[{"has_accepted_license":"1","volume":6,"file":[{"file_id":"5356","date_created":"2018-12-12T10:18:34Z","file_name":"IST-2018-945-v1+1_2012_Schloegl_Review_of.pdf","file_size":2693701,"relation":"main_file","creator":"system","access_level":"open_access","checksum":"195238221c4b0b0f4035f6f6c16ea17c","content_type":"application/pdf","date_updated":"2020-07-14T12:46:35Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by/4.0/","oa_version":"Published Version","citation":{"ama":"Tangermann M, Müller K, Aertsen A, et al. Review of the BCI competition IV. <i>Frontiers in Neuroscience</i>. 2012;6. doi:<a href=\"https://doi.org/10.3389/fnins.2012.00055\">10.3389/fnins.2012.00055</a>","ista":"Tangermann M, Müller K, Aertsen A, Birbaumer N, Braun C, Brunner C, Leeb R, Mehring C, Miller K, Müller Putz G, Nolte G, Pfurtscheller G, Preissl H, Schalk G, Schlögl A, Vidaurre C, Waldert S, Blankertz B. 2012. Review of the BCI competition IV. Frontiers in Neuroscience. 6, 55.","short":"M. Tangermann, K. Müller, A. Aertsen, N. Birbaumer, C. Braun, C. Brunner, R. Leeb, C. Mehring, K. Miller, G. Müller Putz, G. Nolte, G. Pfurtscheller, H. Preissl, G. Schalk, A. Schlögl, C. Vidaurre, S. Waldert, B. Blankertz, Frontiers in Neuroscience 6 (2012).","ieee":"M. Tangermann <i>et al.</i>, “Review of the BCI competition IV,” <i>Frontiers in Neuroscience</i>, vol. 6. Frontiers Research Foundation, 2012.","apa":"Tangermann, M., Müller, K., Aertsen, A., Birbaumer, N., Braun, C., Brunner, C., … Blankertz, B. (2012). Review of the BCI competition IV. <i>Frontiers in Neuroscience</i>. Frontiers Research Foundation. <a href=\"https://doi.org/10.3389/fnins.2012.00055\">https://doi.org/10.3389/fnins.2012.00055</a>","mla":"Tangermann, Michael, et al. “Review of the BCI Competition IV.” <i>Frontiers in Neuroscience</i>, vol. 6, 55, Frontiers Research Foundation, 2012, doi:<a href=\"https://doi.org/10.3389/fnins.2012.00055\">10.3389/fnins.2012.00055</a>.","chicago":"Tangermann, Michael, Klaus Müller, Ad Aertsen, Niels Birbaumer, Christoph Braun, Clemens Brunner, Robert Leeb, et al. “Review of the BCI Competition IV.” <i>Frontiers in Neuroscience</i>. Frontiers Research Foundation, 2012. <a href=\"https://doi.org/10.3389/fnins.2012.00055\">https://doi.org/10.3389/fnins.2012.00055</a>."},"pubrep_id":"945","day":"13","month":"07","ddc":["004"],"file_date_updated":"2020-07-14T12:46:35Z","publication_status":"published","status":"public","acknowledgement":"The studies were in part or completely supported by the Bundesministerium für Bildung und Forschung (BMBF), Fkz 01IB001A, 01GQ0850, by the German Science Foundation (DFG, contract MU 987/3-2), by the European ICT Programme Projects FP7-224631 and 216886, the World Class University Program through the National Research Foundation of Korea funded by the Ministry of Education, Science, and Technology (Grant R31-10008), the US Army Research Office [W911NF-08-1-0216 (Gerwin Schalk) and W911NF-07-1-0415 (Gerwin Schalk)] and the NIH [EB006356 (Gerwin Schalk) and EB000856 (Gerwin Schalk), the WIN-Kolleg of the Heidelberg Academy of Sciences and Humanities, German Federal Ministry of Education and Research grants 01GQ0420, 01GQ0761, 01GQ0762, and 01GQ0830, German Research Foundation grants 550/B5 and C6, and by a scholarship from the German National Academic Foundation. This paper only reflects the authors’ views and funding agencies are not liable for any use that may be made of the information contained herein.\r\n","abstract":[{"text":"The BCI competition IV stands in the tradition of prior BCI competitions that aim to provide high quality neuroscientific data for open access to the scientific community. As experienced already in prior competitions not only scientists from the narrow field of BCI compete, but scholars with a broad variety of backgrounds and nationalities. They include high specialists as well as students.The goals of all BCI competitions have always been to challenge with respect to novel paradigms and complex data. We report on the following challenges: (1) asynchronous data, (2) synthetic, (3) multi-class continuous data, (4) sessionto-session transfer, (5) directionally modulated MEG, (6) finger movements recorded by ECoG. As after past competitions, our hope is that winning entries may enhance the analysis methods of future BCIs.","lang":"eng"}],"doi":"10.3389/fnins.2012.00055","title":"Review of the BCI competition IV","author":[{"full_name":"Tangermann, Michael","last_name":"Tangermann","first_name":"Michael"},{"first_name":"Klaus","full_name":"Müller, Klaus","last_name":"Müller"},{"first_name":"Ad","last_name":"Aertsen","full_name":"Aertsen, Ad"},{"first_name":"Niels","last_name":"Birbaumer","full_name":"Birbaumer, Niels"},{"first_name":"Christoph","full_name":"Braun, Christoph","last_name":"Braun"},{"last_name":"Brunner","full_name":"Brunner, Clemens","first_name":"Clemens"},{"last_name":"Leeb","full_name":"Leeb, Robert","first_name":"Robert"},{"last_name":"Mehring","full_name":"Mehring, Carsten","first_name":"Carsten"},{"first_name":"Kai","full_name":"Miller, Kai","last_name":"Miller"},{"first_name":"Gernot","last_name":"Müller Putz","full_name":"Müller Putz, Gernot"},{"first_name":"Guido","full_name":"Nolte, Guido","last_name":"Nolte"},{"first_name":"Gert","full_name":"Pfurtscheller, Gert","last_name":"Pfurtscheller"},{"first_name":"Hubert","full_name":"Preissl, Hubert","last_name":"Preissl"},{"first_name":"Gerwin","full_name":"Schalk, Gerwin","last_name":"Schalk"},{"last_name":"Schlögl","full_name":"Schlögl, Alois","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100"},{"last_name":"Vidaurre","full_name":"Vidaurre, Carmen","first_name":"Carmen"},{"last_name":"Waldert","full_name":"Waldert, Stephan","first_name":"Stephan"},{"full_name":"Blankertz, Benjamin","last_name":"Blankertz","first_name":"Benjamin"}],"_id":"493","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Frontiers Research Foundation","intvolume":"         6","date_published":"2012-07-13T00:00:00Z","date_created":"2018-12-11T11:46:46Z","scopus_import":1,"department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"publist_id":"7327","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"55","publication":"Frontiers in Neuroscience","date_updated":"2021-01-12T08:01:03Z","year":"2012","oa":1},{"volume":13,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"ACM","intvolume":"        13","date_published":"2012-10-01T00:00:00Z","date_created":"2018-12-11T11:46:47Z","oa_version":"None","scopus_import":1,"citation":{"apa":"Boker, U., &#38; Kupferman, O. (2012). Translating to Co-Büchi made tight, unified, and useful. <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM. <a href=\"https://doi.org/10.1145/2362355.2362357\">https://doi.org/10.1145/2362355.2362357</a>","ieee":"U. Boker and O. Kupferman, “Translating to Co-Büchi made tight, unified, and useful,” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 13, no. 4. ACM, 2012.","ama":"Boker U, Kupferman O. Translating to Co-Büchi made tight, unified, and useful. <i>ACM Transactions on Computational Logic (TOCL)</i>. 2012;13(4). doi:<a href=\"https://doi.org/10.1145/2362355.2362357\">10.1145/2362355.2362357</a>","ista":"Boker U, Kupferman O. 2012. Translating to Co-Büchi made tight, unified, and useful. ACM Transactions on Computational Logic (TOCL). 13(4), 29.","short":"U. Boker, O. Kupferman, ACM Transactions on Computational Logic (TOCL) 13 (2012).","chicago":"Boker, Udi, and Orna Kupferman. “Translating to Co-Büchi Made Tight, Unified, and Useful.” <i>ACM Transactions on Computational Logic (TOCL)</i>. ACM, 2012. <a href=\"https://doi.org/10.1145/2362355.2362357\">https://doi.org/10.1145/2362355.2362357</a>.","mla":"Boker, Udi, and Orna Kupferman. “Translating to Co-Büchi Made Tight, Unified, and Useful.” <i>ACM Transactions on Computational Logic (TOCL)</i>, vol. 13, no. 4, 29, ACM, 2012, doi:<a href=\"https://doi.org/10.1145/2362355.2362357\">10.1145/2362355.2362357</a>."},"day":"01","department":[{"_id":"ToHe"}],"publist_id":"7326","month":"10","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","article_number":"29","publication":"ACM Transactions on Computational Logic (TOCL)","date_updated":"2021-01-12T08:01:03Z","abstract":[{"lang":"eng","text":"We solve the longstanding open problems of the blow-up involved in the translations, when possible, of a nondeterministic Büchi word automaton (NBW) to a nondeterministic co-Büchi word automaton (NCW) and to a deterministic co-Büchi word automaton (DCW). For the NBW to NCW translation, the currently known upper bound is 2o(nlog n) and the lower bound is 1.5n. We improve the upper bound to n2n and describe a matching lower bound of 2ω(n). For the NBW to DCW translation, the currently known upper bound is 2o(nlog n). We improve it to 2 o(n), which is asymptotically tight. Both of our upper-bound constructions are based on a simple subset construction, do not involve intermediate automata with richer acceptance conditions, and can be implemented symbolically. We continue and solve the open problems of translating nondeterministic Streett, Rabin, Muller, and parity word automata to NCW and to DCW. Going via an intermediate NBW is not optimal and we describe direct, simple, and asymptotically tight constructions, involving a 2o(n) blow-up. The constructions are variants of the subset construction, providing a unified approach for translating all common classes of automata to NCW and DCW. Beyond the theoretical importance of the results, we point to numerous applications of the new constructions. In particular, they imply a simple subset-construction based translation, when possible, of LTL to deterministic Büchi word automata."