[{"type":"journal_article","ddc":["570","576"],"pubrep_id":"767","intvolume":"       129","month":"01","ec_funded":1,"page":"367 - 379","issue":"2","citation":{"ista":"Toshima J, Horikomi C, Okada A, Hatori M, Nagano M, Masuda A, Yamamoto W, Siekhaus DE, Toshima J. 2016. Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. Journal of Cell Science. 129(2), 367–379.","ieee":"J. Toshima <i>et al.</i>, “Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis,” <i>Journal of Cell Science</i>, vol. 129, no. 2. Company of Biologists, pp. 367–379, 2016.","short":"J. Toshima, C. Horikomi, A. Okada, M. Hatori, M. Nagano, A. Masuda, W. Yamamoto, D.E. Siekhaus, J. Toshima, Journal of Cell Science 129 (2016) 367–379.","mla":"Toshima, Junko, et al. “Srv2/CAP Is Required for Polarized Actin Cable Assembly and Patch Internalization during Clathrin-Mediated Endocytosis.” <i>Journal of Cell Science</i>, vol. 129, no. 2, Company of Biologists, 2016, pp. 367–79, doi:<a href=\"https://doi.org/10.1242/jcs.176651\">10.1242/jcs.176651</a>.","ama":"Toshima J, Horikomi C, Okada A, et al. Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. <i>Journal of Cell Science</i>. 2016;129(2):367-379. doi:<a href=\"https://doi.org/10.1242/jcs.176651\">10.1242/jcs.176651</a>","chicago":"Toshima, Junko, Chika Horikomi, Asuka Okada, Makiko Hatori, Makoto Nagano, Atsushi Masuda, Wataru Yamamoto, Daria E Siekhaus, and Jiro Toshima. “Srv2/CAP Is Required for Polarized Actin Cable Assembly and Patch Internalization during Clathrin-Mediated Endocytosis.” <i>Journal of Cell Science</i>. Company of Biologists, 2016. <a href=\"https://doi.org/10.1242/jcs.176651\">https://doi.org/10.1242/jcs.176651</a>.","apa":"Toshima, J., Horikomi, C., Okada, A., Hatori, M., Nagano, M., Masuda, A., … Toshima, J. (2016). Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.176651\">https://doi.org/10.1242/jcs.176651</a>"},"quality_controlled":"1","publication_status":"published","abstract":[{"lang":"eng","text":"The dynamic assembly and disassembly of actin filaments is essential for the formation and transport of vesicles during endocytosis. In yeast, two types of actin structures, namely cortical patches and cytoplasmic cables, play a direct role in endocytosis, but how their interaction is regulated remains unclear. Here, we show that Srv2/CAP, an evolutionarily conserved actin regulator, is required for efficient endocytosis owing to its role in the formation of the actin patches that aid initial vesicle invagination and of the actin cables that these move along. Deletion of the SRV2 gene resulted in the appearance of aberrant fragmented actin cables that frequently moved past actin patches, the sites of endocytosis. We find that the C-terminal CARP domain of Srv2p is vitally important for the proper assembly of actin patches and cables; we also demonstrate that the N-terminal helical folded domain of Srv2 is required for its localization to actin patches, specifically to the ADP-actin rich region through an interaction with cofilin. These results demonstrate the in vivo roles of Srv2p in the regulation of the actin cytoskeleton during clathrin-mediated endocytosis"}],"language":[{"iso":"eng"}],"publist_id":"5720","department":[{"_id":"DaSi"}],"publisher":"Company of Biologists","file":[{"file_name":"IST-2017-767-v1+1_367.full.pdf","date_updated":"2020-07-14T12:44:56Z","file_size":7176912,"date_created":"2018-12-12T10:11:08Z","relation":"main_file","file_id":"4861","creator":"system","access_level":"open_access","checksum":"2da0a09149a9ed956cdf79a95c17f08a","content_type":"application/pdf"}],"file_date_updated":"2020-07-14T12:44:56Z","scopus_import":1,"publication":"Journal of Cell Science","title":"Srv2/CAP is required for polarized actin cable assembly and patch internalization during clathrin-mediated endocytosis","_id":"1476","date_updated":"2021-01-12T06:51:00Z","project":[{"grant_number":"334077","call_identifier":"FP7","name":"Investigating the role of transporters in invasive migration through junctions","_id":"2536F660-B435-11E9-9278-68D0E5697425"}],"year":"2016","acknowledgement":"We are grateful to Anthony Bretscher (Cornell University, NY) for providing the bni1-12 bnr1Δ (Y4135) strain. J.Y.T. was supported by a Japan Society for the Promotion of Science (JSPS) KAKENHI grant [grant number 26440067]; the Takeda Science Foundation; and the Novartis Foundation (Japan). J.T. was supported by a JSPS KAKENHI grant [grant number 25440054]; the Takeda Science Foundation; and the Kurata Memorial Hitachi Science and Technology Foundation. D.E.S. was supported by the European Union [grant number PCIG12-GA-2012-334077].","has_accepted_license":"1","oa":1,"oa_version":"Published Version","status":"public","author":[{"full_name":"Toshima, Junko","first_name":"Junko","last_name":"Toshima"},{"last_name":"Horikomi","full_name":"Horikomi, Chika","first_name":"Chika"},{"last_name":"Okada","first_name":"Asuka","full_name":"Okada, Asuka"},{"last_name":"Hatori","full_name":"Hatori, Makiko","first_name":"Makiko"},{"last_name":"Nagano","full_name":"Nagano, Makoto","first_name":"Makoto"},{"last_name":"Masuda","full_name":"Masuda, Atsushi","first_name":"Atsushi"},{"first_name":"Wataru","full_name":"Yamamoto, Wataru","last_name":"Yamamoto"},{"last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","first_name":"Daria E"},{"full_name":"Toshima, Jiro","first_name":"Jiro","last_name":"Toshima"}],"doi":"10.1242/jcs.176651","volume":129,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:52:14Z","day":"15","date_published":"2016-01-15T00:00:00Z"},{"issue":"5","ec_funded":1,"page":"878 - 911","month":"08","intvolume":"        82","type":"journal_article","arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/1309.2802","open_access":"1"}],"scopus_import":1,"publication":"Journal of Computer and System Sciences","publisher":"Elsevier","publist_id":"5718","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"abstract":[{"text":"We consider partially observable Markov decision processes (POMDPs) with ω-regular conditions specified as parity objectives. The class of ω-regular languages provides a robust specification language to express properties in verification, and parity objectives are canonical forms to express them. The qualitative analysis problem given a POMDP and a parity objective asks whether there is a strategy to ensure that the objective is satisfied with probability 1 (resp. positive probability). While the qualitative analysis problems are undecidable even for special cases of parity objectives, we establish decidability (with optimal complexity) for POMDPs with all parity objectives under finite-memory strategies. We establish optimal (exponential) memory bounds and EXPTIME-completeness of the qualitative analysis problems under finite-memory strategies for POMDPs with parity objectives. We also present a practical approach, where we design heuristics to deal with the exponential complexity, and have applied our implementation on a number of POMDP examples.","lang":"eng"}],"publication_status":"published","citation":{"ama":"Chatterjee K, Chmelik M, Tracol M. What is decidable about partially observable Markov decision processes with ω-regular objectives. <i>Journal of Computer and System Sciences</i>. 