanding of species decline requires the accurate identification and characterization of EIDs. We explore this issue in the Western honeybee, where increasing mortality of populations in the Northern Hemisphere has caused major concern. Specifically, we investigate the importance of genetic identity of the main suspect in mortality, deformed wing virus (DWV), in driving honeybee loss. Using laboratory experiments and a systematic field survey, we demonstrate that an emerging DWV genotype (DWV-B) is more virulent than the established DWV genotype (DWV-A) and is widespread in the landscape. Furthermore, we show in a simple model that colonies infected with DWV-B collapse sooner than colonies infected with DWV-A. We also identify potential for rapid DWV evolution by revealing extensive genome-wide recombination in vivo. The emergence of DWV-B in naive honeybee populations, including via recombination with DWV-A, could be of significant ecological and economic importance. Our findings emphasize that knowledge of pathogen genetic identity and diversity is critical to understanding drivers of species decline.","lang":"eng"}]},{"type":"research_data_reference","date_created":"2021-07-23T11:45:47Z","citation":{"ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016.","short":"N.H. Barton, (2016).","ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, <a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","chicago":"Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>.","ama":"Barton NH. Data from: How does epistasis influence the response to selection? 2016. doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>","mla":"Barton, Nicholas H. <i>Data from: How Does Epistasis Influence the Response to Selection?</i> Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","apa":"Barton, N. H. (2016). Data from: How does epistasis influence the response to selection? Dryad. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>"},"oa_version":"Published Version","year":"2016","author":[{"first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"month":"09","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"Much of quantitative genetics is based on the ‘infinitesimal model’, under which selection has a negligible effect on the genetic variance. This is typically justified by assuming a very large number of loci with additive effects. However, it applies even when genes interact, provided that the number of loci is large enough that selection on each of them is weak relative to random drift. In the long term, directional selection will change allele frequencies, but even then, the effects of epistasis on the ultimate change in trait mean due to selection may be modest. Stabilising selection can maintain many traits close to their optima, even when the underlying alleles are weakly selected. However, the number of traits that can be optimised is apparently limited to ~4Ne by the ‘drift load’, and this is hard to reconcile with the apparent complexity of many organisms. Just as for the mutation load, this limit can be evaded by a particular form of negative epistasis. A more robust limit is set by the variance in reproductive success. This suggests that selection accumulates information most efficiently in the infinitesimal regime, when selection on individual alleles is weak, and comparable with random drift. A review of evidence on selection strength suggests that although most variance in fitness may be because of alleles with large Nes, substantial amounts of adaptation may be because of alleles in the infinitesimal regime, in which epistasis has modest effects."}],"date_updated":"2025-05-28T11:57:03Z","article_processing_charge":"No","_id":"9710","date_published":"2016-09-23T00:00:00Z","publisher":"Dryad","doi":"10.5061/dryad.s5s7r","related_material":{"record":[{"id":"1199","relation":"used_in_publication","status":"public"}]},"status":"public","title":"Data from: How does epistasis influence the response to selection?","oa":1,"day":"23","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s5s7r"}],"department":[{"_id":"NiBa"}]},{"year":"2016","citation":{"ama":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. 2016. doi:<a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>","apa":"Mcmahon, D., Fürst, M., Caspar, J., Theodorou, P., Brown, M., &#38; Paxton, R. (2016). Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees. Dryad. <a href=\"https://doi.org/10.5061/dryad.4b565\">https://doi.org/10.5061/dryad.4b565</a>","mla":"Mcmahon, Dino, et al. <i>Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees</i>. Dryad, 2016, doi:<a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>.","ieee":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, and R. Paxton, “Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees.” Dryad, 2016.","short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016).","chicago":"Mcmahon, Dino, Matthias Fürst, Jesicca Caspar, Panagiotis Theodorou, Mark Brown, and Robert Paxton. “Data from: A Sting in the Spit: Widespread Cross-Infection of Multiple RNA Viruses across Wild and Managed Bees.” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.4b565\">https://doi.org/10.5061/dryad.4b565</a>.","ista":"Mcmahon D, Fürst M, Caspar J, Theodorou P, Brown M, Paxton R. 2016. Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees, Dryad, <a href=\"https://doi.org/10.5061/dryad.4b565\">10.5061/dryad.4b565</a>."