}],"year":"2012","issue":"4","doi":"10.1145/2362355.2362357","title":"Translating to Co-Büchi made tight, unified, and useful","author":[{"full_name":"Boker, Udi","last_name":"Boker","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi"},{"last_name":"Kupferman","full_name":"Kupferman, Orna","first_name":"Orna"}],"_id":"494"},{"status":"public","publication_status":"published","ec_funded":1,"project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"abstract":[{"lang":"eng","text":"An automaton with advice is a finite state automaton which has access to an additional fixed infinite string called an advice tape. We refine the Myhill-Nerode theorem to characterize the languages of finite strings that are accepted by automata with advice. We do the same for tree automata with advice."}],"doi":"10.4204/EPTCS.96.18","title":"A Myhill Nerode theorem for automata with advice","author":[{"first_name":"Alex","full_name":"Kruckman, Alex","last_name":"Kruckman"},{"id":"2EC51194-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha","full_name":"Rubin, Sasha","last_name":"Rubin"},{"first_name":"John","last_name":"Sheridan","full_name":"Sheridan, John"},{"full_name":"Zax, Ben","last_name":"Zax","first_name":"Ben"}],"_id":"495","has_accepted_license":"1","volume":96,"file":[{"date_created":"2018-12-12T10:15:31Z","file_id":"5152","creator":"system","file_size":97736,"relation":"main_file","file_name":"IST-2018-944-v1+1_2012_Rubin_A_Myhill.pdf","date_updated":"2020-07-14T12:46:35Z","content_type":"application/pdf","checksum":"56277f95edc9d531fa3bdc5f9579fda8","access_level":"open_access"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","conference":{"location":"Napoli, Italy","start_date":"2012-09-06","end_date":"2012-09-08","name":"GandALF: Games, Automata, Logics and Formal Verification"},"citation":{"chicago":"Kruckman, Alex, Sasha Rubin, John Sheridan, and Ben Zax. “A Myhill Nerode Theorem for Automata with Advice.” In <i>Proceedings GandALF 2012</i>, 96:238–46. Open Publishing Association, 2012. <a href=\"https://doi.org/10.4204/EPTCS.96.18\">https://doi.org/10.4204/EPTCS.96.18</a>.","mla":"Kruckman, Alex, et al. “A Myhill Nerode Theorem for Automata with Advice.” <i>Proceedings GandALF 2012</i>, vol. 96, Open Publishing Association, 2012, pp. 238–46, doi:<a href=\"https://doi.org/10.4204/EPTCS.96.18\">10.4204/EPTCS.96.18</a>.","apa":"Kruckman, A., Rubin, S., Sheridan, J., &#38; Zax, B. (2012). A Myhill Nerode theorem for automata with advice. In <i>Proceedings GandALF 2012</i> (Vol. 96, pp. 238–246). Napoli, Italy: Open Publishing Association. <a href=\"https://doi.org/10.4204/EPTCS.96.18\">https://doi.org/10.4204/EPTCS.96.18</a>","ieee":"A. Kruckman, S. Rubin, J. Sheridan, and B. Zax, “A Myhill Nerode theorem for automata with advice,” in <i>Proceedings GandALF 2012</i>, Napoli, Italy, 2012, vol. 96, pp. 238–246.","ista":"Kruckman A, Rubin S, Sheridan J, Zax B. 2012. A Myhill Nerode theorem for automata with advice. Proceedings GandALF 2012. GandALF: Games, Automata, Logics and Formal Verification, EPTCS, vol. 96, 238–246.","short":"A. Kruckman, S. Rubin, J. Sheridan, B. Zax, in:, Proceedings GandALF 2012, Open Publishing Association, 2012, pp. 238–246.","ama":"Kruckman A, Rubin S, Sheridan J, Zax B. A Myhill Nerode theorem for automata with advice. In: <i>Proceedings GandALF 2012</i>. Vol 96. Open Publishing Association; 2012:238-246. doi:<a href=\"https://doi.org/10.4204/EPTCS.96.18\">10.4204/EPTCS.96.18</a>"},"pubrep_id":"944","day":"07","ddc":["004"],"file_date_updated":"2020-07-14T12:46:35Z","month":"10","page":"238 - 246","publication":"Proceedings GandALF 2012","date_updated":"2021-01-12T08:01:04Z","alternative_title":["EPTCS"],"year":"2012","oa":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","publisher":"Open Publishing Association","intvolume":"        96","date_published":"2012-10-07T00:00:00Z","date_created":"2018-12-11T11:46:47Z","scopus_import":1,"department":[{"_id":"KrCh"}],"publist_id":"7325","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"oa":1,"title":"Interpretations in trees with countably many branches","author":[{"last_name":"Rabinovich","full_name":"Rabinovich, Alexander","first_name":"Alexander"},{"full_name":"Rubin, Sasha","last_name":"Rubin","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha"}],"_id":"496","abstract":[{"lang":"eng","text":"We study the expressive power of logical interpretations on the class of scattered trees, namely those with countably many infinite branches. Scattered trees can be thought of as the tree analogue of scattered linear orders. Every scattered tree has an ordinal rank that reflects the structure of its infinite branches. We prove, roughly, that trees and orders of large rank cannot be interpreted in scattered trees of small rank. We consider a quite general notion of interpretation: each element of the interpreted structure is represented by a set of tuples of subsets of the interpreting tree. Our trees are countable, not necessarily finitely branching, and may have finitely many unary predicates as labellings. We also show how to replace injective set-interpretations in (not necessarily scattered) trees by 'finitary' set-interpretations."}],"alternative_title":["LICS"],"year":"2012","doi":"10.1109/LICS.2012.65","project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"date_updated":"2021-01-12T08:01:05Z","status":"public","publication_status":"published","article_number":"6280474","ec_funded":1,"citation":{"short":"A. Rabinovich, S. Rubin, in:, IEEE, 2012.","ama":"Rabinovich A, Rubin S. Interpretations in trees with countably many branches. In: IEEE; 2012. doi:<a href=\"https://doi.org/10.1109/LICS.2012.65\">10.1109/LICS.2012.65</a>","ista":"Rabinovich A, Rubin S. 2012. Interpretations in trees with countably many branches. LICS: Symposium on Logic in Computer Science, LICS, , 6280474.","ieee":"A. Rabinovich and S. Rubin, “Interpretations in trees with countably many branches,” presented at the LICS: Symposium on Logic in Computer Science, Dubrovnik, Croatia, 2012.","apa":"Rabinovich, A., &#38; Rubin, S. (2012). Interpretations in trees with countably many branches. Presented at the LICS: Symposium on Logic in Computer Science, Dubrovnik, Croatia: IEEE. <a href=\"https://doi.org/10.1109/LICS.2012.65\">https://doi.org/10.1109/LICS.2012.65</a>","mla":"Rabinovich, Alexander, and Sasha Rubin. <i>Interpretations in Trees with Countably Many Branches</i>. 6280474, IEEE, 2012, doi:<a href=\"https://doi.org/10.1109/LICS.2012.65\">10.1109/LICS.2012.65</a>.","chicago":"Rabinovich, Alexander, and Sasha Rubin. “Interpretations in Trees with Countably Many Branches.” IEEE, 2012. <a href=\"https://doi.org/10.1109/LICS.2012.65\">https://doi.org/10.1109/LICS.2012.65</a>."},"department":[{"_id":"KrCh"}],"day":"01","month":"01","publist_id":"7324","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2012-01-01T00:00:00Z","date_created":"2018-12-11T11:46:47Z","oa_version":"Preprint","conference":{"end_date":"2012-06-28","start_date":"2012-06-25","location":"Dubrovnik, Croatia","name":"LICS: Symposium on Logic in Computer Science"},"scopus_import":1,"publisher":"IEEE","main_file_link":[{"url":"https://arise.or.at/pubpdf/Interpretations_in_Trees_with_Countably_Many_Branches.pdf","open_access":"1"}],"quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference"},{"citation":{"ieee":"K. Chatterjee, S. Chaubal, and P. Kamath, “Faster algorithms for alternating refinement relations,” presented at the EACSL: European Association for Computer Science Logic, Fontainebleau, France, 2012, vol. 16, pp. 167–182.","apa":"Chatterjee, K., Chaubal, S., &#38; Kamath, P. (2012). Faster algorithms for alternating refinement relations (Vol. 16, pp. 167–182). Presented at the EACSL: European Association for Computer Science Logic, Fontainebleau, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2012.167\">https://doi.org/10.4230/LIPIcs.CSL.2012.167</a>","short":"K. Chatterjee, S. Chaubal, P. Kamath, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 167–182.","ama":"Chatterjee K, Chaubal S, Kamath P. Faster algorithms for alternating refinement relations. In: Vol 16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2012:167-182. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2012.167\">10.4230/LIPIcs.CSL.2012.167</a>","ista":"Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating refinement relations. EACSL: European Association for Computer Science Logic, LIPIcs, vol. 16, 167–182.","chicago":"Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. “Faster Algorithms for Alternating Refinement Relations,” 16:167–82. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012. <a href=\"https://doi.org/10.4230/LIPIcs.CSL.2012.167\">https://doi.org/10.4230/LIPIcs.CSL.2012.167</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Faster Algorithms for Alternating Refinement Relations</i>. Vol. 16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2012, pp. 167–82, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CSL.2012.167\">10.4230/LIPIcs.CSL.2012.167</a>."},"pubrep_id":"943","day":"01","month":"09","file_date_updated":"2020-07-14T12:46:35Z","ddc":["004"],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","conference":{"name":"EACSL: European Association for Computer Science Logic","start_date":"2012-09-03","location":"Fontainebleau, France","end_date":"2012-09-06"},"file":[{"file_id":"4712","date_created":"2018-12-12T10:08:50Z","access_level":"open_access","content_type":"application/pdf","checksum":"f1b0dd99240800db2d7dbf9b5131fe5e","date_updated":"2020-07-14T12:46:35Z","file_name":"IST-2018-943-v1+1_2012_Chatterjee_Faster_Algorithms.pdf","file_size":471236,"relation":"main_file","creator":"system"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"has_accepted_license":"1","volume":16,"title":"Faster algorithms for alternating refinement relations","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Chaubal, Siddhesh","last_name":"Chaubal","first_name":"Siddhesh"},{"first_name":"Pritish","full_name":"Kamath, Pritish","last_name":"Kamath"}],"_id":"497","abstract":[{"text":"One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n 3·m) time as compared to the previous known O(n 6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n·m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm. © Krishnendu Chatterjee, Siddhesh Chaubal, and Pritish Kamath.","lang":"eng"}],"doi":"10.4230/LIPIcs.CSL.2012.167","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"status":"public","publication_status":"published","ec_funded":1,"department":[{"_id":"KrCh"}],"publist_id":"7323","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2012-09-01T00:00:00Z","date_created":"2018-12-11T11:46:48Z","scopus_import":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"        16","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"oa":1,"alternative_title":["LIPIcs"],"year":"2012","date_updated":"2023-02-23T12:23:32Z","related_material":{"record":[{"id":"5378","relation":"earlier_version","status":"public"}]},"page":"167 - 182"},{"date_published":"2012-12-01T00:00:00Z","date_created":"2018-12-11T11:46:48Z","department":[{"_id":"NiBa"}],"publist_id":"7322","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","publisher":"Wiley-Blackwell","intvolume":"         5","year":"2012","oa":1,"page":"913 - 924","publication":"Evolutionary Applications","date_updated":"2021-01-12T08:01:06Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","oa_version":"Published Version","pubrep_id":"942","citation":{"chicago":"Pickup, Melinda, David Field, David Rowell, and Andrew Young. “Predicting Local Adaptation in Fragmented Plant Populations: Implications for Restoration Genetics.” <i>Evolutionary Applications</i>. Wiley-Blackwell, 2012. <a href=\"https://doi.org/10.1111/j.1752-4571.2012.00284.x\">https://doi.org/10.1111/j.1752-4571.2012.00284.x</a>.","mla":"Pickup, Melinda, et al. “Predicting Local Adaptation in Fragmented Plant Populations: Implications for Restoration Genetics.” <i>Evolutionary Applications</i>, vol. 5, no. 8, Wiley-Blackwell, 2012, pp. 913–24, doi:<a href=\"https://doi.org/10.1111/j.1752-4571.2012.00284.x\">10.1111/j.1752-4571.2012.00284.x</a>.","ista":"Pickup M, Field D, Rowell D, Young A. 2012. Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. Evolutionary Applications. 5(8), 913–924.","short":"M. Pickup, D. Field, D. Rowell, A. Young, Evolutionary Applications 5 (2012) 913–924.","ama":"Pickup M, Field D, Rowell D, Young A. Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. <i>Evolutionary Applications</i>. 2012;5(8):913-924. doi:<a href=\"https://doi.org/10.1111/j.1752-4571.2012.00284.x\">10.1111/j.1752-4571.2012.00284.x</a>","ieee":"M. Pickup, D. Field, D. Rowell, and A. Young, “Predicting local adaptation in fragmented plant populations: Implications for restoration genetics,” <i>Evolutionary Applications</i>, vol. 5, no. 8. Wiley-Blackwell, pp. 913–924, 2012.","apa":"Pickup, M., Field, D., Rowell, D., &#38; Young, A. (2012). Predicting local adaptation in fragmented plant populations: Implications for restoration genetics. <i>Evolutionary Applications</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1752-4571.2012.00284.x\">https://doi.org/10.1111/j.1752-4571.2012.00284.x</a>"},"day":"01","file_date_updated":"2020-07-14T12:46:35Z","ddc":["576"],"month":"12","has_accepted_license":"1","volume":5,"tmp":{"short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"file":[{"access_level":"open_access","content_type":"application/pdf","checksum":"233007138606aca5a2f75f7ae1742f43","date_updated":"2020-07-14T12:46:35Z","file_name":"IST-2018-942-v1+1_Pickup_et_al-2012-Evolutionary_Applications.pdf","creator":"system","file_size":396136,"relation":"main_file","file_id":"4821","date_created":"2018-12-12T10:10:33Z"}],"abstract":[{"lang":"eng","text":"Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined whether spatial scale (0.7-600 km), environmental distance, quantitative (QST) and neutral (FST) genetic differentiation, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with QST and local population size for biomass. QST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low FST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration."}],"issue":"8","doi":"10.1111/j.1752-4571.2012.00284.x","title":"Predicting local adaptation in fragmented plant populations: Implications for restoration genetics","author":[{"full_name":"Pickup, Melinda","last_name":"Pickup","id":"2C78037E-F248-11E8-B48F-1D18A9856A87","first_name":"Melinda","orcid":"0000-0001-6118-0541"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Field, David","last_name":"Field","orcid":"0000-0002-4014-8478"},{"full_name":"Rowell, David","last_name":"Rowell","first_name":"David"},{"full_name":"Young, Andrew","last_name":"Young","first_name":"Andrew"}],"_id":"498","publication_status":"published","status":"public","acknowledgement":"We thank Graham Pickup, David Steer, Linda Broadhurst, Lan Li and Carole Elliott for technical assistance. The New\r\nSouth Wales Department of Environment and Climate Change, ACT Parks, Conservation and Lands and the\r\nDepartment of Sustainability and Environment in Victoria provided permits for seed and soil collection. We thank\r\nSpencer C. H. Barrett for comments that improved the quality of the manuscript.\r\n"},{"department":[{"_id":"MiSi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7314","date_published":"2012-04-30T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:46:51Z","intvolume":"       197","publisher":"Rockefeller University Press","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"oa":1,"year":"2012","publication":"Journal of Cell Biology","date_updated":"2021-01-12T08:01:11Z","article_type":"original","page":"347 - 349","day":"30","citation":{"apa":"Sixt, M. K. (2012). Cell migration: Fibroblasts find a new way to get ahead. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201204039\">https://doi.org/10.1083/jcb.201204039</a>","ieee":"M. K. Sixt, “Cell migration: Fibroblasts find a new way to get ahead,” <i>Journal of Cell Biology</i>, vol. 197, no. 3. Rockefeller University Press, pp. 347–349, 2012.","ama":"Sixt MK. Cell migration: Fibroblasts find a new way to get ahead. <i>Journal of Cell Biology</i>. 2012;197(3):347-349. doi:<a href=\"https://doi.org/10.1083/jcb.201204039\">10.1083/jcb.201204039</a>","ista":"Sixt MK. 2012. Cell migration: Fibroblasts find a new way to get ahead. Journal of Cell Biology. 197(3), 347–349.","short":"M.K. Sixt, Journal of Cell Biology 197 (2012) 347–349.","mla":"Sixt, Michael K. “Cell Migration: Fibroblasts Find a New Way to Get Ahead.” <i>Journal of Cell Biology</i>, vol. 197, no. 3, Rockefeller University Press, 2012, pp. 347–49, doi:<a href=\"https://doi.org/10.1083/jcb.201204039\">10.1083/jcb.201204039</a>.","chicago":"Sixt, Michael K. “Cell Migration: Fibroblasts Find a New Way to Get Ahead.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2012. <a href=\"https://doi.org/10.1083/jcb.201204039\">https://doi.org/10.1083/jcb.201204039</a>."