[{"department":[{"_id":"RySh"}],"date_updated":"2026-04-07T08:32:03Z","quality_controlled":"1","day":"02","doi":"10.1007/978-1-4939-3064-7_17","OA_type":"closed access","publication_status":"published","_id":"19990","title":"High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL)","corr_author":"1","publication":"Receptor and Ion Channel Detection in the Brain","oa_version":"None","abstract":[{"text":"Visualizing molecular localization at high resolution contributes to understanding of their functions and roles in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study high-resolution two-dimensional distribution of transmembrane proteins and their tightly associated proteins on platinum-carbon replica. During treatment with SDS, unfixed proteins and intracellular organelle are dissolved and integral membrane proteins captured and stabilized by carbon and platinum deposition are denatured, retaining most of their antigenicity, and exposed on exoplasmic and protoplasmic surfaces of lipid monolayers. The exposure of these antigens on the surface of replica facilitates the accessibility of antibodies and therefore provides higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples and an additional procedure for fluorescence-guided electron microscopy for replica immunolabeling.","lang":"eng"}],"year":"2016","month":"02","type":"book_chapter","publication_identifier":{"eissn":["1940-6045"],"eisbn":["9781493930647"],"issn":["0893-2336"],"isbn":["9781493930630"]},"series_title":"Neuromethods","publisher":"Springer Nature","acknowledgement":"We thank Mitsuru Ikeda for preparing replica images used in Fig. 2.","date_created":"2025-07-10T13:56:06Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","status":"public","page":"233-245","citation":{"chicago":"Harada, Harumi, and Ryuichi Shigemoto. “High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” In <i>Receptor and Ion Channel Detection in the Brain</i>, 233–45. Neuromethods. Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">https://doi.org/10.1007/978-1-4939-3064-7_17</a>.","ista":"Harada H, Shigemoto R. 2016.High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. , 233–245.","ama":"Harada H, Shigemoto R. High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In: <i>Receptor and Ion Channel Detection in the Brain</i>. Neuromethods. Springer Nature; 2016:233-245. doi:<a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">10.1007/978-1-4939-3064-7_17</a>","apa":"Harada, H., &#38; Shigemoto, R. (2016). High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In <i>Receptor and Ion Channel Detection in the Brain</i> (pp. 233–245). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">https://doi.org/10.1007/978-1-4939-3064-7_17</a>","short":"H. Harada, R. Shigemoto, in:, Receptor and Ion Channel Detection in the Brain, Springer Nature, 2016, pp. 233–245.","mla":"Harada, Harumi, and Ryuichi Shigemoto. “High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” <i>Receptor and Ion Channel Detection in the Brain</i>, Springer Nature, 2016, pp. 233–45, doi:<a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">10.1007/978-1-4939-3064-7_17</a>.","ieee":"H. Harada and R. Shigemoto, “High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL),” in <i>Receptor and Ion Channel Detection in the Brain</i>, Springer Nature, 2016, pp. 233–245."},"article_processing_charge":"No","date_published":"2016-02-02T00:00:00Z","author":[{"full_name":"Harada, Harumi","orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","first_name":"Harumi","last_name":"Harada"},{"last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi"}],"language":[{"iso":"eng"}]},{"publisher":"Springer Nature","publication_identifier":{"eisbn":["9781489975027"]},"type":"book_chapter","month":"07","year":"2016","date_published":"2016-07-06T00:00:00Z","article_processing_charge":"No","citation":{"apa":"Sharmanska, V., &#38; Quadrianto, N. (2016). Learning Using Privileged Information. In <i>Encyclopedia of Machine Learning and Data Mining</i> (pp. 1–4). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4899-7502-7_892-1\">https://doi.org/10.1007/978-1-4899-7502-7_892-1</a>","ama":"Sharmanska V, Quadrianto N. Learning Using Privileged Information. In: <i>Encyclopedia of Machine Learning and Data Mining</i>. Springer Nature; 2016:1-4. doi:<a href=\"https://doi.org/10.1007/978-1-4899-7502-7_892-1\">10.1007/978-1-4899-7502-7_892-1</a>","chicago":"Sharmanska, Viktoriia, and Novi Quadrianto. “Learning Using Privileged Information.” In <i>Encyclopedia of Machine Learning and Data Mining</i>, 1–4. Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-1-4899-7502-7_892-1\">https://doi.org/10.1007/978-1-4899-7502-7_892-1</a>.","ista":"Sharmanska V, Quadrianto N. 2016.Learning Using Privileged Information. In: Encyclopedia of Machine Learning and Data Mining. , 1–4.","short":"V. Sharmanska, N. Quadrianto, in:, Encyclopedia of Machine Learning and Data Mining, Springer Nature, 2016, pp. 1–4.","mla":"Sharmanska, Viktoriia, and Novi Quadrianto. “Learning Using Privileged Information.” <i>Encyclopedia of Machine Learning and Data Mining</i>, Springer Nature, 2016, pp. 1–4, doi:<a href=\"https://doi.org/10.1007/978-1-4899-7502-7_892-1\">10.1007/978-1-4899-7502-7_892-1</a>.","ieee":"V. Sharmanska and N. Quadrianto, “Learning Using Privileged Information,” in <i>Encyclopedia of Machine Learning and Data Mining</i>, Springer Nature, 2016, pp. 1–4."},"status":"public","page":"1-4","language":[{"iso":"eng"}],"author":[{"id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","first_name":"Viktoriia","last_name":"Sharmanska","full_name":"Sharmanska, Viktoriia","orcid":"0000-0003-0192-9308"},{"full_name":"Quadrianto, Novi","last_name":"Quadrianto","first_name":"Novi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-07-10T13:57:52Z","quality_controlled":"1","date_updated":"2025-09-23T10:53:13Z","day":"06","department":[{"_id":"ChLa"}],"_id":"19991","corr_author":"1","publication_status":"published","title":"Learning Using Privileged Information","abstract":[{"text":"When applying machine learning techniques to real-world problems, prior knowledge plays a crucial role in enriching the learning system. This prior knowledge is typically defined by domain experts and can be integrated into machine learning algorithms in a variety of ways: as a preference of certain prediction functions over others, as a Bayesian prior over parameters, or as additional information about the samples in the training set used for learning a prediction function. The latter setup is called learning using privileged information (LUPI) and was adopted by Vapnik and Vashist in (Neural Netw, 2009). Formally, LUPI