},"oa_version":"Published Version","date_created":"2021-07-26T09:14:19Z","type":"research_data_reference","article_processing_charge":"No","date_updated":"2023-02-23T10:17:25Z","abstract":[{"lang":"eng","text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"01","author":[{"first_name":"Dino","full_name":"Mcmahon, Dino","last_name":"Mcmahon"},{"orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst","first_name":"Matthias"},{"first_name":"Jesicca","full_name":"Caspar, Jesicca","last_name":"Caspar"},{"last_name":"Theodorou","full_name":"Theodorou, Panagiotis","first_name":"Panagiotis"},{"last_name":"Brown","full_name":"Brown, Mark","first_name":"Mark"},{"first_name":"Robert","last_name":"Paxton","full_name":"Paxton, Robert"}],"status":"public","related_material":{"record":[{"relation":"used_in_publication","id":"1855","status":"public"}]},"doi":"10.5061/dryad.4b565","publisher":"Dryad","date_published":"2016-01-22T00:00:00Z","_id":"9720","department":[{"_id":"SyCr"}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.4b565","open_access":"1"}],"day":"22","title":"Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees","oa":1},{"day":"27","title":"Simulation study to test the robustness of ABC in face of recent times of divergence","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"publisher":"Public Library of Science","doi":"10.1371/journal.pbio.2000234.s016","_id":"9862","status":"public","related_material":{"record":[{"relation":"used_in_publication","id":"1158","status":"public"}]},"author":[{"first_name":"Camille","full_name":"Roux, Camille","last_name":"Roux"},{"orcid":"0000-0001-8441-5075","first_name":"Christelle","last_name":"Fraisse","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"full_name":"Anciaux, Youann","last_name":"Anciaux","first_name":"Youann"},{"first_name":"Nicolas","full_name":"Galtier, Nicolas","last_name":"Galtier"},{"full_name":"Bierne, Nicolas","last_name":"Bierne","first_name":"Nicolas"}],"month":"12","date_updated":"2023-02-21T16:21:20Z","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","year":"2016","date_created":"2021-08-10T08:20:17Z","citation":{"ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation study to test the robustness of ABC in face of recent times of divergence, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>.","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Simulation study to test the robustness of ABC in face of recent times of divergence.” Public Library of Science, 2016.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>","mla":"Roux, Camille, et al. <i>Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation study to test the robustness of ABC in face of recent times of divergence. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>"},"oa_version":"Published Version"},{"status":"public","related_material":{"record":[{"relation":"used_in_publication","id":"1158","status":"public"}]},"doi":"10.1371/journal.pbio.2000234.s017","publisher":"Public Library of Science","_id":"9863","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"day":"27","title":"Accessions of surveyed individuals, geographic locations and summary statistics","year":"2016","date_created":"2021-08-10T08:22:52Z","citation":{"chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Accessions of surveyed individuals, geographic locations and summary statistics, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","ieee":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, and N. Bierne, “Accessions of surveyed individuals, geographic locations and summary statistics.” Public Library of Science, 2016.","mla":"Roux, Camille, et al. <i>Accessions of Surveyed Individuals, Geographic Locations and Summary Statistics</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>.","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>"},"oa_version":"Published Version","type":"research_data_reference","date_updated":"2023-02-21T16:21:20Z","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"12","author":[{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle"},{"last_name":"Romiguier","full_name":"Romiguier, Jonathan","first_name":"Jonathan"},{"first_name":"Youann","last_name":"Anciaux","full_name":"Anciaux, Youann"},{"last_name":"Galtier","full_name":"Galtier, Nicolas","first_name":"Nicolas"},{"last_name":"Bierne","full_name":"Bierne, Nicolas","first_name":"Nicolas"}]},{"_id":"9864","doi":"10.6084/m9.figshare.4315652.v1","publisher":"The Royal Society","date_published":"2016-12-14T00:00:00Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1077"}]},"status":"public","title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","oa":1,"day":"14","main_file_link":[{"open_access":"1","url":"https://doi.org/10.6084/m9.figshare.4315652.v1"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"type":"research_data_reference","citation":{"short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).","ieee":"R. A. Fernandes Redondo, H. de Vladar, T. Włodarski, and J. P. Bollback, “Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family.” The Royal Society, 2016.","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>.","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>","mla":"Fernandes Redondo, Rodrigo A., et al. <i>Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family</i>. The Royal Society, 2016, doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>"},"oa_version":"Published Version","date_created":"2021-08-10T08:29:47Z","year":"2016","author":[{"full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A","orcid":"0000-0002-5837-2793"},{"orcid":"0000-0002-5985-7653","last_name":"de Vladar","full_name":"de Vladar, Harold","id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold"},{"last_name":"Włodarski","full_name":"Włodarski, Tomasz","first_name":"Tomasz"},{"orcid":"0000-0002-4624-4612","first_name":"Jonathan P","last_name":"Bollback","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Bollback, Jonathan P"}],"month":"12","abstract":[{"text":"Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by, first, reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","date_updated":"2025-05-28T11:57:06Z"},{"date_created":"2021-08-10T08:37:20Z","oa_version":"Published Version","citation":{"ista":"Zagórski MP, Burda Z, Wacław B. 2016. ZIP-archived directory containing all data and computer programs, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>.","chicago":"Zagórski, Marcin P, Zdzisław Burda, and Bartłomiej Wacław. “ZIP-Archived Directory Containing All Data and Computer Programs.