},"file_date_updated":"2020-07-14T12:46:36Z","ddc":["570"],"month":"04","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","oa_version":"Published Version","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"file":[{"date_created":"2019-02-12T09:03:09Z","file_id":"5957","file_size":986566,"creator":"kschuh","relation":"main_file","file_name":"2012_CellBiology_Sixt.pdf","checksum":"45c02be33ebd99fc3077d60b9c90bdfa","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:36Z"}],"has_accepted_license":"1","volume":197,"article_processing_charge":"No","author":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"}],"title":"Cell migration: Fibroblasts find a new way to get ahead","_id":"506","issue":"3","doi":"10.1083/jcb.201204039","status":"public","publication_status":"published"},{"publisher":"IST Austria","file":[{"file_name":"IST-2012-002_IST-2012-0002.pdf","file_size":592098,"relation":"main_file","creator":"system","access_level":"open_access","checksum":"a03c08c1589dbb0c96183a8bcf3ab240","content_type":"application/pdf","date_updated":"2020-07-14T12:46:38Z","file_id":"5522","date_created":"2018-12-12T11:54:00Z"}],"has_accepted_license":"1","type":"technical_report","language":[{"iso":"eng"}],"pubrep_id":"10","citation":{"chicago":"Chatterjee, Krishnendu, and Yaron Velner. <i>Mean-Payoff Pushdown Games</i>. IST Austria, 2012. <a href=\"https://doi.org/10.15479/AT:IST-2012-0002\">https://doi.org/10.15479/AT:IST-2012-0002</a>.","mla":"Chatterjee, Krishnendu, and Yaron Velner. <i>Mean-Payoff Pushdown Games</i>. IST Austria, 2012, doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0002\">10.15479/AT:IST-2012-0002</a>.","short":"K. Chatterjee, Y. Velner, Mean-Payoff Pushdown Games, IST Austria, 2012.","ista":"Chatterjee K, Velner Y. 2012. Mean-payoff pushdown games, IST Austria, 33p.","ama":"Chatterjee K, Velner Y. <i>Mean-Payoff Pushdown Games</i>. IST Austria; 2012. doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0002\">10.15479/AT:IST-2012-0002</a>","apa":"Chatterjee, K., &#38; Velner, Y. (2012). <i>Mean-payoff pushdown games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2012-0002\">https://doi.org/10.15479/AT:IST-2012-0002</a>","ieee":"K. Chatterjee and Y. Velner, <i>Mean-payoff pushdown games</i>. IST Austria, 2012."},"department":[{"_id":"KrCh"}],"day":"02","file_date_updated":"2020-07-14T12:46:38Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000","005"],"month":"07","date_published":"2012-07-02T00:00:00Z","date_created":"2018-12-12T11:38:59Z","oa_version":"Published Version","publication_identifier":{"issn":["2664-1690"]},"date_updated":"2023-02-23T11:05:50Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"2956"}]},"publication_status":"published","status":"public","page":"33","oa":1,"title":"Mean-payoff pushdown games","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Velner, Yaron","last_name":"Velner","first_name":"Yaron"}],"_id":"5377","abstract":[{"lang":"eng","text":"Two-player games on graphs are central in many problems in formal verification and program analysis such as synthesis and verification of open systems. In this work we consider solving recursive game graphs (or pushdown game graphs) that can model the control flow of sequential programs with recursion. While pushdown games have been studied before with qualitative objectives, such as reachability and ω-regular objectives, in this work we study for the first time such games with the most well-studied quantitative objective, namely, mean-payoff objectives. In pushdown games two types of strategies are relevant: (1) global strategies, that depend on the entire global history; and (2) modular strategies, that have only local memory and thus do not depend on the context of invocation, but only on the history of the current invocation of the module. Our main results are as follows: (1) One-player pushdown games with mean-payoff objectives under global strategies are decidable in polynomial time. (2) Two- player pushdown games with mean-payoff objectives under global strategies are undecidable. (3) One-player pushdown games with mean-payoff objectives under modular strategies are NP- hard. (4) Two-player pushdown games with mean-payoff objectives under modular strategies can be solved in NP (i.e., both one-player and two-player pushdown games with mean-payoff objectives under modular strategies are NP-complete). We also establish the optimal strategy complexity showing that global strategies for mean-payoff objectives require infinite memory even in one-player pushdown games; and memoryless modular strategies are sufficient in two- player pushdown games. Finally we also show that all the problems have the same complexity if the stack boundedness condition is added, where along with the mean-payoff objective the player must also ensure that the stack height is bounded."}],"alternative_title":["IST Austria Technical Report"],"year":"2012","doi":"10.15479/AT:IST-2012-0002"},{"page":"21","publication_status":"published","status":"public","related_material":{"record":[{"id":"497","relation":"later_version","status":"public"}]},"date_updated":"2023-02-23T12:21:38Z","publication_identifier":{"issn":["2664-1690"]},"doi":"10.15479/AT:IST-2012-0001","year":"2012","alternative_title":["IST Austria Technical Report"],"abstract":[{"text":"One central issue in the formal design and analysis of reactive systems is the notion of refinement that asks whether all behaviors of the implementation is allowed by the specification. The local interpretation of behavior leads to the notion of simulation. Alternating transition systems (ATSs) provide a general model for composite reactive systems, and the simulation relation for ATSs is known as alternating simulation. The simulation relation for fair transition systems is called fair simulation. In this work our main contributions are as follows: (1) We present an improved algorithm for fair simulation with Büchi fairness constraints; our algorithm requires O(n3 · m) time as compared to the previous known O(n6)-time algorithm, where n is the number of states and m is the number of transitions. (2) We present a game based algorithm for alternating simulation that requires O(m2)-time as compared to the previous known O((n · m)2)-time algorithm, where n is the number of states and m is the size of transition relation. (3) We present an iterative algorithm for alternating simulation that matches the time complexity of the game based algorithm, but is more space efficient than the game based algorithm.","lang":"eng"}],"_id":"5378","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"full_name":"Chaubal, Siddhesh","last_name":"Chaubal","first_name":"Siddhesh"},{"first_name":"Pritish","last_name":"Kamath","full_name":"Kamath, Pritish"}],"oa":1,"title":"Faster algorithms for alternating refinement relations","language":[{"iso":"eng"}],"type":"technical_report","has_accepted_license":"1","file":[{"file_name":"IST-2012-0001_IST-2012-0001.pdf","relation":"main_file","file_size":394256,"creator":"system","date_updated":"2020-07-14T12:46:39Z","access_level":"open_access","checksum":"ec8d1857cc7095d3de5107a0162ced37","content_type":"application/pdf","file_id":"5489","date_created":"2018-12-12T11:53:28Z"}],"publisher":"IST Austria","oa_version":"Published Version","date_created":"2018-12-12T11:38:59Z","date_published":"2012-07-04T00:00:00Z","month":"07","file_date_updated":"2020-07-14T12:46:39Z","ddc":["000","005"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"KrCh"}],"day":"04","citation":{"ieee":"K. Chatterjee, S. Chaubal, and P. Kamath, <i>Faster algorithms for alternating refinement relations</i>. IST Austria, 2012.","apa":"Chatterjee, K., Chaubal, S., &#38; Kamath, P. (2012). <i>Faster algorithms for alternating refinement relations</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">https://doi.org/10.15479/AT:IST-2012-0001</a>","ista":"Chatterjee K, Chaubal S, Kamath P. 2012. Faster algorithms for alternating refinement relations, IST Austria, 21p.","short":"K. Chatterjee, S. Chaubal, P. Kamath, Faster Algorithms for Alternating Refinement Relations, IST Austria, 2012.","ama":"Chatterjee K, Chaubal S, Kamath P. <i>Faster Algorithms for Alternating Refinement Relations</i>. IST Austria; 2012. doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">10.15479/AT:IST-2012-0001</a>","chicago":"Chatterjee, Krishnendu, Siddhesh Chaubal, and Pritish Kamath. <i>Faster Algorithms for Alternating Refinement Relations</i>. IST Austria, 2012. <a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">https://doi.org/10.15479/AT:IST-2012-0001</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Faster Algorithms for Alternating Refinement Relations</i>. IST Austria, 2012, doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0001\">10.15479/AT:IST-2012-0001</a>."},"pubrep_id":"14"},{"title":"Approximating marginals using discrete energy minimization","oa":1,"author":[{"id":"476A2FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Filip","full_name":"Korc, Filip","last_name":"Korc"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"},{"last_name":"Lampert","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887"}],"_id":"5396","abstract":[{"lang":"eng","text":"We consider the problem of inference in agraphical model with binary variables. While in theory it is arguably preferable to compute marginal probabilities, in practice researchers often use MAP inference due to the availability of efficient discrete optimization algorithms. We bridge the gap between the two approaches by introducing the Discrete  Marginals technique in which approximate marginals are obtained by minimizing an objective function with unary and pair-wise terms over a discretized domain. This allows the use of techniques originally devel-oped for MAP-MRF inference and learning. We explore two ways to set up the objective function - by discretizing the Bethe free energy and by learning it  from training data. Experimental results show that for certain types of graphs a learned function can out-perform the  Bethe approximation. We also establish a link between the Bethe free energy and submodular functions."