refers to the setting when, in addition to the main data modality, the learning system has access to an extra source of information about the training examples. The additional source of information is only available during training and therefore is called privileged. The main goal of LUPI is to utilize privileged information and to learn a better model in the main data modality than one would learn without the privileged source. As an illustration, for protein classification based on amino-acid sequences, the protein tertiary structure can be considered additional information. Another example is recognizing objects in images; the textual information in the form of image tags contains additional object descriptions and can be used as privileged.","lang":"eng"}],"oa_version":"None","publication":"Encyclopedia of Machine Learning and Data Mining","OA_type":"closed access","doi":"10.1007/978-1-4899-7502-7_892-1"},{"abstract":[{"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.","lang":"eng"}],"intvolume":"         5","publication":"ACS Synthetic Biology","publication_status":"published","title":"An orthogonal permease–inducer–repressor feedback loop shows bistability","day":"05","quality_controlled":"1","publist_id":"6390","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.","language":[{"iso":"eng"}],"author":[{"full_name":"Gnügge, Robert","last_name":"Gnügge","first_name":"Robert"},{"first_name":"Lekshmi","last_name":"Dharmarajan","full_name":"Dharmarajan, Lekshmi"},{"last_name":"Lang","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz"},{"last_name":"Stelling","first_name":"Jörg","full_name":"Stelling, Jörg"}],"isi":1,"article_processing_charge":"No","citation":{"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.","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>.","short":"R. Gnügge, L. Dharmarajan, M. Lang, J. Stelling, ACS Synthetic Biology 5 (2016) 1098–1107.","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>","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>","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.","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>."},"page":"1098 - 1107","month":"05","volume":5,"doi":"10.1021/acssynbio.6b00013","oa_version":"None","_id":"1008","department":[{"_id":"CaGu"}],"external_id":{"isi":["000386196100008"]},"date_updated":"2025-09-22T14:20:45Z","date_created":"2018-12-11T11:49:40Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2016-05-05T00:00:00Z","status":"public","issue":"10","year":"2016","publisher":"American Chemical Society","type":"journal_article"},{"volume":58,"scopus_import":"1","month":"08","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Wolfgang","last_name":"Dvorák","full_name":"Dvorák, Wolfgang"},{"last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H"},{"full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer","first_name":"Veronika"}],"project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"language":[{"iso":"eng"}],"citation":{"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>.","ieee":"K. Chatterjee, W. Dvorák, M. Henzinger, and V. Loitzenbauer, “Conditionally optimal algorithms for generalized Büchi Games,” presented at the MFCS: Mathematical Foundations of Computer Science, Krakow, Poland, 2016, vol. 58.","short":"K. Chatterjee, W. Dvorák, M. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika 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 M, Loitzenbauer V. 2016. Conditionally optimal algorithms for generalized Büchi Games. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 58, 25.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M., &#38; Loitzenbauer, V. (2016). Conditionally optimal algorithms for generalized Büchi Games (Vol. 58). Presented at the MFCS: Mathematical Foundations of Computer Science, 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>","ama":"Chatterjee K, Dvorák W, Henzinger M, 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>"},"article_processing_charge":"No","oa":1,"publist_id":"6317","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","day":"01","quality_controlled":"1","intvolume":"        58","abstract":[{"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}. ","lang":"eng"}],"has_accepted_license":"1","title":"Conditionally optimal algorithms for generalized Büchi Games","publication_status":"published","ec_funded":1,"type":"conference","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ddc":["000","004","006"],"conference":{"start_date":"2016-08-22","name":"MFCS: Mathematical Foundations of Computer Science","end_date":"2016-08-26","location":"Krakow, Poland"},"year":"2016","status":"public","pubrep_id":"779","date_published":"2016-08-01T00:00:00Z","date_created":"2018-12-11T11:49:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-07-10T11:49:55Z","department":[{"_id":"KrCh"}],"file_date_updated":"2018-12-12T10:16:02Z","oa_version":"Published Version","alternative_title":["LIPIcs"],"_id":"1068","article_number":"25","file":[{"relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:16:02Z","date_updated":"2018-12-12T10:16:02Z","access_level":"open_access","creator":"system","file_id":"5187","file_name":"IST-2017-779-v1+1_LIPIcs-MFCS-2016-25.pdf","file_size":632786}],"tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png","short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"doi":"10.4230/LIPIcs.MFCS.2016.25"},{"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).","oa":1,"publist_id":"6314","article_processing_charge":"No","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 für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">https://doi.org/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 für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">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.","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Skolem Problem for Continuous Linear Dynamical Systems,” Vol. 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">https://doi.org/10.4230/LIPIcs.ICALP.2016.100</a>.","short":"V.K. Chonev, J. Ouaknine, J. Worrell, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","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.","mla":"Chonev, Ventsislav K., et al. <i>On the Skolem Problem for Continuous Linear Dynamical Systems</i>. Vol. 55, 100, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">10.4230/LIPIcs.ICALP.2016.100</a>."