[{"quality_controlled":"1","place":"Berlin, Heidelberg","series_title":"FRONTCOLL","month":"09","publication":"Brain-Computer Interfaces","doi":"10.1007/978-3-642-02091-9_18","publisher":"Springer","date_updated":"2024-02-19T09:47:25Z","article_processing_charge":"No","oa_version":"None","date_published":"2010-09-06T00:00:00Z","type":"book_chapter","department":[{"_id":"ScienComp"}],"year":"2010","language":[{"iso":"eng"}],"publication_status":"published","day":"06","date_created":"2024-02-14T09:56:00Z","alternative_title":["The Frontiers Collection"],"page":"331-355","author":[{"full_name":"Schlögl, Alois","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","last_name":"Schlögl"},{"first_name":"Carmen","full_name":"Vidaurre, Carmen","last_name":"Vidaurre"},{"first_name":"Klaus-Robert","full_name":"Müller, Klaus-Robert","last_name":"Müller"}],"acknowledgement":"This work was supported by the EU grants “BrainCom” (FP6-2004-Mobility-5 Grant No 024259) and “Multi-adaptive BCI” (MEIF-CT-2006 Grant No 040666). Furthermore, we thank Matthias Krauledat for fruitful discussions and tools for generating Fig. 5.","_id":"14983","edition":"1","title":"Adaptive Methods in BCI Research - An Introductory Tutorial","abstract":[{"text":"This chapter tackles a difficult challenge: presenting signal processing material to non-experts. This chapter is meant to be comprehensible to people who have some math background, including a course in linear algebra and basic statistics, but do not specialize in mathematics, engineering, or related fields. Some formulas assume the reader is familiar with matrices and basic matrix operations, but not more advanced material. Furthermore, we tried to make the chapter readable even if you skip the formulas. Nevertheless, we include some simple methods to demonstrate the basics of adaptive data processing, then we proceed with some advanced methods that are fundamental in adaptive signal processing, and are likely to be useful in a variety of applications. The advanced algorithms are also online available [30]. In the second part, these techniques are applied to some real-world BCI data.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","editor":[{"last_name":"Graimann","full_name":"Graimann, Bernhard","first_name":"Bernhard"},{"last_name":"Pfurtscheller","first_name":"Gert","full_name":"Pfurtscheller, Gert"},{"last_name":"Allison","full_name":"Allison, Brendan","first_name":"Brendan"}],"citation":{"chicago":"Schlögl, Alois, Carmen Vidaurre, and Klaus-Robert Müller. “Adaptive Methods in BCI Research - An Introductory Tutorial.” In <i>Brain-Computer Interfaces</i>, edited by Bernhard Graimann, Gert Pfurtscheller, and Brendan Allison, 1st ed., 331–55. FRONTCOLL. Berlin, Heidelberg: Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">https://doi.org/10.1007/978-3-642-02091-9_18</a>.","ama":"Schlögl A, Vidaurre C, Müller K-R. Adaptive Methods in BCI Research - An Introductory Tutorial. In: Graimann B, Pfurtscheller G, Allison B, eds. <i>Brain-Computer Interfaces</i>. 1st ed. FRONTCOLL. Berlin, Heidelberg: Springer; 2010:331-355. doi:<a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">10.1007/978-3-642-02091-9_18</a>","mla":"Schlögl, Alois, et al. “Adaptive Methods in BCI Research - An Introductory Tutorial.” <i>Brain-Computer Interfaces</i>, edited by Bernhard Graimann et al., 1st ed., Springer, 2010, pp. 331–55, doi:<a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">10.1007/978-3-642-02091-9_18</a>.","ieee":"A. Schlögl, C. Vidaurre, and K.-R. Müller, “Adaptive Methods in BCI Research - An Introductory Tutorial,” in <i>Brain-Computer Interfaces</i>, 1st ed., B. Graimann, G. Pfurtscheller, and B. Allison, Eds. Berlin, Heidelberg: Springer, 2010, pp. 331–355.","short":"A. Schlögl, C. Vidaurre, K.-R. Müller, in:, B. Graimann, G. Pfurtscheller, B. Allison (Eds.), Brain-Computer Interfaces, 1st ed., Springer, Berlin, Heidelberg, 2010, pp. 331–355.","ista":"Schlögl A, Vidaurre C, Müller K-R. 2010.Adaptive Methods in BCI Research - An Introductory Tutorial. In: Brain-Computer Interfaces. The Frontiers Collection, , 331–355.","apa":"Schlögl, A., Vidaurre, C., &#38; Müller, K.-R. (2010). Adaptive Methods in BCI Research - An Introductory Tutorial. In B. Graimann, G. Pfurtscheller, &#38; B. Allison (Eds.), <i>Brain-Computer Interfaces</i> (1st ed., pp. 331–355). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-02091-9_18\">https://doi.org/10.1007/978-3-642-02091-9_18</a>"},"status":"public","publication_identifier":{"isbn":["9783642020902"],"eisbn":["9783642020919"],"issn":["1612-3018"]}},{"pubrep_id":"24","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","last_name":"Cerny"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rohit","full_name":"Singh, Rohit","last_name":"Singh"}],"page":"17","alternative_title":["IST Austria Technical Report"],"publication_identifier":{"issn":["2664-1690"]},"date_created":"2018-12-12T11:39:03Z","publication_status":"published","day":"07","year":"2010","ddc":["000","005"],"language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"3366"}]},"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:42Z","date_published":"2010-10-07T00:00:00Z","type":"technical_report","status":"public","oa_version":"Published Version","has_accepted_license":"1","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>.","ama":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">10.15479/AT:IST-2010-0004</a>","chicago":"Chatterjee, Krishnendu, Pavol Cerny, Thomas A Henzinger, Arjun Radhakrishna, and Rohit Singh. <i>Quantitative Synthesis for Concurrent Programs</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>.","apa":"Chatterjee, K., Cerny, P., Henzinger, T. A., Radhakrishna, A., &#38; Singh, R. (2010). <i>Quantitative synthesis for concurrent programs</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0004\">https://doi.org/10.15479/AT:IST-2010-0004</a>","ista":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. 2010. Quantitative synthesis for concurrent programs, IST Austria, 17p.","ieee":"K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, <i>Quantitative synthesis for concurrent programs</i>. IST Austria, 2010.","short":"K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative Synthesis for Concurrent Programs, IST Austria, 2010."},"abstract":[{"lang":"eng","text":"We present an algorithmic method for the synthesis of concurrent programs that are optimal with respect to quantitative performance measures. The input consists of a sequential sketch, that is, a program that does not contain synchronization constructs, and of a parametric performance model that assigns costs to actions such as locking, context switching, and idling. The quantitative synthesis problem is to automatically introduce synchronization constructs into the sequential sketch so that both correctness is guaranteed and worst-case (or average-case) performance is optimized. Correctness is formalized as race freedom or linearizability.\r\n\r\nWe show that for worst-case performance, the problem can be modeled\r\nas a 2-player graph game with quantitative (limit-average) objectives, and\r\nfor average-case performance, as a 2 1/2 -player graph game (with probabilistic transitions). In both cases, the optimal correct program is derived from an optimal strategy in the corresponding quantitative game. We prove that the respective game problems are computationally expensive (NP-complete), and present several techniques that overcome the theoretical difficulty in cases of concurrent programs of practical interest.\r\n\r\nWe have implemented a prototype tool and used it for the automatic syn- thesis of programs that access a concurrent list. For certain parameter val- ues, our method automatically synthesizes various classical synchronization schemes for implementing a concurrent list, such as fine-grained locking or a lazy algorithm. For other parameter values, a new, hybrid synchronization style is synthesized, which uses both the lazy approach and coarse-grained locks (instead of standard fine-grained locks). The trade-off occurs because while fine-grained locking tends to decrease the cost that is due to waiting for locks, it increases cache size requirements."