2016;82(5):878-911. doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">10.1016/j.jcss.2016.02.009</a>","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Mathieu Tracol. “What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives.” <i>Journal of Computer and System Sciences</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">https://doi.org/10.1016/j.jcss.2016.02.009</a>.","apa":"Chatterjee, K., Chmelik, M., &#38; Tracol, M. (2016). What is decidable about partially observable Markov decision processes with ω-regular objectives. <i>Journal of Computer and System Sciences</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">https://doi.org/10.1016/j.jcss.2016.02.009</a>","ieee":"K. Chatterjee, M. Chmelik, and M. Tracol, “What is decidable about partially observable Markov decision processes with ω-regular objectives,” <i>Journal of Computer and System Sciences</i>, vol. 82, no. 5. Elsevier, pp. 878–911, 2016.","ista":"Chatterjee K, Chmelik M, Tracol M. 2016. What is decidable about partially observable Markov decision processes with ω-regular objectives. Journal of Computer and System Sciences. 82(5), 878–911.","mla":"Chatterjee, Krishnendu, et al. “What Is Decidable about Partially Observable Markov Decision Processes with ω-Regular Objectives.” <i>Journal of Computer and System Sciences</i>, vol. 82, no. 5, Elsevier, 2016, pp. 878–911, doi:<a href=\"https://doi.org/10.1016/j.jcss.2016.02.009\">10.1016/j.jcss.2016.02.009</a>.","short":"K. Chatterjee, M. Chmelik, M. Tracol, Journal of Computer and System Sciences 82 (2016) 878–911."},"quality_controlled":"1","oa":1,"project":[{"grant_number":"P 23499-N23","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"year":"2016","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"2295"},{"relation":"earlier_version","status":"public","id":"5400"}]},"_id":"1477","date_updated":"2023-02-23T12:24:38Z","title":"What is decidable about partially observable Markov decision processes with ω-regular objectives","date_published":"2016-08-01T00:00:00Z","day":"01","external_id":{"arxiv":["1309.2802"]},"volume":82,"date_created":"2018-12-11T11:52:15Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.jcss.2016.02.009","status":"public","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"full_name":"Chmelik, Martin","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik"},{"last_name":"Tracol","id":"3F54FA38-F248-11E8-B48F-1D18A9856A87","full_name":"Tracol, Mathieu","first_name":"Mathieu"}],"oa_version":"Preprint"},{"publisher":"IOP Publishing Ltd.","file_date_updated":"2020-07-14T12:44:56Z","scopus_import":1,"publication":"New Journal of Physics","file":[{"relation":"main_file","file_size":965607,"date_created":"2018-12-12T10:17:22Z","date_updated":"2020-07-14T12:44:56Z","file_name":"IST-2016-579-v1+1_njp_18_3_035002.pdf","content_type":"application/pdf","checksum":"4f959eabc19d2a2f518318a450a4d424","access_level":"open_access","creator":"system","file_id":"5276"}],"abstract":[{"text":"We consider the Tonks-Girardeau gas subject to a random external potential. If the disorder is such that the underlying one-particle Hamiltonian displays localization (which is known to be generically the case), we show that there is exponential decay of correlations in the many-body eigenstates. Moreover, there is no Bose-Einstein condensation and no superfluidity, even at zero temperature.","lang":"eng"}],"department":[{"_id":"RoSe"}],"publist_id":"5716","language":[{"iso":"eng"}],"publication_status":"published","quality_controlled":"1","citation":{"ama":"Seiringer R, Warzel S. Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. <i>New Journal of Physics</i>. 2016;18(3). doi:<a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">10.1088/1367-2630/18/3/035002</a>","chicago":"Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence of Superfluidity in the Disordered Tonks-Girardeau Gas.” <i>New Journal of Physics</i>. IOP Publishing Ltd., 2016. <a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">https://doi.org/10.1088/1367-2630/18/3/035002</a>.","apa":"Seiringer, R., &#38; Warzel, S. (2016). Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. <i>New Journal of Physics</i>. IOP Publishing Ltd. <a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">https://doi.org/10.1088/1367-2630/18/3/035002</a>","ieee":"R. Seiringer and S. Warzel, “Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas,” <i>New Journal of Physics</i>, vol. 18, no. 3. IOP Publishing Ltd., 2016.","ista":"Seiringer R, Warzel S. 2016. Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas. New Journal of Physics. 18(3), 035002.","short":"R. Seiringer, S. Warzel, New Journal of Physics 18 (2016).","mla":"Seiringer, Robert, and Simone Warzel. “Decay of Correlations and Absence of Superfluidity in the Disordered Tonks-Girardeau Gas.” <i>New Journal of Physics</i>, vol. 18, no. 3, 035002, IOP Publishing Ltd., 2016, doi:<a href=\"https://doi.org/10.1088/1367-2630/18/3/035002\">10.1088/1367-2630/18/3/035002</a>."},"issue":"3","intvolume":"        18","pubrep_id":"579","article_number":"035002","month":"02","ddc":["510","530"],"type":"journal_article","day":"29","date_published":"2016-02-29T00:00:00Z","doi":"10.1088/1367-2630/18/3/035002","date_created":"2018-12-11T11:52:15Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":18,"oa_version":"Published Version","author":[{"orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","first_name":"Robert","last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simone","full_name":"Warzel, Simone","last_name":"Warzel"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","oa":1,"year":"2016","project":[{"grant_number":"P27533_N27","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"has_accepted_license":"1","date_updated":"2021-01-12T06:51:01Z","_id":"1478","title":"Decay of correlations and absence of superfluidity in the disordered Tonks-Girardeau gas"},{"language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"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"}],"date_published":"2016-03-31T00:00:00Z","file":[{"file_id":"5513","content_type":"application/pdf","checksum":"cef516fa091925b5868813e355268fb4","access_level":"open_access","creator":"system","date_created":"2018-12-12T11:53:52Z","file_size":1012204,"date_updated":"2020-07-14T12:46:58Z","file_name":"IST-2016-523-v1+1_main.pdf","relation":"main_file"}],"file_date_updated":"2020-07-14T12:46:58Z","day":"31","publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"status":"public","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-8943-0722","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Velner","full_name":"Velner, Yaron","first_name":"Yaron"}],"citation":{"ieee":"K. Chatterjee, A. Pavlogiannis, and