},"author":[{"last_name":"Chonev","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Ventsislav K","full_name":"Chonev, Ventsislav K"},{"first_name":"Joël","last_name":"Ouaknine","full_name":"Ouaknine, Joël"},{"full_name":"Worrell, James","last_name":"Worrell","first_name":"James"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"volume":55,"month":"08","scopus_import":"1","ec_funded":1,"has_accepted_license":"1","publication_status":"published","title":"On the skolem problem for continuous linear dynamical systems","intvolume":"        55","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"}],"quality_controlled":"1","day":"01","date_created":"2018-12-11T11:49:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2016-08-01T00:00:00Z","pubrep_id":"778","conference":{"name":"ICALP: Automata, Languages and Programming","start_date":"2016-07-12","location":"Rome, Italy","end_date":"2016-07-15"},"year":"2016","ddc":["004","006"],"type":"conference","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","tmp":{"short":"CC BY (4.0)","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)"},"doi":"10.4230/LIPIcs.ICALP.2016.100","alternative_title":["LIPIcs"],"article_number":"100","_id":"1069","file":[{"relation":"main_file","date_created":"2018-12-12T10:16:26Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2018-12-12T10:16:26Z","creator":"system","file_size":521415,"file_name":"IST-2017-778-v1+1_LIPIcs-ICALP-2016-100.pdf","file_id":"5213"}],"file_date_updated":"2018-12-12T10:16:26Z","oa_version":"Published Version","department":[{"_id":"KrCh"}],"date_updated":"2025-06-03T11:32:08Z"},{"abstract":[{"lang":"eng","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. "}],"intvolume":"        55","has_accepted_license":"1","publication_status":"published","title":"Computation tree logic for synchronization properties","ec_funded":1,"day":"01","quality_controlled":"1","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"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.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Computation Tree Logic for Synchronization Properties</i>. Vol. 55, 98, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">10.4230/LIPIcs.ICALP.2016.98</a>.","short":"K. Chatterjee, L. Doyen, in:, Schloss Dagstuhl - Leibniz-Zentrum für 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 für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">https://doi.org/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 für Informatik. <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 für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">10.4230/LIPIcs.ICALP.2016.98</a>"},"article_processing_charge":"No","oa":1,"publist_id":"6313","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","volume":55,"month":"01","scopus_import":"1","file_date_updated":"2018-12-12T10:08:52Z","oa_version":"Published Version","alternative_title":["LIPIcs"],"article_number":"98","_id":"1070","file":[{"access_level":"open_access","date_updated":"2018-12-12T10:08:52Z","file_size":546133,"file_name":"IST-2017-812-v1+1_LIPIcs-ICALP-2016-98.pdf","file_id":"4714","creator":"system","relation":"main_file","date_created":"2018-12-12T10:08:52Z","content_type":"application/pdf"}],"doi":"10.4230/LIPIcs.ICALP.2016.98","tmp":{"short":"CC BY (4.0)","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)"},"date_updated":"2025-06-03T11:18:54Z","department":[{"_id":"KrCh"}],"status":"public","pubrep_id":"812","date_published":"2016-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:49:59Z","type":"conference","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ddc":["005"],"year":"2016","conference":{"end_date":"2016-07-15","location":"Rome, Italy","name":"ICALP: Automata, Languages and Programming","start_date":"2016-07-12"}},{"type":"conference","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","conference":{"end_date":"2016-08-24","location":"Aarhus, Denmark","name":"ESA: European Symposium on Algorithms","start_date":"2016-08-22"},"year":"2016","ddc":["004","006"],"status":"public","pubrep_id":"777","date_published":"2016-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:49:59Z","related_material":{"record":[{"id":"821","relation":"dissertation_contains","status":"public"}]},"date_updated":"2026-04-08T14:22:16Z","department":[{"_id":"KrCh"}],"alternative_title":["LIPIcs"],"_id":"1071","article_number":"28","file":[{"relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:14:31Z","date_updated":"2018-12-12T10:14:31Z","access_level":"open_access","creator":"system","file_id":"5084","file_size":579225,"file_name":"IST-2017-777-v1+1_LIPIcs-ESA-2016-28.pdf"}],"file_date_updated":"2018-12-12T10:14:31Z","oa_version":"Published Version","doi":"10.4230/LIPIcs.ESA.2016.28","tmp":{"short":"CC BY (4.0)","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)"},"volume":57,"scopus_import":"1","month":"08","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.","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 für 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 für Informatik. <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 für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">10.4230/LIPIcs.ESA.2016.28</a>","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 für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">https://doi.org/10.4230/LIPIcs.ESA.2016.28</a>.","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.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016."},"article_processing_charge":"No","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"last_name":"Pavlogiannis","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas"}],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"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"}],"language":[{"iso":"eng"}],"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).","oa":1,"publist_id":"6312","quality_controlled":"1","day":"01","has_accepted_license":"1","publication_status":"published","title":"Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs","intvolume":"        57","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"}],"ec_funded":1},{"file_date_updated":"2018-12-12T10:13:33Z","oa_version":"Published Version","article_number":"16018","_id":"1081","file":[{"date_created":"2018-12-12T10:13:33Z","content_type":"application/pdf","relation":"main_file","file_name":"IST-2017-757-v1+1_celldisc201618.pdf","file_size":5261671,"file_id":"5017","creator":"system","access_level":"open_access","date_updated":"2018-12-12T10:13:33Z"}],"doi":"10.1038/celldisc.2016.18","tmp":{"short":"CC BY (4.0)","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)"},"external_id":{"isi":["000414797400001"]},"date_updated":"2025-09-22T14:19:46Z","department":[{"_id":"EvBe"},{"_id":"JiFr"}],"status":"public","date_published":"2016-07-19T00:00:00Z","pubrep_id":"757","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:50:02Z","type":"journal_article","publisher":"Nature Publishing