}],"year":"2012","alternative_title":["IST Austria Technical Report"],"doi":"10.15479/AT:IST-2012-0003","publication_identifier":{"issn":["2664-1690"]},"date_updated":"2023-02-23T11:13:22Z","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"3124"}]},"status":"public","publication_status":"published","page":"13","citation":{"short":"F. Korc, V. Kolmogorov, C. Lampert, Approximating Marginals Using Discrete Energy Minimization, IST Austria, 2012.","ista":"Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete energy minimization, IST Austria, 13p.","ama":"Korc F, Kolmogorov V, Lampert C. <i>Approximating Marginals Using Discrete Energy Minimization</i>. IST Austria; 2012. doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0003\">10.15479/AT:IST-2012-0003</a>","apa":"Korc, F., Kolmogorov, V., &#38; Lampert, C. (2012). <i>Approximating marginals using discrete energy minimization</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2012-0003\">https://doi.org/10.15479/AT:IST-2012-0003</a>","ieee":"F. Korc, V. Kolmogorov, and C. Lampert, <i>Approximating marginals using discrete energy minimization</i>. IST Austria, 2012.","chicago":"Korc, Filip, Vladimir Kolmogorov, and Christoph Lampert. <i>Approximating Marginals Using Discrete Energy Minimization</i>. IST Austria, 2012. <a href=\"https://doi.org/10.15479/AT:IST-2012-0003\">https://doi.org/10.15479/AT:IST-2012-0003</a>.","mla":"Korc, Filip, et al. <i>Approximating Marginals Using Discrete Energy Minimization</i>. IST Austria, 2012, doi:<a href=\"https://doi.org/10.15479/AT:IST-2012-0003\">10.15479/AT:IST-2012-0003</a>."},"pubrep_id":"36","department":[{"_id":"VlKo"},{"_id":"ChLa"}],"day":"23","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:46:44Z","ddc":["000"],"date_published":"2012-07-23T00:00:00Z","date_created":"2018-12-12T11:39:06Z","oa_version":"Published Version","publisher":"IST Austria","file":[{"file_id":"5490","date_created":"2018-12-12T11:53:29Z","access_level":"open_access","content_type":"application/pdf","checksum":"7e0ba85ad123b13223aaf6cdde2d288c","date_updated":"2020-07-14T12:46:44Z","file_name":"IST-2012-0003_IST-2012-0003.pdf","file_size":618744,"relation":"main_file","creator":"system"}],"has_accepted_license":"1","language":[{"iso":"eng"}],"type":"technical_report"},{"has_accepted_license":"1","type":"report","language":[{"iso":"eng"}],"file":[{"file_id":"5472","date_created":"2018-12-12T11:53:11Z","file_name":"IST-2012-103-v1+1_Actual_state_of_research_data_@_IST_Austria.pdf","relation":"main_file","creator":"system","file_size":238544,"access_level":"open_access","content_type":"application/pdf","checksum":"e0a7c041eea1ca4b70ab6f9ec5177f4e","date_updated":"2020-07-14T12:46:44Z"}],"publisher":"IST Austria","date_published":"2012-11-12T00:00:00Z","oa_version":"Published Version","date_created":"2018-12-12T11:39:06Z","day":"12","department":[{"_id":"E-Lib"}],"citation":{"apa":"Porsche, J. (2012). <i>Actual state of research data @ ISTAustria</i>. IST Austria.","ieee":"J. Porsche, <i>Actual state of research data @ ISTAustria</i>. IST Austria, 2012.","short":"J. Porsche, Actual State of Research Data @ ISTAustria, IST Austria, 2012.","ama":"Porsche J. <i>Actual State of Research Data @ ISTAustria</i>. IST Austria; 2012.","ista":"Porsche J. 2012. Actual state of research data @ ISTAustria, IST Austria,p.","mla":"Porsche, Jana. <i>Actual State of Research Data @ ISTAustria</i>. IST Austria, 2012.","chicago":"Porsche, Jana. <i>Actual State of Research Data @ ISTAustria</i>. IST Austria, 2012."},"pubrep_id":"103","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"11","ddc":["020"],"file_date_updated":"2020-07-14T12:46:44Z","publication_status":"published","status":"public","date_updated":"2020-07-14T23:04:49Z","year":"2012","abstract":[{"lang":"eng","text":"This document is created as a part of the project “Repository for Research Data on IST Austria”. It summarises the actual state of research data at IST Austria, based on survey results. It supports the choice of appropriate software, which would best fit the requirements of their users, the researchers."}],"author":[{"id":"3252EDC2-F248-11E8-B48F-1D18A9856A87","first_name":"Jana","full_name":"Porsche, Jana","last_name":"Porsche"}],"oa":1,"title":"Actual state of research data @ ISTAustria","_id":"5398"},{"file":[{"access_level":"open_access","checksum":"68415837a315de3cc4d120f6019d752c","content_type":"application/pdf","date_updated":"2020-07-14T12:47:10Z","file_name":"2012_ATVA_Gupta.pdf","relation":"main_file","creator":"dernst","file_size":465502,"file_id":"5746","date_created":"2018-12-18T13:07:35Z"}],"has_accepted_license":"1","volume":7561,"article_processing_charge":"No","citation":{"mla":"Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.” <i>Automated Technology for Verification and Analysis</i>, vol. 7561, Springer Berlin Heidelberg, 2012, pp. 107–21, doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">10.1007/978-3-642-33386-6_10</a>.","chicago":"Gupta, Ashutosh. “Improved Single Pass Algorithms for Resolution Proof Reduction.” In <i>Automated Technology for Verification and Analysis</i>, 7561:107–21. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">https://doi.org/10.1007/978-3-642-33386-6_10</a>.","ista":"Gupta A. 2012.Improved Single Pass Algorithms for Resolution Proof Reduction. In: Automated Technology for Verification and Analysis. vol. 7561, 107–121.","short":"A. Gupta, in:, Automated Technology for Verification and Analysis, Springer Berlin Heidelberg, Berlin, Heidelberg, 2012, pp. 107–121.","ama":"Gupta A. Improved Single Pass Algorithms for Resolution Proof Reduction. In: <i>Automated Technology for Verification and Analysis</i>. Vol 7561. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg; 2012:107-121. doi:<a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">10.1007/978-3-642-33386-6_10</a>","ieee":"A. Gupta, “Improved Single Pass Algorithms for Resolution Proof Reduction,” in <i>Automated Technology for Verification and Analysis</i>, vol. 7561, Berlin, Heidelberg: Springer Berlin Heidelberg, 2012, pp. 107–121.","apa":"Gupta, A. (2012). Improved Single Pass Algorithms for Resolution Proof Reduction. In <i>Automated Technology for Verification and Analysis</i> (Vol. 7561, pp. 107–121). Berlin, Heidelberg: Springer Berlin Heidelberg. <a href=\"https://doi.org/10.1007/978-3-642-33386-6_10\">https://doi.org/10.1007/978-3-642-33386-6_10</a>"},"pubrep_id":"180","file_date_updated":"2020-07-14T12:47:10Z","ddc":["005"],"oa_version":"None","conference":{"name":"ATVA 2012","start_date":"2012-10-03","location":"Thiruvananthapuram, Kerala, India","end_date":"2012-10-06"},"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"isbn":["9783642333859","9783642333866"]},"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"}],"status":"public","publication_status":"published","place":"Berlin, Heidelberg","ec_funded":1,"title":"Improved Single Pass Algorithms for Resolution Proof Reduction","author":[{"first_name":"Ashutosh","full_name":"Gupta, Ashutosh","last_name":"Gupta"}],"_id":"5745","doi":"10.1007/978-3-642-33386-6_10","series_title":"LNCS","publisher":"Springer Berlin Heidelberg","intvolume":"      7561","type":"book_chapter","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2012-01-01T00:00:00Z","date_created":"2018-12-18T13:01:46Z","publication":"Automated Technology for Verification and Analysis","date_updated":"2023-09-05T14:15:29Z","page":"107-121","oa":1,"year":"2012"},{"publication_identifier":{"issn":["1812-9471"]},"publication_status":"published","acknowledgement":"This work is supported by the Austrian Science Fund (FWF), Project P22025-N18.\r\n","status":"public","_id":"6588","title":"Elementary solutions of the Bernstein problem on two intervals","author":[{"full_name":"Pausinger, Florian","last_name":"Pausinger","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0002-8379-3768"}],"abstract":[{"text":"First we note that the best polynomial approximation to vertical bar x vertical bar on the set, which consists of an interval on the positive half-axis and a point on the negative half-axis, can be given by means of the classical Chebyshev polynomials. Then we explore the cases when a solution of the related problem on two intervals can be given in elementary functions.","lang":"eng"}],"issue":"1","article_processing_charge":"No","volume":8,"month":"01","citation":{"mla":"Pausinger, Florian. “Elementary Solutions of the Bernstein Problem on Two Intervals.” <i>Journal of Mathematical Physics, Analysis, Geometry</i>, vol. 8, no. 1, B. Verkin Institute for Low Temperature Physics and Engineering, 2012, pp. 63–78.","chicago":"Pausinger, Florian. “Elementary Solutions of the Bernstein Problem on Two Intervals.” <i>Journal of Mathematical Physics, Analysis, Geometry</i>. B. Verkin Institute for Low Temperature Physics and Engineering, 2012.","ista":"Pausinger F. 2012. Elementary solutions of the Bernstein problem on two intervals. Journal of Mathematical Physics, Analysis, Geometry. 