Y. Velner, <i>Quantitative interprocedural analysis</i>. IST Austria, 2016.","ista":"Chatterjee K, Pavlogiannis A, Velner Y. 2016. Quantitative interprocedural analysis, IST Austria, 33p.","mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Interprocedural Analysis</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">10.15479/AT:IST-2016-523-v1-1</a>.","short":"K. Chatterjee, A. Pavlogiannis, Y. Velner, Quantitative Interprocedural Analysis, IST Austria, 2016.","ama":"Chatterjee K, Pavlogiannis A, Velner Y. <i>Quantitative Interprocedural Analysis</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">10.15479/AT:IST-2016-523-v1-1</a>","apa":"Chatterjee, K., Pavlogiannis, A., &#38; Velner, Y. (2016). <i>Quantitative interprocedural analysis</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">https://doi.org/10.15479/AT:IST-2016-523-v1-1</a>","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, and Yaron Velner. <i>Quantitative Interprocedural Analysis</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-523-v1-1\">https://doi.org/10.15479/AT:IST-2016-523-v1-1</a>."},"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T11:39:22Z","publication_status":"published","doi":"10.15479/AT:IST-2016-523-v1-1","has_accepted_license":"1","month":"03","pubrep_id":"523","year":"2016","publication_identifier":{"issn":["2664-1690"]},"page":"33","oa":1,"title":"Quantitative interprocedural analysis","related_material":{"record":[{"relation":"later_version","status":"public","id":"1604"}]},"ddc":["005"],"date_updated":"2023-02-23T10:06:22Z","type":"technical_report","_id":"5445"},{"oa_version":"Published Version","citation":{"chicago":"Anonymous, 1, 2 Anonymous, and 3 Anonymous. <i>Termination and Worst-Case Analysis of Recursive Programs</i>. IST Austria, 2016.","apa":"Anonymous, 1, Anonymous, 2, &#38; Anonymous, 3. (2016). <i>Termination and worst-case analysis of recursive programs</i>. IST Austria.","ama":"Anonymous 1, Anonymous 2, Anonymous 3. <i>Termination and Worst-Case Analysis of Recursive Programs</i>. IST Austria; 2016.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, Termination and Worst-Case Analysis of Recursive Programs, IST Austria, 2016.","mla":"Anonymous, 1, et al. <i>Termination and Worst-Case Analysis of Recursive Programs</i>. IST Austria, 2016.","ista":"Anonymous 1, Anonymous 2, Anonymous 3. 2016. Termination and worst-case analysis of recursive programs, IST Austria, 26p.","ieee":"1 Anonymous, 2 Anonymous, and 3 Anonymous, <i>Termination and worst-case analysis of recursive programs</i>. IST Austria, 2016."},"alternative_title":["IST Austria Technical Report"],"status":"public","author":[{"first_name":"1","full_name":"Anonymous, 1","last_name":"Anonymous"},{"last_name":"Anonymous","full_name":"Anonymous, 2","first_name":"2"},{"full_name":"Anonymous, 3","first_name":"3","last_name":"Anonymous"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2018-12-12T11:39:23Z","abstract":[{"lang":"eng","text":"We study the problem of developing efficient approaches for proving termination of recursive programs with one-dimensional arrays. Ranking functions serve as a sound and complete approach for proving termination of non-recursive programs without array operations. First, we generalize ranking functions to the notion of measure functions, and prove that measure functions (i) provide a sound method to prove termination of recursive programs (with one-dimensional arrays), and (ii) is both sound and complete over recursive programs without array operations. Our second contribution is the synthesis of measure functions of specific forms in polynomial time. More precisely, we prove that (i) polynomial measure functions over recursive programs can be synthesized in polynomial time through Farkas’ Lemma and Handelman’s Theorem, and (ii) measure functions involving logarithm and exponentiation can be synthesized in polynomial time through abstraction of logarithmic or exponential terms and Handelman’s Theorem. A key application of our method is the worst-case analysis of recursive programs. While previous methods obtain worst-case polynomial bounds of the form O(n^k), where k is an integer, our polynomial time methods can synthesize bounds of the form O(n log n), as well as O(n^x), where x is not an integer. We show the applicability of our automated technique to obtain worst-case complexity of classical recursive algorithms such as (i) Merge-Sort, the divideand-\r\nconquer algorithm for the Closest-Pair problem, where we obtain O(n log n) worst-case bound, and (ii) Karatsuba’s algorithm for polynomial multiplication and Strassen’s algorithm for matrix multiplication, where we obtain O(n^x) bound, where x is not an integer and close to the best-known bounds for the respective algorithms. Finally, we present experimental results to demonstrate the\r\neffectiveness of our approach."}],"language":[{"iso":"eng"}],"publisher":"IST Austria","day":"15","file":[{"file_id":"6403","content_type":"application/pdf","checksum":"689069a7abbb34b21516164cbee9e0df","access_level":"open_access","creator":"dernst","date_created":"2019-05-10T13:27:24Z","file_size":686241,"date_updated":"2020-07-14T12:46:58Z","file_name":"popl2017a.pdf","relation":"main_file"},{"relation":"main_file","date_updated":"2020-07-14T12:46:58Z","file_name":"author_names.txt","date_created":"2019-05-10T13:27:31Z","file_size":258,"access_level":"closed","creator":"dernst","content_type":"text/plain","checksum":"fc08022bfbaac07bac047a9407c0bbb3","file_id":"6404"}],"file_date_updated":"2020-07-14T12:46:58Z","date_published":"2016-07-15T00:00:00Z","title":"Termination and worst-case analysis of recursive programs","type":"technical_report","_id":"5446","ddc":["000"],"date_updated":"2020-07-14T23:05:05Z","pubrep_id":"618","year":"2016","month":"07","has_accepted_license":"1","oa":1,"page":"26","publication_identifier":{"issn":["2664-1690"]}},{"publication_status":"published","date_created":"2018-12-12T11:39:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","author":[{"last_name":"Anonymous","first_name":"1","full_name":"Anonymous, 1"},{"last_name":"Anonymous","first_name":"2","full_name":"Anonymous, 2"},{"last_name":"Anonymous","first_name":"3","full_name":"Anonymous, 3"}],"alternative_title":["IST Austria Technical Report"],"citation":{"short":"1 Anonymous, 2 Anonymous, 3 Anonymous, Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds, IST Austria, 2016.","mla":"Anonymous, 1, et al. <i>Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds</i>. IST Austria, 2016.","ista":"Anonymous 1, Anonymous 2, Anonymous 3. 2016. Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds, IST Austria, 20p.","ieee":"1 Anonymous, 2 Anonymous, and 3 Anonymous, <i>Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds</i>. IST Austria, 2016.","chicago":"Anonymous, 1, 2 Anonymous, and 3 Anonymous. <i>Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds</i>. IST Austria, 2016.","apa":"Anonymous, 1, Anonymous, 2, &#38; Anonymous, 3. (2016). <i>Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds</i>. IST Austria.","ama":"Anonymous 1, Anonymous 2, Anonymous 3. <i>Average-Case Analysis of Programs: Automated Recurrence Analysis for Almost-Linear Bounds</i>. IST Austria; 2016."},"oa_version":"Published Version","date_published":"2016-07-15T00:00:00Z","file_date_updated":"2020-07-14T12:46:58Z","file":[{"relation":"main_file","file_size":281,"date_created":"2019-05-10T13:32:16Z","date_updated":"2020-07-14T12:46:58Z","file_name":"listofauthors.txt","checksum":"cf53cdb6d092e68db0b4a0a1506ef8fb","content_type":"text/plain","access_level":"closed","creator":"dernst","file_id":"6406"},{"file_name":"popl2017b.pdf","date_updated":"2020-07-14T12:46:58Z","file_size":563642,"date_created":"2019-05-10T13:32:16Z","relation":"main_file","file_id":"6407","creator":"dernst","access_level":"open_access","checksum":"7bdd94ba13aa0dec9c46887fcf13870b","content_type":"application/pdf"}],"publisher":"IST Austria","day":"15","language":[{"iso":"eng"}],"abstract":[{"text":"We consider the problem of developing automated techniques to aid the average-case complexity analysis of programs. Several classical textbook algorithms have quite efficient average-case complexity, whereas the corresponding worst-case bounds are either inefficient (e.g., QUICK-SORT), or completely ineffective (e.g., COUPONCOLLECTOR). Since the main focus of average-case analysis is to obtain efficient bounds, we consider bounds that are either logarithmic,\r\nlinear, or almost-linear (O(log n), O(n), O(n · log n),\r\nrespectively, where n represents the size of the input). Our main contribution is a sound approach for deriving such average-case bounds for randomized recursive programs. Our approach is efficient (a simple linear-time algorithm), and it is based on (a) the analysis of recurrence relations induced by randomized algorithms, and (b) a guess-and-check technique. Our approach can infer the asymptotically optimal average-case bounds for classical randomized algorithms, including RANDOMIZED-SEARCH, QUICKSORT, QUICK-SELECT, COUPON-COLLECTOR, where the worstcase\r\nbounds are either inefficient (such as linear as compared to logarithmic of average-case, or quadratic as compared to linear or almost-linear of average-case), or ineffective. We have implemented our approach, and the experimental results show that we obtain the bounds efficiently for various classical algorithms.","lang":"eng"}],"ddc":["000"],"date_updated":"2020-07-14T23:05:06Z","_id":"5447","type":"technical_report","title":"Average-case analysis of programs: Automated recurrence analysis for almost-linear bounds","publication_identifier":{"issn":["2664-1690"]},"page":"20","oa":1,"has_accepted_license":"1","month":"07","pubrep_id":"619","year":"2016"},{"oa_version":"Published Version","author":[{"full_name":"Anonymous, 1","first_name":"1","last_name":"Anonymous"},{"last_name":"Anonymous","full_name":"Anonymous, 2","first_name":"2"},{"last_name":"Anonymous","first_name":"3","full_name":"Anonymous, 3"},{"last_name":"Anonymous","first_name":"4","full_name":"Anonymous, 4"}],"status":"public","alternative_title":["IST Austria Technical Report"],"citation":{"chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria, 2016.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, &#38; Anonymous, 4. (2016). <i>Data-centric dynamic partial order reduction</i>. IST Austria.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria; 2016.","mla":"Anonymous, 1, et al. <i>Data-Centric Dynamic Partial Order Reduction</i>. IST Austria, 2016.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Data-Centric Dynamic Partial Order Reduction, IST Austria, 2016.","ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2016. Data-centric dynamic partial order reduction, IST Austria, 20p.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, <i>Data-centric dynamic partial order reduction</i>. IST Austria, 2016."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_created":"2018-12-12T11:39:23Z","abstract":[{"text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence.\r\n1. For acyclic architectures, our algorithm is guaranteed to explore exactly one representative trace from each observation class, while spending polynomial time per class. Hence, our algorithm is optimal wrt the observation equivalence, and in several cases explores exponentially fewer traces than any enumerative method based on the Mazurkiewicz equivalence.\r\n2. For cyclic architectures, we consider an equivalence between traces which is finer than the observation equivalence; but coarser than the Mazurkiewicz equivalence, and in some cases is exponentially coarser. Our data-centric DPOR algorithm remains optimal under this trace equivalence. \r\nFinally, we perform a basic experimental comparison between the existing Mazurkiewicz-based DPOR and our data-centric DPOR on a set of academic benchmarks. Our results show a significant reduction in both running time and the number of explored equivalence classes.","lang":"eng"}],"external_id":{"arxiv":["1610.01188"]},"language":[{"iso":"eng"}],"day":"15","publisher":"IST Austria","date_published":"2016-07-15T00:00:00Z","file":[{"relation":"main_file","date_updated":"2020-07-14T12:46:58Z","file_name":"IST-2016-620-v1+1_main.pdf","date_created":"2018-12-12T11:53:45Z","file_size":538881,"access_level":"open_access","creator":"system","content_type":"application/pdf","checksum":"1d69252d66bcdf782615ddfb911d2957","file_id":"5506"},{"date_created":"2019-05-10T13:30:40Z","file_size":121,"file_name":"authornames.txt","date_updated":"2020-07-14T12:46:58Z","relation":"main_file","file_id":"6405","checksum":"deabb0eb8f237cae4f9542b28b0b6eb2","content_type":"text/plain","creator":"dernst","access_level":"closed"}],"file_date_updated":"2020-07-14T12:46:58Z","arxiv":1,"title":"Data-centric dynamic partial order reduction","ddc":["000"],"date_updated":"2023-02-23T12:27:16Z","type":"technical_report","_id":"5448","related_material":{"record":[{"relation":"later_version","id":"10417","status":"public"},{"status":"public","id":"5456","relation":"later_version"}]},"year":"2016","pubrep_id":"620","has_accepted_license":"1","month":"07","page":"20","oa":1,"publication_identifier":{"issn":["2664-1690"]}},{"oa_version":"Updated Version","alternative_title":["IST Austria Technical Report"],"author":[{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Josef","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"status":"public","citation":{"ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">10.15479/AT:IST-2016-648-v1-1</a>","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Amplification on undirected population structures: Comets beat stars, IST Austria, 22p.