[{"date_updated":"2023-09-19T14:36:19Z","citation":{"ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria, 2015.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components, IST Austria, 2015.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria; 2015.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, & Anonymous, 4. (2015). Algorithms for algebraic path properties in concurrent systems of constant treewidth components. IST Austria.","mla":"Anonymous, 1, et al. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015.","ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2015. Algorithms for algebraic path properties in concurrent systems of constant treewidth components, IST Austria, 22p.","chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components. IST Austria, 2015."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"author":[{"last_name":"Anonymous","full_name":"Anonymous, 1","first_name":"1"},{"first_name":"2","last_name":"Anonymous","full_name":"Anonymous, 2"},{"last_name":"Anonymous","full_name":"Anonymous, 3","first_name":"3"},{"first_name":"4","last_name":"Anonymous","full_name":"Anonymous, 4"}],"title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","file_date_updated":"2020-07-14T12:46:57Z","_id":"5442","type":"technical_report","pubrep_id":"344","status":"public","year":"2015","publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"has_accepted_license":"1","language":[{"iso":"eng"}],"day":"14","file":[{"date_updated":"2020-07-14T12:46:57Z","file_size":658747,"creator":"system","date_created":"2018-12-12T11:53:37Z","file_name":"IST-2015-343-v2+1_main.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"98fd936102f3e057fc321ef6d316001d","file_id":"5498"},{"content_type":"text/plain","access_level":"closed","relation":"main_file","file_id":"6316","checksum":"b31d09b1241b59c75e1f42dadf09d258","date_updated":"2020-07-14T12:46:57Z","file_size":139,"creator":"dernst","date_created":"2019-04-16T12:36:08Z","file_name":"IST-2015-343-v2+2_anonymous.txt"}],"page":"22","date_created":"2018-12-12T11:39:21Z","related_material":{"record":[{"relation":"later_version","id":"1437","status":"public"},{"relation":"later_version","id":"5441","status":"public"},{"id":"6009","status":"public","relation":"later_version"}]},"date_published":"2015-07-14T00:00:00Z","abstract":[{"text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural properties that arise in program analysis.\r\nWe consider that each component of the concurrent system is a graph with constant treewidth, and it is known that the controlflow graphs of most programs have constant treewidth. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis problems (e.g., alias analysis). The study of multiple queries allows us to consider the tradeoff between the resource usage of the \\emph{one-time} preprocessing and for \\emph{each individual} query. The traditional approaches construct the product graph of all components and apply the best-known graph algorithm on the product. In the traditional approach, even the answer to a single query requires the transitive closure computation (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time.\r\n\r\nOur main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, \r\neach subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results that show that the worst-case running times of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (such as improving \r\nthe worst-case bounds for the shortest path problem in general graphs whose current best-known bound has not been improved in five decades). Finally, we provide a prototype implementation of our algorithms which significantly outperforms the existing algorithmic methods on several benchmarks.","lang":"eng"}],"oa_version":"Published Version","oa":1,"alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","scopus_import":1,"month":"07"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Svoreňová, Mária, Jan Kretinsky, Martin Chmelik, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, 259–68. ACM, 2015. https://doi.org/10.1145/2728606.2728608.","ista":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. 2015. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 259–268.","mla":"Svoreňová, Mária, et al. “Temporal Logic Control for Stochastic Linear Systems Using Abstraction Refinement of Probabilistic Games.” Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 259–68, doi:10.1145/2728606.2728608.","apa":"Svoreňová, M., Kretinsky, J., Chmelik, M., Chatterjee, K., Cěrná, I., & Belta, C. (2015). Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control (pp. 259–268). Seattle, WA, United States: ACM. https://doi.org/10.1145/2728606.2728608","ama":"Svoreňová M, Kretinsky J, Chmelik M, Chatterjee K, Cěrná I, Belta C. Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games. In: Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. ACM; 2015:259-268. doi:10.1145/2728606.2728608","short":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, C. Belta, in:, Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 259–268.","ieee":"M. Svoreňová, J. Kretinsky, M. Chmelik, K. Chatterjee, I. Cěrná, and C. Belta, “Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games,” in Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, Seattle, WA, United States, 2015, pp. 259–268."},"date_updated":"2023-09-20T09:43:09Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"title":"Temporal logic control for stochastic linear systems using abstraction refinement of probabilistic games","author":[{"first_name":"Mária","full_name":"Svoreňová, Mária","last_name":"Svoreňová"},{"first_name":"Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik","full_name":"Chmelik, Martin"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Ivana","last_name":"Cěrná","full_name":"Cěrná, Ivana"},{"last_name":"Belta","full_name":"Belta, Cǎlin","first_name":"Cǎlin"}],"publist_id":"5456","_id":"1689","status":"public","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"conference":{"name":"HSCC: Hybrid Systems - Computation and Control","start_date":"2015-04-14","location":"Seattle, WA, United States","end_date":"2015-04-16"},"type":"conference","language":[{"iso":"eng"}],"publication":"Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control","day":"14","publication_status":"published","year":"2015","date_created":"2018-12-11T11:53:29Z","ec_funded":1,"doi":"10.1145/2728606.2728608","related_material":{"record":[{"relation":"later_version","id":"1407","status":"public"}]},"date_published":"2015-04-14T00:00:00Z","page":"259 - 268","oa_version":"Preprint","abstract":[{"lang":"eng","text":"We consider the problem of computing the set of initial states of a dynamical system such that there exists a control strategy to ensure that the trajectories satisfy a temporal logic specification with probability 1 (almost-surely). We focus on discrete-time, stochastic linear dynamics and specifications given as formulas of the Generalized Reactivity(1) fragment of Linear Temporal Logic over linear predicates in the states of the system. We propose a solution based on iterative abstraction-refinement, and turn-based 2-player probabilistic games. While the theoretical guarantee of our algorithm after any finite number of iterations is only a partial solution, we show that if our algorithm terminates, then the result is the set of satisfying initial states. Moreover, for any (partial) solution our algorithm synthesizes witness control strategies to ensure almost-sure satisfaction of the temporal logic specification. We demonstrate our approach on an illustrative case study."}],"month":"04","oa":1,"main_file_link":[{"url":"http://arxiv.org/abs/1410.5387","open_access":"1"}],"publisher":"ACM","scopus_import":1},{"series_title":"Lecture Notes in Computer Science","_id":"1729","status":"public","pubrep_id":"336","type":"conference","conference":{"start_date":"2015-07-18","end_date":"2015-07-24","location":"San Francisco, CA, United States","name":"CAV: Computer Aided Verification"},"ddc":["000"],"date_updated":"2023-09-20T11:13:50Z","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:13Z","oa_version":"Submitted Version","abstract":[{"text":"We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of such sequences produced under a non-preemptive scheduler. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and rules for inserting synchronization. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient, and, since it does not require explicit specifications, is more practical than the conventional approach based on user-provided assertions.","lang":"eng"}],"month":"07","intvolume":" 9207","alternative_title":["LNCS"],"scopus_import":1,"file":[{"file_id":"4715","checksum":"6ff58ac220e2f20cb001ba35d4924495","content_type":"application/pdf","relation":"main_file","access_level":"local","file_name":"IST-2015-336-v1+1_long_version.pdf","date_created":"2018-12-12T10:08:53Z","file_size":481922,"date_updated":"2020-07-14T12:45:13Z","creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1130"},{"relation":"later_version","id":"1338","status":"public"}]},"volume":9207,"ec_funded":1,"project":[{"grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2015. From non-preemptive to preemptive scheduling using synchronization synthesis. 9207, 180–197.","chicago":"Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-21668-3_11.","ieee":"P. Cerny et al., “From non-preemptive to preemptive scheduling using synchronization synthesis,” vol. 9207. Springer, pp. 180–197, 2015.","short":"P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, 9207 (2015) 180–197.","ama":"Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. 