Group","ddc":["580"],"year":"2016","publication":"Cell Discovery","abstract":[{"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.","lang":"eng"}],"intvolume":"         2","has_accepted_license":"1","title":"Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells","publication_status":"published","ec_funded":1,"day":"19","quality_controlled":"1","author":[{"first_name":"Łukasz","last_name":"Łangowski","full_name":"Łangowski, Łukasz"},{"orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T","last_name":"Wabnik","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T"},{"full_name":"Li, Hongjiang","orcid":"0000-0001-5039-9660","first_name":"Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"full_name":"Naramoto, Satoshi","first_name":"Satoshi","last_name":"Naramoto"},{"last_name":"Tanaka","first_name":"Hirokazu","full_name":"Tanaka, Hirokazu"},{"full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","last_name":"Friml"}],"project":[{"grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"isi":1,"citation":{"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.","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>.","short":"Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J. Friml, Cell Discovery 2 (2016).","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>","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>."},"article_processing_charge":"No","oa":1,"publist_id":"6299","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.","volume":2,"scopus_import":"1","month":"07"},{"oa":1,"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.","author":[{"first_name":"Paul","last_name":"Rubel","full_name":"Rubel, Paul"},{"full_name":"Pani, Danilo","last_name":"Pani","first_name":"Danilo"},{"last_name":"Schlögl","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","full_name":"Schlögl, Alois"},{"first_name":"Jocelyne","last_name":"Fayn","full_name":"Fayn, Jocelyne"},{"full_name":"Badilini, Fabio","first_name":"Fabio","last_name":"Badilini"},{"last_name":"Macfarlane","first_name":"Peter","full_name":"Macfarlane, Peter"},{"full_name":"Varri, Alpo","first_name":"Alpo","last_name":"Varri"}],"language":[{"iso":"eng"}],"page":"309-312","article_processing_charge":"No","citation":{"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>","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>","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.","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>.","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.","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>.","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."},"volume":43,"scopus_import":"1","month":"03","publication_identifier":{"issn":["2325-887X"]},"publication":"2016 Computing in Cardiology Conference","intvolume":"        43","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"}],"publication_status":"published","title":"SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography","main_file_link":[{"url":"https://doi.org/10.22489/cinc.2016.090-500","open_access":"1"}],"day":"01","quality_controlled":"1","date_created":"2022-03-03T10:43:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_published":"2016-03-01T00:00:00Z","ddc":["000"],"year":"2016","conference":{"location":"Vancouver, Canada","end_date":"2016-09-14","start_date":"2016-09-11","name":"CinC: Computing in Cardiology"},"type":"conference","publisher":"Computing in Cardiology","doi":"10.22489/cinc.2016.090-500","oa_version":"Published Version","_id":"10810","department":[{"_id":"CampIT"}],"date_updated":"2026-06-18T08:48:07Z"},{"month":"09","scopus_import":"1","volume":28,"publication_identifier":{"isbn":["9780262339360"]},"oa":1,"article_processing_charge":"No","citation":{"ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>, Cancun, Mexico, 2016, vol. 28, pp. 142–143.","mla":"Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>, vol. 28, MIT Press, 2016, pp. 142–43, doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>.","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, 15th International Conference on the Synthesis and Simulation of Living Systems, MIT Press, 2016, pp. 142–143.","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. 15th International Conference on the Synthesis and Simulation of Living Systems. ALIFE 2016: Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.","chicago":"Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>, 28:142–43. MIT Press, 2016. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>.","apa":"Martius, G. S., Hostettler, R., Knoll, A., &#38; Der, R. (2016). Self-organized control of an tendon driven arm by differential extrinsic plasticity. In <i>15th International Conference on the Synthesis and Simulation of Living Systems</i> (Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>","ama":"Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon driven arm by differential extrinsic plasticity. In: <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>. Vol 28. MIT Press; 2016:142-143. doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>"},"page":"142-143","language":[{"iso":"eng"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"author":[{"full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","last_name":"Martius"},{"full_name":"Hostettler, Rafael","last_name":"Hostettler","first_name":"Rafael"},{"full_name":"Knoll, Alois","last_name":"Knoll","first_name":"Alois"},{"full_name":"Der, Ralf","last_name":"Der","first_name":"Ralf"}],"quality_controlled":"1","day":"01","ec_funded":1,"corr_author":"1","title":"Self-organized control of an tendon driven arm by differential extrinsic plasticity","publication_status":"published","has_accepted_license":"1","intvolume":"        28","abstract":[{"lang":"eng","text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with."