[{"publist_id":"4599","file_date_updated":"2020-07-14T12:45:38Z","title":"From model checking to model measuring","author":[{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Otop","full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"related_material":{"record":[{"id":"5417","relation":"earlier_version","status":"public"}]},"month":"08","scopus_import":"1","citation":{"ama":"Henzinger TA, Otop J. From model checking to model measuring. 2013;8052:273-287. doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_20\">10.1007/978-3-642-40184-8_20</a>","apa":"Henzinger, T. A., &#38; Otop, J. (2013). From model checking to model measuring. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Springer. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_20\">https://doi.org/10.1007/978-3-642-40184-8_20</a>","short":"T.A. Henzinger, J. Otop, 8052 (2013) 273–287.","ieee":"T. A. Henzinger and J. Otop, “From model checking to model measuring,” vol. 8052. Springer, pp. 273–287, 2013.","mla":"Henzinger, Thomas A., and Jan Otop. <i>From Model Checking to Model Measuring</i>. Vol. 8052, Springer, 2013, pp. 273–87, doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_20\">10.1007/978-3-642-40184-8_20</a>.","chicago":"Henzinger, Thomas A, and Jan Otop. “From Model Checking to Model Measuring.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_20\">https://doi.org/10.1007/978-3-642-40184-8_20</a>.","ista":"Henzinger TA, Otop J. 2013. From model checking to model measuring. 8052, 273–287."},"pubrep_id":"129","conference":{"location":"Buenos Aires, Argentina","end_date":"2013-08-30","start_date":"2013-08-27","name":"CONCUR: Concurrency Theory"},"publisher":"Springer","oa":1,"status":"public","has_accepted_license":"1","oa_version":"Submitted Version","year":"2013","page":"273 - 287","date_created":"2018-12-11T11:57:00Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We define the model-measuring problem: given a model M and specification φ, what is the maximal distance ρ such that all models M′ within distance ρ from M satisfy (or violate) φ. The model measuring problem presupposes a distance function on models. We concentrate on automatic distance functions, which are defined by weighted automata. The model-measuring problem subsumes several generalizations of the classical model-checking problem, in particular, quantitative model-checking problems that measure the degree of satisfaction of a specification, and robustness problems that measure how much a model can be perturbed without violating the specification. We show that for automatic distance functions, and ω-regular linear-time and branching-time specifications, the model-measuring problem can be solved. We use automata-theoretic model-checking methods for model measuring, replacing the emptiness question for standard word and tree automata by the optimal-weight question for the weighted versions of these automata. We consider weighted automata that accumulate weights by maximizing, summing, discounting, and limit averaging. We give several examples of using the model-measuring problem to compute various notions of robustness and quantitative satisfaction for temporal specifications."}],"alternative_title":["LNCS"],"day":"01","ddc":["005","000"],"series_title":"Lecture Notes in Computer Science","doi":"10.1007/978-3-642-40184-8_20","intvolume":"      8052","publication_status":"published","volume":8052,"quality_controlled":"1","date_published":"2013-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2327","date_updated":"2024-10-21T06:02:58Z","file":[{"relation":"main_file","content_type":"application/pdf","file_size":378587,"access_level":"open_access","checksum":"4c04695c4bfdf2119cd4f5d1babc3e8a","date_created":"2018-12-12T10:17:45Z","date_updated":"2020-07-14T12:45:38Z","file_name":"IST-2013-129-v1+1_concur.pdf","creator":"system","file_id":"5301"}],"department":[{"_id":"ToHe"}],"corr_author":"1","type":"conference"},{"month":"08","related_material":{"record":[{"status":"public","relation":"later_version","id":"717"}]},"author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yaron","full_name":"Velner, Yaron","last_name":"Velner"}],"citation":{"apa":"Chatterjee, K., &#38; Velner, Y. (2013). Hyperplane separation technique for multidimensional mean-payoff games. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentinia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_35\">https://doi.org/10.1007/978-3-642-40184-8_35</a>","ama":"Chatterjee K, Velner Y. Hyperplane separation technique for multidimensional mean-payoff games. 2013;8052:500-515. doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_35\">10.1007/978-3-642-40184-8_35</a>","ieee":"K. Chatterjee and Y. Velner, “Hyperplane separation technique for multidimensional mean-payoff games,” vol. 8052. Springer, pp. 500–515, 2013.","short":"K. Chatterjee, Y. Velner, 8052 (2013) 500–515.","chicago":"Chatterjee, Krishnendu, and Yaron Velner. “Hyperplane Separation Technique for Multidimensional Mean-Payoff Games.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_35\">https://doi.org/10.1007/978-3-642-40184-8_35</a>.","ista":"Chatterjee K, Velner Y. 2013. Hyperplane separation technique for multidimensional mean-payoff games. 8052, 500–515.","mla":"Chatterjee, Krishnendu, and Yaron Velner. <i>Hyperplane Separation Technique for Multidimensional Mean-Payoff Games</i>. Vol. 8052, Springer, 2013, pp. 500–15, doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_35\">10.1007/978-3-642-40184-8_35</a>."},"scopus_import":1,"ec_funded":1,"conference":{"start_date":"2013-08-27","end_date":"2013-08-30","location":"Buenos Aires, Argentinia","name":"CONCUR: Concurrency Theory"},"publisher":"Springer","publist_id":"4597","title":"Hyperplane separation technique for multidimensional mean-payoff games","oa_version":"Preprint","oa":1,"status":"public","doi":"10.1007/978-3-642-40184-8_35","intvolume":"      8052","publication_status":"published","series_title":"Lecture Notes in Computer Science","volume":8052,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1210.3141"}],"external_id":{"arxiv":["1210.3141"]},"date_created":"2018-12-11T11:57:01Z","page":"500 - 515","year":"2013","day":"01","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work, we consider both finite-state game graphs, and recursive game graphs (or pushdown game graphs) that model the control flow of sequential programs with recursion. The objectives we study are multidimensional mean-payoff objectives, where the goal of player 1 is to ensure that the mean-payoff is non-negative in all dimensions. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation. Our main contributions are as follows: (1) We show that finite-state multidimensional mean-payoff games can be solved in polynomial time if the number of dimensions and the maximal absolute value of the weights are fixed; whereas if the number of dimensions is arbitrary, then the problem is known to be coNP-complete. (2) We show that pushdown graphs with multidimensional mean-payoff objectives can be solved in polynomial time. For both (1) and (2) our algorithms are based on hyperplane separation technique. (3) For pushdown games under global strategies both one and multidimensional mean-payoff objectives problems are known to be undecidable, and we show that under modular strategies the multidimensional problem is also undecidable; under modular strategies the one-dimensional problem is NP-complete. We show that if the number of modules, the number of exits, and the maximal absolute value of the weights are fixed, then pushdown games under modular strategies with one-dimensional mean-payoff objectives can be solved in polynomial time, and if either the number of exits or the number of modules is unbounded, then the problem is NP-hard. (4) Finally we show that a fixed parameter tractable algorithm for finite-state multidimensional mean-payoff games or pushdown games under modular strategies with one-dimensional mean-payoff objectives would imply the fixed parameter tractability of parity games."}],"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"department":[{"_id":"KrCh"}],"arxiv":1,"type":"conference","date_published":"2013-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","_id":"2329","date_updated":"2025-09-10T11:00:30Z"},{"file":[{"date_updated":"2020-07-14T12:45:40Z","file_name":"IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf","checksum":"0751ec74b695567e0cdf02aaf9c26829","date_created":"2018-12-12T10:17:36Z","creator":"system","file_id":"5291","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":130026}],"date_updated":"2024-10-09T20:55:15Z","_id":"2410","date_published":"2013-06-13T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","type":"journal_article","corr_author":"1","department":[{"_id":"JoBo"},{"_id":"LifeSc"}],"day":"13","abstract":[{"lang":"eng","text":"Here, we describe a novel virulent bacteriophage that infects Bacillus weihenstephanensis, isolated from soil in Austria. It is the first phage to be discovered that infects this species. Here, we present the complete genome sequence of this podovirus. "}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:57:30Z","year":"2013","volume":1,"intvolume":"         1","doi":"10.1128/genomeA.00216-13","publication_status":"published","ddc":["576"],"status":"public","oa":1,"oa_version":"Published Version","has_accepted_license":"1","title":"Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis","file_date_updated":"2020-07-14T12:45:40Z","issue":"3","publist_id":"4516","publication":"Genome Announcements","publisher":"American Society for Microbiology","pubrep_id":"398","citation":{"mla":"Fernandes Redondo, Rodrigo A., et al. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” <i>Genome Announcements</i>, vol. 1, no. 3, American Society for Microbiology, 2013, doi:<a href=\"https://doi.org/10.1128/genomeA.00216-13\">10.1128/genomeA.00216-13</a>.","chicago":"Fernandes Redondo, Rodrigo A, Anne Kupczok, Gertraud Stift, and Jonathan P Bollback. “Complete Genome Sequence of the Novel Phage MG-B1 Infecting Bacillus Weihenstephanensis.” <i>Genome Announcements</i>. American Society for Microbiology, 2013. <a href=\"https://doi.org/10.1128/genomeA.00216-13\">https://doi.org/10.1128/genomeA.00216-13</a>.","ista":"Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. 2013. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. Genome Announcements. 