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria, 2016.","mla":"Pavlogiannis, Andreas, et al. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">10.15479/AT:IST-2016-648-v1-1</a>.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Amplification on Undirected Population Structures: Comets Beat Stars, IST Austria, 2016."},"doi":"10.15479/AT:IST-2016-648-v1-1","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T11:39:24Z","abstract":[{"text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population.\r\nThe fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure.\r\nAmplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade.\r\nIn this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively.","lang":"eng"}],"department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"day":"09","publisher":"IST Austria","date_published":"2016-11-09T00:00:00Z","file":[{"file_name":"IST-2016-648-v1+1_tr.pdf","date_updated":"2020-07-14T12:46:58Z","file_size":1264221,"date_created":"2018-12-12T11:54:07Z","relation":"main_file","file_id":"5529","creator":"system","access_level":"open_access","content_type":"application/pdf","checksum":"8345a8c1e7d7f0cd92516d182b7fc59e"}],"file_date_updated":"2020-07-14T12:46:58Z","title":"Amplification on undirected population structures: Comets beat stars","date_updated":"2023-02-23T12:22:21Z","ddc":["519"],"type":"technical_report","_id":"5449","related_material":{"record":[{"id":"512","relation":"later_version","status":"public"}]},"year":"2016","pubrep_id":"648","has_accepted_license":"1","month":"11","page":"22","oa":1,"publication_identifier":{"issn":["2664-1690"]}},{"day":"30","publisher":"IST Austria","date_published":"2016-12-30T00:00:00Z","file_date_updated":"2020-07-14T12:46:59Z","file":[{"file_size":1014732,"date_created":"2018-12-12T11:53:04Z","date_updated":"2020-07-14T12:46:59Z","file_name":"IST-2016-728-v1+1_main.pdf","relation":"main_file","file_id":"5465","checksum":"7b8bb17c322c0556acba6ac169fa71c1","content_type":"application/pdf","access_level":"open_access","creator":"system"}],"language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"doi":"10.15479/AT:IST-2016-728-v1-1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T11:39:24Z","publication_status":"published","oa_version":"Published Version","status":"public","author":[{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"alternative_title":["IST Austria Technical Report"],"citation":{"mla":"Pavlogiannis, Andreas, et al. <i>Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">10.15479/AT:IST-2016-728-v1-1</a>.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Strong Amplifiers of Natural Selection, IST Austria, 2016.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Strong amplifiers of natural selection</i>. IST Austria, 2016.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Strong amplifiers of natural selection, IST Austria, 34p.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">https://doi.org/10.15479/AT:IST-2016-728-v1-1</a>.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">https://doi.org/10.15479/AT:IST-2016-728-v1-1</a>","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">10.15479/AT:IST-2016-728-v1-1</a>"},"page":"34","oa":1,"publication_identifier":{"issn":["2664-1690"]},"pubrep_id":"728","year":"2016","has_accepted_license":"1","month":"12","ddc":["000"],"date_updated":"2023-02-23T12:27:05Z","_id":"5451","type":"technical_report","title":"Strong amplifiers of natural selection"},{"date_published":"2016-12-30T00:00:00Z","day":"30","author":[{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef","full_name":"Tkadlec, Josef"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nowak, Martin","first_name":"Martin","last_name":"Nowak"}],"status":"public","oa_version":"Published Version","date_created":"2018-12-12T11:39:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.15479/AT:IST-2017-728-v2-1","has_accepted_license":"1","year":"2016","project":[{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"}],"publication_identifier":{"issn":["2664-1690"]},"oa":1,"title":"Arbitrarily strong amplifiers of natural selection","article_processing_charge":"No","related_material":{"record":[{"id":"5453","status":"public","relation":"later_version"},{"relation":"popular_science","status":"public","id":"5559"}]},"_id":"5452","date_updated":"2024-02-21T13:48:42Z","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"file":[{"file_size":811558,"date_created":"2018-12-12T11:52:59Z","date_updated":"2020-07-14T12:46:59Z","file_name":"IST-2017-728-v2+1_main.pdf","relation":"main_file","file_id":"5460","checksum":"58e895f26c82f560c0f0989bf8b08599","content_type":"application/pdf","access_level":"open_access","creator":"system"}],"file_date_updated":"2020-07-14T12:46:59Z","publisher":"IST Austria","citation":{"ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 32p.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria, 2016.","mla":"Pavlogiannis, Andreas, et al. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">10.15479/AT:IST-2017-728-v2-1</a>.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">10.15479/AT:IST-2017-728-v2-1</a>","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">https://doi.org/10.15479/AT:IST-2017-728-v2-1</a>","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">https://doi.org/10.15479/AT:IST-2017-728-v2-1</a>."},"alternative_title":["IST Austria Technical Report"],"publication_status":"published","month":"12","pubrep_id":"750","ec_funded":1,"page":"32","type":"technical_report","ddc":["000"]},{"author":[{"id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","orcid":"0000-0002-8943-0722"},{"last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1097-9684","first_name":"Josef","full_name":"Tkadlec, Josef"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"status":"public","alternative_title":["IST Austria Technical Report"],"citation":{"ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria, 2016.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 34p.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","mla":"Pavlogiannis, Andreas, et al. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">10.15479/AT:IST-2017-749-v3-1</a>.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">10.15479/AT:IST-2017-749-v3-1</a>","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">https://doi.org/10.15479/AT:IST-2017-749-v3-1</a>.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Arbitrarily strong amplifiers of natural selection</i>. 