8(1), 63–78.","ama":"Pausinger F. Elementary solutions of the Bernstein problem on two intervals. <i>Journal of Mathematical Physics, Analysis, Geometry</i>. 2012;8(1):63-78.","short":"F. Pausinger, Journal of Mathematical Physics, Analysis, Geometry 8 (2012) 63–78.","ieee":"F. Pausinger, “Elementary solutions of the Bernstein problem on two intervals,” <i>Journal of Mathematical Physics, Analysis, Geometry</i>, vol. 8, no. 1. B. Verkin Institute for Low Temperature Physics and Engineering, pp. 63–78, 2012.","apa":"Pausinger, F. (2012). Elementary solutions of the Bernstein problem on two intervals. <i>Journal of Mathematical Physics, Analysis, Geometry</i>. B. Verkin Institute for Low Temperature Physics and Engineering."},"day":"01","oa_version":"Published Version","date_updated":"2023-10-16T09:41:31Z","publication":"Journal of Mathematical Physics, Analysis, Geometry","page":"63-78","article_type":"original","oa":1,"year":"2012","publisher":"B. Verkin Institute for Low Temperature Physics and Engineering","main_file_link":[{"url":"http://mi.mathnet.ru/eng/jmag525","open_access":"1"}],"intvolume":"         8","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","isi":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"date_created":"2019-06-27T08:16:56Z","scopus_import":"1","external_id":{"isi":["000301173600004"]},"date_published":"2012-01-01T00:00:00Z"},{"month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"ama":"Lohse K, Barton NH, Stone G, Melika G. Data from: A likelihood-based comparison of population histories in a parasitoid guild. 2012. doi:<a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">10.5061/DRYAD.0G0FS</a>","ista":"Lohse K, Barton NH, Stone G, Melika G. 2012. Data from: A likelihood-based comparison of population histories in a parasitoid guild, Dryad, <a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">10.5061/DRYAD.0G0FS</a>.","short":"K. Lohse, N.H. Barton, G. Stone, G. Melika, (2012).","apa":"Lohse, K., Barton, N. H., Stone, G., &#38; Melika, G. (2012). Data from: A likelihood-based comparison of population histories in a parasitoid guild. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">https://doi.org/10.5061/DRYAD.0G0FS</a>","ieee":"K. Lohse, N. H. Barton, G. Stone, and G. Melika, “Data from: A likelihood-based comparison of population histories in a parasitoid guild.” Dryad, 2012.","mla":"Lohse, Konrad, et al. <i>Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild</i>. Dryad, 2012, doi:<a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">10.5061/DRYAD.0G0FS</a>.","chicago":"Lohse, Konrad, Nicholas H Barton, Graham Stone, and George Melika. “Data from: A Likelihood-Based Comparison of Population Histories in a Parasitoid Guild.” Dryad, 2012. <a href=\"https://doi.org/10.5061/DRYAD.0G0FS\">https://doi.org/10.5061/DRYAD.0G0FS</a>."},"day":"08","department":[{"_id":"NiBa"}],"date_created":"2023-05-23T17:01:02Z","oa_version":"Published Version","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_published":"2012-06-08T00:00:00Z","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.0g0fs"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"article_processing_charge":"No","type":"research_data_reference","_id":"13075","title":"Data from: A likelihood-based comparison of population histories in a parasitoid guild","oa":1,"author":[{"last_name":"Lohse","full_name":"Lohse, Konrad","first_name":"Konrad"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H"},{"first_name":"Graham","full_name":"Stone, Graham","last_name":"Stone"},{"last_name":"Melika","full_name":"Melika, George","first_name":"George"}],"doi":"10.5061/DRYAD.0G0FS","abstract":[{"lang":"eng","text":"Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, C. semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and - using triplet alignments of intronic loci - quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times."}],"year":"2012","date_updated":"2025-05-28T11:56:58Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2968"}]},"status":"public"},{"abstract":[{"text":"Software model checking, as an undecidable problem, has three possible outcomes: (1) the program satisfies the specification, (2) the program does not satisfy the specification, and (3) the model checker fails. The third outcome usually manifests itself in a space-out, time-out, or one component of the verification tool giving up; in all of these failing cases, significant computation is performed by the verification tool before the failure, but no result is reported. We propose to reformulate the model-checking problem as follows, in order to have the verification tool report a summary of the performed work even in case of failure: given a program and a specification, the model checker returns a condition Ψ - usually a state predicate - such that the program satisfies the specification under the condition Ψ - that is, as long as the program does not leave the states in which Ψ is satisfied. In our experiments, we investigated as one major application of conditional model checking the sequential combination of model checkers with information passing. We give the condition that one model checker produces, as input to a second conditional model checker, such that the verification problem for the second is restricted to the part of the state space that is not covered by the condition, i.e., the second model checker works on the problems that the first model checker could not solve. Our experiments demonstrate that repeated application of conditional model checkers, passing information from one model checker to the next, can significantly improve the verification results and performance, i.e., we can now verify programs that we could not verify before.","lang":"eng"}],"doi":"10.1145/2393596.2393664","author":[{"first_name":"Dirk","last_name":"Beyer","full_name":"Beyer, Dirk"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Mehmet","full_name":"Keremoglu, Mehmet","last_name":"Keremoglu"},{"last_name":"Wendler","full_name":"Wendler, Philipp","first_name":"Philipp"}],"title":"Conditional model checking: A technique to pass information between verifiers","_id":"1384","acknowledgement":"This  research  was  supported  by  the  Canadian  NSERC grant   RGPIN   341819-07,    the   ERC   Advanced   Grant QUAREM, and the Austrian Science Fund NFN RiSE.","publication_status":"published","status":"public","ec_funded":1,"project":[{"grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"conference":{"end_date":"2012-11-16","start_date":"2012-11-11","location":"Cary, NC, USA","name":"FSE: Foundations of Software Engineering"},"oa_version":"Preprint","day":"01","citation":{"ama":"Beyer D, Henzinger TA, Keremoglu M, Wendler P. Conditional model checking: A technique to pass information between verifiers. In: <i>Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering</i>. ACM; 2012. doi:<a href=\"https://doi.org/10.1145/2393596.2393664\">10.1145/2393596.2393664</a>","short":"D. Beyer, T.A. Henzinger, M. Keremoglu, P. Wendler, in:, Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering, ACM, 2012.","ista":"Beyer D, Henzinger TA, Keremoglu M, Wendler P. 2012. Conditional model checking: A technique to pass information between verifiers. Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering. FSE: Foundations of Software Engineering, 57.","apa":"Beyer, D., Henzinger, T. A., Keremoglu, M., &#38; Wendler, P. (2012). Conditional model checking: A technique to pass information between verifiers. In <i>Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering</i>. Cary, NC, USA: ACM. <a href=\"https://doi.org/10.1145/2393596.2393664\">https://doi.org/10.1145/2393596.2393664</a>","ieee":"D. Beyer, T. A. Henzinger, M. Keremoglu, and P. Wendler, “Conditional model checking: A technique to pass information between verifiers,” in <i>Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering</i>, Cary, NC, USA, 2012.","mla":"Beyer, Dirk, et al. “Conditional Model Checking: A Technique to Pass Information between Verifiers.” <i>Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering</i>, 57, ACM, 2012, doi:<a href=\"https://doi.org/10.1145/2393596.2393664\">10.1145/2393596.2393664</a>.","chicago":"Beyer, Dirk, Thomas A Henzinger, Mehmet Keremoglu, and Philipp Wendler. “Conditional Model Checking: A Technique to Pass Information between Verifiers.” In <i>Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering</i>. ACM, 2012. <a href=\"https://doi.org/10.1145/2393596.2393664\">https://doi.org/10.1145/2393596.2393664</a>."