[{"title":"Reversal of an ancient sex chromosome to an autosome in Drosophila","volume":499,"status":"public","intvolume":"       499","day":"18","year":"2013","author":[{"last_name":"Vicoso","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","full_name":"Beatriz Vicoso"},{"full_name":"Bachtrog, Doris","first_name":"Doris","last_name":"Bachtrog"}],"acknowledgement":"Funded by National Institutes of Health grants (R01GM076007 and R01GM093182) and a Packard Fellowship to D.B.","citation":{"ama":"Vicoso B, Bachtrog D. Reversal of an ancient sex chromosome to an autosome in Drosophila. <i>Nature</i>. 2013;499(7458):332-335. doi:<a href=\"https://doi.org/10.1038/nature12235\">10.1038/nature12235</a>","chicago":"Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome to an Autosome in Drosophila.” <i>Nature</i>. Nature Publishing Group, 2013. <a href=\"https://doi.org/10.1038/nature12235\">https://doi.org/10.1038/nature12235</a>.","short":"B. Vicoso, D. Bachtrog, Nature 499 (2013) 332–335.","apa":"Vicoso, B., &#38; Bachtrog, D. (2013). Reversal of an ancient sex chromosome to an autosome in Drosophila. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature12235\">https://doi.org/10.1038/nature12235</a>","mla":"Vicoso, Beatriz, and Doris Bachtrog. “Reversal of an Ancient Sex Chromosome to an Autosome in Drosophila.” <i>Nature</i>, vol. 499, no. 7458, Nature Publishing Group, 2013, pp. 332–35, doi:<a href=\"https://doi.org/10.1038/nature12235\">10.1038/nature12235</a>.","ieee":"B. Vicoso and D. Bachtrog, “Reversal of an ancient sex chromosome to an autosome in Drosophila,” <i>Nature</i>, vol. 499, no. 7458. Nature Publishing Group, pp. 332–335, 2013.","ista":"Vicoso B, Bachtrog D. 2013. Reversal of an ancient sex chromosome to an autosome in Drosophila. Nature. 499(7458), 332–335."},"doi":"10.1038/nature12235","quality_controlled":0,"date_created":"2018-12-11T11:55:05Z","type":"journal_article","_id":"1991","issue":"7458","publication":"Nature","extern":1,"publication_status":"published","publisher":"Nature Publishing Group","publist_id":"5092","date_updated":"2021-01-12T06:54:33Z","abstract":[{"lang":"eng","text":"Although transitions of sex-determination mechanisms are frequent in species with homomorphic sex chromosomes, heteromorphic sex chromosomes are thought to represent a terminal evolutionary stage owing to chromosome-specific adaptations such as dosage compensation or an accumulation of sex-specific mutations. Here we show that an autosome of Drosophila, the dot chromosome, was ancestrally a differentiated X chromosome. We analyse the whole genome of true fruitflies (Tephritidae), flesh flies (Sarcophagidae) and soldier flies (Stratiomyidae) to show that genes located on the dot chromosome of Drosophila are X-linked in outgroup species, whereas Drosophila X-linked genes are autosomal. We date this chromosomal transition to early drosophilid evolution by sequencing the genome of other Drosophilidae. Our results reveal several puzzling aspects of Drosophila dot chromosome biology to be possible remnants of its former life as a sex chromosome, such as its minor feminizing role in sex determination or its targeting by a chromosome-specific regulatory mechanism. We also show that patterns of biased gene expression of the dot chromosome during early embryogenesis, oogenesis and spermatogenesis resemble that of the current X chromosome. Thus, although sex chromosomes are not necessarily evolutionary end points and can revert back to an autosomal inheritance, the highly specialized genome architecture of this former X chromosome suggests that severe fitness costs must be overcome for such a turnover to occur."}],"date_published":"2013-07-18T00:00:00Z","month":"07","page":"332 - 335"},{"title":"TTP: Tool for tumor progression","volume":8044,"status":"public","day":"01","author":[{"orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter"},{"full_name":"Božić, Ivana","last_name":"Božić","first_name":"Ivana"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Martin","last_name":"Nowak","full_name":"Nowak, Martin"}],"department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:55:08Z","oa_version":"Preprint","project":[{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"publication":"Proceedings of 25th Int. Conf. on Computer Aided Verification","type":"conference","_id":"2000","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-07T11:40:43Z","publist_id":"5077","publisher":"Springer","date_published":"2013-01-01T00:00:00Z","month":"01","series_title":"Lecture Notes in Computer Science","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1303.5251"}],"arxiv":1,"intvolume":"      8044","year":"2013","language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"5399"},{"status":"public","id":"1400","relation":"dissertation_contains"}]},"conference":{"location":"St. Petersburg, Russia","start_date":"2013-07-13","end_date":"2013-07-19","name":"CAV: Computer Aided Verification"},"ec_funded":1,"quality_controlled":"1","citation":{"mla":"Reiter, Johannes, et al. “TTP: Tool for Tumor Progression.” <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, vol. 8044, Springer, 2013, pp. 101–06, doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>.","ieee":"J. Reiter, I. Božić, K. Chatterjee, and M. Nowak, “TTP: Tool for tumor progression,” in <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, St. Petersburg, Russia, 2013, vol. 8044, pp. 101–106.","ista":"Reiter J, Božić I, Chatterjee K, Nowak M. 2013. TTP: Tool for tumor progression. Proceedings of 25th Int. Conf. on Computer Aided Verification. CAV: Computer Aided VerificationLecture Notes in Computer Science, LNCS, vol. 8044, 101–106.","chicago":"Reiter, Johannes, Ivana Božić, Krishnendu Chatterjee, and Martin Nowak. “TTP: Tool for Tumor Progression.” In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>, 8044:101–6. Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>.","short":"J. Reiter, I. Božić, K. Chatterjee, M. Nowak, in:, Proceedings of 25th Int. Conf. on Computer Aided Verification, Springer, 2013, pp. 101–106.","apa":"Reiter, J., Božić, I., Chatterjee, K., &#38; Nowak, M. (2013). TTP: Tool for tumor progression. In <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i> (Vol. 8044, pp. 101–106). St. Petersburg, Russia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">https://doi.org/10.1007/978-3-642-39799-8_6</a>","ama":"Reiter J, Božić I, Chatterjee K, Nowak M. TTP: Tool for tumor progression. In: <i>Proceedings of 25th Int. Conf. on Computer Aided Verification</i>. Vol 8044. Lecture Notes in Computer Science. Springer; 2013:101-106. doi:<a href=\"https://doi.org/10.1007/978-3-642-39799-8_6\">10.1007/978-3-642-39799-8_6</a>"},"doi":"10.1007/978-3-642-39799-8_6","abstract":[{"text":"In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics.","lang":"eng"}],"oa":1,"alternative_title":["LNCS"],"page":"101 - 106","external_id":{"arxiv":["1303.5251"]}},{"publist_id":"5067","date_updated":"2021-01-12T06:54:41Z","publisher":"Carnegie Mellon University","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"08","date_published":"2013-08-01T00:00:00Z","abstract":[{"lang":"eng","text":"Traditional statistical methods for confidentiality protection of statistical databases do not scale well to deal with GWAS databases especially in terms of guarantees regarding protection from linkage to external information. The more recent concept of differential privacy, introduced by the cryptographic community, is an approach which provides a rigorous definition of privacy with meaningful privacy guarantees in the presence of arbitrary external information, although the guarantees may come at a serious price in terms of data utility. Building on such notions, we propose new methods to release aggregate GWAS data without compromising an individual’s privacy. We present methods for releasing differentially private minor allele frequencies, chi-square statistics and p-values. We compare these approaches on simulated data and on a GWAS study of canine hair length involving 685 dogs. We also propose a privacy-preserving method for finding genome-wide associations based on a differentially-private approach to penalized logistic regression."}],"oa":1,"page":"137 - 166","main_file_link":[{"open_access":"1","url":"http://repository.cmu.edu/jpc/vol5/iss1/6"}],"status":"public","intvolume":"         5","title":"Privacy-preserving data sharing for genome-wide association studies","volume":5,"language":[{"iso":"eng"}],"day":"01","year":"2013","department":[{"_id":"CaUh"}],"author":[{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"},{"full_name":"Slavkovic, Aleksandra","first_name":"Aleksandra","last_name":"Slavkovic"},{"full_name":"Fienberg, Stephen","last_name":"Fienberg","first_name":"Stephen"}],"publication":"Journal of Privacy and Confidentiality ","_id":"2009","issue":"1","type":"journal_article","article_processing_charge":"No","oa_version":"Published Version","date_created":"2018-12-11T11:55:11Z","quality_controlled":"1","citation":{"ama":"Uhler C, Slavkovic A, Fienberg S. Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. 