[{"oa_version":"Submitted Version","issue":"1","publication":"Plant Cell","day":"20","abstract":[{"lang":"eng","text":"Auxin participates in a multitude of developmental processes, as well as responses to environmental cues. Compared with other plant hormones, auxin exhibits a unique property, as it undergoes directional, cell-to-cell transport facilitated by plasma membrane-localized transport proteins. Among them, a prominent role has been ascribed to the PIN family of auxin efflux facilitators. PIN proteins direct polar auxin transport on account of their asymmetric subcellular localizations. In this review, we provide an overview of the multiple developmental roles of PIN proteins, including the atypical endoplasmic reticulum-localized members of the family, and look at the family from an evolutionary perspective. Next, we cover the cell biological and molecular aspects of PIN function, in particular the establishment of their polar subcellular localization. Hormonal and environmental inputs into the regulation of PIN action are summarized as well."}],"corr_author":"1","publication_status":"published","scopus_import":"1","related_material":{"record":[{"id":"938","status":"public","relation":"dissertation_contains"}]},"title":"PIN-dependent auxin transport: Action, regulation, and evolution","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330589/"}],"department":[{"_id":"JiFr"}],"external_id":{"isi":["000350764700007"],"pmid":["25604445"]},"author":[{"orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","first_name":"Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"page":"20 - 32","_id":"1591","year":"2015","pmid":1,"isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"American Society of Plant Biologists","status":"public","type":"journal_article","date_updated":"2026-04-08T14:20:44Z","intvolume":"        27","doi":"10.1105/tpc.114.134874","publist_id":"5580","date_published":"2015-01-20T00:00:00Z","article_processing_charge":"No","volume":27,"month":"01","oa":1,"citation":{"short":"M. Adamowski, J. Friml, Plant Cell 27 (2015) 20–32.","ista":"Adamowski M, Friml J. 2015. PIN-dependent auxin transport: Action, regulation, and evolution. Plant Cell. 27(1), 20–32.","ama":"Adamowski M, Friml J. PIN-dependent auxin transport: Action, regulation, and evolution. <i>Plant Cell</i>. 2015;27(1):20-32. doi:<a href=\"https://doi.org/10.1105/tpc.114.134874\">10.1105/tpc.114.134874</a>","chicago":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” <i>Plant Cell</i>. American Society of Plant Biologists, 2015. <a href=\"https://doi.org/10.1105/tpc.114.134874\">https://doi.org/10.1105/tpc.114.134874</a>.","mla":"Adamowski, Maciek, and Jiří Friml. “PIN-Dependent Auxin Transport: Action, Regulation, and Evolution.” <i>Plant Cell</i>, vol. 27, no. 1, American Society of Plant Biologists, 2015, pp. 20–32, doi:<a href=\"https://doi.org/10.1105/tpc.114.134874\">10.1105/tpc.114.134874</a>.","ieee":"M. Adamowski and J. Friml, “PIN-dependent auxin transport: Action, regulation, and evolution,” <i>Plant Cell</i>, vol. 27, no. 1. American Society of Plant Biologists, pp. 20–32, 2015.","apa":"Adamowski, M., &#38; Friml, J. (2015). PIN-dependent auxin transport: Action, regulation, and evolution. <i>Plant Cell</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1105/tpc.114.134874\">https://doi.org/10.1105/tpc.114.134874</a>"},"date_created":"2018-12-11T11:52:54Z","language":[{"iso":"eng"}],"quality_controlled":"1"},{"page":"140 - 157","_id":"1607","year":"2015","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Springer","status":"public","type":"conference","date_updated":"2026-04-08T14:22:16Z","intvolume":"      9206","doi":"10.1007/978-3-319-21690-4_9","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","publist_id":"5560","date_published":"2015-07-16T00:00:00Z","month":"07","article_processing_charge":"No","volume":9206,"oa":1,"citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for quantitative verification in constant treewidth graphs. In: Vol 9206. Springer; 2015:140-157. doi:<a href=\"https://doi.org/10.1007/978-3-319-21690-4_9\">10.1007/978-3-319-21690-4_9</a>","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs,” 9206:140–57. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-21690-4_9\">https://doi.org/10.1007/978-3-319-21690-4_9</a>.","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2015). Faster algorithms for quantitative verification in constant treewidth graphs (Vol. 9206, pp. 140–157). Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-319-21690-4_9\">https://doi.org/10.1007/978-3-319-21690-4_9</a>","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for quantitative verification in constant treewidth graphs,” presented at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015, vol. 9206, pp. 140–157.","mla":"Chatterjee, Krishnendu, et al. <i>Faster Algorithms for Quantitative Verification in Constant Treewidth Graphs</i>. Vol. 9206, Springer, 2015, pp. 140–57, doi:<a href=\"https://doi.org/10.1007/978-3-319-21690-4_9\">10.1007/978-3-319-21690-4_9</a>.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2015. Faster algorithms for quantitative verification in constant treewidth graphs. CAV: Computer Aided Verification, LNCS, vol. 9206, 140–157.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Springer, 2015, pp. 140–157."},"date_created":"2018-12-11T11:52:59Z","arxiv":1,"conference":{"location":"San Francisco, CA, United States","start_date":"2015-07-18","name":"CAV: Computer Aided Verification","end_date":"2015-07-24"},"language":[{"iso":"eng"}],"quality_controlled":"1","ec_funded":1,"oa_version":"Preprint","project":[{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"day":"16","abstract":[{"lang":"eng","text":"We consider the core algorithmic problems related to verification of systems with respect to three classical quantitative properties, namely, the mean-payoff property, the ratio property, and the minimum initial credit for energy property. The algorithmic problem given a graph and a quantitative property asks to compute the optimal value (the infimum value over all traces) from every node of the graph. We consider graphs with constant treewidth, and it is well-known that the control-flow graphs of most programs have constant treewidth. Let n denote the number of nodes of a graph, m the number of edges (for constant treewidth graphs m=O(n)) and W the largest absolute value of the weights. Our main theoretical results are as follows. First, for constant treewidth graphs we present an algorithm that approximates the mean-payoff value within a multiplicative factor of ϵ in time O(n⋅log(n/ϵ)) and linear space, as compared to the classical algorithms that require quadratic time. Second, for the ratio property we present an algorithm that for constant treewidth graphs works in time O(n⋅log(|a⋅b|))=O(n⋅log(n⋅W)), when the output is ab, as compared to the previously best known algorithm with running time O(n2⋅log(n⋅W)). Third, for the minimum initial credit problem we show that (i) for general graphs the problem can be solved in O(n2⋅m) time and the associated decision problem can be solved in O(n⋅m) time, improving the previous known O(n3⋅m⋅log(n⋅W)) and O(n2⋅m) bounds, respectively; and (ii) for constant treewidth graphs we present an algorithm that requires O(n⋅logn) time, improving the previous known O(n4⋅log(n⋅W)) bound. We have implemented some of our algorithms and show that they present a significant speedup on standard benchmarks."}],"publication_status":"published","corr_author":"1","scopus_import":"1","alternative_title":["LNCS"],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5430"},{"id":"5437","status":"public","relation":"earlier_version"},{"id":"821","status":"public","relation":"dissertation_contains"}]},"title":"Faster algorithms for quantitative verification in constant treewidth graphs","main_file_link":[{"url":"http://arxiv.org/abs/1504.07384","open_access":"1"}],"department":[{"_id":"KrCh"}],"external_id":{"isi":["000364182900009"],"arxiv":["1504.07384"]},"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722"}]},{"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722"},{"full_name":"Goyal, Prateesh","last_name":"Goyal","first_name":"Prateesh"}],"external_id":{"arxiv":["1410.7724"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1410.7724"}],"department":[{"_id":"KrCh"}],"title":"Faster algorithms for algebraic path properties in recursive state machines with constant treewidth","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"821"}]},"publication_status":"published","scopus_import":1,"publication":"ACM SIGPLAN Notices","issue":"1","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"day":"01","abstract":[{"text":"Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, etc. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring, and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, etc. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in a very important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect that we consider is that the control flow graphs for most programs have constant treewidth. Our main contributions are simple and implementable algorithms that supportmultiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing, but can answer subsequent queries significantly faster as compared to the current best-known solutions for several important problems, such as interprocedural reachability and shortest path. We provide a prototype implementation for interprocedural reachability and intraprocedural shortest path that gives a significant speed-up on several benchmarks.","lang":"eng"}],"ec_funded":1,"oa_version":"Preprint","language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2018-12-11T11:52:58Z","arxiv":1,"conference":{"location":"Mumbai, India","start_date":"2015-01-15","end_date":"2015-01-17","name":"SIGPLAN: Symposium on Principles of Programming Languages"},"volume":50,"month":"01","oa":1,"citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. <i>ACM SIGPLAN Notices</i>. 