1(3).","short":"R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013).","ieee":"R. A. Fernandes Redondo, A. Kupczok, G. Stift, and J. P. Bollback, “Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis,” <i>Genome Announcements</i>, vol. 1, no. 3. American Society for Microbiology, 2013.","ama":"Fernandes Redondo RA, Kupczok A, Stift G, Bollback JP. Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. <i>Genome Announcements</i>. 2013;1(3). doi:<a href=\"https://doi.org/10.1128/genomeA.00216-13\">10.1128/genomeA.00216-13</a>","apa":"Fernandes Redondo, R. A., Kupczok, A., Stift, G., &#38; Bollback, J. P. (2013). Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis. <i>Genome Announcements</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/genomeA.00216-13\">https://doi.org/10.1128/genomeA.00216-13</a>"},"scopus_import":1,"month":"06","author":[{"orcid":"0000-0002-5837-2793","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","first_name":"Rodrigo A","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo"},{"last_name":"Kupczok","full_name":"Kupczok, Anne","first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"},{"id":"2DB195CA-F248-11E8-B48F-1D18A9856A87","first_name":"Gertraud","full_name":"Stift, Gertraud","last_name":"Stift"},{"last_name":"Bollback","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87"}]},{"department":[{"_id":"JoBo"}],"corr_author":"1","type":"journal_article","quality_controlled":"1","date_published":"2013-02-26T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2412","date_updated":"2025-09-29T14:15:59Z","file":[{"file_size":518729,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5268","creator":"system","date_created":"2018-12-12T10:17:15Z","checksum":"029c7e0b198c19312b66ecce3cabb22f","file_name":"IST-2015-397-v1+1_1471-2148-13-54.pdf","date_updated":"2020-07-14T12:45:40Z"}],"ddc":["576"],"doi":"10.1186/1471-2148-13-54","publication_status":"published","intvolume":"        13","volume":13,"external_id":{"isi":["000321524500001"]},"year":"2013","date_created":"2018-12-11T11:57:31Z","page":"54 - 54","abstract":[{"text":"Background: The CRISPR/Cas system is known to act as an adaptive and heritable immune system in Eubacteria and Archaea. Immunity is encoded in an array of spacer sequences. Each spacer can provide specific immunity to invasive elements that carry the same or a similar sequence. Even in closely related strains, spacer content is very dynamic and evolves quickly. Standard models of nucleotide evolutioncannot be applied to quantify its rate of change since processes other than single nucleotide changes determine its evolution.Methods We present probabilistic models that are specific for spacer content evolution. They account for the different processes of insertion and deletion. Insertions can be constrained to occur on one end only or are allowed to occur throughout the array. One deletion event can affect one spacer or a whole fragment of adjacent spacers. Parameters of the underlying models are estimated for a pair of arrays by maximum likelihood using explicit ancestor enumeration.Results Simulations show that parameters are well estimated on average under the models presented here. There is a bias in the rate estimation when including fragment deletions. The models also estimate times between pairs of strains. But with increasing time, spacer overlap goes to zero, and thus there is an upper bound on the distance that can be estimated. Spacer content similarities are displayed in a distance based phylogeny using the estimated times.We use the presented models to analyze different Yersinia pestis data sets and find that the results among them are largely congruent. The models also capture the variation in diversity of spacers among the data sets. A comparison of spacer-based phylogenies and Cas gene phylogenies shows that they resolve very different time scales for this data set.Conclusions The simulations and data analyses show that the presented models are useful for quantifying spacer content evolution and for displaying spacer content similarities of closely related strains in a phylogeny. This allows for comparisons of different CRISPR arrays or for comparisons between CRISPR arrays and nucleotide substitution rates.","lang":"eng"}],"language":[{"iso":"eng"}],"day":"26","has_accepted_license":"1","oa_version":"Published Version","oa":1,"status":"public","author":[{"full_name":"Kupczok, Anne","last_name":"Kupczok","first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jonathan P","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","full_name":"Bollback, Jonathan P"}],"month":"02","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","pubrep_id":"397","citation":{"ieee":"A. Kupczok and J. P. Bollback, “Probabilistic models for CRISPR spacer content evolution ,” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1. BioMed Central, pp. 54–54, 2013.","short":"A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54.","ama":"Kupczok A, Bollback JP. Probabilistic models for CRISPR spacer content evolution . <i>BMC Evolutionary Biology</i>. 2013;13(1):54-54. doi:<a href=\"https://doi.org/10.1186/1471-2148-13-54\">10.1186/1471-2148-13-54</a>","apa":"Kupczok, A., &#38; Bollback, J. P. (2013). Probabilistic models for CRISPR spacer content evolution . <i>BMC Evolutionary Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2148-13-54\">https://doi.org/10.1186/1471-2148-13-54</a>","mla":"Kupczok, Anne, and Jonathan P. Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” <i>BMC Evolutionary Biology</i>, vol. 13, no. 1, BioMed Central, 2013, pp. 54–54, doi:<a href=\"https://doi.org/10.1186/1471-2148-13-54\">10.1186/1471-2148-13-54</a>.","chicago":"Kupczok, Anne, and Jonathan P Bollback. “Probabilistic Models for CRISPR Spacer Content Evolution .” <i>BMC Evolutionary Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2148-13-54\">https://doi.org/10.1186/1471-2148-13-54</a>.","ista":"Kupczok A, Bollback JP. 2013. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 13(1), 54–54."},"publisher":"BioMed Central","isi":1,"publication":"BMC Evolutionary Biology","publist_id":"4514","file_date_updated":"2020-07-14T12:45:40Z","issue":"1","article_processing_charge":"No","title":"Probabilistic models for CRISPR spacer content evolution "},{"quality_controlled":"1","publication_identifier":{"eisbn":["9783527671632"],"isbn":["9783527411986 "]},"date_published":"2013-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","_id":"2413","date_updated":"2025-06-03T11:46:23Z","department":[{"_id":"GaTk"}],"oa_version":"None","type":"book_chapter","publist_id":"4513","editor":[{"last_name":"Meyer","full_name":"Meyer, Misha","first_name":"Misha"},{"first_name":"Z.","last_name":"Pesenson","full_name":"Pesenson, Z."}],"year":"2013","date_created":"2018-12-11T11:57:31Z","alternative_title":["Reviews of Nonlinear Dynamics and Complexity"],"abstract":[{"lang":"eng","text":"Progress in understanding the global brain dynamics has remained slow to date in large part because of the highly multiscale nature of brain activity. Indeed, normal brain dynamics is characterized by complex interactions between multiple levels: from the microscopic scale of single neurons to the mesoscopic level of local groups of neurons, and finally to the macroscopic level of the whole brain. Among the most difficult tasks are those of identifying which scales are significant for a given particular function and describing how the scales affect each other. It is important to realize that the scales of time and space are linked together, or even intertwined, and that causal inference is far more ambiguous between than within levels. We approach this problem from the perspective of our recent work on simultaneous recording from micro- and macroelectrodes in the human brain. We propose a physiological description of these multilevel interactions, based on phase–amplitude coupling of neuronal oscillations that operate at multiple frequencies and on different spatial scales. Specifically, the amplitude of the oscillations on a particular spatial scale is modulated by phasic variations in neuronal excitability induced by lower frequency oscillations that emerge on a larger spatial scale. Following this general principle, it is possible to scale up or scale down the multiscale brain dynamics. It is expected that large-scale network oscillations in the low-frequency range, mediating downward effects, may play an important role in attention and consciousness."}],"language":[{"iso":"eng"}],"title":"Neuronal oscillations scale up and scale down the brain dynamics ","article_processing_charge":"No","day":"01","author":[{"first_name":"Mario","full_name":"Valderrama, Mario","last_name":"Valderrama"},{"first_name":"Vicente","orcid":"0000-0002-8790-1914","id":"421234E8-F248-11E8-B48F-1D18A9856A87","last_name":"Botella Soler","full_name":"Botella Soler, Vicente"},{"first_name":"Michel","full_name":"Le Van Quyen, Michel","last_name":"Le Van Quyen"}],"publication_status":"published","doi":"10.1002/9783527671632.ch08","month":"08","scopus_import":"1","citation":{"chicago":"Valderrama, Mario, Vicente Botella Soler, and Michel Le Van Quyen. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” In <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>, edited by Misha Meyer and Z. Pesenson. Wiley, 2013. <a href=\"https://doi.org/10.1002/9783527671632.ch08\">https://doi.org/10.1002/9783527671632.ch08</a>.","mla":"Valderrama, Mario, et al. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .” <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>, edited by Misha Meyer and Z. Pesenson, Wiley, 2013, doi:<a href=\"https://doi.org/10.1002/9783527671632.ch08\">10.1002/9783527671632.ch08</a>.","ista":"Valderrama M, Botella Soler V, Le Van Quyen M. 2013.Neuronal oscillations scale up and scale down the brain dynamics . In: Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain. Reviews of Nonlinear Dynamics and Complexity, .","ieee":"M. Valderrama, V. Botella Soler, and M. Le Van Quyen, “Neuronal oscillations scale up and scale down the brain dynamics ,” in <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>, M. Meyer and Z. Pesenson, Eds. Wiley, 2013.","short":"M. Valderrama, V. Botella Soler, M. Le Van Quyen, in:, M. Meyer, Z. Pesenson (Eds.), Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, Wiley, 2013.","apa":"Valderrama, M., Botella Soler, V., &#38; Le Van Quyen, M. (2013). Neuronal oscillations scale up and scale down the brain dynamics . In M. Meyer &#38; Z. Pesenson (Eds.), <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>. Wiley. <a href=\"https://doi.org/10.1002/9783527671632.ch08\">https://doi.org/10.1002/9783527671632.ch08</a>","ama":"Valderrama M, Botella Soler V, Le Van Quyen M. Neuronal oscillations scale up and scale down the brain dynamics . In: Meyer M, Pesenson Z, eds. <i>Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain</i>. Wiley; 2013. doi:<a href=\"https://doi.org/10.1002/9783527671632.ch08\">10.1002/9783527671632.ch08</a>"},"publisher":"Wiley","publication":"Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain"},{"month":"07","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Jakub","full_name":"Ła̧Cki, Jakub","last_name":"Ła̧Cki"}],"citation":{"ieee":"K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013.","short":"K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558.","ama":"Chatterjee K, Ła̧Cki J. Faster algorithms for Markov decision processes with low treewidth. 