[{"file":[{"creator":"system","checksum":"0b2ef8c4037ffccc6902d93081af24f7","date_created":"2018-12-12T10:16:33Z","relation":"main_file","file_name":"IST-2012-43-v1+1_GIST-_A_solver_for_probabilistic_games.pdf","date_updated":"2020-07-14T12:46:28Z","access_level":"open_access","file_size":293605,"file_id":"5221","content_type":"application/pdf"}],"ddc":["004"],"abstract":[{"text":"GIST is a tool that (a) solves the qualitative analysis problem of turn-based probabilistic games with ω-regular objectives; and (b) synthesizes reasonable environment assumptions for synthesis of unrealizable specifications. Our tool provides the first and efficient implementations of several reduction-based techniques to solve turn-based probabilistic games, and uses the analysis of turn-based probabilistic games for synthesizing environment assumptions for unrealizable specifications.","lang":"eng"}],"date_published":"2010-07-01T00:00:00Z","status":"public","quality_controlled":"1","has_accepted_license":"1","article_processing_charge":"No","scopus_import":1,"month":"07","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Barbara","full_name":"Jobstmann, Barbara","last_name":"Jobstmann"},{"last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5393"}]},"language":[{"iso":"eng"}],"ec_funded":1,"arxiv":1,"oa_version":"Submitted Version","doi":"10.1007/978-3-642-14295-6_57","page":"665 - 669","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"43","publisher":"Springer","oa":1,"intvolume":"      6174","volume":6174,"publist_id":"1068","external_id":{"arxiv":["1004.2367"]},"title":"GIST: A solver for probabilistic games","day":"01","year":"2010","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"citation":{"short":"K. Chatterjee, T.A. Henzinger, B. Jobstmann, A. Radhakrishna, in:, Springer, 2010, pp. 665–669.","apa":"Chatterjee, K., Henzinger, T. A., Jobstmann, B., &#38; Radhakrishna, A. (2010). GIST: A solver for probabilistic games (Vol. 6174, pp. 665–669). Presented at the CAV: Computer Aided Verification, Edinburgh, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-642-14295-6_57\">https://doi.org/10.1007/978-3-642-14295-6_57</a>","ista":"Chatterjee K, Henzinger TA, Jobstmann B, Radhakrishna A. 2010. GIST: A solver for probabilistic games. CAV: Computer Aided Verification, LNCS, vol. 6174, 665–669.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Arjun Radhakrishna. “GIST: A Solver for Probabilistic Games,” 6174:665–69. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-14295-6_57\">https://doi.org/10.1007/978-3-642-14295-6_57</a>.","mla":"Chatterjee, Krishnendu, et al. <i>GIST: A Solver for Probabilistic Games</i>. Vol. 6174, Springer, 2010, pp. 665–69, doi:<a href=\"https://doi.org/10.1007/978-3-642-14295-6_57\">10.1007/978-3-642-14295-6_57</a>.","ama":"Chatterjee K, Henzinger TA, Jobstmann B, Radhakrishna A. GIST: A solver for probabilistic games. In: Vol 6174. Springer; 2010:665-669. doi:<a href=\"https://doi.org/10.1007/978-3-642-14295-6_57\">10.1007/978-3-642-14295-6_57</a>","ieee":"K. Chatterjee, T. A. Henzinger, B. Jobstmann, and A. Radhakrishna, “GIST: A solver for probabilistic games,” presented at the CAV: Computer Aided Verification, Edinburgh, UK, 2010, vol. 6174, pp. 665–669."},"date_updated":"2023-02-23T12:24:17Z","_id":"4388","project":[{"_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"COMponent-Based Embedded Systems design Techniques","grant_number":"215543"},{"grant_number":"214373","call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems"}],"file_date_updated":"2020-07-14T12:46:28Z","conference":{"location":"Edinburgh, UK","start_date":"2010-07-15","end_date":"2010-07-17","name":"CAV: Computer Aided Verification"},"date_created":"2018-12-11T12:08:36Z","alternative_title":["LNCS"],"publication_status":"published"},{"year":"2010","publist_id":"1069","title":"Robustness of sequential circuits","day":"23","date_created":"2018-12-11T12:08:36Z","publication_status":"published","department":[{"_id":"ToHe"}],"citation":{"ieee":"L. Doyen, T. A. Henzinger, A. Legay, and D. Nickovic, “Robustness of sequential circuits,” presented at the ACSD: Application of Concurrency to System Design, 2010, pp. 77–84.","chicago":"Doyen, Laurent, Thomas A Henzinger, Axel Legay, and Dejan Nickovic. “Robustness of Sequential Circuits,” 77–84. IEEE, 2010. <a href=\"https://doi.org/10.1109/ACSD.2010.26\">https://doi.org/10.1109/ACSD.2010.26</a>.","mla":"Doyen, Laurent, et al. <i>Robustness of Sequential Circuits</i>. IEEE, 2010, pp. 77–84, doi:<a href=\"https://doi.org/10.1109/ACSD.2010.26\">10.1109/ACSD.2010.26</a>.","ama":"Doyen L, Henzinger TA, Legay A, Nickovic D. Robustness of sequential circuits. In: IEEE; 2010:77-84. doi:<a href=\"https://doi.org/10.1109/ACSD.2010.26\">10.1109/ACSD.2010.26</a>","short":"L. Doyen, T.A. Henzinger, A. Legay, D. Nickovic, in:, IEEE, 2010, pp. 77–84.","apa":"Doyen, L., Henzinger, T. A., Legay, A., &#38; Nickovic, D. (2010). Robustness of sequential circuits (pp. 77–84). Presented at the ACSD: Application of Concurrency to System Design, IEEE. <a href=\"https://doi.org/10.1109/ACSD.2010.26\">https://doi.org/10.1109/ACSD.2010.26</a>","ista":"Doyen L, Henzinger TA, Legay A, Nickovic D. 2010. Robustness of sequential circuits. ACSD: Application of Concurrency to System Design, 77–84."},"date_updated":"2021-01-12T07:56:36Z","_id":"4389","file_date_updated":"2020-07-14T12:46:28Z","conference":{"name":"ACSD: Application of Concurrency to System Design"},"has_accepted_license":"1","scopus_import":1,"month":"08","author":[{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Axel","full_name":"Legay, Axel","last_name":"Legay"},{"first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","last_name":"Nickovic","full_name":"Nickovic, Dejan"}],"file":[{"file_size":159920,"access_level":"open_access","content_type":"application/pdf","file_id":"4733","file_name":"IST-2012-44-v1+1_Robustness_of_sequential_circuits.pdf","date_updated":"2020-07-14T12:46:28Z","relation":"main_file","date_created":"2018-12-12T10:09:10Z","creator":"system","checksum":"42b2952bfc6b6974617bd554842b904a"}],"ddc":["004"],"abstract":[{"text":"Digital components play a central role in the design of complex embedded systems. These components are interconnected with other, possibly analog, devices and the physical environment. This environment cannot be entirely captured and can provide inaccurate input data to the component. It is thus important for digital components to have a robust behavior, i.e. the presence of a small change in the input sequences should not result in a drastic change in the output sequences. In this paper, we study a notion of robustness for sequential circuits. However, since sequential circuits may have parts that are naturally discontinuous (e.g., digital controllers with switching behavior), we need a flexible framework that accommodates this fact and leaves discontinuous parts of the circuit out from the robustness analysis. As a consequence, we consider sequential circuits that have their input variables partitioned into two disjoint sets: control and disturbance variables. Our contributions are (1) a definition of robustness for sequential circuits as a form of continuity with respect to disturbance variables, (2) the characterization of the exact class of sequential circuits that are robust according to our definition, (3) an algorithm to decide whether a sequential circuit is robust or not.","lang":"eng"}],"date_published":"2010-08-23T00:00:00Z","status":"public","quality_controlled":"1","publisher":"IEEE","oa":1,"language":[{"iso":"eng"}],"oa_version":"Submitted Version","doi":"10.1109/ACSD.2010.26","page":"77 - 84","type":"conference","pubrep_id":"44","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"year":"2010","volume":6174,"publist_id":"1066","title":"Model checking of linearizability of concurrent list implementations","day":"01","date_created":"2018-12-11T12:08:36Z","alternative_title":["LNCS"],"publication_status":"published","department":[{"_id":"ToHe"}],"citation":{"ieee":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, “Model checking of linearizability of concurrent list implementations,” presented at the CAV: Computer Aided Verification, Edinburgh, UK, 2010, vol. 6174, pp. 465–479.","short":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, in:, Springer, 2010, pp. 465–479.","apa":"Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., &#38; Alur, R. (2010). Model checking of linearizability of concurrent list implementations (Vol. 6174, pp. 465–479). Presented at the CAV: Computer Aided Verification, Edinburgh, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-642-14295-6_41\">https://doi.org/10.1007/978-3-642-14295-6_41</a>","ista":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking of linearizability of concurrent list implementations. CAV: Computer Aided Verification, LNCS, vol. 6174, 465–479.","chicago":"Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and Rajeev Alur. “Model Checking of Linearizability of Concurrent List Implementations,” 6174:465–79. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-14295-6_41\">https://doi.org/10.1007/978-3-642-14295-6_41</a>.","mla":"Cerny, Pavol, et al. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. Vol. 6174, Springer, 2010, pp. 465–79, doi:<a href=\"https://doi.org/10.1007/978-3-642-14295-6_41\">10.1007/978-3-642-14295-6_41</a>.","ama":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. Model checking of linearizability of concurrent list implementations. In: Vol 6174. Springer; 2010:465-479. doi:<a href=\"https://doi.org/10.1007/978-3-642-14295-6_41\">10.1007/978-3-642-14295-6_41</a>"},"date_updated":"2023-02-23T12:24:12Z","_id":"4390","file_date_updated":"2020-07-14T12:46:28Z","conference":{"name":"CAV: Computer Aided Verification","end_date":"2010-07-17","start_date":"2010-07-15","location":"Edinburgh, UK"},"has_accepted_license":"1","article_processing_charge":"No","month":"07","author":[{"full_name":"Cerny, Pavol","last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna"},{"orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien","full_name":"Zufferey, Damien","last_name":"Zufferey"},{"full_name":"Chaudhuri, Swarat","last_name":"Chaudhuri","first_name":"Swarat"},{"last_name":"Alur","full_name":"Alur, Rajeev","first_name":"Rajeev"}],"file":[{"date_updated":"2020-07-14T12:46:28Z","file_name":"2010_CAV_Cerny.pdf","content_type":"application/pdf","file_id":"7873","file_size":3633276,"access_level":"open_access","checksum":"2eb211ce40b3c4988bce3a3592980704","creator":"dernst","relation":"main_file","date_created":"2020-05-19T16:31:56Z"}],"ddc":["000"],"abstract":[{"lang":"eng","text":"Concurrent data structures with fine-grained synchronization are notoriously difficult to implement correctly. The difficulty of reasoning about these implementations does not stem from the number of variables or the program size, but rather from the large number of possible interleavings. These implementations are therefore prime candidates for model checking. We introduce an algorithm for verifying linearizability of singly-linked heap-based concurrent data structures. We consider a model consisting of an unbounded heap where each vertex stores an element from an unbounded data domain, with a restricted set of operations for testing and updating pointers and data elements. Our main result is that linearizability is decidable for programs that invoke a fixed number of methods, possibly in parallel. This decidable fragment covers many of the common implementation techniques — fine-grained locking, lazy synchronization, and lock-free synchronization. We also show how the technique can be used to verify optimistic implementations with the help of programmer annotations. We developed a verification tool CoLT and evaluated it on a representative sample of Java implementations of the concurrent set data structure. The tool verified linearizability of a number of implementations, found a known error in a lock-free implementation and proved that the corrected version is linearizable."}],"date_published":"2010-07-01T00:00:00Z","status":"public","quality_controlled":"1","oa":1,"publisher":"Springer","intvolume":"      6174","related_material":{"record":[{"status":"public","id":"5391","relation":"earlier_version"}]},"language":[{"iso":"eng"}],"oa_version":"Submitted Version","page":"465 - 479","doi":"10.1007/978-3-642-14295-6_41","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"27"},{"quality_controlled":"1","series_title":"Essays in Memory of Amir Pnueli","status":"public","date_published":"2010-07-29T00:00:00Z","abstract":[{"lang":"eng","text":"While a boolean notion of correctness is given by a preorder on systems and properties, a quantitative notion of correctness is defined by a distance function on systems and properties, where the distance between a system and a property provides a measure of “fit” or “desirability.” In this article, we explore several ways how the simulation preorder can be generalized to a distance function. This is done by equipping the classical simulation game between a system and a property with quantitative objectives. In particular, for systems that satisfy a property, a quantitative simulation game can measure the “robustness” of the satisfaction, that is, how much the system can deviate from its nominal behavior while still satisfying the property. For systems that violate a property, a quantitative simulation game can measure the “seriousness” of the violation, that is, how much the property has to be modified so that it is satisfied by the system. These distances can be computed in polynomial time, since the computation reduces to the value problem in limit average games with constant weights. Finally, we demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes. "}],"author":[{"full_name":"Cerny, Pavol","last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun"}],"month":"07","scopus_import":1,"editor":[{"first_name":"Zohar","full_name":"Manna, Zohar","last_name":"Manna"},{"first_name":"Doron","full_name":"Peled, Doron","last_name":"Peled"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","doi":"10.1007/978-3-642-13754-9_3","page":"42 - 60","publication":"Time For Verification: Essays in Memory of Amir Pnueli","oa_version":"None","language":[{"iso":"eng"}],"ec_funded":1,"intvolume":"      6200","publisher":"Springer","day":"29","title":"Quantitative Simulation Games","publist_id":"1064","volume":6200,"year":"2010","project":[{"grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"25F1337C-B435-11E9-9278-68D0E5697425","name":"Design for Embedded Systems","grant_number":"214373"}],"_id":"4392","date_updated":"2021-01-12T07:56:38Z","citation":{"ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Quantitative Simulation Games,” in <i>Time For Verification: Essays in Memory of Amir Pnueli</i>, vol. 6200, Z. Manna and D. Peled, Eds. Springer, 2010, pp. 42–60.","mla":"Cerny, Pavol, et al. “Quantitative Simulation Games.” <i>Time For Verification: Essays in Memory of Amir Pnueli</i>, edited by Zohar Manna and Doron Peled, vol. 6200, Springer, 2010, pp. 42–60, doi:<a href=\"https://doi.org/10.1007/978-3-642-13754-9_3\">10.1007/978-3-642-13754-9_3</a>.","ama":"Cerny P, Henzinger TA, Radhakrishna A. Quantitative Simulation Games. In: Manna Z, Peled D, eds. <i>Time For Verification: Essays in Memory of Amir Pnueli</i>. Vol 6200. Essays in Memory of Amir Pnueli. Springer; 2010:42-60. doi:<a href=\"https://doi.org/10.1007/978-3-642-13754-9_3\">10.1007/978-3-642-13754-9_3</a>","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Quantitative Simulation Games.” In <i>Time For Verification: Essays in Memory of Amir Pnueli</i>, edited by Zohar Manna and Doron Peled, 6200:42–60. Essays in Memory of Amir Pnueli. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-13754-9_3\">https://doi.org/10.1007/978-3-642-13754-9_3</a>.","apa":"Cerny, P., Henzinger, T. A., &#38; Radhakrishna, A. (2010). Quantitative Simulation Games. In Z. Manna &#38; D. Peled (Eds.), <i>Time For Verification: Essays in Memory of Amir Pnueli</i> (Vol. 6200, pp. 42–60). Springer. <a href=\"https://doi.org/10.1007/978-3-642-13754-9_3\">https://doi.org/10.1007/978-3-642-13754-9_3</a>","ista":"Cerny P, Henzinger TA, Radhakrishna A. 2010.Quantitative Simulation Games. In: Time For Verification: Essays in Memory of Amir Pnueli. LNCS, vol. 6200, 42–60.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, in:, Z. Manna, D. Peled (Eds.), Time For Verification: Essays in Memory of Amir Pnueli, Springer, 2010, pp. 42–60."},"department":[{"_id":"ToHe"}],"publication_status":"published","alternative_title":["LNCS"],"date_created":"2018-12-11T12:08:37Z"},{"ddc":["005"],"abstract":[{"text":"Boolean notions of correctness are formalized by preorders on systems. Quantitative measures of correctness can be formalized by real-valued distance functions between systems, where the distance between implementation and specification provides a measure of “fit” or “desirability.” We extend the simulation preorder to the quantitative setting, by making each player of a simulation game pay a certain price for her choices. We use the resulting games with quantitative objectives to define three different simulation distances. The correctness distance measures how much the specification must be changed in order to be satisfied by the implementation. The coverage distance measures how much the implementation restricts the degrees of freedom offered by the specification. The robustness distance measures how much a system can deviate from the implementation description without violating the specification. We consider these distances for safety as well as liveness specifications. The distances can be computed in polynomial time for safety specifications, and for liveness specifications given by weak fairness constraints. We show that the distance functions satisfy the triangle inequality, that the distance between two systems does not increase under parallel composition with a third system, and that the distance between two systems can be bounded from above and below by distances between abstractions of the two systems. These properties suggest that our simulation distances provide an appropriate basis for a quantitative theory of discrete systems. We also demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes.","lang":"eng"}],"date_published":"2010-11-01T00:00:00Z","file":[{"date_created":"2018-12-12T10:15:12Z","relation":"main_file","checksum":"ea567903676ba8afe0507ee11313dce5","creator":"system","file_id":"5130","content_type":"application/pdf","access_level":"open_access","file_size":198913,"file_name":"IST-2012-42-v1+1_Simulation_distances.pdf","date_updated":"2020-07-14T12:46:28Z"}],"quality_controlled":"1","status":"public","has_accepted_license":"1","month":"11","author":[{"first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","full_name":"Cerny, Pavol"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna"}],"scopus_import":1,"language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Submitted Version","related_material":{"record":[{"relation":"later_version","id":"3249","status":"public"},{"relation":"earlier_version","id":"5389","status":"public"}]},"type":"conference","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pubrep_id":"42","page":"235 - 268","doi":"10.1007/978-3-642-15375-4_18","intvolume":"      6269","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publist_id":"1065","acknowledgement":"This work was partially supported by the European Union project COMBEST and the European Network of Excellence ArtistDesign.","volume":6269,"title":"Simulation distances","day":"01","year":"2010","department":[{"_id":"ToHe"}],"citation":{"ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Simulation distances,” presented at the CONCUR: Concurrency Theory, Paris, France, 2010, vol. 6269, pp. 235–268.","ama":"Cerny P, Henzinger TA, Radhakrishna A. Simulation distances. In: Vol 6269. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:235-268. doi:<a href=\"https://doi.org/10.1007/978-3-642-15375-4_18\">10.1007/978-3-642-15375-4_18</a>","mla":"Cerny, Pavol, et al. <i>Simulation Distances</i>. Vol. 6269, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 235–68, doi:<a href=\"https://doi.org/10.1007/978-3-642-15375-4_18\">10.1007/978-3-642-15375-4_18</a>.","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Simulation Distances,” 6269:235–68. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. <a href=\"https://doi.org/10.1007/978-3-642-15375-4_18\">https://doi.org/10.1007/978-3-642-15375-4_18</a>.","ista":"Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances. CONCUR: Concurrency Theory, LNCS, vol. 6269, 235–268.","apa":"Cerny, P., Henzinger, T. A., &#38; Radhakrishna, A. (2010). Simulation distances (Vol. 6269, pp. 235–268). Presented at the CONCUR: Concurrency Theory, Paris, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/978-3-642-15375-4_18\">https://doi.org/10.1007/978-3-642-15375-4_18</a>","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 235–268."},"file_date_updated":"2020-07-14T12:46:28Z","project":[{"grant_number":"215543","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques"},{"grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Design for Embedded Systems"}],"conference":{"name":"CONCUR: Concurrency Theory","end_date":"2010-09-03","start_date":"2010-08-31","location":"Paris, France"},"date_updated":"2023-02-23T12:24:04Z","_id":"4393","date_created":"2018-12-11T12:08:37Z","publication_status":"published","alternative_title":["LNCS"]},{"date_created":"2018-12-11T12:08:38Z","publication_status":"published","alternative_title":["LNCS"],"citation":{"ieee":"D. Beyer, T. A. Henzinger, G. Théoduloz, and D. Zufferey, “Shape refinement through explicit heap analysis,” presented at the FASE: Fundamental Approaches To Software Engineering, Paphos, Cyprus, 2010, vol. 6013, pp. 263–277.","mla":"Beyer, Dirk, et al. <i>Shape Refinement through Explicit Heap Analysis</i>. Edited by David Rosenblum and Gabriele Taenzer, vol. 6013, Springer, 2010, pp. 263–77, doi:<a href=\"https://doi.org/10.1007/978-3-642-12029-9_19\">10.1007/978-3-642-12029-9_19</a>.","ama":"Beyer D, Henzinger TA, Théoduloz G, Zufferey D. Shape refinement through explicit heap analysis. In: Rosenblum D, Taenzer G, eds. Vol 6013. Springer; 2010:263-277. doi:<a href=\"https://doi.org/10.1007/978-3-642-12029-9_19\">10.1007/978-3-642-12029-9_19</a>","chicago":"Beyer, Dirk, Thomas A Henzinger, Grégory Théoduloz, and Damien Zufferey. “Shape Refinement through Explicit Heap Analysis.” edited by David Rosenblum and Gabriele Taenzer, 6013:263–77. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-12029-9_19\">https://doi.org/10.1007/978-3-642-12029-9_19</a>.","apa":"Beyer, D., Henzinger, T. A., Théoduloz, G., &#38; Zufferey, D. (2010). Shape refinement through explicit heap analysis. In D. Rosenblum &#38; G. Taenzer (Eds.) (Vol. 6013, pp. 263–277). Presented at the FASE: Fundamental Approaches To Software Engineering, Paphos, Cyprus: Springer. <a href=\"https://doi.org/10.1007/978-3-642-12029-9_19\">https://doi.org/10.1007/978-3-642-12029-9_19</a>","ista":"Beyer D, Henzinger TA, Théoduloz G, Zufferey D. 2010. Shape refinement through explicit heap analysis. FASE: Fundamental Approaches To Software Engineering, LNCS, vol. 6013, 263–277.","short":"D. Beyer, T.A. Henzinger, G. Théoduloz, D. Zufferey, in:, D. Rosenblum, G. Taenzer (Eds.), Springer, 2010, pp. 263–277."},"department":[{"_id":"ToHe"}],"conference":{"start_date":"2010-03-20","location":"Paphos, Cyprus","name":"FASE: Fundamental Approaches To Software Engineering","end_date":"2010-03-28"},"file_date_updated":"2020-07-14T12:46:29Z","project":[{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"_id":"4396","date_updated":"2021-01-12T07:56:40Z","year":"2010","publist_id":"1061","volume":6013,"day":"21","title":"Shape refinement through explicit heap analysis","intvolume":"      6013","oa":1,"publisher":"Springer","oa_version":"Submitted Version","language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","pubrep_id":"41","type":"conference","page":"263 - 277","doi":"10.1007/978-3-642-12029-9_19","has_accepted_license":"1","editor":[{"first_name":"David","last_name":"Rosenblum","full_name":"Rosenblum, David"},{"first_name":"Gabriele","last_name":"Taenzer","full_name":"Taenzer, Gabriele"}],"author":[{"first_name":"Dirk","last_name":"Beyer","full_name":"Beyer, Dirk"},{"first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"first_name":"Grégory","full_name":"Théoduloz, Grégory","last_name":"Théoduloz"},{"full_name":"Zufferey, Damien","last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736","first_name":"Damien"}],"month":"04","scopus_import":1,"date_published":"2010-04-21T00:00:00Z","ddc":["004"],"abstract":[{"text":"Shape analysis is a promising technique to prove program properties about recursive data structures. The challenge is to automatically determine the data-structure type, and to supply the shape analysis with the necessary information about the data structure. We present a stepwise approach to the selection of instrumentation predicates for a TVLA-based shape analysis, which takes us a step closer towards the fully automatic verification of data structures. The approach uses two techniques to guide the refinement of shape abstractions: (1) during program exploration, an explicit heap analysis collects sample instances of the heap structures, which are used to identify the data structures that are manipulated by the program; and (2) during abstraction refinement along an infeasible error path, we consider different possible heap abstractions and choose the coarsest one that eliminates the infeasible path. We have implemented this combined approach for automatic shape refinement as an extension of the software model checker BLAST. Example programs from a data-structure library that manipulate doubly-linked lists and trees were successfully verified by our tool.","lang":"eng"}],"file":[{"file_size":312147,"access_level":"open_access","content_type":"application/pdf","file_id":"5332","date_updated":"2020-07-14T12:46:29Z","file_name":"IST-2012-41-v1+1_Shape_refinement_through_explicit_heap_analysis.pdf","relation":"main_file","date_created":"2018-12-12T10:18:13Z","creator":"system","checksum":"7d26e59a9681487d7283eba337292b2c"}],"quality_controlled":"1","status":"public"},{"date_published":"2010-09-01T00:00:00Z","publist_id":"2780","abstract":[{"text":"Classical models of gene flow fail in three ways: they cannot explain large-scale patterns; they predict much more genetic diversity than is observed; and they assume that loosely linked genetic loci evolve independently. We propose a new model that deals with these problems. Extinction events kill some fraction of individuals in a region. These are replaced by offspring from a small number of parents, drawn from the preexisting population. This model of evolution forwards in time corresponds to a backwards model, in which ancestral lineages jump to a new location if they are hit by an event, and may coalesce with other lineages that are hit by the same event. We derive an expression for the identity in allelic state, and show that, over scales much larger than the largest event, this converges to the classical value derived by Wright and Malécot. However, rare events that cover large areas cause low genetic diversity, large-scale patterns, and correlations in ancestry between unlinked loci.","lang":"eng"}],"volume":64,"acknowledgement":"This work has made use of the resources provided by the Edinburgh Compute and Data Facility (ECDF). The ECDF is partially supported by the eDIKT initiative. NHB is supported in part by EPSRC Grant EP/E066070/1; JK is supported by EPSRC Grant EP/E066070/1; and AME is supported in part by EPSRC Grant EP/E065945/1.","quality_controlled":"1","day":"01","title":"A new model for extinction and recolonization in two dimensions: Quantifying phylogeography","status":"public","issue":"9","year":"2010","author":[{"last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"full_name":"Kelleher, Jerome","last_name":"Kelleher","first_name":"Jerome"},{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"}],"month":"09","scopus_import":1,"oa_version":"None","publication":"Evolution","citation":{"ieee":"N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for extinction and recolonization in two dimensions: Quantifying phylogeography,” <i>Evolution</i>, vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.","mla":"Barton, Nicholas H., et al. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” <i>Evolution</i>, vol. 64, no. 9, Wiley-Blackwell, 2010, pp. 2701–15, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">10.1111/j.1558-5646.2010.01019.x</a>.","ama":"Barton NH, Kelleher J, Etheridge A. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. <i>Evolution</i>. 2010;64(9):2701-2715. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">10.1111/j.1558-5646.2010.01019.x</a>","chicago":"Barton, Nicholas H, Jerome Kelleher, and Alison Etheridge. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” <i>Evolution</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">https://doi.org/10.1111/j.1558-5646.2010.01019.x</a>.","ista":"Barton NH, Kelleher J, Etheridge A. 2010. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. 64(9), 2701–2715.","apa":"Barton, N. H., Kelleher, J., &#38; Etheridge, A. (2010). A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. <i>Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">https://doi.org/10.1111/j.1558-5646.2010.01019.x</a>","short":"N.H. Barton, J. Kelleher, A. Etheridge, Evolution 64 (2010) 2701–2715."},"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","doi":"10.1111/j.1558-5646.2010.01019.x","_id":"474","page":"2701 - 2715","date_updated":"2021-01-12T08:00:52Z","intvolume":"        64","publisher":"Wiley-Blackwell","date_created":"2018-12-11T11:46:40Z","publication_status":"published"},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"intvolume":"         8","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"oa_version":"Published Version","language":[{"iso":"eng"}],"doi":"10.4230/LIPIcs.FSTTCS.2010.1","page":"1 - 12","pubrep_id":"948","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","has_accepted_license":"1","scopus_import":1,"author":[{"last_name":"Alur","full_name":"Alur, Rajeev","first_name":"Rajeev"},{"full_name":"Cerny, Pavol","last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"}],"month":"01","file":[{"date_created":"2018-12-12T10:08:29Z","relation":"main_file","checksum":"5845be5aa19791830f7407d8853f2df0","creator":"system","file_id":"4690","content_type":"application/pdf","access_level":"open_access","file_size":492344,"date_updated":"2020-07-14T12:46:35Z","file_name":"IST-2018-948-v1+1_2011_Cerny_Expressiveness_of.pdf"}],"date_published":"2010-01-01T00:00:00Z","ddc":["005"],"abstract":[{"lang":"eng","text":"Streaming string transducers [1] define (partial) functions from input strings to output strings. A streaming string transducer makes a single pass through the input string and uses a finite set of variables that range over strings from the output alphabet. At every step, the transducer processes an input symbol, and updates all the variables in parallel using assignments whose right-hand-sides are concatenations of output symbols and variables with the restriction that a variable can be used at most once in a right-hand-side expression. It has been shown that streaming string transducers operating on strings over infinite data domains are of interest in algorithmic verification of list-processing programs, as they lead to PSPACE decision procedures for checking pre/post conditions and for checking semantic equivalence, for a well-defined class of heap-manipulating programs. In order to understand the theoretical expressiveness of streaming transducers, we focus on streaming transducers processing strings over finite alphabets, given the existence of a robust and well-studied class of &quot;regular&quot; transductions for this case. Such regular transductions can be defined either by two-way deterministic finite-state transducers, or using a logical MSO-based characterization. Our main result is that the expressiveness of streaming string transducers coincides exactly with this class of regular transductions. "}],"status":"public","quality_controlled":"1","date_created":"2018-12-11T11:46:45Z","alternative_title":["LIPIcs"],"publication_status":"published","citation":{"short":"R. Alur, P. Cerny, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12.","ista":"Alur R, Cerny P. 2010. Expressiveness of streaming string transducers. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 8, 1–12.","apa":"Alur, R., &#38; Cerny, P. (2010). Expressiveness of streaming string transducers (Vol. 8, pp. 1–12). Presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Chennai, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1</a>","chicago":"Alur, Rajeev, and Pavol Cerny. “Expressiveness of Streaming String Transducers,” 8:1–12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1</a>.","ama":"Alur R, Cerny P. Expressiveness of streaming string transducers. In: Vol 8. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:1-12. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">10.4230/LIPIcs.FSTTCS.2010.1</a>","mla":"Alur, Rajeev, and Pavol Cerny. <i>Expressiveness of Streaming String Transducers</i>. Vol. 8, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">10.4230/LIPIcs.FSTTCS.2010.1</a>.","ieee":"R. Alur and P. Cerny, “Expressiveness of streaming string transducers,” presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Chennai, India, 2010, vol. 8, pp. 1–12."},"department":[{"_id":"ToHe"}],"_id":"488","date_updated":"2021-01-12T08:01:00Z","conference":{"location":"Chennai, India","start_date":"2010-12-15","end_date":"2010-12-18","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science"},"file_date_updated":"2020-07-14T12:46:35Z","year":"2010","volume":8,"publist_id":"7331","day":"01","title":"Expressiveness of streaming string transducers"},{"alternative_title":["EPTCS"],"publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1006.1404v1","open_access":"1"}],"date_created":"2018-12-11T11:46:45Z","date_updated":"2021-01-12T08:01:01Z","_id":"489","conference":{"location":"Minori, Amalfi Coast, Italy","start_date":"2010-06-17","end_date":"2010-06-18","name":"GandALF: Games, Automata, Logic, and Formal Verification"},"department":[{"_id":"KrCh"}],"citation":{"ieee":"J. Cristau, C. David, and F. Horn, “How do we remember the past in randomised strategies? ,” in <i>Proceedings of GandALF 2010</i>, Minori, Amalfi Coast, Italy, 2010, vol. 25, pp. 30–39.","ama":"Cristau J, David C, Horn F. How do we remember the past in randomised strategies? . In: <i>Proceedings of GandALF 2010</i>. Vol 25. Open Publishing Association; 2010:30-39. doi:<a href=\"https://doi.org/10.4204/EPTCS.25.7\">10.4204/EPTCS.25.7</a>","mla":"Cristau, Julien, et al. “How Do We Remember the Past in Randomised Strategies? .” <i>Proceedings of GandALF 2010</i>, vol. 25, Open Publishing Association, 2010, pp. 30–39, doi:<a href=\"https://doi.org/10.4204/EPTCS.25.7\">10.4204/EPTCS.25.7</a>.","chicago":"Cristau, Julien, Claire David, and Florian Horn. “How Do We Remember the Past in Randomised Strategies? .” In <i>Proceedings of GandALF 2010</i>, 25:30–39. Open Publishing Association, 2010. <a href=\"https://doi.org/10.4204/EPTCS.25.7\">https://doi.org/10.4204/EPTCS.25.7</a>.","ista":"Cristau J, David C, Horn F. 2010. How do we remember the past in randomised strategies? . Proceedings of GandALF 2010. GandALF: Games, Automata, Logic, and Formal Verification, EPTCS, vol. 25, 30–39.","apa":"Cristau, J., David, C., &#38; Horn, F. (2010). How do we remember the past in randomised strategies? . In <i>Proceedings of GandALF 2010</i> (Vol. 25, pp. 30–39). Minori, Amalfi Coast, Italy: Open Publishing Association. <a href=\"https://doi.org/10.4204/EPTCS.25.7\">https://doi.org/10.4204/EPTCS.25.7</a>","short":"J. Cristau, C. David, F. Horn, in:, Proceedings of GandALF 2010, Open Publishing Association, 2010, pp. 30–39."