2015;50(1):97-109. doi:<a href=\"https://doi.org/10.1145/2676726.2676979\">10.1145/2676726.2676979</a>","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, Andreas Pavlogiannis, and Prateesh Goyal. “Faster Algorithms for Algebraic Path Properties in Recursive State Machines with Constant Treewidth.” <i>ACM SIGPLAN Notices</i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2676726.2676979\">https://doi.org/10.1145/2676726.2676979</a>.","apa":"Chatterjee, K., Ibsen-Jensen, R., Pavlogiannis, A., &#38; Goyal, P. (2015). Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. <i>ACM SIGPLAN Notices</i>. Mumbai, India: ACM. <a href=\"https://doi.org/10.1145/2676726.2676979\">https://doi.org/10.1145/2676726.2676979</a>","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Algebraic Path Properties in Recursive State Machines with Constant Treewidth.” <i>ACM SIGPLAN Notices</i>, vol. 50, no. 1, ACM, 2015, pp. 97–109, doi:<a href=\"https://doi.org/10.1145/2676726.2676979\">10.1145/2676726.2676979</a>.","ieee":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, and P. Goyal, “Faster algorithms for algebraic path properties in recursive state machines with constant treewidth,” <i>ACM SIGPLAN Notices</i>, vol. 50, no. 1. ACM, pp. 97–109, 2015.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A, Goyal P. 2015. Faster algorithms for algebraic path properties in recursive state machines with constant treewidth. ACM SIGPLAN Notices. 50(1), 97–109.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, P. Goyal, ACM SIGPLAN Notices 50 (2015) 97–109."},"date_published":"2015-01-01T00:00:00Z","acknowledgement":"We thank anonymous reviewers for helpful comments to improve the presentation of the paper.","doi":"10.1145/2676726.2676979","publist_id":"5565","publisher":"ACM","status":"public","type":"journal_article","date_updated":"2026-04-08T14:22:16Z","intvolume":"        50","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"97 - 109","_id":"1602","year":"2015"},{"author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","first_name":"Andreas"},{"last_name":"Velner","first_name":"Yaron","full_name":"Velner, Yaron"}],"title":"Quantitative interprocedural analysis","department":[{"_id":"KrCh"}],"scopus_import":1,"corr_author":"1","publication_status":"published","pubrep_id":"523","related_material":{"record":[{"id":"5445","status":"public","relation":"earlier_version"},{"relation":"dissertation_contains","status":"public","id":"821"}]},"oa_version":"None","ec_funded":1,"project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"We consider the quantitative analysis problem for interprocedural control-flow graphs (ICFGs). The input consists of an ICFG, a positive weight function that assigns every transition a positive integer-valued number, and a labelling of the transitions (events) as good, bad, and neutral events. The weight function assigns to each transition a numerical value that represents ameasure of how good or bad an event is. The quantitative analysis problem asks whether there is a run of the ICFG where the ratio of the sum of the numerical weights of good events versus the sum of weights of bad events in the long-run is at least a given threshold (or equivalently, to compute the maximal ratio among all valid paths in the ICFG). The quantitative analysis problem for ICFGs can be solved in polynomial time, and we present an efficient and practical algorithm for the problem. We show that several problems relevant for static program analysis, such as estimating the worst-case execution time of a program or the average energy consumption of a mobile application, can be modeled in our framework. We have implemented our algorithm as a tool in the Java Soot framework. We demonstrate the effectiveness of our approach with two case studies. First, we show that our framework provides a sound approach (no false positives) for the analysis of inefficiently-used containers. Second, we show that our approach can also be used for static profiling of programs which reasons about methods that are frequently invoked. Our experimental results show that our tool scales to relatively large benchmarks, and discovers relevant and useful information that can be used to optimize performance of the programs.","lang":"eng"}],"day":"01","publication":"Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT ","issue":"1","conference":{"name":"SIGPLAN: Symposium on Principles of Programming Languages","end_date":"2015-01-17","location":"Mumbai, India","start_date":"2015-01-15"},"date_created":"2018-12-11T11:52:59Z","publication_identifier":{"isbn":["978-1-4503-3300-9"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2015-01-01T00:00:00Z","citation":{"short":"K. Chatterjee, A. Pavlogiannis, Y. Velner, Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT  50 (2015) 539–551.","ista":"Chatterjee K, Pavlogiannis A, Velner Y. 2015. Quantitative interprocedural analysis. Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT . 50(1), 539–551.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. “Quantitative Interprocedural Analysis.” <i>Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT </i>. ACM, 2015. <a href=\"https://doi.org/10.1145/2676726.2676968\">https://doi.org/10.1145/2676726.2676968</a>.","ama":"Chatterjee K, Pavlogiannis A, Velner Y. Quantitative interprocedural analysis. <i>Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT </i>. 2015;50(1):539-551. doi:<a href=\"https://doi.org/10.1145/2676726.2676968\">10.1145/2676726.2676968</a>","ieee":"K. Chatterjee, A. Pavlogiannis, and Y. Velner, “Quantitative interprocedural analysis,” <i>Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT </i>, vol. 50, no. 1. ACM, pp. 539–551, 2015.","mla":"Chatterjee, Krishnendu, et al. “Quantitative Interprocedural Analysis.” <i>Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT </i>, vol. 50, no. 1, ACM, 2015, pp. 539–51, doi:<a href=\"https://doi.org/10.1145/2676726.2676968\">10.1145/2676726.2676968</a>.","apa":"Chatterjee, K., Pavlogiannis, A., &#38; Velner, Y. (2015). Quantitative interprocedural analysis. <i>Proceedings of the 42nd Annual ACM SIGPLAN-SIGACT </i>. Mumbai, India: ACM. <a href=\"https://doi.org/10.1145/2676726.2676968\">https://doi.org/10.1145/2676726.2676968</a>"},"volume":50,"month":"01","intvolume":"        50","publisher":"ACM","status":"public","type":"journal_article","date_updated":"2026-04-08T14:22:16Z","publist_id":"5563","doi":"10.1145/2676726.2676968","year":"2015","page":"539 - 551","_id":"1604","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"conference":{"start_date":"2014-12-02","location":"Rome, Italy","name":"RTSS: Real-Time Systems Symposium","end_date":"2014-12-05"},"date_created":"2018-12-11T11:53:37Z","quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2015-01-15T00:00:00Z","citation":{"apa":"Chatterjee, K., Pavlogiannis, A., Kößler, A., &#38; Schmid, U. (2015). A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In <i>Real-Time Systems Symposium</i> (Vol. 2015, pp. 118–127). Rome, Italy: IEEE. <a href=\"https://doi.org/10.1109/RTSS.2014.9\">https://doi.org/10.1109/RTSS.2014.9</a>","mla":"Chatterjee, Krishnendu, et al. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” <i>Real-Time Systems Symposium</i>, vol. 2015, no. January, IEEE, 2015, pp. 118–27, doi:<a href=\"https://doi.org/10.1109/RTSS.2014.9\">10.1109/RTSS.2014.9</a>.","ieee":"K. Chatterjee, A. Pavlogiannis, A. Kößler, and U. Schmid, “A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks,” in <i>Real-Time Systems Symposium</i>, Rome, Italy, 2015, vol. 2015, no. January, pp. 118–127.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Alexander Kößler, and Ulrich Schmid. “A Framework for Automated Competitive Analysis of On-Line Scheduling of Firm-Deadline Tasks.” In <i>Real-Time Systems Symposium</i>, 2015:118–27. IEEE, 2015. <a href=\"https://doi.org/10.1109/RTSS.2014.9\">https://doi.org/10.1109/RTSS.2014.9</a>.","ama":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. In: <i>Real-Time Systems Symposium</i>. Vol 2015. IEEE; 2015:118-127. doi:<a href=\"https://doi.org/10.1109/RTSS.2014.9\">10.1109/RTSS.2014.9</a>","ista":"Chatterjee K, Pavlogiannis A, Kößler A, Schmid U. 2015. A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks. Real-Time Systems Symposium. RTSS: Real-Time Systems Symposium vol. 2015, 118–127.","short":"K. Chatterjee, A. Pavlogiannis, A. Kößler, U. Schmid, in:, Real-Time Systems Symposium, IEEE, 2015, pp. 118–127."