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5388","title":"Quantitative synthesis for concurrent programs","date_updated":"2023-02-23T11:24:08Z","publisher":"IST Austria","doi":"10.15479/AT:IST-2010-0004","month":"10","file":[{"content_type":"application/pdf","date_created":"2018-12-12T11:53:53Z","file_id":"5515","creator":"system","relation":"main_file","file_name":"IST-2010-0004_IST-2010-0004.pdf","access_level":"open_access","checksum":"da38782d2388a6fa32109d10bb9bad67","date_updated":"2020-07-14T12:46:42Z","file_size":429101}],"oa":1},{"pubrep_id":"25","author":[{"id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","full_name":"Cerny, Pavol","last_name":"Cerny"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun"}],"alternative_title":["IST Austria Technical Report"],"page":"24","date_created":"2018-12-12T11:39:03Z","publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","day":"04","language":[{"iso":"eng"}],"ddc":["005"],"year":"2010","related_material":{"record":[{"relation":"later_version","status":"public","id":"3249"},{"id":"4393","status":"public","relation":"later_version"}]},"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:42Z","date_published":"2010-06-04T00:00:00Z","type":"technical_report","status":"public","oa_version":"Published Version","has_accepted_license":"1","citation":{"short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, Simulation Distances, IST Austria, 2010.","ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, <i>Simulation distances</i>. IST Austria, 2010.","ista":"Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances, IST Austria, 24p.","apa":"Cerny, P., Henzinger, T. A., &#38; Radhakrishna, A. (2010). <i>Simulation distances</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>","chicago":"Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. <i>Simulation Distances</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">https://doi.org/10.15479/AT:IST-2010-0003</a>.","ama":"Cerny P, Henzinger TA, Radhakrishna A. <i>Simulation Distances</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>","mla":"Cerny, Pavol, et al. <i>Simulation Distances</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0003\">10.15479/AT:IST-2010-0003</a>."},"abstract":[{"text":"Boolean notions of correctness are formalized by preorders on systems. Quantitative measures of correctness can be formalized by real-valued distance functions between systems, where the distance between implementation and specification provides a measure of “fit” or “desirability.” We extend the simulation preorder to the quantitative setting, by making each player of a simulation game pay a certain price for her choices. We use the resulting games with quantitative objectives to define three different simulation distances. The correctness distance measures how much the specification must be changed in order to be satisfied by the implementation. The coverage distance measures how much the im- plementation restricts the degrees of freedom offered by the specification. The robustness distance measures how much a system can deviate from the implementation description without violating the specification. We consider these distances for safety as well as liveness specifications. The distances can be computed in polynomial time for safety specifications, and for liveness specifications given by weak fairness constraints. We show that the distance functions satisfy the triangle inequality, that the distance between two systems does not increase under parallel composition with a third system, and that the distance between two systems can be bounded from above and below by distances between abstractions of the two systems. These properties suggest that our simulation distances provide an appropriate basis for a quantitative theory of discrete systems. We also demonstrate how the robustness distance can be used to measure how many transmission errors are tolerated by error correcting codes.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"5389","doi":"10.15479/AT:IST-2010-0003","publisher":"IST Austria","date_updated":"2023-02-23T12:09:16Z","title":"Simulation distances","month":"06","file":[{"checksum":"284ded99764e32a583a8ea83fcea254b","access_level":"open_access","file_name":"IST-2010-0003_IST-2010-0003.pdf","file_size":367246,"date_updated":"2020-07-14T12:46:42Z","file_id":"5547","date_created":"2018-12-12T11:54:25Z","content_type":"application/pdf","creator":"system","relation":"main_file"}],"oa":1},{"has_accepted_license":"1","citation":{"ieee":"K. Chatterjee and N. Fijalkow, <i>Topological, automata-theoretic and logical characterization of finitary languages</i>. IST Austria, 2010.","short":"K. Chatterjee, N. Fijalkow, Topological, Automata-Theoretic and Logical Characterization of Finitary Languages, IST Austria, 2010.","apa":"Chatterjee, K., &#38; Fijalkow, N. (2010). <i>Topological, automata-theoretic and logical characterization of finitary languages</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">https://doi.org/10.15479/AT:IST-2010-0002</a>","ista":"Chatterjee K, Fijalkow N. 2010. Topological, automata-theoretic and logical characterization of finitary languages, IST Austria, 21p.","chicago":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">https://doi.org/10.15479/AT:IST-2010-0002</a>.","mla":"Chatterjee, Krishnendu, and Nathanaël Fijalkow. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">10.15479/AT:IST-2010-0002</a>.","ama":"Chatterjee K, Fijalkow N. <i>Topological, Automata-Theoretic and Logical Characterization of Finitary Languages</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0002\">10.15479/AT:IST-2010-0002</a>"},"oa_version":"Published Version","status":"public","type":"technical_report","date_published":"2010-06-04T00:00:00Z","oa":1,"file":[{"checksum":"283d3604d76dd4d5161585d4c8625fbe","access_level":"open_access","file_name":"IST-2010-0002_IST-2010-0002.pdf","file_size":395662,"date_updated":"2020-07-14T12:46:43Z","file_id":"5532","date_created":"2018-12-12T11:54:10Z","content_type":"application/pdf","relation":"main_file","creator":"system"}],"month":"06","_id":"5390","doi":"10.15479/AT:IST-2010-0002","publisher":"IST Austria","date_updated":"2020-07-14T23:04:41Z","title":"Topological, automata-theoretic and logical characterization of finitary languages","abstract":[{"text":"The class of ω regular languages provide a robust specification language in verification. Every ω-regular condition can be decomposed into a safety part and a liveness part. The liveness part ensures that something good happens “eventually.” Two main strengths of the classical, infinite-limit formulation of liveness are robustness (independence from the granularity of transitions) and simplicity (abstraction of complicated time bounds). However, the classical liveness formulation suffers from the drawback that the time until something good happens may be unbounded. A stronger formulation of liveness, so-called finitary liveness, overcomes this drawback, while still retaining robustness and simplicity. Finitary liveness requires that there exists an unknown, fixed bound b such that something good happens within b transitions. In this work we consider the finitary parity and Streett (fairness) conditions. We present the topological, automata-theoretic and logical characterization of finitary languages defined by finitary parity and Streett conditions. We (a) show that the finitary parity and Streett languages are Σ2-complete; (b) present a complete characterization of the expressive power of various classes of automata with finitary and infinitary conditions (in particular we show that non-deterministic finitary parity and Streett automata cannot be determinized to deterministic finitary parity or Streett automata); and (c) show that the languages defined by non-deterministic finitary parity automata exactly characterize the star-free fragment of ωB-regular languages.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","day":"04","publication_identifier":{"issn":["2664-1690"]},"date_created":"2018-12-12T11:39:03Z","alternative_title":["IST Austria Technical Report"],"page":"21","pubrep_id":"26","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fijalkow","full_name":"Fijalkow, Nathanaël","first_name":"Nathanaël"}],"file_date_updated":"2020-07-14T12:46:43Z","department":[{"_id":"KrCh"}],"year":"2010","language":[{"iso":"eng"}],"ddc":["000"]},{"status":"public","date_published":"2010-04-19T00:00:00Z","type":"technical_report","citation":{"short":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, Model Checking of Linearizability of Concurrent List Implementations, IST Austria, 2010.","ieee":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, <i>Model checking of linearizability of concurrent list implementations</i>. IST Austria, 2010.","apa":"Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., &#38; Alur, R. (2010). <i>Model checking of linearizability of concurrent list implementations</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">https://doi.org/10.15479/AT:IST-2010-0001</a>","ista":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking of linearizability of concurrent list implementations, IST Austria, 27p.","chicago":"Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and Rajeev Alur. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria, 2010. <a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">https://doi.org/10.15479/AT:IST-2010-0001</a>.","mla":"Cerny, Pavol, et al. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria, 2010, doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">10.15479/AT:IST-2010-0001</a>.","ama":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. <i>Model Checking of Linearizability of Concurrent List Implementations</i>. IST Austria; 2010. doi:<a href=\"https://doi.org/10.15479/AT:IST-2010-0001\">10.15479/AT:IST-2010-0001</a>"},"has_accepted_license":"1","oa_version":"Published Version","doi":"10.15479/AT:IST-2010-0001","date_updated":"2023-02-23T12:09:09Z","title":"Model checking of linearizability of concurrent list implementations","publisher":"IST Austria","_id":"5391","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Concurrent data structures with fine-grained synchronization are notoriously difficult to implement correctly. The difficulty of reasoning about these implementations does not stem from the number of variables or the program size, but rather from the large number of possible interleavings. These implementations are therefore prime candidates for model checking. We introduce an algorithm for verifying linearizability of singly-linked heap-based concurrent data structures. We consider a model consisting of an unbounded heap where each node consists an element from an unbounded data domain, with a restricted set of operations for testing and updating pointers and data elements. Our main result is that linearizability is decidable for programs that invoke a fixed number of methods, possibly in parallel. This decidable fragment covers many of the common implementation techniques — fine-grained locking, lazy synchronization, and lock-free synchronization. We also show how the technique can be used to verify optimistic implementations with the help of programmer annotations. We developed a verification tool CoLT and evaluated it on a representative sample of Java implementations of the concurrent set data structure. The tool verified linearizability of a number of implementations, found a known error in a lock-free imple- mentation and proved that the corrected version is linearizable."}],"oa":1,"file":[{"creator":"system","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T11:53:44Z","file_id":"5505","date_updated":"2020-07-14T12:46:43Z","file_size":372286,"file_name":"IST-2010-0001_IST-2010-0001.pdf","access_level":"open_access","checksum":"986645caad7dd85a6a091488f6c646dc"}],"month":"04","page":"27","alternative_title":["IST Austria Technical Report"],"author":[{"last_name":"Cerny","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol"},{"first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna"},{"full_name":"Zufferey, Damien","first_name":"Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","last_name":"Zufferey","orcid":"0000-0002-3197-8736"},{"first_name":"Swarat","full_name":"Chaudhuri, Swarat","last_name":"Chaudhuri"},{"last_name":"Alur","full_name":"Alur, Rajeev","first_name":"Rajeev"}],"pubrep_id":"27","day":"19","publication_status":"published","publication_identifier":{"issn":["2664-1690"]},"date_created":"2018-12-12T11:39:04Z","related_material":{"record":[{"id":"4390","status":"public","relation":"later_version"}]},"language":[{"iso":"eng"}],"year":"2010","ddc":["004"],"file_date_updated":"2020-07-14T12:46:43Z","department":[{"_id":"ToHe"}]},{"extern":"1","quality_controlled":"1","month":"05","publication":"Science","doi":"10.1126/science.1186366","publisher":"American Association for the Advancement of Science","date_updated":"2021-12-14T08:35:37Z","article_processing_charge":"No","oa_version":"None","article_type":"original","external_id":{"pmid":["20395474 "]},"volume":328,"type":"journal_article","date_published":"2010-05-14T00:00:00Z","department":[{"_id":"DaZi"}],"year":"2010","language":[{"iso":"eng"}],"publication_status":"published","day":"14","date_created":"2021-06-04T08:26:08Z","page":"916-919","author":[{"full_name":"Zemach, Assaf ","first_name":"Assaf ","last_name":"Zemach"},{"last_name":"McDaniel","first_name":"Ivy E.","full_name":"McDaniel, Ivy E."},{"last_name":"Silva","first_name":"Pedro","full_name":"Silva, Pedro"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"keyword":["Multidisciplinary"],"pmid":1,"_id":"9452","title":"Genome-wide evolutionary analysis of eukaryotic DNA methylation","abstract":[{"text":"Eukaryotic cytosine methylation represses transcription but also occurs in the bodies of active genes, and the extent of methylation biology conservation is unclear. We quantified DNA methylation in 17 eukaryotic genomes and found that gene body methylation is conserved between plants and animals, whereas selective methylation of transposons is not. We show that methylation of plant transposons in the CHG context extends to green algae and that exclusion of histone H2A.Z from methylated DNA is conserved between plants and animals, and we present evidence for RNA-directed DNA methylation of fungal genes. Our data demonstrate that extant DNA methylation systems are mosaics of conserved and derived features, and indicate that gene body methylation is an ancient property of eukaryotic genomes.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"       328","citation":{"ieee":"A. Zemach, I. E. McDaniel, P. Silva, and D. Zilberman, “Genome-wide evolutionary analysis of eukaryotic DNA methylation,” <i>Science</i>, vol. 328, no. 5980. American Association for the Advancement of Science, pp. 916–919, 2010.","short":"A. Zemach, I.E. McDaniel, P. Silva, D. Zilberman, Science 328 (2010) 916–919.","ista":"Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 328(5980), 916–919.","apa":"Zemach, A., McDaniel, I. E., Silva, P., &#38; Zilberman, D. (2010). Genome-wide evolutionary analysis of eukaryotic DNA methylation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1186366\">https://doi.org/10.1126/science.1186366</a>","chicago":"Zemach, Assaf , Ivy E. McDaniel, Pedro Silva, and Daniel Zilberman. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” <i>Science</i>. American Association for the Advancement of Science, 2010. <a href=\"https://doi.org/10.1126/science.1186366\">https://doi.org/10.1126/science.1186366</a>.","ama":"Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. <i>Science</i>. 2010;328(5980):916-919. doi:<a href=\"https://doi.org/10.1126/science.1186366\">10.1126/science.1186366</a>","mla":"Zemach, Assaf, et al. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” <i>Science</i>, vol. 328, no. 5980, American Association for the Advancement of Science, 2010, pp. 916–19, doi:<a href=\"https://doi.org/10.1126/science.1186366\">10.1126/science.1186366</a>."},"status":"public","scopus_import":"1","publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"issue":"5980"},{"volume":107,"date_published":"2010-10-26T00:00:00Z","type":"journal_article","article_type":"original","oa_version":"Published Version","external_id":{"pmid":["20937895"]},"article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences","date_updated":"2021-12-14T08:40:02Z","doi":"10.1073/pnas.1009695107","publisher":"National Academy of Sciences","month":"10","extern":"1","quality_controlled":"1","oa":1,"author":[{"first_name":"Assaf","full_name":"Zemach, Assaf","last_name":"Zemach"},{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"last_name":"Silva","first_name":"Pedro","full_name":"Silva, Pedro"},{"first_name":"Jessica A.","full_name":"Rodrigues, Jessica A.","last_name":"Rodrigues"},{"last_name":"Dotson","full_name":"Dotson, Bradley","first_name":"Bradley"},{"first_name":"Matthew D.","full_name":"Brooks, Matthew D.","last_name":"Brooks"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"page":"18729-18734","date_created":"2021-06-07T09:31:01Z","publication_status":"published","day":"26","language":[{"iso":"eng"}],"year":"2010","department":[{"_id":"DaZi"}],"status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1009695107"}],"intvolume":"       107","citation":{"ama":"Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2010;107(43):18729-18734. doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>","mla":"Zemach, Assaf, et al. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43, National Academy of Sciences, 2010, pp. 18729–34, doi:<a href=\"https://doi.org/10.1073/pnas.1009695107\">10.1073/pnas.1009695107</a>.","chicago":"Zemach, Assaf, M. Yvonne Kim, Pedro Silva, Jessica A. Rodrigues, Bradley Dotson, Matthew D. Brooks, and Daniel Zilberman. “Local DNA Hypomethylation Activates Genes in Rice Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2010. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>.","ista":"Zemach A, Kim MY, Silva P, Rodrigues JA, Dotson B, Brooks MD, Zilberman D. 2010. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 107(43), 18729–18734.","apa":"Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M. D., &#38; Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1009695107\">https://doi.org/10.1073/pnas.1009695107</a>","ieee":"A. Zemach <i>et al.</i>, “Local DNA hypomethylation activates genes in rice endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 107, no. 43. National Academy of Sciences, pp. 18729–18734, 2010.","short":"A. Zemach, M.Y. Kim, P. Silva, J.A. Rodrigues, B. Dotson, M.D. Brooks, D. Zilberman, Proceedings of the National Academy of Sciences 107 (2010) 18729–18734."},"abstract":[{"text":"Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9485","title":"Local DNA hypomethylation activates genes in rice endosperm","pmid":1,"issue":"43","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"scopus_import":"1"},{"publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"issue":"17","scopus_import":"1","citation":{"short":"A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785.","ieee":"A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the pursuit of safer sex,” <i>Current Biology</i>, vol. 20, no. 17. Elsevier, pp. R780–R785, 2010.","apa":"Zemach, A., &#38; Zilberman, D. (2010). Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>","ista":"Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 20(17), R780–R785.","chicago":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">https://doi.org/10.1016/j.cub.2010.07.007</a>.","mla":"Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” <i>Current Biology</i>, vol. 20, no. 17, Elsevier, 2010, pp. R780–85, doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>.","ama":"Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. <i>Current Biology</i>. 