},"year":"2010","title":"How do we remember the past in randomised strategies? ","day":"09","volume":25,"publist_id":"7332","publisher":"Open Publishing Association","oa":1,"intvolume":"        25","page":"30 - 39","doi":"10.4204/EPTCS.25.7","type":"conference","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"Proceedings of GandALF 2010","oa_version":"Published Version","scopus_import":1,"month":"06","author":[{"first_name":"Julien","last_name":"Cristau","full_name":"Cristau, Julien"},{"first_name":"Claire","last_name":"David","full_name":"David, Claire"},{"last_name":"Horn","full_name":"Horn, Florian","first_name":"Florian","id":"37327ACE-F248-11E8-B48F-1D18A9856A87"}],"status":"public","quality_controlled":"1","abstract":[{"text":"Graph games of infinite length are a natural model for open reactive processes: one player represents the controller, trying to ensure a given specification, and the other represents a hostile environment. The evolution of the system depends on the decisions of both players, supplemented by chance. In this work, we focus on the notion of randomised strategy. More specifically, we show that three natural definitions may lead to very different results: in the most general cases, an almost-surely winning situation may become almost-surely losing if the player is only allowed to use a weaker notion of strategy. In more reasonable settings, translations exist, but they require infinite memory, even in simple cases. Finally, some traditional problems becomes undecidable for the strongest type of strategies.","lang":"eng"}],"date_published":"2010-06-09T00:00:00Z"},{"volume":37,"date_published":"2010-12-01T00:00:00Z","publist_id":"7284","abstract":[{"lang":"eng","text":"Any programming error that can be revealed before compiling a program saves precious time for the programmer. While integrated development environments already do a good job by detecting, e.g., data-flow abnormalities, current static analysis tools suffer from false positives (&quot;noise&quot;) or require strong user interaction. We propose to avoid this deficiency by defining a new class of errors. A program fragment is doomed if its execution will inevitably fail, regardless of which state it is started in. We use a formal verification method to identify such errors fully automatically and, most significantly, without producing noise. We report on experiments with a prototype tool."}],"status":"public","day":"01","quality_controlled":"1","title":"Doomed program points","issue":"2-3","year":"2010","scopus_import":1,"author":[{"first_name":"Jochen","last_name":"Hoenicke","full_name":"Hoenicke, Jochen"},{"first_name":"Kari","last_name":"Leino","full_name":"Leino, Kari"},{"full_name":"Podelski, Andreas","last_name":"Podelski","first_name":"Andreas"},{"full_name":"Schäf, Martin","last_name":"Schäf","first_name":"Martin"},{"first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","last_name":"Wies","full_name":"Wies, Thomas"}],"month":"12","publication":"Formal Methods in System Design","citation":{"ieee":"J. Hoenicke, K. Leino, A. Podelski, M. Schäf, and T. Wies, “Doomed program points,” <i>Formal Methods in System Design</i>, vol. 37, no. 2–3. Springer, pp. 171–199, 2010.","ama":"Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. Doomed program points. <i>Formal Methods in System Design</i>. 2010;37(2-3):171-199. doi:<a href=\"https://doi.org/10.1007/s10703-010-0102-0\">10.1007/s10703-010-0102-0</a>","mla":"Hoenicke, Jochen, et al. “Doomed Program Points.” <i>Formal Methods in System Design</i>, vol. 37, no. 2–3, Springer, 2010, pp. 171–99, doi:<a href=\"https://doi.org/10.1007/s10703-010-0102-0\">10.1007/s10703-010-0102-0</a>.","chicago":"Hoenicke, Jochen, Kari Leino, Andreas Podelski, Martin Schäf, and Thomas Wies. “Doomed Program Points.” <i>Formal Methods in System Design</i>. Springer, 2010. <a href=\"https://doi.org/10.1007/s10703-010-0102-0\">https://doi.org/10.1007/s10703-010-0102-0</a>.","apa":"Hoenicke, J., Leino, K., Podelski, A., Schäf, M., &#38; Wies, T. (2010). Doomed program points. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-010-0102-0\">https://doi.org/10.1007/s10703-010-0102-0</a>","ista":"Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. 2010. Doomed program points. Formal Methods in System Design. 37(2–3), 171–199.","short":"J. Hoenicke, K. Leino, A. Podelski, M. Schäf, T. Wies, Formal Methods in System Design 37 (2010) 171–199."},"oa_version":"None","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"_id":"533","doi":"10.1007/s10703-010-0102-0","page":"171 - 199","date_updated":"2021-01-12T08:01:28Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publisher":"Springer","date_created":"2018-12-11T11:47:01Z","intvolume":"        37","publication_status":"published"},{"status":"public","title":"Quantitative synthesis for concurrent programs","day":"07","file":[{"content_type":"application/pdf","file_id":"5515","file_size":429101,"access_level":"open_access","file_name":"IST-2010-0004_IST-2010-0004.pdf","date_updated":"2020-07-14T12:46:42Z","relation":"main_file","date_created":"2018-12-12T11:53:53Z","checksum":"da38782d2388a6fa32109d10bb9bad67","creator":"system"}],"abstract":[{"lang":"eng","text":"We present an algorithmic method for the synthesis of concurrent programs that are optimal with respect to quantitative performance measures. The input consists of a sequential sketch, that is, a program that does not contain synchronization constructs, and of a parametric performance model that assigns costs to actions such as locking, context switching, and idling. The quantitative synthesis problem is to automatically introduce synchronization constructs into the sequential sketch so that both correctness is guaranteed and worst-case (or average-case) performance is optimized. Correctness is formalized as race freedom or linearizability.\r\n\r\nWe show that for worst-case performance, the problem can be modeled\r\nas a 2-player graph game with quantitative (limit-average) objectives, and\r\nfor average-case performance, as a 2 1/2 -player graph game (with probabilistic transitions). In both cases, the optimal correct program is derived from an optimal strategy in the corresponding quantitative game. We prove that the respective game problems are computationally expensive (NP-complete), and present several techniques that overcome the theoretical difficulty in cases of concurrent programs of practical interest.\r\n\r\nWe have implemented a prototype tool and used it for the automatic syn- thesis of programs that access a concurrent list. For certain parameter val- ues, our method automatically synthesizes various classical synchronization schemes for implementing a concurrent list, such as fine-grained locking or a lazy algorithm. For other parameter values, a new, hybrid synchronization style is synthesized, which uses both the lazy approach and coarse-grained locks (instead of standard fine-grained locks). The trade-off occurs because while fine-grained locking tends to decrease the cost that is due to waiting for locks, it increases cache size requirements."}],"ddc":["000","005"],"date_published":"2010-10-07T00:00:00Z","month":"10","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"last_name":"Cerny","full_name":"Cerny, Pavol","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A"},{"last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rohit","full_name":"Singh, Rohit","last_name":"Singh"}],"year":"2010","has_accepted_license":"1","date_updated":"2023-02-23T11:24:08Z","_id":"5388","doi":"10.15479/AT:IST-2010-0004","page":"17","type":"technical_report","file_date_updated":"2020-07-14T12:46:42Z","pubrep_id":"24","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2664-1690"]},"related_material":{"record":[{"status":"public","id":"3366","relation":"later_version"}]},"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"language":[{"iso":"eng"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>.","ama":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>","chicago":"Chatterjee, Krishnendu, Pavol Cerny, Thomas A Henzinger, Arjun Radhakrishna, and Rohit Singh. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>.","apa":"Chatterjee, K., Cerny, P., Henzinger, T. A., Radhakrishna, A., &#38; Singh, R. (2010). <i>Quantitative synthesis for concurrent programs</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>","ista":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. 2010. Quantitative synthesis for concurrent programs, IST Austria, 17p.","short":"K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative Synthesis for Concurrent Programs, IST Austria, 2010.","ieee":"K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, <i>Quantitative synthesis for concurrent programs</i>. IST Austria, 2010."},"oa_version":"Published Version","alternative_title":["IST Austria Technical Report"],"publication_status":"published","oa":1,"publisher":"IST Austria","date_created":"2018-12-12T11:39:03Z"},{"related_material":{"record":[{"status":"public","id":"3249","relation":"later_version"},{"relation":"later_version","id":"4393","status":"public"}]},"department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"citation":{"ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, <i>Simulation distances</i>. IST Austria, 2010.","ista":"Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances, IST Austria, 24p.","apa":"Cerny, P., Henzinger, T. A., &#38; Radhakrishna, A. (2010). <i>Simulation distances</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, Simulation Distances, IST Austria, 2010.","mla":"Cerny, Pavol, et al. <i>Simulation Distances</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>.","ama":"Cerny P, Henzinger TA, Radhakrishna A. <i>Simulation Distances</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. <i>Simulation Distances</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>."