[{"date_created":"2018-12-11T11:57:30Z","oa_version":"Published Version","publist_id":"4517","publication":"Algorithms for Molecular Biology","title":"Accuracy of phylogeny reconstruction methods combining overlapping gene data sets ","department":[{"_id":"JoBo"}],"publisher":"BioMed Central","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"}],"_id":"2409","has_accepted_license":"1","year":"2010","volume":5,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","citation":{"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>.","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.","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>","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>","short":"A. Kupczok, H. Schmidt, A. Von Haeseler, Algorithms for Molecular Biology 5 (2010).","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>.","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."},"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).","oa":1,"status":"public","issue":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:45:40Z","article_number":"37","scopus_import":1,"quality_controlled":"1","pubrep_id":"939","date_published":"2010-12-06T00:00:00Z","author":[{"last_name":"Kupczok","first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Kupczok, Anne"},{"first_name":"Heiko","last_name":"Schmidt","full_name":"Schmidt, Heiko"},{"full_name":"Von Haeseler, Arndt","first_name":"Arndt","last_name":"Von Haeseler"}],"doi":"10.1186/1748-7188-5-37","date_updated":"2021-01-12T06:57:18Z","intvolume":"         5","file":[{"checksum":"e2497285388bc4da629bafb46662eb43","file_name":"IST-2018-939-v1+1_2010_Kupczok_Accuracy_of.pdf","file_size":723929,"file_id":"4739","date_updated":"2020-07-14T12:45:40Z","date_created":"2018-12-12T10:09:16Z","content_type":"application/pdf","creator":"system","access_level":"open_access","relation":"main_file"}],"publication_status":"published","month":"12","language":[{"iso":"eng"}],"ddc":["576"],"day":"06"},{"type":"journal_article","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","page":"2701 - 2715","volume":64,"publication_status":"published","year":"2010","intvolume":"        64","_id":"474","day":"01","issue":"9","status":"public","acknowledgement":"This work has made use of the resources provided by the Edinburgh Compute and Data Facility (ECDF). The ECDF is partially supported by the eDIKT initiative. NHB is supported in part by EPSRC Grant EP/E066070/1; JK is supported by EPSRC Grant EP/E066070/1; and AME is supported in part by EPSRC Grant EP/E065945/1.","language":[{"iso":"eng"}],"month":"09","citation":{"apa":"Barton, N. H., Kelleher, J., &#38; Etheridge, A. (2010). A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. <i>Evolution</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">https://doi.org/10.1111/j.1558-5646.2010.01019.x</a>","chicago":"Barton, Nicholas H, Jerome Kelleher, and Alison Etheridge. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” <i>Evolution</i>. Wiley-Blackwell, 2010. <a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">https://doi.org/10.1111/j.1558-5646.2010.01019.x</a>.","ieee":"N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for extinction and recolonization in two dimensions: Quantifying phylogeography,” <i>Evolution</i>, vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.","short":"N.H. Barton, J. Kelleher, A. Etheridge, Evolution 64 (2010) 2701–2715.","mla":"Barton, Nicholas H., et al. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” <i>Evolution</i>, vol. 64, no. 9, Wiley-Blackwell, 2010, pp. 2701–15, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">10.1111/j.1558-5646.2010.01019.x</a>.","ista":"Barton NH, Kelleher J, Etheridge A. 2010. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. 64(9), 2701–2715.","ama":"Barton NH, Kelleher J, Etheridge A. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. <i>Evolution</i>. 2010;64(9):2701-2715. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2010.01019.x\">10.1111/j.1558-5646.2010.01019.x</a>"},"publisher":"Wiley-Blackwell","department":[{"_id":"NiBa"}],"title":"A new model for extinction and recolonization in two dimensions: Quantifying phylogeography","publication":"Evolution","publist_id":"2780","oa_version":"None","date_created":"2018-12-11T11:46:40Z","date_updated":"2021-01-12T08:00:52Z","doi":"10.1111/j.1558-5646.2010.01019.x","author":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jerome","last_name":"Kelleher","full_name":"Kelleher, Jerome"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"}],"date_published":"2010-09-01T00:00:00Z","quality_controlled":"1","scopus_import":1,"abstract":[{"text":"Classical models of gene flow fail in three ways: they cannot explain large-scale patterns; they predict much more genetic diversity than is observed; and they assume that loosely linked genetic loci evolve independently. We propose a new model that deals with these problems. Extinction events kill some fraction of individuals in a region. These are replaced by offspring from a small number of parents, drawn from the preexisting population. This model of evolution forwards in time corresponds to a backwards model, in which ancestral lineages jump to a new location if they are hit by an event, and may coalesce with other lineages that are hit by the same event. We derive an expression for the identity in allelic state, and show that, over scales much larger than the largest event, this converges to the classical value derived by Wright and Malécot. However, rare events that cover large areas cause low genetic diversity, large-scale patterns, and correlations in ancestry between unlinked