2013;8044:543-558. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">10.1007/978-3-642-39799-8_36</a>","apa":"Chatterjee, K., &#38; Ła̧Cki, J. (2013). Faster algorithms for Markov decision processes with low treewidth. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">https://doi.org/10.1007/978-3-642-39799-8_36</a>","chicago":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. “Faster Algorithms for Markov Decision Processes with Low Treewidth.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">https://doi.org/10.1007/978-3-642-39799-8_36</a>.","mla":"Chatterjee, Krishnendu, and Jakub Ła̧Cki. <i>Faster Algorithms for Markov Decision Processes with Low Treewidth</i>. Vol. 8044, Springer, 2013, pp. 543–58, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_36\">10.1007/978-3-642-39799-8_36</a>.","ista":"Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes with low treewidth. 8044, 543–558."},"scopus_import":1,"conference":{"name":"CAV: Computer Aided Verification","start_date":"2013-07-13","end_date":"2013-07-19","location":"St. Petersburg, Russia"},"publisher":"Springer","ec_funded":1,"publist_id":"4459","title":"Faster algorithms for Markov decision processes with low treewidth","oa_version":"Preprint","oa":1,"status":"public","publication_status":"published","intvolume":"      8044","doi":"10.1007/978-3-642-39799-8_36","series_title":"Lecture Notes in Computer Science","volume":8044,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.0084"}],"external_id":{"arxiv":["1304.0084"]},"date_created":"2018-12-11T11:57:42Z","page":"543 - 558","year":"2013","day":"01","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","name":"Game Theory","call_identifier":"FWF"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"abstract":[{"lang":"eng","text":"We consider two core algorithmic problems for probabilistic verification: the maximal end-component decomposition and the almost-sure reachability set computation for Markov decision processes (MDPs). For MDPs with treewidth k, we present two improved static algorithms for both the problems that run in time O(n·k 2.38·2k ) and O(m·logn· k), respectively, where n is the number of states and m is the number of edges, significantly improving the previous known O(n·k·√n· k) bound for low treewidth. We also present decremental algorithms for both problems for MDPs with constant treewidth that run in amortized logarithmic time, which is a huge improvement over the previously known algorithms that require amortized linear time."}],"department":[{"_id":"KrCh"}],"arxiv":1,"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2013-07-01T00:00:00Z","quality_controlled":"1","_id":"2444","date_updated":"2020-08-11T10:09:47Z"},{"volume":8044,"intvolume":"      8044","doi":"10.1007/978-3-642-39799-8_68","publication_status":"published","ddc":["000","004"],"day":"01","abstract":[{"text":"We develop program synthesis techniques that can help programmers fix concurrency-related bugs. We make two new contributions to synthesis for concurrency, the first improving the efficiency of the synthesized code, and the second improving the efficiency of the synthesis procedure itself. The first contribution is to have the synthesis procedure explore a variety of (sequential) semantics-preserving program transformations. Classically, only one such transformation has been considered, namely, the insertion of synchronization primitives (such as locks). Based on common manual bug-fixing techniques used by Linux device-driver developers, we explore additional, more efficient transformations, such as the reordering of independent instructions. The second contribution is to speed up the counterexample-guided removal of concurrency bugs within the synthesis procedure by considering partial-order traces (instead of linear traces) as counterexamples. A partial-order error trace represents a set of linear (interleaved) traces of a concurrent program all of which lead to the same error. By eliminating a partial-order error trace, we eliminate in a single iteration of the synthesis procedure all linearizations of the partial-order trace. We evaluated our techniques on several simplified examples of real concurrency bugs that occurred in Linux device drivers.","lang":"eng"}],"alternative_title":["LNCS"],"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"page":"951 - 967","date_created":"2018-12-11T11:57:42Z","year":"2013","type":"conference","department":[{"_id":"ToHe"}],"file":[{"file_id":"5158","creator":"system","file_name":"IST-2014-199-v1+1_cav2013-final.pdf","date_updated":"2020-07-14T12:45:40Z","date_created":"2018-12-12T10:15:37Z","checksum":"70c70ca5487faba82262c63e1b678a27","access_level":"open_access","file_size":365548,"content_type":"application/pdf","relation":"main_file"}],"date_updated":"2026-04-09T10:54:00Z","_id":"2445","date_published":"2013-07-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","conference":{"name":"CAV: Computer Aided Verification","end_date":"2013-07-19","location":"St. Petersburg, Russia","start_date":"2013-07-13"},"ec_funded":1,"publisher":"Springer","citation":{"ista":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. 2013. Efficient synthesis for concurrency by semantics-preserving transformations. CAV: Computer Aided Verification, LNCS, vol. 8044, 951–967.","mla":"Cerny, Pavol, et al. <i>Efficient Synthesis for Concurrency by Semantics-Preserving Transformations</i>. Vol. 8044, Springer, 2013, pp. 951–67, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">10.1007/978-3-642-39799-8_68</a>.","chicago":"Cerny, Pavol, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, and Thorsten Tarrach. “Efficient Synthesis for Concurrency by Semantics-Preserving Transformations,” 8044:951–67. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">https://doi.org/10.1007/978-3-642-39799-8_68</a>.","apa":"Cerny, P., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., &#38; Tarrach, T. (2013). Efficient synthesis for concurrency by semantics-preserving transformations (Vol. 8044, pp. 951–967). Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">https://doi.org/10.1007/978-3-642-39799-8_68</a>","ama":"Cerny P, Henzinger TA, Radhakrishna A, Ryzhyk L, Tarrach T. Efficient synthesis for concurrency by semantics-preserving transformations. In: Vol 8044. Springer; 2013:951-967. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_68\">10.1007/978-3-642-39799-8_68</a>","ieee":"P. Cerny, T. A. Henzinger, A. Radhakrishna, L. Ryzhyk, and T. Tarrach, “Efficient synthesis for concurrency by semantics-preserving transformations,” presented at the CAV: Computer Aided Verification, St. Petersburg, Russia, 2013, vol. 8044, pp. 951–967.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer, 2013, pp. 951–967."},"pubrep_id":"199","scopus_import":1,"month":"07","author":[{"full_name":"Cerny, Pavol","last_name":"Cerny","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun"},{"first_name":"Leonid","full_name":"Ryzhyk, Leonid","last_name":"Ryzhyk"},{"last_name":"Tarrach","full_name":"Tarrach, Thorsten","first_name":"Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4409-8487"}],"related_material":{"record":[{"status":"public","id":"1130","relation":"dissertation_contains"}]},"title":"Efficient synthesis for concurrency by semantics-preserving transformations","file_date_updated":"2020-07-14T12:45:40Z","publist_id":"4458","oa_version":"Submitted Version","has_accepted_license":"1","status":"public","oa":1},{"oa_version":"Preprint","status":"public","oa":1,"ec_funded":1,"conference":{"name":"CAV: Computer Aided Verification","start_date":"2013-07-13","location":"St. Petersburg, Russia","end_date":"2013-07-19"},"publisher":"Springer","citation":{"chicago":"Chatterjee, Krishnendu, Andreas Gaiser, and Jan Kretinsky. “Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">https://doi.org/10.1007/978-3-642-39799-8_37</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Automata with Generalized Rabin Pairs for Probabilistic Model Checking and LTL Synthesis</i>. Vol. 8044, Springer, 2013, pp. 559–75, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">10.1007/978-3-642-39799-8_37</a>.","ista":"Chatterjee K, Gaiser A, Kretinsky J. 2013. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 8044, 559–575.","short":"K. Chatterjee, A. Gaiser, J. Kretinsky, 8044 (2013) 559–575.","ieee":"K. Chatterjee, A. Gaiser, and J. Kretinsky, “Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis,” vol. 8044. Springer, pp. 559–575, 2013.","apa":"Chatterjee, K., Gaiser, A., &#38; Kretinsky, J. (2013). Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">https://doi.org/10.1007/978-3-642-39799-8_37</a>","ama":"Chatterjee K, Gaiser A, Kretinsky J. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 2013;8044:559-575. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_37\">10.1007/978-3-642-39799-8_37</a>"},"scopus_import":1,"month":"07","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Andreas","last_name":"Gaiser","full_name":"Gaiser, Andreas"},{"orcid":"0000-0002-8122-2881","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Kretinsky, Jan","last_name":"Kretinsky"}],"title":"Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis","publist_id":"4457","type":"conference","arxiv":1,"department":[{"_id":"KrCh"}],"date_updated":"2020-08-11T10:09:47Z","_id":"2446","date_published":"2013-07-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","external_id":{"arxiv":["1304.5281"]},"volume":8044,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.5281"}],"publication_status":"published","doi":"10.1007/978-3-642-39799-8_37","intvolume":"      8044","series_title":"Lecture Notes in Computer Science","day":"01","language":[{"iso":"eng"}],"project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"The model-checking problem for probabilistic systems crucially relies on the translation of LTL to deterministic Rabin automata (DRW). Our recent Safraless translation [KE12, GKE12] for the LTL(F,G) fragment produces smaller automata as compared to the traditional approach. In this work, instead of DRW we consider deterministic automata with acceptance condition given as disjunction of generalized Rabin pairs (DGRW). The Safraless translation of LTL(F,G) formulas to DGRW results in smaller automata as compared to DRW. We present algorithms for probabilistic model-checking as well as game solving for DGRW conditions. Our new algorithms lead to improvement both in terms of theoretical bounds as well as practical evaluation. We compare PRISM with and without our new translation, and show that the new translation leads to significant improvements."}],"alternative_title":["LNCS"],"page":"559 - 575","date_created":"2018-12-11T11:57:42Z","year":"2013"},{"month":"07","author":[{"full_name":"Piskac, Ruzica","last_name":"Piskac","first_name":"Ruzica"},{"last_name":"Wies","full_name":"Wies, Thomas","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"},{"id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736","first_name":"Damien","full_name":"Zufferey, Damien","last_name":"Zufferey"}],"citation":{"ista":"Piskac R, Wies T, Zufferey D. 2013. Automating separation logic using SMT. 8044, 773–789.","chicago":"Piskac, Ruzica, Thomas Wies, and Damien Zufferey. “Automating Separation Logic Using SMT.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">https://doi.org/10.1007/978-3-642-39799-8_54</a>.","mla":"Piskac, Ruzica, et al. <i>Automating Separation Logic Using SMT</i>. Vol. 8044, Springer, 2013, pp. 773–89, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">10.1007/978-3-642-39799-8_54</a>.","ieee":"R. Piskac, T. Wies, and D. Zufferey, “Automating separation logic using SMT,” vol. 8044. Springer, pp. 773–789, 2013.","short":"R. Piskac, T. Wies, D. Zufferey, 8044 (2013) 773–789.","ama":"Piskac R, Wies T, Zufferey D. Automating separation logic using SMT. 2013;8044:773-789. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">10.1007/978-3-642-39799-8_54</a>","apa":"Piskac, R., Wies, T., &#38; Zufferey, D. (2013). Automating separation logic using SMT. Presented at the CAV: Computer Aided Verification, St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_54\">https://doi.org/10.1007/978-3-642-39799-8_54</a>"},"scopus_import":1,"conference":{"end_date":"2013-07-19","start_date":"2013-07-13","location":"St. Petersburg, Russia","name":"CAV: Computer Aided Verification"},"publisher":"Springer","publist_id":"4456","file_date_updated":"2020-07-14T12:45:41Z","title":"Automating separation logic using SMT","article_processing_charge":"No","has_accepted_license":"1","oa_version":"Submitted Version","oa":1,"status":"public","doi":"10.1007/978-3-642-39799-8_54","publication_status":"published","intvolume":"      8044","ddc":["000"],"series_title":"Lecture Notes in Computer Science","volume":8044,"page":"773 - 789","date_created":"2018-12-11T11:57:43Z","year":"2013","day":"01","abstract":[{"lang":"eng","text":"Separation logic (SL) has gained widespread popularity because of its ability to succinctly express complex invariants of a program’s heap configurations. Several specialized provers have been developed for decidable SL fragments. However, these provers cannot be easily extended or combined with solvers for other theories that are important in program verification, e.g., linear arithmetic. In this paper, we present a reduction of decidable SL fragments to a decidable first-order theory that fits well into the satisfiability modulo theories (SMT) framework. We show how to use this reduction to automate satisfiability, entailment, frame inference, and abduction problems for separation logic using SMT solvers. Our approach provides a simple method of integrating separation logic into existing verification tools that provide SMT backends, and an elegant way of combining SL fragments with other decidable first-order theories. We implemented this approach in a verification tool and applied it to heap-manipulating programs whose verification involves reasoning in theory combinations.\r\n"}],"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"department":[{"_id":"ToHe"}],"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2013-07-01T00:00:00Z","quality_controlled":"1","_id":"2447","file":[{"access_level":"open_access","file_size":309182,"content_type":"application/pdf","relation":"main_file","file_id":"7859","creator":"dernst","date_updated":"2020-07-14T12:45:41Z","file_name":"2013_CAV_Piskac.pdf","checksum":"2e866932ab688f47ecd504acb4d5c7d4","date_created":"2020-05-15T11:13:01Z"}],"date_updated":"2020-08-11T10:09:47Z"},{"article_number":"e25688","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"abstract":[{"text":"Cell-to-cell directional flow of the phytohormone auxin is primarily established by polar localization of the PIN auxin transporters, a process tightly regulated at multiple levels by auxin itself. We recently reported that, in the context of strong auxin flows, activity of the vacuolar ZIFL1.1 transporter is required for fine-tuning of polar auxin transport rates in the Arabidopsis root. In particular, ZIFL1.1 function protects plasma-membrane stability of the PIN2 carrier in epidermal root tip cells under conditions normally triggering PIN2 degradation. Here, we show that ZIFL1.1 activity at the root tip also promotes PIN1 plasma-membrane abundance in central cylinder cells, thus supporting the notion that ZIFL1.1 acts as a general positive modulator of polar auxin transport in roots.","lang":"eng"}],"day":"10","year":"2013","date_created":"2018-12-11T11:57:43Z","intvolume":"         8","publication_status":"published","doi":"10.4161/psb.25688","external_id":{"pmid":["23857365"]},"volume":8,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091088/"}],"quality_controlled":"1","date_published":"2013-07-10T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-04-15T07:48:02Z","_id":"2448","department":[{"_id":"JiFr"}],"type":"journal_article","publist_id":"4455","article_processing_charge":"No","title":"ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip","issue":"10","scopus_import":"1","citation":{"mla":"Remy, Estelle, et al. “ZIFL1.1 Transporter Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” <i>Plant Signaling &#38; Behavior</i>, vol. 8, no. 10, e25688, Taylor &#38; Francis, 2013, doi:<a href=\"https://doi.org/10.4161/psb.25688\">10.4161/psb.25688</a>.","chicago":"Remy, Estelle, Pawel Baster, Jiří Friml, and Paula Duque. “ZIFL1.1 Transporter Modulates Polar Auxin Transport by Stabilizing Membrane Abundance of Multiple PINs in Arabidopsis Root Tip.” <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis, 2013. <a href=\"https://doi.org/10.4161/psb.25688\">https://doi.org/10.4161/psb.25688</a>.","ista":"Remy E, Baster P, Friml J, Duque P. 2013. ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. Plant Signaling &#38; Behavior. 8(10), e25688.","apa":"Remy, E., Baster, P., Friml, J., &#38; Duque, P. (2013). ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. <i>Plant Signaling &#38; Behavior</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.4161/psb.25688\">https://doi.org/10.4161/psb.25688</a>","ama":"Remy E, Baster P, Friml J, Duque P. ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip. <i>Plant Signaling &#38; Behavior</i>. 2013;8(10). doi:<a href=\"https://doi.org/10.4161/psb.25688\">10.4161/psb.25688</a>","ieee":"E. Remy, P. Baster, J. Friml, and P. Duque, “ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip,” <i>Plant Signaling &#38; Behavior</i>, vol. 8, no. 10. Taylor &#38; Francis, 2013.","short":"E. Remy, P. Baster, J. Friml, P. Duque, Plant Signaling &#38; Behavior 8 (2013)."},"author":[{"full_name":"Remy, Estelle","last_name":"Remy","first_name":"Estelle"},{"first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","last_name":"Baster","full_name":"Baster, Pawel"},{"full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí"},{"last_name":"Duque","full_name":"Duque, Paula","first_name":"Paula"}],"month":"07","publication":"Plant Signaling & Behavior","ec_funded":1,"publisher":"Taylor & Francis","status":"public","oa":1,"article_type":"original","pmid":1,"oa_version":"Submitted Version"},{"year":"2013","page":"1849 - 1862","date_created":"2018-12-11T11:57:44Z","abstract":[{"lang":"eng","text":"Intracellular protein routing is mediated by vesicular transport which is tightly regulated in eukaryotes. The protein and lipid homeostasis depends on coordinated delivery of de novo synthesized or recycled cargoes to the plasma membrane by exocytosis and their subsequent removal by rerouting them for recycling or degradation. Here, we report the characterization of protein affected trafficking 3 (pat3) mutant that we identified by an epifluorescence-based forward genetic screen for mutants defective in subcellular distribution of Arabidopsis auxin transporter PIN1–GFP. While pat3 displays largely normal plant morphology and development in nutrient-rich conditions, it shows strong ectopic intracellular accumulations of different plasma membrane cargoes in structures that resemble prevacuolar compartments (PVC) with an aberrant morphology. Genetic mapping revealed that pat3 is defective in vacuolar protein sorting 35A (VPS35A), a putative subunit of the retromer complex that mediates retrograde trafficking between the PVC and trans-Golgi network. Similarly, a mutant defective in another retromer subunit, vps29, shows comparable subcellular defects in PVC morphology and protein accumulation. Thus, our data provide evidence that the retromer components VPS35A and VPS29 are essential for normal PVC morphology and normal trafficking of plasma membrane proteins in plants. In addition, we show that, out of the three VPS35 retromer subunits present in Arabidopsis thaliana genome, the VPS35 homolog A plays a prevailing role in trafficking to the lytic vacuole, presenting another level of complexity in the retromer-dependent vacuolar sorting. "}],"language":[{"iso":"eng"}],"day":"01","publication_status":"published","doi":"10.1093/mp/sst044","intvolume":"         6","volume":6,"external_id":{"isi":["000327541200010"]},"quality_controlled":"1","date_published":"2013-11-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2449","date_updated":"2025-09-29T14:14:22Z","department":[{"_id":"JiFr"}],"corr_author":"1","type":"journal_article","publist_id":"4454","issue":"6","title":"Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis","article_processing_charge":"No","author":[{"first_name":"Tomasz","full_name":"Nodzyński, Tomasz","last_name":"Nodzyński"},{"first_name":"Murguel","last_name":"Feraru","full_name":"Feraru, Murguel"},{"last_name":"Hirsch","full_name":"Hirsch, Sibylle","first_name":"Sibylle"},{"last_name":"De Rycke","full_name":"De Rycke, Riet","first_name":"Riet"},{"last_name":"Nicuales","full_name":"Nicuales, Claudiu","first_name":"Claudiu"},{"first_name":"Jelle","full_name":"Van Leene, Jelle","last_name":"Van Leene"},{"full_name":"De Jaeger, Geert","last_name":"De Jaeger","first_name":"Geert"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}],"month":"11","scopus_import":"1","citation":{"apa":"Nodzyński, T., Feraru, M., Hirsch, S., De Rycke, R., Nicuales, C., Van Leene, J., … Friml, J. (2013). Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. <i>Molecular Plant</i>. Cell Press. <a href=\"https://doi.org/10.1093/mp/sst044\">https://doi.org/10.1093/mp/sst044</a>","ama":"Nodzyński T, Feraru M, Hirsch S, et al. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. <i>Molecular Plant</i>. 2013;6(6):1849-1862. doi:<a href=\"https://doi.org/10.1093/mp/sst044\">10.1093/mp/sst044</a>","ieee":"T. Nodzyński <i>et al.</i>, “Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis,” <i>Molecular Plant</i>, vol. 6, no. 6. Cell Press, pp. 1849–1862, 2013.","short":"T. Nodzyński, M. Feraru, S. Hirsch, R. De Rycke, C. Nicuales, J. Van Leene, G. De Jaeger, S. Vanneste, J. Friml, Molecular Plant 6 (2013) 1849–1862.","mla":"Nodzyński, Tomasz, et al. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” <i>Molecular Plant</i>, vol. 6, no. 6, Cell Press, 2013, pp. 1849–62, doi:<a href=\"https://doi.org/10.1093/mp/sst044\">10.1093/mp/sst044</a>.","ista":"Nodzyński T, Feraru M, Hirsch S, De Rycke R, Nicuales C, Van Leene J, De Jaeger G, Vanneste S, Friml J. 2013. Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis. Molecular Plant. 6(6), 1849–1862.","chicago":"Nodzyński, Tomasz, Murguel Feraru, Sibylle Hirsch, Riet De Rycke, Claudiu Nicuales, Jelle Van Leene, Geert De Jaeger, Steffen Vanneste, and Jiří Friml. “Retromer Subunits VPS35A and VPS29 Mediate Prevacuolar Compartment (PVC) Function in Arabidopsis.” <i>Molecular Plant</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1093/mp/sst044\">https://doi.org/10.1093/mp/sst044</a>."},"publisher":"Cell Press","publication":"Molecular Plant","isi":1,"status":"public","oa_version":"None"},{"article_number":"103","abstract":[{"lang":"eng","text":"We introduce a new method for efficiently simulating liquid with extreme amounts of spatial adaptivity. Our method combines several key components to drastically speed up the simulation of large-scale fluid phenomena: We leverage an alternative Eulerian tetrahedral mesh discretization to significantly reduce the complexity of the pressure solve while increasing the robustness with respect to element quality and removing the possibility of locking. Next, we enable subtle free-surface phenomena by deriving novel second-order boundary conditions consistent with our discretization. We couple this discretization with a spatially adaptive Fluid-Implicit Particle (FLIP) method, enabling efficient, robust, minimally-dissipative simulations that can undergo sharp changes in spatial resolution while minimizing artifacts. Along the way, we provide a new method for generating a smooth and detailed surface from a set of particles with variable sizes. Finally, we explore several new sizing functions for determining spatially adaptive simulation resolutions, and we show how to couple them to our simulator. We combine each of these elements to produce a simulation algorithm that is capable of creating animations at high maximum resolutions while avoiding common pitfalls like inaccurate boundary conditions and inefficient computation."}],"language":[{"iso":"eng"}],"day":"01","year":"2013","date_created":"2018-12-11T11:57:50Z","ddc":["000"],"intvolume":"        32","doi":"10.1145/2461912.2461982","publication_status":"published","external_id":{"isi":["000321840100072"]},"volume":32,"quality_controlled":"1","date_published":"2013-07-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-29T14:13:52Z","file":[{"creator":"system","file_id":"5279","date_updated":"2020-07-14T12:45:41Z","file_name":"IST-2016-605-v1+1_tetflip_fixed.pdf","checksum":"aeea6b0ff2b27c695aeb8408c7d2fc50","date_created":"2018-12-12T10:17:25Z","access_level":"open_access","file_size":8601561,"content_type":"application/pdf","relation":"main_file"}],"_id":"2466","department":[{"_id":"ChWo"}],"type":"journal_article","publist_id":"4436","title":"Highly adaptive liquid simulations on tetrahedral meshes","article_processing_charge":"No","file_date_updated":"2020-07-14T12:45:41Z","issue":"4","scopus_import":"1","pubrep_id":"605","citation":{"ama":"Ando R, Thuerey N, Wojtan C. Highly adaptive liquid simulations on tetrahedral meshes. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461982\">10.1145/2461912.2461982</a>","apa":"Ando, R., Thuerey, N., &#38; Wojtan, C. (2013). Highly adaptive liquid simulations on tetrahedral meshes. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461982\">https://doi.org/10.1145/2461912.2461982</a>","ieee":"R. Ando, N. Thuerey, and C. Wojtan, “Highly adaptive liquid simulations on tetrahedral meshes,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","short":"R. Ando, N. Thuerey, C. Wojtan, ACM Transactions on Graphics 32 (2013).","ista":"Ando R, Thuerey N, Wojtan C. 2013. Highly adaptive liquid simulations on tetrahedral meshes. ACM Transactions on Graphics. 32(4), 103.","mla":"Ando, Ryoichi, et al. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, 103, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461982\">10.1145/2461912.2461982</a>.","chicago":"Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “Highly Adaptive Liquid Simulations on Tetrahedral Meshes.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461982\">https://doi.org/10.1145/2461912.2461982</a>."},"author":[{"full_name":"Ando, Ryoichi","last_name":"Ando","first_name":"Ryoichi"},{"first_name":"Nils","full_name":"Thuerey, Nils","last_name":"Thuerey"},{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","last_name":"Wojtan","full_name":"Wojtan, Christopher J"}],"month":"07","publication":"ACM Transactions on Graphics","isi":1,"publisher":"ACM","status":"public","oa":1,"has_accepted_license":"1","oa_version":"Submitted Version"},{"department":[{"_id":"ChWo"}],"type":"journal_article","date_published":"2013-07-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","_id":"2467","file":[{"access_level":"open_access","file_size":3514674,"content_type":"application/pdf","relation":"main_file","file_id":"4768","creator":"system","date_updated":"2020-07-14T12:45:41Z","file_name":"IST-2016-604-v1+1_toptop2013.pdf","checksum":"9c8425d62246996ca632c5a01870515b","date_created":"2018-12-12T10:09:43Z"}],"date_updated":"2025-09-29T14:13:25Z","doi":"10.1145/2461912.2462027","publication_status":"published","intvolume":"        32","ddc":["000"],"volume":32,"external_id":{"isi":["000321840100003"]},"article_number":"34","date_created":"2018-12-11T11:57:50Z","year":"2013","day":"01","abstract":[{"text":"This paper presents a method for computing topology changes for triangle meshes in an interactive geometric modeling environment. Most triangle meshes in practice do not exhibit desirable geometric properties, so we develop a solution that is independent of standard assumptions and robust to geometric errors. Specifically, we provide the first method for topology change applicable to arbitrary non-solid, non-manifold, non-closed, self-intersecting surfaces. We prove that this new method for topology change produces the expected conventional results when applied to solid (closed, manifold, non-self-intersecting) surfaces---that is, we prove a backwards-compatibility property relative to prior work. Beyond solid surfaces, we present empirical evidence that our method remains tolerant to a variety of surface aberrations through the incorporation of a novel error correction scheme. Finally, we demonstrate how topology change applied to non-solid objects enables wholly new and useful behaviors.","lang":"eng"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","oa_version":"Submitted Version","oa":1,"status":"public","month":"07","author":[{"last_name":"Bernstein","full_name":"Bernstein, Gilbert","first_name":"Gilbert"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"}],"pubrep_id":"604","citation":{"ieee":"G. Bernstein and C. Wojtan, “Putting holes in holey geometry: Topology change for arbitrary surfaces,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","short":"G. Bernstein, C. Wojtan, ACM Transactions on Graphics 32 (2013).","apa":"Bernstein, G., &#38; Wojtan, C. (2013). Putting holes in holey geometry: Topology change for arbitrary surfaces. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2462027\">https://doi.org/10.1145/2461912.2462027</a>","ama":"Bernstein G, Wojtan C. Putting holes in holey geometry: Topology change for arbitrary surfaces. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2462027\">10.1145/2461912.2462027</a>","chicago":"Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2462027\">https://doi.org/10.1145/2461912.2462027</a>.","mla":"Bernstein, Gilbert, and Chris Wojtan. “Putting Holes in Holey Geometry: Topology Change for Arbitrary Surfaces.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, 34, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2462027\">10.1145/2461912.2462027</a>.","ista":"Bernstein G, Wojtan C. 2013. Putting holes in holey geometry: Topology change for arbitrary surfaces. ACM Transactions on Graphics. 32(4), 34."