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We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)","lang":"eng"}],"file_date_updated":"2020-07-14T12:47:00Z","file":[{"file_id":"5594","checksum":"950f85b80427d357bfeff09608ba02e9","content_type":"application/zip","creator":"system","access_level":"open_access","date_created":"2018-12-12T13:02:27Z","file_size":4468543,"file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","date_updated":"2020-07-14T12:47:00Z","relation":"main_file"}],"date_published":"2016-02-19T00:00:00Z","publisher":"Institute of Science and Technology Austria","day":"19","citation":{"mla":"Ellis, Thomas, and David Field. <i>Flower Colour Data and Phylogeny (NEXUS) Files</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","short":"T. Ellis, D. Field, (2016).","ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016.","ista":"Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","apa":"Ellis, T., &#38; Field, D. (2016). Flower colour data and phylogeny (NEXUS) files. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>","chicago":"Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS) Files.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>.","ama":"Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>"},"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"author":[{"last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8511-0254","first_name":"Thomas","full_name":"Ellis, Thomas"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","full_name":"Field, David","orcid":"0000-0002-4014-8478"}],"status":"public","oa_version":"Published Version","datarep_id":"34","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T12:31:29Z","doi":"10.15479/AT:ISTA:34","license":"https://creativecommons.org/publicdomain/zero/1.0/","month":"02","has_accepted_license":"1","year":"2016","oa":1,"article_processing_charge":"No","title":"Flower colour data and phylogeny (NEXUS) files","related_material":{"record":[{"id":"1382","relation":"research_paper","status":"public"}]},"_id":"5550","type":"research_data","date_updated":"2024-02-21T13:49:54Z","ddc":["576"]},{"file":[{"content_type":"application/zip","checksum":"aa3eb85d52b110cd192aa23147c4d4f3","creator":"system","access_level":"open_access","file_id":"5640","relation":"main_file","date_created":"2018-12-12T13:05:12Z","file_size":32775,"file_name":"IST-2016-35-v1+1_array_data.zip","date_updated":"2020-07-14T12:47:01Z"}],"file_date_updated":"2020-07-14T12:47:01Z","date_published":"2016-02-19T00:00:00Z","day":"19","publisher":"Institute of Science and Technology Austria","department":[{"_id":"NiBa"}],"abstract":[{"lang":"eng","text":"Data from array experiments investigating pollinator behaviour on snapdragons in controlled conditions, and their effect on plant mating. Data were collected as part of Tom Ellis' PhD thesis , submitted February 2016.\r\n\r\nWe placed a total of 36 plants in a grid inside a closed organza tent, with a single hive of commercially bred bumblebees (Bombus hortorum). We used only the yellow-flowered Antirrhinum majus striatum and the magenta-flowered Antirrhinum majus pseudomajus, at ratios of 6:36, 12:24, 18:18, 24:12 and 30:6.\r\n\r\nAfter 24 hours to learn how to deal with snapdragons, I observed pollinators foraging on plants, and recorded the transitions between plants. Thereafter seeds on plants were allowed to develops. A sample of these were grown to maturity when their flower colour could be determined, and they were scored as yellow, magenta, or hybrid."}],"datarep_id":"35","date_created":"2018-12-12T12:31:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.15479/AT:ISTA:35","citation":{"ama":"Ellis T. Data on pollinator observations and offpsring phenotypes. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>","apa":"Ellis, T. (2016). Data on pollinator observations and offpsring phenotypes. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>","chicago":"Ellis, Thomas. “Data on Pollinator Observations and Offpsring Phenotypes.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:35\">https://doi.org/10.15479/AT:ISTA:35</a>.","ista":"Ellis T. 2016. Data on pollinator observations and offpsring phenotypes, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>.","ieee":"T. Ellis, “Data on pollinator observations and offpsring phenotypes.” Institute of Science and Technology Austria, 2016.","short":"T. Ellis, (2016).","mla":"Ellis, Thomas. <i>Data on Pollinator Observations and Offpsring Phenotypes</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:35\">10.15479/AT:ISTA:35</a>."},"status":"public","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"author":[{"orcid":"0000-0002-8511-0254","first_name":"Thomas","full_name":"Ellis, Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","oa":1,"month":"02","contributor":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240"}],"has_accepted_license":"1","year":"2016","related_material":{"record":[{"relation":"research_paper","status":"public","id":"1398"}]},"type":"research_data","_id":"5551","date_updated":"2024-02-21T13:51:27Z","article_processing_charge":"No","title":"Data on pollinator observations and offpsring phenotypes"},{"oa_version":"Published Version","citation":{"ista":"Ellis T. 2016. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data., Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>.","ieee":"T. Ellis, “Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.” Institute of Science and Technology Austria, 2016.","mla":"Ellis, Thomas. <i>Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.</i> Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>.","short":"T. Ellis, (2016).","ama":"Ellis T. Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:36\">10.15479/AT:ISTA:36</a>","apa":"Ellis, T. (2016). Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:36\">https://doi.org/10.15479/AT:ISTA:36</a>","chicago":"Ellis, Thomas. “Pollinator Visitation Data for Wild Antirrhinum Majus Plants, with Phenotypic and Frequency Data.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:36\">https://doi.org/10.15479/AT:ISTA:36</a>."},"author":[{"orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas","first_name":"Thomas","last_name":"Ellis","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87"}],"status":"public","doi":"10.15479/AT:ISTA:36","datarep_id":"36","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T12:31:30Z","abstract":[{"lang":"eng","text":"Data on pollinator visitation to wild snapdragons in a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted February 2016).\r\n\r\nSnapdragon flowers have a mouth-like structure which pollinators must open to access nectar. We placed 5mm cellophane tags in these mouths, which are held in place by the pressure of the flower until a pollinator visits. When she opens the flower, the tag drops out, and one can infer a visit. We surveyed plants over multiple days in 2010, 2011 and 2012.\r\n\r\nAlso included are data on phenotypic and demographic variables which may be explanatory variables for pollinator visitation."