loci.","lang":"eng"}]},{"file_date_updated":"2020-07-14T12:46:35Z","conference":{"name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","end_date":"2010-12-18","location":"Chennai, India","start_date":"2010-12-15"},"tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_updated":"2021-01-12T08:01:00Z","doi":"10.4230/LIPIcs.FSTTCS.2010.1","alternative_title":["LIPIcs"],"date_published":"2010-01-01T00:00:00Z","author":[{"last_name":"Alur","first_name":"Rajeev","full_name":"Alur, Rajeev"},{"first_name":"Pavol","last_name":"Cerny","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"}],"pubrep_id":"948","quality_controlled":"1","scopus_import":1,"file":[{"file_size":492344,"checksum":"5845be5aa19791830f7407d8853f2df0","file_name":"IST-2018-948-v1+1_2011_Cerny_Expressiveness_of.pdf","date_updated":"2020-07-14T12:46:35Z","file_id":"4690","content_type":"application/pdf","date_created":"2018-12-12T10:08:29Z","relation":"main_file","access_level":"open_access","creator":"system"}],"publication_status":"published","intvolume":"         8","ddc":["005"],"day":"01","month":"01","language":[{"iso":"eng"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"}],"title":"Expressiveness of streaming string transducers","publist_id":"7331","date_created":"2018-12-11T11:46:45Z","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Streaming string transducers [1] define (partial) functions from input strings to output strings. A streaming string transducer makes a single pass through the input string and uses a finite set of variables that range over strings from the output alphabet. At every step, the transducer processes an input symbol, and updates all the variables in parallel using assignments whose right-hand-sides are concatenations of output symbols and variables with the restriction that a variable can be used at most once in a right-hand-side expression. It has been shown that streaming string transducers operating on strings over infinite data domains are of interest in algorithmic verification of list-processing programs, as they lead to PSPACE decision procedures for checking pre/post conditions and for checking semantic equivalence, for a well-defined class of heap-manipulating programs. In order to understand the theoretical expressiveness of streaming transducers, we focus on streaming transducers processing strings over finite alphabets, given the existence of a robust and well-studied class of &quot;regular&quot; transductions for this case. Such regular transductions can be defined either by two-way deterministic finite-state transducers, or using a logical MSO-based characterization. Our main result is that the expressiveness of streaming string transducers coincides exactly with this class of regular transductions. "}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","volume":8,"page":"1 - 12","year":"2010","has_accepted_license":"1","_id":"488","oa":1,"status":"public","citation":{"apa":"Alur, R., &#38; Cerny, P. (2010). Expressiveness of streaming string transducers (Vol. 8, pp. 1–12). Presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Chennai, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1</a>","chicago":"Alur, Rajeev, and Pavol Cerny. “Expressiveness of Streaming String Transducers,” 8:1–12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1</a>.","ieee":"R. Alur and P. Cerny, “Expressiveness of streaming string transducers,” presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Chennai, India, 2010, vol. 8, pp. 1–12.","mla":"Alur, Rajeev, and Pavol Cerny. <i>Expressiveness of Streaming String Transducers</i>. Vol. 8, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">10.4230/LIPIcs.FSTTCS.2010.1</a>.","ista":"Alur R, Cerny P. 2010. Expressiveness of streaming string transducers. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 8, 1–12.","short":"R. Alur, P. Cerny, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12.","ama":"Alur R, Cerny P. Expressiveness of streaming string transducers. In: Vol 8. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:1-12. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1\">10.4230/LIPIcs.FSTTCS.2010.1</a>"}},{"main_file_link":[{"url":"https://arxiv.org/abs/1006.1404v1","open_access":"1"}],"intvolume":"        25","publication_status":"published","day":"09","language":[{"iso":"eng"}],"month":"06","conference":{"name":"GandALF: Games, Automata, Logic, and Formal Verification","end_date":"2010-06-18","location":"Minori, Amalfi Coast, Italy","start_date":"2010-06-17"},"date_published":"2010-06-09T00:00:00Z","author":[{"full_name":"Cristau, Julien","first_name":"Julien","last_name":"Cristau"},{"first_name":"Claire","last_name":"David","full_name":"David, Claire"},{"first_name":"Florian","last_name":"Horn","full_name":"Horn, Florian","id":"37327ACE-F248-11E8-B48F-1D18A9856A87"}],"alternative_title":["EPTCS"],"date_updated":"2021-01-12T08:01:01Z","doi":"10.4204/EPTCS.25.7","scopus_import":1,"quality_controlled":"1","page":"30 - 39","volume":25,"type":"conference","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"489","year":"2010","oa":1,"status":"public","citation":{"ama":"Cristau J, David C, Horn F. How do we remember the past in randomised strategies? . In: <i>Proceedings of GandALF 2010</i>. Vol 25. Open Publishing Association; 2010:30-39. doi:<a href=\"https://doi.org/10.4204/EPTCS.25.7\">10.4204/EPTCS.25.7</a>","ista":"Cristau J, David C, Horn F. 2010. How do we remember the past in randomised strategies? . Proceedings of GandALF 2010. GandALF: Games, Automata, Logic, and Formal Verification, EPTCS, vol. 25, 30–39.","short":"J. Cristau, C. David, F. Horn, in:, Proceedings of GandALF 2010, Open Publishing Association, 2010, pp. 30–39.","mla":"Cristau, Julien, et al. “How Do We Remember the Past in Randomised Strategies? .” <i>Proceedings of GandALF 2010</i>, vol. 25, Open Publishing Association, 2010, pp. 30–39, doi:<a href=\"https://doi.org/10.4204/EPTCS.25.7\">10.4204/EPTCS.25.7</a>.","ieee":"J. Cristau, C. David, and F. Horn, “How do we remember the past in randomised strategies? ,” in <i>Proceedings of GandALF 2010</i>, Minori, Amalfi Coast, Italy, 2010, vol. 25, pp. 30–39.","chicago":"Cristau, Julien, Claire David, and Florian Horn. “How Do We Remember the Past in Randomised Strategies? .” In <i>Proceedings of GandALF 2010</i>, 25:30–39. Open Publishing Association, 2010. <a href=\"https://doi.org/10.4204/EPTCS.25.7\">https://doi.org/10.4204/EPTCS.25.7</a>.","apa":"Cristau, J., David, C., &#38; Horn, F. (2010). How do we remember the past in randomised strategies? . In <i>Proceedings of GandALF 2010</i> (Vol. 