[{"editor":[{"last_name":"Owe","first_name":"Olaf","full_name":"Owe, Olaf"},{"first_name":"Martin","last_name":"Steffen","full_name":"Steffen, Martin"},{"first_name":"Jan Arne","last_name":"Telle","full_name":"Telle, Jan Arne"}],"external_id":{"arxiv":["1104.3211"]},"abstract":[{"lang":"eng","text":"In two-player games on graph, the players construct an infinite path through the game graph and get a reward computed by a payoff function over infinite paths. Over weighted graphs, the typical and most studied payoff functions compute the limit-average or the discounted sum of the rewards along the path. Besides their simple definition, these two payoff functions enjoy the property that memoryless optimal strategies always exist. In an attempt to construct other simple payoff functions, we define a class of payoff functions which compute an (infinite) weighted average of the rewards. This new class contains both the limit-average and the discounted sum functions, and we show that they are the only members of this class which induce memoryless optimal strategies, showing that there is essentially no other simple payoff functions."}],"date_updated":"2025-06-11T08:12:32Z","department":[{"_id":"KrCh"}],"arxiv":1,"date_published":"2011-04-16T00:00:00Z","publisher":"Springer","conference":{"location":"Oslo, Norway","start_date":"2011-08-22","name":"FCT: Fundamentals of Computation Theory","end_date":"2011-08-25"},"language":[{"iso":"eng"}],"oa_version":"Submitted Version","citation":{"chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Rohit Singh. “On Memoryless Quantitative Objectives.” edited by Olaf Owe, Martin Steffen, and Jan Arne Telle, 6914:148–59. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-22953-4_13\">https://doi.org/10.1007/978-3-642-22953-4_13</a>.","ieee":"K. Chatterjee, L. Doyen, and R. Singh, “On memoryless quantitative objectives,” presented at the FCT: Fundamentals of Computation Theory, Oslo, Norway, 2011, vol. 6914, pp. 148–159.","mla":"Chatterjee, Krishnendu, et al. <i>On Memoryless Quantitative Objectives</i>. Edited by Olaf Owe et al., vol. 6914, Springer, 2011, pp. 148–59, doi:<a href=\"https://doi.org/10.1007/978-3-642-22953-4_13\">10.1007/978-3-642-22953-4_13</a>.","ista":"Chatterjee K, Doyen L, Singh R. 2011. On memoryless quantitative objectives. FCT: Fundamentals of Computation Theory, LNCS, vol. 6914, 148–159.","apa":"Chatterjee, K., Doyen, L., &#38; Singh, R. (2011). On memoryless quantitative objectives. In O. Owe, M. Steffen, &#38; J. A. Telle (Eds.) (Vol. 6914, pp. 148–159). Presented at the FCT: Fundamentals of Computation Theory, Oslo, Norway: Springer. <a href=\"https://doi.org/10.1007/978-3-642-22953-4_13\">https://doi.org/10.1007/978-3-642-22953-4_13</a>","ama":"Chatterjee K, Doyen L, Singh R. On memoryless quantitative objectives. In: Owe O, Steffen M, Telle JA, eds. Vol 6914. Springer; 2011:148-159. doi:<a href=\"https://doi.org/10.1007/978-3-642-22953-4_13\">10.1007/978-3-642-22953-4_13</a>","short":"K. Chatterjee, L. Doyen, R. Singh, in:, O. Owe, M. Steffen, J.A. Telle (Eds.), Springer, 2011, pp. 148–159."},"publist_id":"3270","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Laurent","last_name":"Doyen","full_name":"Doyen, Laurent"},{"full_name":"Singh, Rohit","first_name":"Rohit","last_name":"Singh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3351","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1104.3211"}],"doi":"10.1007/978-3-642-22953-4_13","oa":1,"year":"2011","publication_status":"published","status":"public","type":"conference","quality_controlled":"1","alternative_title":["LNCS"],"page":"148 - 159","title":"On memoryless quantitative objectives","intvolume":"      6914","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"volume":6914,"month":"04","article_processing_charge":"No","day":"16","scopus_import":"1","date_created":"2018-12-11T12:02:50Z"},{"publist_id":"3267","citation":{"short":"J. Fisher, D. Harel, T.A. Henzinger, Communications of the ACM 54 (2011) 72–82.","ama":"Fisher J, Harel D, Henzinger TA. Biology as reactivity. <i>Communications of the ACM</i>. 2011;54(10):72-82. doi:<a href=\"https://doi.org/10.1145/2001269.2001289\">10.1145/2001269.2001289</a>","apa":"Fisher, J., Harel, D., &#38; Henzinger, T. A. (2011). Biology as reactivity. <i>Communications of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/2001269.2001289\">https://doi.org/10.1145/2001269.2001289</a>","ista":"Fisher J, Harel D, Henzinger TA. 2011. Biology as reactivity. Communications of the ACM. 54(10), 72–82.","mla":"Fisher, Jasmin, et al. “Biology as Reactivity.” <i>Communications of the ACM</i>, vol. 54, no. 10, ACM, 2011, pp. 72–82, doi:<a href=\"https://doi.org/10.1145/2001269.2001289\">10.1145/2001269.2001289</a>.","ieee":"J. Fisher, D. Harel, and T. A. Henzinger, “Biology as reactivity,” <i>Communications of the ACM</i>, vol. 54, no. 10. ACM, pp. 72–82, 2011.","chicago":"Fisher, Jasmin, David Harel, and Thomas A Henzinger. “Biology as Reactivity.” <i>Communications of the ACM</i>. ACM, 2011. <a href=\"https://doi.org/10.1145/2001269.2001289\">https://doi.org/10.1145/2001269.2001289</a>."},"oa_version":"None","language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"last_name":"Fisher","first_name":"Jasmin","full_name":"Fisher, Jasmin"},{"full_name":"Harel, David","first_name":"David","last_name":"Harel"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"ToHe"}],"date_updated":"2025-09-30T09:06:32Z","abstract":[{"lang":"eng","text":"Exploring the connection of biology with reactive systems to better understand living systems."}],"isi":1,"external_id":{"isi":["000296022500019"]},"issue":"10","publisher":"ACM","date_published":"2011-10-01T00:00:00Z","article_processing_charge":"No","month":"10","volume":54,"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}],"intvolume":"        54","title":"Biology as reactivity","page":"72 - 82","publication":"Communications of the ACM","date_created":"2018-12-11T12:02:50Z","ec_funded":1,"scopus_import":"1","day":"01","doi":"10.1145/2001269.2001289","_id":"3352","quality_controlled":"1","status":"public","type":"journal_article","year":"2011","publication_status":"published"},{"date_published":"2011-10-13T00:00:00Z","publisher":"IEEE","conference":{"start_date":"2011-09-05","location":"Aachen, Germany","name":"QEST: Quantitative Evaluation of Systems","end_date":"2011-09-08"},"ddc":["000","004"],"abstract":[{"lang":"eng","text":"Byzantine Fault Tolerant (BFT) protocols aim to improve the reliability of distributed systems. They enable systems to tolerate arbitrary failures in a bounded number of nodes. BFT protocols are usually proven correct for certain safety and liveness properties. However, recent studies have shown that the performance of state-of-the-art BFT protocols decreases drastically in the presence of even a single malicious node. This motivates a formal quantitative analysis of BFT protocols to investigate their performance characteristics under different scenarios. We present HyPerf, a new hybrid methodology based on model checking and simulation techniques for evaluating the performance of BFT protocols. We build a transition system corresponding to a BFT protocol and systematically explore the set of behaviors allowed by the protocol. We associate certain timing information with different operations in the protocol, like cryptographic operations and message transmission. After an elaborate state exploration, we use the time information to evaluate the performance characteristics of the protocol using simulation techniques. We integrate our framework in Mace, a tool for building and verifying distributed systems. We evaluate the performance of PBFT using our framework. We describe two different use-cases of our methodology. For the benign operation of the protocol, we use the time information as random variables to compute the probability distribution of the execution times. In the presence of faults, we estimate the worst-case performance of the protocol for various attacks that can be employed by malicious nodes. Our results show the importance of hybrid techniques in systematically analyzing the performance of large-scale systems."}],"date_updated":"2024-10-09T20:54:27Z","department":[{"_id":"ToHe"}],"corr_author":"1","author":[{"id":"584C6850-E996-11E9-805B-F01764644770","first_name":"Raluca","last_name":"Halalai","full_name":"Halalai, Raluca"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Singh, Vasu","last_name":"Singh","first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"oa_version":"Submitted Version","citation":{"chicago":"Halalai, Raluca, Thomas A Henzinger, and Vasu Singh. “Quantitative Evaluation of BFT Protocols,” 255–64. IEEE, 2011. <a href=\"https://doi.org/10.1109/QEST.2011.40\">https://doi.org/10.1109/QEST.2011.40</a>.","ieee":"R. Halalai, T. A. Henzinger, and V. Singh, “Quantitative evaluation of BFT protocols,” presented at the QEST: Quantitative Evaluation of Systems, Aachen, Germany, 2011, pp. 255–264.","ista":"Halalai R, Henzinger TA, Singh V. 2011. Quantitative evaluation of BFT protocols. QEST: Quantitative Evaluation of Systems, 255–264.","mla":"Halalai, Raluca, et al. <i>Quantitative Evaluation of BFT Protocols</i>. IEEE, 2011, pp. 255–64, doi:<a href=\"https://doi.org/10.1109/QEST.2011.40\">10.1109/QEST.2011.40</a>.","apa":"Halalai, R., Henzinger, T. A., &#38; Singh, V. (2011). Quantitative evaluation of BFT protocols (pp. 255–264). Presented at the QEST: Quantitative Evaluation of Systems, Aachen, Germany: IEEE. <a href=\"https://doi.org/10.1109/QEST.2011.40\">https://doi.org/10.1109/QEST.2011.40</a>","short":"R. Halalai, T.A. Henzinger, V. Singh, in:, IEEE, 2011, pp. 255–264.","ama":"Halalai R, Henzinger TA, Singh V. Quantitative evaluation of BFT protocols. In: IEEE; 2011:255-264. doi:<a href=\"https://doi.org/10.1109/QEST.2011.40\">10.1109/QEST.2011.40</a>"},"publist_id":"3260","file_date_updated":"2020-07-14T12:46:09Z","year":"2011","publication_status":"published","status":"public","type":"conference","quality_controlled":"1","_id":"3355","doi":"10.1109/QEST.2011.40","oa":1,"has_accepted_license":"1","day":"13","pubrep_id":"84","scopus_import":1,"date_created":"2018-12-11T12:02:51Z","page":"255 - 264","title":"Quantitative evaluation of BFT protocols","file":[{"date_created":"2018-12-12T10:07:49Z","checksum":"4dc8750ab7921f51de992000b13d1b01","relation":"main_file","file_id":"4648","creator":"system","access_level":"open_access","file_name":"IST-2012-84-v1+1_Quantitative_evaluation_of_BFT_protocols.