},"volume":2015,"month":"01","article_processing_charge":"No","intvolume":"      2015","date_updated":"2026-04-08T14:22:16Z","type":"conference","publisher":"IEEE","status":"public","publist_id":"5417","doi":"10.1109/RTSS.2014.9","year":"2015","_id":"1714","page":"118 - 127","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"external_id":{"isi":["000569750000012"]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","first_name":"Andreas","orcid":"0000-0002-8943-0722"},{"last_name":"Kößler","first_name":"Alexander","full_name":"Kößler, Alexander"},{"last_name":"Schmid","full_name":"Schmid, Ulrich","first_name":"Ulrich"}],"title":"A framework for automated competitive analysis of on-line scheduling of firm-deadline tasks","department":[{"_id":"KrCh"}],"scopus_import":"1","publication_status":"published","related_material":{"record":[{"id":"5423","relation":"earlier_version","status":"public"},{"id":"821","relation":"dissertation_contains","status":"public"}]},"oa_version":"None","day":"15","abstract":[{"text":"We present a flexible framework for the automated competitive analysis of on-line scheduling algorithms for firm-deadline real-time tasks based on multi-objective graphs: Given a task set and an on-line scheduling algorithm specified as a labeled transition system, along with some optional safety, liveness, and/or limit-average constraints for the adversary, we automatically compute the competitive ratio of the algorithm w.r.t. A clairvoyant scheduler. We demonstrate the flexibility and power of our approach by comparing the competitive ratio of several on-line algorithms, including Dover, that have been proposed in the past, for various task sets. Our experimental results reveal that none of these algorithms is universally optimal, in the sense that there are task sets where other schedulers provide better performance. Our framework is hence a very useful design tool for selecting optimal algorithms for a given application.","lang":"eng"}],"issue":"January","publication":"Real-Time Systems Symposium"},{"oa_version":"Published Version","project":[{"call_identifier":"FWF","name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","_id":"2529486C-B435-11E9-9278-68D0E5697425","grant_number":"T 560-B17"},{"_id":"2527D5CC-B435-11E9-9278-68D0E5697425","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","call_identifier":"FWF","grant_number":"I812-B12"}],"day":"12","abstract":[{"text":"3D amoeboid cell migration is central to many developmental and disease-related processes such as cancer metastasis. Here, we identify a unique prototypic amoeboid cell migration mode in early zebrafish embryos, termed stable-bleb migration. Stable-bleb cells display an invariant polarized balloon-like shape with exceptional migration speed and persistence. Progenitor cells can be reversibly transformed into stable-bleb cells irrespective of their primary fate and motile characteristics by increasing myosin II activity through biochemical or mechanical stimuli. Using a combination of theory and experiments, we show that, in stable-bleb cells, cortical contractility fluctuations trigger a stochastic switch into amoeboid motility, and a positive feedback between cortical flows and gradients in contractility maintains stable-bleb cell polarization. We further show that rearward cortical flows drive stable-bleb cell migration in various adhesive and non-adhesive environments, unraveling a highly versatile amoeboid migration phenotype.","lang":"eng"}],"ddc":["570"],"issue":"4","publication":"Cell","scopus_import":"1","corr_author":"1","publication_status":"published","pubrep_id":"484","has_accepted_license":"1","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"961"}]},"title":"Cortical contractility triggers a stochastic switch to fast amoeboid cell motility","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"file_name":"IST-2016-484-v1+1_1-s2.0-S0092867415000094-main.pdf","checksum":"228d3edf40627d897b3875088a0ac51f","file_id":"5003","creator":"system","date_created":"2018-12-12T10:13:21Z","relation":"main_file","date_updated":"2020-07-14T12:45:01Z","access_level":"open_access","content_type":"application/pdf","file_size":4362653}],"external_id":{"isi":["000349208800011"]},"author":[{"orcid":"0000-0003-4088-8633","first_name":"Verena","last_name":"Ruprecht","full_name":"Ruprecht, Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2670-2217","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","full_name":"Wieser, Stefan","last_name":"Wieser","first_name":"Stefan"},{"full_name":"Callan Jones, Andrew","first_name":"Andrew","last_name":"Callan Jones"},{"orcid":"0000-0002-5920-9090","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Smutny","full_name":"Smutny, Michael"},{"id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","full_name":"Morita, Hitoshi","last_name":"Morita","first_name":"Hitoshi"},{"orcid":"0000-0002-6453-8075","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","first_name":"Keisuke","last_name":"Sako","full_name":"Sako, Keisuke"},{"full_name":"Barone, Vanessa","first_name":"Vanessa","last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2676-3367"},{"last_name":"Ritsch Marte","first_name":"Monika","full_name":"Ritsch Marte, Monika"},{"full_name":"Sixt, Michael K","last_name":"Sixt","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179"},{"first_name":"Raphaël","full_name":"Voituriez, Raphaël","last_name":"Voituriez"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"year":"2015","page":"673 - 685","acknowledged_ssus":[{"_id":"SSU"}],"_id":"1537","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"intvolume":"       160","publisher":"Cell Press","type":"journal_article","status":"public","date_updated":"2026-04-08T14:22:39Z","publist_id":"5634","doi":"10.1016/j.cell.2015.01.008","acknowledgement":"We would like to thank R. Hausschild and E. Papusheva for technical assistance and the service facilities at the IST Austria for continuous support. The caRhoA plasmid was a kind gift of T. Kudoh and A. Takesono. We thank M. Piel and E. Paluch for exchanging unpublished data. ","date_published":"2015-02-12T00:00:00Z","file_date_updated":"2020-07-14T12:45:01Z","citation":{"short":"V. Ruprecht, S. Wieser, A. Callan Jones, M. Smutny, H. Morita, K. Sako, V. Barone, M. Ritsch Marte, M.K. Sixt, R. Voituriez, C.-P.J. Heisenberg, Cell 160 (2015) 673–685.","ista":"Ruprecht V, Wieser S, Callan Jones A, Smutny M, Morita H, Sako K, Barone V, Ritsch Marte M, Sixt MK, Voituriez R, Heisenberg C-PJ. 2015. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. Cell. 160(4), 673–685.","chicago":"Ruprecht, Verena, Stefan Wieser, Andrew Callan Jones, Michael Smutny, Hitoshi Morita, Keisuke Sako, Vanessa Barone, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” <i>Cell</i>. Cell Press, 2015. <a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">https://doi.org/10.1016/j.cell.2015.01.008</a>.","ama":"Ruprecht V, Wieser S, Callan Jones A, et al. Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. <i>Cell</i>. 2015;160(4):673-685. doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">10.1016/j.cell.2015.01.008</a>","mla":"Ruprecht, Verena, et al. “Cortical Contractility Triggers a Stochastic Switch to Fast Amoeboid Cell Motility.” <i>Cell</i>, vol. 160, no. 4, Cell Press, 2015, pp. 673–85, doi:<a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">10.1016/j.cell.2015.01.008</a>.","ieee":"V. Ruprecht <i>et al.</i>, “Cortical contractility triggers a stochastic switch to fast amoeboid cell motility,” <i>Cell</i>, vol. 160, no. 4. Cell Press, pp. 673–685, 2015.","apa":"Ruprecht, V., Wieser, S., Callan Jones, A., Smutny, M., Morita, H., Sako, K., … Heisenberg, C.-P. J. (2015). Cortical contractility triggers a stochastic switch to fast amoeboid cell motility. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2015.01.008\">https://doi.org/10.1016/j.cell.2015.01.008</a>"},"article_processing_charge":"No","month":"02","volume":160,"oa":1,"date_created":"2018-12-11T11:52:35Z","quality_controlled":"1","language":[{"iso":"eng"}]},{"quality_controlled":"1","language":[{"iso":"eng"}],"conference":{"location":"San Francisco, CA, United States","start_date":"2015-07-18","end_date":"2015-07-24","name":"CAV: Computer Aided Verification"},"date_created":"2018-12-11T11:53:42Z","citation":{"mla":"Cerny, Pavol, et al. <i>From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis</i>. Vol. 9207, Springer, 2015, pp. 180–97, doi:<a href=\"https://doi.org/10.1007/978-3-319-21668-3_11\">10.1007/978-3-319-21668-3_11</a>.","ieee":"P. Cerny <i>et al.</i>, “From non-preemptive to preemptive scheduling using synchronization synthesis,” vol. 9207. Springer, pp. 180–197, 2015.","apa":"Cerny, P., Clarke, E., Henzinger, T. A., Radhakrishna, A., Ryzhyk, L., Samanta, R., &#38; Tarrach, T. (2015). From non-preemptive to preemptive scheduling using synchronization synthesis. Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-319-21668-3_11\">https://doi.org/10.1007/978-3-319-21668-3_11</a>","chicago":"Cerny, Pavol, Edmund Clarke, Thomas A Henzinger, Arjun Radhakrishna, Leonid Ryzhyk, Roopsha Samanta, and Thorsten Tarrach. “From Non-Preemptive to Preemptive Scheduling Using Synchronization Synthesis.” Lecture Notes in Computer Science. Springer, 2015. <a href=\"https://doi.org/10.1007/978-3-319-21668-3_11\">https://doi.org/10.1007/978-3-319-21668-3_11</a>.","ama":"Cerny P, Clarke E, Henzinger TA, et al. From non-preemptive to preemptive scheduling using synchronization synthesis. 2015;9207:180-197. doi:<a href=\"https://doi.org/10.1007/978-3-319-21668-3_11\">10.1007/978-3-319-21668-3_11</a>","short":"P. Cerny, E. Clarke, T.A. Henzinger, A. Radhakrishna, L. Ryzhyk, R. Samanta, T. Tarrach, 9207 (2015) 180–197.","ista":"Cerny P, Clarke E, Henzinger TA, Radhakrishna A, Ryzhyk L, Samanta R, Tarrach T. 2015. From non-preemptive to preemptive scheduling using synchronization synthesis. 9207, 180–197."