[{"project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"}],"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:39Z","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:57:01Z","oa":1,"year":"2013","citation":{"ama":"Henzinger TA, Sezgin A, Vafeiadis V. Aspect-oriented linearizability proofs. 2013;8052:242-256. doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">10.1007/978-3-642-40184-8_18</a>","ieee":"T. A. Henzinger, A. Sezgin, and V. Vafeiadis, “Aspect-oriented linearizability proofs,” vol. 8052. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, pp. 242–256, 2013.","apa":"Henzinger, T. A., Sezgin, A., &#38; Vafeiadis, V. (2013). Aspect-oriented linearizability proofs. Presented at the CONCUR: Concurrency Theory, Buenos Aires, Argentina: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">https://doi.org/10.1007/978-3-642-40184-8_18</a>","mla":"Henzinger, Thomas A., et al. <i>Aspect-Oriented Linearizability Proofs</i>. Vol. 8052, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 242–56, doi:<a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">10.1007/978-3-642-40184-8_18</a>.","ista":"Henzinger TA, Sezgin A, Vafeiadis V. 2013. Aspect-oriented linearizability proofs. 8052, 242–256.","chicago":"Henzinger, Thomas A, Ali Sezgin, and Viktor Vafeiadis. “Aspect-Oriented Linearizability Proofs.” Lecture Notes in Computer Science. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. <a href=\"https://doi.org/10.1007/978-3-642-40184-8_18\">https://doi.org/10.1007/978-3-642-40184-8_18</a>.","short":"T.A. Henzinger, A. Sezgin, V. Vafeiadis, 8052 (2013) 242–256."},"abstract":[{"lang":"eng","text":"Linearizability of concurrent data structures is usually proved by monolithic simulation arguments relying on identifying the so-called linearization points. Regrettably, such proofs, whether manual or automatic, are often complicated and scale poorly to advanced non-blocking concurrency patterns, such as helping and optimistic updates.\r\nIn response, we propose a more modular way of checking linearizability of concurrent queue algorithms that does not involve identifying linearization points. We reduce the task of proving linearizability with respect to the queue specification to establishing four basic properties, each of which can be proved independently by simpler arguments. As a demonstration of our approach, we verify the Herlihy and Wing queue, an algorithm that is challenging to verify by a simulation proof."}],"alternative_title":["LNCS"],"oa_version":"Submitted Version","file":[{"file_name":"IST-2014-197-v1+1_main-queue-verification.pdf","file_id":"4721","checksum":"bdbb520de91751fe0136309ad4ef67e4","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:39Z","file_size":337059,"date_created":"2018-12-12T10:08:58Z","creator":"system"}],"month":"08","volume":8052,"department":[{"_id":"ToHe"}],"pubrep_id":"197","date_published":"2013-08-01T00:00:00Z","related_material":{"record":[{"id":"1832","status":"public","relation":"later_version"}]},"author":[{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"full_name":"Sezgin, Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","first_name":"Ali","last_name":"Sezgin"},{"last_name":"Vafeiadis","full_name":"Vafeiadis, Viktor","first_name":"Viktor"}],"_id":"2328","day":"01","status":"public","conference":{"name":"CONCUR: Concurrency Theory","end_date":"2013-08-30","start_date":"2013-08-27","location":"Buenos Aires, Argentina"},"publication_status":"published","doi":"10.1007/978-3-642-40184-8_18","ec_funded":1,"page":"242 - 256","scopus_import":1,"has_accepted_license":"1","type":"conference","ddc":["000","004"],"date_updated":"2025-09-23T07:56:19Z","series_title":"Lecture Notes in Computer Science","title":"Aspect-oriented linearizability proofs","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publist_id":"4598","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"      8052"},{"oa_version":"Preprint","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."}],"citation":{"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.","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>.","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>.","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>","ista":"Chatterjee K, Velner Y. 2013. Hyperplane separation technique for multidimensional mean-payoff games. 8052, 500–515.","short":"K. Chatterjee, Y. Velner, 8052 (2013) 500–515."},"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1210.3141"}],"month":"08","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:57:01Z","project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","year":"2013","oa":1,"related_material":{"record":[{"id":"717","status":"public","relation":"later_version"}]},"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Yaron","full_name":"Velner, Yaron","last_name":"Velner"}],"_id":"2329","external_id":{"arxiv":["1210.3141"]},"volume":8052,"department":[{"_id":"KrCh"}],"date_published":"2013-08-01T00:00:00Z","page":"500 - 515","ec_funded":1,"type":"conference","scopus_import":1,"day":"01","publication_status":"published","status":"public","conference":{"end_date":"2013-08-30","name":"CONCUR: Concurrency Theory","start_date":"2013-08-27","location":"Buenos Aires, Argentinia"},"doi":"10.1007/978-3-642-40184-8_35","publist_id":"4597","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Hyperplane separation technique for multidimensional mean-payoff games","publisher":"Springer","intvolume":"      8052","arxiv":1,"date_updated":"2025-09-10T11:00:30Z","series_title":"Lecture Notes in Computer Science"},{"date_published":"2013-02-01T00:00:00Z","date_updated":"2021-01-12T06:57:17Z","volume":162,"intvolume":"       162","_id":"2404","author":[{"last_name":"Frank","full_name":"Frank, Rupert L","first_name":"Rupert"},{"last_name":"Lewin","first_name":"Mathieu","full_name":"Lewin, Mathieu"},{"first_name":"Élliott","full_name":"Lieb, Élliott H","last_name":"Lieb"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Robert Seiringer","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"title":"A positive density analogue of the Lieb-Thirring inequality","publisher":"Duke University Press","publist_id":"4521","oa":1,"year":"2013","doi":"10.1215/00127094-2019477","issue":"3","quality_controlled":0,"extern":1,"status":"public","publication_status":"published","date_created":"2018-12-11T11:57:28Z","day":"01","month":"02","type":"journal_article","main_file_link":[{"url":"http://arxiv.org/abs/1108.4246","open_access":"1"}],"publication":"Duke Mathematical Journal","abstract":[{"text":"The Lieb-Thirring inequalities give a bound on the negative eigenvalues of a Schrödinger operator in terms of an Lp-norm of the potential. These are dual to bounds on the H1-norms of a system of orthonormal