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:09Z","file_size":272017}],"month":"10"},{"year":"2011","publication_status":"published","type":"conference","status":"public","quality_controlled":"1","date_published":"2011-01-01T00:00:00Z","publisher":"Springer","conference":{"location":"Tarragona, Spain","start_date":"2011-05-26","name":"LATA: Language and Automata Theory and Applications","end_date":"2011-05-31"},"alternative_title":["LNCS"],"editor":[{"last_name":"Dediu","first_name":"Adrian-Horia","full_name":"Dediu, Adrian-Horia"},{"full_name":"Inenaga, Shunsuke","first_name":"Shunsuke","last_name":"Inenaga"},{"full_name":"Martín-Vide, Carlos","first_name":"Carlos","last_name":"Martín-Vide"}],"_id":"3357","doi":"10.1007/978-3-642-21254-3_17","abstract":[{"text":"We consider two-player graph games whose objectives are request-response condition, i.e conjunctions of conditions of the form \"if a state with property Rq is visited, then later a state with property Rp is visited\". The winner of such games can be decided in EXPTIME and the problem is known to be NP-hard. In this paper, we close this gap by showing that this problem is, in fact, EXPTIME-complete. We show that the problem becomes PSPACE-complete if we only consider games played on DAGs, and NP-complete or PTIME-complete if there is only one player (depending on whether he wants to enforce or spoil the request-response condition). We also present near-optimal bounds on the memory needed to design winning strategies for each player, in each case.","lang":"eng"}],"date_updated":"2024-10-09T20:54:27Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"day":"01","corr_author":"1","scopus_import":1,"date_created":"2018-12-11T12:02:52Z","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Horn, Florian","id":"37327ACE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Horn"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","page":"227 - 237","language":[{"iso":"eng"}],"title":"The complexity of request-response games","oa_version":"None","intvolume":"      6638","volume":6638,"citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “The Complexity of Request-Response Games.” edited by Adrian-Horia Dediu, Shunsuke Inenaga, and Carlos Martín-Vide, 6638:227–37. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-21254-3_17\">https://doi.org/10.1007/978-3-642-21254-3_17</a>.","ieee":"K. Chatterjee, T. A. Henzinger, and F. Horn, “The complexity of request-response games,” presented at the LATA: Language and Automata Theory and Applications, Tarragona, Spain, 2011, vol. 6638, pp. 227–237.","mla":"Chatterjee, Krishnendu, et al. <i>The Complexity of Request-Response Games</i>. Edited by Adrian-Horia Dediu et al., vol. 6638, Springer, 2011, pp. 227–37, doi:<a href=\"https://doi.org/10.1007/978-3-642-21254-3_17\">10.1007/978-3-642-21254-3_17</a>.","ista":"Chatterjee K, Henzinger TA, Horn F. 2011. The complexity of request-response games. LATA: Language and Automata Theory and Applications, LNCS, vol. 6638, 227–237.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Horn, F. (2011). The complexity of request-response games. In A.-H. Dediu, S. Inenaga, &#38; C. Martín-Vide (Eds.) (Vol. 6638, pp. 227–237). Presented at the LATA: Language and Automata Theory and Applications, Tarragona, Spain: Springer. <a href=\"https://doi.org/10.1007/978-3-642-21254-3_17\">https://doi.org/10.1007/978-3-642-21254-3_17</a>","ama":"Chatterjee K, Henzinger TA, Horn F. The complexity of request-response games. In: Dediu A-H, Inenaga S, Martín-Vide C, eds. Vol 6638. Springer; 2011:227-237. doi:<a href=\"https://doi.org/10.1007/978-3-642-21254-3_17\">10.1007/978-3-642-21254-3_17</a>","short":"K. Chatterjee, T.A. Henzinger, F. Horn, in:, A.-H. Dediu, S. Inenaga, C. Martín-Vide (Eds.), Springer, 2011, pp. 227–237."},"month":"01","publist_id":"3258"},{"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"last_name":"Singh","first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","full_name":"Singh, Vasu"},{"id":"447BFB88-F248-11E8-B48F-1D18A9856A87","last_name":"Wies","first_name":"Thomas","full_name":"Wies, Thomas"},{"orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien","last_name":"Zufferey","first_name":"Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"10","corr_author":"1","scopus_import":"1","date_created":"2018-12-11T12:02:53Z","citation":{"mla":"Henzinger, Thomas A., et al. <i>Scheduling Large Jobs by Abstraction Refinement</i>. ACM, 2011, pp. 329–42, doi:<a href=\"https://doi.org/10.1145/1966445.1966476\">10.1145/1966445.1966476</a>.","ista":"Henzinger TA, Singh V, Wies T, Zufferey D. 2011. Scheduling large jobs by abstraction refinement. EuroSys, 329–342.","ieee":"T. A. Henzinger, V. Singh, T. Wies, and D. Zufferey, “Scheduling large jobs by abstraction refinement,” presented at the EuroSys, Salzburg, Austria, 2011, pp. 329–342.","chicago":"Henzinger, Thomas A, Vasu Singh, Thomas Wies, and Damien Zufferey. “Scheduling Large Jobs by Abstraction Refinement,” 329–42. ACM, 2011. <a href=\"https://doi.org/10.1145/1966445.1966476\">https://doi.org/10.1145/1966445.1966476</a>.","ama":"Henzinger TA, Singh V, Wies T, Zufferey D. Scheduling large jobs by abstraction refinement. In: ACM; 2011:329-342. doi:<a href=\"https://doi.org/10.1145/1966445.1966476\">10.1145/1966445.1966476</a>","short":"T.A. Henzinger, V. Singh, T. Wies, D. Zufferey, in:, ACM, 2011, pp. 329–342.","apa":"Henzinger, T. A., Singh, V., Wies, T., &#38; Zufferey, D. (2011). Scheduling large jobs by abstraction refinement (pp. 329–342). Presented at the EuroSys, Salzburg, Austria: ACM. <a href=\"https://doi.org/10.1145/1966445.1966476\">https://doi.org/10.1145/1966445.1966476</a>"},"article_processing_charge":"No","month":"04","publist_id":"3257","language":[{"iso":"eng"}],"page":"329 - 342","title":"Scheduling large jobs by abstraction refinement","oa_version":"Published Version","publisher":"ACM","conference":{"end_date":"2011-04-13","name":"EuroSys","location":"Salzburg, Austria","start_date":"2011-04-10"},"year":"2011","publication_status":"published","type":"conference","status":"public","quality_controlled":"1","date_published":"2011-04-10T00:00:00Z","abstract":[{"text":"The static scheduling problem often arises as a fundamental problem in real-time systems and grid computing. We consider the problem of statically scheduling a large job expressed as a task graph on a large number of computing nodes, such as a data center. This paper solves the large-scale static scheduling problem using abstraction refinement, a technique commonly used in formal verification to efficiently solve computationally hard problems. A scheduler based on abstraction refinement first attempts to solve the scheduling problem with abstract representations of the job and the computing resources. As abstract representations are generally small, the scheduling can be done reasonably fast. If the obtained schedule does not meet specified quality conditions (like data center utilization or schedule makespan) then the scheduler refines the job and data center abstractions and, again solves the scheduling problem. We develop different schedulers based on abstraction refinement. We implemented these schedulers and used them to schedule task graphs from various computing domains on simulated data centers with realistic topologies. We compared the speed of scheduling and the quality of the produced schedules with our abstraction refinement schedulers against a baseline scheduler that does not use any abstraction. We conclude that abstraction refinement techniques give a significant speed-up compared to traditional static scheduling heuristics, at a reasonable cost in the quality of the produced schedules. We further used our static schedulers in an actual system that we deployed on Amazon EC2 and compared it against the Hadoop dynamic scheduler for large MapReduce jobs. Our experiments indicate that there is great potential for static scheduling techniques.","lang":"eng"}],"oa":1,"date_updated":"2026-06-18T18:44:21Z","department":[{"_id":"ToHe"}],"ddc":["000"],"_id":"3358","main_file_link":[{"url":"http://cs.nyu.edu/wies/publ/scheduling_large_jobs_by_abstraction_refinement.pdf","open_access":"1"}],"doi":"10.1145/1966445.1966476"},{"conference":{"name":"EMSOFT: Embedded Software ","end_date":"2011-10-14","start_date":"2011-10-09","location":"Taipei; Taiwan"},"publisher":"ACM","date_published":"2011-10-09T00:00:00Z","quality_controlled":"1","type":"conference","status":"public","publication_status":"published","year":"2011","department":[{"_id":"ToHe"}],"date_updated":"2024-10-21T06:03:04Z","abstract":[{"lang":"eng","text":"Motivated by improvements in constraint-solving technology and by the increase of routinely available computational power, partial-program synthesis is emerging as an effective approach for increasing programmer productivity. The goal of the approach is to allow the programmer to specify a part of her intent imperatively (that is, give a partial program) and a part of her intent declaratively, by specifying which conditions need to be achieved or maintained. The task of the synthesizer is to construct a program that satisfies the specification. As an example, consider a partial program where threads access shared data without using any synchronization mechanism, and a declarative specification that excludes data races and deadlocks. The task of the synthesizer is then to place locks into the program code in order for the program to meet the specification.\r\n\r\nIn this paper, we argue that quantitative objectives are needed in partial-program synthesis in order to produce higher-quality programs, while enabling simpler specifications. Returning to the example, the synthesizer could construct a naive solution that uses one global lock for shared data. This can be prevented either by constraining the solution space further (which is error-prone and partly defeats the point of synthesis), or by optimizing a quantitative objective that models performance. Other quantitative notions useful in synthesis include fault tolerance, robustness, resource (memory, power) consumption, and information flow."