2010;20(17):R780-R785. doi:<a href=\"https://doi.org/10.1016/j.cub.2010.07.007\">10.1016/j.cub.2010.07.007</a>"},"intvolume":"        20","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2010.07.007","open_access":"1"}],"status":"public","pmid":1,"title":"Evolution of eukaryotic DNA methylation and the pursuit of safer sex","_id":"9489","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","abstract":[{"lang":"eng","text":"Cytosine methylation is an ancient process with conserved enzymology but diverse biological functions that include defense against transposable elements and regulation of gene expression. Here we will discuss the evolution and biological significance of eukaryotic DNA methylation, the likely drivers of that evolution, and major remaining mysteries."}],"day":"14","publication_status":"published","date_created":"2021-06-07T09:45:27Z","page":"R780-R785","author":[{"first_name":"Assaf","full_name":"Zemach, Assaf","last_name":"Zemach"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"}],"department":[{"_id":"DaZi"}],"language":[{"iso":"eng"}],"year":"2010","external_id":{"pmid":["20833323"]},"oa_version":"Published Version","article_type":"review","type":"journal_article","date_published":"2010-09-14T00:00:00Z","volume":20,"quality_controlled":"1","oa":1,"extern":"1","month":"09","doi":"10.1016/j.cub.2010.07.007","date_updated":"2021-12-14T08:52:34Z","publisher":"Elsevier","publication":"Current Biology","article_processing_charge":"No"},{"day":"20","date_created":"2021-08-02T09:45:39Z","author":[{"last_name":"Rosas","first_name":"Ulises","full_name":"Rosas, Ulises"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"},{"full_name":"Copsey, Lucy","first_name":"Lucy","last_name":"Copsey"},{"last_name":"Barbier De Reuille","first_name":"Pierre","full_name":"Barbier De Reuille, Pierre"},{"first_name":"Enrico","full_name":"Coen, Enrico","last_name":"Coen"}],"department":[{"_id":"NiBa"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"3779"}]},"year":"2010","citation":{"short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010).","ieee":"U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Heterosis and the drift load.” Public Library of Science, 2010.","apa":"Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., &#38; Coen, E. (2010). Heterosis and the drift load. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">https://doi.org/10.1371/journal.pbio.1000429.s003</a>","ista":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Heterosis and the drift load, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">10.1371/journal.pbio.1000429.s003</a>.","chicago":"Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Heterosis and the Drift Load.” Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">https://doi.org/10.1371/journal.pbio.1000429.s003</a>.","mla":"Rosas, Ulises, et al. <i>Heterosis and the Drift Load</i>. Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">10.1371/journal.pbio.1000429.s003</a>.","ama":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Heterosis and the drift load. 2010. doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429.s003\">10.1371/journal.pbio.1000429.s003</a>"},"oa_version":"Published Version","status":"public","date_published":"2010-07-20T00:00:00Z","type":"research_data_reference","month":"07","doi":"10.1371/journal.pbio.1000429.s003","publisher":"Public Library of Science","title":"Heterosis and the drift load","date_updated":"2023-02-23T11:42:17Z","_id":"9764","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"department":[{"_id":"ToHe"}],"year":"2010","language":[{"iso":"eng"}],"day":"01","publication_status":"published","date_created":"2022-03-21T08:14:35Z","conference":{"start_date":"2010-04-25","name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning","location":"Dakar, Senegal","end_date":"2010-05-01"},"page":"103-118","author":[{"last_name":"Blanc","full_name":"Blanc, Régis","first_name":"Régis"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","last_name":"Henzinger"},{"last_name":"Hottelier","full_name":"Hottelier, Thibaud","first_name":"Thibaud"},{"last_name":"Kovács","first_name":"Laura","full_name":"Kovács, Laura"}],"oa":1,"series_title":"LNCS","quality_controlled":"1","place":"Berlin, Heidelberg","month":"05","publisher":"Springer Nature","date_updated":"2022-06-13T07:44:21Z","doi":"10.1007/978-3-642-17511-4_7","publication":"Logic for Programming, Artificial Intelligence, and Reasoning","article_processing_charge":"No","oa_version":"Submitted Version","type":"conference","date_published":"2010-05-01T00:00:00Z","volume":6355,"scopus_import":"1","publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"],"eisbn":["9783642175114"],"isbn":["9783642175107"]},"acknowledgement":"This work was supported in part by the Swiss NSF. The fourth author is supported by an FWF Hertha Firnberg Research grant (T425-N23).","title":"ABC: Algebraic Bound Computation for loops","_id":"10908","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We present ABC, a software tool for automatically computing symbolic upper bounds on the number of iterations of nested program loops. The system combines static analysis of programs with symbolic summation techniques to derive loop invariant relations between program variables. Iteration bounds are obtained from the inferred invariants, by replacing variables with bounds on their greatest values. We have successfully applied ABC to a large number of examples. The derived symbolic bounds express non-trivial polynomial relations over loop variables. We also report on results to automatically infer symbolic expressions over harmonic numbers as upper bounds on loop iteration counts."}],"intvolume":"      6355","citation":{"apa":"Blanc, R., Henzinger, T. A., Hottelier, T., &#38; Kovács, L. (2010). ABC: Algebraic Bound Computation for loops. In E. M. Clarke &#38; A. Voronkov (Eds.), <i>Logic for Programming, Artificial Intelligence, and Reasoning</i> (Vol. 6355, pp. 103–118). Berlin, Heidelberg: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">https://doi.org/10.1007/978-3-642-17511-4_7</a>","ista":"Blanc R, Henzinger TA, Hottelier T, Kovács L. 2010. ABC: Algebraic Bound Computation for loops. Logic for Programming, Artificial Intelligence, and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and ReasoningLNCS vol. 6355, 103–118.","short":"R. Blanc, T.A. Henzinger, T. Hottelier, L. Kovács, in:, E.M. Clarke, A. Voronkov (Eds.), Logic for Programming, Artificial Intelligence, and Reasoning, Springer Nature, Berlin, Heidelberg, 2010, pp. 103–118.","ieee":"R. Blanc, T. A. Henzinger, T. Hottelier, and L. Kovács, “ABC: Algebraic Bound Computation for loops,” in <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>, Dakar, Senegal, 2010, vol. 6355, pp. 103–118.","mla":"Blanc, Régis, et al. “ABC: Algebraic Bound Computation for Loops.” <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>, edited by Edmund M Clarke and Andrei Voronkov, vol. 6355, Springer Nature, 2010, pp. 103–18, doi:<a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">10.1007/978-3-642-17511-4_7</a>.","ama":"Blanc R, Henzinger TA, Hottelier T, Kovács L. ABC: Algebraic Bound Computation for loops. In: Clarke EM, Voronkov A, eds. <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>. Vol 6355. LNCS. Berlin, Heidelberg: Springer Nature; 2010:103-118. doi:<a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">10.1007/978-3-642-17511-4_7</a>","chicago":"Blanc, Régis, Thomas A Henzinger, Thibaud Hottelier, and Laura Kovács. “ABC: Algebraic Bound Computation for Loops.” In <i>Logic for Programming, Artificial Intelligence, and Reasoning</i>, edited by Edmund M Clarke and Andrei Voronkov, 6355:103–18. LNCS. Berlin, Heidelberg: Springer Nature, 2010. <a href=\"https://doi.org/10.1007/978-3-642-17511-4_7\">https://doi.org/10.1007/978-3-642-17511-4_7</a>."},"editor":[{"last_name":"Clarke","full_name":"Clarke, Edmund M","first_name":"Edmund M"},{"full_name":"Voronkov, Andrei","first_name":"Andrei","last_name":"Voronkov"}],"main_file_link":[{"open_access":"1","url":"https://infoscience.epfl.ch/record/186096"}],"status":"public"},{"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We focus on the volume measure, that is, the 1-norm of a cycle. Two main results are presented. First, we prove the problem is NP-hard to approximate within any constant factor. Second, we prove that for homology of dimension two or higher, the problem is NP-hard to approximate even when the Betti number is O(1). A side effect is the inapproximability of the problem of computing the nonbounding cycle with the smallest volume, and computing cycles representing a homology basis with the minimal total volume. We also discuss other geometric measures (diameter and radius) and show their disadvantages in homology localization. Our work is restricted to homology over the ℤ2 field.","lang":"eng"}],"title":"Hardness results for homology localization","doi":"10.1137/1.9781611973075.129","date_updated":"2023-02-23T11:19:46Z","publisher":"Society for Industrial and Applied Mathematics","_id":"10909","publication":"Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms","month":"02","quality_controlled":"1","acknowledgement":"Partially supported by the Austrian Science Fund under grantFSP-S9103-N04 and P20134-N13.","type":"conference","date_published":"2010-02-01T00:00:00Z","status":"public","oa_version":"None","citation":{"ama":"Chen C, Freedman D. Hardness results for homology localization. In: <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>. Society for Industrial and Applied Mathematics; 2010:1594-1604. doi:<a href=\"https://doi.org/10.1137/1.9781611973075.129\">10.1137/1.9781611973075.129</a>","mla":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Society for Industrial and Applied Mathematics, 2010, pp. 1594–604, doi:<a href=\"https://doi.org/10.1137/1.9781611973075.129\">10.1137/1.9781611973075.129</a>.","chicago":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” In <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, 1594–1604. Society for Industrial and Applied Mathematics, 2010. <a href=\"https://doi.org/10.1137/1.9781611973075.129\">https://doi.org/10.1137/1.9781611973075.129</a>.","ista":"Chen C, Freedman D. 2010. Hardness results for homology localization. Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1594–1604.","apa":"Chen, C., &#38; Freedman, D. (2010). Hardness results for homology localization. In <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i> (pp. 1594–1604). Austin, TX, United States: Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/1.9781611973075.129\">https://doi.org/10.1137/1.9781611973075.129</a>","ieee":"C. Chen and D. Freedman, “Hardness results for homology localization,” in <i>Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms</i>, Austin, TX, United States, 2010, pp. 1594–1604.","short":"C. Chen, D. Freedman, in:, Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2010, pp. 1594–1604."},"scopus_import":"1","related_material":{"record":[{"relation":"later_version","status":"public","id":"3267"}]},"language":[{"iso":"eng"}],"year":"2010","department":[{"_id":"HeEd"}],"author":[{"last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","full_name":"Chen, Chao"},{"full_name":"Freedman, Daniel","first_name":"Daniel","last_name":"Freedman"}],"conference":{"name":"SODA: Symposium on Discrete Algorithms","start_date":"2010-01-17","end_date":"2010-01-19","location":"Austin, TX, United States"},"page":"1594-1604","date_created":"2022-03-21T08:24:07Z","publication_identifier":{"eisbn":["9781611973075"]},"day":"01","publication_status":"published"},{"status":"public","citation":{"mla":"Kupczok, Anne, et al. “Accuracy of Phylogeny Reconstruction Methods Combining Overlapping Gene Data Sets .” <i>Algorithms for Molecular Biology</i>, vol. 5, no. 1, 37, BioMed Central, 2010, doi:<a href=\"https://doi.org/10.1186/1748-7188-5-37\">10.1186/1748-7188-5-37</a>.","ama":"Kupczok A, Schmidt H, Von Haeseler A. Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . <i>Algorithms for Molecular Biology</i>. 2010;5(1). doi:<a href=\"https://doi.org/10.1186/1748-7188-5-37\">10.1186/1748-7188-5-37</a>","chicago":"Kupczok, Anne, Heiko Schmidt, and Arndt Von Haeseler. “Accuracy of Phylogeny Reconstruction Methods Combining Overlapping Gene Data Sets .” <i>Algorithms for Molecular Biology</i>. BioMed Central, 2010. <a href=\"https://doi.org/10.1186/1748-7188-5-37\">https://doi.org/10.1186/1748-7188-5-37</a>.","apa":"Kupczok, A., Schmidt, H., &#38; Von Haeseler, A. (2010). Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . <i>Algorithms for Molecular Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/1748-7188-5-37\">https://doi.org/10.1186/1748-7188-5-37</a>","ista":"Kupczok A, Schmidt H, Von Haeseler A. 2010. Accuracy of phylogeny reconstruction methods combining overlapping gene data sets . Algorithms for Molecular Biology. 5(1), 37.","short":"A. Kupczok, H. Schmidt, A. Von Haeseler, Algorithms for Molecular Biology 5 (2010).","ieee":"A. Kupczok, H. Schmidt, and A. Von Haeseler, “Accuracy of phylogeny reconstruction methods combining overlapping gene data sets ,” <i>Algorithms for Molecular Biology</i>, vol. 5, no. 1. BioMed Central, 2010."},"intvolume":"         5","has_accepted_license":"1","title":"Accuracy of phylogeny reconstruction methods combining overlapping gene data sets ","_id":"2409","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Background: The availability of many gene alignments with overlapping taxon sets raises the question of which strategy is the best to infer species phylogenies from multiple gene information. Methods and programs abound that use the gene alignment in different ways to reconstruct the species tree. In particular, different methods combine the original data at different points along the way from the underlying sequences to the final tree. Accordingly, they are classified into superalignment, supertree and medium-level approaches. Here, we present a simulation study to compare different methods from each of these three approaches.\r\n\r\nResults: We observe that superalignment methods usually outperform the other approaches over a wide range of parameters including sparse data and gene-specific evolutionary parameters. In the presence of high incongruency among gene trees, however, other combination methods show better performance than the superalignment approach. Surprisingly, some supertree and medium-level methods exhibit, on average, worse results than a single gene phylogeny with complete taxon information.\r\n\r\nConclusions: For some methods, using the reconstructed gene tree as an estimation of the species tree is superior to the combination of incomplete information. Superalignment usually performs best since it is less susceptible to stochastic error. Supertree methods can outperform superalignment in the presence of gene-tree conflict.","lang":"eng"}],"acknowledgement":"Financial support from the Wiener Wissenschafts-, Forschungs- and Technologiefonds (WWTF) is greatly appreciated. A.v.H. acknowledges support from the German Research Foundation (DFG, SPP-1174).","issue":"1","scopus_import":1,"file_date_updated":"2020-07-14T12:45:40Z","type":"journal_article","date_published":"2010-12-06T00:00:00Z","volume":5,"oa_version":"Published Version","publisher":"BioMed Central","date_updated":"2021-01-12T06:57:18Z","doi":"10.1186/1748-7188-5-37","publication":"Algorithms for Molecular Biology","quality_controlled":"1","oa":1,"file":[{"access_level":"open_access","file_name":"IST-2018-939-v1+1_2010_Kupczok_Accuracy_of.pdf","checksum":"e2497285388bc4da629bafb46662eb43","date_updated":"2020-07-14T12:45:40Z","file_size":723929,"content_type":"application/pdf","file_id":"4739","date_created":"2018-12-12T10:09:16Z","relation":"main_file","creator":"system"}],"article_number":"37","month":"12","author":[{"last_name":"Kupczok","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Anne","full_name":"Kupczok, Anne"},{"last_name":"Schmidt","full_name":"Schmidt, Heiko","first_name":"Heiko"},{"first_name":"Arndt","full_name":"Von Haeseler, Arndt","last_name":"Von Haeseler"}],"pubrep_id":"939","day":"06","publist_id":"4517","publication_status":"published","date_created":"2018-12-11T11:57:30Z","year":"2010","language":[{"iso":"eng"}],"ddc":["576"],"department":[{"_id":"JoBo"}],"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)"}},{"day":"01","publist_id":"3337","publication_status":"published","date_created":"2018-12-11T12:02:33Z","page":"1389 - 1410","author":[{"id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","full_name":"Weissman, Daniel","last_name":"Weissman"},{"full_name":"Feldman, Marcus","first_name":"Marcus","last_name":"Feldman"},{"full_name":"Fisher, Daniel","first_name":"Daniel","last_name":"Fisher"}],"department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"year":"2010","oa_version":"Submitted Version","date_published":"2010-12-01T00:00:00Z","type":"journal_article","project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7"}],"volume":186,"quality_controlled":"1","oa":1,"month":"12","doi":"10.1534/genetics.110.123240","date_updated":"2021-01-12T07:42:31Z","publisher":"Genetics Society of America","publication":"Genetics","issue":"4","scopus_import":1,"citation":{"ieee":"D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing in sexual populations,” <i>Genetics</i>, vol. 186, no. 4. Genetics Society of America, pp. 1389–1410, 2010.","short":"D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410.","apa":"Weissman, D., Feldman, M., &#38; Fisher, D. (2010). The rate of fitness-valley crossing in sexual populations. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.110.123240\">https://doi.org/10.1534/genetics.110.123240</a>","ista":"Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing in sexual populations. Genetics. 186(4), 1389–1410.","chicago":"Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley Crossing in Sexual Populations.” <i>Genetics</i>. Genetics Society of America, 2010. <a href=\"https://doi.org/10.1534/genetics.110.123240\">https://doi.org/10.1534/genetics.110.123240</a>.","mla":"Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.” <i>Genetics</i>, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410, doi:<a href=\"https://doi.org/10.1534/genetics.110.123240\">10.1534/genetics.110.123240</a>.","ama":"Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual populations. <i>Genetics</i>. 