},"oa":1,"month":"07","volume":9207,"article_processing_charge":"No","date_published":"2015-07-01T00:00:00Z","file_date_updated":"2025-06-26T07:12:35Z","publist_id":"5398","doi":"10.1007/978-3-319-21668-3_11","intvolume":"      9207","date_updated":"2026-04-09T10:54:00Z","type":"conference","status":"public","publisher":"Springer","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","series_title":"Lecture Notes in Computer Science","isi":1,"OA_type":"green","year":"2015","_id":"1729","page":"180 - 197","author":[{"full_name":"Cerny, Pavol","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny"},{"full_name":"Clarke, Edmund","first_name":"Edmund","last_name":"Clarke"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","first_name":"Arjun","full_name":"Radhakrishna, Arjun"},{"last_name":"Ryzhyk","first_name":"Leonid","full_name":"Ryzhyk, Leonid"},{"id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","first_name":"Roopsha","full_name":"Samanta, Roopsha","last_name":"Samanta"},{"full_name":"Tarrach, Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","last_name":"Tarrach","first_name":"Thorsten","orcid":"0000-0003-4409-8487"}],"external_id":{"isi":["000491470400011"]},"department":[{"_id":"ToHe"}],"file":[{"file_name":"IST-2015-336-v1+1_long_version.pdf","checksum":"6ff58ac220e2f20cb001ba35d4924495","file_id":"4715","creator":"system","date_updated":"2025-06-26T07:12:35Z","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:08:53Z","content_type":"application/pdf","file_size":481922}],"title":"From non-preemptive to preemptive scheduling using synchronization synthesis","OA_place":"repository","related_material":{"record":[{"relation":"later_version","status":"public","id":"1338"},{"status":"public","relation":"dissertation_contains","id":"1130"}]},"has_accepted_license":"1","pubrep_id":"336","alternative_title":["LNCS"],"scopus_import":"1","publication_status":"published","day":"01","abstract":[{"text":"We present a computer-aided programming approach to concurrency. The approach allows programmers to program assuming a friendly, non-preemptive scheduler, and our synthesis procedure inserts synchronization to ensure that the final program works even with a preemptive scheduler. The correctness specification is implicit, inferred from the non-preemptive behavior. Let us consider sequences of calls that the program makes to an external interface. The specification requires that any such sequence produced under a preemptive scheduler should be included in the set of such sequences produced under a non-preemptive scheduler. The solution is based on a finitary abstraction, an algorithm for bounded language inclusion modulo an independence relation, and rules for inserting synchronization. We apply the approach to device-driver programming, where the driver threads call the software interface of the device and the API provided by the operating system. Our experiments demonstrate that our synthesis method is precise and efficient, and, since it does not require explicit specifications, is more practical than the conventional approach based on user-provided assertions.","lang":"eng"}],"ddc":["000"],"project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"}],"oa_version":"Submitted Version","ec_funded":1},{"ec_funded":1,"oa_version":"Published Version","issue":"11","publication":"PLoS Genetics","ddc":["576"],"day":"06","abstract":[{"lang":"eng","text":"Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics."}],"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"}],"publication_status":"published","scopus_import":"1","related_material":{"record":[{"id":"9712","relation":"research_data","status":"public"},{"id":"1131","status":"public","relation":"dissertation_contains"}]},"has_accepted_license":"1","pubrep_id":"463","title":"Dynamics of transcription factor binding site evolution","file":[{"checksum":"a4e72fca5ccf40ddacf4d08c8e46b554","file_id":"4657","creator":"system","date_updated":"2020-07-14T12:45:10Z","relation":"main_file","access_level":"open_access","date_created":"2018-12-12T10:07:58Z","file_name":"IST-2016-463-v1+1_journal.pgen.1005639.pdf","content_type":"application/pdf","file_size":2580778}],"department":[{"_id":"NiBa"},{"_id":"CaGu"},{"_id":"GaTk"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000366179000022"]},"author":[{"first_name":"Murat","full_name":"Tugrul, Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","last_name":"Tugrul","orcid":"0000-0002-8523-0758"},{"orcid":"0000-0003-2361-3953","id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","last_name":"Paixao","full_name":"Paixao, Tiago","first_name":"Tiago"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455"}],"_id":"1666","year":"2015","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-04-09T10:52:40Z","publisher":"Public Library of Science","type":"journal_article","status":"public","intvolume":"        11","doi":"10.1371/journal.pgen.1005639","publist_id":"5483","file_date_updated":"2020-07-14T12:45:10Z","date_published":"2015-11-06T00:00:00Z","oa":1,"month":"11","volume":11,"article_processing_charge":"No","citation":{"chicago":"Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>.","ama":"Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. 2015;11(11). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>","apa":"Tugrul, M., Paixao, T., Barton, N. H., &#38; Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1005639\">https://doi.org/10.1371/journal.pgen.1005639</a>","ieee":"M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” <i>PLoS Genetics</i>, vol. 11, no. 11. Public Library of Science, 2015.","mla":"Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” <i>PLoS Genetics</i>, vol. 11, no. 11, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1005639\">10.1371/journal.pgen.1005639</a>.","ista":"Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11).","short":"M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015)."},"date_created":"2018-12-11T11:53:21Z","language":[{"iso":"eng"}],"quality_controlled":"1"},{"year":"2015","page":"144","_id":"1401","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Science and Technology Austria","status":"public","type":"dissertation","date_updated":"2026-04-09T14:25:49Z","publist_id":"5806","doi":"10.15479/at:ista:1401","acknowledgement":"I would like to thank my supervisor, Christoph Lampert, for guidance throughout my studies and for patience in transforming me into a scientist, and my thesis committee, Chris Wojtan and Horst Bischof, for their help and advice. \r\n\r\nI would like to thank Elisabeth Hacker who perfectly assisted all my administrative needs and was always nice and friendly to me, and the campus team for making the IST Austria campus my second home. \r\nI was honored to collaborate with brilliant researchers and to learn from their experience. Undoubtedly, I learned most of all from Novi Quadrianto: brainstorming our projects and getting exciting results was the most enjoyable part of my work – thank you! I am also grateful to David Knowles, Zoubin Ghahramani, Daniel Hernández-Lobato, Kristian Kersting and Anastasia Pentina for the fantastic projects we worked on together, and to Kristen Grauman and Adriana Kovashka for the exceptional experience working with user studies. I would like to thank my colleagues at IST Austria and my office mates who shared their happy moods, scientific breakthroughs and thought-provoking conversations with me: Chao, Filip, Rustem, Asya, Sameh, Alex, Vlad, Mayu, Neel, Csaba, Thomas, Vladimir, Cristina, Alex Z., Avro, Amelie and Emilie, Andreas H. and Andreas E., Chris, Lena, Michael, Ali and Ipek, Vera, Igor, Katia. Special thanks to Morten for the countless games of table soccer we played together and the tournaments we teamed up for: we will definitely win next time:) A very warm hug to Asya for always being so inspiring and supportive to me, and for helping me to increase the proportion of female computer scientists in our group. ","supervisor":[{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2015-04-01T00:00:00Z","file_date_updated":"2021-11-17T13:47:24Z","citation":{"short":"V. Sharmanska, Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views, Institute of Science and Technology Austria, 2015.","ista":"Sharmanska V. 2015. Learning with attributes for object recognition: Parametric and non-parametrics views. Institute of Science and Technology Austria.","chicago":"Sharmanska, Viktoriia. “Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views.” Institute of Science and Technology Austria, 2015. <a href=\"https://doi.org/10.15479/at:ista:1401\">https://doi.org/10.15479/at:ista:1401</a>.","ama":"Sharmanska V. Learning with attributes for object recognition: Parametric and non-parametrics views. 2015. doi:<a href=\"https://doi.org/10.15479/at:ista:1401\">10.15479/at:ista:1401</a>","mla":"Sharmanska, Viktoriia. <i>Learning with Attributes for Object Recognition: Parametric and Non-Parametrics Views</i>. Institute of Science and Technology Austria, 2015, doi:<a href=\"https://doi.org/10.15479/at:ista:1401\">10.15479/at:ista:1401</a>.","ieee":"V. Sharmanska, “Learning with attributes for object recognition: Parametric and non-parametrics views,” Institute of Science and Technology Austria, 2015.","apa":"Sharmanska, V. (2015). <i>Learning with attributes for object recognition: Parametric and non-parametrics views</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:1401\">https://doi.org/10.15479/at:ista:1401</a>"},"month":"04","article_processing_charge":"No","oa":1,"date_created":"2018-12-11T11:51:48Z","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"oa_version":"Published Version","ddc":["000"],"day":"01","abstract":[{"text":"The human ability to recognize objects in complex scenes has driven research in the computer vision field over couple of decades. This thesis focuses on the object recognition task in images. That is, given the image, we want the computer system to be able to predict the class of the object that appears in the image. A recent successful attempt to bridge semantic understanding of the image perceived by humans and by computers uses attribute-based models. Attributes are semantic properties of the objects shared across different categories, which humans and computers can decide on. To explore the attribute-based models we take a statistical machine learning approach, and address two key learning challenges in view of object recognition task: learning augmented attributes as mid-level discriminative feature representation, and learning with attributes as privileged information. Our main contributions are parametric and non-parametric models and algorithms to solve these frameworks. In the parametric approach, we explore an autoencoder model combined with the large margin nearest neighbor principle for mid-level feature learning, and linear support vector machines for learning with privileged information. In the non-parametric approach, we propose a supervised Indian Buffet Process for automatic augmentation of semantic attributes, and explore the Gaussian Processes classification framework for learning with privileged