}],"doi":"10.1145/2038642.2038666","_id":"3359","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Pavol","last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"}],"ec_funded":1,"date_created":"2018-12-11T12:02:53Z","acknowledgement":"This work was partially supported by the ERC Advanced Grant QUAREM, the FWF NFN Grant S11402-N23 (RiSE), and the EU NOE Grant ArtistDesign.","corr_author":"1","scopus_import":"1","day":"09","publist_id":"3256","month":"10","citation":{"ieee":"P. Cerny and T. A. Henzinger, “From boolean to quantitative synthesis,” presented at the EMSOFT: Embedded Software , Taipei; Taiwan, 2011, pp. 149–154.","chicago":"Cerny, Pavol, and Thomas A Henzinger. “From Boolean to Quantitative Synthesis,” 149–54. ACM, 2011. <a href=\"https://doi.org/10.1145/2038642.2038666\">https://doi.org/10.1145/2038642.2038666</a>.","mla":"Cerny, Pavol, and Thomas A. Henzinger. <i>From Boolean to Quantitative Synthesis</i>. ACM, 2011, pp. 149–54, doi:<a href=\"https://doi.org/10.1145/2038642.2038666\">10.1145/2038642.2038666</a>.","ista":"Cerny P, Henzinger TA. 2011. From boolean to quantitative synthesis. EMSOFT: Embedded Software , 149–154.","short":"P. Cerny, T.A. Henzinger, in:, ACM, 2011, pp. 149–154.","ama":"Cerny P, Henzinger TA. From boolean to quantitative synthesis. In: ACM; 2011:149-154. doi:<a href=\"https://doi.org/10.1145/2038642.2038666\">10.1145/2038642.2038666</a>","apa":"Cerny, P., &#38; Henzinger, T. A. (2011). From boolean to quantitative synthesis (pp. 149–154). Presented at the EMSOFT: Embedded Software , Taipei; Taiwan: ACM. <a href=\"https://doi.org/10.1145/2038642.2038666\">https://doi.org/10.1145/2038642.2038666</a>"},"project":[{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","call_identifier":"FWF"},{"call_identifier":"FP7","name":"Design for Embedded Systems","grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425"}],"oa_version":"None","title":"From boolean to quantitative synthesis","page":"149 - 154","language":[{"iso":"eng"}]},{"ddc":["004"],"department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T07:42:56Z","abstract":[{"text":"A discounted-sum automaton (NDA) is a nondeterministic finite automaton with edge weights, which values a run by the discounted sum of visited edge weights. More precisely, the weight in the i-th position of the run is divided by lambda^i, where the discount factor lambda is a fixed rational number greater than 1. Discounted summation is a common and useful measuring scheme, especially for infinite sequences, which reflects the assumption that earlier weights are more important than later weights. Determinizing automata is often essential, for example, in formal verification, where there are polynomial algorithms for comparing two deterministic NDAs, while the equivalence problem for NDAs is not known to be decidable. Unfortunately, however, discounted-sum automata are, in general, not determinizable: it is currently known that for every rational discount factor 1 &lt; lambda &lt; 2, there is an NDA with lambda (denoted lambda-NDA) that cannot be determinized. We provide positive news, showing that every NDA with an integral factor is determinizable. We also complete the picture by proving that the integers characterize exactly the discount factors that guarantee determinizability: we show that for every non-integral rational factor lambda, there is a nondeterminizable lambda-NDA. Finally, we prove that the class of NDAs with integral discount factors enjoys closure under the algebraic operations min, max, addition, and subtraction, which is not the case for general NDAs nor for deterministic NDAs. This shows that for integral discount factors, the class of NDAs forms an attractive specification formalism in quantitative formal verification. All our results hold equally for automata over finite words and for automata over infinite words. ","lang":"eng"}],"date_published":"2011-08-31T00:00:00Z","conference":{"location":"Bergen, Norway","start_date":"2011-09-12","name":"CSL: Computer Science Logic","end_date":"2011-09-15"},"publisher":"Springer","oa_version":"Published Version","language":[{"iso":"eng"}],"publist_id":"3255","citation":{"chicago":"Boker, Udi, and Thomas A Henzinger. “Determinizing Discounted-Sum Automata,” 12:82–96. Springer, 2011. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2011.82\">https://doi.org/10.4230/LIPIcs.CSL.2011.82</a>.","ieee":"U. Boker and T. A. Henzinger, “Determinizing discounted-sum automata,” presented at the CSL: Computer Science Logic, Bergen, Norway, 2011, vol. 12, pp. 82–96.","mla":"Boker, Udi, and Thomas A. Henzinger. <i>Determinizing Discounted-Sum Automata</i>. Vol. 12, Springer, 2011, pp. 82–96, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2011.82\">10.4230/LIPIcs.CSL.2011.82</a>.","ista":"Boker U, Henzinger TA. 2011. Determinizing discounted-sum automata. CSL: Computer Science Logic, LIPIcs, vol. 12, 82–96.","apa":"Boker, U., &#38; Henzinger, T. A. (2011). Determinizing discounted-sum automata (Vol. 12, pp. 82–96). Presented at the CSL: Computer Science Logic, Bergen, Norway: Springer. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2011.82\">https://doi.org/10.4230/LIPIcs.CSL.2011.82</a>","short":"U. Boker, T.A. Henzinger, in:, Springer, 2011, pp. 82–96.","ama":"Boker U, Henzinger TA. Determinizing discounted-sum automata. In: Vol 12. Springer; 2011:82-96. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2011.82\">10.4230/LIPIcs.CSL.2011.82</a>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Boker, Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","last_name":"Boker","first_name":"Udi"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.4230/LIPIcs.CSL.2011.82","_id":"3360","has_accepted_license":"1","oa":1,"quality_controlled":"1","status":"public","type":"conference","publication_status":"published","year":"2011","file_date_updated":"2020-07-14T12:46:10Z","alternative_title":["LIPIcs"],"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"COMponent-Based Embedded Systems design Techniques","grant_number":"215543","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Design for Embedded Systems","grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425"}],"intvolume":"        12","page":"82 - 96","title":"Determinizing discounted-sum automata","month":"08","file":[{"access_level":"open_access","relation":"main_file","creator":"system","file_id":"4803","date_created":"2018-12-12T10:10:17Z","checksum":"250603c6be8ccad4fbd4d7b24221f0ee","file_size":504270,"content_type":"application/pdf","date_updated":"2020-07-14T12:46:10Z","file_name":"IST-2012-82-v1+1_Determinizing_discounted-sum_automata.pdf"}],"volume":12,"date_created":"2018-12-11T12:02:53Z","ec_funded":1,"scopus_import":1,"day":"31","pubrep_id":"82","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"}},{"date_published":"2011-06-27T00:00:00Z","publisher":"IEEE","conference":{"end_date":"2011-06-29","name":"CSF: Computer Security Foundations","start_date":"2011-06-27","location":"Cernay-la-Ville, France"},"isi":1,"external_id":{"isi":["000300766400014"]},"ddc":["000","005"],"abstract":[{"text":"In this paper, we investigate the computational complexity of quantitative information flow (QIF) problems. Information-theoretic quantitative relaxations of noninterference (based on Shannon entropy)have been introduced to enable more fine-grained reasoning about programs in situations where limited information flow is acceptable. The QIF bounding problem asks whether the information flow in a given program is bounded by a constant $d$. Our first result is that the QIF bounding problem is PSPACE-complete. The QIF memoryless synthesis problem asks whether it is possible to resolve nondeterministic choices in a given partial program in such a way that in the resulting deterministic program, the quantitative information flow is bounded by a given constant $d$. Our second result is that the QIF memoryless synthesis problem is also EXPTIME-complete. The QIF memoryless synthesis problem generalizes to QIF general synthesis problem which does not impose the memoryless requirement (that is, by allowing the synthesized program to have more variables then the original partial program). Our third result is that the QIF general synthesis problem is EXPTIME-hard.","lang":"eng"}],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"date_updated":"2025-09-30T09:04:15Z","corr_author":"1","author":[{"full_name":"Cerny, Pavol","last_name":"Cerny","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Submitted Version","language":[{"iso":"eng"}],"citation":{"short":"P. Cerny, K. Chatterjee, T.A. Henzinger, in:, IEEE, 2011, pp. 205–217.","ama":"Cerny P, Chatterjee K, Henzinger TA. The complexity of quantitative information flow problems. In: IEEE; 2011:205-217. doi:<a href=\"https://doi.org/10.1109/CSF.2011.21\">10.1109/CSF.2011.21</a>","apa":"Cerny, P., Chatterjee, K., &#38; Henzinger, T. A. (2011). The complexity of quantitative information flow problems (pp. 205–217). Presented at the CSF: Computer Security Foundations, Cernay-la-Ville, France: IEEE. <a href=\"https://doi.org/10.1109/CSF.2011.21\">https://doi.org/10.1109/CSF.2011.21</a>","ieee":"P. Cerny, K. Chatterjee, and T. A. Henzinger, “The complexity of quantitative information flow problems,” presented at the CSF: Computer Security Foundations, Cernay-la-Ville, France, 2011, pp. 205–217.","chicago":"Cerny, Pavol, Krishnendu Chatterjee, and Thomas A Henzinger. “The Complexity of Quantitative Information Flow Problems,” 205–17. IEEE, 2011. <a href=\"https://doi.org/10.1109/CSF.2011.21\">https://doi.org/10.1109/CSF.2011.21</a>.","mla":"Cerny, Pavol, et al. <i>The Complexity of Quantitative Information Flow Problems</i>. IEEE, 2011, pp. 205–17, doi:<a href=\"https://doi.org/10.1109/CSF.2011.21\">10.1109/CSF.2011.21</a>.","ista":"Cerny P, Chatterjee K, Henzinger TA. 2011. The complexity of quantitative information flow problems. CSF: Computer Security Foundations, 205–217."},"publist_id":"3254","type":"conference","status":"public","year":"2011","file_date_updated":"2020-07-14T12:46:10Z","publication_status":"published","quality_controlled":"1","doi":"10.1109/CSF.2011.21","_id":"3361","oa":1,"has_accepted_license":"1","day":"27","pubrep_id":"81","date_created":"2018-12-11T12:02:54Z","ec_funded":1,"scopus_import":"1","page":"205 - 217","title":"The complexity of quantitative information flow problems","project":[{"call_identifier":"FP7","grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"file":[{"date_updated":"2020-07-14T12:46:10Z","content_type":"application/pdf","file_size":299069,"file_name":"IST-2012-81-v1+1_The_complexity_of_quantitative_information_flow_problems.pdf","access_level":"open_access","date_created":"2018-12-12T10:10:07Z","checksum":"1a25be0c62459fc7640db88af08ff63a","file_id":"4792","creator":"system","relation":"main_file"}],"month":"06","article_processing_charge":"No"},{"file":[{"date_created":"2020-05-19T16:17:48Z","checksum":"6bf2453d8e52e979ddb58d17325bad26","creator":"dernst","file_id":"7870","relation":"main_file","access_level":"open_access","file_name":"2011_CONCUR_Fisher.