2010;186(4):1389-1410. doi:<a href=\"https://doi.org/10.1534/genetics.110.123240\">10.1534/genetics.110.123240</a>"},"intvolume":"       186","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/","open_access":"1"}],"status":"public","ec_funded":1,"acknowledgement":"This work was supported in part by a Robert N. Noyce Stanford Graduate Fellowship and European Research Council grant 250152 (to D.B.W.) and by National Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer for their helpful suggestions. ","title":"The rate of fitness-valley crossing in sexual populations","_id":"3303","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population. ","lang":"eng"}]},{"volume":19,"type":"journal_article","date_published":"2010-03-01T00:00:00Z","status":"public","oa_version":"None","intvolume":"        19","citation":{"apa":"Senn, H., Goodman, S., Swanson, G., Barton, N. H., &#38; Pemberton, J. (2010). Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. <i>Molecular Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-294X.2009.04497.x\">https://doi.org/10.1111/j.1365-294X.2009.04497.x</a>","ista":"Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. 2010. Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. Molecular Ecology. 19(5), 910–924.","short":"H. Senn, S. Goodman, G. Swanson, N.H. Barton, J. Pemberton, Molecular Ecology 19 (2010) 910–924.","ieee":"H. Senn, S. Goodman, G. Swanson, N. H. Barton, and J. Pemberton, “Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland,” <i>Molecular Ecology</i>, vol. 19, no. 5. Wiley-Blackwell, pp. 910–924, 2010.","mla":"Senn, Helen, et al. “Investigating Temporal Changes in Hybridisation and Introgression between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on the Kintyre Peninsula, Scotland.” <i>Molecular Ecology</i>, vol. 19, no. 5, Wiley-Blackwell, 2010, pp. 910–24, doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2009.04497.x\">10.1111/j.1365-294X.2009.04497.x</a>.","ama":"Senn H, Goodman S, Swanson G, Barton NH, Pemberton J. Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland. <i>Molecular Ecology</i>. 2010;19(5):910-924. doi:<a href=\"https://doi.org/10.1111/j.1365-294X.2009.04497.x\">10.1111/j.1365-294X.2009.04497.x</a>","chicago":"Senn, Helen, Simon Goodman, Graeme Swanson, Nicholas H Barton, and Josephine Pemberton. “Investigating Temporal Changes in Hybridisation and Introgression between Invasive Sika (Cervus Nippon) and Native Red Deer (Cervus Elaphus) on the Kintyre Peninsula, Scotland.” <i>Molecular Ecology</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1111/j.1365-294X.2009.04497.x\">https://doi.org/10.1111/j.1365-294X.2009.04497.x</a>."},"abstract":[{"lang":"eng","text":"We investigated temporal changes in hybridization and introgression between native red deer (Cervus elaphus) and invasive Japanese sika (Cervus nippon) on the Kintyre Peninsula, Scotland, over 15 years, through analysis of 1513 samples of deer at 20 microsatellite loci and a mtDNA marker. We found no evidence that either the proportion of recent hybrids, or the levels of introgression had changed over the study period. Nevertheless, in one population where the two species have been in contact since ∼1970, 44% of individuals sampled during the study were hybrids. This suggests that hybridization between these species can proceed fairly rapidly. By analysing the number of alleles that have introgressed from polymorphic red deer into the genetically homogenous sika population, we reconstructed the haplotypes of red deer alleles introduced by backcrossing. Five separate hybridization events could account for all the recently hybridized sika-like individuals found across a large section of the Peninsula. Although we demonstrate that low rates of F1 hybridization can lead to substantial introgression, the progress of hybridization and introgression appears to be unpredictable over the short timescales."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3604","publication":"Molecular Ecology","publisher":"Wiley-Blackwell","date_updated":"2021-01-12T07:44:36Z","doi":"10.1111/j.1365-294X.2009.04497.x","title":"Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland","month":"03","quality_controlled":"1","issue":"5","author":[{"first_name":"Helen","full_name":"Senn, Helen","last_name":"Senn"},{"full_name":"Goodman, Simon","first_name":"Simon","last_name":"Goodman"},{"last_name":"Swanson","first_name":"Graeme","full_name":"Swanson, Graeme"},{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"},{"last_name":"Pemberton","first_name":"Josephine","full_name":"Pemberton, Josephine"}],"page":"910 - 924","date_created":"2018-12-11T12:04:12Z","publist_id":"2779","publication_status":"published","day":"01","scopus_import":1,"language":[{"iso":"eng"}],"year":"2010","department":[{"_id":"NiBa"}]},{"language":[{"iso":"eng"}],"year":"2010","scopus_import":1,"department":[{"_id":"PeJo"}],"page":"406 - 415","issue":"6","author":[{"full_name":"Guzmán, José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José","last_name":"Guzmán"},{"last_name":"Schmidt","full_name":"Schmidt, Hartmut","first_name":"Hartmut"},{"first_name":"Heike","full_name":"Franke, Heike","last_name":"Franke"},{"first_name":"Ute","full_name":"Krügel, Ute","last_name":"Krügel"},{"last_name":"Eilers","full_name":"Eilers, Jens","first_name":"Jens"},{"last_name":"Illes","full_name":"Illes, Peter","first_name":"Peter"},{"last_name":"Gerevich","full_name":"Gerevich, Zoltan","first_name":"Zoltan"}],"day":"01","publist_id":"2512","publication_status":"published","date_created":"2018-12-11T12:04:47Z","publisher":"Elsevier","title":"P2Y1 receptors inhibit long-term depression in the prefrontal cortex.","doi":"10.1016/j.neuropharm.2010.05.013","date_updated":"2021-01-12T07:51:42Z","_id":"3718","publication":"Neuropharmacology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Long-term depression (LTD) is a form of synaptic plasticity that may contribute to information storage in the central nervous system. Here we report that LTD can be elicited in layer 5 pyramidal neurons of the rat prefrontal cortex by pairing low frequency stimulation with a modest postsynaptic depolarization. The induction of LTD required the activation of both metabotropic glutamate receptors of the mGlu1 subtype and voltage-sensitive Ca(2+) channels (VSCCs) of the T/R, P/Q and N types, leading to the stimulation of intracellular inositol trisphosphate (IP3) receptors by IP3 and Ca(2+). The subsequent release of Ca(2+) from intracellular stores activated the protein phosphatase cascade involving calcineurin and protein phosphatase 1. The activation of purinergic P2Y(1) receptors blocked LTD. This effect was prevented by P2Y(1) receptor antagonists and was absent in mice lacking P2Y(1) but not P2Y(2) receptors. We also found that activation of P2Y(1) receptors inhibits Ca(2+) transients via VSCCs in the apical dendrites and spines of pyramidal neurons. In addition, we show that the release of ATP under hypoxia is able to inhibit LTD by acting on postsynaptic P2Y(1) receptors. In conclusion, these data suggest that the reduction of Ca(2+) influx via VSCCs caused by the activation of P2Y(1) receptors by ATP is the possible mechanism for the inhibition of LTD in prefrontal cortex."}],"quality_controlled":"1","acknowledgement":" The financial support of the Deutsche Forschungsgemeinschaft (IL 20/12-1, KI 677/2-4) is gratefully acknowledged.\r\nWe thank B. H. Koller (Department of Genetics and Molecular Biology, University of North Carolina at Chapel Hill, NC, USA) for the generous supply of P2Y1−/− and P2Y2−/− mice. We are grateful to Dr. A. Schulz for reanalysing the genotype of the P2Y1−/− mice. The authors thank P. Jonas and U. Heinemann for many helpful comments and A-K. Krause, L Feige and M. Eberts for their excellent technical support.","month":"11","status":"public","date_published":"2010-11-01T00:00:00Z","type":"journal_article","volume":59,"citation":{"chicago":"Guzmán, José, Hartmut Schmidt, Heike Franke, Ute Krügel, Jens Eilers, Peter Illes, and Zoltan Gerevich. “P2Y1 Receptors Inhibit Long-Term Depression in the Prefrontal Cortex.” <i>Neuropharmacology</i>. Elsevier, 2010. <a href=\"https://doi.org/10.1016/j.neuropharm.2010.05.013\">https://doi.org/10.1016/j.neuropharm.2010.05.013</a>.","mla":"Guzmán, José, et al. “P2Y1 Receptors Inhibit Long-Term Depression in the Prefrontal Cortex.” <i>Neuropharmacology</i>, vol. 59, no. 6, Elsevier, 2010, pp. 406–15, doi:<a href=\"https://doi.org/10.1016/j.neuropharm.2010.05.013\">10.1016/j.neuropharm.2010.05.013</a>.","ama":"Guzmán J, Schmidt H, Franke H, et al. P2Y1 receptors inhibit long-term depression in the prefrontal cortex. <i>Neuropharmacology</i>. 2010;59(6):406-415. doi:<a href=\"https://doi.org/10.1016/j.neuropharm.2010.05.013\">10.1016/j.neuropharm.2010.05.013</a>","ieee":"J. Guzmán <i>et al.</i>, “P2Y1 receptors inhibit long-term depression in the prefrontal cortex.,” <i>Neuropharmacology</i>, vol. 59, no. 6. Elsevier, pp. 406–415, 2010.","short":"J. Guzmán, H. Schmidt, H. Franke, U. Krügel, J. Eilers, P. Illes, Z. Gerevich, Neuropharmacology 59 (2010) 406–415.","apa":"Guzmán, J., Schmidt, H., Franke, H., Krügel, U., Eilers, J., Illes, P., &#38; Gerevich, Z. (2010). P2Y1 receptors inhibit long-term depression in the prefrontal cortex. <i>Neuropharmacology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuropharm.2010.05.013\">https://doi.org/10.1016/j.neuropharm.2010.05.013</a>","ista":"Guzmán J, Schmidt H, Franke H, Krügel U, Eilers J, Illes P, Gerevich Z. 2010. P2Y1 receptors inhibit long-term depression in the prefrontal cortex. Neuropharmacology. 