information. A thorough experimental analysis shows the effectiveness of the proposed models in both parametric and non-parametric views.","lang":"eng"}],"corr_author":"1","publication_status":"published","OA_place":"publisher","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"title":"Learning with attributes for object recognition: Parametric and non-parametrics views","department":[{"_id":"ChLa"},{"_id":"GradSch"}],"main_file_link":[{"url":"http://users.sussex.ac.uk/~nq28/viktoriia/Thesis_Sharmanska.pdf"}],"file":[{"success":1,"file_name":"2015_Thesis_Sharmanska.pdf","date_updated":"2021-02-22T11:33:17Z","relation":"main_file","access_level":"open_access","date_created":"2021-02-22T11:33:17Z","checksum":"3605b402bb6934e09ae4cf672c84baf7","file_id":"9177","creator":"dernst","file_size":7964342,"content_type":"application/pdf"},{"content_type":"application/pdf","file_size":7372241,"file_name":"2015_Thesis_Sharmanska_pdfa.pdf","checksum":"e37593b3ee75bf3180629df2d6ca8f4e","file_id":"10297","creator":"cchlebak","date_created":"2021-11-16T14:40:45Z","access_level":"closed","relation":"main_file","date_updated":"2021-11-17T13:47:24Z"}],"degree_awarded":"PhD","author":[{"orcid":"0000-0003-0192-9308","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","first_name":"Viktoriia","full_name":"Sharmanska, Viktoriia","last_name":"Sharmanska"}]},{"doi":"10.1016/j.jco.2015.06.002","acknowledgement":"F.P. is supported by the Graduate School of IST Austria, A.M.S is supported by the Centre for Stochastic Geometry and Advanced Bioimaging funded by a grant from the Villum Foundation.","publist_id":"5320","date_updated":"2026-04-09T14:26:05Z","type":"journal_article","status":"public","publisher":"Academic Press","intvolume":"        31","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"1792","page":"773 - 797","year":"2015","language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2018-12-11T11:54:02Z","month":"12","volume":31,"article_processing_charge":"No","citation":{"short":"F. Pausinger, A. Svane, Journal of Complexity 31 (2015) 773–797.","ista":"Pausinger F, Svane A. 2015. A Koksma-Hlawka inequality for general discrepancy systems. Journal of Complexity. 31(6), 773–797.","chicago":"Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” <i>Journal of Complexity</i>. Academic Press, 2015. <a href=\"https://doi.org/10.1016/j.jco.2015.06.002\">https://doi.org/10.1016/j.jco.2015.06.002</a>.","ama":"Pausinger F, Svane A. A Koksma-Hlawka inequality for general discrepancy systems. <i>Journal of Complexity</i>. 2015;31(6):773-797. doi:<a href=\"https://doi.org/10.1016/j.jco.2015.06.002\">10.1016/j.jco.2015.06.002</a>","ieee":"F. Pausinger and A. Svane, “A Koksma-Hlawka inequality for general discrepancy systems,” <i>Journal of Complexity</i>, vol. 31, no. 6. Academic Press, pp. 773–797, 2015.","mla":"Pausinger, Florian, and Anne Svane. “A Koksma-Hlawka Inequality for General Discrepancy Systems.” <i>Journal of Complexity</i>, vol. 31, no. 6, Academic Press, 2015, pp. 773–97, doi:<a href=\"https://doi.org/10.1016/j.jco.2015.06.002\">10.1016/j.jco.2015.06.002</a>.","apa":"Pausinger, F., &#38; Svane, A. (2015). A Koksma-Hlawka inequality for general discrepancy systems. <i>Journal of Complexity</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jco.2015.06.002\">https://doi.org/10.1016/j.jco.2015.06.002</a>"},"date_published":"2015-12-01T00:00:00Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1399"}]},"publication_status":"published","corr_author":"1","scopus_import":"1","publication":"Journal of Complexity","issue":"6","day":"01","abstract":[{"text":"Motivated by recent ideas of Harman (Unif. Distrib. Theory, 2010) we develop a new concept of variation of multivariate functions on a compact Hausdorff space with respect to a collection D of subsets. We prove a general version of the Koksma-Hlawka theorem that holds for this notion of variation and discrepancy with respect to D. As special cases, we obtain Koksma-Hlawka inequalities for classical notions, such as extreme or isotropic discrepancy. For extreme discrepancy, our result coincides with the usual Koksma-Hlawka theorem. We show that the space of functions of bounded D-variation contains important discontinuous functions and is closed under natural algebraic operations. Finally, we illustrate the results on concrete integration problems from integral geometry and stereology.","lang":"eng"}],"oa_version":"None","author":[{"first_name":"Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","last_name":"Pausinger","full_name":"Pausinger, Florian","orcid":"0000-0002-8379-3768"},{"last_name":"Svane","first_name":"Anne","full_name":"Svane, Anne"}],"external_id":{"isi":["000362926900001"]},"department":[{"_id":"HeEd"}],"title":"A Koksma-Hlawka inequality for general discrepancy systems"},{"title":"Biological auctions with multiple rewards","department":[{"_id":"KrCh"}],"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528522/","open_access":"1"}],"external_id":{"pmid":["26180069"],"isi":["000362305500021"]},"author":[{"orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","first_name":"Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kanodia, Ayush","last_name":"Kanodia","first_name":"Ayush"},{"full_name":"Gupta, Raghav","last_name":"Gupta","first_name":"Raghav"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"}],"oa_version":"Submitted Version","day":"15","abstract":[{"lang":"eng","text":"The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards."}],"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","issue":"1812","scopus_import":"1","publication_status":"published","corr_author":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"1400"}]},"date_published":"2015-07-15T00:00:00Z","citation":{"ista":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. 2015. Biological auctions with multiple rewards. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1812).","short":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, K. Chatterjee, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015).","ama":"Reiter J, Kanodia A, Gupta R, Nowak M, Chatterjee K. Biological auctions with multiple rewards. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2015;282(1812). doi:<a href=\"https://doi.org/10.1098/rspb.2015.1041\">10.1098/rspb.2015.1041</a>","chicago":"Reiter, Johannes, Ayush Kanodia, Raghav Gupta, Martin Nowak, and Krishnendu Chatterjee. “Biological Auctions with Multiple Rewards.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society, 2015. <a href=\"https://doi.org/10.1098/rspb.2015.1041\">https://doi.org/10.1098/rspb.2015.1041</a>.","apa":"Reiter, J., Kanodia, A., Gupta, R., Nowak, M., &#38; Chatterjee, K. (2015). Biological auctions with multiple rewards. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rspb.2015.1041\">https://doi.org/10.1098/rspb.2015.1041</a>","ieee":"J. Reiter, A. Kanodia, R. Gupta, M. Nowak, and K. Chatterjee, “Biological auctions with multiple rewards,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1812. Royal Society, 2015.","mla":"Reiter, Johannes, et al. “Biological Auctions with Multiple Rewards.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1812, Royal Society, 2015, doi:<a href=\"https://doi.org/10.1098/rspb.2015.1041\">10.1098/rspb.2015.1041</a>."},"oa":1,"month":"07","article_processing_charge":"No","volume":282,"date_created":"2018-12-11T11:53:35Z","quality_controlled":"1","language":[{"iso":"eng"}],"pmid":1,"year":"2015","_id":"1709","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"article_type":"original","intvolume":"       282","date_updated":"2026-04-09T14:26:23Z","type":"journal_article","publisher":"Royal Society","status":"public","publist_id":"5425","acknowledgement":"This work was supported by grants from the John Templeton Foundation, ERC Start Grant (279307: Graph Games), FWF NFN Grant (No S11407N23 RiSE/SHiNE), FWF Grant (No P23499N23) and a Microsoft faculty fellows award.","doi":"10.1098/rspb.2015.1041"},{"date_updated":"2026-04-09T14:26:24Z","publisher":"Institute of Science and Technology Austria","publication_status":"published","type":"dissertation","corr_author":"1","status":"public","related_material":{"record":[{"id":"2000","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"1709"},{"id":"2858","relation":"part_of_dissertation","status":"public"},{"id":"2816","status":"public","relation":"part_of_dissertation"},{"id":"2247","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"3260"},{"id":"3157","relation":"part_of_dissertation","status":"public"}]},"OA_place":"publisher","publist_id":"5807","supervisor":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"}],"alternative_title":["ISTA Thesis"],"oa_version":"None","year":"2015","_id":"1400","page":"183","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","abstract":[{"lang":"eng","text":"Cancer results from an uncontrolled growth of abnormal cells. Sequentially accumulated genetic and epigenetic alterations decrease cell death and increase cell replication. We used mathematical models to quantify the effect of driver gene mutations. The recently developed targeted therapies can lead to dramatic regressions. However, in solid cancers, clinical responses are often short-lived because resistant cancer cells evolve. We estimated that approximately 50 different mutations can confer resistance to a typical targeted therapeutic agent. We find that resistant cells are likely to be present in expanded subclones before the start of the treatment. The dominant strategy to prevent the evolution of resistance is combination therapy. Our analytical results suggest that in most patients, dual therapy, but not monotherapy, can result in long-term disease control. However, long-term control can only occur if there are no possible mutations in the genome that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous therapy with two drugs is much more likely to result in long-term disease control than sequential therapy with the same drugs. To improve our understanding of the underlying subclonal evolution we reconstruct the evolutionary history of a patient's cancer from next-generation sequencing data of spatially-distinct DNA samples. Using a quantitative measure of genetic relatedness, we found that pancreatic cancers and their metastases demonstrated a higher level of relatedness than that expected for any two cells randomly taken from a normal tissue. This minimal amount of genetic divergence among advanced lesions indicates that genetic heterogeneity, when quantitatively defined, is not a fundamental feature of the natural history of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics finds evidence for seeding patterns of metastases and can directly be used to discover rules governing the evolution of solid malignancies to transform cancer into a more predictable disease."