},"scopus_import":"1","publisher":"ACM","publication":"ACM Transactions on Graphics","isi":1,"publist_id":"4435","issue":"4","file_date_updated":"2020-07-14T12:45:41Z","article_processing_charge":"No","title":"Putting holes in holey geometry: Topology change for arbitrary surfaces"},{"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2013-07-01T00:00:00Z","_id":"2468","date_updated":"2025-09-29T14:12:53Z","file":[{"file_size":5813685,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4761","creator":"system","date_created":"2018-12-12T10:09:37Z","checksum":"53d905e0180e23ef3e813b969ffed4e1","file_name":"IST-2016-603-v1+1_liquidError_web.pdf","date_updated":"2020-07-14T12:45:41Z"}],"department":[{"_id":"ChWo"}],"corr_author":"1","type":"journal_article","article_number":"68","year":"2013","date_created":"2018-12-11T11:57:50Z","abstract":[{"lang":"eng","text":"Our work concerns the combination of an Eulerian liquid simulation with a high-resolution surface tracker (e.g. the level set method or a Lagrangian triangle mesh). The naive application of a high-resolution surface tracker to a low-resolution velocity field can produce many visually disturbing physical and topological artifacts that limit their use in practice. We address these problems by defining an error function which compares the current state of the surface tracker to the set of physically valid surface states. By reducing this error with a gradient descent technique, we introduce a novel physics-based surface fairing method. Similarly, by treating this error function as a potential energy, we derive a new surface correction force that mimics the vortex sheet equations. We demonstrate our results with both level set and mesh-based surface trackers."}],"language":[{"iso":"eng"}],"day":"01","ddc":["000"],"doi":"10.1145/2461912.2461991","intvolume":"        32","publication_status":"published","volume":32,"external_id":{"isi":["000321840100037"]},"oa":1,"status":"public","has_accepted_license":"1","oa_version":"Submitted Version","publist_id":"4434","file_date_updated":"2020-07-14T12:45:41Z","issue":"4","title":"Liquid surface tracking with error compensation","article_processing_charge":"No","author":[{"last_name":"Bojsen-Hansen","full_name":"Bojsen-Hansen, Morten","orcid":"0000-0002-4417-3224","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","first_name":"Morten"},{"first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","last_name":"Wojtan"}],"month":"07","scopus_import":"1","pubrep_id":"603","citation":{"short":"M. Bojsen-Hansen, C. Wojtan, ACM Transactions on Graphics 32 (2013).","ieee":"M. Bojsen-Hansen and C. Wojtan, “Liquid surface tracking with error compensation,” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4. ACM, 2013.","apa":"Bojsen-Hansen, M., &#38; Wojtan, C. (2013). Liquid surface tracking with error compensation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2461912.2461991\">https://doi.org/10.1145/2461912.2461991</a>","ama":"Bojsen-Hansen M, Wojtan C. Liquid surface tracking with error compensation. <i>ACM Transactions on Graphics</i>. 2013;32(4). doi:<a href=\"https://doi.org/10.1145/2461912.2461991\">10.1145/2461912.2461991</a>","chicago":"Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” <i>ACM Transactions on Graphics</i>. ACM, 2013. <a href=\"https://doi.org/10.1145/2461912.2461991\">https://doi.org/10.1145/2461912.2461991</a>.","ista":"Bojsen-Hansen M, Wojtan C. 2013. Liquid surface tracking with error compensation. ACM Transactions on Graphics. 32(4), 68.","mla":"Bojsen-Hansen, Morten, and Chris Wojtan. “Liquid Surface Tracking with Error Compensation.” <i>ACM Transactions on Graphics</i>, vol. 32, no. 4, 68, ACM, 2013, doi:<a href=\"https://doi.org/10.1145/2461912.2461991\">10.1145/2461912.2461991</a>."},"publisher":"ACM","publication":"ACM Transactions on Graphics","isi":1},{"department":[{"_id":"CaHe"}],"type":"journal_article","corr_author":"1","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2013-07-22T00:00:00Z","date_updated":"2025-09-29T14:12:25Z","file":[{"file_size":247320,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5881","creator":"dernst","date_created":"2019-01-24T15:40:22Z","checksum":"6a424b2f007b41d4955a9135793b2162","file_name":"2013_CurrentBiology_Maitre.pdf","date_updated":"2020-07-14T12:45:41Z"}],"_id":"2469","ddc":["570"],"publication_status":"published","doi":"10.1016/j.cub.2013.06.019","intvolume":"        23","external_id":{"isi":["000322414200018"],"pmid":["23885883"]},"volume":23,"abstract":[{"text":"Cadherins are transmembrane proteins that mediate cell–cell adhesion in animals. By regulating contact formation and stability, cadherins play a crucial role in tissue morphogenesis and homeostasis. Here, we review the three major  unctions of cadherins in cell–cell contact formation and stability. Two of those functions lead to a decrease in interfacial ension at the forming cell–cell contact, thereby promoting contact expansion — first, by providing adhesion tension that lowers interfacial tension at the cell–cell contact, and second, by signaling to the actomyosin cytoskeleton in order to reduce cortex tension and thus interfacial tension at the contact. The third function of cadherins in cell–cell contact formation is to stabilize the contact by resisting mechanical forces that pull on the contact.","lang":"eng"}],"language":[{"iso":"eng"}],"day":"22","year":"2013","date_created":"2018-12-11T11:57:51Z","page":"R626 - R633","has_accepted_license":"1","pmid":1,"oa_version":"Published Version","status":"public","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"scopus_import":"1","citation":{"ieee":"J.-L. Maître and C.-P. J. Heisenberg, “Three functions of cadherins in cell adhesion,” <i>Current Biology</i>, vol. 23, no. 14. Cell Press, pp. R626–R633, 2013.","short":"J.-L. Maître, C.-P.J. Heisenberg, Current Biology 23 (2013) R626–R633.","apa":"Maître, J.-L., &#38; Heisenberg, C.-P. J. (2013). Three functions of cadherins in cell adhesion. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">https://doi.org/10.1016/j.cub.2013.06.019</a>","ama":"Maître J-L, Heisenberg C-PJ. Three functions of cadherins in cell adhesion. <i>Current Biology</i>. 2013;23(14):R626-R633. doi:<a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">10.1016/j.cub.2013.06.019</a>","ista":"Maître J-L, Heisenberg C-PJ. 2013. Three functions of cadherins in cell adhesion. Current Biology. 23(14), R626–R633.","mla":"Maître, Jean-Léon, and Carl-Philipp J. Heisenberg. “Three Functions of Cadherins in Cell Adhesion.” <i>Current Biology</i>, vol. 23, no. 14, Cell Press, 2013, pp. R626–33, doi:<a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">10.1016/j.cub.2013.06.019</a>.","chicago":"Maître, Jean-Léon, and Carl-Philipp J Heisenberg. “Three Functions of Cadherins in Cell Adhesion.” <i>Current Biology</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.cub.2013.06.019\">https://doi.org/10.1016/j.cub.2013.06.019</a>."},"author":[{"id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3688-1474","first_name":"Jean-Léon","last_name":"Maître","full_name":"Maître, Jean-Léon"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"month":"07","isi":1,"publication":"Current Biology","publisher":"Cell Press","publist_id":"4433","title":"Three functions of cadherins in cell adhesion","article_processing_charge":"No","file_date_updated":"2020-07-14T12:45:41Z","issue":"14"},{"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"chicago":"Čovanová, Milada, Michael Sauer, Jan Rychtář, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0070050\">https://doi.org/10.1371/journal.pone.0070050</a>.","mla":"Čovanová, Milada, et al. “Overexpression of the Auxin Binding PROTEIN1 Modulates PIN-Dependent Auxin Transport in Tobacco Cells.” <i>PLoS One</i>, vol. 8, no. 7, e70050, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0070050\">10.1371/journal.pone.0070050</a>.","ista":"Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. 2013. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. PLoS One. 8(7), e70050.","short":"M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, E. Zažímalová, PLoS One 8 (2013).","ieee":"M. Čovanová, M. Sauer, J. Rychtář, J. Friml, J. Petrášek, and E. Zažímalová, “Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells,” <i>PLoS One</i>, vol. 8, no. 7. Public Library of Science, 2013.","apa":"Čovanová, M., Sauer, M., Rychtář, J., Friml, J., Petrášek, J., &#38; Zažímalová, E. (2013). Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0070050\">https://doi.org/10.1371/journal.pone.0070050</a>","ama":"Čovanová M, Sauer M, Rychtář J, Friml J, Petrášek J, Zažímalová E. Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells. <i>PLoS One</i>. 2013;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0070050\">10.1371/journal.pone.0070050</a>"},"pubrep_id":"413","author":[{"first_name":"Milada","last_name":"Čovanová","full_name":"Čovanová, Milada"},{"full_name":"Sauer, Michael","last_name":"Sauer","first_name":"Michael"},{"first_name":"Jan","full_name":"Rychtář, Jan","last_name":"Rychtář"},{"full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Jan","last_name":"Petrášek","full_name":"Petrášek, Jan"},{"first_name":"Eva","full_name":"Zažímalová, Eva","last_name":"Zažímalová"}],"month":"07","publication":"PLoS One","isi":1,"publisher":"Public Library of Science","publist_id":"4432","article_processing_charge":"No","title":"Overexpression of the auxin binding PROTEIN1 modulates PIN-dependent auxin transport in tobacco cells","issue":"7","file_date_updated":"2020-07-14T12:45:41Z","has_accepted_license":"1","oa_version":"Published Version","status":"public","oa":1,"ddc":["570"],"intvolume":"         8","doi":"10.1371/journal.pone.0070050","publication_status":"published","external_id":{"isi":["000325211000181"]},"volume":8,"article_number":"e70050","abstract":[{"text":"Background:Auxin binding protein 1 (ABP1) is a putative auxin receptor and its function is indispensable for plant growth and development. ABP1 has been shown to be involved in auxin-dependent regulation of cell division and expansion, in plasma-membrane-related processes such as changes in transmembrane potential, and in the regulation of clathrin-dependent endocytosis. However, the ABP1-regulated downstream pathway remains elusive.Methodology/Principal Findings:Using auxin transport assays and quantitative analysis of cellular morphology we show that ABP1 regulates auxin efflux from tobacco BY-2 cells. The overexpression of ABP1can counterbalance increased auxin efflux and auxin starvation phenotypes caused by the overexpression of PIN auxin efflux carrier. Relevant mechanism involves the ABP1-controlled vesicle trafficking processes, including positive regulation of endocytosis of PIN auxin efflux carriers, as indicated by fluorescence recovery after photobleaching (FRAP) and pharmacological manipulations.Conclusions/Significance:The findings indicate the involvement of ABP1 in control of rate of auxin transport