25, pp. 30–39). Minori, Amalfi Coast, Italy: Open Publishing Association. <a href=\"https://doi.org/10.4204/EPTCS.25.7\">https://doi.org/10.4204/EPTCS.25.7</a>"},"department":[{"_id":"KrCh"}],"title":"How do we remember the past in randomised strategies? ","publication":"Proceedings of GandALF 2010","publisher":"Open Publishing Association","oa_version":"Published Version","date_created":"2018-12-11T11:46:45Z","publist_id":"7332","abstract":[{"text":"Graph games of infinite length are a natural model for open reactive processes: one player represents the controller, trying to ensure a given specification, and the other represents a hostile environment. The evolution of the system depends on the decisions of both players, supplemented by chance. In this work, we focus on the notion of randomised strategy. More specifically, we show that three natural definitions may lead to very different results: in the most general cases, an almost-surely winning situation may become almost-surely losing if the player is only allowed to use a weaker notion of strategy. In more reasonable settings, translations exist, but they require infinite memory, even in simple cases. Finally, some traditional problems becomes undecidable for the strongest type of strategies.","lang":"eng"}]},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":37,"page":"171 - 199","year":"2010","publication_status":"published","_id":"533","intvolume":"        37","issue":"2-3","day":"01","status":"public","month":"12","language":[{"iso":"eng"}],"citation":{"apa":"Hoenicke, J., Leino, K., Podelski, A., Schäf, M., &#38; Wies, T. (2010). Doomed program points. <i>Formal Methods in System Design</i>. Springer. <a href=\"https://doi.org/10.1007/s10703-010-0102-0\">https://doi.org/10.1007/s10703-010-0102-0</a>","chicago":"Hoenicke, Jochen, Kari Leino, Andreas Podelski, Martin Schäf, and Thomas Wies. “Doomed Program Points.” <i>Formal Methods in System Design</i>. Springer, 2010. <a href=\"https://doi.org/10.1007/s10703-010-0102-0\">https://doi.org/10.1007/s10703-010-0102-0</a>.","ieee":"J. Hoenicke, K. Leino, A. Podelski, M. Schäf, and T. Wies, “Doomed program points,” <i>Formal Methods in System Design</i>, vol. 37, no. 2–3. Springer, pp. 171–199, 2010.","mla":"Hoenicke, Jochen, et al. “Doomed Program Points.” <i>Formal Methods in System Design</i>, vol. 37, no. 2–3, Springer, 2010, pp. 171–99, doi:<a href=\"https://doi.org/10.1007/s10703-010-0102-0\">10.1007/s10703-010-0102-0</a>.","short":"J. Hoenicke, K. Leino, A. Podelski, M. Schäf, T. Wies, Formal Methods in System Design 37 (2010) 171–199.","ista":"Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. 2010. Doomed program points. Formal Methods in System Design. 37(2–3), 171–199.","ama":"Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. Doomed program points. <i>Formal Methods in System Design</i>. 2010;37(2-3):171-199. doi:<a href=\"https://doi.org/10.1007/s10703-010-0102-0\">10.1007/s10703-010-0102-0</a>"},"publisher":"Springer","publication":"Formal Methods in System Design","title":"Doomed program points","department":[{"_id":"ToHe"}],"publist_id":"7284","date_created":"2018-12-11T11:47:01Z","oa_version":"None","date_updated":"2021-01-12T08:01:28Z","doi":"10.1007/s10703-010-0102-0","author":[{"full_name":"Hoenicke, Jochen","first_name":"Jochen","last_name":"Hoenicke"},{"first_name":"Kari","last_name":"Leino","full_name":"Leino, Kari"},{"full_name":"Podelski, Andreas","last_name":"Podelski","first_name":"Andreas"},{"full_name":"Schäf, Martin","first_name":"Martin","last_name":"Schäf"},{"last_name":"Wies","first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","full_name":"Wies, Thomas"}],"date_published":"2010-12-01T00:00:00Z","quality_controlled":"1","scopus_import":1,"abstract":[{"lang":"eng","text":"Any programming error that can be revealed before compiling a program saves precious time for the programmer. While integrated development environments already do a good job by detecting, e.g., data-flow abnormalities, current static analysis tools suffer from false positives (&quot;noise&quot;) or require strong user interaction. We propose to avoid this deficiency by defining a new class of errors. A program fragment is doomed if its execution will inevitably fail, regardless of which state it is started in. We use a formal verification method to identify such errors fully automatically and, most significantly, without producing noise. We report on experiments with a prototype tool."}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"technical_report","page":"17","has_accepted_license":"1","year":"2010","file":[{"file_id":"5515","date_updated":"2020-07-14T12:46:42Z","file_size":429101,"checksum":"da38782d2388a6fa32109d10bb9bad67","file_name":"IST-2010-0004_IST-2010-0004.pdf","relation":"main_file","creator":"system","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T11:53:53Z"}],"publication_status":"published","_id":"5388","ddc":["000","005"],"day":"07","oa":1,"status":"public","month":"10","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"citation":{"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>","ieee":"K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, <i>Quantitative synthesis for concurrent programs</i>. IST Austria, 2010.","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>.","short":"K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative Synthesis for Concurrent Programs, IST Austria, 2010.","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>.","ista":"Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. 2010. Quantitative synthesis for concurrent programs, IST Austria, 17p.","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>"},"publisher":"IST Austria","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:42Z","title":"Quantitative synthesis for concurrent programs","date_created":"2018-12-12T11:39:03Z","oa_version":"Published Version","date_updated":"2023-02-23T11:24:08Z","alternative_title":["IST Austria Technical Report"],"related_material":{"record":[{"id":"3366","relation":"later_version","status":"public"}]},"doi":"10.15479/AT:IST-2010-0004","date_published":"2010-10-07T00:00:00Z","pubrep_id":"24","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Pavol","last_name":"Cerny","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna","first_name":"Arjun"},{"last_name":"Singh","first_name":"Rohit","full_name":"Singh, Rohit"}],"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."