functions. Here we extend these bounds to analogous inequalities for perturbations of the Fermi sea of noninteracting particles (i.e., for perturbations of the continuous spectrum of the Laplacian by local potentials).","lang":"eng"}],"citation":{"chicago":"Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “A Positive Density Analogue of the Lieb-Thirring Inequality.” <i>Duke Mathematical Journal</i>. Duke University Press, 2013. <a href=\"https://doi.org/10.1215/00127094-2019477\">https://doi.org/10.1215/00127094-2019477</a>.","mla":"Frank, Rupert, et al. “A Positive Density Analogue of the Lieb-Thirring Inequality.” <i>Duke Mathematical Journal</i>, vol. 162, no. 3, Duke University Press, 2013, pp. 435–95, doi:<a href=\"https://doi.org/10.1215/00127094-2019477\">10.1215/00127094-2019477</a>.","apa":"Frank, R., Lewin, M., Lieb, É., &#38; Seiringer, R. (2013). A positive density analogue of the Lieb-Thirring inequality. <i>Duke Mathematical Journal</i>. Duke University Press. <a href=\"https://doi.org/10.1215/00127094-2019477\">https://doi.org/10.1215/00127094-2019477</a>","ista":"Frank R, Lewin M, Lieb É, Seiringer R. 2013. A positive density analogue of the Lieb-Thirring inequality. Duke Mathematical Journal. 162(3), 435–495.","short":"R. Frank, M. Lewin, É. Lieb, R. Seiringer, Duke Mathematical Journal 162 (2013) 435–495.","ama":"Frank R, Lewin M, Lieb É, Seiringer R. A positive density analogue of the Lieb-Thirring inequality. <i>Duke Mathematical Journal</i>. 2013;162(3):435-495. doi:<a href=\"https://doi.org/10.1215/00127094-2019477\">10.1215/00127094-2019477</a>","ieee":"R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “A positive density analogue of the Lieb-Thirring inequality,” <i>Duke Mathematical Journal</i>, vol. 162, no. 3. Duke University Press, pp. 435–495, 2013."},"page":"435 - 495"},{"volume":319,"date_updated":"2021-01-12T06:57:17Z","date_published":"2013-04-01T00:00:00Z","publist_id":"4522","title":"Symmetry of bipolaron bound states for small Coulomb repulsion","publisher":"Springer","intvolume":"       319","_id":"2405","author":[{"last_name":"Frank","first_name":"Rupert","full_name":"Frank, Rupert L"},{"first_name":"Élliott","full_name":"Lieb, Élliott H","last_name":"Lieb"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","full_name":"Robert Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"extern":1,"date_created":"2018-12-11T11:57:28Z","status":"public","day":"01","publication_status":"published","quality_controlled":0,"doi":"10.1007/s00220-012-1604-y","issue":"2","year":"2013","oa":1,"page":"557 - 573","publication":"Communications in Mathematical Physics","citation":{"ieee":"R. Frank, É. Lieb, and R. Seiringer, “Symmetry of bipolaron bound states for small Coulomb repulsion,” <i>Communications in Mathematical Physics</i>, vol. 319, no. 2. Springer, pp. 557–573, 2013.","ama":"Frank R, Lieb É, Seiringer R. Symmetry of bipolaron bound states for small Coulomb repulsion. <i>Communications in Mathematical Physics</i>. 2013;319(2):557-573. doi:<a href=\"https://doi.org/10.1007/s00220-012-1604-y\">10.1007/s00220-012-1604-y</a>","short":"R. Frank, É. Lieb, R. Seiringer, Communications in Mathematical Physics 319 (2013) 557–573.","chicago":"Frank, Rupert, Élliott Lieb, and Robert Seiringer. “Symmetry of Bipolaron Bound States for Small Coulomb Repulsion.” <i>Communications in Mathematical Physics</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s00220-012-1604-y\">https://doi.org/10.1007/s00220-012-1604-y</a>.","apa":"Frank, R., Lieb, É., &#38; Seiringer, R. (2013). Symmetry of bipolaron bound states for small Coulomb repulsion. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-012-1604-y\">https://doi.org/10.1007/s00220-012-1604-y</a>","mla":"Frank, Rupert, et al. “Symmetry of Bipolaron Bound States for Small Coulomb Repulsion.” <i>Communications in Mathematical Physics</i>, vol. 319, no. 2, Springer, 2013, pp. 557–73, doi:<a href=\"https://doi.org/10.1007/s00220-012-1604-y\">10.1007/s00220-012-1604-y</a>.","ista":"Frank R, Lieb É, Seiringer R. 2013. Symmetry of bipolaron bound states for small Coulomb repulsion. Communications in Mathematical Physics. 319(2), 557–573."},"abstract":[{"lang":"eng","text":"We consider the bipolaron in the Pekar-Tomasevich approximation and address the question whether the ground state is spherically symmetric or not. Numerical analysis has, so far, not completely settled the question. Our contribution is to prove rigorously that the ground state remains spherical for small values of the electron-electron Coulomb repulsion."}],"type":"journal_article","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1201.3954"}],"month":"04"},{"month":"02","type":"journal_article","publication":"European Physical Journal: Special Topics","abstract":[{"lang":"eng","text":"We study the effects of random scatterers on the ground state of the one-dimensional Lieb-Liniger model of interacting bosons on the unit interval. We prove that, in the Gross-Pitaevskii limit, Bose Einstein condensation takes place in the whole parameter range considered. The character of the wave function of the condensate, however, depends in an essential way on the interplay between randomness and the strength of the two-body interaction. For low density of scatterers or strong interactions the wave function extends over the whole interval. High density of scatterers and weak interaction, on the other hand, leads to localization of the wave function in a fragmented subset of the unit interval."}],"citation":{"short":"R. Seiringer, J. Yngvason, V. Zagrebnov, European Physical Journal: Special Topics 217 (2013) 103–107.","chicago":"Seiringer, Robert, Jakob Yngvason, and Valentin Zagrebnov. “Condensation of Interacting Bosons in a Random Potential.” <i>European Physical Journal: Special Topics</i>. Springer, 2013. <a href=\"https://doi.org/10.1140/epjst/e2013-01759-5\">https://doi.org/10.1140/epjst/e2013-01759-5</a>.","apa":"Seiringer, R., Yngvason, J., &#38; Zagrebnov, V. (2013). Condensation of interacting bosons in a random potential. <i>European Physical Journal: Special Topics</i>. Springer. <a href=\"https://doi.org/10.1140/epjst/e2013-01759-5\">https://doi.org/10.1140/epjst/e2013-01759-5</a>","mla":"Seiringer, Robert, et al. “Condensation of Interacting Bosons in a Random Potential.” <i>European Physical Journal: Special Topics</i>, vol. 217, no. 1, Springer, 2013, pp. 103–07, doi:<a href=\"https://doi.org/10.1140/epjst/e2013-01759-5\">10.1140/epjst/e2013-01759-5</a>.","ista":"Seiringer R, Yngvason J, Zagrebnov V. 2013. Condensation of interacting bosons in a random potential. European Physical Journal: Special Topics. 