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">https://doi.org/10.1371/journal.pcbi.1005218.s009</a>.","short":"M.P. Zagórski, Z. Burda, B. Wacław, (2016).","ieee":"M. P. Zagórski, Z. Burda, and B. Wacław, “ZIP-archived directory containing all data and computer programs.” Public Library of Science, 2016.","mla":"Zagórski, Marcin P., et al. <i>ZIP-Archived Directory Containing All Data and Computer Programs</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>.","apa":"Zagórski, M. P., Burda, Z., &#38; Wacław, B. (2016). ZIP-archived directory containing all data and computer programs. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">https://doi.org/10.1371/journal.pcbi.1005218.s009</a>","ama":"Zagórski MP, Burda Z, Wacław B. ZIP-archived directory containing all data and computer programs. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005218.s009\">10.1371/journal.pcbi.1005218.s009</a>"},"year":"2016","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-02-21T16:24:29Z","article_processing_charge":"No","month":"12","author":[{"orcid":"0000-0001-7896-7762","first_name":"Marcin P","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","full_name":"Zagórski, Marcin P"},{"last_name":"Burda","full_name":"Burda, Zdzisław","first_name":"Zdzisław"},{"last_name":"Wacław","full_name":"Wacław, Bartłomiej","first_name":"Bartłomiej"}],"related_material":{"record":[{"id":"1167","relation":"used_in_publication","status":"public"}]},"status":"public","_id":"9866","publisher":"Public Library of Science","date_published":"2016-12-09T00:00:00Z","doi":"10.1371/journal.pcbi.1005218.s009","department":[{"_id":"AnKi"}],"title":"ZIP-archived directory containing all data and computer programs","day":"09"},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"In the beginning of our experiment, subjects were asked to read a few pages on their computer screens that would explain the rules of the subsequent game. Here, we provide these instructions, translated from German.","lang":"eng"}],"date_updated":"2023-02-21T16:59:01Z","article_processing_charge":"No","month":"10","author":[{"orcid":"0000-0001-5116-955X","last_name":"Hilbe","full_name":"Hilbe, Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"full_name":"Hagel, Kristin","last_name":"Hagel","first_name":"Kristin"},{"first_name":"Manfred","last_name":"Milinski","full_name":"Milinski, Manfred"}],"date_created":"2021-08-10T08:42:00Z","citation":{"ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental game instructions.” Public Library of Science, 2016.","short":"C. Hilbe, K. Hagel, M. Milinski, (2016).","ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental game instructions, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>.","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Game Instructions.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">https://doi.org/10.1371/journal.pone.0163867.s008</a>.","ama":"Hilbe C, Hagel K, Milinski M. Experimental game instructions. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>","apa":"Hilbe, C., Hagel, K., &#38; Milinski, M. (2016). Experimental game instructions. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">https://doi.org/10.1371/journal.pone.0163867.s008</a>","mla":"Hilbe, Christian, et al. <i>Experimental Game Instructions</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s008\">10.1371/journal.pone.0163867.s008</a>."},"oa_version":"Published Version","year":"2016","type":"research_data_reference","department":[{"_id":"KrCh"}],"title":"Experimental game instructions","day":"04","related_material":{"record":[{"status":"public","id":"1322","relation":"used_in_publication"}]},"status":"public","_id":"9867","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0163867.s008"},{"status":"public","related_material":{"record":[{"status":"public","id":"1322","relation":"used_in_publication"}]},"publisher":"Public Library of Science","date_published":"2016-10-04T00:00:00Z","doi":"10.1371/journal.pone.0163867.s009","_id":"9868","department":[{"_id":"KrCh"}],"day":"04","title":"Experimental data","year":"2016","date_created":"2021-08-10T08:45:00Z","oa_version":"Published Version","citation":{"ieee":"C. Hilbe, K. Hagel, and M. Milinski, “Experimental data.” Public Library of Science, 2016.","short":"C. Hilbe, K. Hagel, M. Milinski, (2016).","ista":"Hilbe C, Hagel K, Milinski M. 2016. Experimental data, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>.","chicago":"Hilbe, Christian, Kristin Hagel, and Manfred Milinski. “Experimental Data.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">https://doi.org/10.1371/journal.pone.0163867.s009</a>.","ama":"Hilbe C, Hagel K, Milinski M. Experimental data. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>","apa":"Hilbe, C., Hagel, K., &#38; Milinski, M. (2016). Experimental data. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">https://doi.org/10.1371/journal.pone.0163867.s009</a>","mla":"Hilbe, Christian, et al. <i>Experimental Data</i>. Public Library of Science, 2016, doi:<a href=\"https://doi.org/10.1371/journal.pone.0163867.s009\">10.1371/journal.pone.0163867.s009</a>."},"type":"research_data_reference","date_updated":"2023-02-21T16:59:01Z","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"text":"The raw data file containing the experimental decisions of all our study subjects.","lang":"eng"}],"author":[{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","full_name":"Hilbe, Christian","last_name":"Hilbe","first_name":"Christian","orcid":"0000-0001-5116-955X"},{"full_name":"Hagel, Kristin","last_name":"Hagel","first_name":"Kristin"},{"first_name":"Manfred","full_name":"Milinski, Manfred","last_name":"Milinski"}],"month":"10"}]