}],"department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","day":"19","file":[{"file_name":"IST-2016-36-v1+1_tag_assay_archive.zip","date_updated":"2020-07-14T12:47:01Z","file_size":44905,"date_created":"2018-12-12T13:03:07Z","relation":"main_file","file_id":"5625","creator":"system","access_level":"open_access","content_type":"application/zip","checksum":"cbc61b523d4d475a04a737d50dc470ef"}],"file_date_updated":"2020-07-14T12:47:01Z","date_published":"2016-02-19T00:00:00Z","article_processing_charge":"No","title":"Pollinator visitation data for wild Antirrhinum majus plants, with phenotypic and frequency data.","_id":"5552","type":"research_data","date_updated":"2024-02-21T13:51:40Z","related_material":{"record":[{"relation":"research_paper","status":"public","id":"1398"}]},"year":"2016","month":"02","has_accepted_license":"1","contributor":[{"first_name":"David","last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"oa":1},{"related_material":{"record":[{"status":"public","id":"1398","relation":"research_paper"}]},"_id":"5553","type":"research_data","ddc":["576"],"date_updated":"2024-02-21T13:51:14Z","title":"Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012","article_processing_charge":"No","oa":1,"month":"02","has_accepted_license":"1","contributor":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","contributor_type":"project_manager","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"year":"2016","datarep_id":"37","date_created":"2018-12-12T12:31:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.15479/AT:ISTA:37","keyword":["paternity assignment","pedigree","matting patterns","assortative mating","Antirrhinum majus","frequency-dependent selection","plant-pollinator interaction"],"citation":{"apa":"Field, D., &#38; Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>","chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>.","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>","short":"D. Field, T. Ellis, (2016).","mla":"Field, David, and Thomas Ellis. <i>Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","ieee":"D. Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016."},"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"author":[{"last_name":"Field","id":"419049E2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4014-8478","full_name":"Field, David","first_name":"David"},{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","full_name":"Ellis, Thomas","first_name":"Thomas","orcid":"0000-0002-8511-0254"}],"status":"public","oa_version":"Published Version","file":[{"creator":"system","access_level":"open_access","content_type":"application/zip","checksum":"4ae751b1fa4897fa216241f975a57313","file_id":"5620","relation":"main_file","file_name":"IST-2016-37-v1+1_paternity_archive.zip","date_updated":"2020-07-14T12:47:01Z","date_created":"2018-12-12T13:03:02Z","file_size":132808}],"file_date_updated":"2020-07-14T12:47:01Z","date_published":"2016-02-19T00:00:00Z","publisher":"Institute of Science and Technology Austria","day":"19","department":[{"_id":"NiBa"}],"abstract":[{"text":"Genotypic, phenotypic and demographic data for 2128 wild snapdragons and 1127 open-pollinated progeny from a natural hybrid zone, collected as part of Tom Ellis' PhD thesis (submitted) February 2016).\r\n\r\nTissue samples were sent to LGC Genomics in Berlin for DNA extraction, and genotyping at 70 SNP markers by KASPR genotyping. 29 of these SNPs failed to amplify reliably, and have been removed from this dataset.\r\n\r\nOther data were retreived from an online database of this population at www.antspec.org.","lang":"eng"}]},{"datarep_id":"43","date_created":"2018-12-12T12:31:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.15479/AT:ISTA:43","citation":{"apa":"Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>","chicago":"Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>.","ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>","mla":"Tugrul, Murat. <i>Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>.","short":"M. Tugrul, (2016).","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016.","ista":"Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>."},"keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"author":[{"last_name":"Tugrul","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8523-0758","first_name":"Murat","full_name":"Tugrul, Murat"}],"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","oa_version":"Published Version","file":[{"checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","content_type":"application/zip","creator":"system","access_level":"open_access","file_id":"5626","relation":"main_file","date_created":"2018-12-12T13:03:08Z","file_size":1123495,"file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip","date_updated":"2020-07-14T12:47:01Z"}],"file_date_updated":"2020-07-14T12:47:01Z","date_published":"2016-05-12T00:00:00Z","publisher":"Institute of Science and Technology Austria","day":"12","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"abstract":[{"lang":"eng","text":"The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution."}],"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"1131"}]},"type":"research_data","_id":"5554","date_updated":"2024-02-21T13:50:34Z","article_processing_charge":"No","title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","oa":1,"month":"05","has_accepted_license":"1","contributor":[{"last_name":"Steinrück","contributor_type":"researcher","id":"2C023F40-F248-11E8-B48F-1D18A9856A87","first_name":"Magdalena"},{"first_name":"Fabienne","last_name":"Jesse","contributor_type":"researcher","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87"}],"year":"2016"},{"oa":1,"has_accepted_license":"1","month":"07","year":"2016","ddc":["570"],"date_updated":"2024-02-21T13:50:06Z","_id":"5555","type":"research_data","title":"Fiji script to determine average speed and direction of migration of cells","article_processing_charge":"No","date_published":"2016-07-08T00:00:00Z","file_date_updated":"2020-07-14T12:47:02Z","file":[{"checksum":"9f96cddbcd4ed689f48712ffe234d5e5","content_type":"application/zip","access_level":"open_access","creator":"system","file_id":"5621","relation":"main_file","file_size":20692,"date_created":"2018-12-12T13:03:03Z","date_updated":"2020-07-14T12:47:02Z","file_name":"IST-2016-44-v1+1_migrationAnalyzer.zip"}],"day":"08","publisher":"Institute of Science and Technology Austria","department":[{"_id":"Bio"}],"abstract":[{"lang":"eng","text":"This FIJI script calculates the population average of the migration speed as a function of time of all cells from wide field microscopy movies."}],"date_created":"2018-12-12T12:31:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","datarep_id":"44","doi":"10.15479/AT:ISTA:44","author":[{"full_name":"Hauschild, Robert","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild"}],"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","citation":{"ama":"Hauschild R. Fiji script to determine average speed and direction of migration of cells. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:44\">10.15479/AT:ISTA:44</a>","apa":"Hauschild, R. (2016). Fiji script to determine average speed and direction of migration of cells. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:44\">https://doi.org/10.15479/AT:ISTA:44</a>","chicago":"Hauschild, Robert. “Fiji Script to Determine Average Speed and Direction of Migration of Cells.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:44\">https://doi.org/10.15479/AT:ISTA:44</a>.","ieee":"R. Hauschild, “Fiji script to determine average speed and direction of migration of cells.” Institute of Science and Technology Austria, 2016.","ista":"Hauschild R. 2016. Fiji script to determine average speed and direction of migration of cells, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:44\">10.15479/AT:ISTA:44</a>.","mla":"Hauschild, Robert. <i>Fiji Script to Determine Average Speed and Direction of Migration of Cells</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:44\">10.15479/AT:ISTA:44</a>.","short":"R. Hauschild, (2016)."},"keyword":["cell migration","wide field microscopy","FIJI"],"oa_version":"Published Version"},{"article_processing_charge":"No","title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","ddc":["571"],"date_updated":"2024-02-21T13:51:53Z","_id":"5556","type":"research_data","related_material":{"record":[{"relation":"used_in_publication","id":"8431","status":"deleted"},{"status":"public","id":"1029","relation":"research_paper"}]},"year":"2016","has_accepted_license":"1","month":"08","oa":1,"oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"author":[{"full_name":"Lukacisin, Martin","first_name":"Martin","orcid":"0000-0001-6549-4177","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisin"},{"last_name":"Landon","first_name":"Matthieu","full_name":"Landon, Matthieu"},{"last_name":"Jajoo","full_name":"Jajoo, Rishi","first_name":"Rishi"}],"status":"public","citation":{"ista":"Lukacisin M, Landon M, Jajoo R. 2016. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>.","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016.","short":"M. Lukacisin, M. Landon, R. Jajoo, (2016).","mla":"Lukacisin, Martin, et al. <i>MATLAB Analysis Code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.”</i> Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>.","ama":"Lukacisin M, Landon M, Jajoo R. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:45\">https://doi.org/10.15479/AT:ISTA:45</a>.","apa":"Lukacisin, M., Landon, M., &#38; Jajoo, R. (2016). MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:45\">https://doi.org/10.15479/AT:ISTA:45</a>"},"keyword":["transcription","pausing","backtracking","polymerase","RNA","NET-seq","nucleosome","basepairing"],"license":"https://creativecommons.org/licenses/by-sa/4.0/","doi":"10.15479/AT:ISTA:45","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T12:31:31Z","datarep_id":"45","abstract":[{"text":"MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions","lang":"eng"}],"department":[{"_id":"ToBo"}],"publisher":"Institute of Science and Technology Austria","day":"25","date_published":"2016-08-25T00:00:00Z","file_date_updated":"2020-07-14T12:47:02Z","file":[{"file_id":"5616","content_type":"application/zip","checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","creator":"system","access_level":"open_access","date_created":"2018-12-12T13:02:58Z","file_size":296722548,"file_name":"IST-2016-45-v1+1_PaperCode.zip","date_updated":"2020-07-14T12:47:02Z","relation":"main_file"}]},{"_id":"5557","type":"research_data","ddc":["006"],"date_updated":"2024-02-21T13:50:21Z","title":"Synthetic discrete tomography problems","article_processing_charge":"No","oa":1,"year":"2016","month":"09","contributor":[{"first_name":"Jan","contributor_type":"data_collector","last_name":"Kuske"}],"has_accepted_license":"1","doi":"10.15479/AT:ISTA:46","datarep_id":"46","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-12T12:31:31Z","oa_version":"Published Version","keyword":["discrete tomography"],"citation":{"chicago":"Swoboda, Paul. “Synthetic Discrete Tomography Problems.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:46\">https://doi.org/10.15479/AT:ISTA:46</a>.","apa":"Swoboda, P. 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Swoboda, “Synthetic discrete tomography problems.” Institute of Science and Technology Austria, 2016."},"author":[{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","first_name":"Paul","full_name":"Swoboda, Paul"}],"tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","publisher":"Institute of Science and Technology Austria","day":"20","file":[{"file_id":"5645","access_level":"open_access","creator":"system","checksum":"aa5a16a0dc888da7186fb8fc45e88439","content_type":"application/zip","date_updated":"2020-07-14T12:47:02Z","file_name":"IST-2016-46-v1+1_discrete_tomography_synthetic.zip","date_created":"2018-12-12T13:05:19Z","file_size":36058401,"relation":"main_file"}],"file_date_updated":"2020-07-14T12:47:02Z","date_published":"2016-09-20T00:00:00Z","abstract":[{"text":"Small synthetic discrete tomography problems.\r\nSizes are 32x32, 64z64 and 256x256.\r\nProjection angles are 2, 4, and 6.\r\nNumber of labels are 3 and 5.","lang":"eng"}],"department":[{"_id":"VlKo"}]},{"related_material":{"record":[{"status":"public","relation":"other","id":"1122"}]},"ddc":["004"],"date_updated":"2024-02-21T13:50:48Z","type":"research_data","_id":"5558","article_processing_charge":"No","title":"Tracking, Correcting and Absorbing Water Surface Waves","oa":1,"has_accepted_license":"1","month":"09","pubrep_id":"640","year":"2016","date_created":"2018-12-12T12:31:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","datarep_id":"48","doi":"10.15479/AT:ISTA:48","author":[{"orcid":"0000-0002-4417-3224","full_name":"Bojsen-Hansen, Morten","first_name":"Morten","last_name":"Bojsen-Hansen","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","citation":{"ama":"Bojsen-Hansen M. 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Bojsen-Hansen, (2016).","mla":"Bojsen-Hansen, Morten. <i>Tracking, Correcting and Absorbing Water Surface Waves</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>."},"oa_version":"Published Version","date_published":"2016-09-23T00:00:00Z","file":[{"checksum":"5b1b256ad796fbddb4b7729f5e45e444","content_type":"application/x-bzip2","access_level":"open_access","creator":"system","file_id":"5589","relation":"main_file","file_size":55237885,"date_created":"2018-12-12T13:02:18Z","date_updated":"2020-07-14T12:47:02Z","file_name":"IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2"}],"file_date_updated":"2020-07-14T12:47:02Z","publisher":"Institute of Science and Technology Austria","day":"23","department":[{"_id":"ChWo"}],"publist_id":"6238","abstract":[{"lang":"eng","text":"PhD thesis LaTeX source code"}]}]