}],"publication":"15th International Conference on the Synthesis and Simulation of Living Systems","conference":{"start_date":"2016-07-04","name":"ALIFE 2016: Conference on the Synthesis and Simulation of Living Systems","end_date":"2016-07-08","location":"Cancun, Mexico"},"year":"2016","ddc":["610"],"publisher":"MIT Press","type":"conference","date_created":"2020-07-05T22:00:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2016-09-01T00:00:00Z","status":"public","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"date_updated":"2025-07-10T11:55:05Z","tmp":{"short":"CC BY (4.0)","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)"},"doi":"10.7551/978-0-262-33936-0-ch029","_id":"8094","file":[{"content_type":"application/pdf","date_created":"2020-07-06T12:59:09Z","relation":"main_file","creator":"cziletti","file_id":"8096","file_name":"2016_ProcALIFE_Martius.pdf","file_size":678670,"checksum":"cff63e7a4b8ac466ba51a9c84153a940","date_updated":"2020-07-14T12:48:09Z","access_level":"open_access"}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:48:09Z"},{"external_id":{"pmid":["27760113"]},"date_updated":"2021-12-14T07:55:30Z","extern":"1","department":[{"_id":"DaZi"}],"oa_version":"Submitted Version","_id":"9456","doi":"10.1038/nature20110","type":"journal_article","article_type":"letter_note","publisher":"Springer Nature ","issue":"7626","pmid":1,"year":"2016","status":"public","date_published":"2016-10-27T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2021-06-04T11:34:55Z","day":"27","quality_controlled":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/","open_access":"1"}],"publication":"Nature","intvolume":"       538","abstract":[{"text":"The discovery of introns four decades ago was one of the most unexpected findings in molecular biology. Introns are sequences interrupting genes that must be removed as part of messenger RNA production. Genome sequencing projects have shown that most eukaryotic genes contain at least one intron, and frequently many. Comparison of these genomes reveals a history of long evolutionary periods during which few introns were gained, punctuated by episodes of rapid, extensive gain. However, although several detailed mechanisms for such episodic intron generation have been proposed, none has been empirically supported on a genomic scale. Here we show how short, non-autonomous DNA transposons independently generated hundreds to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte Aureococcus anophagefferens. Each transposon carries one splice site. The other splice site is co-opted from the gene sequence that is duplicated upon transposon insertion, allowing perfect splicing out of the RNA. The distributions of sequences that can be co-opted are biased with respect to codons, and phasing of transposon-generated introns is similarly biased. These transposons insert between pre-existing nucleosomes, so that multiple nearby insertions generate nucleosome-sized intervening segments. Thus, transposon insertion and sequence co-option may explain the intron phase biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall, the two independent examples of proliferating elements illustrate a general DNA transposon mechanism that can plausibly account for episodes of rapid, extensive intron gain during eukaryotic evolution.","lang":"eng"}],"title":"Mechanism for DNA transposons to generate introns on genomic scales","publication_status":"published","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"volume":538,"scopus_import":"1","month":"10","author":[{"first_name":"Jason T.","last_name":"Huff","full_name":"Huff, Jason T."},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"},{"last_name":"Roy","first_name":"Scott W.","full_name":"Roy, Scott W."}],"language":[{"iso":"eng"}],"page":"533-536","citation":{"chicago":"Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>. Springer Nature , 2016. <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>.","ista":"Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate introns on genomic scales. Nature. 538(7626), 533–536.","ama":"Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. 2016;538(7626):533-536. doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>","apa":"Huff, J. T., Zilberman, D., &#38; Roy, S. W. (2016). Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. Springer Nature . <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>","short":"J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.","mla":"Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>, vol. 538, no. 7626, Springer Nature , 2016, pp. 533–36, doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>.","ieee":"J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to generate introns on genomic scales,” <i>Nature</i>, vol. 538, no. 7626. Springer Nature , pp. 533–536, 2016."},"article_processing_charge":"No","oa":1},{"date_published":"2016-12-27T00:00:00Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-06-07T06:21:39Z","publisher":"National Academy of Sciences","article_type":"original","type":"journal_article","year":"2016","pmid":1,"issue":"52","_id":"9473","oa_version":"Published Version","doi":"10.1073/pnas.1619074114","extern":"1","date_updated":"2023-05-08T11:00:40Z","external_id":{"pmid":["27956643"]},"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"citation":{"ama":"Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15132-15137. doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>","apa":"Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L., … Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>","ista":"Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 113(52), 15132–15137.","chicago":"Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman, Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>.","short":"P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman, X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.","ieee":"P.-H. Hsieh <i>et al.</i>, “Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15132–15137, 2016.","mla":"Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15132–37, doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>."},"article_processing_charge":"No","page":"15132-15137","language":[{"iso":"eng"}],"author":[{"full_name":"Hsieh, Ping-Hung","last_name":"Hsieh","first_name":"Ping-Hung"},{"last_name":"He","first_name":"Shengbo","full_name":"He, Shengbo"},{"first_name":"Toby","last_name":"Buttress","full_name":"Buttress, Toby"},{"last_name":"Gao","first_name":"Hongbo","full_name":"Gao, Hongbo"},{"full_name":"Couchman, Matthew","last_name":"Couchman","first_name":"Matthew"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"}],"oa":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"scopus_import":"1","month":"12","volume":113,"publication_status":"published","title":"Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues","abstract":[{"lang":"eng","text":"Cytosine DNA methylation regulates the expression of eukaryotic genes and transposons. Methylation is copied by methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Transgenerational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of transgenerational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases. We find that DNA methylation dependency on these enzymes is similar in sperm, vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin in vegetative cells, likely reflecting transcription of heterochromatic transposons in this cell type. We also show that lack of histone H1, which elevates heterochromatic DNA methylation in somatic tissues, does not have this effect in pollen. Instead, levels of CG methylation in wild-type sperm and vegetative cells, as well as in wild-type microspores from which both pollen cell types originate, are substantially higher than in wild-type somatic tissues and similar to those of H1-depleted roots. Our results demonstrate that the mechanisms of methylation maintenance are similar between pollen and somatic cells, but the efficiency of CG methylation is higher in pollen, allowing methylation patterns to be accurately inherited across generations."