}],"day":"01","date_created":"2018-12-11T11:51:48Z","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","author":[{"orcid":"0000-0002-0170-7353","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter","full_name":"Reiter, Johannes"}],"language":[{"iso":"eng"}],"title":"The subclonal evolution of cancer","date_published":"2015-04-01T00:00:00Z","citation":{"apa":"Reiter, J. (2015). <i>The subclonal evolution of cancer</i>. Institute of Science and Technology Austria.","mla":"Reiter, Johannes. <i>The Subclonal Evolution of Cancer</i>. Institute of Science and Technology Austria, 2015.","ieee":"J. Reiter, “The subclonal evolution of cancer,” Institute of Science and Technology Austria, 2015.","ama":"Reiter J. The subclonal evolution of cancer. 2015.","chicago":"Reiter, Johannes. “The Subclonal Evolution of Cancer.” Institute of Science and Technology Austria, 2015.","ista":"Reiter J. 2015. The subclonal evolution of cancer. Institute of Science and Technology Austria.","short":"J. Reiter, The Subclonal Evolution of Cancer, Institute of Science and Technology Austria, 2015."},"department":[{"_id":"KrCh"}],"article_processing_charge":"No","month":"04"},{"oa_version":"Submitted Version","ec_funded":1,"ddc":["000"],"day":"01","abstract":[{"lang":"eng","text":"We extend the theory of input-output conformance with operators for merge and quotient. The former is useful when testing against multiple requirements or views. The latter can be used to generate tests for patches of an already tested system. Both operators can combine systems with different action alphabets, which is usually the case when constructing complex systems and specifications from parts, for instance different views as well as newly defined functionality of a~previous version of the system."}],"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems","call_identifier":"FWF"},{"grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","publication_status":"published","has_accepted_license":"1","related_material":{"record":[{"id":"1155","relation":"dissertation_contains","status":"public"}]},"pubrep_id":"625","alternative_title":["Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering "],"title":"Complete composition operators for IOCO-testing theory","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"file":[{"content_type":"application/pdf","file_size":467561,"file_name":"IST-2016-625-v1+1_conf-cbse-BenesDHKN15.pdf","file_id":"5303","checksum":"c6ce681035c163a158751f240cb7d389","creator":"system","date_created":"2018-12-12T10:17:46Z","relation":"main_file","date_updated":"2020-07-14T12:44:59Z","access_level":"open_access"}],"external_id":{"isi":["000380554800013"]},"author":[{"full_name":"Beneš, Nikola","last_name":"Beneš","first_name":"Nikola"},{"full_name":"Daca, Przemyslaw","last_name":"Daca","id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A"},{"orcid":"0000-0002-8122-2881","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","last_name":"Kretinsky","first_name":"Jan"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","first_name":"Dejan"}],"year":"2015","_id":"1502","page":"101 - 110","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"date_updated":"2026-04-15T10:02:12Z","status":"public","type":"conference","publisher":"ACM","publist_id":"5676","doi":"10.1145/2737166.2737175","acknowledgement":"This research was funded in part by the European Research Council (ERC) under grant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects S11402-N23(RiSE) and Z211-N23 (Wittgestein Award), by People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement 291734, and by the ARTEMIS JU under grant agreement 295373 (nSafeCer).  Jan Křetínský has been partially supported by the Czech Science Foundation, grant No.  P202/12/G061.  Nikola Beneš has been supported by the\r\nMEYS project No. CZ.1.07/2.3.00/30.0009 Employment of Newly Graduated Doctors of Science for Scientific Excellence.","date_published":"2015-05-01T00:00:00Z","file_date_updated":"2020-07-14T12:44:59Z","citation":{"ista":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. 2015. Complete composition operators for IOCO-testing theory. CBSE: Component-Based Software Engineering , Proceedings of the 18th International ACM SIGSOFT Symposium on Component-Based Software Engineering , , 101–110.","short":"N. Beneš, P. Daca, T.A. Henzinger, J. Kretinsky, D. Nickovic, in:, ACM, 2015, pp. 101–110.","chicago":"Beneš, Nikola, Przemyslaw Daca, Thomas A Henzinger, Jan Kretinsky, and Dejan Nickovic. “Complete Composition Operators for IOCO-Testing Theory,” 101–10. ACM, 2015. <a href=\"https://doi.org/10.1145/2737166.2737175\">https://doi.org/10.1145/2737166.2737175</a>.","ama":"Beneš N, Daca P, Henzinger TA, Kretinsky J, Nickovic D. Complete composition operators for IOCO-testing theory. In: ACM; 2015:101-110. doi:<a href=\"https://doi.org/10.1145/2737166.2737175\">10.1145/2737166.2737175</a>","apa":"Beneš, N., Daca, P., Henzinger, T. A., Kretinsky, J., &#38; Nickovic, D. (2015). Complete composition operators for IOCO-testing theory (pp. 101–110). Presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada: ACM. <a href=\"https://doi.org/10.1145/2737166.2737175\">https://doi.org/10.1145/2737166.2737175</a>","mla":"Beneš, Nikola, et al. <i>Complete Composition Operators for IOCO-Testing Theory</i>. ACM, 2015, pp. 101–10, doi:<a href=\"https://doi.org/10.1145/2737166.2737175\">10.1145/2737166.2737175</a>.","ieee":"N. Beneš, P. Daca, T. A. Henzinger, J. Kretinsky, and D. Nickovic, “Complete composition operators for IOCO-testing theory,” presented at the CBSE: Component-Based Software Engineering , Montreal, QC, Canada, 2015, pp. 101–110."},"oa":1,"month":"05","article_processing_charge":"No","conference":{"start_date":"2015-05-04","location":"Montreal, QC, Canada","name":"CBSE: Component-Based Software Engineering ","end_date":"2015-05-08"},"date_created":"2018-12-11T11:52:24Z","quality_controlled":"1","publication_identifier":{"isbn":["978-1-4503-3471-6"]},"language":[{"iso":"eng"}]},{"date_published":"2015-10-01T00:00:00Z","citation":{"short":"K. Chatterjee, M. Chmelik, P. Daca, Formal Methods in System Design 47 (2015) 230–264.","ista":"Chatterjee K, Chmelik M, Daca P. 2015. CEGAR for compositional analysis of qualitative properties in Markov decision processes. Formal Methods in System Design. 47(2), 230–264.","ama":"Chatterjee K, Chmelik M, Daca P. CEGAR for compositional analysis of qualitative properties in Markov decision processes. <i>Formal Methods in System Design</i>. 2015;47(2):230-264. doi:<a href=\"https://doi.org/10.1007/s10703-015-0235-2\">10.1007/s10703-015-0235-2</a>","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” <i>Formal Methods in System Design</i>. Springer, 2015. <a href=\"https://doi.org/10.1007/s10703-015-0235-2\">https://doi.org/10.1007/s10703-015-0235-2</a>.","ieee":"K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for compositional analysis of qualitative properties in Markov decision processes,” <i>Formal Methods in System Design</i>, vol. 47, no. 2. Springer, pp. 230–264, 2015.","mla":"Chatterjee, Krishnendu, et al. “CEGAR for Compositional Analysis of Qualitative Properties in Markov Decision Processes.” <i>Formal Methods in System Design</i>, vol. 47, no. 2, Springer, 2015, pp. 230–64, doi:<a href=\"https://doi.org/10.1007/s10703-015-0235-2\">10.1007/s10703-015-0235-2</a>.","apa":"Chatterjee, K., Chmelik, M., &#38; Daca, P. (2015). CEGAR for compositional analysis of qualitative properties in Markov decision processes. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-015-0235-2\">https://doi.org/10.1007/s10703-015-0235-2</a>"},"article_processing_charge":"No","month":"10","volume":47,"oa":1,"date_created":"2018-12-11T11:52:23Z","arxiv":1,"quality_controlled":"1","language":[{"iso":"eng"}],"year":"2015","page":"230 - 264","_id":"1501","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"intvolume":"        47","publisher":"Springer","type":"journal_article","status":"public","date_updated":"2026-04-15T10:02:12Z","publist_id":"5677","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No. P23499- N23, FWF NFN Grant No. S11407-N23, FWF Grant S11403-N23 (RiSE), and FWF Grant Z211-N23 (Wittgenstein Award), ERC Start Grant (279307: Graph Games), Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (Quantitative Reactive Modeling).","doi":"10.1007/s10703-015-0235-2","title":"CEGAR for compositional analysis of qualitative properties in Markov decision processes","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1405.0835"}],"external_id":{"isi":["000361752300003"],"arxiv":["1405.0835"]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Chmelik, Martin","first_name":"Martin","last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Przemyslaw","full_name":"Daca, Przemyslaw","last_name":"Daca","id":"49351290-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Preprint","ec_funded":1,"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems. We focus on qualitative properties for MDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation of MDPs with respect to qualitative properties, and present discrete graph algorithms with quadratic complexity to compute the simulation relation. We present an automated technique for assume-guarantee style reasoning for compositional analysis of two-player games by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We show a tight link between two-player games and MDPs, and as a consequence the results for games are lifted to MDPs with qualitative properties. We have implemented our algorithms and show that the compositional analysis leads to significant improvements. 