across plasma membrane emphasizing the role of ABP1 in regulation of PIN activity at the plasma membrane, and highlighting the relevance of ABP1 for the formation of developmentally important, PIN-dependent auxin gradients.","lang":"eng"}],"language":[{"iso":"eng"}],"day":"23","year":"2013","date_created":"2018-12-11T11:57:51Z","department":[{"_id":"JiFr"}],"type":"journal_article","quality_controlled":"1","date_published":"2013-07-23T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-29T14:11:54Z","file":[{"date_updated":"2020-07-14T12:45:41Z","file_name":"IST-2016-413-v1+1_journal.pone.0070050.pdf","checksum":"2d47ef47616ef4de1d517d146548184e","date_created":"2018-12-12T10:08:21Z","creator":"system","file_id":"4681","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":2294955}],"_id":"2470"},{"volume":8,"external_id":{"isi":["000323114200054"]},"ddc":["570"],"doi":"10.1371/journal.pone.0070013","intvolume":"         8","publication_status":"published","year":"2013","date_created":"2018-12-11T11:57:51Z","abstract":[{"text":"The impact of disulfide bonds on protein stability goes beyond simple equilibrium thermodynamics effects associated with the conformational entropy of the unfolded state. Indeed, disulfide crosslinks may play a role in the prevention of dysfunctional association and strongly affect the rates of irreversible enzyme inactivation, highly relevant in biotechnological applications. While these kinetic-stability effects remain poorly understood, by analogy with proposed mechanisms for processes of protein aggregation and fibrillogenesis, we propose that they may be determined by the properties of sparsely-populated, partially-unfolded intermediates. Here we report the successful design, on the basis of high temperature molecular-dynamics simulations, of six thermodynamically and kinetically stabilized variants of phytase from Citrobacter braakii (a biotechnologically important enzyme) with one, two or three engineered disulfides. Activity measurements and 3D crystal structure determination demonstrate that the engineered crosslinks do not cause dramatic alterations in the native structure. The inactivation kinetics for all the variants displays a strongly non-Arrhenius temperature dependence, with the time-scale for the irreversible denaturation process reaching a minimum at a given temperature within the range of the denaturation transition. We show this striking feature to be a signature of a key role played by a partially unfolded, intermediate state/ensemble. Energetic and mutational analyses confirm that the intermediate is highly unfolded (akin to a proposed critical intermediate in the misfolding of the prion protein), a result that explains the observed kinetic stabilization. Our results provide a rationale for the kinetic-stability consequences of disulfide-crosslink engineering and an experimental methodology to arrive at energetic/structural descriptions of the sparsely populated and elusive intermediates that play key roles in irreversible protein denaturation.","lang":"eng"}],"language":[{"iso":"eng"}],"day":"30","article_number":"e70013","type":"journal_article","department":[{"_id":"HaJa"}],"_id":"2471","date_updated":"2025-09-29T14:10:56Z","file":[{"access_level":"open_access","file_size":1323666,"content_type":"application/pdf","relation":"main_file","file_id":"5124","creator":"system","date_updated":"2020-07-14T12:45:41Z","file_name":"IST-2016-414-v1+1_journal.pone.0070013.pdf","checksum":"c0c96cc76ed7ef0d036a31a7e33c9a37","date_created":"2018-12-12T10:15:07Z"}],"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2013-07-30T00:00:00Z","publisher":"Public Library of Science","isi":1,"publication":"PLoS One","author":[{"first_name":"Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","last_name":"Sanchez Romero","full_name":"Sanchez Romero, Inmaculada"},{"full_name":"Ariza, Antonio","last_name":"Ariza","first_name":"Antonio"},{"full_name":"Wilson, Keith","last_name":"Wilson","first_name":"Keith"},{"last_name":"Skjøt","full_name":"Skjøt, Michael","first_name":"Michael"},{"full_name":"Vind, Jesper","last_name":"Vind","first_name":"Jesper"},{"first_name":"Leonardo","full_name":"De Maria, Leonardo","last_name":"De Maria"},{"first_name":"Lars","full_name":"Skov, Lars","last_name":"Skov"},{"full_name":"Sánchez Ruiz, Jose","last_name":"Sánchez Ruiz","first_name":"Jose"}],"month":"07","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"citation":{"apa":"Sanchez-Romero, I., Ariza, A., Wilson, K., Skjøt, M., Vind, J., De Maria, L., … Sánchez Ruiz, J. (2013). Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0070013\">https://doi.org/10.1371/journal.pone.0070013</a>","ama":"Sanchez-Romero I, Ariza A, Wilson K, et al. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. <i>PLoS One</i>. 2013;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0070013\">10.1371/journal.pone.0070013</a>","ieee":"I. Sanchez-Romero <i>et al.</i>, “Mechanism of protein kinetic stabilization by engineered disulfide crosslinks,” <i>PLoS One</i>, vol. 8, no. 7. Public Library of Science, 2013.","short":"I. Sanchez-Romero, A. Ariza, K. Wilson, M. Skjøt, J. Vind, L. De Maria, L. Skov, J. Sánchez Ruiz, PLoS One 8 (2013).","ista":"Sanchez-Romero I, Ariza A, Wilson K, Skjøt M, Vind J, De Maria L, Skov L, Sánchez Ruiz J. 2013. Mechanism of protein kinetic stabilization by engineered disulfide crosslinks. PLoS One. 8(7), e70013.","mla":"Sanchez-Romero, Inmaculada, et al. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” <i>PLoS One</i>, vol. 8, no. 7, e70013, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0070013\">10.1371/journal.pone.0070013</a>.","chicago":"Sanchez-Romero, Inmaculada, Antonio Ariza, Keith Wilson, Michael Skjøt, Jesper Vind, Leonardo De Maria, Lars Skov, and Jose Sánchez Ruiz. “Mechanism of Protein Kinetic Stabilization by Engineered Disulfide Crosslinks.” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0070013\">https://doi.org/10.1371/journal.pone.0070013</a>."},"pubrep_id":"414","issue":"7","file_date_updated":"2020-07-14T12:45:41Z","title":"Mechanism of protein kinetic stabilization by engineered disulfide crosslinks","article_processing_charge":"No","publist_id":"4430","oa_version":"Published Version","has_accepted_license":"1","oa":1,"status":"public"},{"has_accepted_license":"1","oa_version":"Published Version","status":"public","oa":1,"citation":{"ieee":"C. Cazzonelli <i>et al.</i>, “Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development,” <i>PLoS One</i>, vol. 8, no. 7. Public Library of Science, 2013.","short":"C. Cazzonelli, M. Vanstraelen, S. Simon, K. Yin, A. Carron Arthur, N. Nisar, G. Tarle, A. Cuttriss, I. Searle, E. Benková, U. Mathesius, J. Masle, J. Friml, B. Pogson, PLoS One 8 (2013).","ama":"Cazzonelli C, Vanstraelen M, Simon S, et al. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. <i>PLoS One</i>. 2013;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0070069\">10.1371/journal.pone.0070069</a>","apa":"Cazzonelli, C., Vanstraelen, M., Simon, S., Yin, K., Carron Arthur, A., Nisar, N., … Pogson, B. (2013). Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0070069\">https://doi.org/10.1371/journal.pone.0070069</a>","mla":"Cazzonelli, Christopher, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” <i>PLoS One</i>, vol. 8, no. 7, e70069, Public Library of Science, 2013, doi:<a href=\"https://doi.org/10.1371/journal.pone.0070069\">10.1371/journal.pone.0070069</a>.","chicago":"Cazzonelli, Christopher, Marleen Vanstraelen, Sibu Simon, Kuide Yin, Ashley Carron Arthur, Nazia Nisar, Gauri Tarle, et al. “Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development.” <i>PLoS One</i>. Public Library of Science, 2013. <a href=\"https://doi.org/10.1371/journal.pone.0070069\">https://doi.org/10.1371/journal.pone.0070069</a>.","ista":"Cazzonelli C, Vanstraelen M, Simon S, Yin K, Carron Arthur A, Nisar N, Tarle G, Cuttriss A, Searle I, Benková E, Mathesius U, Masle J, Friml J, Pogson B. 2013. Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development. PLoS One. 8(7), e70069."},"pubrep_id":"393","scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"month":"07","author":[{"last_name":"Cazzonelli","full_name":"Cazzonelli, Christopher","first_name":"Christopher"},{"full_name":"Vanstraelen, Marleen","last_name":"Vanstraelen","first_name":"Marleen"},{"last_name":"Simon","full_name":"Simon, Sibu","first_name":"Sibu","id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1998-6741"},{"last_name":"Yin","full_name":"Yin, Kuide","first_name":"Kuide"},{"first_name":"Ashley","last_name":"Carron Arthur","full_name":"Carron Arthur, Ashley"},{"first_name":"Nazia","full_name":"Nisar, Nazia","last_name":"Nisar"},{"first_name":"Gauri","full_name":"Tarle, Gauri","last_name":"Tarle"},{"full_name":"Cuttriss, Abby","last_name":"Cuttriss","first_name":"Abby"},{"full_name":"Searle, Iain","last_name":"Searle","first_name":"Iain"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","first_name":"Eva","full_name":"Benková, Eva","last_name":"Benková"},{"first_name":"Ulrike","full_name":"Mathesius, Ulrike","last_name":"Mathesius"},{"full_name":"Masle, Josette","last_name":"Masle","first_name":"Josette"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí"},{"first_name":"Barry","last_name":"Pogson","full_name":"Pogson, Barry"}],"publication":"PLoS One","isi":1,"publisher":"Public Library of Science","ec_funded":1,"publist_id":"4431","title":"Role of the Arabidopsis PIN6 auxin transporter in auxin homeostasis and auxin-mediated development","article_processing_charge":"No","issue":"7","file_date_updated":"2020-07-14T12:45:41Z","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2013-07-29T00:00:00Z","quality_controlled":"1","file":[{"file_size":9003465,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","creator":"system","file_id":"5222","checksum":"3be71828b6c2ba9c90eb7056e3f7f57a","date_created":"2018-12-12T10:16:34Z","date_updated":"2020-07-14T12:45:41Z","file_name":"IST-2015-393-v1+1_journal.pone.0070069.pdf"}],"date_updated":"2025-09-29T14:11:25Z","_id":"2472","publication_status":"published","intvolume":"         8","doi":"10.1371/journal.pone.0070069","ddc":["580","570"],"external_id":{"isi":["000323369700128"]},"volume":8,"article_number":"e70069","day":"29","abstract":[{"text":"Plant-specific PIN-formed (PIN) efflux transporters for the plant hormone auxin are required for tissue-specific directional auxin transport and cellular auxin homeostasis. The Arabidopsis PIN protein family has