2015;9207:180-197. doi:10.1007/978-3-319-21668-3_11","apa":"Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., & Tarrach, T. (2015). From non-preemptive to preemptive scheduling using synchronization synthesis. Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21668-3_11","mla":"Cerny, Pavol, et al. From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis. Vol. 9207, Springer, 2015, pp. 180–97, doi:10.1007/978-3-319-21668-3_11."},"title":"From non-preemptive to preemptive scheduling using synchronization synthesis","author":[{"last_name":"Cerny","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"},{"last_name":"Clarke","full_name":"Clarke, Edmund","first_name":"Edmund"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ryzhyk","full_name":"Ryzhyk, Leonid","first_name":"Leonid"},{"last_name":"Samanta","full_name":"Samanta, Roopsha","first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tarrach","full_name":"Tarrach, Thorsten","orcid":"0000-0003-4409-8487","first_name":"Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"5398","publisher":"Springer","quality_controlled":"1","day":"01","has_accepted_license":"1","year":"2015","doi":"10.1007/978-3-319-21668-3_11","date_published":"2015-07-01T00:00:00Z","date_created":"2018-12-11T11:53:42Z","page":"180 - 197"},{"_id":"1835","series_title":"Lecture Notes in Computer Science","status":"public","type":"conference","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2015-04-11","end_date":"2015-04-18","location":"London, United Kingdom"},"date_updated":"2023-09-20T11:06:03Z","department":[{"_id":"ToHe"},{"_id":"CaGu"},{"_id":"NiBa"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The behaviour of gene regulatory networks (GRNs) is typically analysed using simulation-based statistical testing-like methods. In this paper, we demonstrate that we can replace this approach by a formal verification-like method that gives higher assurance and scalability. We focus on Wagner’s weighted GRN model with varying weights, which is used in evolutionary biology. In the model, weight parameters represent the gene interaction strength that may change due to genetic mutations. For a property of interest, we synthesise the constraints over the parameter space that represent the set of GRNs satisfying the property. We experimentally show that our parameter synthesis procedure computes the mutational robustness of GRNs –an important problem of interest in evolutionary biology– more efficiently than the classical simulation method. We specify the property in linear temporal logics. We employ symbolic bounded model checking and SMT solving to compute the space of GRNs that satisfy the property, which amounts to synthesizing a set of linear constraints on the weights."}],"month":"04","intvolume":" 9035","alternative_title":["LNCS"],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1410.7704"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":9035,"related_material":{"record":[{"relation":"later_version","id":"1351","status":"public"}]},"ec_funded":1,"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. 2015. Model checking gene regulatory networks. 9035, 469–483.","chicago":"Giacobbe, Mirco, Calin C Guet, Ashutosh Gupta, Thomas A Henzinger, Tiago Paixao, and Tatjana Petrov. “Model Checking Gene Regulatory Networks.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-46681-0_47.","apa":"Giacobbe, M., Guet, C. C., Gupta, A., Henzinger, T. A., Paixao, T., & Petrov, T. (2015). Model checking gene regulatory networks. Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, London, United Kingdom: Springer. https://doi.org/10.1007/978-3-662-46681-0_47","ama":"Giacobbe M, Guet CC, Gupta A, Henzinger TA, Paixao T, Petrov T. Model checking gene regulatory networks. 2015;9035:469-483. doi:10.1007/978-3-662-46681-0_47","short":"M. Giacobbe, C.C. Guet, A. Gupta, T.A. Henzinger, T. Paixao, T. Petrov, 9035 (2015) 469–483.","ieee":"M. Giacobbe, C. C. Guet, A. Gupta, T. A. Henzinger, T. Paixao, and T. Petrov, “Model checking gene regulatory networks,” vol. 9035. Springer, pp. 469–483, 2015.","mla":"Giacobbe, Mirco, et al. Model Checking Gene Regulatory Networks. Vol. 9035, Springer, 2015, pp. 469–83, doi:10.1007/978-3-662-46681-0_47."},"title":"Model checking gene regulatory networks","author":[{"full_name":"Giacobbe, Mirco","orcid":"0000-0001-8180-0904","last_name":"Giacobbe","first_name":"Mirco","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","full_name":"Gupta, Ashutosh","last_name":"Gupta"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Paixao","orcid":"0000-0003-2361-3953","full_name":"Paixao, Tiago","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago"},{"last_name":"Petrov","orcid":"0000-0002-9041-0905","full_name":"Petrov, Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana"}],"publist_id":"5267","acknowledgement":"SNSF Early Postdoc.Mobility Fellowship, the grant number P2EZP2 148797.