},"month":"11","year":"2012","oa":1,"article_number":"57","publication":"Proceedings of the ACM SIGSOFT 20th International Symposium on the Foundations of Software Engineering","date_updated":"2021-01-12T06:50:18Z","date_published":"2012-11-01T00:00:00Z","scopus_import":1,"date_created":"2018-12-11T11:51:42Z","department":[{"_id":"ToHe"}],"publist_id":"5826","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.6926"}],"publisher":"ACM"},{"issue":"6100","abstract":[{"text":"The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation before fertilization, but the targeting preferences, mechanism, and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell and preferentially targets small, AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA–directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes and likely contributes to stable silencing of transposable elements across generations.","lang":"eng"}],"doi":"10.1126/science.1224839","author":[{"first_name":"Christian A.","last_name":"Ibarra","full_name":"Ibarra, Christian A."},{"last_name":"Feng","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi"},{"full_name":"Schoft, Vera K.","last_name":"Schoft","first_name":"Vera K."},{"last_name":"Hsieh","full_name":"Hsieh, Tzung-Fu","first_name":"Tzung-Fu"},{"first_name":"Rie","full_name":"Uzawa, Rie","last_name":"Uzawa"},{"first_name":"Jessica A.","last_name":"Rodrigues","full_name":"Rodrigues, Jessica A."},{"first_name":"Assaf","last_name":"Zemach","full_name":"Zemach, Assaf"},{"last_name":"Chumak","full_name":"Chumak, Nina","first_name":"Nina"},{"first_name":"Adriana","full_name":"Machlicova, Adriana","last_name":"Machlicova"},{"last_name":"Nishimura","full_name":"Nishimura, Toshiro","first_name":"Toshiro"},{"first_name":"Denisse","full_name":"Rojas, Denisse","last_name":"Rojas"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"first_name":"Hisashi","full_name":"Tamaru, Hisashi","last_name":"Tamaru"},{"orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman"}],"title":"Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes","_id":"9451","publication_status":"published","status":"public","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"oa_version":"Published Version","day":"14","citation":{"chicago":"Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” <i>Science</i>. American Association for the Advancement of Science, 2012. <a href=\"https://doi.org/10.1126/science.1224839\">https://doi.org/10.1126/science.1224839</a>.","mla":"Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes.” <i>Science</i>, vol. 337, no. 6100, American Association for the Advancement of Science, 2012, pp. 1360–64, doi:<a href=\"https://doi.org/10.1126/science.1224839\">10.1126/science.1224839</a>.","apa":"Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1224839\">https://doi.org/10.1126/science.1224839</a>","ieee":"C. A. Ibarra <i>et al.</i>, “Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes,” <i>Science</i>, vol. 337, no. 6100. American Association for the Advancement of Science, pp. 1360–1364, 2012.","ista":"Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A, Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman D. 2012. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science. 337(6100), 1360–1364.","ama":"Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. <i>Science</i>. 2012;337(6100):1360-1364. doi:<a href=\"https://doi.org/10.1126/science.1224839\">10.1126/science.1224839</a>","short":"C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues, A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H. Tamaru, D. Zilberman, Science 337 (2012) 1360–1364."},"pmid":1,"ddc":["580"],"month":"09","has_accepted_license":"1","volume":337,"article_processing_charge":"No","year":"2012","oa":1,"article_type":"original","page":"1360-1364","publication":"Science","date_updated":"2021-12-14T08:28:51Z","date_published":"2012-09-14T00:00:00Z","external_id":{"pmid":["22984074"]},"extern":"1","scopus_import":"1","date_created":"2021-06-04T07:51:31Z","department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"       337","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/","open_access":"1"}],"publisher":"American Association for the Advancement of Science"},{"date_created":"2021-06-07T10:55:27Z","scopus_import":"1","external_id":{"pmid":["23071449"]},"extern":"1","date_published":"2012-10-11T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"publisher":"Public Library of Science","main_file_link":[{"url":"https://doi.org/10.1371/journal.pgen.1002988","open_access":"1"}],"intvolume":"         8","year":"2012","oa":1,"article_number":"e1002988","article_type":"original","date_updated":"2021-12-14T08:29:57Z","publication":"PLoS Genetics","oa_version":"Published Version","pmid":1,"month":"10","citation":{"chicago":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” <i>PLoS Genetics</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pgen.1002988\">https://doi.org/10.1371/journal.pgen.1002988</a>.","mla":"Coleman-Derr, Devin, and Daniel Zilberman. “Deposition of Histone Variant H2A.Z within Gene Bodies Regulates Responsive Genes.” <i>PLoS Genetics</i>, vol. 8, no. 10, e1002988, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002988\">10.1371/journal.pgen.1002988</a>.","ieee":"D. Coleman-Derr and D. Zilberman, “Deposition of histone variant H2A.Z within gene bodies regulates responsive genes,” <i>PLoS Genetics</i>, vol. 8, no. 10. Public Library of Science, 2012.","apa":"Coleman-Derr, D., &#38; Zilberman, D. (2012). Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1002988\">https://doi.org/10.1371/journal.pgen.1002988</a>","ama":"Coleman-Derr D, Zilberman D. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. <i>PLoS Genetics</i>. 2012;8(10). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002988\">10.1371/journal.pgen.1002988</a>","ista":"Coleman-Derr D, Zilberman D. 2012. Deposition of histone variant H2A.Z within gene bodies regulates responsive genes. PLoS Genetics. 8(10), e1002988.","short":"D. Coleman-Derr, D. Zilberman, PLoS Genetics 8 (2012)."},"day":"11","volume":8,"article_processing_charge":"No","doi":"10.1371/journal.pgen.1002988","abstract":[{"lang":"eng","text":"The regulation of eukaryotic chromatin relies on interactions between many epigenetic factors, including histone modifications, DNA methylation, and the incorporation of histone variants. H2A.Z, one of the most conserved but enigmatic histone variants that is enriched at the transcriptional start sites of genes, has been implicated in a variety of chromosomal processes. Recently, we reported a genome-wide anticorrelation between H2A.Z and DNA methylation, an epigenetic hallmark of heterochromatin that has also been found in the bodies of active genes in plants and animals. Here, we investigate the basis of this anticorrelation using a novel h2a.z loss-of-function line in Arabidopsis thaliana. Through genome-wide bisulfite sequencing, we demonstrate that loss of H2A.Z in Arabidopsis has only a minor effect on the level or profile of DNA methylation in genes, and we propose that the global anticorrelation between DNA methylation and H2A.Z is primarily caused by the exclusion of H2A.Z from methylated DNA. RNA sequencing and genomic mapping of H2A.Z show that H2A.Z enrichment across gene bodies, rather than at the TSS, is correlated with lower transcription levels and higher measures of gene responsiveness. Loss of H2A.Z causes misregulation of many genes that are disproportionately associated with response to environmental and developmental stimuli. We propose that H2A.Z deposition in gene bodies promotes variability in levels and patterns of gene expression, and that a major function of genic DNA methylation is to exclude H2A.Z from constitutively expressed genes."}],"issue":"10","_id":"9497","title":"Deposition of histone variant H2A.Z within gene bodies regulates responsive genes","author":[{"full_name":"Coleman-Derr, Devin","last_name":"Coleman-Derr","first_name":"Devin"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"publication_status":"published","status":"public","publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]}},{"oa_version":"Published Version","pmid":1,"month":"03","day":"22","citation":{"chicago":"Kim, Sang Yeol, Jungeun Lee, Leor Eshed-Williams, Daniel Zilberman, and Z. Renee Sung. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” <i>PLoS Genetics</i>. Public Library of Science, 2012. <a href=\"https://doi.org/10.1371/journal.pgen.1002512\">https://doi.org/10.1371/journal.pgen.1002512</a>.","mla":"Kim, Sang Yeol, et al. “EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development.” <i>PLoS Genetics</i>, vol. 8, no. 3, e1002512, Public Library of Science, 2012, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002512\">10.1371/journal.pgen.1002512</a>.","ama":"Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. <i>PLoS Genetics</i>. 2012;8(3). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1002512\">10.1371/journal.pgen.1002512</a>","ista":"Kim SY, Lee J, Eshed-Williams L, Zilberman D, Sung ZR. 2012. EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. PLoS Genetics. 8(3), e1002512.","short":"S.Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, Z.R. Sung, PLoS Genetics 8 (2012).","apa":"Kim, S. Y., Lee, J., Eshed-Williams, L., Zilberman, D., &#38; Sung, Z. R. (2012). EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1002512\">https://doi.org/10.1371/journal.pgen.1002512</a>","ieee":"S. Y. Kim, J. Lee, L. Eshed-Williams, D. Zilberman, and Z. R. Sung, “EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development,” <i>PLoS Genetics</i>, vol. 8, no. 3. Public Library of Science, 2012."