been shown to play important roles in developmental processes such as embryogenesis, organogenesis, vascular tissue differentiation, root meristem patterning and tropic growth. Here we analyzed roles of the less characterised Arabidopsis PIN6 auxin transporter. PIN6 is auxin-inducible and is expressed during multiple auxin-regulated developmental processes. Loss of pin6 function interfered with primary root growth and lateral root development. Misexpression of PIN6 affected auxin transport and interfered with auxin homeostasis in other growth processes such as shoot apical dominance, lateral root primordia development, adventitious root formation, root hair outgrowth and root waving. These changes in auxin-regulated growth correlated with a reduction in total auxin transport as well as with an altered activity of DR5-GUS auxin response reporter. Overall, the data indicate that PIN6 regulates auxin homeostasis during plant development.","lang":"eng"}],"language":[{"iso":"eng"}],"project":[{"_id":"253FCA6A-B435-11E9-9278-68D0E5697425","grant_number":"207362","call_identifier":"FP7","name":"Hormonal cross-talk in plant organogenesis"},{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:57:52Z","year":"2013"},{"publist_id":"4428","file_date_updated":"2020-07-14T12:45:41Z","issue":"8","article_processing_charge":"No","title":"Genetic hitch-hiking in spatially extended populations","author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"},{"first_name":"Jerome","last_name":"Kelleher","full_name":"Kelleher, Jerome"},{"full_name":"Véber, Amandine","last_name":"Véber","first_name":"Amandine"}],"month":"01","scopus_import":"1","citation":{"chicago":"Barton, Nicholas H, Alison Etheridge, Jerome Kelleher, and Amandine Véber. “Genetic Hitch-Hiking in Spatially Extended Populations.” <i>Theoretical Population Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">https://doi.org/10.1016/j.tpb.2012.12.001</a>.","mla":"Barton, Nicholas H., et al. “Genetic Hitch-Hiking in Spatially Extended Populations.” <i>Theoretical Population Biology</i>, vol. 87, no. 8, Elsevier, 2013, pp. 75–89, doi:<a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">10.1016/j.tpb.2012.12.001</a>.","ista":"Barton NH, Etheridge A, Kelleher J, Véber A. 2013. Genetic hitch-hiking in spatially extended populations. Theoretical Population Biology. 87(8), 75–89.","short":"N.H. Barton, A. Etheridge, J. Kelleher, A. Véber, Theoretical Population Biology 87 (2013) 75–89.","ieee":"N. H. Barton, A. Etheridge, J. Kelleher, and A. Véber, “Genetic hitch-hiking in spatially extended populations,” <i>Theoretical Population Biology</i>, vol. 87, no. 8. Elsevier, pp. 75–89, 2013.","apa":"Barton, N. H., Etheridge, A., Kelleher, J., &#38; Véber, A. (2013). Genetic hitch-hiking in spatially extended populations. <i>Theoretical Population Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">https://doi.org/10.1016/j.tpb.2012.12.001</a>","ama":"Barton NH, Etheridge A, Kelleher J, Véber A. Genetic hitch-hiking in spatially extended populations. <i>Theoretical Population Biology</i>. 2013;87(8):75-89. doi:<a href=\"https://doi.org/10.1016/j.tpb.2012.12.001\">10.1016/j.tpb.2012.12.001</a>"},"pubrep_id":"118","publisher":"Elsevier","ec_funded":1,"isi":1,"publication":"Theoretical Population Biology","oa":1,"status":"public","has_accepted_license":"1","oa_version":"Submitted Version","year":"2013","page":"75 - 89","date_created":"2018-12-11T11:57:52Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"When a mutation with selective advantage s spreads through a panmictic population, it may cause two lineages at a linked locus to coalesce; the probability of coalescence is exp(−2rT), where T∼log(2Ns)/s is the time to fixation, N is the number of haploid individuals, and r is the recombination rate. Population structure delays fixation, and so weakens the effect of a selective sweep. However, favourable alleles spread through a spatially continuous population behind a narrow wavefront; ancestral lineages are confined at the tip of this front, and so coalesce rapidly. In extremely dense populations, coalescence is dominated by rare fluctuations ahead of the front. However, we show that for moderate densities, a simple quasi-deterministic approximation applies: the rate of coalescence within the front is λ∼2g(η)/(ρℓ), where ρ is the population density and  is the characteristic scale of the wavefront; g(η) depends only on the strength of random drift,  . The net effect of a sweep on coalescence also depends crucially on whether two lineages are ever both within the wavefront at the same time: even in the extreme case when coalescence within the front is instantaneous, the net rate of coalescence may be lower than in a single panmictic population. Sweeps can also have a substantial impact on the rate of gene flow. A single lineage will jump to a new location when it is hit by a sweep, with mean square displacement  ; this can be substantial if the species’ range, L, is large, even if the species-wide rate of sweeps per map length, Λ/R, is small. This effect is half as strong in two dimensions. In contrast, the rate of coalescence between lineages, at random locations in space and on the genetic map, is proportional to (c/L)(Λ/R), where c is the wavespeed: thus, on average, one-dimensional structure is likely to reduce coalescence due to sweeps, relative to panmixis. In two dimensions, genes must move along the front before they can coalesce; this process is rapid, being dominated by rare fluctuations. This leads to a dramatically higher rate of coalescence within the wavefront than if lineages simply diffused along the front. Nevertheless, the net rate of coalescence due to a sweep through a two-dimensional population is likely to be lower than it would be with panmixis."}],"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"day":"03","ddc":["570"],"intvolume":"        87","doi":"10.1016/j.tpb.2012.12.001","publication_status":"published","volume":87,"external_id":{"isi":["000322688800008"]},"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2013-01-03T00:00:00Z","_id":"2473","date_updated":"2025-09-29T14:10:28Z","file":[{"date_created":"2018-12-12T10:18:54Z","checksum":"4274ec1f433b838a7d5b941cc9684ca7","file_name":"IST-2013-118-v1+1_bartonetalRevision.pdf","date_updated":"2020-07-14T12:45:41Z","creator":"system","file_id":"5376","relation":"main_file","content_type":"application/pdf","file_size":1706282,"access_level":"open_access"}],"department":[{"_id":"NiBa"}],"corr_author":"1","type":"journal_article"},{"oa_version":"None","status":"public","publisher":"IEEE","isi":1,"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","author":[{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert"},{"first_name":"Hannes","full_name":"Nickisch, Hannes","last_name":"Nickisch"},{"first_name":"Stefan","last_name":"Harmeling","full_name":"Harmeling, Stefan"}],"month":"07","scopus_import":"1","citation":{"mla":"Lampert, Christoph, et al. “Attribute-Based Classification for Zero-Shot Learning of Object Categories.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 3, IEEE, 2013, pp. 453–65, doi:<a href=\"https://doi.org/10.1109/TPAMI.2013.140\">10.1109/TPAMI.2013.140</a>.","ista":"Lampert C, Nickisch H, Harmeling S. 2013. Attribute-based classification for zero-shot learning of object categories. IEEE Transactions on Pattern Analysis and Machine Intelligence. 36(3), 453–465.","chicago":"Lampert, Christoph, Hannes Nickisch, and Stefan Harmeling. “Attribute-Based Classification for Zero-Shot Learning of Object Categories.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2013. <a href=\"https://doi.org/10.1109/TPAMI.2013.140\">https://doi.org/10.1109/TPAMI.2013.140</a>.","short":"C. Lampert, H. Nickisch, S. Harmeling, IEEE Transactions on Pattern Analysis and Machine Intelligence 36 (2013) 453–465.","ieee":"C. Lampert, H. Nickisch, and S. Harmeling, “Attribute-based classification for zero-shot learning of object categories,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 36, no. 3. IEEE, pp. 453–465, 2013.","ama":"Lampert C, Nickisch H, Harmeling S. Attribute-based classification for zero-shot learning of object categories. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2013;36(3):453-465. doi:<a href=\"https://doi.org/10.1109/TPAMI.2013.140\">10.1109/TPAMI.2013.140</a>","apa":"Lampert, C., Nickisch, H., &#38; Harmeling, S. (2013). Attribute-based classification for zero-shot learning of object categories. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/TPAMI.2013.140\">https://doi.org/10.1109/TPAMI.2013.140</a>"},"issue":"3","article_processing_charge":"No","title":"Attribute-based classification for zero-shot learning of object categories","publist_id":"4385","type":"journal_article","department":[{"_id":"ChLa"}],"_id":"2516","date_updated":"2025-09-29T14:09:57Z","quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2013-07-30T00:00:00Z","volume":36,"external_id":{"isi":["000331450100005"]},"intvolume":"        36","doi":"10.1109/TPAMI.2013.140","publication_status":"published","year":"2013","date_created":"2018-12-11T11:58:08Z","page":"453 - 465","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We study the problem of object recognition for categories for which we have no training examples, a task also called zero-data or zero-shot learning. This situation has hardly been studied in computer vision research, even though it occurs frequently: the world contains tens of thousands of different object classes and for only few of them image collections have been formed and suitably annotated. To tackle the problem we introduce attribute-based classification: objects are identified based on a high-level description that is phrased in terms of semantic attributes, such as the object's color or shape. Because the identification of each such property transcends the specific learning task at hand, the attribute classifiers can be pre-learned independently, e.g. from existing image datasets unrelated to the current task. Afterwards, new classes can be detected based on their attribute representation, without the need for a new training phase. In this paper we also introduce a new dataset, Animals with Attributes, of over 30,000 images of 50 animal classes, annotated with 85 semantic attributes. Extensive experiments on this and two more datasets show that attribute-based classification indeed is able to categorize images without access to any training images of the target classes."}],"day":"30"}]