2013;5(1):137-166. doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>","ieee":"C. Uhler, A. Slavkovic, and S. Fienberg, “Privacy-preserving data sharing for genome-wide association studies,” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1. Carnegie Mellon University, pp. 137–166, 2013.","ista":"Uhler C, Slavkovic A, Fienberg S. 2013. Privacy-preserving data sharing for genome-wide association studies. Journal of Privacy and Confidentiality . 5(1), 137–166.","mla":"Uhler, Caroline, et al. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>, vol. 5, no. 1, Carnegie Mellon University, 2013, pp. 137–66, doi:<a href=\"https://doi.org/10.29012/jpc.v5i1.629\">10.29012/jpc.v5i1.629</a>.","apa":"Uhler, C., Slavkovic, A., &#38; Fienberg, S. (2013). Privacy-preserving data sharing for genome-wide association studies. <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>","short":"C. Uhler, A. Slavkovic, S. Fienberg, Journal of Privacy and Confidentiality  5 (2013) 137–166.","chicago":"Uhler, Caroline, Aleksandra Slavkovic, and Stephen Fienberg. “Privacy-Preserving Data Sharing for Genome-Wide Association Studies.” <i>Journal of Privacy and Confidentiality </i>. Carnegie Mellon University, 2013. <a href=\"https://doi.org/10.29012/jpc.v5i1.629\">https://doi.org/10.29012/jpc.v5i1.629</a>."},"doi":"10.29012/jpc.v5i1.629"},{"day":"01","status":"public","volume":41,"title":"Geometry of the faithfulness assumption in causal inference","type":"journal_article","_id":"2010","issue":"2","publication":"The Annals of Statistics","oa_version":"Published Version","date_created":"2018-12-11T11:55:11Z","department":[{"_id":"CaUh"}],"author":[{"full_name":"Uhler, Caroline","orcid":"0000-0002-7008-0216","last_name":"Uhler","first_name":"Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Garvesh","last_name":"Raskutti","full_name":"Raskutti, Garvesh"},{"first_name":"Peter","last_name":"Bühlmann","full_name":"Bühlmann, Peter"},{"last_name":"Yu","first_name":"Bin","full_name":"Yu, Bin"}],"date_published":"2013-04-01T00:00:00Z","month":"04","publisher":"Institute of Mathematical Statistics","date_updated":"2021-01-12T06:54:42Z","publist_id":"5066","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","main_file_link":[{"open_access":"1","url":"www.doi.org/10.1214/12-AOS1080"}],"scopus_import":1,"language":[{"iso":"eng"}],"year":"2013","intvolume":"        41","arxiv":1,"doi":"10.1214/12-AOS1080","citation":{"apa":"Uhler, C., Raskutti, G., Bühlmann, P., &#38; Yu, B. (2013). Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>","short":"C. Uhler, G. Raskutti, P. Bühlmann, B. Yu, The Annals of Statistics 41 (2013) 436–463.","chicago":"Uhler, Caroline, Garvesh Raskutti, Peter Bühlmann, and Bin Yu. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>. Institute of Mathematical Statistics, 2013. <a href=\"https://doi.org/10.1214/12-AOS1080\">https://doi.org/10.1214/12-AOS1080</a>.","ista":"Uhler C, Raskutti G, Bühlmann P, Yu B. 2013. Geometry of the faithfulness assumption in causal inference. The Annals of Statistics. 41(2), 436–463.","ieee":"C. Uhler, G. Raskutti, P. Bühlmann, and B. Yu, “Geometry of the faithfulness assumption in causal inference,” <i>The Annals of Statistics</i>, vol. 41, no. 2. Institute of Mathematical Statistics, pp. 436–463, 2013.","mla":"Uhler, Caroline, et al. “Geometry of the Faithfulness Assumption in Causal Inference.” <i>The Annals of Statistics</i>, vol. 41, no. 2, Institute of Mathematical Statistics, 2013, pp. 436–63, doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>.","ama":"Uhler C, Raskutti G, Bühlmann P, Yu B. Geometry of the faithfulness assumption in causal inference. <i>The Annals of Statistics</i>. 2013;41(2):436-463. doi:<a href=\"https://doi.org/10.1214/12-AOS1080\">10.1214/12-AOS1080</a>"},"quality_controlled":"1","oa":1,"abstract":[{"text":"Many algorithms for inferring causality rely heavily on the faithfulness assumption. The main justification for imposing this assumption is that the set of unfaithful distributions has Lebesgue measure zero, since it can be seen as a collection of hypersurfaces in a hypercube. However, due to sampling error the faithfulness condition alone is not sufficient for statistical estimation, and strong-faithfulness has been proposed and assumed to achieve uniform or high-dimensional consistency. In contrast to the plain faithfulness assumption, the set of distributions that is not strong-faithful has nonzero Lebesgue measure and in fact, can be surprisingly large as we show in this paper. We study the strong-faithfulness condition from a geometric and combinatorial point of view and give upper and lower bounds on the Lebesgue measure of strong-faithful distributions for various classes of directed acyclic graphs. Our results imply fundamental limitations for the PC-algorithm and potentially also for other algorithms based on partial correlation testing in the Gaussian case.","lang":"eng"}],"external_id":{"arxiv":["1207.0547"]},"page":"436 - 463"},{"keyword":["Organic Chemistry"],"abstract":[{"text":"We report a method for preparing electrode–molecule–electrode junctions that incorporate nonsymmetrical azobenzene dithiols. Our approach is based on sequential deprotection of thiol moieties originally carrying two different protecting groups. The azobenzene derivatives retained their switching properties within monolayers and permitted the photocontrol of electrical conductance.","lang":"eng"}],"page":"2370-2374","intvolume":"        24","publication_identifier":{"eissn":["1437-2096"],"issn":["0936-5214"]},"language":[{"iso":"eng"}],"year":"2013","extern":"1","citation":{"apa":"Ely, T., Das, S., Li, W., Kundu, P., Tirosh, E., Cahen, D., … Klajn, R. (2013). Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol. <i>Synlett</i>. Georg Thieme Verlag. <a href=\"https://doi.org/10.1055/s-0033-1340087\">https://doi.org/10.1055/s-0033-1340087</a>","short":"T. Ely, S. Das, W. Li, P. Kundu, E. Tirosh, D. Cahen, A. Vilan, R. Klajn, Synlett 24 (2013) 2370–2374.","chicago":"Ely, Tal, Sanjib Das, Wenjie Li, Pintu Kundu, Einat Tirosh, David Cahen, Ayelet Vilan, and Rafal Klajn. “Photocontrol of Electrical Conductance with a Nonsymmetrical Azobenzene Dithiol.” <i>Synlett</i>. Georg Thieme Verlag, 2013. <a href=\"https://doi.org/10.1055/s-0033-1340087\">https://doi.org/10.1055/s-0033-1340087</a>.","ieee":"T. Ely <i>et al.</i>, “Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol,” <i>Synlett</i>, vol. 24, no. 18. Georg Thieme Verlag, pp. 2370–2374, 2013.","ista":"Ely T, Das S, Li W, Kundu P, Tirosh E, Cahen D, Vilan A, Klajn R. 2013. Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol. Synlett. 24(18), 2370–2374.","mla":"Ely, Tal, et al. “Photocontrol of Electrical Conductance with a Nonsymmetrical Azobenzene Dithiol.” <i>Synlett</i>, vol. 24, no. 18, Georg Thieme Verlag, 2013, pp. 2370–74, doi:<a href=\"https://doi.org/10.1055/s-0033-1340087\">10.1055/s-0033-1340087</a>.","ama":"Ely T, Das S, Li W, et al. Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol. <i>Synlett</i>. 2013;24(18):2370-2374. doi:<a href=\"https://doi.org/10.1055/s-0033-1340087\">10.1055/s-0033-1340087</a>"},"doi":"10.1055/s-0033-1340087","quality_controlled":"1","publisher":"Georg Thieme Verlag","date_updated":"2023-08-08T07:47:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_published":"2013-10-22T00:00:00Z","month":"10","article_type":"original","scopus_import":"1","status":"public","title":"Photocontrol of electrical conductance with a nonsymmetrical azobenzene dithiol","volume":24,"day":"22","author":[{"first_name":"Tal","last_name":"Ely","full_name":"Ely, Tal"},{"first_name":"Sanjib","last_name":"Das","full_name":"Das, Sanjib"},{"last_name":"Li","first_name":"Wenjie","full_name":"Li, Wenjie"},{"last_name":"Kundu","first_name":"Pintu","full_name":"Kundu, Pintu"},{"first_name":"Einat","last_name":"Tirosh","full_name":"Tirosh, Einat"},{"first_name":"David","last_name":"Cahen","full_name":"Cahen, David"},{"full_name":"Vilan, Ayelet","last_name":"Vilan","first_name":"Ayelet"},{"first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","last_name":"Klajn","full_name":"Klajn, Rafal"}],"type":"journal_article","issue":"18","_id":"13405","article_processing_charge":"No","publication":"Synlett","oa_version":"None","date_created":"2023-08-01T09:47:17Z"},{"author":[{"first_name":"Sanjib","last_name":"Das","full_name":"Das, Sanjib"},{"full_name":"Ranjan, Priyadarshi","first_name":"Priyadarshi","last_name":"Ranjan"},{"full_name":"Maiti, Pradipta Sankar","last_name":"Maiti","first_name":"Pradipta Sankar"},{"full_name":"Singh, Gurvinder","first_name":"Gurvinder","last_name":"Singh"},{"full_name":"Leitus, Gregory","first_name":"Gregory","last_name":"Leitus"},{"full_name":"Klajn, Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"}],"issue":"3","_id":"13406","type":"journal_article","article_processing_charge":"No","publication":"Advanced Materials","date_created":"2023-08-01T09:47:30Z","oa_version":"None","status":"public","volume":25,"title":"Dual-responsive nanoparticles and their self-assembly","day":"18","scopus_import":"1","publisher":"Wiley","date_updated":"2023-08-08T07:49:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_published":"2013-01-18T00:00:00Z","month":"01","article_type":"original","extern":"1","citation":{"short":"S. Das, P. Ranjan, P.S. Maiti, G. Singh, G. Leitus, R. Klajn, Advanced Materials 25 (2013) 422–426.","chicago":"Das, Sanjib, Priyadarshi Ranjan, Pradipta Sankar Maiti, Gurvinder Singh, Gregory Leitus, and Rafal Klajn. “Dual-Responsive Nanoparticles and Their Self-Assembly.” <i>Advanced Materials</i>. Wiley, 2013. <a href=\"https://doi.org/10.1002/adma.201201734\">https://doi.org/10.1002/adma.201201734</a>.","apa":"Das, S., Ranjan, P., Maiti, P. S., Singh, G., Leitus, G., &#38; Klajn, R. (2013). Dual-responsive nanoparticles and their self-assembly. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.201201734\">https://doi.org/10.1002/adma.201201734</a>","mla":"Das, Sanjib, et al. “Dual-Responsive Nanoparticles and Their Self-Assembly.” <i>Advanced Materials</i>, vol. 25, no. 3, Wiley, 2013, pp. 422–26, doi:<a href=\"https://doi.org/10.1002/adma.201201734\">10.1002/adma.201201734</a>.","ieee":"S. Das, P. Ranjan, P. S. Maiti, G. Singh, G. Leitus, and R. Klajn, “Dual-responsive nanoparticles and their self-assembly,” <i>Advanced Materials</i>, vol. 25, no. 3. Wiley, pp. 422–426, 2013.","ista":"Das S, Ranjan P, Maiti PS, Singh G, Leitus G, Klajn R. 2013. Dual-responsive nanoparticles and their self-assembly. Advanced Materials. 25(3), 422–426.","ama":"Das S, Ranjan P, Maiti PS, Singh G, Leitus G, Klajn R. Dual-responsive nanoparticles and their self-assembly. <i>Advanced Materials</i>. 2013;25(3):422-426. doi:<a href=\"https://doi.org/10.1002/adma.201201734\">10.1002/adma.201201734</a>"},"doi":"10.1002/adma.201201734","quality_controlled":"1","pmid":1,"intvolume":"        25","publication_identifier":{"issn":["0935-9648"]},"language":[{"iso":"eng"}],"year":"2013","external_id":{"pmid":["22933327"]},"page":"422-426","keyword":["Mechanical Engineering","Mechanics of Materials","General Materials Science"],"abstract":[{"text":"Dual-responsive nanoparticles are designed by functionalizing magnetic cores with light-responsive ligands. These materials respond to both light and magnetic fields and can be assembled into various higher-order structures, depending on the relative contributions of these two stimuli.","lang":"eng"}]},{"abstract":[{"text":"We study two-player zero-sum games over infinite-state graphs equipped with ωB and finitary conditions. Our first contribution is about the strategy complexity, i.e the memory required for winning strategies: we prove that over general infinite-state graphs, memoryless strategies are sufficient for finitary Büchi, and finite-memory suffices for finitary parity games. We then study pushdown games with boundedness conditions, with two contributions. First we prove a collapse result for pushdown games with ωB-conditions, implying the decidability of solving these games. Second we consider pushdown games with finitary parity along with stack boundedness conditions, and show that solving these games is EXPTIME-complete.","lang":"eng"}],"oa":1,"ddc":["000"],"file":[{"creator":"system","file_size":547296,"checksum":"b7091a3866db573c0db5ec486952255e","date_updated":"2020-07-14T12:44:47Z","access_level":"open_access","date_created":"2018-12-12T10:13:38Z","file_id":"5023","relation":"main_file","file_name":"IST-2016-624-v1+1_ChKr_Infinite-state_games_2013_17.pdf","content_type":"application/pdf"}],"alternative_title":["LIPIcs"],"page":"181 - 196","has_accepted_license":"1","intvolume":"        23","year":"2013","language":[{"iso":"eng"}],"conference":{"end_date":"2013-09-05","start_date":"203-09-02","location":"Torino, Italy","name":"CSL: Computer Science Logic"},"quality_controlled":"1","ec_funded":1,"citation":{"ista":"Chatterjee K, Fijalkow N. 2013. Infinite-state games with finitary conditions. 22nd EACSL Annual Conference on Computer Science Logic. CSL: Computer Science LogicLeibniz International Proceedings in Informatics, LIPIcs, vol. 23, 181–196.","ieee":"K. Chatterjee and N. Fijalkow, “Infinite-state games with finitary conditions,” in <i>22nd EACSL Annual Conference on Computer Science Logic</i>, Torino, Italy, 2013, vol. 23, pp. 181–196.","mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with Finitary Conditions.” <i>22nd EACSL Annual Conference on Computer Science Logic</i>, vol. 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–96, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">10.4230/LIPIcs.CSL.2013.181</a>.","apa":"Chatterjee, K., &#38; Fijalkow, N. (2013). Infinite-state games with finitary conditions. In <i>22nd EACSL Annual Conference on Computer Science Logic</i> (Vol. 23, pp. 181–196). Torino, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">https://doi.org/10.4230/LIPIcs.CSL.2013.181</a>","short":"K. Chatterjee, N. Fijalkow, in:, 22nd EACSL Annual Conference on Computer Science Logic, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013, pp. 181–196.","chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. “Infinite-State Games with Finitary Conditions.” In <i>22nd EACSL Annual Conference on Computer Science Logic</i>, 23:181–96. Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2013. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">https://doi.org/10.4230/LIPIcs.CSL.2013.181</a>.","ama":"Chatterjee K, Fijalkow N. Infinite-state games with finitary conditions. In: <i>22nd EACSL Annual Conference on Computer Science Logic</i>. Vol 23. Leibniz International Proceedings in Informatics. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2013:181-196. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2013.181\">10.4230/LIPIcs.CSL.2013.181</a>"},"doi":"10.4230/LIPIcs.CSL.2013.181","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T06:50:14Z","publist_id":"5837","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_published":"2013-09-01T00:00:00Z","month":"09","series_title":"Leibniz International Proceedings in Informatics","scopus_import":1,"title":"Infinite-state games with finitary conditions","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":23,"status":"public","day":"01","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Fijalkow, Nathanaël","last_name":"Fijalkow","first_name":"Nathanaël"}],"department":[{"_id":"KrCh"}],"pubrep_id":"624","date_created":"2018-12-11T11:51:39Z","oa_version":"Published Version","project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF","grant_number":"S11407"},{"grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"publication":"22nd EACSL Annual Conference on Computer Science Logic","file_date_updated":"2020-07-14T12:44:47Z","_id":"1374","type":"conference"},{"page":"18 - 25","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T12:24:53Z","publist_id":"5835","publisher":"IEEE","abstract":[{"text":"We consider the distributed synthesis problem for temporal logic specifications. Traditionally, the problem has been studied for LTL, and the previous results show that the problem is decidable iff there is no information fork in the architecture. We consider the problem for fragments of LTL and our main results are as follows: (1) We show that the problem is undecidable for architectures with information forks even for the fragment of LTL with temporal operators restricted to next and eventually. (2) For specifications restricted to globally along with non-nested next operators, we establish decidability (in EXPSPACE) for star architectures where the processes receive disjoint inputs, whereas we establish undecidability for architectures containing an information fork-meet structure. (3) Finally, we consider LTL without the next operator, and establish decidability (NEXPTIME-complete) for all architectures for a fragment that consists of a set of safety assumptions, and a set of guarantees where each guarantee is a safety, reachability, or liveness condition.","lang":"eng"}],"month":"12","date_published":"2013-12-11T00:00:00Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"},{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"}],"related_material":{"record":[{"id":"5406","status":"public","relation":"earlier_version"}]},"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"conference":{"name":"FMCAD: Formal Methods in Computer-Aided Design","location":"Portland, OR, United States","end_date":"2013-10-23","start_date":"2013-10-20"},"date_created":"2018-12-11T11:51:40Z","quality_controlled":"1","oa_version":"None","ec_funded":1,"citation":{"ama":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. Distributed synthesis for LTL fragments. In: <i>13th International Conference on Formal Methods in Computer-Aided Design</i>. IEEE; 2013:18-25. doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">10.1109/FMCAD.2013.6679386</a>","ista":"Chatterjee K, Henzinger TA, Otop J, Pavlogiannis A. 2013. Distributed synthesis for LTL fragments. 13th International Conference on Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 18–25.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and A. Pavlogiannis, “Distributed synthesis for LTL fragments,” in <i>13th International Conference on Formal Methods in Computer-Aided Design</i>, Portland, OR, United States, 2013, pp. 18–25.","mla":"Chatterjee, Krishnendu, et al. “Distributed Synthesis for LTL Fragments.” <i>13th International Conference on Formal Methods in Computer-Aided Design</i>, IEEE, 2013, pp. 18–25, doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">10.1109/FMCAD.2013.6679386</a>.