},"article_processing_charge":"No","volume":8,"doi":"10.1371/journal.pgen.1002512","issue":"3","abstract":[{"lang":"eng","text":"EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination. Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment levels of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying cell fates during growth and differentiation. H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism."}],"_id":"9499","author":[{"first_name":"Sang Yeol","last_name":"Kim","full_name":"Kim, Sang Yeol"},{"first_name":"Jungeun","last_name":"Lee","full_name":"Lee, Jungeun"},{"last_name":"Eshed-Williams","full_name":"Eshed-Williams, Leor","first_name":"Leor"},{"orcid":"0000-0002-0123-8649","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","full_name":"Zilberman, Daniel"},{"full_name":"Sung, Z. Renee","last_name":"Sung","first_name":"Z. Renee"}],"title":"EMF1 and PRC2 cooperate to repress key regulators of Arabidopsis development","publication_status":"published","status":"public","publication_identifier":{"issn":["1553-7390"],"eissn":["1553-7404"]},"scopus_import":"1","date_created":"2021-06-07T11:07:56Z","external_id":{"pmid":["22457632"]},"date_published":"2012-03-22T00:00:00Z","extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaZi"}],"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1371/journal.pgen.1002512"}],"intvolume":"         8","publisher":"Public Library of Science","year":"2012","oa":1,"article_type":"original","article_number":"e1002512","date_updated":"2021-12-14T08:31:14Z","publication":"PLoS Genetics"},{"publication_identifier":{"issn":["0959-437X"]},"status":"public","publication_status":"published","author":[{"full_name":"Huff, Jason T.","last_name":"Huff","first_name":"Jason T."},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"title":"Regulation of biological accuracy, precision, and memory by plant chromatin organization","_id":"9528","issue":"2","abstract":[{"lang":"eng","text":"Accumulating evidence points toward diverse functions for plant chromatin. Remarkable progress has been made over the last few years in elucidating the mechanisms for a number of these functions. Activity of the histone demethylase IBM1 accurately targets DNA methylation to silent repeats and transposable elements, not to genes. A genetic screen uncovered the surprising role of H2A.Z-containing nucleosomes in sensing precise differences in ambient temperature and consequent gene regulation. Precise maintenance of chromosome number is assured by a histone modification that suppresses inappropriate DNA replication and by centromeric histone H3 regulation of chromosome segregation. Histones and noncoding RNAs regulate FLOWERING LOCUS C, the expression of which quantitatively measures the duration of cold exposure, functioning as memory of winter. These findings are a testament to the power of using plants to research chromatin organization, and demonstrate examples of how chromatin functions to achieve biological accuracy, precision, and memory."}],"doi":"10.1016/j.gde.2012.01.007","volume":22,"article_processing_charge":"No","citation":{"mla":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” <i>Current Opinion in Genetics and Development</i>, vol. 22, no. 2, Elsevier, 2012, pp. 132–38, doi:<a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">10.1016/j.gde.2012.01.007</a>.","chicago":"Huff, Jason T., and Daniel Zilberman. “Regulation of Biological Accuracy, Precision, and Memory by Plant Chromatin Organization.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2012. <a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">https://doi.org/10.1016/j.gde.2012.01.007</a>.","apa":"Huff, J. T., &#38; Zilberman, D. (2012). Regulation of biological accuracy, precision, and memory by plant chromatin organization. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">https://doi.org/10.1016/j.gde.2012.01.007</a>","ieee":"J. T. Huff and D. Zilberman, “Regulation of biological accuracy, precision, and memory by plant chromatin organization,” <i>Current Opinion in Genetics and Development</i>, vol. 22, no. 2. Elsevier, pp. 132–138, 2012.","ama":"Huff JT, Zilberman D. Regulation of biological accuracy, precision, and memory by plant chromatin organization. <i>Current Opinion in Genetics and Development</i>. 2012;22(2):132-138. doi:<a href=\"https://doi.org/10.1016/j.gde.2012.01.007\">10.1016/j.gde.2012.01.007</a>","short":"J.T. Huff, D. Zilberman, Current Opinion in Genetics and Development 22 (2012) 132–138.","ista":"Huff JT, Zilberman D. 2012. Regulation of biological accuracy, precision, and memory by plant chromatin organization. Current Opinion in Genetics and Development. 22(2), 132–138."},"pmid":1,"month":"04","oa_version":"None","publication":"Current Opinion in Genetics and Development","date_updated":"2021-12-14T08:32:38Z","article_type":"review","page":"132-138","year":"2012","intvolume":"        22","publisher":"Elsevier","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2012-04-01T00:00:00Z","external_id":{"pmid":["22336527"]},"extern":"1","scopus_import":"1","date_created":"2021-06-08T08:58:52Z"},{"page":"147-154","article_type":"review","publication":"Cold Spring Harbor Symposia on Quantitative Biology","date_updated":"2021-12-14T08:33:09Z","year":"2012","oa":1,"type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Cold Spring Harbor Laboratory Press","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/sqb.2012.77.014944"}],"intvolume":"        77","external_id":{"pmid":["23250988"]},"extern":"1","date_published":"2012-12-18T00:00:00Z","date_created":"2021-06-08T13:01:23Z","scopus_import":"1","department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","status":"public","publication_identifier":{"issn":["0091-7451"],"eissn":["1943-4456"]},"abstract":[{"text":"The most well-studied function of DNA methylation in eukaryotic cells is the transcriptional silencing of genes and transposons. More recent results showed that many eukaryotes methylate the bodies of genes as well and that this methylation correlates with transcriptional activity rather than repression. The purpose of gene body methylation remains mysterious, but is potentially related to the histone variant H2A.Z. Studies in plants and animals have shown that the genome-wide distributions of H2A.Z and DNA methylation are strikingly anticorrelated. Furthermore, we and other investigators have shown that this relationship is likely to be the result of an ancient but unknown mechanism by which DNA methylation prevents the incorporation of H2A.Z. Recently, we discovered strong correlations between the presence of H2A.Z within gene bodies, the degree to which a gene's expression varies across tissue types or environmental conditions, and transcriptional misregulation in an h2a.z mutant. We propose that one basal function of gene body methylation is the establishment of constitutive expression patterns within housekeeping genes by excluding H2A.Z from their bodies.","lang":"eng"}],"doi":"10.1101/sqb.2012.77.014944","title":"DNA methylation, H2A.Z, and the regulation of constitutive expression","author":[{"first_name":"D.","last_name":"Coleman-Derr","full_name":"Coleman-Derr, D."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"_id":"9535","article_processing_charge":"No","volume":77,"oa_version":"Published Version","citation":{"apa":"Coleman-Derr, D., &#38; Zilberman, D. (2012). DNA methylation, H2A.Z, and the regulation of constitutive expression. <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">https://doi.org/10.1101/sqb.2012.77.014944</a>","ieee":"D. Coleman-Derr and D. Zilberman, “DNA methylation, H2A.Z, and the regulation of constitutive expression,” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 77. Cold Spring Harbor Laboratory Press, pp. 147–154, 2012.","ista":"Coleman-Derr D, Zilberman D. 2012. DNA methylation, H2A.Z, and the regulation of constitutive expression. Cold Spring Harbor Symposia on Quantitative Biology. 77, 147–154.","short":"D. Coleman-Derr, D. Zilberman, Cold Spring Harbor Symposia on Quantitative Biology 77 (2012) 147–154.","ama":"Coleman-Derr D, Zilberman D. DNA methylation, H2A.Z, and the regulation of constitutive expression. <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. 2012;77:147-154. doi:<a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">10.1101/sqb.2012.77.014944</a>","mla":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 77, Cold Spring Harbor Laboratory Press, 2012, pp. 147–54, doi:<a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">10.1101/sqb.2012.77.014944</a>.","chicago":"Coleman-Derr, D., and Daniel Zilberman. “DNA Methylation, H2A.Z, and the Regulation of Constitutive Expression.” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Cold Spring Harbor Laboratory Press, 2012. <a href=\"https://doi.org/10.1101/sqb.2012.77.014944\">https://doi.org/10.1101/sqb.2012.77.014944</a>."},"day":"18","month":"12","pmid":1}]