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:10Z","file_size":337125}],"volume":6901,"article_processing_charge":"No","month":"01","page":"404 - 418","title":"Dynamic reactive modules","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"}],"intvolume":"      6901","day":"01","ec_funded":1,"date_created":"2018-12-11T12:02:54Z","scopus_import":1,"oa":1,"has_accepted_license":"1","doi":"10.1007/978-3-642-23217-6_27","_id":"3362","alternative_title":["LNCS"],"status":"public","type":"conference","file_date_updated":"2020-07-14T12:46:10Z","publication_status":"published","year":"2011","quality_controlled":"1","citation":{"apa":"Fisher, J., Henzinger, T. A., Nickovic, D., Piterman, N., Singh, A., &#38; Vardi, M. (2011). Dynamic reactive modules (Vol. 6901, pp. 404–418). Presented at the CONCUR: Concurrency Theory, Aachen, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.1007/978-3-642-23217-6_27\">https://doi.org/10.1007/978-3-642-23217-6_27</a>","ama":"Fisher J, Henzinger TA, Nickovic D, Piterman N, Singh A, Vardi M. Dynamic reactive modules. In: Vol 6901. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2011:404-418. doi:<a href=\"https://doi.org/10.1007/978-3-642-23217-6_27\">10.1007/978-3-642-23217-6_27</a>","short":"J. Fisher, T.A. Henzinger, D. Nickovic, N. Piterman, A. Singh, M. Vardi, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2011, pp. 404–418.","chicago":"Fisher, Jasmin, Thomas A Henzinger, Dejan Nickovic, Nir Piterman, Anmol Singh, and Moshe Vardi. “Dynamic Reactive Modules,” 6901:404–18. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2011. <a href=\"https://doi.org/10.1007/978-3-642-23217-6_27\">https://doi.org/10.1007/978-3-642-23217-6_27</a>.","ieee":"J. Fisher, T. A. Henzinger, D. Nickovic, N. Piterman, A. Singh, and M. Vardi, “Dynamic reactive modules,” presented at the CONCUR: Concurrency Theory, Aachen, Germany, 2011, vol. 6901, pp. 404–418.","mla":"Fisher, Jasmin, et al. <i>Dynamic Reactive Modules</i>. Vol. 6901, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2011, pp. 404–18, doi:<a href=\"https://doi.org/10.1007/978-3-642-23217-6_27\">10.1007/978-3-642-23217-6_27</a>.","ista":"Fisher J, Henzinger TA, Nickovic D, Piterman N, Singh A, Vardi M. 2011. Dynamic reactive modules. CONCUR: Concurrency Theory, LNCS, vol. 6901, 404–418."},"publist_id":"3253","oa_version":"Submitted Version","language":[{"iso":"eng"}],"author":[{"full_name":"Fisher, Jasmin","last_name":"Fisher","first_name":"Jasmin"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Piterman","first_name":"Nir","full_name":"Piterman, Nir"},{"last_name":"Singh","first_name":"Anmol","full_name":"Singh, Anmol"},{"full_name":"Vardi, Moshe","first_name":"Moshe","last_name":"Vardi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"State-transition systems communicating by shared variables have been the underlying model of choice for applications of model checking. Such formalisms, however, have difficulty with modeling process creation or death and communication reconfigurability. Here, we introduce “dynamic reactive modules” (DRM), a state-transition modeling formalism that supports dynamic reconfiguration and creation/death of processes. The resulting formalism supports two types of variables, data variables and reference variables. Reference variables enable changing the connectivity between processes and referring to instances of processes. We show how this new formalism supports parallel composition and refinement through trace containment. DRM provide a natural language for modeling (and ultimately reasoning about) biological systems and multiple threads communicating through shared variables."}],"department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T07:42:57Z","ddc":["000"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","conference":{"start_date":"2011-09-06","location":"Aachen, Germany","name":"CONCUR: Concurrency Theory","end_date":"2011-09-09"},"date_published":"2011-01-01T00:00:00Z"},{"date_created":"2018-12-11T12:02:54Z","ec_funded":1,"day":"01","month":"04","article_processing_charge":"No","project":[{"_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"214373","name":"Design for Embedded Systems"}],"title":"The decidability frontier for probabilistic automata on infinite words","page":"19","publication_status":"submitted","year":"2011","type":"preprint","status":"public","oa":1,"_id":"3363","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1104.0127"}],"doi":"10.48550/arXiv.1104.0127","article_number":"1104.0127","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger"},{"last_name":"Tracol","first_name":"Mathieu","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","full_name":"Tracol, Mathieu"}],"corr_author":"1","publist_id":"3251","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Mathieu Tracol. “The Decidability Frontier for Probabilistic Automata on Infinite Words.” ArXiv, n.d. <a href=\"https://doi.org/10.48550/arXiv.1104.0127\">https://doi.org/10.48550/arXiv.1104.0127</a>.","ieee":"K. Chatterjee, T. A. Henzinger, and M. Tracol, “The decidability frontier for probabilistic automata on infinite words.” ArXiv.","mla":"Chatterjee, Krishnendu, et al. <i>The Decidability Frontier for Probabilistic Automata on Infinite Words</i>. 1104.0127, ArXiv, doi:<a href=\"https://doi.org/10.48550/arXiv.1104.0127\">10.48550/arXiv.1104.0127</a>.","ista":"Chatterjee K, Henzinger TA, Tracol M. The decidability frontier for probabilistic automata on infinite words. 1104.0127.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Tracol, M. (n.d.). The decidability frontier for probabilistic automata on infinite words. ArXiv. <a href=\"https://doi.org/10.48550/arXiv.1104.0127\">https://doi.org/10.48550/arXiv.1104.0127</a>","ama":"Chatterjee K, Henzinger TA, Tracol M. The decidability frontier for probabilistic automata on infinite words. doi:<a href=\"https://doi.org/10.48550/arXiv.1104.0127\">10.48550/arXiv.1104.0127</a>","short":"K. Chatterjee, T.A. Henzinger, M. Tracol, (n.d.)."},"language":[{"iso":"eng"}],"oa_version":"Preprint","publisher":"ArXiv","date_published":"2011-04-01T00:00:00Z","arxiv":1,"date_updated":"2025-06-26T09:19:59Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"abstract":[{"text":"We consider probabilistic automata on infinite words with acceptance defined by safety, reachability, Büchi, coBüchi, and limit-average conditions. We consider quantitative and qualitative decision problems. We present extensions and adaptations of proofs for probabilistic finite automata and present a complete characterization of the decidability and undecidability frontier of the quantitative and qualitative decision problems for probabilistic automata on infinite words.","lang":"eng"}],"external_id":{"arxiv":["1104.0127"]}},{"oa_version":"Submitted Version","language":[{"iso":"eng"}],"publist_id":"3249","citation":{"apa":"Didier, F., Henzinger, T. A., Mateescu, M., &#38; Wolf, V. (2011). Approximation of event probabilities in noisy cellular processes. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2010.10.022\">https://doi.org/10.1016/j.tcs.2010.10.022</a>","ama":"Didier F, Henzinger TA, Mateescu M, Wolf V. Approximation of event probabilities in noisy cellular processes. <i>Theoretical Computer Science</i>. 2011;412(21):2128-2141. doi:<a href=\"https://doi.org/10.1016/j.tcs.2010.10.022\">10.1016/j.tcs.2010.10.022</a>","short":"F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, Theoretical Computer Science 412 (2011) 2128–2141.","ista":"Didier F, Henzinger TA, Mateescu M, Wolf V. 2011. Approximation of event probabilities in noisy cellular processes. Theoretical Computer Science. 412(21), 2128–2141.","mla":"Didier, Frédéric, et al. “Approximation of Event Probabilities in Noisy Cellular Processes.” <i>Theoretical Computer Science</i>, vol. 412, no. 21, Elsevier, 2011, pp. 2128–41, doi:<a href=\"https://doi.org/10.1016/j.tcs.2010.10.022\">10.1016/j.tcs.2010.10.022</a>.","chicago":"Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Approximation of Event Probabilities in Noisy Cellular Processes.” <i>Theoretical Computer Science</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.tcs.2010.10.022\">https://doi.org/10.1016/j.tcs.2010.10.022</a>.","ieee":"F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Approximation of event probabilities in noisy cellular processes,” <i>Theoretical Computer Science</i>, vol. 412, no. 21. Elsevier, pp. 2128–2141, 2011."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Didier, Frédéric","last_name":"Didier","first_name":"Frédéric"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Mateescu, Maria","first_name":"Maria","last_name":"Mateescu"},{"full_name":"Wolf, Verena","last_name":"Wolf","first_name":"Verena"}],"external_id":{"isi":["000290078000005"]},"isi":1,"ddc":["000","004"],"department":[{"_id":"ToHe"}],"date_updated":"2025-09-30T09:03:30Z","abstract":[{"text":"Molecular noise, which arises from the randomness of the discrete events in the cell, significantly influences fundamental biological processes. Discrete-state continuous-time stochastic models (CTMC) can be used to describe such effects, but the calculation of the probabilities of certain events is computationally expensive. We present a comparison of two analysis approaches for CTMC. On one hand, we estimate the probabilities of interest using repeated Gillespie simulation and determine the statistical accuracy that we obtain. On the other hand, we apply a numerical reachability analysis that approximates the probability distributions of the system at several time instances. We use examples of cellular processes to demonstrate the superiority of the reachability analysis if accurate results are required.","lang":"eng"}],"date_published":"2011-05-06T00:00:00Z","issue":"21","publisher":"Elsevier","related_material":{"record":[{"id":"4535","status":"public","relation":"earlier_version"}]},"intvolume":"       412","page":"2128 - 2141","title":"Approximation of event probabilities in noisy cellular processes","article_processing_charge":"No","month":"05","file":[{"access_level":"open_access","relation":"main_file","file_id":"4862","creator":"system","date_created":"2018-12-12T10:11:09Z","checksum":"e5503e25ce020d753e06b3431e16841e","file_size":230503,"date_updated":"2020-07-14T12:46:10Z","content_type":"application/pdf","file_name":"IST-2012-79-v1+1_Approximation_of_event_probabilities_in_noisy_cellular_processes.pdf"}],"volume":412,"date_created":"2018-12-11T12:02:55Z","scopus_import":"1","day":"06","pubrep_id":"79","publication":"Theoretical Computer