}]},{"publication_status":"published","file":[{"date_updated":"2020-07-14T12:46:42Z","file_id":"5547","file_name":"IST-2010-0003_IST-2010-0003.pdf","checksum":"284ded99764e32a583a8ea83fcea254b","file_size":367246,"access_level":"open_access","creator":"system","relation":"main_file","date_created":"2018-12-12T11:54:25Z","content_type":"application/pdf"}],"year":"2010","has_accepted_license":"1","_id":"5389","type":"technical_report","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"24","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"month":"06","citation":{"ieee":"P. Cerny, T. A. Henzinger, and A. Radhakrishna, <i>Simulation distances</i>. IST Austria, 2010.","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>.","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>","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>","ista":"Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances, IST Austria, 24p.","short":"P. Cerny, T.A. Henzinger, A. Radhakrishna, Simulation Distances, IST Austria, 2010.","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>."},"day":"04","ddc":["005"],"status":"public","oa":1,"oa_version":"Published Version","date_created":"2018-12-12T11:39:03Z","publisher":"IST Austria","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:42Z","title":"Simulation distances","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"}],"alternative_title":["IST Austria Technical Report"],"date_updated":"2023-02-23T12:09:16Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"3249"},{"status":"public","relation":"later_version","id":"4393"}]},"doi":"10.15479/AT:IST-2010-0003","pubrep_id":"25","author":[{"last_name":"Cerny","first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna","first_name":"Arjun"}],"date_published":"2010-06-04T00:00:00Z"},{"_id":"5390","publication_status":"published","file":[{"checksum":"283d3604d76dd4d5161585d4c8625fbe","file_name":"IST-2010-0002_IST-2010-0002.pdf","file_size":395662,"file_id":"5532","date_updated":"2020-07-14T12:46:43Z","date_created":"2018-12-12T11:54:10Z","content_type":"application/pdf","access_level":"open_access","creator":"system","relation":"main_file"}],"year":"2010","has_accepted_license":"1","page":"21","type":"technical_report","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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>","ista":"Chatterjee K, Fijalkow N. 2010. Topological, automata-theoretic and logical characterization of finitary languages, IST Austria, 21p.","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>.","short":"K. Chatterjee, N. Fijalkow, Topological, Automata-Theoretic and Logical Characterization of Finitary Languages, IST Austria, 2010.","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>.","ieee":"K. Chatterjee and N. Fijalkow, <i>Topological, automata-theoretic and logical characterization of finitary languages</i>. 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>"},"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"month":"06","status":"public","oa":1,"day":"04","ddc":["000"],"oa_version":"Published Version","date_created":"2018-12-12T11:39:03Z","title":"Topological, automata-theoretic and logical characterization of finitary languages","file_date_updated":"2020-07-14T12:46:43Z","department":[{"_id":"KrCh"}],"publisher":"IST Austria","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"}],"pubrep_id":"26","date_published":"2010-06-04T00:00:00Z","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Fijalkow, Nathanaël","first_name":"Nathanaël","last_name":"Fijalkow"}],"alternative_title":["IST Austria Technical Report"],"date_updated":"2020-07-14T23:04:41Z","doi":"10.15479/AT:IST-2010-0002"},{"_id":"5391","file":[{"content_type":"application/pdf","date_created":"2018-12-12T11:53:44Z","relation":"main_file","access_level":"open_access","creator":"system","file_size":372286,"file_name":"IST-2010-0001_IST-2010-0001.pdf","checksum":"986645caad7dd85a6a091488f6c646dc","file_id":"5505","date_updated":"2020-07-14T12:46:43Z"}],"year":"2010","has_accepted_license":"1","publication_status":"published","page":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"technical_report","citation":{"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>.","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>","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>","ista":"Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. 2010. Model checking of linearizability of concurrent list implementations, IST Austria, 27p.","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>.","short":"P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, Model Checking of Linearizability of Concurrent List Implementations, IST Austria, 2010."},"month":"04","publication_identifier":{"issn":["2664-1690"]},"language":[{"iso":"eng"}],"oa":1,"status":"public","ddc":["004"],"day":"19","date_created":"2018-12-12T11:39:04Z","oa_version":"Published Version","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:46:43Z","title":"Model checking of linearizability of concurrent list implementations","publisher":"IST Austria","abstract":[{"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.","lang":"eng"}],"author":[{"full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","first_name":"Pavol","last_name":"Cerny"},{"last_name":"Radhakrishna","first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun"},{"full_name":"Zufferey, Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien","orcid":"0000-0002-3197-8736","last_name":"Zufferey"},{"full_name":"Chaudhuri, Swarat","last_name":"Chaudhuri","first_name":"Swarat"},{"full_name":"Alur, Rajeev","first_name":"Rajeev","last_name":"Alur"}],"pubrep_id":"27","date_published":"2010-04-19T00:00:00Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"4390"}]},"doi":"10.15479/AT:IST-2010-0001","alternative_title":["IST Austria Technical Report"],"date_updated":"2023-02-23T12:09:09Z"},{"status":"public","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.","publication_identifier":{"isbn":["9783642020902"],"issn":["1612-3018"],"eisbn":["9783642020919"]},"citation":{"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>","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>.","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.","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>.","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>"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","page":"331-355","edition":"1","year":"2010","place":"Berlin, Heidelberg","_id":"14983","series_title":"FRONTCOLL","abstract":[{"lang":"eng","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."