},"oa_version":"Published Version","date_updated":"2023-02-23T12:09:16Z","_id":"5389","doi":"10.15479/AT:IST-2010-0003","page":"24","file_date_updated":"2020-07-14T12:46:42Z","type":"technical_report","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2664-1690"]},"pubrep_id":"25","date_created":"2018-12-12T11:39:03Z","publisher":"IST Austria","oa":1,"alternative_title":["IST Austria Technical Report"],"publication_status":"published","file":[{"content_type":"application/pdf","file_id":"5547","file_size":367246,"access_level":"open_access","file_name":"IST-2010-0003_IST-2010-0003.pdf","date_updated":"2020-07-14T12:46:42Z","relation":"main_file","date_created":"2018-12-12T11:54:25Z","checksum":"284ded99764e32a583a8ea83fcea254b","creator":"system"}],"ddc":["005"],"abstract":[{"text":"Boolean notions of correctness are formalized by preorders on systems. Quantitative measures of correctness can be formalized by real-valued distance functions between systems, where the distance between implementation and specification provides a measure of “fit” or “desirability.” We extend the simulation preorder to the quantitative setting, by making each player of a simulation game pay a certain price for her choices. We use the resulting games with quantitative objectives to define three different simulation distances. The correctness distance measures how much the specification must be changed in order to be satisfied by the implementation. The coverage distance measures how much the im- plementation restricts the degrees of freedom offered by the specification. The robustness distance measures how much a system can deviate from the implementation description without violating the specification. We consider these distances for safety as well as liveness specifications. The distances can be computed in polynomial time for safety specifications, and for liveness specifications given by weak fairness constraints. We show that the distance functions satisfy the triangle inequality, that the distance between two systems does not increase under parallel composition with a third system, and that the distance between two systems can be bounded from above and below by distances between abstractions of the two systems. These properties suggest that our simulation distances provide an appropriate basis for a quantitative theory of discrete systems. We also demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes.","lang":"eng"}],"date_published":"2010-06-04T00:00:00Z","status":"public","title":"Simulation distances","day":"04","year":"2010","has_accepted_license":"1","month":"06","author":[{"first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","full_name":"Cerny, Pavol"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna"}]},{"alternative_title":["IST Austria Technical Report"],"publication_status":"published","date_created":"2018-12-12T11:39:03Z","oa":1,"publisher":"IST Austria","_id":"5390","doi":"10.15479/AT:IST-2010-0002","page":"21","date_updated":"2020-07-14T23:04:41Z","pubrep_id":"26","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2664-1690"]},"type":"technical_report","file_date_updated":"2020-07-14T12:46:43Z","citation":{"mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">10.15479/AT:IST-2010-0002</a>.","ama":"Chatterjee K, Fijalkow N. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">10.15479/AT:IST-2010-0002</a>","chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">https://doi.org/10.15479/AT:IST-2010-0002</a>.","ista":"Chatterjee K, Fijalkow N. 2010. Topological, automata-theoretic and logical characterization of finitary languages, IST Austria, 21p.","apa":"Chatterjee, K., &#38; Fijalkow, N. (2010). <i>Topological, automata-theoretic and logical characterization of finitary languages</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">https://doi.org/10.15479/AT:IST-2010-0002</a>","short":"K. Chatterjee, N. Fijalkow, Topological, Automata-Theoretic and Logical Characterization of Finitary Languages, IST Austria, 2010.","ieee":"K. Chatterjee and N. Fijalkow, <i>Topological, automata-theoretic and logical characterization of finitary languages</i>. IST Austria, 2010."},"oa_version":"Published Version","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Fijalkow, Nathanaël","last_name":"Fijalkow","first_name":"Nathanaël"}],"month":"06","year":"2010","has_accepted_license":"1","status":"public","day":"04","title":"Topological, automata-theoretic and logical characterization of finitary languages","file":[{"content_type":"application/pdf","file_id":"5532","file_size":395662,"access_level":"open_access","date_updated":"2020-07-14T12:46:43Z","file_name":"IST-2010-0002_IST-2010-0002.pdf","relation":"main_file","date_created":"2018-12-12T11:54:10Z","checksum":"283d3604d76dd4d5161585d4c8625fbe","creator":"system"}],"date_published":"2010-06-04T00:00:00Z","abstract":[{"text":"The class of ω regular languages provide a robust specification language in verification. Every ω-regular condition can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. In this work we consider the finitary parity and Streett (fairness) conditions. We present the topological, automata-theoretic and logical characterization of finitary languages defined by finitary parity and Streett conditions. We (a) show that the finitary parity and Streett languages are Σ2-complete; (b) present a complete characterization of the expressive power of various classes of automata with finitary and infinitary conditions (in particular we show that non-deterministic finitary parity and Streett automata cannot be determinized to deterministic finitary parity or Streett automata); and (c) show that the languages defined by non-deterministic finitary parity automata exactly characterize the star-free fragment of ωB-regular languages.","lang":"eng"}],"ddc":["000"]},{"author":[{"full_name":"Cerny, Pavol","last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"},{"last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"},{"id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736","first_name":"Damien","full_name":"Zufferey, Damien","last_name":"Zufferey"},{"first_name":"Swarat","last_name":"Chaudhuri","full_name":"Chaudhuri, Swarat"},{"first_name":"Rajeev","last_name":"Alur","full_name":"Alur, Rajeev"}],"month":"04","has_accepted_license":"1","year":"2010","day":"19","title":"Model checking of linearizability of concurrent list implementations","status":"public","date_published":"2010-04-19T00:00:00Z","ddc":["004"],"abstract":[{"text":"Concurrent data structures with fine-grained synchronization are notoriously difficult to implement correctly. The difficulty of reasoning about these implementations does not stem from the number of variables or the program size, but rather from the large number of possible interleavings. These implementations are therefore prime candidates for model checking. We introduce an algorithm for verifying linearizability of singly-linked heap-based concurrent data structures. We consider a model consisting of an unbounded heap where each node consists an element from an unbounded data domain, with a restricted set of operations for testing and updating pointers and data elements. Our main result is that linearizability is decidable for programs that invoke a fixed number of methods, possibly in parallel. This decidable fragment covers many of the common implementation techniques — fine-grained locking, lazy synchronization, and lock-free synchronization. We also show how the technique can be used to verify optimistic implementations with the help of programmer annotations. We developed a verification tool CoLT and evaluated it on a representative sample of Java implementations of the concurrent set data structure. The tool verified linearizability of a number of implementations, found a known error in a lock-free imple- mentation and proved that the corrected version is linearizable.","lang":"eng"}],"file":[{"relation":"main_file","date_created":"2018-12-12T11:53:44Z","creator":"system","checksum":"986645caad7dd85a6a091488f6c646dc","file_size":372286,"access_level":"open_access","content_type":"application/pdf","file_id":"5505","date_updated":"2020-07-14T12:46:43Z","file_name":"IST-2010-0001_IST-2010-0001.pdf"}],"publication_status":"published","alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","oa":1,"date_created":"2018-12-12T11:39:04Z","publication_identifier":{"issn":["2664-1690"]},"pubrep_id":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:46:43Z","type":"technical_report","_id":"5391","page":"27","doi":"10.15479/AT:IST-2010-0001","date_updated":"2023-02-23T12:09:09Z","citation":{"ama":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">10.15479/AT:IST-2010-0001</a>","mla":"Cerny, Pavol, et al. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">10.15479/AT:IST-2010-0001</a>.","chicago":"Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and Rajeev Alur. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">https://doi.org/10.15479/AT:IST-2010-0001</a>.","ista":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking of linearizability of concurrent list implementations, IST Austria, 27p.","apa":"Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., &#38; Alur, R. (2010). <i>Model checking of linearizability of concurrent list implementations</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">https://doi.org/10.15479/AT:IST-2010-0001</a>","short":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, Model Checking of Linearizability of Concurrent List Implementations, IST Austria, 2010.","ieee":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, <i>Model checking of linearizability of concurrent list implementations</i>. IST Austria, 2010."},"oa_version":"Published Version","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"4390"}]}},{"scopus_import":"1","article_processing_charge":"No","author":[{"first_name":"Assaf ","full_name":"Zemach, Assaf ","last_name":"Zemach"},{"first_name":"Ivy E.","full_name":"McDaniel, Ivy E.","last_name":"McDaniel"},{"last_name":"Silva","full_name":"Silva, Pedro","first_name":"Pedro"},{"full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel"}],"month":"05","article_type":"original","status":"public","quality_controlled":"1","date_published":"2010-05-14T00:00:00Z","abstract":[{"text":"Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes.","lang":"eng"}],"publisher":"American Association for the Advancement of Science","intvolume":"       328","doi":"10.1126/science.1186366","page":"916-919","keyword":["Multidisciplinary"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"type":"journal_article","extern":"1","oa_version":"None","publication":"Science","language":[{"iso":"eng"}],"issue":"5980","year":"2010","external_id":{"pmid":["20395474 "]},"day":"14","title":"Genome-wide evolutionary analysis of eukaryotic DNA methylation","volume":328,"publication_status":"published","date_created":"2021-06-04T08:26:08Z","pmid":1,"_id":"9452","date_updated":"2021-12-14T08:35:37Z","citation":{"ieee":"A. Zemach, I. E. McDaniel, P. Silva, and D. Zilberman, “Genome-wide evolutionary analysis of eukaryotic DNA methylation,” <i>Science</i>, vol. 328, no. 5980. American Association for the Advancement of Science, pp. 916–919, 2010.","short":"A. Zemach, I.E. McDaniel, P. Silva, D. Zilberman, Science 328 (2010) 916–919.","apa":"Zemach, A., McDaniel, I. E., Silva, P., &#38; Zilberman, D. (2010). Genome-wide evolutionary analysis of eukaryotic DNA methylation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1186366\">https://doi.org/10.1126/science.1186366</a>","ista":"Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 328(5980), 916–919.","chicago":"Zemach, Assaf , Ivy E. McDaniel, Pedro Silva, and Daniel Zilberman. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” <i>Science</i>. American Association for the Advancement of Science, 2010. <a href=\"https://doi.org/10.1126/science.1186366\">https://doi.org/10.1126/science.1186366</a>.","ama":"Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. <i>Science</i>. 2010;328(5980):916-919. doi:<a href=\"https://doi.org/10.1126/science.1186366\">10.1126/science.1186366</a>","mla":"Zemach, Assaf, et al. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” <i>Science</i>, vol. 328, no. 5980, American Association for the Advancement of Science, 2010, pp. 916–19, doi:<a href=\"https://doi.org/10.1126/science.1186366\">10.1126/science.1186366</a>."},"department":[{"_id":"DaZi"}]},{"quality_controlled":"1","article_type":"original","status":"public","date_published":"2010-10-26T00:00:00Z","abstract":[{"lang":"eng","text":"Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops."}],"author":[{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"},{"first_name":"M. Yvonne","last_name":"Kim","full_name":"Kim, M. Yvonne"},{"first_name":"Pedro","last_name":"Silva","full_name":"Silva, Pedro"},{"first_name":"Jessica A.","full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues"},{"last_name":"Dotson","full_name":"Dotson, Bradley","first_name":"Bradley"},{"full_name":"Brooks, Matthew D.","last_name":"Brooks","first_name":"Matthew D."},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman"}],"month":"10","scopus_import":"1","article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"type":"journal_article","page":"18729-18734","doi":"10.1073/pnas.1009695107","oa_version":"Published Version","publication":"Proceedings of the National Academy of Sciences","language":[{"iso":"eng"}],"extern":"1","intvolume":"       107","publisher":"National Academy of Sciences","oa":1,"day":"26","title":"Local DNA hypomethylation activates genes in rice endosperm","external_id":{"pmid":["20937895"]},"volume":107,"issue":"43","year":"2010","_id":"9485","date_updated":"2021-12-14T08:40:02Z","citation":{"ieee":"A. Zemach <i>et al.</i>, “Local DNA hypomethylation activates genes in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43. National Academy of Sciences, pp. 18729–18734, 2010.","short":"A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D. Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734.","ista":"Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D. 2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 107(43), 18729–18734.","apa":"Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M. D., &#38; Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>","chicago":"Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>.","mla":"Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43, National Academy of Sciences, 2010, pp. 18729–34, doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>.","ama":"Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2010;107(43):18729-18734. doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>"},"department":[{"_id":"DaZi"}],"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1009695107","open_access":"1"}],"publication_status":"published","pmid":1,"date_created":"2021-06-07T09:31:01Z"},{"intvolume":"        20","oa":1,"publisher":"Elsevier","publication":"Current Biology","oa_version":"Published Version","language":[{"iso":"eng"}],"extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"type":"journal_article","page":"R780-R785","doi":"10.1016/j.cub.2010.07.007","author":[{"last_name":"Zemach","full_name":"Zemach, Assaf","first_name":"Assaf"},{"last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649"}],"month":"09","article_processing_charge":"No","scopus_import":"1","date_published":"2010-09-14T00:00:00Z","abstract":[{"lang":"eng","text":"Cytosine methylation is an ancient process with conserved enzymology but diverse biological functions that include defense against transposable elements and regulation of gene expression. Here we will discuss the evolution and biological significance of eukaryotic DNA methylation, the likely drivers of that evolution, and major remaining mysteries."}],"quality_controlled":"1","article_type":"review","status":"public","pmid":1,"date_created":"2021-06-07T09:45:27Z","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2010.07.007","open_access":"1"}],"citation":{"ieee":"A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the pursuit of safer sex,” <i>Current Biology</i>, vol. 20, no. 17. Elsevier, pp. R780–R785, 2010.","ama":"Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. 2010;20(17):R780-R785. doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>","mla":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>, vol. 20, no. 17, Elsevier, 2010, pp. R780–85, doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>.","chicago":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>.","ista":"Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 20(17), R780–R785.","apa":"Zemach, A., &#38; Zilberman, D. (2010). Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>","short":"A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785."},"department":[{"_id":"DaZi"}],"_id":"9489","date_updated":"2021-12-14T08:52:34Z","issue":"17","year":"2010","volume":20,"day":"14","title":"Evolution of eukaryotic DNA methylation and the pursuit of safer sex","external_id":{"pmid":["20833323"]}},{"doi":"10.1371/journal.pbio.1000429.s003","_id":"9764","date_updated":"2023-02-23T11:42:17Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","related_material":{"record":[{"id":"3779","relation":"used_in_publication","status":"public"}]},"citation":{"ieee":"U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Heterosis and the drift load.” Public Library of Science, 2010.","short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010).","apa":"Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., &#38; Coen, E. (2010). Heterosis and the drift load. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">https://doi.org/10.1371/journal.pbio.1000429.s003</a>","ista":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Heterosis and the drift load, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">10.1371/journal.pbio.1000429.s003</a>.","chicago":"Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Heterosis and the Drift Load.” Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">https://doi.org/10.1371/journal.pbio.1000429.s003</a>.","mla":"Rosas, Ulises, et al. <i>Heterosis and the Drift Load</i>. Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">10.1371/journal.pbio.1000429.s003</a>.","ama":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Heterosis and the drift load. 2010. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">10.1371/journal.pbio.1000429.s003</a>"},"oa_version":"Published Version","department":[{"_id":"NiBa"}],"date_created":"2021-08-02T09:45:39Z","publisher":"Public Library of Science","status":"public","day":"20","title":"Heterosis and the drift load","date_published":"2010-07-20T00:00:00Z","article_processing_charge":"No","author":[{"first_name":"Ulises","full_name":"Rosas, Ulises","last_name":"Rosas"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton"},{"last_name":"Copsey","full_name":"Copsey, Lucy","first_name":"Lucy"},{"first_name":"Pierre","last_name":"Barbier De Reuille","full_name":"Barbier De Reuille, Pierre"},{"first_name":"Enrico","full_name":"Coen, Enrico","last_name":"Coen"}],"month":"07","year":"2010"},{"year":"2009","month":"11","author":[{"full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"scopus_import":1,"abstract":[{"text":"Sex and recombination have long been seen as adaptations that facilitate natural selection by generating favorable variations. If recombination is to aid selection, there must be negative linkage disequilibria—favorable alleles must be found together less often than expected by chance. These negative linkage disequilibria can be generated directly by selection, but this must involve negative epistasis of just the right strength, which is not expected, from either experiment or theory. Random drift provides a more general source of negative associations: Favorable mutations almost always arise on different genomes, and negative associations tend to persist, precisely because they shield variation from selection.\r\n\r\nWe can understand how recombination aids adaptation by determining the maximum possible rate of adaptation. With unlinked loci, this rate increases only logarithmically with the influx of favorable mutations. With a linear genome, a scaling argument shows that in a large population, the rate of adaptive substitution depends only on the expected rate in the absence of interference, divided by the total rate of recombination. A two-locus approximation predicts an upper bound on the rate of substitution, proportional to recombination rate.\r\n\r\nIf associations between linked loci do impede adaptation, there can be substantial selection for modifiers that increase recombination. Whether this can account for the maintenance of high rates of sex and recombination depends on the extent of selection. It is clear that the rate of species-wide substitutions is typically far too low to generate appreciable selection for recombination. However, local sweeps within a subdivided population may be effective.","lang":"eng"}],"date_published":"2009-11-10T00:00:00Z","publist_id":"2708","acknowledgement":"Royal Society and the Engineering and Physical Sciences for support (GR/ T11753/01)","volume":74,"title":"Why sex and recombination? ","quality_controlled":"1","day":"10","status":"public","intvolume":"        74","publisher":"Cold Spring Harbor Laboratory Press","date_created":"2018-12-11T12:04:33Z","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"oa_version":"None","citation":{"mla":"Barton, Nicholas H. “Why Sex and Recombination? .” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 74, Cold Spring Harbor Laboratory Press, 2009, pp. 187–95, doi:<a href=\"https://doi.org/10.1101/sqb.2009.74.030\">10.1101/sqb.2009.74.030</a>.","ama":"Barton NH. Why sex and recombination? . In: <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Vol 74. Cold Spring Harbor Laboratory Press; 2009:187-195. doi:<a href=\"https://doi.org/10.1101/sqb.2009.74.030\">10.1101/sqb.2009.74.030</a>","chicago":"Barton, Nicholas H. “Why Sex and Recombination? .” In <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, 74:187–95. Cold Spring Harbor Laboratory Press, 2009. <a href=\"https://doi.org/10.1101/sqb.2009.74.030\">https://doi.org/10.1101/sqb.2009.74.030</a>.","apa":"Barton, N. H. (2009). Why sex and recombination? . In <i>Cold Spring Harbor Symposia on Quantitative Biology</i> (Vol. 74, pp. 187–195). Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/sqb.2009.74.030\">https://doi.org/10.1101/sqb.2009.74.030</a>","ista":"Barton NH. 2009.Why sex and recombination? . In: Cold Spring Harbor Symposia on Quantitative Biology. vol. 74, 187–195.","short":"N.H. Barton, in:, Cold Spring Harbor Symposia on Quantitative Biology, Cold Spring Harbor Laboratory Press, 2009, pp. 187–195.","ieee":"N. H. Barton, “Why sex and recombination? ,” in <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 74, Cold Spring Harbor Laboratory Press, 2009, pp. 187–195."},"publication":"Cold Spring Harbor Symposia on Quantitative Biology","type":"book_chapter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:45:04Z","page":"187 - 195","_id":"3675","doi":"10.1101/sqb.2009.74.030"},{"issue":"2","year":"2009","day":"21","title":"On the application of statistical physics to evolutionary biology","volume":259,"acknowledgement":"This work was supported by a Royal Society/Wolfson Award, and by grants EP/T11753/01, EP/C546318/01 from the EPSRC.\r\nWe are grateful to M. Cates, H.P. de Vladar and G. Sella, and to two anonymous referees, for their helpful comments.","publist_id":"2452","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-00554594/document"}],"publication_status":"published","date_created":"2018-12-11T12:05:06Z","_id":"3775","date_updated":"2021-01-12T07:52:06Z","citation":{"mla":"Barton, Nicholas H., and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” <i>Journal of Theoretical Biology</i>, vol. 259, no. 2, Elsevier, 2009, pp. 317–24, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">10.1016/j.jtbi.2009.03.019</a>.","ama":"Barton NH, Coe J. On the application of statistical physics to evolutionary biology. <i>Journal of Theoretical Biology</i>. 2009;259(2):317-324. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">10.1016/j.jtbi.2009.03.019</a>","chicago":"Barton, Nicholas H, and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” <i>Journal of Theoretical Biology</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">https://doi.org/10.1016/j.jtbi.2009.03.019</a>.","apa":"Barton, N. H., &#38; Coe, J. (2009). On the application of statistical physics to evolutionary biology. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">https://doi.org/10.1016/j.jtbi.2009.03.019</a>","ista":"Barton NH, Coe J. 2009. On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. 259(2), 317–324.","short":"N.H. Barton, J. Coe, Journal of Theoretical Biology 259 (2009) 317–324.","ieee":"N. H. Barton and J. Coe, “On the application of statistical physics to evolutionary biology,” <i>Journal of Theoretical Biology</i>, vol. 259, no. 2. Elsevier, pp. 317–324, 2009."},"department":[{"_id":"NiBa"}],"scopus_import":1,"author":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"},{"first_name":"Jason","full_name":"Coe, Jason","last_name":"Coe"}],"month":"07","status":"public","quality_controlled":"1","date_published":"2009-07-21T00:00:00Z","abstract":[{"text":"There is a close analogy between statistical thermodynamics and the evolution of allele frequencies under mutation, selection and random drift. Wright's formula for the stationary distribution of allele frequencies is analogous to the Boltzmann distribution in statistical physics. Population size, 2N, plays the role of the inverse temperature, 1/kT, and determines the magnitude of random fluctuations. Log mean fitness, View the MathML source, tends to increase under selection, and is analogous to a (negative) energy; a potential function, U, increases under mutation in a similar way. An entropy, SH, can be defined which measures the deviation from the distribution of allele frequencies expected under random drift alone; the sum View the MathML source gives a free fitness that increases as the population evolves towards its stationary distribution. Usually, we observe the distribution of a few quantitative traits that depend on the frequencies of very many alleles. The mean and variance of such traits are analogous to observable quantities in statistical thermodynamics. Thus, we can define an entropy, SΩ, which measures the volume of allele frequency space that is consistent with the observed trait distribution. The stationary distribution of the traits is View the MathML source; this applies with arbitrary epistasis and dominance. The entropies SΩ, SH are distinct, but converge when there are so many alleles that traits fluctuate close to their expectations. Populations tend to evolve towards states that can be realised in many ways (i.e., large SΩ), which may lead to a substantial drop below the adaptive peak; we illustrate this point with a simple model of genetic redundancy. This analogy with statistical thermodynamics brings together previous ideas in a general framework, and justifies a maximum entropy approximation to the dynamics of quantitative traits.","lang":"eng"}],"publisher":"Elsevier","oa":1,"intvolume":"       259","doi":"10.1016/j.jtbi.2009.03.019","page":"317 - 324","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","oa_version":"Submitted Version","publication":"Journal of Theoretical Biology","language":[{"iso":"eng"}]}]