Science","doi":"10.1016/j.tcs.2010.10.022","_id":"3364","has_accepted_license":"1","oa":1,"quality_controlled":"1","status":"public","type":"journal_article","year":"2011","file_date_updated":"2020-07-14T12:46:10Z","publication_status":"published"},{"alternative_title":["LNCS"],"quality_controlled":"1","file_date_updated":"2020-07-14T12:46:10Z","year":"2011","publication_status":"published","type":"conference","status":"public","has_accepted_license":"1","oa":1,"_id":"3365","doi":"10.1007/978-3-642-19835-9_24","scopus_import":1,"date_created":"2018-12-11T12:02:55Z","pubrep_id":"77","day":"29","month":"09","volume":6605,"file":[{"access_level":"open_access","creator":"system","file_id":"5022","relation":"main_file","date_created":"2018-12-12T10:13:37Z","checksum":"762e52eb296f6dbfbf2a75d98b8ebaee","file_size":475661,"date_updated":"2020-07-14T12:46:10Z","content_type":"application/pdf","file_name":"IST-2012-77-v1+1_QUASY-_quantitative_synthesis_tool.pdf"}],"intvolume":"      6605","page":"267 - 271","title":"QUASY: quantitative synthesis tool","conference":{"location":"Saarbrucken, Germany","start_date":"2011-03-26","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2011-04-03"},"publisher":"Springer","date_published":"2011-09-29T00:00:00Z","date_updated":"2021-01-12T07:42:58Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"We present the tool Quasy, a quantitative synthesis tool. Quasy takes qualitative and quantitative specifications and automatically constructs a system that satisfies the qualitative specification and optimizes the quantitative specification, if such a system exists. The user can choose between a system that satisfies and optimizes the specifications (a) under all possible environment behaviors or (b) under the most-likely environment behaviors given as a probability distribution on the possible input sequences. Quasy solves these two quantitative synthesis problems by reduction to instances of 2-player games and Markov Decision Processes (MDPs) with quantitative winning objectives. Quasy can also be seen as a game solver for quantitative games. Most notable, it can solve lexicographic mean-payoff games with 2 players, MDPs with mean-payoff objectives, and ergodic MDPs with mean-payoff parity objectives."}],"ddc":["000","005"],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Jobstmann, Barbara","first_name":"Barbara","last_name":"Jobstmann"},{"last_name":"Singh","first_name":"Rohit","full_name":"Singh, Rohit"}],"publist_id":"3248","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Barbara Jobstmann, and Rohit Singh. “QUASY: Quantitative Synthesis Tool,” 6605:267–71. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-19835-9_24\">https://doi.org/10.1007/978-3-642-19835-9_24</a>.","ieee":"K. Chatterjee, T. A. Henzinger, B. Jobstmann, and R. Singh, “QUASY: quantitative synthesis tool,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Saarbrucken, Germany, 2011, vol. 6605, pp. 267–271.","ista":"Chatterjee K, Henzinger TA, Jobstmann B, Singh R. 2011. QUASY: quantitative synthesis tool. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 6605, 267–271.","mla":"Chatterjee, Krishnendu, et al. <i>QUASY: Quantitative Synthesis Tool</i>. Vol. 6605, Springer, 2011, pp. 267–71, doi:<a href=\"https://doi.org/10.1007/978-3-642-19835-9_24\">10.1007/978-3-642-19835-9_24</a>.","apa":"Chatterjee, K., Henzinger, T. A., Jobstmann, B., &#38; Singh, R. (2011). QUASY: quantitative synthesis tool (Vol. 6605, pp. 267–271). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Saarbrucken, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-642-19835-9_24\">https://doi.org/10.1007/978-3-642-19835-9_24</a>","ama":"Chatterjee K, Henzinger TA, Jobstmann B, Singh R. QUASY: quantitative synthesis tool. In: Vol 6605. Springer; 2011:267-271. doi:<a href=\"https://doi.org/10.1007/978-3-642-19835-9_24\">10.1007/978-3-642-19835-9_24</a>","short":"K. Chatterjee, T.A. Henzinger, B. Jobstmann, R. Singh, in:, Springer, 2011, pp. 267–271."},"language":[{"iso":"eng"}],"oa_version":"Submitted Version"},{"alternative_title":["LNCS"],"quality_controlled":"1","file_date_updated":"2020-07-14T12:46:10Z","publication_status":"published","year":"2011","status":"public","type":"conference","has_accepted_license":"1","oa":1,"_id":"3366","doi":"10.1007/978-3-642-22110-1_20","scopus_import":"1","date_created":"2018-12-11T12:02:55Z","ec_funded":1,"pubrep_id":"76","day":"21","article_processing_charge":"No","month":"04","volume":6806,"file":[{"checksum":"c033689355f45742dc7c99b5af13ce7a","date_created":"2018-12-12T10:15:51Z","relation":"main_file","creator":"system","file_id":"5174","access_level":"open_access","file_name":"IST-2012-76-v1+1_Quantitative_synthesis_for_concurrent_programs.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:10Z","file_size":508946}],"intvolume":"      6806","project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989"},{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"call_identifier":"FP7","grant_number":"214373","name":"Design for Embedded Systems","_id":"25F1337C-B435-11E9-9278-68D0E5697425"}],"page":"243 - 259","title":"Quantitative synthesis for concurrent programs","conference":{"name":"CAV: Computer Aided Verification","end_date":"2011-07-20","start_date":"2011-07-14","location":"Snowbird, USA"},"publisher":"Springer","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5388"}]},"date_published":"2011-04-21T00:00:00Z","date_updated":"2024-10-21T06:03:04Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"abstract":[{"lang":"eng","text":"We present an algorithmic method for the quantitative, performance-aware synthesis of concurrent programs. The input consists of a nondeterministic partial program and of a parametric performance model. The nondeterminism allows the programmer to omit which (if any) synchronization construct is used at a particular program location. The performance model, specified as a weighted automaton, can capture system architectures by assigning different costs to actions such as locking, context switching, and memory and cache accesses. The quantitative synthesis problem is to automatically resolve the nondeterminism of the partial program so that both correctness is guaranteed and performance is optimal. As is standard for shared memory concurrency, correctness is formalized &quot;specification free&quot;, in particular as race freedom or deadlock freedom. For worst-case (average-case) performance, we show that the problem can be reduced to 2-player graph games (with probabilistic transitions) with quantitative objectives. While we show, using game-theoretic methods, that the synthesis problem is Nexp-complete, we present an algorithmic method and an implementation that works efficiently for concurrent programs and performance models of practical interest. We have implemented a prototype tool and used it to synthesize finite-state concurrent programs that exhibit different programming patterns, for several performance models representing different architectures. "}],"editor":[{"full_name":"Gopalakrishnan, Ganesh","first_name":"Ganesh","last_name":"Gopalakrishnan"},{"full_name":"Qadeer, Shaz","last_name":"Qadeer","first_name":"Shaz"}],"ddc":["000","004"],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","first_name":"Pavol","full_name":"Cerny, Pavol"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","last_name":"Radhakrishna"},{"last_name":"Singh","first_name":"Rohit","full_name":"Singh, Rohit"}],"corr_author":"1","publist_id":"3247","citation":{"apa":"Cerny, P., Chatterjee, K., Henzinger, T. A., Radhakrishna, A., &#38; Singh, R. (2011). Quantitative synthesis for concurrent programs. In G. Gopalakrishnan &#38; S. Qadeer (Eds.) (Vol. 6806, pp. 243–259). Presented at the CAV: Computer Aided Verification, Snowbird, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-22110-1_20\">https://doi.org/10.1007/978-3-642-22110-1_20</a>","short":"P. Cerny, K. Chatterjee, T.A. Henzinger, A. Radhakrishna, R. Singh, in:, G. Gopalakrishnan, S. Qadeer (Eds.), Springer, 2011, pp. 243–259.","ama":"Cerny P, Chatterjee K, Henzinger TA, Radhakrishna A, Singh R. Quantitative synthesis for concurrent programs. In: Gopalakrishnan G, Qadeer S, eds. Vol 6806. Springer; 2011:243-259. doi:<a href=\"https://doi.org/10.1007/978-3-642-22110-1_20\">10.1007/978-3-642-22110-1_20</a>","chicago":"Cerny, Pavol, Krishnendu Chatterjee, Thomas A Henzinger, Arjun Radhakrishna, and Rohit Singh. “Quantitative Synthesis for Concurrent Programs.” edited by Ganesh Gopalakrishnan and Shaz Qadeer, 6806:243–59. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-22110-1_20\">https://doi.org/10.1007/978-3-642-22110-1_20</a>.","ieee":"P. Cerny, K. Chatterjee, T. A. Henzinger, A. Radhakrishna, and R. Singh, “Quantitative synthesis for concurrent programs,” presented at the CAV: Computer Aided Verification, Snowbird, USA, 2011, vol. 6806, pp. 243–259.","ista":"Cerny P, Chatterjee K, Henzinger TA, Radhakrishna A, Singh R. 2011. Quantitative synthesis for concurrent programs. CAV: Computer Aided Verification, LNCS, vol. 6806, 243–259.","mla":"Cerny, Pavol, et al. <i>Quantitative Synthesis for Concurrent Programs</i>. Edited by Ganesh Gopalakrishnan and Shaz Qadeer, vol. 6806, Springer, 2011, pp. 243–59, doi:<a href=\"https://doi.org/10.1007/978-3-642-22110-1_20\">10.1007/978-3-642-22110-1_20</a>."},"language":[{"iso":"eng"}],"oa_version":"Submitted Version"},{"quality_controlled":"1","date_published":"2011-06-13T00:00:00Z","year":"2011","publication_status":"published","status":"public","type":"conference","conference":{"end_date":"2011-06-15","name":"SoCG: Symposium on Computational Geometry","start_date":"2011-06-13","location":"Paris, France"},"publisher":"ACM","related_material":{"record":[{"relation":"later_version","status":"public","id":"2939"}]},"_id":"3367","doi":"10.1145/1998196.1998228","date_updated":"2025-09-29T13:26:20Z","department":[{"_id":"HeEd"}],"abstract":[{"lang":"eng","text":"In this paper, we present the first output-sensitive algorithm to compute the persistence diagram of a filtered simplicial complex. For any Γ&gt;0, it returns only those homology classes with persistence at least Γ. Instead of the classical reduction via column operations, our algorithm performs rank computations on submatrices of the boundary matrix. For an arbitrary constant δ ∈ (0,1), the running time is O(C(1-δ)ΓR(n)log n), where C(1-δ)Γ is the number of homology classes with persistence at least (1-δ)Γ, n is the total number of simplices, and R(n) is the complexity of computing the rank of an n x n matrix with O(n) nonzero entries. Depending on the choice of the rank algorithm, this yields a deterministic O(C(1-δ)Γn2.376) algorithm, a O(C(1-δ)Γn2.28) Las-Vegas algorithm, or a O(C(1-δ)Γn2+ε) Monte-Carlo algorithm for an arbitrary ε&gt;0."