217(1), 103–107.","ieee":"R. Seiringer, J. Yngvason, and V. Zagrebnov, “Condensation of interacting bosons in a random potential,” <i>European Physical Journal: Special Topics</i>, vol. 217, no. 1. Springer, pp. 103–107, 2013.","ama":"Seiringer R, Yngvason J, Zagrebnov V. Condensation of interacting bosons in a random potential. <i>European Physical Journal: Special Topics</i>. 2013;217(1):103-107. doi:<a href=\"https://doi.org/10.1140/epjst/e2013-01759-5\">10.1140/epjst/e2013-01759-5</a>"},"page":"103 - 107","year":"2013","doi":"10.1140/epjst/e2013-01759-5","issue":"1","quality_controlled":0,"extern":1,"publication_status":"published","status":"public","date_created":"2018-12-11T11:57:29Z","day":"01","intvolume":"       217","_id":"2406","author":[{"full_name":"Robert Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"},{"full_name":"Yngvason, Jakob","first_name":"Jakob","last_name":"Yngvason"},{"full_name":"Zagrebnov, Valentin A","first_name":"Valentin","last_name":"Zagrebnov"}],"title":"Condensation of interacting bosons in a random potential","publisher":"Springer","publist_id":"4520","date_published":"2013-02-01T00:00:00Z","date_updated":"2021-01-12T06:57:17Z","volume":217},{"volume":322,"date_published":"2013-09-01T00:00:00Z","date_updated":"2021-01-12T06:57:18Z","publisher":"Springer","title":"The excitation spectrum for weakly interacting Bosons in a trap","publist_id":"4518","_id":"2408","author":[{"first_name":"Philip","full_name":"Grech, Philip","last_name":"Grech"},{"orcid":"0000-0002-6781-0521","last_name":"Seiringer","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Robert Seiringer"}],"intvolume":"       322","quality_controlled":0,"date_created":"2018-12-11T11:57:29Z","publication_status":"published","day":"01","status":"public","extern":1,"year":"2013","oa":1,"issue":"2","doi":"10.1007/s00220-013-1736-8","abstract":[{"text":"We investigate the low-energy excitation spectrum of a Bose gas confined in a trap, with weak long-range repulsive interactions. In particular, we prove that the spectrum can be described in terms of the eigenvalues of an effective one-particle operator, as predicted by the Bogoliubov approximation.","lang":"eng"}],"citation":{"short":"P. Grech, R. Seiringer, Communications in Mathematical Physics 322 (2013) 559–591.","chicago":"Grech, Philip, and Robert Seiringer. “The Excitation Spectrum for Weakly Interacting Bosons in a Trap.” <i>Communications in Mathematical Physics</i>. Springer, 2013. <a href=\"https://doi.org/10.1007/s00220-013-1736-8\">https://doi.org/10.1007/s00220-013-1736-8</a>.","apa":"Grech, P., &#38; Seiringer, R. (2013). The excitation spectrum for weakly interacting Bosons in a trap. <i>Communications in Mathematical Physics</i>. Springer. <a href=\"https://doi.org/10.1007/s00220-013-1736-8\">https://doi.org/10.1007/s00220-013-1736-8</a>","ista":"Grech P, Seiringer R. 2013. The excitation spectrum for weakly interacting Bosons in a trap. Communications in Mathematical Physics. 322(2), 559–591.","mla":"Grech, Philip, and Robert Seiringer. “The Excitation Spectrum for Weakly Interacting Bosons in a Trap.” <i>Communications in Mathematical Physics</i>, vol. 322, no. 2, Springer, 2013, pp. 559–91, doi:<a href=\"https://doi.org/10.1007/s00220-013-1736-8\">10.1007/s00220-013-1736-8</a>.","ieee":"P. Grech and R. Seiringer, “The excitation spectrum for weakly interacting Bosons in a trap,” <i>Communications in Mathematical Physics</i>, vol. 322, no. 2. Springer, pp. 559–591, 2013.","ama":"Grech P, Seiringer R. The excitation spectrum for weakly interacting Bosons in a trap. <i>Communications in Mathematical Physics</i>. 2013;322(2):559-591. doi:<a href=\"https://doi.org/10.1007/s00220-013-1736-8\">10.1007/s00220-013-1736-8</a>"},"publication":"Communications in Mathematical Physics","page":"559 - 591","month":"09","type":"journal_article","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1205.5259"}]},{"volume":1,"pubrep_id":"398","date_published":"2013-06-13T00:00:00Z","department":[{"_id":"JoBo"},{"_id":"LifeSc"}],"author":[{"first_name":"Rodrigo A","id":"409D5C96-F248-11E8-B48F-1D18A9856A87","full_name":"Fernandes Redondo, Rodrigo A","last_name":"Fernandes Redondo","orcid":"0000-0002-5837-2793"},{"last_name":"Kupczok","full_name":"Kupczok, Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Anne"},{"last_name":"Stift","full_name":"Stift, Gertraud","id":"2DB195CA-F248-11E8-B48F-1D18A9856A87","first_name":"Gertraud"},{"full_name":"Bollback, Jonathan P","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","last_name":"Bollback"}],"_id":"2410","file_date_updated":"2020-07-14T12:45:40Z","quality_controlled":"1","date_created":"2018-12-11T11:57:30Z","language":[{"iso":"eng"}],"oa":1,"year":"2013","issue":"3","citation":{"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>","short":"R.A. Fernandes Redondo, A. Kupczok, G. Stift, J.P. Bollback, Genome Announcements 1 (2013).","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).","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>.","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>"},"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. "}],"file":[{"content_type":"application/pdf","access_level":"open_access","checksum":"0751ec74b695567e0cdf02aaf9c26829","relation":"main_file","file_name":"IST-2015-398-v1+1_Genome_Announc.-2013-Redondo-.pdf","file_id":"5291","creator":"system","date_created":"2018-12-12T10:17:36Z","file_size":130026,"date_updated":"2020-07-14T12:45:40Z"}],"oa_version":"Published Version","month":"06","ddc":["576"],"date_updated":"2024-10-09T20:55:15Z","corr_author":"1","publisher":"American Society for Microbiology","title":"Complete genome sequence of the novel phage MG-B1 infecting bacillus weihenstephanensis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4516","intvolume":"         1","status":"public","day":"13","publication_status":"published","doi":"10.1128/genomeA.00216-13","publication":"Genome Announcements","scopus_import":1,"type":"journal_article","has_accepted_license":"1"},{"publication_status":"published","status":"public","day":"26","doi":"10.1186/1471-2148-13-54","page":"54 - 54","publication":"BMC Evolutionary Biology","type":"journal_article","has_accepted_license":"1","scopus_import":"1","date_updated":"2025-09-29T14:15:59Z","ddc":["576"],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"4514","publisher":"BioMed Central","corr_author":"1","title":"Probabilistic models for CRISPR spacer content evolution ","article_processing_charge":"No","intvolume":"        13","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:57:31Z","file_date_updated":"2020-07-14T12:45:40Z","quality_controlled":"1","issue":"1","oa":1,"year":"2013","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa_version":"Published Version","file":[{"file_size":518729,"date_updated":"2020-07-14T12:45:40Z","creator":"system","date_created":"2018-12-12T10:17:15Z","file_name":"IST-2015-397-v1+1_1471-2148-13-54.pdf","file_id":"5268","relation":"main_file","checksum":"029c7e0b198c19312b66ecce3cabb22f","access_level":"open_access","content_type":"application/pdf"}],"license":"https://creativecommons.org/licenses/by/4.0/","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.","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>","short":"A. Kupczok, J.P. Bollback, BMC Evolutionary Biology 13 (2013) 54–54.","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>.","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>.","ista":"Kupczok A, Bollback JP. 2013. Probabilistic models for CRISPR spacer content evolution . BMC Evolutionary Biology. 