}],"publisher":"Springer","publication":"Brain-Computer Interfaces","department":[{"_id":"ScienComp"}],"title":"Adaptive Methods in BCI Research - An Introductory Tutorial","date_created":"2024-02-14T09:56:00Z","oa_version":"None","day":"06","month":"09","language":[{"iso":"eng"}],"publication_status":"published","article_processing_charge":"No","doi":"10.1007/978-3-642-02091-9_18","date_updated":"2024-02-19T09:47:25Z","alternative_title":["The Frontiers Collection"],"author":[{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl","first_name":"Alois"},{"full_name":"Vidaurre, Carmen","last_name":"Vidaurre","first_name":"Carmen"},{"full_name":"Müller, Klaus-Robert","last_name":"Müller","first_name":"Klaus-Robert"}],"date_published":"2010-09-06T00:00:00Z","editor":[{"full_name":"Graimann, Bernhard","last_name":"Graimann","first_name":"Bernhard"},{"full_name":"Pfurtscheller, Gert","last_name":"Pfurtscheller","first_name":"Gert"},{"full_name":"Allison, Brendan","first_name":"Brendan","last_name":"Allison"}],"quality_controlled":"1"},{"date_updated":"2021-12-14T08:35:37Z","doi":"10.1126/science.1186366","article_processing_charge":"No","date_published":"2010-05-14T00:00:00Z","author":[{"full_name":"Zemach, Assaf ","first_name":"Assaf ","last_name":"Zemach"},{"last_name":"McDaniel","first_name":"Ivy E.","full_name":"McDaniel, Ivy E."},{"full_name":"Silva, Pedro","last_name":"Silva","first_name":"Pedro"},{"first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"quality_controlled":"1","scopus_import":"1","keyword":["Multidisciplinary"],"publication_status":"published","intvolume":"       328","day":"14","pmid":1,"language":[{"iso":"eng"}],"month":"05","publisher":"American Association for the Advancement of Science","department":[{"_id":"DaZi"}],"title":"Genome-wide evolutionary analysis of eukaryotic DNA methylation","publication":"Science","oa_version":"None","date_created":"2021-06-04T08:26:08Z","extern":"1","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"}],"type":"journal_article","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"916-919","volume":328,"year":"2010","_id":"9452","article_type":"original","external_id":{"pmid":["20395474 "]},"issue":"5980","status":"public","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"citation":{"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>","short":"A. Zemach, I.E. McDaniel, P. Silva, D. Zilberman, Science 328 (2010) 916–919.","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>.","ista":"Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 328(5980), 916–919.","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>.","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.","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>"}},{"publisher":"National Academy of Sciences","publication":"Proceedings of the National Academy of Sciences","title":"Local DNA hypomethylation activates genes in rice endosperm","department":[{"_id":"DaZi"}],"date_created":"2021-06-07T09:31:01Z","oa_version":"Published Version","extern":"1","abstract":[{"lang":"eng","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."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","volume":107,"page":"18729-18734","year":"2010","_id":"9485","issue":"43","article_type":"original","external_id":{"pmid":["20937895"]},"oa":1,"status":"public","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"citation":{"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>.","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.","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>","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>","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.","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.","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>."},"article_processing_charge":"No","doi":"10.1073/pnas.1009695107","date_updated":"2021-12-14T08:40:02Z","author":[{"full_name":"Zemach, Assaf","last_name":"Zemach","first_name":"Assaf"},{"full_name":"Kim, M. Yvonne","last_name":"Kim","first_name":"M. Yvonne"},{"full_name":"Silva, Pedro","first_name":"Pedro","last_name":"Silva"},{"full_name":"Rodrigues, Jessica A.","first_name":"Jessica A.","last_name":"Rodrigues"},{"first_name":"Bradley","last_name":"Dotson","full_name":"Dotson, Bradley"},{"full_name":"Brooks, Matthew D.","last_name":"Brooks","first_name":"Matthew D."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","first_name":"Daniel"}],"date_published":"2010-10-26T00:00:00Z","quality_controlled":"1","scopus_import":"1","publication_status":"published","intvolume":"       107","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1009695107","open_access":"1"}],"day":"26","pmid":1,"month":"10","language":[{"iso":"eng"}]},{"date_created":"2021-06-07T09:45:27Z","oa_version":"Published Version","publisher":"Elsevier","publication":"Current Biology","department":[{"_id":"DaZi"}],"title":"Evolution of eukaryotic DNA methylation and the pursuit of safer sex","extern":"1","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."}],"year":"2010","_id":"9489","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","volume":20,"page":"R780-R785","publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"citation":{"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>","ista":"Zemach A, Zilberman D. 2010. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 20(17), R780–R785.","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>.","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.","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>.","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>"},"issue":"17","article_type":"review","external_id":{"pmid":["20833323"]},"status":"public","oa":1,"quality_controlled":"1","scopus_import":"1","article_processing_charge":"No","doi":"10.1016/j.cub.2010.07.007","date_updated":"2021-12-14T08:52:34Z","author":[{"first_name":"Assaf","last_name":"Zemach","full_name":"Zemach, Assaf"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"}],"date_published":"2010-09-14T00:00:00Z","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2010.07.007"}],"intvolume":"        20","month":"09","language":[{"iso":"eng"}],"day":"14","pmid":1},{"language":[{"iso":"eng"}],"month":"07","pmid":1,"day":"15","intvolume":"       137","publication_status":"published","scopus_import":"1","keyword":["Developmental Biology","Molecular Biology","Anther Tapetum","Arabidopsis","Cell Fate Establishment","EMS1","Reproductive Cell Lineage"],"quality_controlled":"1","date_published":"2010-07-15T00:00:00Z","author":[{"full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","last_name":"Feng","orcid":"0000-0002-4008-1234"},{"full_name":"Dickinson, Hugh G.","first_name":"Hugh G.","last_name":"Dickinson"}],"date_updated":"2023-05-08T10:57:11Z","doi":"10.1242/dev.049320","article_processing_charge":"No","citation":{"apa":"Feng, X., &#38; Dickinson, H. G. (2010). Tapetal cell fate, lineage and proliferation in the Arabidopsis anther. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.049320\">https://doi.org/10.1242/dev.049320</a>","ieee":"X. Feng and H. G. Dickinson, “Tapetal cell fate, lineage and proliferation in the Arabidopsis anther,” <i>Development</i>, vol. 137, no. 14. The Company of Biologists, pp. 2409–2416, 2010.","chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation in the Arabidopsis Anther.” <i>Development</i>. The Company of Biologists, 2010. <a href=\"https://doi.org/10.1242/dev.049320\">https://doi.org/10.1242/dev.049320</a>.","ista":"Feng X, Dickinson HG. 2010. Tapetal cell fate, lineage and proliferation in the Arabidopsis anther. Development. 137(14), 2409–2416.","mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation in the Arabidopsis Anther.” <i>Development</i>, vol. 137, no. 14, The Company of Biologists, 2010, pp. 2409–16, doi:<a href=\"https://doi.org/10.1242/dev.049320\">10.1242/dev.049320</a>.","short":"X. Feng, H.G. Dickinson, Development 137 (2010) 2409–2416.","ama":"Feng X, Dickinson HG. Tapetal cell fate, lineage and proliferation in the Arabidopsis anther. <i>Development</i>. 2010;137(14):2409-2416. doi:<a href=\"https://doi.org/10.1242/dev.049320\">10.1242/dev.049320</a>"},"publication_identifier":{"issn":["1477-9129","0950-1991"]},"acknowledgement":"We thank the following for providing mutant lines and reagents: Hong Ma, De Ye, Sacco De Vries, and Rod Scott for providing the pA9::Barnase lines and information on A9 expression patterns. Carla Galinha and Paolo Piazza gave valuable help with in situ hybridisation and qRT-PCR, respectively, and we acknowledge Qing Zhang, Helen Prescott and Matthew Dicks for providing excellent technical assistance. We are indebted to Miltos Tsiantis and Angela Hay for helpful discussion, and the research was funded by Oxford University through a Clarendon Scholarship to X.F., with additional financial support from Magdalen College (Oxford).","status":"public","article_type":"original","external_id":{"pmid":["20570940"]},"issue":"14","_id":"12199","year":"2010","page":"2409-2416","volume":137,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"The four microsporangia of the flowering plant anther develop from archesporial cells in the L2 of the primordium. Within each microsporangium, developing microsporocytes are surrounded by concentric monolayers of tapetal, middle layer and endothecial cells. How this intricate array of tissues, each containing relatively few cells, is established in an organ possessing no formal meristems is poorly understood. We describe here the pivotal role of the LRR receptor kinase EXCESS MICROSPOROCYTES 1 (EMS1) in forming the monolayer of tapetal nurse cells in Arabidopsis. Unusually for plants, tapetal cells are specified very early in development, and are subsequently stimulated to proliferate by a receptor-like kinase (RLK) complex that includes EMS1. Mutations in members of this EMS1 signalling complex and its putative ligand result in male-sterile plants in which tapetal initials fail to proliferate. Surprisingly, these cells continue to develop, isolated at the locular periphery. Mutant and wild-type microsporangia expand at similar rates and the ‘tapetal’ space at the periphery of mutant locules becomes occupied by microsporocytes. However, induction of late expression of EMS1 in the few tapetal initials in ems1 plants results in their proliferation to generate a functional tapetum, and this proliferation suppresses microsporocyte number. Our experiments also show that integrity of the tapetal monolayer is crucial for the maintenance of the polarity of divisions within it. This unexpected autonomy of the tapetal ‘lineage’ is discussed in the context of tissue development in complex plant organs, where constancy in size, shape and cell number is crucial.","lang":"eng"}],"extern":"1","oa_version":"None","date_created":"2023-01-16T09:21:54Z","title":"Tapetal cell fate, lineage and proliferation in the Arabidopsis anther","department":[{"_id":"XiFe"}],"publication":"Development","publisher":"The Company of Biologists"},{"publication_status":"published","intvolume":"        38","language":[{"iso":"eng"}],"month":"03","day":"22","pmid":1,"quality_controlled":"1","scopus_import":"1","keyword":["Biochemistry","Anther Development","Arabidopsis","Cell Fate","Microsporangium","Polarity","Receptor Kinase"],"date_updated":"2023-05-08T10:57:59Z","doi":"10.1042/bst0380571","article_processing_charge":"No","author":[{"id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","last_name":"Feng","first_name":"Xiaoqi"},{"full_name":"Dickinson, Hugh G.","last_name":"Dickinson","first_name":"Hugh G."