59(6), 406–415."},"intvolume":"        59","oa_version":"None"},{"volume":40,"date_published":"2010-10-30T00:00:00Z","type":"conference","oa_version":"Submitted Version","external_id":{"arxiv":["1011.0496"]},"publisher":"Open Publishing Association","date_updated":"2023-02-23T11:15:19Z","month":"10","file":[{"file_size":907155,"date_updated":"2020-07-14T12:46:14Z","checksum":"eaaba991a86fff37606b0eb5196878e8","file_name":"Lumpability_abstractions_of_rule-based_systems.pdf","access_level":"open_access","creator":"kschuh","relation":"main_file","date_created":"2019-01-31T12:09:09Z","file_id":"5904","content_type":"application/pdf"}],"oa":1,"quality_controlled":"1","author":[{"last_name":"Feret","first_name":"Jérôme","full_name":"Feret, Jérôme"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Koeppl, Heinz","first_name":"Heinz","last_name":"Koeppl"},{"orcid":"0000-0002-9041-0905","last_name":"Petrov","full_name":"Petrov, Tatjana","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["EPTCS"],"page":"142-161","conference":{"start_date":"2010-08-23","name":"MECBIC: Membrane Computing and Biologically Inspired Process Calculi","location":"Jena, Germany","end_date":"2010-08-23"},"arxiv":1,"date_created":"2018-12-11T12:04:47Z","publist_id":"2511","publication_status":"published","day":"30","ddc":["570"],"year":"2010","language":[{"iso":"eng"}],"related_material":{"record":[{"id":"3168","status":"public","relation":"later_version"}]},"department":[{"_id":"ToHe"},{"_id":"CaGu"}],"status":"public","has_accepted_license":"1","citation":{"ista":"Feret J, Henzinger TA, Koeppl H, Petrov T. 2010. Lumpability abstractions of rule-based systems. MECBIC: Membrane Computing and Biologically Inspired Process Calculi, EPTCS, vol. 40, 142–161.","apa":"Feret, J., Henzinger, T. A., Koeppl, H., &#38; Petrov, T. (2010). Lumpability abstractions of rule-based systems (Vol. 40, pp. 142–161). Presented at the MECBIC: Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany: Open Publishing Association.","short":"J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, in:, Open Publishing Association, 2010, pp. 142–161.","ieee":"J. Feret, T. A. Henzinger, H. Koeppl, and T. Petrov, “Lumpability abstractions of rule-based systems,” presented at the MECBIC: Membrane Computing and Biologically Inspired Process Calculi, Jena, Germany, 2010, vol. 40, pp. 142–161.","ama":"Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule-based systems. In: Vol 40. Open Publishing Association; 2010:142-161.","mla":"Feret, Jérôme, et al. <i>Lumpability Abstractions of Rule-Based Systems</i>. Vol. 40, Open Publishing Association, 2010, pp. 142–61.","chicago":"Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability Abstractions of Rule-Based Systems,” 40:142–61. Open Publishing Association, 2010."},"intvolume":"        40","abstract":[{"text":"The induction of a signaling pathway is characterized by transient complex formation and mutual posttranslational modification of proteins. To faithfully capture this combinatorial process in a math- ematical model is an important challenge in systems biology. Exploiting the limited context on which most binding and modification events are conditioned, attempts have been made to reduce the com- binatorial complexity by quotienting the reachable set of molecular species, into species aggregates while preserving the deterministic semantics of the thermodynamic limit. Recently we proposed a quotienting that also preserves the stochastic semantics and that is complete in the sense that the semantics of individual species can be recovered from the aggregate semantics. In this paper we prove that this quotienting yields a sufficient condition for weak lumpability and that it gives rise to a backward Markov bisimulation between the original and aggregated transition system. We illustrate the framework on a case study of the EGF/insulin receptor crosstalk.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"3719","title":"Lumpability abstractions of rule-based systems","acknowledgement":"Jérôme Feret’s contribution was partially supported by the ABSTRACTCELL ANR-Chair of Excellence. Heinz Koeppl acknowledges the support from the Swiss National Science Foundation, grant no. 200020-117975/1. Tatjana Petrov acknowledges the support from SystemsX.ch, the Swiss Initiative in Systems Biology.","scopus_import":1,"file_date_updated":"2020-07-14T12:46:14Z"},{"author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240"}],"pubrep_id":"524","day":"17","publication_status":"published","publist_id":"2454","date_created":"2018-12-11T12:05:05Z","year":"2010","ddc":["570","576"],"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"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)"},"date_published":"2010-06-17T00:00:00Z","type":"journal_article","volume":6,"oa_version":"Published Version","publisher":"Public Library of Science","date_updated":"2021-01-12T07:52:05Z","doi":"10.1371/journal.pgen.1000987","publication":"PLoS Genetics","oa":1,"quality_controlled":"1","file":[{"file_size":349965,"date_updated":"2020-07-14T12:46:15Z","checksum":"5c14de2680ab483cb835096c99ee734d","access_level":"open_access","file_name":"IST-2016-524-v1+1_journal.pgen.1000987.PDF","creator":"system","relation":"main_file","file_id":"5075","date_created":"2018-12-12T10:14:24Z","content_type":"application/pdf"}],"article_number":"e1000987","month":"06","issue":"6","scopus_import":1,"file_date_updated":"2020-07-14T12:46:15Z","status":"public","citation":{"short":"N.H. Barton, PLoS Genetics 6 (2010).","ieee":"N. H. Barton, “Understanding adaptation in large populations,” <i>PLoS Genetics</i>, vol. 6, no. 6. Public Library of Science, 2010.","ista":"Barton NH. 2010. Understanding adaptation in large populations. PLoS Genetics. 6(6), e1000987.","apa":"Barton, N. H. (2010). Understanding adaptation in large populations. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1000987\">https://doi.org/10.1371/journal.pgen.1000987</a>","chicago":"Barton, Nicholas H. “Understanding Adaptation in Large Populations.” <i>PLoS Genetics</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pgen.1000987\">https://doi.org/10.1371/journal.pgen.1000987</a>.","ama":"Barton NH. Understanding adaptation in large populations. <i>PLoS Genetics</i>. 2010;6(6). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1000987\">10.1371/journal.pgen.1000987</a>","mla":"Barton, Nicholas H. “Understanding Adaptation in Large Populations.” <i>PLoS Genetics</i>, vol. 6, no. 6, e1000987, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1000987\">10.1371/journal.pgen.1000987</a>."},"intvolume":"         6","has_accepted_license":"1","title":"Understanding adaptation in large populations","_id":"3772","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"pmid":1,"acknowledgement":"The author thanks the Werner-Gren Foundation and the Royal Swedish Academy of Sciences for organizing the symposium on the ‘Origin of Species’. He also thanks Reinhard Bürger, and two anonymous referees, for their helpful comments.\r\n","abstract":[{"text":"If distinct biological species are to coexist in sympatry, they must be reproductively isolated and must exploit different limiting resources. A two-niche Levene model is analysed, in which habitat preference and survival depend on underlying additive traits. The population genetics of preference and viability are equivalent. However, there is a linear trade-off between the chances of settling in either niche, whereas viabilities may be constrained arbitrarily. With a convex trade-off, a sexual population evolves a single generalist genotype, whereas with a concave trade-off, disruptive selection favours maximal variance. A pure habitat preference evolves to global linkage equilibrium if mating occurs in a single pool, but remarkably, evolves to pairwise linkage equilibrium within niches if mating is within those niches--independent of the genetics. With a concave trade-off, the population shifts sharply between a unimodal distribution with high gene flow and a bimodal distribution with strong isolation, as the underlying genetic variance increases. However, these alternative states are only simultaneously stable for a narrow parameter range. A sharp threshold is only seen if survival in the 'wrong' niche is low; otherwise, strong isolation is impossible. Gene flow from divergent demes makes speciation much easier in parapatry than in sympatry.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"3773","title":"What role does natural selection play in speciation?","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pubmed/20439284","open_access":"1"}],"citation":{"apa":"Barton, N. H. (2010). What role does natural selection play in speciation? <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rstb.2010.0001\">https://doi.org/10.1098/rstb.2010.0001</a>","ista":"Barton NH. 2010. What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1547), 1825–1840.","ieee":"N. H. Barton, “What role does natural selection play in speciation?,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1547. Royal Society, pp. 1825–1840, 2010.