13(1), 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"}],"isi":1,"month":"02","volume":13,"external_id":{"isi":["000321524500001"]},"date_published":"2013-02-26T00:00:00Z","pubrep_id":"397","department":[{"_id":"JoBo"}],"author":[{"last_name":"Kupczok","full_name":"Kupczok, Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Anne"},{"full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P","orcid":"0000-0002-4624-4612","last_name":"Bollback"}],"_id":"2412"},{"date_published":"2013-08-01T00:00:00Z","department":[{"_id":"GaTk"}],"publication_identifier":{"isbn":["9783527411986 "],"eisbn":["9783527671632"]},"date_updated":"2025-06-03T11:46:23Z","publisher":"Wiley","title":"Neuronal oscillations scale up and scale down the brain dynamics ","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","editor":[{"last_name":"Meyer","first_name":"Misha","full_name":"Meyer, Misha"},{"last_name":"Pesenson","first_name":"Z.","full_name":"Pesenson, Z."}],"publist_id":"4513","author":[{"last_name":"Valderrama","first_name":"Mario","full_name":"Valderrama, Mario"},{"last_name":"Botella Soler","orcid":"0000-0002-8790-1914","full_name":"Botella Soler, Vicente","id":"421234E8-F248-11E8-B48F-1D18A9856A87","first_name":"Vicente"},{"last_name":"Le Van Quyen","first_name":"Michel","full_name":"Le Van Quyen, Michel"}],"_id":"2413","article_processing_charge":"No","quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:57:31Z","status":"public","day":"01","year":"2013","doi":"10.1002/9783527671632.ch08","citation":{"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>","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.","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>.","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>","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, .","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>.","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."},"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."}],"publication":"Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain","oa_version":"None","month":"08","scopus_import":"1","type":"book_chapter"},{"department":[{"_id":"JiFr"}],"date_published":"2013-12-01T00:00:00Z","external_id":{"isi":["000330955300012"]},"volume":200,"author":[{"id":"4542EF9A-F248-11E8-B48F-1D18A9856A87","first_name":"Sibu","full_name":"Simon, Sibu","last_name":"Simon","orcid":"0000-0002-1998-6741"},{"last_name":"Kubeš","first_name":"Martin","full_name":"Kubeš, Martin"},{"first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","full_name":"Baster, Pawel","last_name":"Baster"},{"last_name":"Robert","first_name":"Stéphanie","full_name":"Robert, Stéphanie"},{"full_name":"Dobrev, Petre","first_name":"Petre","last_name":"Dobrev"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Petrášek","full_name":"Petrášek, Jan","first_name":"Jan"},{"first_name":"Eva","full_name":"Zažímalová, Eva","last_name":"Zažímalová"}],"_id":"2443","issue":"4","oa":1,"year":"2013","date_created":"2018-12-11T11:57:41Z","language":[{"iso":"eng"}],"quality_controlled":"1","project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","grant_number":"282300"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/nph.12437"}],"isi":1,"acknowledgement":"The authors thank Dr Christian Luschnig (University of Natural Resources and Life Sciences (BOKU), Vienna, Austria) for the anti-PIN2 antibody, Professor Mark Estelle (University of California, San Diego, CA, USA) for tir1-1 mutant seeds and, last but not least, to Dr David Morris for critical reading of the manuscript. We also thank Markéta Pařezová and Jana Stýblová for excellent technical assistance. This work was supported by the Grant Agency of the Czech Republic (P305/11/0797 to E.Z. and 13-40637S to J.F.), the Central European Institute of Technology project CZ.1.05/1.1.00/02.0068 from the European Regional Development Fund and by a European Research Council starting independent research grant ERC-2011-StG-20101109-PSDP (to J.F.).","month":"12","oa_version":"Published Version","abstract":[{"text":"The mode of action of auxin is based on its non-uniform distribution within tissues and organs. Despite the wide use of several auxin analogues in research and agriculture, little is known about the specificity of different auxin-related transport and signalling processes towards these compounds. Using seedlings of Arabidopsis thaliana and suspension-cultured cells of Nicotiana tabacum (BY-2), the physiological activity of several auxin analogues was investigated, together with their capacity to induce auxin-dependent gene expression, to inhibit endocytosis and to be transported across the plasma membrane. This study shows that the specificity criteria for different auxin-related processes vary widely. Notably, the special behaviour of some synthetic auxin analogues suggests that they might be useful tools in investigations of the molecular mechanism of auxin action. Thus, due to their differential stimulatory effects on DR5 expression, indole-3-propionic (IPA) and 2,4,5-trichlorophenoxy acetic (2,4,5-T) acids can serve in studies of TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALLING F-BOX (TIR1/AFB)-mediated auxin signalling, and 5-fluoroindole-3-acetic acid (5-F-IAA) can help to discriminate between transcriptional and non-transcriptional pathways of auxin signalling. The results demonstrate that the major determinants for the auxin-like physiological potential of a particular compound are very complex and involve its chemical and metabolic stability, its ability to distribute in tissues in a polar manner and its activity towards auxin signalling machinery.","lang":"eng"}],"citation":{"ieee":"S. Simon <i>et al.</i>, “Defining the selectivity of processes along the auxin response chain: A study using auxin analogues,” <i>New Phytologist</i>, vol. 200, no. 4. Wiley, pp. 1034–1048, 2013.","ama":"Simon S, Kubeš M, Baster P, et al. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. 