}],"date_published":"2010-03-22T00:00:00Z","year":"2010","_id":"12200","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"571-576","volume":38,"publication_identifier":{"issn":["0300-5127","1470-8752"]},"citation":{"mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning of the <i>Arabidopsis</i> Anther.” <i>Biochemical Society Transactions</i>, vol. 38, no. 2, Portland Press Ltd., 2010, pp. 571–76, doi:<a href=\"https://doi.org/10.1042/bst0380571\">10.1042/bst0380571</a>.","short":"X. Feng, H.G. Dickinson, Biochemical Society Transactions 38 (2010) 571–576.","ista":"Feng X, Dickinson HG. 2010. Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther. Biochemical Society Transactions. 38(2), 571–576.","ama":"Feng X, Dickinson HG. Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther. <i>Biochemical Society Transactions</i>. 2010;38(2):571-576. doi:<a href=\"https://doi.org/10.1042/bst0380571\">10.1042/bst0380571</a>","apa":"Feng, X., &#38; Dickinson, H. G. (2010). Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther. <i>Biochemical Society Transactions</i>. Portland Press Ltd. <a href=\"https://doi.org/10.1042/bst0380571\">https://doi.org/10.1042/bst0380571</a>","ieee":"X. Feng and H. G. Dickinson, “Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther,” <i>Biochemical Society Transactions</i>, vol. 38, no. 2. Portland Press Ltd., pp. 571–576, 2010.","chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning of the <i>Arabidopsis</i> Anther.” <i>Biochemical Society Transactions</i>. Portland Press Ltd., 2010. <a href=\"https://doi.org/10.1042/bst0380571\">https://doi.org/10.1042/bst0380571</a>."},"article_type":"original","external_id":{"pmid":["20298223"]},"issue":"2","status":"public","oa_version":"None","date_created":"2023-01-16T09:22:18Z","publisher":"Portland Press Ltd.","title":"Cell–cell interactions during patterning of the <i>Arabidopsis</i> anther","department":[{"_id":"XiFe"}],"publication":"Biochemical Society Transactions","extern":"1","abstract":[{"lang":"eng","text":"Key steps in the evolution of the angiosperm anther include the patterning of the concentrically organized microsporangium and the incorporation of four such microsporangia into a leaf-like structure. Mutant studies in the model plant Arabidopsis thaliana are leading to an increasingly accurate picture of (i) the cell lineages culminating in the different cell types present in the microsporangium (the microsporocytes, the tapetum, and the middle and endothecial layers), and (ii) some of the genes responsible for specifying their fates. However, the processes that confer polarity on the developing anther and position the microsporangia within it remain unclear. Certainly, data from a range of experimental strategies suggest that hormones play a central role in establishing polarity and the patterning of the anther initial, and may be responsible for locating the microsporangia. But the fact that microsporangia were originally positioned externally suggests that their development is likely to be autonomous, perhaps with the reproductive cells generating signals controlling the growth and division of the investing anther epidermis. These possibilities are discussed in the context of the expression of genes which initiate and maintain male and female reproductive development, and in the perspective of our current views of anther evolution."}]},{"year":"2010","_id":"9764","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","month":"07","citation":{"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>","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>.","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.","short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010).","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>.","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>"},"day":"20","status":"public","date_created":"2021-08-02T09:45:39Z","oa_version":"Published Version","publisher":"Public Library of Science","title":"Heterosis and the drift load","department":[{"_id":"NiBa"}],"article_processing_charge":"No","date_updated":"2023-02-23T11:42:17Z","related_material":{"record":[{"id":"3779","status":"public","relation":"used_in_publication"}]},"doi":"10.1371/journal.pbio.1000429.s003","author":[{"last_name":"Rosas","first_name":"Ulises","full_name":"Rosas, Ulises"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"},{"first_name":"Lucy","last_name":"Copsey","full_name":"Copsey, Lucy"},{"first_name":"Pierre","last_name":"Barbier De Reuille","full_name":"Barbier De Reuille, Pierre"},{"full_name":"Coen, Enrico","first_name":"Enrico","last_name":"Coen"}],"date_published":"2010-07-20T00:00:00Z"},{"date_created":"2018-12-11T12:04:12Z","oa_version":"None","publist_id":"2779","publication":"Molecular Ecology","department":[{"_id":"NiBa"}],"title":"Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland","publisher":"Wiley-Blackwell","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."}],"scopus_import":1,"quality_controlled":"1","date_published":"2010-03-01T00:00:00Z","author":[{"first_name":"Helen","last_name":"Senn","full_name":"Senn, Helen"},{"full_name":"Goodman, Simon","last_name":"Goodman","first_name":"Simon"},{"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"},{"first_name":"Josephine","last_name":"Pemberton","full_name":"Pemberton, Josephine"}],"doi":"10.1111/j.1365-294X.2009.04497.x","date_updated":"2021-01-12T07:44:36Z","_id":"3604","intvolume":"        19","year":"2010","publication_status":"published","volume":19,"page":"910 - 