}],"intvolume":"       113","publication":"Proceedings of the National Academy of Sciences","quality_controlled":"1","day":"27","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1619074114","open_access":"1"}]},{"publication_status":"published","title":"DNA demethylation is initiated in the central cells of Arabidopsis and rice","abstract":[{"lang":"eng","text":"Cytosine methylation is a DNA modification with important regulatory functions in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive DNA demethylation, which is required for proper gene expression in the endosperm, a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm cell carried in the pollen and a female central cell. Endosperm DNA demethylation is observed specifically on the chromosomes inherited from the central cell in Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase in Arabidopsis. DEMETER is expressed in the central cell before fertilization, suggesting that endosperm demethylation patterns are inherited from the central cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed to contribute to central cell demethylation. However, with the exception of three maize genes, central cell DNA methylation has not been directly measured, leaving the origin and mechanism of endosperm demethylation uncertain. Here, we report genome-wide analysis of DNA methylation in the central cells of Arabidopsis and rice—species that diverged 150 million years ago—as well as in rice egg cells. We find that DNA demethylation in both species is initiated in central cells, which requires DEMETER in Arabidopsis. However, we do not observe a global reduction of CG methylation that would be indicative of lowered MET1 activity; on the contrary, CG methylation efficiency is elevated in female gametes compared with nonsexual tissues. Our results demonstrate that locus-specific, active DNA demethylation in the central cell is the origin of maternal chromosome hypomethylation in the endosperm."}],"intvolume":"       113","publication":"Proceedings of the National Academy of Sciences","quality_controlled":"1","day":"27","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1619047114","open_access":"1"}],"citation":{"ieee":"K. Park <i>et al.</i>, “DNA demethylation is initiated in the central cells of Arabidopsis and rice,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.","mla":"Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>.","ista":"Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 113(52), 15138–15143.","chicago":"Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun, Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>.","ama":"Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15138-15143. doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>","apa":"Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten, S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>","short":"K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman, R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy of Sciences 113 (2016) 15138–15143."},"article_processing_charge":"No","page":"15138-15143","language":[{"iso":"eng"}],"author":[{"first_name":"Kyunghyuk","last_name":"Park","full_name":"Park, Kyunghyuk"},{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"full_name":"Vickers, Martin","last_name":"Vickers","first_name":"Martin"},{"full_name":"Park, Jin-Sup","first_name":"Jin-Sup","last_name":"Park"},{"full_name":"Hyun, Youbong","last_name":"Hyun","first_name":"Youbong"},{"full_name":"Okamoto, Takashi","last_name":"Okamoto","first_name":"Takashi"},{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."},{"last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi"},{"last_name":"Choi","first_name":"Yeonhee","full_name":"Choi, Yeonhee"},{"first_name":"Stefan","last_name":"Scholten","full_name":"Scholten, Stefan"}],"oa":1,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"month":"12","scopus_import":"1","volume":113,"_id":"9477","oa_version":"Published Version","doi":"10.1073/pnas.1619047114","extern":"1","date_updated":"2023-05-08T11:00:07Z","external_id":{"pmid":["27956642"]},"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"date_published":"2016-12-27T00:00:00Z","status":"public","keyword":["Multidisciplinary"],"date_created":"2021-06-07T07:10:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"National Academy of Sciences","article_type":"original","type":"journal_article","year":"2016","pmid":1,"issue":"52"},{"oa_version":"None","_id":"948","alternative_title":["Advances in Neural Information Processing Systems"],"date_updated":"2025-06-03T11:18:32Z","department":[{"_id":"GaTk"}],"date_published":"2016-01-01T00:00:00Z","status":"public","date_created":"2018-12-11T11:49:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Neural Information Processing Systems Foundation","type":"conference","year":"2016","conference":{"start_date":"2016-12-05","name":"NIPS: Neural Information Processing Systems","end_date":"2016-12-10","location":"Barcelona, Spaine"},"abstract":[{"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.","lang":"eng"}],"intvolume":"        29","publication_status":"published","title":"Neurons equipped with intrinsic plasticity learn stimulus intensity statistics","ec_funded":1,"day":"01","quality_controlled":"1","main_file_link":[{"url":"https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics","open_access":"1"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Monk, Travis","last_name":"Monk","first_name":"Travis"},{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","last_name":"Savin","full_name":"Savin, Cristina"},{"full_name":"Lücke, Jörg","first_name":"Jörg","last_name":"Lücke"}],"citation":{"short":"T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems Foundation, 2016, pp. 4285–4293.","chicago":"Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems Foundation, 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.","ama":"Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems Foundation; 2016:4285-4293.","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 Foundation.","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.","mla":"Monk, Travis, et al. <i>Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics</i>. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 4285–93."},"article_processing_charge":"No","page":"4285 - 4293","publist_id":"6469","oa":1,"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)","month":"01","scopus_import":"1","volume":29},{"year":"2016","month":"05","type":"research_data_reference","publisher":"Dryad","oa":1,"date_created":"2021-07-23T08:30:38Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","date_published":"2016-05-06T00:00:00Z","article_processing_charge":"No","citation":{"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>","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>","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>.","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>.","short":"D. Mcmahon, M. Natsopoulou, V. Doublet, M. Fürst, S. Weging, M. Brown, A. Gogol Döring, R. Paxton, (2016).","ieee":"D. Mcmahon <i>et al.</i>, “Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss.” Dryad, 2016.","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>."},"author":[{"full_name":"Mcmahon, Dino","last_name":"Mcmahon","first_name":"Dino"},{"last_name":"Natsopoulou","first_name":"Myrsini","full_name":"Natsopoulou, Myrsini"},{"full_name":"Doublet, Vincent","first_name":"Vincent","last_name":"Doublet"},{"full_name":"Fürst, Matthias","orcid":"0000-0002-3712-925X","first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","last_name":"Fürst"},{"first_name":"Silvio","last_name":"Weging","full_name":"Weging, Silvio"},{"last_name":"Brown","first_name":"Mark","full_name":"Brown, Mark"},{"full_name":"Gogol Döring, Andreas","first_name":"Andreas","last_name":"Gogol Döring"},{"first_name":"Robert","last_name":"Paxton","full_name":"Paxton, Robert"}],"department":[{"_id":"SyCr"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.cq7t1"}],"date_updated":"2025-09-22T08:59:29Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1262"}]},"day":"06","doi":"10.5061/dryad.cq7t1","_id":"9704","title":"Data from: Elevated virulence of an emerging viral genotype as a driver of honeybee loss","oa_version":"Published Version","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"}]},{"department":[{"_id":"NiBa"}],"main_file_link":[{"url":"https://doi.org/10.5061/dryad.s5s7r","open_access":"1"}],"day":"23","date_updated":"2025-04-15T07:11:02Z","related_material":{"record":[{"relation":"used_in_publication","id":"1199","status":"public"}]},"doi":"10.5061/dryad.s5s7r","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."}],"oa_version":"Published Version","title":"Data from: How does epistasis influence the response to selection?","_id":"9710","year":"2016","month":"09","type":"research_data_reference","publisher":"Dryad","oa":1,"date_created":"2021-07-23T11:45:47Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"status":"public","citation":{"short":"N.H. Barton, (2016).","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>","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>","chicago":"Barton, Nicholas H. “Data from: How Does Epistasis Influence the Response to Selection?” Dryad, 2016. <a href=\"https://doi.org/10.5061/dryad.s5s7r\">https://doi.org/10.5061/dryad.s5s7r</a>.","ista":"Barton NH. 2016. Data from: How does epistasis influence the response to selection?, Dryad, <a href=\"https://doi.org/10.5061/dryad.s5s7r\">10.5061/dryad.s5s7r</a>.","ieee":"N. H. Barton, “Data from: How does epistasis influence the response to selection?” Dryad, 2016.","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>."},"date_published":"2016-09-23T00:00:00Z","article_processing_charge":"No"},{"doi":"10.5061/dryad.4b565","oa_version":"Published Version","abstract":[{"text":"Summary: Declining populations of bee pollinators are a cause of concern, with major repercussions for biodiversity loss and food security. RNA viruses associated with honeybees represent a potential threat to other insect pollinators, but the extent of this threat is poorly understood. This study aims to attain a detailed understanding of the current and ongoing risk of emerging infectious disease (EID) transmission between managed and wild pollinator species across a wide range of RNA viruses. Within a structured large-scale national survey across 26 independent sites, we quantify the prevalence and pathogen loads of multiple RNA viruses in co-occurring managed honeybee (Apis mellifera) and wild bumblebee (Bombus spp.) populations. We then construct models that compare virus prevalence between wild and managed pollinators. Multiple RNA viruses associated with honeybees are widespread in sympatric wild bumblebee populations. Virus prevalence in honeybees is a significant predictor of virus prevalence in bumblebees, but we remain cautious in speculating over the principle direction of pathogen transmission. We demonstrate species-specific differences in prevalence, indicating significant variation in disease susceptibility or tolerance. Pathogen loads within individual bumblebees may be high and in the case of at least one RNA virus, prevalence is higher in wild bumblebees than in managed honeybee populations. Our findings indicate widespread transmission of RNA viruses between managed and wild bee pollinators, pointing to an interconnected network of potential disease pressures within and among pollinator species. In the context of the biodiversity crisis, our study emphasizes the importance of targeting a wide range of pathogens and defining host associations when considering potential drivers of population decline.","lang":"eng"}],"title":"Data from: A sting in the spit: widespread cross-infection of multiple RNA viruses across wild and managed bees","_id":"9720","main_file_link":[{"url":"https://doi.org/10.5061/dryad.4b565","open_access":"1"}],"department":[{"_id":"SyCr"}],"day":"22","date_updated":"2025-09-23T07:26:23Z","related_material":{"record":[{"relation":"used_in_publication","id":"1855","status":"public"}]},"date_created":"2021-07-26T09:14:19Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","oa":1,"author":[{"last_name":"Mcmahon","first_name":"Dino","full_name":"Mcmahon, Dino"},{"last_name":"Fürst","first_name":"Matthias","id":"393B1196-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3712-925X","full_name":"Fürst, Matthias"},{"first_name":"Jesicca","last_name":"Caspar","full_name":"Caspar, Jesicca"},{"last_name":"Theodorou","first_name":"Panagiotis","full_name":"Theodorou, Panagiotis"},{"first_name":"Mark","last_name":"Brown","full_name":"Brown, Mark"},{"first_name":"Robert","last_name":"Paxton","full_name":"Paxton, Robert"}],"article_processing_charge":"No","citation":{"short":"D. Mcmahon, M. Fürst, J. Caspar, P. Theodorou, M. Brown, R. Paxton, (2016).","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>","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>","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>.","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."