2013;200(4):1034-1048. doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>","short":"S. Simon, M. Kubeš, P. Baster, S. Robert, P. Dobrev, J. Friml, J. Petrášek, E. Zažímalová, New Phytologist 200 (2013) 1034–1048.","chicago":"Simon, Sibu, Martin Kubeš, Pawel Baster, Stéphanie Robert, Petre Dobrev, Jiří Friml, Jan Petrášek, and Eva Zažímalová. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>. Wiley, 2013. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>.","ista":"Simon S, Kubeš M, Baster P, Robert S, Dobrev P, Friml J, Petrášek J, Zažímalová E. 2013. Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. New Phytologist. 200(4), 1034–1048.","mla":"Simon, Sibu, et al. “Defining the Selectivity of Processes along the Auxin Response Chain: A Study Using Auxin Analogues.” <i>New Phytologist</i>, vol. 200, no. 4, Wiley, 2013, pp. 1034–48, doi:<a href=\"https://doi.org/10.1111/nph.12437\">10.1111/nph.12437</a>.","apa":"Simon, S., Kubeš, M., Baster, P., Robert, S., Dobrev, P., Friml, J., … Zažímalová, E. (2013). Defining the selectivity of processes along the auxin response chain: A study using auxin analogues. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.12437\">https://doi.org/10.1111/nph.12437</a>"},"article_type":"original","date_updated":"2025-09-29T14:15:18Z","article_processing_charge":"No","intvolume":"       200","publist_id":"4460","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Defining the selectivity of processes along the auxin response chain: A study using auxin analogues","publisher":"Wiley","doi":"10.1111/nph.12437","status":"public","day":"01","publication_status":"published","type":"journal_article","scopus_import":"1","page":"1034 - 1048","publication":"New Phytologist","ec_funded":1},{"page":"543 - 558","ec_funded":1,"type":"conference","scopus_import":1,"publication_status":"published","conference":{"name":"CAV: Computer Aided Verification","end_date":"2013-07-19","location":"St. Petersburg, Russia","start_date":"2013-07-13"},"day":"01","status":"public","doi":"10.1007/978-3-642-39799-8_36","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4459","publisher":"Springer","title":"Faster algorithms for Markov decision processes with low treewidth","intvolume":"      8044","arxiv":1,"series_title":"Lecture Notes in Computer Science","date_updated":"2020-08-11T10:09:47Z","oa_version":"Preprint","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."}],"alternative_title":["LNCS"],"citation":{"ieee":"K. Chatterjee and J. Ła̧Cki, “Faster algorithms for Markov decision processes with low treewidth,” vol. 8044. Springer, pp. 543–558, 2013.","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>","short":"K. Chatterjee, J. Ła̧Cki, 8044 (2013) 543–558.","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>.","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>","ista":"Chatterjee K, Ła̧Cki J. 2013. Faster algorithms for Markov decision processes with low treewidth. 8044, 543–558.","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>."},"main_file_link":[{"url":"http://arxiv.org/abs/1304.0084","open_access":"1"}],"month":"07","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:57:42Z","quality_controlled":"1","project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"call_identifier":"FWF","grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"oa":1,"year":"2013","_id":"2444","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"first_name":"Jakub","full_name":"Ła̧Cki, Jakub","last_name":"Ła̧Cki"}],"external_id":{"arxiv":["1304.0084"]},"volume":8044,"date_published":"2013-07-01T00:00:00Z","department":[{"_id":"KrCh"}]},{"_id":"2445","author":[{"last_name":"Cerny","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun"},{"last_name":"Ryzhyk","first_name":"Leonid","full_name":"Ryzhyk, Leonid"},{"full_name":"Tarrach, Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","first_name":"Thorsten","last_name":"Tarrach","orcid":"0000-0003-4409-8487"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1130"}]},"pubrep_id":"199","date_published":"2013-07-01T00:00:00Z","department":[{"_id":"ToHe"}],"volume":8044,"month":"07","oa_version":"Submitted Version","file":[{"checksum":"70c70ca5487faba82262c63e1b678a27","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5158","file_name":"IST-2014-199-v1+1_cav2013-final.pdf","date_created":"2018-12-12T10:15:37Z","creator":"system","date_updated":"2020-07-14T12:45:40Z","file_size":365548}],"alternative_title":["LNCS"],"citation":{"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.","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>","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, T. Tarrach, in:, Springer, 2013, pp. 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>.","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.","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>","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>."},"abstract":[{"lang":"eng","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."}],"year":"2013","oa":1,"date_created":"2018-12-11T11:57:42Z","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:45:40Z","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","intvolume":"      8044","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4458","publisher":"Springer","title":"Efficient synthesis for concurrency by semantics-preserving transformations","date_updated":"2025-04-15T08:11:59Z","ddc":["000","004"],"type":"conference","has_accepted_license":"1","scopus_import":1,"page":"951 - 967","ec_funded":1,"doi":"10.1007/978-3-642-39799-8_68","publication_status":"published","day":"01","status":"public","conference":{"location":"St. Petersburg, Russia","start_date":"2013-07-13","name":"CAV: Computer Aided Verification","end_date":"2013-07-19"}},{"department":[{"_id":"KrCh"}],"date_published":"2013-07-01T00:00:00Z","external_id":{"arxiv":["1304.5281"]},"volume":8044,"_id":"2446","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Gaiser, Andreas","first_name":"Andreas","last_name":"Gaiser"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","full_name":"Kretinsky, Jan","orcid":"0000-0002-8122-2881","last_name":"Kretinsky"}],"oa":1,"year":"2013","project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:57:42Z","month":"07","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1304.5281"}],"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>.","ista":"Chatterjee K, Gaiser A, Kretinsky J. 2013. Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis. 8044, 559–575.","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>","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>.","short":"K. Chatterjee, A. Gaiser, J. Kretinsky, 8044 (2013) 559–575.","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>","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."