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1825–1840.","mla":"Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1547, Royal Society, 2010, pp. 1825–40, doi:<a href=\"https://doi.org/10.1098/rstb.2010.0001\">10.1098/rstb.2010.0001</a>.","ama":"Barton NH. What role does natural selection play in speciation? <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2010;365(1547):1825-1840. doi:<a href=\"https://doi.org/10.1098/rstb.2010.0001\">10.1098/rstb.2010.0001</a>","chicago":"Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, 2010. <a href=\"https://doi.org/10.1098/rstb.2010.0001\">https://doi.org/10.1098/rstb.2010.0001</a>."},"intvolume":"       365","status":"public","scopus_import":1,"issue":"1547","month":"06","quality_controlled":"1","oa":1,"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","date_updated":"2021-01-12T07:52:06Z","doi":"10.1098/rstb.2010.0001","publisher":"Royal Society","oa_version":"Submitted Version","external_id":{"pmid":["20439284"]},"volume":365,"date_published":"2010-06-12T00:00:00Z","type":"journal_article","department":[{"_id":"NiBa"}],"year":"2010","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:05:05Z","publication_status":"published","publist_id":"2455","day":"12","author":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"page":"1825 - 1840"},{"issue":"2","scopus_import":1,"citation":{"short":"H. Senn, G. Swanson, S. Goodman, N.H. Barton, J. Pemberton, Journal of Animal Ecology 79 (2010) 414–425.","ieee":"H. Senn, G. Swanson, S. Goodman, N. H. Barton, and J. Pemberton, “Phenotypic correlates of hybridisation between red and sika deer (genus Cervus),” <i>Journal of Animal Ecology</i>, vol. 79, no. 2. Wiley-Blackwell, pp. 414–425, 2010.","ista":"Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. 2010. Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). Journal of Animal Ecology. 79(2), 414–425.","apa":"Senn, H., Swanson, G., Goodman, S., Barton, N. H., &#38; Pemberton, J. (2010). Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). <i>Journal of Animal Ecology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1365-2656.2009.01633.x\">https://doi.org/10.1111/j.1365-2656.2009.01633.x</a>","chicago":"Senn, Helen, Graeme Swanson, Simon Goodman, Nicholas H Barton, and Josephine Pemberton. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus Cervus).” <i>Journal of Animal Ecology</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1111/j.1365-2656.2009.01633.x\">https://doi.org/10.1111/j.1365-2656.2009.01633.x</a>.","ama":"Senn H, Swanson G, Goodman S, Barton NH, Pemberton J. Phenotypic correlates of hybridisation between red and sika deer (genus Cervus). <i>Journal of Animal Ecology</i>. 2010;79(2):414-425. doi:<a href=\"https://doi.org/10.1111/j.1365-2656.2009.01633.x\">10.1111/j.1365-2656.2009.01633.x</a>","mla":"Senn, Helen, et al. “Phenotypic Correlates of Hybridisation between Red and Sika Deer (Genus Cervus).” <i>Journal of Animal Ecology</i>, vol. 79, no. 2, Wiley-Blackwell, 2010, pp. 414–25, doi:<a href=\"https://doi.org/10.1111/j.1365-2656.2009.01633.x\">10.1111/j.1365-2656.2009.01633.x</a>."},"intvolume":"        79","status":"public","acknowledgement":"This project was funded through a NERC studentship to HVS which was CASE partnered by the Macaulay Institute.\r\nWe thank the Forestry Commission Scotland rangers for all their help with providing the larder data for and samples from red and sika deer, Stephen Senn and Jarrod Hadfield for statistical advice and Steve Albon for helpful comments on the manuscript.","pmid":1,"_id":"3774","title":"Phenotypic correlates of hybridisation between red and sika deer (genus Cervus)","abstract":[{"text":"1. Hybridisation with an invasive species has the potential to alter the phenotype and hence the ecology of a native counterpart. 2. Here data from populations of native red deer Cervus elaphus and invasive sika deer Cervus nippon in Scotland is used to assess the extent to which hybridisation between them is causing phenotypic change. This is done by regression of phenotypic traits against genetic hybrid scores. 3. Hybridisation is causing increases in the body weight of sika-like deer and decreases in the body weight of red-like females. Hybridisation is causing increases in jaw length and increases in incisor arcade breadth in sika-like females. Hybridisation is also causing decreases in incisor arcade breadth in red-like females. 4. There is currently no evidence that hybridisation is causing changes in the kidney fat weight or pregnancy rates of either population. 5. Increased phenotypic similarity between the two species is likely to lead to further hybridisation. The ecological consequences of this are difficult to predict.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publist_id":"2453","day":"01","date_created":"2018-12-11T12:05:06Z","page":"414 - 425","author":[{"last_name":"Senn","first_name":"Helen","full_name":"Senn, Helen"},{"first_name":"Graeme","full_name":"Swanson, Graeme","last_name":"Swanson"},{"first_name":"Simon","full_name":"Goodman, Simon","last_name":"Goodman"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"full_name":"Pemberton, Josephine","first_name":"Josephine","last_name":"Pemberton"}],"department":[{"_id":"NiBa"}],"year":"2010","language":[{"iso":"eng"}],"oa_version":"None","external_id":{"pmid":["20002231"]},"volume":79,"type":"journal_article","date_published":"2010-03-01T00:00:00Z","quality_controlled":"1","month":"03","publication":"Journal of Animal Ecology","doi":"10.1111/j.1365-2656.2009.01633.x","date_updated":"2021-01-12T07:52:06Z","publisher":"Wiley-Blackwell"},{"issue":"1552","file_date_updated":"2020-07-14T12:46:15Z","scopus_import":1,"citation":{"mla":"Barton, Nicholas H. “Genetic Linkage and Natural Selection.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1552, Royal Society, 2010, pp. 2559–69, doi:<a href=\"https://doi.org/10.1098/rstb.2010.0106\">10.1098/rstb.2010.0106</a>.","ama":"Barton NH. Genetic linkage and natural selection. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2010;365(1552):2559-2569. doi:<a href=\"https://doi.org/10.1098/rstb.2010.0106\">10.1098/rstb.2010.0106</a>","chicago":"Barton, Nicholas H. “Genetic Linkage and Natural Selection.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society, 2010. <a href=\"https://doi.org/10.1098/rstb.2010.0106\">https://doi.org/10.1098/rstb.2010.0106</a>.","apa":"Barton, N. H. (2010). Genetic linkage and natural selection. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rstb.2010.0106\">https://doi.org/10.1098/rstb.2010.0106</a>","ista":"Barton NH. 2010. Genetic linkage and natural selection. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1552), 2559–2569.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 2559–2569.","ieee":"N. H. Barton, “Genetic linkage and natural selection,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1552. Royal Society, pp. 2559–2569, 2010."},"intvolume":"       365","has_accepted_license":"1","status":"public","acknowledgement":"Royal Society and Wolfson Foundation for their support\r\nWe would like to thank Brian Charlesworth and Sally Otto for their helpful comments.","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The prevalence of recombination in eukaryotes poses one of the most puzzling questions in biology. The most compelling general explanation is that recombination facilitates selection by breaking down the negative associations generated by random drift (i.e. Hill-Robertson interference, HRI). I classify the effects of HRI owing to: deleterious mutation, balancing selection and selective sweeps on: neutral diversity, rates of adaptation and the mutation load. These effects are mediated primarily by the density of deleterious mutations and of selective sweeps. Sequence polymorphism and divergence suggest that these rates may be high enough to cause significant interference even in genomic regions of high recombination. However, neither seems able to generate enough variance in fitness to select strongly for high rates of recombination. It is plausible that spatial and temporal fluctuations in selection generate much more fitness variance, and hence selection for recombination, than can be explained by uniformly deleterious mutations or species-wide selective sweeps."}],"title":"Genetic linkage and natural selection","_id":"3776","date_created":"2018-12-11T12:05:06Z","day":"27","publist_id":"2450","publication_status":"published","author":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"pubrep_id":"555","page":"2559 - 2569","department":[{"_id":"NiBa"}],"language":[{"iso":"eng"}],"year":"2010","ddc":["570"],"oa_version":"Submitted Version","type":"journal_article","date_published":"2010-08-27T00:00:00Z","volume":365,"month":"08","file":[{"checksum":"4d8aade10db030124ab158b622e337e0","file_name":"IST-2016-555-v1+1_RS2009_revised.pdf","access_level":"open_access","file_size":250255,"date_updated":"2020-07-14T12:46:15Z","date_created":"2018-12-12T10:14:40Z","file_id":"5093","content_type":"application/pdf","creator":"system","relation":"main_file"}],"oa":1,"quality_controlled":"1","doi":"10.1098/rstb.2010.0106","publisher":"Royal Society","date_updated":"2021-01-12T07:52:07Z","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences"}]