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Pausinger, On the Approximation of Intrinsic Volumes, Institute of Science and Technology Austria, 2015."},"department":[{"_id":"HeEd"}],"month":"06","article_processing_charge":"No","title":"On the approximation of intrinsic volumes","date_published":"2015-06-01T00:00:00Z","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1662"},{"id":"1792","status":"public","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"2255"}]},"OA_place":"publisher","publist_id":"5808","alternative_title":["ISTA Thesis"],"supervisor":[{"orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert"}],"date_updated":"2026-04-16T10:09:04Z","corr_author":"1","status":"public","publication_status":"published","publisher":"Institute of Science and Technology Austria","type":"dissertation","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","abstract":[{"lang":"eng","text":"This thesis is concerned with the computation and approximation of intrinsic volumes. Given a smooth body M and a certain digital approximation of it, we develop algorithms to approximate various intrinsic volumes of M using only measurements taken from its digital approximations. The crucial idea behind our novel algorithms is to link the recent theory of persistent homology to the theory of intrinsic volumes via the Crofton formula from integral geometry and, in particular, via Euler characteristic computations. Our main contributions are a multigrid convergent digital algorithm to compute the first intrinsic volume of a solid body in R^n as well as an appropriate integration pipeline to approximate integral-geometric integrals defined over the Grassmannian manifold."}],"day":"01","oa_version":"None","year":"2015","_id":"1399","page":"144"},{"title":"Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA","file":[{"content_type":"application/pdf","file_size":931707,"file_name":"IST-2016-720-v1+1_OANA_OA-Empfehlungen_12-11-2015.pdf","file_id":"5317","creator":"system","checksum":"a495fe253bbc7615b1d60e9e85c94408","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:45:00Z","date_created":"2018-12-12T10:17:59Z"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"E-Lib"}],"author":[{"first_name":"Bruno","last_name":"Bauer","full_name":"Bauer, Bruno"},{"last_name":"Blechl","full_name":"Blechl, Guido","first_name":"Guido"},{"last_name":"Bock","first_name":"Christoph","full_name":"Bock, Christoph"},{"first_name":"Patrick","id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","full_name":"Danowski, Patrick","last_name":"Danowski","orcid":"0000-0002-6026-4409"},{"first_name":"Andreas","last_name":"Ferus","full_name":"Ferus, Andreas"},{"last_name":"Graschopf","first_name":"Anton","full_name":"Graschopf, Anton"},{"first_name":"Thomas","last_name":"König","full_name":"König, Thomas"},{"full_name":"Mayer, Katja","first_name":"Katja","last_name":"Mayer"},{"last_name":"Reckling","first_name":"Falk","full_name":"Reckling, Falk"},{"first_name":"Katharina","full_name":"Rieck, Katharina","last_name":"Rieck"},{"first_name":"Peter","last_name":"Seitz","full_name":"Seitz, Peter"},{"last_name":"Stöger","first_name":"Herwig","full_name":"Stöger, Herwig"},{"last_name":"Welzig","first_name":"Elvira","full_name":"Welzig, Elvira"}],"oa_version":"Published Version","issue":"3","publication":"VÖB Mitteilungen","ddc":["020"],"day":"12","abstract":[{"text":"Based on 16 recommendations, efforts should be made to achieve the following goal: By 2025, all scholarly publication activity in Austria should be Open Access. In other words, the final versions of all scholarly publications resulting from the support of public resources must be freely accessible on the Internet without delay (Gold Open Access). The resources required to meet this obligation shall be provided to the authors, or the cost of the publication venues shall be borne directly by the research organisations.","lang":"eng"}],"publication_status":"published","scopus_import":"1","pubrep_id":"720","OA_place":"publisher","has_accepted_license":"1","file_date_updated":"2020-07-14T12:45:00Z","date_published":"2015-11-12T00:00:00Z","volume":68,"month":"11","article_processing_charge":"No","oa":1,"citation":{"chicago":"Bauer, Bruno, Guido Blechl, Christoph Bock, Patrick Danowski, Andreas Ferus, Anton Graschopf, Thomas König, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” <i>VÖB Mitteilungen</i>. Verein Österreichischer Bibliothekare, 2015. <a href=\"https://doi.org/10.5281/zenodo.33178\">https://doi.org/10.5281/zenodo.33178</a>.","ama":"Bauer B, Blechl G, Bock C, et al. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. <i>VÖB Mitteilungen</i>. 2015;68(3):580-607. doi:<a href=\"https://doi.org/10.5281/zenodo.33178\">10.5281/zenodo.33178</a>","apa":"Bauer, B., Blechl, G., Bock, C., Danowski, P., Ferus, A., Graschopf, A., … Welzig, E. (2015). Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. <i>VÖB Mitteilungen</i>. Verein Österreichischer Bibliothekare. <a href=\"https://doi.org/10.5281/zenodo.33178\">https://doi.org/10.5281/zenodo.33178</a>","mla":"Bauer, Bruno, et al. “Arbeitsgruppe „Nationale Strategie“ Des Open Access Network Austria OANA.” <i>VÖB Mitteilungen</i>, vol. 68, no. 3, Verein Österreichischer Bibliothekare, 2015, pp. 580–607, doi:<a href=\"https://doi.org/10.5281/zenodo.33178\">10.5281/zenodo.33178</a>.","ieee":"B. Bauer <i>et al.</i>, “Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA,” <i>VÖB Mitteilungen</i>, vol. 68, no. 3. Verein Österreichischer Bibliothekare, pp. 580–607, 2015.","ista":"Bauer B, Blechl G, Bock C, Danowski P, Ferus A, Graschopf A, König T, Mayer K, Reckling F, Rieck K, Seitz P, Stöger H, Welzig E. 2015. Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA. VÖB Mitteilungen. 68(3), 580–607.","short":"B. Bauer, G. Blechl, C. Bock, P. Danowski, A. Ferus, A. Graschopf, T. König, K. Mayer, F. Reckling, K. Rieck, P. Seitz, H. Stöger, E. 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Hall, (2015).","chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Data from: Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Non-Mutator Bacteria.” Dryad, 2015. <a href=\"https://doi.org/10.5061/dryad.cj910\">https://doi.org/10.5061/dryad.cj910</a>.","ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria. 2015. doi:<a href=\"https://doi.org/10.5061/dryad.cj910\">10.5061/dryad.cj910</a>","apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &#38; Hall, A. R. (2015). Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria. Dryad. <a href=\"https://doi.org/10.5061/dryad.cj910\">https://doi.org/10.5061/dryad.cj910</a>","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. 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Dryad, 2015, doi:<a href=\"https://doi.org/10.5061/dryad.cj910\">10.5061/dryad.cj910</a>."},"date_published":"2015-12-21T00:00:00Z","title":"Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria","author":[{"first_name":"Sébastien","full_name":"Wielgoss, Sébastien","last_name":"Wielgoss"},{"orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"},{"first_name":"Anna M.","last_name":"Bischofberger","full_name":"Bischofberger, Anna M."},{"full_name":"Hall, Alex R.","last_name":"Hall","first_name":"Alex R."}],"date_created":"2021-07-26T08:44:04Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"21","abstract":[{"lang":"eng","text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance."}],"_id":"9719","year":"2015","oa_version":"Published Version","doi":"10.5061/dryad.cj910","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"5749"}]},"status":"public","type":"research_data_reference","publisher":"Dryad","date_updated":"2026-04-29T05:57:01Z"},{"main_file_link":[{"url":"https://arxiv.org/abs/1504.08259","open_access":"1"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"title":"Edit distance for pushdown automata","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4783-0389"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","full_name":"Otop, Jan","last_name":"Otop"}],"external_id":{"isi":["000364317900010"],"arxiv":["1504.08259"]},"publication":"42nd International Colloquium on Automata, Languages, and Programming","issue":"Part II","abstract":[{"lang":"eng","text":"The edit distance between two words w1, w2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w1 to w2. The edit distance generalizes to languages L1,L2, where the edit distance is the minimal number k such that for every word from L1 there exists a word in L2 with edit distance at most k. We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to pushdown automata is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). 