},"alternative_title":["LNCS"],"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","date_updated":"2020-08-11T10:09:47Z","series_title":"Lecture Notes in Computer Science","arxiv":1,"intvolume":"      8044","title":"Automata with generalized Rabin pairs for probabilistic model checking and LTL synthesis","publisher":"Springer","publist_id":"4457","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-642-39799-8_37","conference":{"end_date":"2013-07-19","name":"CAV: Computer Aided Verification","location":"St. Petersburg, Russia","start_date":"2013-07-13"},"publication_status":"published","day":"01","status":"public","scopus_import":1,"type":"conference","ec_funded":1,"page":"559 - 575"},{"doi":"10.1007/978-3-642-39799-8_54","status":"public","publication_status":"published","conference":{"location":"St. Petersburg, Russia","start_date":"2013-07-13","name":"CAV: Computer Aided Verification","end_date":"2013-07-19"},"day":"01","scopus_import":1,"has_accepted_license":"1","type":"conference","page":"773 - 789","ddc":["000"],"date_updated":"2020-08-11T10:09:47Z","series_title":"Lecture Notes in Computer Science","intvolume":"      8044","article_processing_charge":"No","title":"Automating separation logic using SMT","publisher":"Springer","publist_id":"4456","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"year":"2013","quality_controlled":"1","file_date_updated":"2020-07-14T12:45:41Z","date_created":"2018-12-11T11:57:43Z","language":[{"iso":"eng"}],"month":"07","abstract":[{"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","lang":"eng"}],"citation":{"ieee":"R. Piskac, T. Wies, and D. Zufferey, “Automating separation logic using SMT,” vol. 8044. Springer, pp. 773–789, 2013.","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>","short":"R. Piskac, T. Wies, D. Zufferey, 8044 (2013) 773–789.","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>","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>.","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>."},"alternative_title":["LNCS"],"oa_version":"Submitted Version","file":[{"date_created":"2020-05-15T11:13:01Z","creator":"dernst","date_updated":"2020-07-14T12:45:41Z","file_size":309182,"checksum":"2e866932ab688f47ecd504acb4d5c7d4","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2013_CAV_Piskac.pdf","file_id":"7859"}],"department":[{"_id":"ToHe"}],"date_published":"2013-07-01T00:00:00Z","volume":8044,"author":[{"full_name":"Piskac, Ruzica","first_name":"Ruzica","last_name":"Piskac"},{"id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","full_name":"Wies, Thomas","last_name":"Wies"},{"last_name":"Zufferey","orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien","first_name":"Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"}],"_id":"2447"},{"publisher":"Taylor & Francis","title":"ZIFL1.1 transporter modulates polar auxin transport by stabilizing membrane abundance of multiple PINs in Arabidopsis root tip","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4455","intvolume":"         8","pmid":1,"article_processing_charge":"No","date_updated":"2025-04-15T07:48:02Z","article_type":"original","ec_funded":1,"publication":"Plant Signaling & Behavior","scopus_import":"1","type":"journal_article","publication_status":"published","status":"public","day":"10","doi":"10.4161/psb.25688","_id":"2448","author":[{"last_name":"Remy","first_name":"Estelle","full_name":"Remy, Estelle"},{"last_name":"Baster","full_name":"Baster, Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel"},{"full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml"},{"last_name":"Duque","full_name":"Duque, Paula","first_name":"Paula"}],"external_id":{"pmid":["23857365"]},"volume":8,"article_number":"e25688","date_published":"2013-07-10T00:00:00Z","department":[{"_id":"JiFr"}],"abstract":[{"lang":"eng","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."}],"citation":{"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.","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>","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>.","short":"E. Remy, P. Baster, J. Friml, P. Duque, Plant Signaling &#38; Behavior 8 (2013)."},"oa_version":"Submitted Version","month":"07","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4091088/","open_access":"1"}],"project":[{"call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"quality_controlled":"1","date_created":"2018-12-11T11:57:43Z","language":[{"iso":"eng"}],"year":"2013","oa":1,"issue":"10"},{"title":"Retromer subunits VPS35A and VPS29 mediate prevacuolar compartment (PVC) function in Arabidopsis","corr_author":"1","publisher":"Cell Press","publist_id":"4454","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"         6","article_processing_charge":"No","date_updated":"2025-09-29T14:14:22Z","publication":"Molecular Plant","page":"1849 - 1862","scopus_import":"1","type":"journal_article","status":"public","publication_status":"published","day":"01","doi":"10.1093/mp/sst044","author":[{"full_name":"Nodzyński, Tomasz","first_name":"Tomasz","last_name":"Nodzyński"},{"last_name":"Feraru","first_name":"Murguel","full_name":"Feraru, Murguel"},{"full_name":"Hirsch, Sibylle","first_name":"Sibylle","last_name":"Hirsch"},{"first_name":"Riet","full_name":"De Rycke, Riet","last_name":"De Rycke"},{"last_name":"Nicuales","full_name":"Nicuales, Claudiu","first_name":"Claudiu"},{"last_name":"Van Leene","first_name":"Jelle","full_name":"Van Leene, Jelle"},{"last_name":"De Jaeger","first_name":"Geert","full_name":"De Jaeger, Geert"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jirí"}],"_id":"2449","external_id":{"isi":["000327541200010"]},"volume":6,"department":[{"_id":"JiFr"}],"date_published":"2013-11-01T00:00:00Z","abstract":[{"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. ","lang":"eng"}],"citation":{"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.","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>.","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.","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>.","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>","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.","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>"},"oa_version":"None","month":"11","isi":1,"quality_controlled":"1","date_created":"2018-12-11T11:57:44Z","language":[{"iso":"eng"}],"year":"2013","issue":"6"},{"date_published":"2013-07-01T00:00:00Z","date_updated":"2021-01-12T06:57:33Z","publisher":"Walter de Gruyter","title":"Inhomogeneous cubic congruences and rational points on del Pezzo surfaces","publist_id":"7659","author":[{"last_name":"Baier","first_name":"Stephan","full_name":"Baier, Stephan"},{"first_name":"Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Timothy Browning","orcid":"0000-0002-8314-0177","last_name":"Browning"}],"_id":"245","quality_controlled":0,"date_created":"2018-12-11T11:45:24Z","publication_status":"published","day":"01","status":"public","extern":1,"year":"2013","oa":1,"issue":"680","doi":"10.1515/crelle.2012.039","abstract":[{"lang":"eng","text":"For given non-zero integers a, b, q we investigate the density of solutions (x; y) ∈ ℤ2 to the binary cubic congruence ax2 + by3 ≡ 0 mod q, and use it to establish the Manin conjecture for a singular del Pezzo surface of degree 2 defined over ℚ."