}],"corr_author":"1","scopus_import":1,"date_created":"2018-12-11T12:02:56Z","day":"13","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Chen","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao"},{"id":"36E4574A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Kerber","full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299"}],"page":"207 - 216","title":"An output sensitive algorithm for persistent homology","language":[{"iso":"eng"}],"oa_version":"None","article_processing_charge":"No","month":"06","publist_id":"3245","citation":{"apa":"Chen, C., &#38; Kerber, M. (2011). An output sensitive algorithm for persistent homology (pp. 207–216). Presented at the SoCG: Symposium on Computational Geometry, Paris, France: ACM. <a href=\"https://doi.org/10.1145/1998196.1998228\">https://doi.org/10.1145/1998196.1998228</a>","ama":"Chen C, Kerber M. An output sensitive algorithm for persistent homology. In: ACM; 2011:207-216. doi:<a href=\"https://doi.org/10.1145/1998196.1998228\">10.1145/1998196.1998228</a>","short":"C. Chen, M. Kerber, in:, ACM, 2011, pp. 207–216.","chicago":"Chen, Chao, and Michael Kerber. “An Output Sensitive Algorithm for Persistent Homology,” 207–16. ACM, 2011. <a href=\"https://doi.org/10.1145/1998196.1998228\">https://doi.org/10.1145/1998196.1998228</a>.","ieee":"C. Chen and M. Kerber, “An output sensitive algorithm for persistent homology,” presented at the SoCG: Symposium on Computational Geometry, Paris, France, 2011, pp. 207–216.","mla":"Chen, Chao, and Michael Kerber. <i>An Output Sensitive Algorithm for Persistent Homology</i>. ACM, 2011, pp. 207–16, doi:<a href=\"https://doi.org/10.1145/1998196.1998228\">10.1145/1998196.1998228</a>.","ista":"Chen C, Kerber M. 2011. An output sensitive algorithm for persistent homology. SoCG: Symposium on Computational Geometry, 207–216."}},{"author":[{"full_name":"Pernia-Andrade, Alejandro","id":"36963E98-F248-11E8-B48F-1D18A9856A87","first_name":"Alejandro","last_name":"Pernia-Andrade"},{"first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","citation":{"ista":"Pernia-Andrade A, Jonas PM. 2011. The multiple faces of RIM. Neuron. 69(2), 185–187.","mla":"Pernia-Andrade, Alejandro, and Peter M. Jonas. “The Multiple Faces of RIM.” <i>Neuron</i>, vol. 69, no. 2, Elsevier, 2011, pp. 185–87, doi:<a href=\"https://doi.org/10.1016/j.neuron.2011.01.010\">10.1016/j.neuron.2011.01.010</a>.","chicago":"Pernia-Andrade, Alejandro, and Peter M Jonas. “The Multiple Faces of RIM.” <i>Neuron</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.neuron.2011.01.010\">https://doi.org/10.1016/j.neuron.2011.01.010</a>.","ieee":"A. Pernia-Andrade and P. M. Jonas, “The multiple faces of RIM,” <i>Neuron</i>, vol. 69, no. 2. Elsevier, pp. 185–187, 2011.","apa":"Pernia-Andrade, A., &#38; Jonas, P. M. (2011). The multiple faces of RIM. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2011.01.010\">https://doi.org/10.1016/j.neuron.2011.01.010</a>","short":"A. Pernia-Andrade, P.M. Jonas, Neuron 69 (2011) 185–187.","ama":"Pernia-Andrade A, Jonas PM. The multiple faces of RIM. <i>Neuron</i>. 2011;69(2):185-187. doi:<a href=\"https://doi.org/10.1016/j.neuron.2011.01.010\">10.1016/j.neuron.2011.01.010</a>"},"publist_id":"3243","oa_version":"None","language":[{"iso":"eng"}],"publisher":"Elsevier","issue":"2","date_published":"2011-01-27T00:00:00Z","abstract":[{"lang":"eng","text":"Rab3 interacting molecules (RIMs) are highly enriched in the active zones of presynaptic terminals. It is generally thought that they operate as effectors of the small G protein Rab3. Three recent papers, by Han et al. (this issue of Neuron), Deng et al. (this issue of Neuron), and Kaeser et al. (a recent issue of Cell), shed new light on the functional role of RIM in presynaptic terminals. First, RIM tethers Ca2+ channels to active zones. Second, RIM contributes to priming of synaptic vesicles by interacting with another presynaptic protein, Munc13."}],"department":[{"_id":"PeJo"}],"date_updated":"2025-09-30T09:01:26Z","isi":1,"external_id":{"isi":["000286792900002"]},"publication":"Neuron","day":"27","date_created":"2018-12-11T12:02:56Z","scopus_import":"1","volume":69,"article_processing_charge":"No","month":"01","page":"185 - 187","title":"The multiple faces of RIM","intvolume":"        69","status":"public","type":"journal_article","year":"2011","publication_status":"published","quality_controlled":"1","doi":"10.1016/j.neuron.2011.01.010","_id":"3369"},{"day":"01","date_created":"2018-12-11T12:02:57Z","publication":"Systematic Biology","page":"218 - 225","title":"Consequences of different null models on the tree shape bias of supertree methods","intvolume":"        60","volume":60,"article_processing_charge":"No","month":"03","publication_status":"published","year":"2011","type":"journal_article","status":"public","quality_controlled":"1","main_file_link":[{"url":"http://eprints.cs.univie.ac.at/3226/","open_access":"1"}],"_id":"3370","doi":"10.1093/sysbio/syq086","oa":1,"corr_author":"1","author":[{"last_name":"Kupczok","first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Kupczok, Anne"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"oa_version":"Submitted Version","citation":{"ieee":"A. Kupczok, “Consequences of different null models on the tree shape bias of supertree methods,” <i>Systematic Biology</i>, vol. 60, no. 2. Oxford University Press, pp. 218–225, 2011.","chicago":"Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias of Supertree Methods.” <i>Systematic Biology</i>. Oxford University Press, 2011. <a href=\"https://doi.org/10.1093/sysbio/syq086\">https://doi.org/10.1093/sysbio/syq086</a>.","mla":"Kupczok, Anne. “Consequences of Different Null Models on the Tree Shape Bias of Supertree Methods.” <i>Systematic Biology</i>, vol. 60, no. 2, Oxford University Press, 2011, pp. 218–25, doi:<a href=\"https://doi.org/10.1093/sysbio/syq086\">10.1093/sysbio/syq086</a>.","ista":"Kupczok A. 2011. Consequences of different null models on the tree shape bias of supertree methods. Systematic Biology. 60(2), 218–225.","short":"A. Kupczok, Systematic Biology 60 (2011) 218–225.","ama":"Kupczok A. Consequences of different null models on the tree shape bias of supertree methods. <i>Systematic Biology</i>. 2011;60(2):218-225. doi:<a href=\"https://doi.org/10.1093/sysbio/syq086\">10.1093/sysbio/syq086</a>","apa":"Kupczok, A. (2011). Consequences of different null models on the tree shape bias of supertree methods. <i>Systematic Biology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/sysbio/syq086\">https://doi.org/10.1093/sysbio/syq086</a>"},"publist_id":"3241","date_published":"2011-03-01T00:00:00Z","publisher":"Oxford University Press","issue":"2","external_id":{"isi":["000287255100009"]},"isi":1,"abstract":[{"lang":"eng","text":"Supertree methods are widely applied and give rise to new conclusions about phylogenies (e.g., Bininda-Emonds et al. 2007). Although several desiderata for supertree methods exist (Wilkinson, Thorley, et al. 2004), only few of them have been studied in greater detail, examples include shape bias (Wilkinson et al. 2005) or pareto properties (Wilkinson et al. 2007). Here I look more closely at two matrix representation methods, matrix representation with compatibility (MRC) and matrix representation with parsimony (MRP). Different null models of random data are studied and the resulting tree shapes are investigated. Thereby I consider unrooted trees and a bias in tree shape is determined by a tree balance measure. The measure for unrooted trees is a modification of a tree balance measure for rooted trees. I observe that depending on the underlying null model of random data, the methods may resolve conflict in favor of more balanced tree shapes. The analyses refer only to trees with the same taxon set, also known as the consensus setting (e.g., Wilkinson et al. 2007), but I will be able to draw conclusions on how to deal with missing data."}],"date_updated":"2025-09-30T08:59:18Z","department":[{"_id":"JoBo"}]},{"publication_status":"published","file_date_updated":"2020-07-14T12:46:11Z","year":"2011","type":"journal_article","status":"public","quality_controlled":"1","_id":"3371","doi":"10.1091/mbc.E10-12-0958","article_type":"original","oa":1,"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"pubrep_id":"373","day":"15","scopus_import":"1","date_created":"2018-12-11T12:02:57Z","publication":"Molecular Biology and Evolution","page":"724","title":"Cells on the move in Philadelphia","intvolume":"        22","volume":22,"file":[{"file_name":"IST-2015-373-v1+1_Mol._Biol._Cell-2011-Sixt-724.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:11Z","file_size":105421,"checksum":"3467986ab7a64e7694ffd1013b5d9da9","date_created":"2018-12-12T10:17:29Z","creator":"system","file_id":"5283","relation":"main_file","access_level":"open_access"}],"article_processing_charge":"No","month":"03","date_published":"2011-03-15T00:00:00Z","publisher":"Oxford University Press","issue":"6","ddc":["570"],"isi":1,"external_id":{"isi":["000288368200010"]},"abstract":[{"text":"The Minisymposium “Cell Migration and Motility” was attended by approximately 500 visitors and covered a broad range of questions in the field using diverse model systems. Topics comprised actin dynamics, cell polarity, force transduction, signal transduction, bar- rier transmigration, and chemotactic guidance.","lang":"eng"}],"date_updated":"2025-09-30T08:58:51Z","department":[{"_id":"MiSi"}],"author":[{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"},{"full_name":"Parent, Carole","first_name":"Carole","last_name":"Parent"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"short":"M.K. Sixt, C. Parent, Molecular Biology and Evolution 22 (2011) 724.","ama":"Sixt MK, Parent C. Cells on the move in Philadelphia. <i>Molecular Biology and Evolution</i>. 2011;22(6):724. doi:<a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">10.1091/mbc.E10-12-0958</a>","apa":"Sixt, M. K., &#38; Parent, C. (2011). Cells on the move in Philadelphia. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">https://doi.org/10.1091/mbc.E10-12-0958</a>","ieee":"M. K. Sixt and C. Parent, “Cells on the move in Philadelphia,” <i>Molecular Biology and Evolution</i>, vol. 22, no. 6. Oxford University Press, p. 724, 2011.","chicago":"Sixt, Michael K, and Carole Parent. “Cells on the Move in Philadelphia.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2011. <a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">https://doi.org/10.1091/mbc.E10-12-0958</a>.","mla":"Sixt, Michael K., and Carole Parent. “Cells on the Move in Philadelphia.” <i>Molecular Biology and Evolution</i>, vol. 22, no. 6, Oxford University Press, 2011, p. 724, doi:<a href=\"https://doi.org/10.1091/mbc.E10-12-0958\">10.1091/mbc.E10-12-0958</a>.","ista":"Sixt MK, Parent C. 2011. Cells on the move in Philadelphia. Molecular Biology and Evolution. 22(6), 724."