\r\n","quality_controlled":"1","publisher":"Springer","oa":1,"day":"01","year":"2015","doi":"10.1007/978-3-662-46681-0_47","date_published":"2015-04-01T00:00:00Z","date_created":"2018-12-11T11:54:16Z","page":"469 - 483"},{"date_published":"2015-10-01T00:00:00Z","doi":"10.12688/f1000research.7143.1","date_created":"2018-12-11T11:52:26Z","has_accepted_license":"1","year":"2015","day":"01","publication":"F1000 Research ","publisher":"F1000 Research","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by ERC Independent Research grant (ERC-2011-StG-20101109-PSDP to JF). JM internship was supported by the grant “Action Austria – Slovakia”.\r\nData associated with the article are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication). \r\n\r\nData availability: \r\nF1000Research: Dataset 1. Dataset 1, 10.5256/f1000research.7143.d104552\r\n\r\nF1000Research: Dataset 2. Dataset 2, 10.5256/f1000research.7143.d104553\r\n\r\nF1000Research: Dataset 3. Dataset 3, 10.5256/f1000research.7143.d104554","publist_id":"5668","author":[{"id":"483727CA-F248-11E8-B48F-1D18A9856A87","first_name":"Jaroslav","full_name":"Michalko, Jaroslav","last_name":"Michalko"},{"first_name":"Marta","id":"4342E402-F248-11E8-B48F-1D18A9856A87","full_name":"Dravecka, Marta","orcid":"0000-0002-2519-8004","last_name":"Dravecka"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bollenbach","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"}],"article_processing_charge":"No","title":"Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene","citation":{"chicago":"Michalko, Jaroslav, Marta Lukacisinova, Mark Tobias Bollenbach, and Jiří Friml. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” F1000 Research . F1000 Research, 2015. https://doi.org/10.12688/f1000research.7143.1.","ista":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. 2015. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 4.","mla":"Michalko, Jaroslav, et al. “Embryo-Lethal Phenotypes in Early Abp1 Mutants Are Due to Disruption of the Neighboring BSM Gene.” F1000 Research , vol. 4, F1000 Research, 2015, doi:10.12688/f1000research.7143.1.","ieee":"J. Michalko, M. Lukacisinova, M. T. Bollenbach, and J. Friml, “Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene,” F1000 Research , vol. 4. F1000 Research, 2015.","short":"J. Michalko, M. Lukacisinova, M.T. Bollenbach, J. Friml, F1000 Research 4 (2015).","apa":"Michalko, J., Lukacisinova, M., Bollenbach, M. T., & Friml, J. (2015). Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . F1000 Research. https://doi.org/10.12688/f1000research.7143.1","ama":"Michalko J, Lukacisinova M, Bollenbach MT, Friml J. Embryo-lethal phenotypes in early abp1 mutants are due to disruption of the neighboring BSM gene. F1000 Research . 2015;4. doi:10.12688/f1000research.7143.1"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"volume":4,"ec_funded":1,"publication_status":"published","file":[{"file_name":"IST-2016-497-v1+1_10.12688_f1000research.7143.1_20151102.pdf","date_created":"2018-12-12T10:16:12Z","creator":"system","file_size":4414248,"date_updated":"2020-07-14T12:44:59Z","checksum":"8beae5cbe988e1060265ae7de2ee8306","file_id":"5198","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"10","intvolume":" 4","abstract":[{"text":"The Auxin Binding Protein1 (ABP1) has been identified based on its ability to bind auxin with high affinity and studied for a long time as a prime candidate for the extracellular auxin receptor responsible for mediating in particular the fast non-transcriptional auxin responses. However, the contradiction between the embryo-lethal phenotypes of the originally described Arabidopsis T-DNA insertional knock-out alleles (abp1-1 and abp1-1s) and the wild type-like phenotypes of other recently described loss-of-function alleles (abp1-c1 and abp1-TD1) questions the biological importance of ABP1 and relevance of the previous genetic studies. Here we show that there is no hidden copy of the ABP1 gene in the Arabidopsis genome but the embryo-lethal phenotypes of abp1-1 and abp1-1s alleles are very similar to the knock-out phenotypes of the neighboring gene, BELAYA SMERT (BSM). Furthermore, the allelic complementation test between bsm and abp1 alleles shows that the embryo-lethality in the abp1-1 and abp1-1s alleles is caused by the off-target disruption of the BSM locus by the T-DNA insertions. This clarifies the controversy of different phenotypes among published abp1 knock-out alleles and asks for reflections on the developmental role of ABP1.","lang":"eng"}],"oa_version":"Published Version","department":[{"_id":"JiFr"},{"_id":"ToBo"}],"file_date_updated":"2020-07-14T12:44:59Z","date_updated":"2023-10-10T14:10:24Z","ddc":["570"],"type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","pubrep_id":"497","_id":"1509"}]