924","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","citation":{"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>","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.","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>.","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.","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>.","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>"},"month":"03","language":[{"iso":"eng"}],"status":"public","issue":"5","day":"01"},{"scopus_import":1,"abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","date_published":"2010-11-01T00:00:00Z","author":[{"full_name":"Guzmán, José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","first_name":"José","last_name":"Guzmán"},{"last_name":"Schmidt","first_name":"Hartmut","full_name":"Schmidt, Hartmut"},{"full_name":"Franke, Heike","last_name":"Franke","first_name":"Heike"},{"full_name":"Krügel, Ute","first_name":"Ute","last_name":"Krügel"},{"first_name":"Jens","last_name":"Eilers","full_name":"Eilers, Jens"},{"last_name":"Illes","first_name":"Peter","full_name":"Illes, Peter"},{"full_name":"Gerevich, Zoltan","last_name":"Gerevich","first_name":"Zoltan"}],"doi":"10.1016/j.neuropharm.2010.05.013","date_updated":"2021-01-12T07:51:42Z","oa_version":"None","date_created":"2018-12-11T12:04:47Z","publist_id":"2512","title":"P2Y1 receptors inhibit long-term depression in the prefrontal cortex.","department":[{"_id":"PeJo"}],"publication":"Neuropharmacology","publisher":"Elsevier","citation":{"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>.","short":"J. Guzmán, H. Schmidt, H. Franke, U. Krügel, J. Eilers, P. Illes, Z. Gerevich, Neuropharmacology 59 (2010) 406–415.","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.","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>","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>","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.","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>."},"language":[{"iso":"eng"}],"month":"11","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.","status":"public","day":"01","issue":"6","_id":"3718","intvolume":"        59","publication_status":"published","year":"2010","page":"406 - 415","volume":59,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"conference":{"start_date":"2010-08-23","location":"Jena, Germany","end_date":"2010-08-23","name":"MECBIC: Membrane Computing and Biologically Inspired Process Calculi"},"file_date_updated":"2020-07-14T12:46:14Z","quality_controlled":"1","scopus_import":1,"alternative_title":["EPTCS"],"date_updated":"2023-02-23T11:15:19Z","related_material":{"record":[{"relation":"later_version","status":"public","id":"3168"}]},"author":[{"first_name":"Jérôme","last_name":"Feret","full_name":"Feret, Jérôme"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Koeppl, Heinz","last_name":"Koeppl","first_name":"Heinz"},{"full_name":"Petrov, Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","first_name":"Tatjana","orcid":"0000-0002-9041-0905","last_name":"Petrov"}],"date_published":"2010-10-30T00:00:00Z","publication_status":"published","file":[{"file_name":"Lumpability_abstractions_of_rule-based_systems.pdf","checksum":"eaaba991a86fff37606b0eb5196878e8","file_size":907155,"file_id":"5904","date_updated":"2020-07-14T12:46:14Z","date_created":"2019-01-31T12:09:09Z","content_type":"application/pdf","access_level":"open_access","creator":"kschuh","relation":"main_file"}],"intvolume":"        40","language":[{"iso":"eng"}],"month":"10","day":"30","ddc":["570"],"publist_id":"2511","oa_version":"Submitted Version","date_created":"2018-12-11T12:04:47Z","publisher":"Open Publishing Association","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"title":"Lumpability abstractions of rule-based systems","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"}],"arxiv":1,"has_accepted_license":"1","year":"2010","_id":"3719","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"142-161","volume":40,"citation":{"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.","chicago":"Feret, Jérôme, Thomas A Henzinger, Heinz Koeppl, and Tatjana Petrov. “Lumpability Abstractions of Rule-Based Systems,” 40:142–61. Open Publishing Association, 2010.","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.","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.","short":"J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, in:, Open Publishing Association, 2010, pp. 142–161.","mla":"Feret, Jérôme, et al. <i>Lumpability Abstractions of Rule-Based Systems</i>. Vol. 40, Open Publishing Association, 2010, pp. 142–61.","ama":"Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule-based systems. In: Vol 40. Open Publishing Association; 2010:142-161."},"external_id":{"arxiv":["1011.0496"]},"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.","status":"public","oa":1},{"oa":1,"status":"public","issue":"6","citation":{"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>.","ieee":"N. H. Barton, “Understanding adaptation in large populations,” <i>PLoS Genetics</i>, vol. 6, no. 6. Public Library of Science, 2010.","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>.","ista":"Barton NH. 2010. Understanding adaptation in large populations. PLoS Genetics. 6(6), e1000987.","short":"N.H. Barton, PLoS Genetics 6 (2010).","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>"},"volume":6,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","_id":"3772","has_accepted_license":"1","year":"2010","publication":"PLoS Genetics","title":"Understanding adaptation in large populations","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","date_created":"2018-12-11T12:05:05Z","oa_version":"Published Version","publist_id":"2454","ddc":["570","576"],"day":"17","month":"06","language":[{"iso":"eng"}],"intvolume":"         6","file":[{"file_id":"5075","date_updated":"2020-07-14T12:46:15Z","file_size":349965,"file_name":"IST-2016-524-v1+1_journal.pgen.1000987.PDF","checksum":"5c14de2680ab483cb835096c99ee734d","relation":"main_file","creator":"system","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:14:24Z"}],"publication_status":"published","author":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"pubrep_id":"524","date_published":"2010-06-17T00:00:00Z","date_updated":"2021-01-12T07:52:05Z","doi":"10.1371/journal.pgen.1000987","scopus_import":1,"quality_controlled":"1","file_date_updated":"2020-07-14T12:46:15Z","article_number":"e1000987","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}}]