},"publist_id":"3238"},{"publication":"Nature","pmid":1,"day":"23","scopus_import":"1","date_created":"2018-12-11T12:02:57Z","volume":471,"article_processing_charge":"No","month":"03","title":"Inclusive fitness theory and eusociality","page":"E1 - E4","intvolume":"       471","publication_status":"published","year":"2011","status":"public","type":"journal_article","quality_controlled":"1","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3836173/","open_access":"1"}],"_id":"3372","doi":"10.1038/nature09831","author":[{"last_name":"Abbot","first_name":"Patrick","full_name":"Abbot, Patrick"},{"first_name":"Jun","last_name":"Abe","full_name":"Abe, Jun"},{"full_name":"Alcock, John","last_name":"Alcock","first_name":"John"},{"first_name":"Samuel","last_name":"Alizon","full_name":"Alizon, Samuel"},{"last_name":"Alpedrinha","first_name":"Joao","full_name":"Alpedrinha, Joao"},{"full_name":"Andersson, Malte","first_name":"Malte","last_name":"Andersson"},{"first_name":"Jean","last_name":"Andre","full_name":"Andre, Jean"},{"first_name":"Minus","last_name":"Van Baalen","full_name":"Van Baalen, Minus"},{"last_name":"Balloux","first_name":"Francois","full_name":"Balloux, Francois"},{"full_name":"Balshine, Sigal","last_name":"Balshine","first_name":"Sigal"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"},{"first_name":"Leo","last_name":"Beukeboom","full_name":"Beukeboom, Leo"},{"full_name":"Biernaskie, Jay","last_name":"Biernaskie","first_name":"Jay"},{"first_name":"Trine","last_name":"Bilde","full_name":"Bilde, Trine"},{"first_name":"Gerald","last_name":"Borgia","full_name":"Borgia, Gerald"},{"first_name":"Michael","last_name":"Breed","full_name":"Breed, Michael"},{"last_name":"Brown","first_name":"Sam","full_name":"Brown, Sam"},{"full_name":"Bshary, Redouan","first_name":"Redouan","last_name":"Bshary"},{"first_name":"Angus","last_name":"Buckling","full_name":"Buckling, Angus"},{"full_name":"Burley, Nancy","last_name":"Burley","first_name":"Nancy"},{"first_name":"Max","last_name":"Burton Chellew","full_name":"Burton Chellew, Max"},{"full_name":"Cant, Michael","first_name":"Michael","last_name":"Cant"},{"first_name":"Michel","last_name":"Chapuisat","full_name":"Chapuisat, Michel"},{"full_name":"Charnov, Eric","first_name":"Eric","last_name":"Charnov"},{"full_name":"Clutton Brock, Tim","first_name":"Tim","last_name":"Clutton Brock"},{"full_name":"Cockburn, Andrew","last_name":"Cockburn","first_name":"Andrew"},{"full_name":"Cole, Blaine","last_name":"Cole","first_name":"Blaine"},{"full_name":"Colegrave, Nick","last_name":"Colegrave","first_name":"Nick"},{"full_name":"Cosmides, Leda","first_name":"Leda","last_name":"Cosmides"},{"last_name":"Couzin","first_name":"Iain","full_name":"Couzin, Iain"},{"last_name":"Coyne","first_name":"Jerry","full_name":"Coyne, Jerry"},{"full_name":"Creel, Scott","last_name":"Creel","first_name":"Scott"},{"last_name":"Crespi","first_name":"Bernard","full_name":"Crespi, Bernard"},{"full_name":"Curry, Robert","first_name":"Robert","last_name":"Curry"},{"first_name":"Sasha","last_name":"Dall","full_name":"Dall, Sasha"},{"full_name":"Day, Troy","first_name":"Troy","last_name":"Day"},{"first_name":"Janis","last_name":"Dickinson","full_name":"Dickinson, Janis"},{"first_name":"Lee","last_name":"Dugatkin","full_name":"Dugatkin, Lee"},{"last_name":"El Mouden","first_name":"Claire","full_name":"El Mouden, Claire"},{"full_name":"Emlen, Stephen","last_name":"Emlen","first_name":"Stephen"},{"full_name":"Evans, Jay","first_name":"Jay","last_name":"Evans"},{"full_name":"Ferriere, Regis","last_name":"Ferriere","first_name":"Regis"},{"last_name":"Field","first_name":"Jeremy","full_name":"Field, Jeremy"},{"full_name":"Foitzik, Susanne","first_name":"Susanne","last_name":"Foitzik"},{"last_name":"Foster","first_name":"Kevin","full_name":"Foster, Kevin"},{"full_name":"Foster, William","last_name":"Foster","first_name":"William"},{"first_name":"Charles","last_name":"Fox","full_name":"Fox, Charles"},{"last_name":"Gadau","first_name":"Juergen","full_name":"Gadau, Juergen"},{"first_name":"Sylvain","last_name":"Gandon","full_name":"Gandon, Sylvain"},{"full_name":"Gardner, Andy","last_name":"Gardner","first_name":"Andy"},{"last_name":"Gardner","first_name":"Michael","full_name":"Gardner, Michael"},{"last_name":"Getty","first_name":"Thomas","full_name":"Getty, Thomas"},{"last_name":"Goodisman","first_name":"Michael","full_name":"Goodisman, Michael"},{"last_name":"Grafen","first_name":"Alan","full_name":"Grafen, Alan"},{"full_name":"Grosberg, Rick","last_name":"Grosberg","first_name":"Rick"},{"last_name":"Grozinger","first_name":"Christina","full_name":"Grozinger, Christina"},{"full_name":"Gouyon, Pierre","first_name":"Pierre","last_name":"Gouyon"},{"last_name":"Gwynne","first_name":"Darryl","full_name":"Gwynne, Darryl"},{"full_name":"Harvey, Paul","first_name":"Paul","last_name":"Harvey"},{"last_name":"Hatchwell","first_name":"Ben","full_name":"Hatchwell, Ben"},{"full_name":"Heinze, Jürgen","last_name":"Heinze","first_name":"Jürgen"},{"full_name":"Helantera, Heikki","first_name":"Heikki","last_name":"Helantera"},{"full_name":"Helms, Ken","first_name":"Ken","last_name":"Helms"},{"full_name":"Hill, Kim","last_name":"Hill","first_name":"Kim"},{"full_name":"Jiricny, Natalie","last_name":"Jiricny","first_name":"Natalie"},{"last_name":"Johnstone","first_name":"Rufus","full_name":"Johnstone, Rufus"},{"last_name":"Kacelnik","first_name":"Alex","full_name":"Kacelnik, Alex"},{"last_name":"Kiers","first_name":"E Toby","full_name":"Kiers, E Toby"},{"first_name":"Hanna","last_name":"Kokko","full_name":"Kokko, Hanna"},{"last_name":"Komdeur","first_name":"Jan","full_name":"Komdeur, Jan"},{"full_name":"Korb, Judith","last_name":"Korb","first_name":"Judith"},{"first_name":"Daniel","last_name":"Kronauer","full_name":"Kronauer, Daniel"},{"last_name":"Kümmerli","first_name":"Rolf","full_name":"Kümmerli, Rolf"},{"last_name":"Lehmann","first_name":"Laurent","full_name":"Lehmann, Laurent"},{"first_name":"Timothy","last_name":"Linksvayer","full_name":"Linksvayer, Timothy"},{"first_name":"Sébastien","last_name":"Lion","full_name":"Lion, Sébastien"},{"full_name":"Lyon, Bruce","first_name":"Bruce","last_name":"Lyon"},{"last_name":"Marshall","first_name":"James","full_name":"Marshall, James"},{"full_name":"Mcelreath, Richard","last_name":"Mcelreath","first_name":"Richard"},{"full_name":"Michalakis, Yannis","first_name":"Yannis","last_name":"Michalakis"},{"first_name":"Richard","last_name":"Michod","full_name":"Michod, Richard"},{"full_name":"Mock, Douglas","first_name":"Douglas","last_name":"Mock"},{"last_name":"Monnin","first_name":"Thibaud","full_name":"Monnin, Thibaud"},{"full_name":"Montgomerie, Robert","last_name":"Montgomerie","first_name":"Robert"},{"first_name":"Allen","last_name":"Moore","full_name":"Moore, Allen"},{"last_name":"Mueller","first_name":"Ulrich","full_name":"Mueller, Ulrich"},{"first_name":"Ronald","last_name":"Noë","full_name":"Noë, Ronald"},{"last_name":"Okasha","first_name":"Samir","full_name":"Okasha, Samir"},{"full_name":"Pamilo, Pekka","first_name":"Pekka","last_name":"Pamilo"},{"full_name":"Parker, Geoff","first_name":"Geoff","last_name":"Parker"},{"full_name":"Pedersen, Jes","first_name":"Jes","last_name":"Pedersen"},{"first_name":"Ido","last_name":"Pen","full_name":"Pen, Ido"},{"first_name":"David","last_name":"Pfennig","full_name":"Pfennig, David"},{"first_name":"David","last_name":"Queller","full_name":"Queller, David"},{"last_name":"Rankin","first_name":"Daniel","full_name":"Rankin, Daniel"},{"full_name":"Reece, Sarah","last_name":"Reece","first_name":"Sarah"},{"full_name":"Reeve, Hudson","first_name":"Hudson","last_name":"Reeve"},{"last_name":"Reuter","first_name":"Max","full_name":"Reuter, Max"},{"last_name":"Roberts","first_name":"Gilbert","full_name":"Roberts, Gilbert"},{"full_name":"Robson, Simon","last_name":"Robson","first_name":"Simon"},{"first_name":"Denis","last_name":"Roze","full_name":"Roze, Denis"},{"full_name":"Rousset, Francois","last_name":"Rousset","first_name":"Francois"},{"full_name":"Rueppell, Olav","last_name":"Rueppell","first_name":"Olav"},{"first_name":"Joel","last_name":"Sachs","full_name":"Sachs, Joel"},{"full_name":"Santorelli, Lorenzo","first_name":"Lorenzo","last_name":"Santorelli"},{"last_name":"Schmid Hempel","first_name":"Paul","full_name":"Schmid Hempel, Paul"},{"full_name":"Schwarz, Michael","last_name":"Schwarz","first_name":"Michael"},{"full_name":"Scott Phillips, Tom","first_name":"Tom","last_name":"Scott Phillips"},{"first_name":"Janet","last_name":"Shellmann Sherman","full_name":"Shellmann Sherman, Janet"},{"full_name":"Sherman, Paul","last_name":"Sherman","first_name":"Paul"},{"full_name":"Shuker, David","last_name":"Shuker","first_name":"David"},{"full_name":"Smith, Jeff","first_name":"Jeff","last_name":"Smith"},{"full_name":"Spagna, Joseph","last_name":"Spagna","first_name":"Joseph"},{"full_name":"Strassmann, Beverly","first_name":"Beverly","last_name":"Strassmann"},{"full_name":"Suarez, Andrew","last_name":"Suarez","first_name":"Andrew"},{"first_name":"Liselotte","last_name":"Sundström","full_name":"Sundström, Liselotte"},{"last_name":"Taborsky","first_name":"Michael","full_name":"Taborsky, Michael"},{"full_name":"Taylor, Peter","first_name":"Peter","last_name":"Taylor"},{"full_name":"Thompson, Graham","last_name":"Thompson","first_name":"Graham"},{"full_name":"Tooby, John","last_name":"Tooby","first_name":"John"},{"first_name":"Neil","last_name":"Tsutsui","full_name":"Tsutsui, Neil"},{"first_name":"Kazuki","last_name":"Tsuji","full_name":"Tsuji, Kazuki"},{"first_name":"Stefano","last_name":"Turillazzi","full_name":"Turillazzi, Stefano"},{"full_name":"Úbeda, Francisco","first_name":"Francisco","last_name":"Úbeda"},{"first_name":"Edward","last_name":"Vargo","full_name":"Vargo, Edward"},{"full_name":"Voelkl, Bernard","first_name":"Bernard","last_name":"Voelkl"},{"full_name":"Wenseleers, Tom","first_name":"Tom","last_name":"Wenseleers"},{"full_name":"West, Stuart","first_name":"Stuart","last_name":"West"},{"last_name":"West Eberhard","first_name":"Mary","full_name":"West Eberhard, Mary"},{"full_name":"Westneat, David","last_name":"Westneat","first_name":"David"},{"full_name":"Wiernasz, Diane","last_name":"Wiernasz","first_name":"Diane"},{"full_name":"Wild, Geoff","first_name":"Geoff","last_name":"Wild"},{"first_name":"Richard","last_name":"Wrangham","full_name":"Wrangham, Richard"},{"first_name":"Andrew","last_name":"Young","full_name":"Young, Andrew"},{"full_name":"Zeh, David","first_name":"David","last_name":"Zeh"},{"last_name":"Zeh","first_name":"Jeanne","full_name":"Zeh, Jeanne"},{"last_name":"Zink","first_name":"Andrew","full_name":"Zink, Andrew"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"short":"P. Abbot, J. Abe, J. Alcock, S. Alizon, J. Alpedrinha, M. Andersson, J. Andre, M. Van