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Pavlogiannis, A. (2013). Distributed synthesis for LTL fragments. In <i>13th International Conference on Formal Methods in Computer-Aided Design</i> (pp. 18–25). Portland, OR, United States: IEEE. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">https://doi.org/10.1109/FMCAD.2013.6679386</a>","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Andreas Pavlogiannis. “Distributed Synthesis for LTL Fragments.” In <i>13th International Conference on Formal Methods in Computer-Aided Design</i>, 18–25. IEEE, 2013. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679386\">https://doi.org/10.1109/FMCAD.2013.6679386</a>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, A. Pavlogiannis, in:, 13th International Conference on Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 18–25."},"project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"doi":"10.1109/FMCAD.2013.6679386","publication":"13th International Conference on Formal Methods in Computer-Aided Design","_id":"1376","type":"conference","title":"Distributed synthesis for LTL fragments","status":"public","day":"11","year":"2013","language":[{"iso":"eng"}]},{"department":[{"_id":"ToHe"}],"author":[{"full_name":"Hofferek, Georg","last_name":"Hofferek","first_name":"Georg"},{"last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","first_name":"Ashutosh","full_name":"Gupta, Ashutosh"},{"full_name":"Könighofer, Bettina","last_name":"Könighofer","first_name":"Bettina"},{"full_name":"Jiang, Jie","first_name":"Jie","last_name":"Jiang"},{"full_name":"Bloem, Roderick","last_name":"Bloem","first_name":"Roderick"}],"publication":"2013 Formal Methods in Computer-Aided Design","_id":"1385","type":"conference","oa_version":"Preprint","date_created":"2018-12-11T11:51:43Z","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF"},{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989"}],"status":"public","title":"Synthesizing multiple boolean functions using interpolation on a single proof","day":"11","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1308.4767"}],"publist_id":"5825","date_updated":"2021-01-12T06:50:19Z","publisher":"IEEE","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","date_published":"2013-12-11T00:00:00Z","acknowledgement":"This research was supported by the European Commission through project\r\nDIAMOND  (FP7-2009-IST-4-248613), and  QUAINT  (I774-N23),  ","conference":{"location":"Portland, OR, United States","start_date":"2013-10-20","end_date":"2013-10-23","name":"FMCAD: Formal Methods in Computer-Aided Design"},"ec_funded":1,"quality_controlled":"1","citation":{"ama":"Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. Synthesizing multiple boolean functions using interpolation on a single proof. In: <i>2013 Formal Methods in Computer-Aided Design</i>. IEEE; 2013:77-84. doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">10.1109/FMCAD.2013.6679394</a>","mla":"Hofferek, Georg, et al. “Synthesizing Multiple Boolean Functions Using Interpolation on a Single Proof.” <i>2013 Formal Methods in Computer-Aided Design</i>, IEEE, 2013, pp. 77–84, doi:<a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">10.1109/FMCAD.2013.6679394</a>.","ista":"Hofferek G, Gupta A, Könighofer B, Jiang J, Bloem R. 2013. Synthesizing multiple boolean functions using interpolation on a single proof. 2013 Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 77–84.","ieee":"G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, and R. Bloem, “Synthesizing multiple boolean functions using interpolation on a single proof,” in <i>2013 Formal Methods in Computer-Aided Design</i>, Portland, OR, United States, 2013, pp. 77–84.","short":"G. Hofferek, A. Gupta, B. Könighofer, J. Jiang, R. Bloem, in:, 2013 Formal Methods in Computer-Aided Design, IEEE, 2013, pp. 77–84.","chicago":"Hofferek, Georg, Ashutosh Gupta, Bettina Könighofer, Jie Jiang, and Roderick Bloem. “Synthesizing Multiple Boolean Functions Using Interpolation on a Single Proof.” In <i>2013 Formal Methods in Computer-Aided Design</i>, 77–84. IEEE, 2013. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">https://doi.org/10.1109/FMCAD.2013.6679394</a>.","apa":"Hofferek, G., Gupta, A., Könighofer, B., Jiang, J., &#38; Bloem, R. (2013). Synthesizing multiple boolean functions using interpolation on a single proof. In <i>2013 Formal Methods in Computer-Aided Design</i> (pp. 77–84). Portland, OR, United States: IEEE. <a href=\"https://doi.org/10.1109/FMCAD.2013.6679394\">https://doi.org/10.1109/FMCAD.2013.6679394</a>"},"doi":"10.1109/FMCAD.2013.6679394","arxiv":1,"language":[{"iso":"eng"}],"year":"2013","external_id":{"arxiv":["1308.4767"]},"page":"77 - 84","abstract":[{"text":"It is often difficult to correctly implement a Boolean controller for a complex system, especially when concurrency is involved. Yet, it may be easy to formally specify a controller. For instance, for a pipelined processor it suffices to state that the visible behavior of the pipelined system should be identical to a non-pipelined reference system (Burch-Dill paradigm). We present a novel procedure to efficiently synthesize multiple Boolean control signals from a specification given as a quantified first-order formula (with a specific quantifier structure). Our approach uses uninterpreted functions to abstract details of the design. We construct an unsatisfiable SMT formula from the given specification. Then, from just one proof of unsatisfiability, we use a variant of Craig interpolation to compute multiple coordinated interpolants that implement the Boolean control signals. Our method avoids iterative learning and back-substitution of the control functions. We applied our approach to synthesize a controller for a simple two-stage pipelined processor, and present first experimental results.","lang":"eng"}],"oa":1},{"file":[{"creator":"dernst","checksum":"98bc02e3793072e279ec8d364b381ff3","file_size":276982,"date_updated":"2020-07-14T12:44:48Z","access_level":"open_access","date_created":"2020-05-15T11:05:50Z","file_id":"7857","file_name":"2013_ICALP_Boker.pdf","relation":"main_file","content_type":"application/pdf"}],"abstract":[{"text":"Choices made by nondeterministic word automata depend on both the past (the prefix of the word read so far) and the future (the suffix yet to be read). In several applications, most notably synthesis, the future is diverse or unknown, leading to algorithms that are based on deterministic automata. Hoping to retain some of the advantages of nondeterministic automata, researchers have studied restricted classes of nondeterministic automata. Three such classes are nondeterministic automata that are good for trees (GFT; i.e., ones that can be expanded to tree automata accepting the derived tree languages, thus whose choices should satisfy diverse futures), good for games (GFG; i.e., ones whose choices depend only on the past), and determinizable by pruning (DBP; i.e., ones that embody equivalent deterministic automata). The theoretical properties and relative merits of the different classes are still open, having vagueness on whether they really differ from deterministic automata. In particular, while DBP ⊆ GFG ⊆ GFT, it is not known whether every GFT automaton is GFG and whether every GFG automaton is DBP. Also open is the possible succinctness of GFG and GFT automata compared to deterministic automata. We study these problems for ω-regular automata with all common acceptance conditions. We show that GFT=GFG⊃DBP, and describe a determinization construction for GFG automata.","lang":"eng"}],"ddc":["000"],"oa":1,"alternative_title":["LNCS"],"page":"89 - 100","intvolume":"      7966","has_accepted_license":"1","language":[{"iso":"eng"}],"year":"2013","acknowledgement":"and ERC Grant QUALITY.","conference":{"name":"ICALP: Automata, Languages and Programming","start_date":"2013-07-08","end_date":"2013-07-12","location":"Riga, Latvia"},"ec_funded":1,"quality_controlled":"1","doi":"10.1007/978-3-642-39212-2_11","citation":{"ama":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. Nondeterminism in the presence of a diverse or unknown future. 2013;7966(PART 2):89-100. doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">10.1007/978-3-642-39212-2_11</a>","mla":"Boker, Udi, et al. <i>Nondeterminism in the Presence of a Diverse or Unknown Future</i>. Vol. 7966, no. PART 2, Springer, 2013, pp. 89–100, doi:<a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">10.1007/978-3-642-39212-2_11</a>.","ista":"Boker U, Kuperberg D, Kupferman O, Skrzypczak M. 2013. Nondeterminism in the presence of a diverse or unknown future. 7966(PART 2), 89–100.","ieee":"U. Boker, D. Kuperberg, O. Kupferman, and M. Skrzypczak, “Nondeterminism in the presence of a diverse or unknown future,” vol. 7966, no. PART 2. Springer, pp. 89–100, 2013.","chicago":"Boker, Udi, Denis Kuperberg, Orna Kupferman, and Michał Skrzypczak. “Nondeterminism in the Presence of a Diverse or Unknown Future.” Lecture Notes in Computer Science. Springer, 2013. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">https://doi.org/10.1007/978-3-642-39212-2_11</a>.","short":"U. Boker, D. Kuperberg, O. Kupferman, M. Skrzypczak, 7966 (2013) 89–100.","apa":"Boker, U., Kuperberg, D., Kupferman, O., &#38; Skrzypczak, M. (2013). Nondeterminism in the presence of a diverse or unknown future. Presented at the ICALP: Automata, Languages and Programming, Riga, Latvia: Springer. <a href=\"https://doi.org/10.1007/978-3-642-39212-2_11\">https://doi.org/10.1007/978-3-642-39212-2_11</a>"},"publist_id":"5823","date_updated":"2020-08-11T10:09:09Z","publisher":"Springer","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2013-07-01T00:00:00Z","month":"07","scopus_import":1,"series_title":"Lecture Notes in Computer Science","status":"public","volume":7966,"title":"Nondeterminism in the presence of a diverse or unknown future","day":"01","department":[{"_id":"ToHe"}],"author":[{"full_name":"Boker, Udi","first_name":"Udi","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","last_name":"Boker"},{"last_name":"Kuperberg","first_name":"Denis","full_name":"Kuperberg, Denis"},{"first_name":"Orna","last_name":"Kupferman","full_name":"Kupferman, Orna"},{"last_name":"Skrzypczak","first_name":"Michał","full_name":"Skrzypczak, Michał"}],"file_date_updated":"2020-07-14T12:44:48Z","issue":"PART 2","_id":"1387","article_processing_charge":"No","type":"conference","oa_version":"Submitted Version","date_created":"2018-12-11T11:51:44Z","project":[{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"}]},{"_id":"1405","article_processing_charge":"No","type":"dissertation","file_date_updated":"2021-11-17T13:47:58Z","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"}],"date_created":"2018-12-11T11:51:50Z","oa_version":"Published Version","department":[{"_id":"ToHe"},{"_id":"GradSch"}],"author":[{"last_name":"Zufferey","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien","orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien"}],"day":"05","status":"public","title":"Analysis of dynamic message passing programs","main_file_link":[{"url":"http://dzufferey.github.io/files/2013_thesis.pdf"}],"month":"09","date_published":"2013-09-05T00:00:00Z","publisher":"Institute of Science and Technology Austria","publist_id":"5802","date_updated":"2023-09-07T11:36:37Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","citation":{"ama":"Zufferey D. Analysis of dynamic message passing programs. 2013. doi:<a href=\"https://doi.org/10.15479/at:ista:1405\">10.15479/at:ista:1405</a>","chicago":"Zufferey, Damien. “Analysis of Dynamic Message Passing Programs.” Institute of Science and Technology Austria, 2013. <a href=\"https://doi.org/10.15479/at:ista:1405\">https://doi.org/10.15479/at:ista:1405</a>.","short":"D. Zufferey, Analysis of Dynamic Message Passing Programs, Institute of Science and Technology Austria, 2013.","apa":"Zufferey, D. (2013). <i>Analysis of dynamic message passing programs</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:1405\">https://doi.org/10.15479/at:ista:1405</a>","mla":"Zufferey, Damien. <i>Analysis of Dynamic Message Passing Programs</i>. Institute of Science and Technology Austria, 2013, doi:<a href=\"https://doi.org/10.15479/at:ista:1405\">10.15479/at:ista:1405</a>.","ista":"Zufferey D. 2013. Analysis of dynamic message passing programs. Institute of Science and Technology Austria.","ieee":"D. Zufferey, “Analysis of dynamic message passing programs,” Institute of Science and Technology Austria, 2013."},"doi":"10.15479/at:ista:1405","ec_funded":1,"acknowledgement":"This work was supported in part by the Austrian Science Fund NFN RiSE (Rigorous Systems Engineering) and by the ERC Advanced Grant QUAREM (Quantitative Reactve Modeling).\r\nChapter 2, 3, and 4 are joint work with Thomas A. Henzinger and Thomas Wies. Chapter 2 was published in FoSSaCS 2010 as “Forward Analysis of Depth-Bounded Processes” [112]. Chapter 3 was published in VMCAI 2012 as “Ideal Abstractions for Well-Structured Transition Systems” [114]. Chap- ter 5.1 is joint work with Kshitij Bansal, Eric Koskinen, and Thomas Wies. It was published in TACAS 2013 as “Structural Counter Abstraction” [13]. The author’s contribution in this part is mostly related to the implementation. The theory required to understand the method and its implementation is quickly recalled to make the thesis self-contained, but should not be considered as a contribution. For the details of the methods, we refer the reader to the orig- inal publication [13] and the corresponding technical report [14]. Chapter 5.2 is ongoing work with Shahram Esmaeilsabzali, Rupak Majumdar, and Thomas Wies. I also would like to thank the people who supported over the past 4 years. My advisor Thomas A. Henzinger who gave me a lot of freedom to work on projects I was interested in. My collaborators, especially Thomas Wies with whom I worked since the beginning. The members of my thesis committee, Viktor Kun- cak and Rupak Majumdar, who also agreed to advise me. Simon Aeschbacher, Pavol Cerny, Cezara Dragoi, Arjun Radhakrishna, my family, friends and col- leagues who created an enjoyable environment. ","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"2847"},{"relation":"part_of_dissertation","id":"3251","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"4361"}]},"publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"year":"2013","has_accepted_license":"1","alternative_title":["ISTA Thesis"],"page":"134","supervisor":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"file":[{"date_updated":"2021-02-22T11:28:36Z","creator":"dernst","file_size":1514906,"checksum":"ed2d7b52933d134e8dc69d569baa284e","relation":"main_file","file_name":"2013_Zufferey_thesis_final.pdf","content_type":"application/pdf","success":1,"date_created":"2021-02-22T11:28:36Z","access_level":"open_access","file_id":"9176"},{"date_updated":"2021-11-17T13:47:58Z","creator":"cchlebak","checksum":"cecc4c4b14225bee973d32e3dba91a55","file_size":1378313,"file_name":"2013_Zufferey_thesis_final_pdfa.pdf","relation":"main_file","content_type":"application/pdf","date_created":"2021-11-16T14:42:52Z","access_level":"closed","file_id":"10298"}],"oa":1,"ddc":["000"],"degree_awarded":"PhD","abstract":[{"lang":"eng","text":"Motivated by the analysis of highly dynamic message-passing systems, i.e. unbounded thread creation, mobility, etc. we present a framework for the analysis of depth-bounded systems. Depth-bounded systems are one of the most expressive known fragment of the π-calculus for which interesting verification problems are still decidable. Even though they are infinite state systems depth-bounded systems are well-structured, thus can be analyzed algorithmically. We give an interpretation of depth-bounded systems as graph-rewriting systems. This gives more flexibility and ease of use to apply depth-bounded systems to other type of systems like shared memory concurrency.\r\n\r\nFirst, we develop an adequate domain of limits for depth-bounded systems, a prerequisite for the effective representation of downward-closed sets. Downward-closed sets are needed by forward saturation-based algorithms to represent potentially infinite sets of states. Then, we present an abstract interpretation framework to compute the covering set of well-structured transition systems. Because, in general, the covering set is not computable, our abstraction over-approximates the actual covering set. Our abstraction captures the essence of acceleration based-algorithms while giving up enough precision to ensure convergence. We have implemented the analysis in the PICASSO tool and show that it is accurate in practice. Finally, we build some further analyses like termination using the covering set as starting point."}]},{"alternative_title":["ISTA Thesis"],"page":"123","supervisor":[{"full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"abstract":[{"text":"Epithelial spreading is a critical part of various developmental and wound repair processes. Here we use zebrafish epiboly as a model system to study the cellular and molecular mechanisms underlying the spreading of epithelial sheets. During zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the embryo to eventually cover the entire yolk cell by the end of gastrulation. The EVL leading edge is anchored through tight junctions to the yolk syncytial layer (YSL), where directly adjacent to the EVL margin a contractile actomyosin ring is formed that is thought to drive EVL epiboly. The prevalent view in the field was that the contractile ring exerts a pulling force on the EVL margin, which pulls the EVL towards the vegetal pole. However, how this force is generated and how it affects EVL morphology still remains elusive. Moreover, the cellular mechanisms mediating the increase in EVL surface area, while maintaining tissue integrity and function are still unclear. Here we show that the YSL actomyosin ring pulls on the EVL margin by two distinct force-generating mechanisms. One mechanism is based on contraction of the ring around its circumference, as previously proposed. The second mechanism is based on actomyosin retrogade flows, generating force through resistance against the substrate. The latter can function at any epiboly stage even in situations where the contraction-based mechanism is unproductive. Additionally, we demonstrate that during epiboly the EVL is subjected to anisotropic tension, which guides the orientation of EVL cell division along the main axis (animal-vegetal) of tension. The influence of tension in cell division orientation involves cell elongation and requires myosin-2 activity for proper spindle alignment. Strikingly, we reveal that tension-oriented cell divisions release anisotropic tension within the EVL and that in the absence of such divisions, EVL cells undergo ectopic fusions. We conclude that forces applied to the EVL by the action of the YSL actomyosin ring generate a tension anisotropy in the EVL that orients cell divisions, which in turn limit tissue tension increase thereby facilitating tissue spreading.","lang":"eng"}],"degree_awarded":"PhD","date_published":"2013-10-01T00:00:00Z","month":"10","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","publisher":"Institute of Science and Technology Austria","publist_id":"5801","date_updated":"2023-09-07T11:36:07Z","citation":{"ama":"Campinho P. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. 2013.","short":"P. Campinho, Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading, Institute of Science and Technology Austria, 2013.","chicago":"Campinho, Pedro. “Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading.” Institute of Science and Technology Austria, 2013.","apa":"Campinho, P. (2013). <i>Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading</i>. Institute of Science and Technology Austria.","mla":"Campinho, Pedro. <i>Mechanics of Zebrafish Epiboly: Tension-Oriented Cell Divisions Limit Anisotropic Tissue Tension in Epithelial Spreading</i>. Institute of Science and Technology Austria, 2013.","ista":"Campinho P. 2013. Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading. Institute of Science and Technology Austria.","ieee":"P. Campinho, “Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading,” Institute of Science and Technology Austria, 2013."},"date_created":"2018-12-11T11:51:50Z","oa_version":"None","article_processing_charge":"No","_id":"1406","type":"dissertation","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"author":[{"last_name":"Campinho","first_name":"Pedro","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8526-5416","full_name":"Campinho, Pedro"}],"department":[{"_id":"CaHe"}],"year":"2013","day":"01","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"title":"Mechanics of zebrafish epiboly: Tension-oriented cell divisions limit anisotropic tissue tension in epithelial spreading","status":"public"},{"abstract":[{"lang":"eng","text":"We give a cohomological interpretation of both the Kac polynomial and the refined Donaldson-Thomas-invariants of quivers. This interpretation yields a proof of a conjecture of Kac from 1982 and gives a new perspective on recent work of Kontsevich-Soibelman. Thisis achieved by computing, via an arithmetic Fourier transform, the dimensions of the isotypical components of the cohomology of associated Nakajima quiver varieties under the action of a Weyl group. The generating function of the corresponding Poincare polynomials is an extension of Hua's formula for Kac polynomials of quivers involving Hall-Littlewood symmetric functions. The resulting formulae contain a wide range of information on the geometry of the quiver varieties."}],"oa":1,"month":"01","date_published":"2013-01-01T00:00:00Z","publication_status":"published","date_updated":"2021-01-12T06:50:47Z","publist_id":"5754","publisher":"Princeton University Press","main_file_link":[{"url":"http://arxiv.org/abs/1204.2375","open_access":"1"}],"page":"1147 - 1168","day":"01","year":"2013","title":"Positivity for Kac polynomials and DT-invariants of quivers","volume":177,"intvolume":"       177","status":"public","date_created":"2018-12-11T11:52:02Z","quality_controlled":0,"doi":"10.4007/annals.2013.177.3.8","citation":{"ama":"Hausel T, Letellier E, Rodríguez Villegas F. Positivity for Kac polynomials and DT-invariants of quivers. <i>Annals of Mathematics</i>. 2013;177(3):1147-1168. doi:<a href=\"https://doi.org/10.4007/annals.2013.177.3.8\">10.4007/annals.2013.177.3.8</a>","apa":"Hausel, T., Letellier, E., &#38; Rodríguez Villegas, F. (2013). Positivity for Kac polynomials and DT-invariants of quivers. <i>Annals of Mathematics</i>. Princeton University Press. <a href=\"https://doi.org/10.4007/annals.2013.177.3.8\">https://doi.org/10.4007/annals.2013.177.3.8</a>","chicago":"Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Positivity for Kac Polynomials and DT-Invariants of Quivers.” <i>Annals of Mathematics</i>. Princeton University Press, 2013. <a href=\"https://doi.org/10.4007/annals.2013.177.3.8\">https://doi.org/10.4007/annals.2013.177.3.8</a>.","short":"T. Hausel, E. Letellier, F. Rodríguez Villegas, Annals of Mathematics 177 (2013) 1147–1168.","ista":"Hausel T, Letellier E, Rodríguez Villegas F. 2013. Positivity for Kac polynomials and DT-invariants of quivers. Annals of Mathematics. 177(3), 1147–1168.","ieee":"T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Positivity for Kac polynomials and DT-invariants of quivers,” <i>Annals of Mathematics</i>, vol. 177, no. 3. Princeton University Press, pp. 1147–1168, 2013.","mla":"Hausel, Tamás, et al. “Positivity for Kac Polynomials and DT-Invariants of Quivers.” <i>Annals of Mathematics</i>, vol. 177, no. 3, Princeton University Press, 2013, pp. 1147–68, doi:<a href=\"https://doi.org/10.4007/annals.2013.177.3.8\">10.4007/annals.2013.177.3.8</a>."},"publication":"Annals of Mathematics","extern":1,"type":"journal_article","_id":"1442","issue":"3","author":[{"last_name":"Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamas","full_name":"Tamas Hausel"},{"full_name":"Letellier, Emmanuel","last_name":"Letellier","first_name":"Emmanuel"},{"first_name":"Fernando","last_name":"Rodríguez Villegas","full_name":"Rodríguez Villegas, Fernando"}],"acknowledgement":"The first author thanks the Royal Society for funding his research 2005-2012 in the form of a Royal Society University Research Fellowship as well as the Mathematical Institute and Wadham College in Oxford for a very productive environment. The second author is supported by Agence Nationale de la Recherche grant\nANR-09-JCJC-0102-01. The third author is supported by the NSF grant DMS-1101484 and a Research Scholarship from the Clay Mathematical Institute."},{"publication_status":"published","publisher":"International Press","date_updated":"2021-01-12T06:50:47Z","publist_id":"5753","oa":1,"abstract":[{"lang":"eng","text":"Here we survey several results and conjectures on the cohomology of the total space of the Hitchin system: the moduli space of semi-stable rank n and degree d Higgs bundles on a complex algebraic curve C. The picture emerging is a dynamic mixture of ideas originating in theoretical physics such as gauge theory and mirror symmetry, Weil conjectures in arithmetic algebraic geometry, representation theory of finite groups of Lie type and Langlands duality in number theory."}],"month":"03","date_published":"2013-03-15T00:00:00Z","alternative_title":["Advanced Lectures in Mathematics"],"page":"29 - 70","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1102.1717"}],"title":"Global topology of the Hitchin system","volume":25,"intvolume":"        25","status":"public","year":"2013","day":"15","author":[{"full_name":"Tamas Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamas","last_name":"Hausel"}],"citation":{"apa":"Hausel, T. (2013). Global topology of the Hitchin system. In <i>Handbook of Moduli: Volume II</i> (Vol. 25, pp. 29–70). International Press.","short":"T. Hausel, in:, Handbook of Moduli: Volume II, International Press, 2013, pp. 29–70.","chicago":"Hausel, Tamás. “Global Topology of the Hitchin System.” In <i>Handbook of Moduli: Volume II</i>, 25:29–70. International Press, 2013.","ieee":"T. Hausel, “Global topology of the Hitchin system,” in <i>Handbook of Moduli: Volume II</i>, vol. 25, International Press, 2013, pp. 29–70.","ista":"Hausel T. 2013.Global topology of the Hitchin system. In: Handbook of Moduli: Volume II. Advanced Lectures in Mathematics, vol. 25, 29–70.","mla":"Hausel, Tamás. “Global Topology of the Hitchin System.” <i>Handbook of Moduli: Volume II</i>, vol. 25, International Press, 2013, pp. 29–70.","ama":"Hausel T. Global topology of the Hitchin system. In: <i>Handbook of Moduli: Volume II</i>. Vol 25. International Press; 2013:29-70."},"date_created":"2018-12-11T11:52:03Z","quality_controlled":0,"type":"book_chapter","_id":"1443","extern":1,"publication":"Handbook of Moduli: Volume II"},{"title":"Arithmetic harmonic analysis on character and quiver varieties II","volume":234,"status":"public","intvolume":"       234","day":"15","year":"2013","author":[{"full_name":"Tamas Hausel","last_name":"Hausel","first_name":"Tamas","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Letellier, Emmanuel","last_name":"Letellier","first_name":"Emmanuel"},{"full_name":"Rodríguez Villegas, Fernando","last_name":"Rodríguez Villegas","first_name":"Fernando"}],"acknowledgement":"During the preparation of this paper TH was supported by a Royal Society University Research Fellowship at the University of Oxford. EL was supported by ANR-09-JCJC-0102-01. FRV was supported by NSF grant DMS-0200605, an FRA from the University of Texas at Austin, EPSRC grant EP/G027110/1, Visiting Fellowships at All Souls and Wadham Colleges in Oxford and a Research Scholarship from the Clay Mathematical Institute.","date_created":"2018-12-11T11:52:12Z","quality_controlled":0,"citation":{"ama":"Hausel T, Letellier E, Rodríguez Villegas F. Arithmetic harmonic analysis on character and quiver varieties II. <i>Advances in Mathematics</i>. 