}],"citation":{"short":"S. Baier, T.D. Browning, Journal Fur Die Reine Und Angewandte Mathematik (2013) 69–151.","chicago":"Baier, Stephan, and Timothy D Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” <i>Journal Fur Die Reine Und Angewandte Mathematik</i>. Walter de Gruyter, 2013. <a href=\"https://doi.org/10.1515/crelle.2012.039\">https://doi.org/10.1515/crelle.2012.039</a>.","ista":"Baier S, Browning TD. 2013. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. (680), 69–151.","apa":"Baier, S., &#38; Browning, T. D. (2013). Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. <i>Journal Fur Die Reine Und Angewandte Mathematik</i>. Walter de Gruyter. <a href=\"https://doi.org/10.1515/crelle.2012.039\">https://doi.org/10.1515/crelle.2012.039</a>","mla":"Baier, Stephan, and Timothy D. Browning. “Inhomogeneous Cubic Congruences and Rational Points on Del Pezzo Surfaces.” <i>Journal Fur Die Reine Und Angewandte Mathematik</i>, no. 680, Walter de Gruyter, 2013, pp. 69–151, doi:<a href=\"https://doi.org/10.1515/crelle.2012.039\">10.1515/crelle.2012.039</a>.","ieee":"S. Baier and T. D. Browning, “Inhomogeneous cubic congruences and rational points on del Pezzo surfaces,” <i>Journal fur die Reine und Angewandte Mathematik</i>, no. 680. Walter de Gruyter, pp. 69–151, 2013.","ama":"Baier S, Browning TD. Inhomogeneous cubic congruences and rational points on del Pezzo surfaces. <i>Journal fur die Reine und Angewandte Mathematik</i>. 2013;(680):69-151. doi:<a href=\"https://doi.org/10.1515/crelle.2012.039\">10.1515/crelle.2012.039</a>"},"publication":"Journal fur die Reine und Angewandte Mathematik","page":"69 - 151","month":"07","type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1011.3434","open_access":"1"}]},{"citation":{"short":"J. Liu, S. Menhi, J. Topping, J. Friml, K. Lindsey, Frontiers in Plant Science 4 (2013).","mla":"Liu, Junli, et al. “Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis Root Development.” <i>Frontiers in Plant Science</i>, vol. 4, no. 75, Frontiers Research Foundation, 2013, doi:<a href=\"https://doi.org/10.3389/fpls.2013.00075\">10.3389/fpls.2013.00075</a>.","apa":"Liu, J., Menhi, S., Topping, J., Friml, J., &#38; Lindsey, K. (2013). Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. <i>Frontiers in Plant Science</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fpls.2013.00075\">https://doi.org/10.3389/fpls.2013.00075</a>","ista":"Liu J, Menhi S, Topping J, Friml J, Lindsey K. 2013. Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. Frontiers in Plant Science. 4(75).","chicago":"Liu, Junli, Saher Menhi, Jennifer Topping, Jiří Friml, and Keith Lindsey. “Interaction of PLS and PIN and Hormonal Crosstalk in Arabidopsis Root Development.” <i>Frontiers in Plant Science</i>. Frontiers Research Foundation, 2013. <a href=\"https://doi.org/10.3389/fpls.2013.00075\">https://doi.org/10.3389/fpls.2013.00075</a>.","ieee":"J. Liu, S. Menhi, J. Topping, J. Friml, and K. Lindsey, “Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development,” <i>Frontiers in Plant Science</i>, vol. 4, no. 75. Frontiers Research Foundation, 2013.","ama":"Liu J, Menhi S, Topping J, Friml J, Lindsey K. Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development. <i>Frontiers in Plant Science</i>. 2013;4(75). doi:<a href=\"https://doi.org/10.3389/fpls.2013.00075\">10.3389/fpls.2013.00075</a>"},"abstract":[{"lang":"eng","text":"Understanding how hormones and genes interact to coordinate plant growth is a major challenge in developmental biology. The activities of auxin, ethylene, and cytokinin depend on cellular context and exhibit either synergistic or antagonistic interactions. Here we use experimentation and network construction to elucidate the role of the interaction of the POLARIS peptide (PLS) and the auxin efflux carrier PIN proteins in the crosstalk of three hormones (auxin, ethylene, and cytokinin) in Arabidopsis root development. In ethylene hypersignaling mutants such as polaris (pls), we show experimentally that expression of both PIN1 and PIN2 significantly increases. This relationship is analyzed in the context of the crosstalk between auxin, ethylene, and cytokinin: in pls, endogenous auxin, ethylene and cytokinin concentration decreases, approximately remains unchanged and increases, respectively. Experimental data are integrated into a hormonal crosstalk network through combination with information in literature. Network construction reveals that the regulation of both PIN1 and PIN2 is predominantly via ethylene signaling. In addition, it is deduced that the relationship between cytokinin and PIN1 and PIN2 levels implies a regulatory role of cytokinin in addition to its regulation to auxin, ethylene, and PLS levels. We discuss how the network of hormones and genes coordinates plant growth by simultaneously regulating the activities of auxin, ethylene, and cytokinin signaling pathways.hormonal crosstalk, root development, auxin flux, PIN proteins, PLS protein, signaling network"}],"publication":"Frontiers in Plant Science","month":"04","type":"journal_article","quality_controlled":0,"publication_status":"published","day":"01","date_created":"2018-12-11T11:57:44Z","status":"public","extern":1,"year":"2013","issue":"75","doi":"10.3389/fpls.2013.00075","publisher":"Frontiers Research Foundation","title":"Interaction of PLS and PIN and hormonal crosstalk in Arabidopsis root development","publist_id":"4453","author":[{"last_name":"Liu","first_name":"Junli","full_name":"Liu, Junli"},{"first_name":"Saher","full_name":"Menhi, Saher","last_name":"Menhi"},{"first_name":"Jennifer","full_name":"Topping, Jennifer","last_name":"Topping"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml"},{"last_name":"Lindsey","full_name":"Lindsey, Keith","first_name":"Keith"}],"_id":"2450","intvolume":"         4","volume":4,"date_published":"2013-04-01T00:00:00Z","date_updated":"2021-01-12T06:57:34Z"},{"publisher":"BioMed Central","title":"Single-cell-based system to monitor carrier driven cellular auxin homeostasis","publist_id":"4451","_id":"2452","author":[{"last_name":"Barbez","first_name":"Elke","full_name":"Barbez, Elke"},{"first_name":"Martina","full_name":"Laňková, Martina","last_name":"Laňková"},{"last_name":"Pařezová","full_name":"Pařezová, Markéta","first_name":"Markéta"},{"last_name":"Maizel","full_name":"Maizel, Alexis","first_name":"Alexis"},{"last_name":"Zažímalová","first_name":"Eva","full_name":"Zažímalová, Eva"},{"first_name":"Jan","full_name":"Petrášek, Jan","last_name":"Petrášek"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Jirí