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Springer Nature, 2015. <a href=\"https://doi.org/10.1007/978-3-662-47666-6_10\">https://doi.org/10.1007/978-3-662-47666-6_10</a>.","ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. Edit distance for pushdown automata. In: <i>42nd International Colloquium on Automata, Languages, and Programming</i>. Vol 9135. Springer Nature; 2015:121-133. doi:<a href=\"https://doi.org/10.1007/978-3-662-47666-6_10\">10.1007/978-3-662-47666-6_10</a>","apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., &#38; Otop, J. (2015). Edit distance for pushdown automata. In <i>42nd International Colloquium on Automata, Languages, and Programming</i> (Vol. 9135, pp. 121–133). Kyoto, Japan: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-47666-6_10\">https://doi.org/10.1007/978-3-662-47666-6_10</a>","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, “Edit distance for pushdown automata,” in <i>42nd International Colloquium on Automata, Languages, and Programming</i>, Kyoto, Japan, 2015, vol. 9135, no. Part II, pp. 121–133.","mla":"Chatterjee, Krishnendu, et al. “Edit Distance for Pushdown Automata.” <i>42nd International Colloquium on Automata, Languages, and Programming</i>, vol. 9135, no. Part II, Springer Nature, 2015, pp. 121–33, doi:<a href=\"https://doi.org/10.1007/978-3-662-47666-6_10\">10.1007/978-3-662-47666-6_10</a>.","ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for pushdown automata. 42nd International Colloquium on Automata, Languages, and Programming. ICALP: Automata, Languages and Programming, LNCS, vol. 9135, 121–133.","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, in:, 42nd International Colloquium on Automata, Languages, and Programming, Springer Nature, 2015, pp. 121–133."},"date_published":"2015-07-01T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"isbn":["978-3-662-47665-9"]},"arxiv":1,"date_created":"2018-12-11T11:53:01Z","conference":{"start_date":"2015-07-06","location":"Kyoto, Japan","end_date":"2015-07-10","name":"ICALP: Automata, Languages and Programming"},"isi":1,"OA_type":"green","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1610","page":"121 - 133","year":"2015","doi":"10.1007/978-3-662-47666-6_10","acknowledgement":"This research was funded in part by the European Research Council (ERC) under\r\ngrant agreement 267989 (QUAREM), by the Austrian Science Fund (FWF) projects\r\nS11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), FWF Grant No P23499-\r\nN23, FWF NFN Grant No S11407-N23 (RiSE), ERC Start grant (279307: Graph\r\nGames), and MSR faculty fellows award.","publist_id":"5556","date_updated":"2026-04-29T06:14:48Z","status":"public","type":"conference","publisher":"Springer Nature","intvolume":"      9135"},{"oa_version":"Published Version","year":"2015","_id":"5438","page":"15","day":"05","abstract":[{"text":"The edit distance between two words w1, w2 is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform w1 to w2. The edit distance generalizes to languages L1, L2, where the edit distance is the minimal number k such that for every word from L1 there exists a word in L2 with edit distance at most k. We study the edit distance computation problem between pushdown automata and their subclasses.\r\nThe problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for deciding whether, for a given threshold k, the edit distance from a pushdown automaton to a finite automaton is at most k. ","lang":"eng"}],"ddc":["004"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-04-29T06:14:48Z","publisher":"IST Austria","publication_status":"published","status":"public","type":"technical_report","related_material":{"record":[{"id":"465","relation":"later_version","status":"public"},{"status":"public","relation":"later_version","id":"1610"}]},"has_accepted_license":"1","pubrep_id":"334","alternative_title":["IST Austria Technical Report"],"doi":"10.15479/AT:IST-2015-334-v1-1","title":"Edit distance for pushdown automata","date_published":"2015-05-05T00:00:00Z","file_date_updated":"2020-07-14T12:46:55Z","citation":{"ista":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. 2015. Edit distance for pushdown automata, IST Austria, 15p.","short":"K. Chatterjee, T.A. Henzinger, R. Ibsen-Jensen, J. Otop, Edit Distance for Pushdown Automata, IST Austria, 2015.","apa":"Chatterjee, K., Henzinger, T. A., Ibsen-Jensen, R., &#38; Otop, J. (2015). <i>Edit distance for pushdown automata</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2015-334-v1-1\">https://doi.org/10.15479/AT:IST-2015-334-v1-1</a>","mla":"Chatterjee, Krishnendu, et al. <i>Edit Distance for Pushdown Automata</i>. IST Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-334-v1-1\">10.15479/AT:IST-2015-334-v1-1</a>.","ieee":"K. Chatterjee, T. A. Henzinger, R. Ibsen-Jensen, and J. Otop, <i>Edit distance for pushdown automata</i>. IST Austria, 2015.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Rasmus Ibsen-Jensen, and Jan Otop. <i>Edit Distance for Pushdown Automata</i>. IST Austria, 2015. <a href=\"https://doi.org/10.15479/AT:IST-2015-334-v1-1\">https://doi.org/10.15479/AT:IST-2015-334-v1-1</a>.","ama":"Chatterjee K, Henzinger TA, Ibsen-Jensen R, Otop J. <i>Edit Distance for Pushdown Automata</i>. IST Austria; 2015. doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-334-v1-1\">10.15479/AT:IST-2015-334-v1-1</a>"},"department":[{"_id":"KrCh"}],"oa":1,"file":[{"file_id":"5518","creator":"system","checksum":"8a5f2d77560e552af87eb1982437a43b","relation":"main_file","date_updated":"2020-07-14T12:46:55Z","access_level":"open_access","date_created":"2018-12-12T11:53:56Z","file_name":"IST-2015-334-v1+1_report.pdf","content_type":"application/pdf","file_size":422573}],"month":"05","date_created":"2018-12-12T11:39:20Z","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"orcid":"0000-0003-4783-0389","first_name":"Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","full_name":"Ibsen-Jensen, Rasmus","last_name":"Ibsen-Jensen"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan"}]},{"title":"Quantifying the determinants of evolutionary dynamics leading to drug resistance","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"ToBo"}],"file":[{"file_size":1387760,"content_type":"application/pdf","date_created":"2018-12-12T10:09:00Z","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:45:07Z","creator":"system","checksum":"0e82e3279f50b15c6c170c042627802b","file_id":"4723","file_name":"IST-2016-468-v1+1_journal.pbio.1002299.pdf"}],"external_id":{"isi":["000365898900011"]},"author":[{"full_name":"Chevereau, Guillaume","id":"424D78A0-F248-11E8-B48F-1D18A9856A87","last_name":"Chevereau","first_name":"Guillaume"},{"orcid":"0000-0002-2519-8004","full_name":"Dravecka, Marta","first_name":"Marta","last_name":"Dravecka","id":"4342E402-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tugce","full_name":"Batur, Tugce","last_name":"Batur"},{"last_name":"Guvenek","first_name":"Aysegul","full_name":"Guvenek, Aysegul"},{"last_name":"Ayhan","full_name":"Ayhan, Dilay","first_name":"Dilay"},{"last_name":"Toprak","full_name":"Toprak, Erdal","first_name":"Erdal"},{"orcid":"0000-0003-4398-476X","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","first_name":"Mark Tobias"}],"oa_version":"Published Version","ec_funded":1,"project":[{"_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth","grant_number":"RGP0042/2013"},{"grant_number":"P27201-B22","name":"Revealing the mechanisms underlying drug interactions","call_identifier":"FWF","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"303507","_id":"25E83C2C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Optimality principles in responses to antibiotics"}],"day":"18","ddc":["570"],"abstract":[{"text":"The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the “morbidostat”, a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations—an almost paradoxical behavior since this drug causes DNA damage and increases the mutation rate. Overall, we identified novel quantitative characteristics of the evolutionary landscape that provide the conceptual foundation for predicting the dynamics of drug resistance evolution.","lang":"eng"}],"publication":"PLoS Biology","issue":"11","scopus_import":"1","publication_status":"published","corr_author":"1","pubrep_id":"468","has_accepted_license":"1","related_material":{"record":[{"id":"9711","status":"public","relation":"research_data"},{"status":"public","relation":"research_data","id":"9765"},{"id":"6263","status":"public","relation":"dissertation_contains"}]},"article_number":"e1002299","date_published":"2015-11-18T00:00:00Z","file_date_updated":"2020-07-14T12:45:07Z","citation":{"chicago":"Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” <i>PLoS Biology</i>. Public Library of Science, 2015. <a href=\"https://doi.org/10.1371/journal.pbio.1002299\">https://doi.org/10.1371/journal.pbio.1002299</a>.","ama":"Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of evolutionary dynamics leading to drug resistance. <i>PLoS Biology</i>. 2015;13(11). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299\">10.1371/journal.pbio.1002299</a>","apa":"Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak, E., &#38; Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary dynamics leading to drug resistance. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1002299\">https://doi.org/10.1371/journal.pbio.1002299</a>","mla":"Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” <i>PLoS Biology</i>, vol. 13, no. 11, e1002299, Public Library of Science, 2015, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1002299\">10.1371/journal.pbio.1002299</a>.","ieee":"G. Chevereau <i>et al.</i>, “Quantifying the determinants of evolutionary dynamics leading to drug resistance,” <i>PLoS Biology</i>, vol. 13, no. 11. Public Library of Science, 2015.","ista":"Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 13(11), e1002299.","short":"G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak, M.T. Bollenbach, PLoS Biology 13 (2015)."},"volume":13,"article_processing_charge":"No","month":"11","oa":1,"date_created":"2018-12-11T11:53:04Z","quality_controlled":"1","language":[{"iso":"eng"}],"year":"2015","_id":"1619","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","isi":1,"intvolume":"        13","publisher":"Public Library of Science","status":"public","type":"journal_article","date_updated":"2026-05-12T22:31:04Z","publist_id":"5547","doi":"10.1371/journal.pbio.1002299"}]