},"date_published":"2016-01-22T00:00:00Z","status":"public","month":"01","year":"2016","publisher":"Dryad","type":"research_data_reference"},{"title":"Simulation study to test the robustness of ABC in face of recent times of divergence","_id":"9862","oa_version":"Published Version","doi":"10.1371/journal.pbio.2000234.s016","date_updated":"2025-09-22T09:55:08Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1158"}]},"day":"27","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"citation":{"ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Simulation study to test the robustness of ABC in face of recent times of divergence. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Simulation study to test the robustness of ABC in face of recent times of divergence. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>","chicago":"Roux, Camille, Christelle Fraisse, Jonathan Romiguier, Youann Anciaux, Nicolas Galtier, and Nicolas Bierne. “Simulation Study to Test the Robustness of ABC in Face of Recent Times of Divergence.” Public Library of Science, 2016. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">https://doi.org/10.1371/journal.pbio.2000234.s016</a>.","ista":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. 2016. Simulation study to test the robustness of ABC in face of recent times of divergence, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s016\">10.1371/journal.pbio.2000234.s016</a>.","short":"C. Roux, C. Fraisse, J. Romiguier, Y. Anciaux, N. Galtier, N. Bierne, (2016).","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>.","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."},"article_processing_charge":"No","status":"public","author":[{"full_name":"Roux, Camille","first_name":"Camille","last_name":"Roux"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jonathan","last_name":"Romiguier","full_name":"Romiguier, Jonathan"},{"last_name":"Anciaux","first_name":"Youann","full_name":"Anciaux, Youann"},{"last_name":"Galtier","first_name":"Nicolas","full_name":"Galtier, Nicolas"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"date_created":"2021-08-10T08:20:17Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","type":"research_data_reference","month":"12","year":"2016"},{"type":"research_data_reference","publisher":"Public Library of Science","year":"2016","month":"12","author":[{"first_name":"Camille","last_name":"Roux","full_name":"Roux, Camille"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Romiguier, Jonathan","first_name":"Jonathan","last_name":"Romiguier"},{"last_name":"Anciaux","first_name":"Youann","full_name":"Anciaux, Youann"},{"full_name":"Galtier, Nicolas","first_name":"Nicolas","last_name":"Galtier"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"status":"public","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>.","ama":"Roux C, Fraisse C, Romiguier J, Anciaux Y, Galtier N, Bierne N. Accessions of surveyed individuals, geographic locations and summary statistics. 2016. doi:<a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">10.1371/journal.pbio.2000234.s017</a>","apa":"Roux, C., Fraisse, C., Romiguier, J., Anciaux, Y., Galtier, N., &#38; Bierne, N. (2016). Accessions of surveyed individuals, geographic locations and summary statistics. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.2000234.s017\">https://doi.org/10.1371/journal.pbio.2000234.s017</a>","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>."},"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-08-10T08:22:52Z","day":"27","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1158"}]},"date_updated":"2025-09-22T09:55:09Z","department":[{"_id":"BeVi"},{"_id":"NiBa"}],"oa_version":"Published Version","title":"Accessions of surveyed individuals, geographic locations and summary statistics","_id":"9863","doi":"10.1371/journal.pbio.2000234.s017"},{"month":"12","year":"2016","publisher":"The Royal Society","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-08-10T08:29:47Z","oa":1,"article_processing_charge":"No","citation":{"short":"R.A. Fernandes Redondo, H. de Vladar, T. Włodarski, J.P. Bollback, (2016).","ista":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. 2016. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family, The Royal Society, <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>.","chicago":"Fernandes Redondo, Rodrigo A, Harold de Vladar, Tomasz Włodarski, and Jonathan P Bollback. “Data from Evolutionary Interplay between Structure, Energy and Epistasis in the Coat Protein of the ΦX174 Phage Family.” The Royal Society, 2016. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>.","ama":"Fernandes Redondo RA, de Vladar H, Włodarski T, Bollback JP. Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. 2016. doi:<a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">10.6084/m9.figshare.4315652.v1</a>","apa":"Fernandes Redondo, R. A., de Vladar, H., Włodarski, T., &#38; Bollback, J. P. (2016). Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. The Royal Society. <a href=\"https://doi.org/10.6084/m9.figshare.4315652.v1\">https://doi.org/10.6084/m9.figshare.4315652.v1</a>","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.","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>."},"date_published":"2016-12-14T00:00:00Z","status":"public","author":[{"orcid":"0000-0002-5837-2793","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","first_name":"Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87"},{"last_name":"de Vladar","id":"2A181218-F248-11E8-B48F-1D18A9856A87","first_name":"Harold","orcid":"0000-0002-5985-7653","full_name":"de Vladar, Harold"},{"first_name":"Tomasz","last_name":"Włodarski","full_name":"Włodarski, Tomasz"},{"id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","last_name":"Bollback","full_name":"Bollback, Jonathan P","orcid":"0000-0002-4624-4612"}],"main_file_link":[{"url":"https://doi.org/10.6084/m9.figshare.4315652.v1","open_access":"1"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"related_material":{"record":[{"relation":"used_in_publication","id":"1077","status":"public"}]},"date_updated":"2025-07-10T11:49:59Z","day":"14","doi":"10.6084/m9.figshare.4315652.v1","_id":"9864","title":"Data from evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family","oa_version":"Published Version","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"}]}]