Baalen, F. Balloux, S. Balshine, N.H. Barton, L. Beukeboom, J. Biernaskie, T. Bilde, G. Borgia, M. Breed, S. Brown, R. Bshary, A. Buckling, N. Burley, M. Burton Chellew, M. Cant, M. Chapuisat, E. Charnov, T. Clutton Brock, A. Cockburn, B. Cole, N. Colegrave, L. Cosmides, I. Couzin, J. Coyne, S. Creel, B. Crespi, R. Curry, S. Dall, T. Day, J. Dickinson, L. Dugatkin, C. El Mouden, S. Emlen, J. Evans, R. Ferriere, J. Field, S. Foitzik, K. Foster, W. Foster, C. Fox, J. Gadau, S. Gandon, A. Gardner, M. Gardner, T. Getty, M. Goodisman, A. Grafen, R. Grosberg, C. Grozinger, P. Gouyon, D. Gwynne, P. Harvey, B. Hatchwell, J. Heinze, H. Helantera, K. Helms, K. Hill, N. Jiricny, R. Johnstone, A. Kacelnik, E.T. Kiers, H. Kokko, J. Komdeur, J. Korb, D. Kronauer, R. Kümmerli, L. Lehmann, T. Linksvayer, S. Lion, B. Lyon, J. Marshall, R. Mcelreath, Y. Michalakis, R. Michod, D. Mock, T. Monnin, R. Montgomerie, A. Moore, U. Mueller, R. Noë, S. Okasha, P. Pamilo, G. Parker, J. Pedersen, I. Pen, D. Pfennig, D. Queller, D. Rankin, S. Reece, H. Reeve, M. Reuter, G. Roberts, S. Robson, D. Roze, F. Rousset, O. Rueppell, J. Sachs, L. Santorelli, P. Schmid Hempel, M. Schwarz, T. Scott Phillips, J. Shellmann Sherman, P. Sherman, D. Shuker, J. Smith, J. Spagna, B. Strassmann, A. Suarez, L. Sundström, M. Taborsky, P. Taylor, G. Thompson, J. Tooby, N. Tsutsui, K. Tsuji, S. Turillazzi, F. Úbeda, E. Vargo, B. Voelkl, T. Wenseleers, S. West, M. West Eberhard, D. Westneat, D. Wiernasz, G. Wild, R. Wrangham, A. Young, D. Zeh, J. Zeh, A. Zink, Nature 471 (2011) E1–E4.","ama":"Abbot P, Abe J, Alcock J, et al. Inclusive fitness theory and eusociality. <i>Nature</i>. 2011;471(7339):E1-E4. doi:<a href=\"https://doi.org/10.1038/nature09831\">10.1038/nature09831</a>","apa":"Abbot, P., Abe, J., Alcock, J., Alizon, S., Alpedrinha, J., Andersson, M., … Zink, A. (2011). Inclusive fitness theory and eusociality. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature09831\">https://doi.org/10.1038/nature09831</a>","ista":"Abbot P et al. 2011. Inclusive fitness theory and eusociality. Nature. 471(7339), E1–E4.","mla":"Abbot, Patrick, et al. “Inclusive Fitness Theory and Eusociality.” <i>Nature</i>, vol. 471, no. 7339, Nature Publishing Group, 2011, pp. E1–4, doi:<a href=\"https://doi.org/10.1038/nature09831\">10.1038/nature09831</a>.","ieee":"P. Abbot <i>et al.</i>, “Inclusive fitness theory and eusociality,” <i>Nature</i>, vol. 471, no. 7339. Nature Publishing Group, pp. E1–E4, 2011.","chicago":"Abbot, Patrick, Jun Abe, John Alcock, Samuel Alizon, Joao Alpedrinha, Malte Andersson, Jean Andre, et al. “Inclusive Fitness Theory and Eusociality.” <i>Nature</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/nature09831\">https://doi.org/10.1038/nature09831</a>."},"publist_id":"3237","language":[{"iso":"eng"}],"oa_version":"Submitted Version","publisher":"Nature Publishing Group","issue":"7339","date_published":"2011-03-23T00:00:00Z","abstract":[{"lang":"eng","text":"Nowak et al.1 argue that inclusive fitness theory has been of little value in explaining the natural world, and that it has led to negligible progress in explaining the evolution of eusociality. However, we believe that their arguments are based upon a misunderstanding of evolutionary theory and a misrepresentation of the empirical literature. We will focus our comments on three general issues."}],"date_updated":"2025-09-30T08:58:00Z","department":[{"_id":"NiBa"}],"isi":1,"external_id":{"isi":["000288702200001"],"pmid":["21430721"]}},{"arxiv":1,"date_published":"2011-04-01T00:00:00Z","publisher":"IOP Publishing","issue":"15","isi":1,"external_id":{"isi":["000289199800002"],"arxiv":["1101.4240"]},"abstract":[{"text":"Genetic regulatory networks enable cells to respond to changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits has deepened our understanding of what kinds of computations genetic regulatory networks can perform, and with what reliability. These advances have motivated researchers to look for connections between the architecture and function of genetic regulatory networks. Transmitting information between a network's inputs and outputs has been proposed as one such possible measure of function, relevant in certain biological contexts. Here we summarize recent developments in the application of information theory to gene regulatory networks. We first review basic concepts in information theory necessary for understanding recent work. We then discuss the functional complexity of gene regulation, which arises from the molecular nature of the regulatory interactions. We end by reviewing some experiments that support the view that genetic networks responsible for early development of multicellular organisms might be maximizing transmitted 'positional information'.","lang":"eng"}],"department":[{"_id":"GaTk"}],"date_updated":"2025-09-30T08:56:23Z","corr_author":"1","author":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper"},{"last_name":"Walczak","first_name":"Aleksandra","full_name":"Walczak, Aleksandra"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Submitted Version","language":[{"iso":"eng"}],"citation":{"ama":"Tkačik G, Walczak A. Information transmission in genetic regulatory networks a review. <i>Journal of Physics: Condensed Matter</i>. 2011;23(15). doi:<a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">10.1088/0953-8984/23/15/153102</a>","short":"G. Tkačik, A. Walczak, Journal of Physics: Condensed Matter 23 (2011).","apa":"Tkačik, G., &#38; Walczak, A. (2011). Information transmission in genetic regulatory networks a review. <i>Journal of Physics: Condensed Matter</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">https://doi.org/10.1088/0953-8984/23/15/153102</a>","ista":"Tkačik G, Walczak A. 2011. Information transmission in genetic regulatory networks a review. Journal of Physics: Condensed Matter. 23(15), 153102.","mla":"Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” <i>Journal of Physics: Condensed Matter</i>, vol. 23, no. 15, 153102, IOP Publishing, 2011, doi:<a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">10.1088/0953-8984/23/15/153102</a>.","ieee":"G. Tkačik and A. Walczak, “Information transmission in genetic regulatory networks a review,” <i>Journal of Physics: Condensed Matter</i>, vol. 23, no. 15. IOP Publishing, 2011.","chicago":"Tkačik, Gašper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” <i>Journal of Physics: Condensed Matter</i>. IOP Publishing, 2011. <a href=\"https://doi.org/10.1088/0953-8984/23/15/153102\">https://doi.org/10.1088/0953-8984/23/15/153102</a>."},"publist_id":"3233","status":"public","type":"journal_article","publication_status":"published","year":"2011","quality_controlled":"1","article_number":"153102","doi":"10.1088/0953-8984/23/15/153102","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1101.4240"}],"_id":"3374","oa":1,"day":"01","date_created":"2018-12-11T12:02:58Z","scopus_import":"1","publication":"Journal of Physics: Condensed Matter","title":"Information transmission in genetic regulatory networks a review","intvolume":"        23","volume":23,"article_processing_charge":"No","month":"04"},{"quality_controlled":"1","publication_status":"published","year":"2011","status":"public","type":"journal_article","oa":1,"_id":"3376","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143497/","open_access":"1"}],"doi":"10.1016/j.molcel.2011.04.016","publication":"Molecular Cell","scopus_import":"1","acknowledgement":"This work was supported by a Feodor Lynen Fellowship of the Alexander von Humboldt Foundation (to T.B.).","date_created":"2018-12-11T12:02:59Z","day":"20","article_processing_charge":"No","month":"05","volume":42,"intvolume":"        42","page":"413 - 425","title":"Resolution of gene regulatory conflicts caused by combinations of antibiotics","issue":"4","publisher":"Cell Press","date_published":"2011-05-20T00:00:00Z","date_updated":"2025-09-30T08:54:28Z","department":[{"_id":"ToBo"}],"abstract":[{"lang":"eng","text":"Regulatory conflicts occur when two signals that individually trigger opposite cellular responses are present simultaneously. Here, we investigate regulatory conflicts in the bacterial response to antibiotic combinations. We use an Escherichia coli promoter-GFP library to study the transcriptional response of many promoters to either additive or antagonistic drug pairs at fine two-dimensional (2D) resolution of drug concentration. Surprisingly, we find that this data set can be characterized as a linear sum of only two principal components. Component one, accounting for over 70% of the response, represents the response to growth inhibition by the drugs. Component two describes how regulatory conflicts are resolved. For the additive drug pair, conflicts are resolved by linearly interpolating the single drug responses, while for the antagonistic drug pair, the growth-limiting drug dominates the response. Importantly, for a given drug pair, the same conflict resolution strategy applies to almost all genes. These results provide a recipe for predicting gene expression responses to antibiotic combinations."}],"isi":1,"external_id":{"isi":["000291113800005"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X"},{"first_name":"Roy","last_name":"Kishony","full_name":"Kishony, Roy"}],"publist_id":"3231","citation":{"short":"M.T. Bollenbach, R. Kishony, Molecular Cell 42 (2011) 413–425.","ama":"Bollenbach MT, Kishony R. Resolution of gene regulatory conflicts caused by combinations of antibiotics. <i>Molecular Cell</i>. 2011;42(4):413-425. doi:<a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">10.1016/j.molcel.2011.04.016</a>","apa":"Bollenbach, M. T., &#38; Kishony, R. (2011). Resolution of gene regulatory conflicts caused by combinations of antibiotics. <i>Molecular Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">https://doi.org/10.1016/j.molcel.2011.04.016</a>","ieee":"M. T. Bollenbach and R. Kishony, “Resolution of gene regulatory conflicts caused by combinations of antibiotics,” <i>Molecular Cell</i>, vol. 42, no. 4. Cell Press, pp. 413–425, 2011.","chicago":"Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” <i>Molecular Cell</i>. Cell Press, 2011. <a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">https://doi.org/10.1016/j.molcel.2011.04.016</a>.","ista":"Bollenbach MT, Kishony R. 2011. Resolution of gene regulatory conflicts caused by combinations of antibiotics. Molecular Cell. 42(4), 413–425.","mla":"Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” <i>Molecular Cell</i>, vol. 42, no. 4, Cell Press, 2011, pp. 413–25, doi:<a href=\"https://doi.org/10.1016/j.molcel.2011.04.016\">10.1016/j.molcel.2011.04.016</a>."},"language":[{"iso":"eng"}],"oa_version":"Submitted Version"}]