2013;234:85-128. doi:<a href=\"https://doi.org/10.1016/j.aim.2012.10.009\">10.1016/j.aim.2012.10.009</a>","apa":"Hausel, T., Letellier, E., &#38; Rodríguez Villegas, F. (2013). Arithmetic harmonic analysis on character and quiver varieties II. <i>Advances in Mathematics</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.aim.2012.10.009\">https://doi.org/10.1016/j.aim.2012.10.009</a>","short":"T. Hausel, E. Letellier, F. Rodríguez Villegas, Advances in Mathematics 234 (2013) 85–128.","chicago":"Hausel, Tamás, Emmanuel Letellier, and Fernando Rodríguez Villegas. “Arithmetic Harmonic Analysis on Character and Quiver Varieties II.” <i>Advances in Mathematics</i>. Academic Press, 2013. <a href=\"https://doi.org/10.1016/j.aim.2012.10.009\">https://doi.org/10.1016/j.aim.2012.10.009</a>.","ista":"Hausel T, Letellier E, Rodríguez Villegas F. 2013. Arithmetic harmonic analysis on character and quiver varieties II. Advances in Mathematics. 234, 85–128.","ieee":"T. Hausel, E. Letellier, and F. Rodríguez Villegas, “Arithmetic harmonic analysis on character and quiver varieties II,” <i>Advances in Mathematics</i>, vol. 234. Academic Press, pp. 85–128, 2013.","mla":"Hausel, Tamás, et al. “Arithmetic Harmonic Analysis on Character and Quiver Varieties II.” <i>Advances in Mathematics</i>, vol. 234, Academic Press, 2013, pp. 85–128, doi:<a href=\"https://doi.org/10.1016/j.aim.2012.10.009\">10.1016/j.aim.2012.10.009</a>."},"doi":"10.1016/j.aim.2012.10.009","publication":"Advances in Mathematics","extern":1,"_id":"1469","type":"journal_article","publication_status":"published","publist_id":"5724","date_updated":"2021-01-12T06:50:57Z","publisher":"Academic Press","abstract":[{"text":"We study connections between the topology of generic character varieties of fundamental groups of punctured Riemann surfaces, Macdonald polynomials, quiver representations, Hilbert schemes on Cx × Cx, modular forms and multiplicities in tensor products of irreducible characters of finite general linear groups.","lang":"eng"}],"date_published":"2013-02-15T00:00:00Z","month":"02","page":"85 - 128"},{"acknowledgement":"Mark Andrea A. de Cataldo was partially supported by N.S.A. and N.S.F. Tamás Hausel was supported by a Royal Society University Research Fellowship. Luca Migliorini was partially supported by PRIN 2007 project \"Spazi di moduli e teoria di Lie\"","author":[{"full_name":"De Cataldo, Mark A","first_name":"Mark","last_name":"De Cataldo"},{"last_name":"Hausel","id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","first_name":"Tamas","full_name":"Tamas Hausel"},{"first_name":"Luca","last_name":"Migliorini","full_name":"Migliorini, Luca"}],"publication":"Journal of Singularities","extern":1,"_id":"1470","type":"journal_article","quality_controlled":0,"date_created":"2018-12-11T11:52:12Z","citation":{"short":"M. De Cataldo, T. Hausel, L. Migliorini, Journal of Singularities 7 (2013) 23–38.","chicago":"De Cataldo, Mark, Tamás Hausel, and Luca Migliorini. “Exchange between Perverse and Weight Filtration for the Hilbert Schemes of Points of Two Surfaces.” <i>Journal of Singularities</i>. Worldwide Center of Mathematics, 2013. <a href=\"https://doi.org/10.5427/jsing.2013.7c\">https://doi.org/10.5427/jsing.2013.7c</a>.","apa":"De Cataldo, M., Hausel, T., &#38; Migliorini, L. (2013). Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces. <i>Journal of Singularities</i>. Worldwide Center of Mathematics. <a href=\"https://doi.org/10.5427/jsing.2013.7c\">https://doi.org/10.5427/jsing.2013.7c</a>","mla":"De Cataldo, Mark, et al. “Exchange between Perverse and Weight Filtration for the Hilbert Schemes of Points of Two Surfaces.” <i>Journal of Singularities</i>, vol. 7, Worldwide Center of Mathematics, 2013, pp. 23–38, doi:<a href=\"https://doi.org/10.5427/jsing.2013.7c\">10.5427/jsing.2013.7c</a>.","ieee":"M. De Cataldo, T. Hausel, and L. Migliorini, “Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces,” <i>Journal of Singularities</i>, vol. 7. Worldwide Center of Mathematics, pp. 23–38, 2013.","ista":"De Cataldo M, Hausel T, Migliorini L. 2013. Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces. Journal of Singularities. 7, 23–38.","ama":"De Cataldo M, Hausel T, Migliorini L. Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces. <i>Journal of Singularities</i>. 2013;7:23-38. doi:<a href=\"https://doi.org/10.5427/jsing.2013.7c\">10.5427/jsing.2013.7c</a>"},"doi":"10.5427/jsing.2013.7c","status":"public","intvolume":"         7","volume":7,"title":"Exchange between perverse and weight filtration for the Hilbert schemes of points of two surfaces","day":"01","year":"2013","page":"23 - 38","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1012.2583"}],"date_updated":"2021-01-12T06:50:58Z","publist_id":"5725","publisher":"Worldwide Center of Mathematics","publication_status":"published","date_published":"2013-01-01T00:00:00Z","month":"01","abstract":[{"text":"We show that a natural isomorphism between the rational cohomology groups of the two zero-dimensional Hilbert schemes of n-points of two surfaces, the affine plane minus the axes and the cotangent bundle of an elliptic curve, exchanges the weight filtration on the first set of cohomology groups with the perverse Leray filtration associated with a natural fibration on the second set of cohomology groups. We discuss some associated hard Lefschetz phenomena.","lang":"eng"}],"oa":1},{"oa_version":"Published Version","pubrep_id":"104","date_created":"2018-12-12T11:39:07Z","citation":{"ama":"Reiter J, Bozic I, Chatterjee K, Nowak M. <i>TTP: Tool for Tumor Progression</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-104-v1-1\">10.15479/AT:IST-2013-104-v1-1</a>","ista":"Reiter J, Bozic I, Chatterjee K, Nowak M. 2013. TTP: Tool for Tumor Progression, IST Austria, 17p.","ieee":"J. Reiter, I. Bozic, K. Chatterjee, and M. Nowak, <i>TTP: Tool for Tumor Progression</i>. IST Austria, 2013.","mla":"Reiter, Johannes, et al. <i>TTP: Tool for Tumor Progression</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-104-v1-1\">10.15479/AT:IST-2013-104-v1-1</a>.","apa":"Reiter, J., Bozic, I., Chatterjee, K., &#38; Nowak, M. (2013). <i>TTP: Tool for Tumor Progression</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-104-v1-1\">https://doi.org/10.15479/AT:IST-2013-104-v1-1</a>","short":"J. Reiter, I. Bozic, K. Chatterjee, M. Nowak, TTP: Tool for Tumor Progression, IST Austria, 2013.","chicago":"Reiter, Johannes, Ivana Bozic, Krishnendu Chatterjee, and Martin Nowak. <i>TTP: Tool for Tumor Progression</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-104-v1-1\">https://doi.org/10.15479/AT:IST-2013-104-v1-1</a>."},"doi":"10.15479/AT:IST-2013-104-v1-1","file_date_updated":"2020-07-14T12:46:44Z","_id":"5399","type":"technical_report","author":[{"full_name":"Reiter, Johannes","orcid":"0000-0002-0170-7353","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","last_name":"Reiter"},{"full_name":"Bozic, Ivana","last_name":"Bozic","first_name":"Ivana"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"related_material":{"record":[{"id":"2000","status":"public","relation":"later_version"}]},"department":[{"_id":"KrCh"}],"day":"11","year":"2013","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"title":"TTP: Tool for Tumor Progression","has_accepted_license":"1","status":"public","page":"17","alternative_title":["IST Austria Technical Report"],"abstract":[{"lang":"eng","text":"In this work we present a flexible tool for tumor progression, which simulates the evolutionary dynamics of cancer. Tumor progression implements a multi-type branching process where the key parameters are the fitness landscape, the mutation rate, and the average time of cell division. The fitness of a cancer cell depends on the mutations it has accumulated. The input to our tool could be any fitness landscape, mutation rate, and cell division time, and the tool produces the growth dynamics and all relevant statistics."}],"oa":1,"ddc":["000"],"file":[{"file_id":"5542","date_created":"2018-12-12T11:54:20Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"IST-2013-104-v1+1_tumortool.pdf","file_size":1471954,"checksum":"2cc8c6e157eca1271128db80bb3dec80","creator":"system","date_updated":"2020-07-14T12:46:44Z"}],"date_published":"2013-01-11T00:00:00Z","month":"01","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T10:23:57Z","publisher":"IST Austria"},{"file":[{"creator":"system","checksum":"cbba40210788a1b22c6cf06433b5ed6f","file_size":483407,"date_updated":"2020-07-14T12:46:44Z","access_level":"open_access","date_created":"2018-12-12T11:53:06Z","file_id":"5467","file_name":"IST-2013-109-v1+1_What_is_Decidable_about_Partially_Observable_Markov_Decision_Processes_with_ω-Regular_Objectives.pdf","relation":"main_file","content_type":"application/pdf"}],"month":"02","date_published":"2013-02-20T00:00:00Z","abstract":[{"lang":"eng","text":"We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages extends regular languages to infinite strings and provides a robust specification language to express all properties used in verification, and parity objectives are canonical forms to express ω-regular conditions. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satis- fied with probability 1 (resp. positive probability). While the qualitative analysis problems are known to be undecidable even for very special cases of parity objectives, we establish decidability (with optimal complexity) of the qualitative analysis problems for POMDPs with all parity objectives under finite- memory strategies. We establish asymptotically optimal (exponential) memory bounds and EXPTIME- completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives."}],"oa":1,"ddc":["000","005"],"date_updated":"2023-02-23T10:36:45Z","publisher":"IST Austria","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"41","alternative_title":["IST Austria Technical Report"],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"day":"20","year":"2013","status":"public","title":"What is decidable about partially observable Markov decision processes with ω-regular objectives","has_accepted_license":"1","file_date_updated":"2020-07-14T12:46:44Z","type":"technical_report","_id":"5400","date_created":"2018-12-12T11:39:07Z","oa_version":"Published Version","pubrep_id":"109","doi":"10.15479/AT:IST-2013-109-v1-1","citation":{"ama":"Chatterjee K, Chmelik M, Tracol M. <i>What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives</i>. IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-109-v1-1\">10.15479/AT:IST-2013-109-v1-1</a>","ista":"Chatterjee K, Chmelik M, Tracol M. 2013. What is decidable about partially observable Markov decision processes with ω-regular objectives, IST Austria, 41p.","ieee":"K. Chatterjee, M. Chmelik, and M. Tracol, <i>What is decidable about partially observable Markov decision processes with ω-regular objectives</i>. IST Austria, 2013.","mla":"Chatterjee, Krishnendu, et al. <i>What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives</i>. IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-109-v1-1\">10.15479/AT:IST-2013-109-v1-1</a>.","apa":"Chatterjee, K., Chmelik, M., &#38; Tracol, M. (2013). <i>What is decidable about partially observable Markov decision processes with ω-regular objectives</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-109-v1-1\">https://doi.org/10.15479/AT:IST-2013-109-v1-1</a>","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. <i>What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives</i>. IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-109-v1-1\">https://doi.org/10.15479/AT:IST-2013-109-v1-1</a>.","short":"K. Chatterjee, M. Chmelik, M. Tracol, What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives, IST Austria, 2013."},"department":[{"_id":"KrCh"}],"author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Chmelik","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin"},{"last_name":"Tracol","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","first_name":"Mathieu","full_name":"Tracol, Mathieu"}],"related_material":{"record":[{"id":"1477","status":"public","relation":"later_version"},{"relation":"later_version","id":"2295","status":"public"}]}},{"language":[{"iso":"eng"}],"day":"20","year":"2013","status":"public","title":"Initiatives and projects related to RD","has_accepted_license":"1","_id":"5401","type":"report","file_date_updated":"2020-07-14T12:46:45Z","citation":{"ama":"Porsche J. <i>Initiatives and Projects Related to RD</i>. IST Austria; 2013.","short":"J. Porsche, Initiatives and Projects Related to RD, IST Austria, 2013.","chicago":"Porsche, Jana. <i>Initiatives and Projects Related to RD</i>. IST Austria, 2013.","apa":"Porsche, J. (2013). <i>Initiatives and projects related to RD</i>. IST Austria.","mla":"Porsche, Jana. <i>Initiatives and Projects Related to RD</i>. IST Austria, 2013.","ista":"Porsche J. 2013. Initiatives and projects related to RD, IST Austria,p.","ieee":"J. Porsche, <i>Initiatives and projects related to RD</i>. IST Austria, 2013."},"date_created":"2018-12-12T11:39:07Z","pubrep_id":"113","oa_version":"Published Version","department":[{"_id":"E-Lib"}],"author":[{"full_name":"Porsche, Jana","last_name":"Porsche","first_name":"Jana","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2013-03-20T00:00:00Z","month":"03","file":[{"date_updated":"2020-07-14T12:46:45Z","file_size":151208,"checksum":"d68712db838432ecdacf9ffb1de8f8a6","creator":"system","content_type":"application/pdf","file_name":"IST-2013-113-v1+1_Initiatives_and_projects_related_to_RD.pdf","relation":"main_file","file_id":"5536","date_created":"2018-12-12T11:54:14Z","access_level":"open_access"}],"oa":1,"ddc":["020"],"abstract":[{"lang":"eng","text":"This document is created as a part of the project “Repository for Research Data at IST Austria”. It summarises the actual initiatives, projects and standards related to the project. It supports the preparation of standards and specifications for the project, which should be considered and followed to ensure interoperability and visibility of the uploaded data."}],"publisher":"IST Austria","date_updated":"2020-07-14T23:04:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published"},{"alternative_title":["IST Austria Technical Report"],"page":"16","date_published":"2013-06-12T00:00:00Z","month":"06","file":[{"relation":"main_file","file_name":"IST-2013-123-v1+1_main-concur2013.pdf","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T11:53:19Z","file_id":"5480","date_updated":"2020-07-14T12:46:45Z","creator":"system","file_size":249790,"checksum":"ce580605ae9756a8c99d7b403ebb8eed"}],"ddc":["000","004"],"oa":1,"abstract":[{"text":"Linearizability requires that the outcome of calls by competing threads to a concurrent data structure is the same as some sequential execution where each thread has exclusive access to the data structure. In an ordered data structure, such as a queue or a stack, linearizability is ensured by requiring threads commit in the order dictated by the sequential semantics of the data structure; e.g., in a concurrent queue implementation a dequeue can only remove the oldest element. \r\nIn this paper, we investigate the impact of this strict ordering, by comparing what linearizability allows to what existing implementations do. We first give an operational definition for linearizability which allows us to build the most general linearizable implementation as a transition system for any given sequential specification. We then use this operational definition to categorize linearizable implementations based on whether they are bound or free. In a bound implementation, whenever all threads observe the same logical state, the updates to the logical state and the temporal order of commits coincide. All existing queue implementations we know of are bound. We then proceed to present, to the best of our knowledge, the first ever free queue implementation. Our experiments show that free implementations have the potential for better performance by suffering less from contention.","lang":"eng"}],"publisher":"IST Austria","date_updated":"2020-07-14T23:04:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","type":"technical_report","_id":"5402","file_date_updated":"2020-07-14T12:46:45Z","citation":{"apa":"Henzinger, T. A., &#38; Sezgin, A. (2013). <i>How free is your linearizable concurrent data structure?</i> IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">https://doi.org/10.15479/AT:IST-2013-123-v1-1</a>","chicago":"Henzinger, Thomas A, and Ali Sezgin. <i>How Free Is Your Linearizable Concurrent Data Structure?</i> IST Austria, 2013. <a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">https://doi.org/10.15479/AT:IST-2013-123-v1-1</a>.","short":"T.A. Henzinger, A. Sezgin, How Free Is Your Linearizable Concurrent Data Structure?, IST Austria, 2013.","ieee":"T. A. Henzinger and A. Sezgin, <i>How free is your linearizable concurrent data structure?</i> IST Austria, 2013.","ista":"Henzinger TA, Sezgin A. 2013. How free is your linearizable concurrent data structure?, IST Austria, 16p.","mla":"Henzinger, Thomas A., and Ali Sezgin. <i>How Free Is Your Linearizable Concurrent Data Structure?</i> IST Austria, 2013, doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">10.15479/AT:IST-2013-123-v1-1</a>.","ama":"Henzinger TA, Sezgin A. <i>How Free Is Your Linearizable Concurrent Data Structure?</i> IST Austria; 2013. doi:<a href=\"https://doi.org/10.15479/AT:IST-2013-123-v1-1\">10.15479/AT:IST-2013-123-v1-1</a>"},"doi":"10.15479/AT:IST-2013-123-v1-1","date_created":"2018-12-12T11:39:07Z","pubrep_id":"123","oa_version":"Published Version","department":[{"_id":"ToHe"}],"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Sezgin, Ali","first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87","last_name":"Sezgin"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"year":"2013","day":"12","status":"public","has_accepted_license":"1","title":"How free is your linearizable concurrent data structure?"}]