Friml"},{"last_name":"Kleine Vehn","first_name":"Jürgen","full_name":"Kleine-Vehn, Jürgen"}],"intvolume":"        13","volume":13,"date_published":"2013-02-01T00:00:00Z","date_updated":"2021-01-12T06:57:34Z","abstract":[{"text":"Background: Abundance and distribution of the plant hormone auxin play important roles in plant development. Besides other metabolic processes, various auxin carriers control the cellular level of active auxin and, hence, are major regulators of cellular auxin homeostasis. Despite the developmental importance of auxin transporters, a simple medium-to-high throughput approach to assess carrier activities is still missing. Here we show that carrier driven depletion of cellular auxin correlates with reduced nuclear auxin signaling in tobacco Bright Yellow-2 (BY-2) cell cultures.Results: We developed an easy to use transient single-cell-based system to detect carrier activity. We use the relative changes in signaling output of the auxin responsive promoter element DR5 to indirectly visualize auxin carrier activity. The feasibility of the transient approach was demonstrated by pharmacological and genetic interference with auxin signaling and transport. As a proof of concept, we provide visual evidence that the prominent auxin transport proteins PIN-FORMED (PIN)2 and PIN5 regulate cellular auxin homeostasis at the plasma membrane and endoplasmic reticulum (ER), respectively. Our data suggest that PIN2 and PIN5 have different sensitivities to the auxin transport inhibitor 1-naphthylphthalamic acid (NPA). Also the putative PIN-LIKES (PILS) auxin carrier activity at the ER is insensitive to NPA in our system, indicating that NPA blocks intercellular, but not intracellular auxin transport.Conclusions: This single-cell-based system is a useful tool by which the activity of putative auxin carriers, such as PINs, PILS and WALLS ARE THIN1 (WAT1), can be indirectly visualized in a medium-to-high throughput manner. Moreover, our single cell system might be useful to investigate also other hormonal signaling pathways, such as cytokinin.","lang":"eng"}],"citation":{"ieee":"E. Barbez <i>et al.</i>, “Single-cell-based system to monitor carrier driven cellular auxin homeostasis,” <i>BMC Plant Biology</i>, vol. 13, no. 1. BioMed Central, 2013.","ama":"Barbez E, Laňková M, Pařezová M, et al. Single-cell-based system to monitor carrier driven cellular auxin homeostasis. <i>BMC Plant Biology</i>. 2013;13(1). doi:<a href=\"https://doi.org/10.1186/1471-2229-13-20\">10.1186/1471-2229-13-20</a>","short":"E. Barbez, M. Laňková, M. Pařezová, A. Maizel, E. Zažímalová, J. Petrášek, J. Friml, J. Kleine Vehn, BMC Plant Biology 13 (2013).","apa":"Barbez, E., Laňková, M., Pařezová, M., Maizel, A., Zažímalová, E., Petrášek, J., … Kleine Vehn, J. (2013). Single-cell-based system to monitor carrier driven cellular auxin homeostasis. <i>BMC Plant Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1471-2229-13-20\">https://doi.org/10.1186/1471-2229-13-20</a>","ista":"Barbez E, Laňková M, Pařezová M, Maizel A, Zažímalová E, Petrášek J, Friml J, Kleine Vehn J. 2013. Single-cell-based system to monitor carrier driven cellular auxin homeostasis. BMC Plant Biology. 13(1).","mla":"Barbez, Elke, et al. “Single-Cell-Based System to Monitor Carrier Driven Cellular Auxin Homeostasis.” <i>BMC Plant Biology</i>, vol. 13, no. 1, BioMed Central, 2013, doi:<a href=\"https://doi.org/10.1186/1471-2229-13-20\">10.1186/1471-2229-13-20</a>.","chicago":"Barbez, Elke, Martina Laňková, Markéta Pařezová, Alexis Maizel, Eva Zažímalová, Jan Petrášek, Jiří Friml, and Jürgen Kleine Vehn. “Single-Cell-Based System to Monitor Carrier Driven Cellular Auxin Homeostasis.” <i>BMC Plant Biology</i>. BioMed Central, 2013. <a href=\"https://doi.org/10.1186/1471-2229-13-20\">https://doi.org/10.1186/1471-2229-13-20</a>."},"publication":"BMC Plant Biology","month":"02","type":"journal_article","quality_controlled":0,"date_created":"2018-12-11T11:57:45Z","day":"01","publication_status":"published","status":"public","extern":1,"year":"2013","issue":"1","doi":"10.1186/1471-2229-13-20"},{"date_updated":"2021-01-12T06:57:36Z","date_published":"2013-01-01T00:00:00Z","volume":18,"intvolume":"        18","author":[{"full_name":"Viaene, Tom","first_name":"Tom","last_name":"Viaene"},{"last_name":"Delwiche","full_name":"Delwiche, Charles","first_name":"Charles"},{"last_name":"Rensing","first_name":"Stefan","full_name":"Rensing, Stefan"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"_id":"2457","publist_id":"4446","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Origin and evolution of PIN auxin transporters in the green lineage","publisher":"Cell Press","doi":"10.1016/j.tplants.2012.08.009","issue":"1","year":"2013","extern":"1","status":"public","publication_status":"published","day":"01","date_created":"2018-12-11T11:57:46Z","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","month":"01","oa_version":"None","page":"5 - 10","publication":"Trends in Plant Science","citation":{"ama":"Viaene T, Delwiche C, Rensing S, Friml J. Origin and evolution of PIN auxin transporters in the green lineage. <i>Trends in Plant Science</i>. 2013;18(1):5-10. doi:<a href=\"https://doi.org/10.1016/j.tplants.2012.08.009\">10.1016/j.tplants.2012.08.009</a>","ieee":"T. Viaene, C. Delwiche, S. Rensing, and J. Friml, “Origin and evolution of PIN auxin transporters in the green lineage,” <i>Trends in Plant Science</i>, vol. 18, no. 1. Cell Press, pp. 5–10, 2013.","chicago":"Viaene, Tom, Charles Delwiche, Stefan Rensing, and Jiří Friml. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” <i>Trends in Plant Science</i>. Cell Press, 2013. <a href=\"https://doi.org/10.1016/j.tplants.2012.08.009\">https://doi.org/10.1016/j.tplants.2012.08.009</a>.","mla":"Viaene, Tom, et al. “Origin and Evolution of PIN Auxin Transporters in the Green Lineage.” <i>Trends in Plant Science</i>, vol. 18, no. 1, Cell Press, 2013, pp. 5–10, doi:<a href=\"https://doi.org/10.1016/j.tplants.2012.08.009\">10.1016/j.tplants.2012.08.009</a>.","apa":"Viaene, T., Delwiche, C., Rensing, S., &#38; Friml, J. (2013). Origin and evolution of PIN auxin transporters in the green lineage. <i>Trends in Plant Science</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.tplants.2012.08.009\">https://doi.org/10.1016/j.tplants.2012.08.009</a>","ista":"Viaene T, Delwiche C, Rensing S, Friml J. 2013. Origin and evolution of PIN auxin transporters in the green lineage. Trends in Plant Science. 18(1), 5–10.","short":"T. Viaene, C. Delwiche, S. Rensing, J. Friml, Trends in Plant Science 18 (2013) 5–10."}}]