[{"doi":"10.1007/978-3-642-17511-4_7","intvolume":"      6355","corr_author":"1","day":"01","citation":{"ista":"Blanc R, Henzinger TA, Hottelier T, Kovács L. 2010. ABC: Algebraic Bound Computation for loops. Logic for Programming, Artificial Intelligence, and Reasoning. LPAR: Logic for Programming, Artificial Intelligence and ReasoningLNCS vol. 6355, 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>.","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>.","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>","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.","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>"},"quality_controlled":"1","date_created":"2022-03-21T08:14:35Z","scopus_import":"1","conference":{"start_date":"2010-04-25","name":"LPAR: Logic for Programming, Artificial Intelligence and Reasoning","location":"Dakar, Senegal","end_date":"2010-05-01"},"article_processing_charge":"No","oa":1,"editor":[{"last_name":"Clarke","full_name":"Clarke, Edmund M","first_name":"Edmund M"},{"full_name":"Voronkov, Andrei","last_name":"Voronkov","first_name":"Andrei"}],"abstract":[{"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.","lang":"eng"}],"volume":6355,"author":[{"last_name":"Blanc","full_name":"Blanc, Régis","first_name":"Régis"},{"full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"last_name":"Hottelier","full_name":"Hottelier, Thibaud","first_name":"Thibaud"},{"last_name":"Kovács","full_name":"Kovács, Laura","first_name":"Laura"}],"external_id":{"isi":["000309668000007"]},"date_published":"2010-05-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","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).","year":"2010","publication":"Logic for Programming, Artificial Intelligence, and Reasoning","page":"103-118","language":[{"iso":"eng"}],"_id":"10908","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783642175107"],"issn":["0302-9743"],"eisbn":["9783642175114"]},"isi":1,"date_updated":"2025-09-30T09:51:13Z","department":[{"_id":"ToHe"}],"title":"ABC: Algebraic Bound Computation for loops","month":"05","place":"Berlin, Heidelberg","main_file_link":[{"open_access":"1","url":"https://infoscience.epfl.ch/record/186096"}],"oa_version":"Submitted Version","series_title":"LNCS","publication_status":"published","type":"conference","publisher":"Springer Nature"},{"_id":"10909","related_material":{"record":[{"id":"3267","relation":"later_version","status":"public"}]},"doi":"10.1137/1.9781611973075.129","citation":{"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>.","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>.","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>","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.","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>","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.","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."},"quality_controlled":"1","date_created":"2022-03-21T08:24:07Z","scopus_import":"1","corr_author":"1","day":"01","publication_identifier":{"eisbn":["9781611973075"]},"conference":{"start_date":"2010-01-17","location":"Austin, TX, United States","name":"SODA: Symposium on Discrete Algorithms","end_date":"2010-01-19"},"date_updated":"2025-09-30T09:22:32Z","article_processing_charge":"No","title":"Hardness results for homology localization","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"}],"department":[{"_id":"HeEd"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2010-02-01T00:00:00Z","month":"02","author":[{"first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Chao"},{"first_name":"Daniel","last_name":"Freedman","full_name":"Freedman, Daniel"}],"acknowledgement":"Partially supported by the Austrian Science Fund under grantFSP-S9103-N04 and P20134-N13.","status":"public","type":"conference","publication_status":"published","publisher":"Society for Industrial and Applied Mathematics","oa_version":"None","year":"2010","page":"1594-1604","language":[{"iso":"eng"}],"publication":"Proceedings of the 2010 Annual ACM-SIAM Symposium on Discrete Algorithms"},{"title":"Accuracy of phylogeny reconstruction methods combining overlapping gene data sets","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"department":[{"_id":"JoBo"}],"date_updated":"2025-09-30T09:48:29Z","isi":1,"_id":"2409","oa_version":"Published Version","type":"journal_article","publication_status":"published","publisher":"BioMed Central","month":"12","file_date_updated":"2020-07-14T12:45:40Z","oa":1,"ddc":["576"],"abstract":[{"lang":"eng","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."}],"has_accepted_license":"1","article_processing_charge":"No","article_number":"37","day":"06","scopus_import":"1","citation":{"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.","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>","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.","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>","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>."},"date_created":"2018-12-11T11:57:30Z","quality_controlled":"1","doi":"10.1186/1748-7188-5-37","intvolume":"         5","issue":"1","publication":"Algorithms for Molecular Biology","language":[{"iso":"eng"}],"year":"2010","status":"public","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).","author":[{"first_name":"Anne","last_name":"Kupczok","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Kupczok, Anne"},{"full_name":"Schmidt, Heiko","last_name":"Schmidt","first_name":"Heiko"},{"first_name":"Arndt","last_name":"Von Haeseler","full_name":"Von Haeseler, Arndt"}],"external_id":{"isi":["000286183400001"]},"publist_id":"4517","volume":5,"date_published":"2010-12-06T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pubrep_id":"939","file":[{"date_updated":"2020-07-14T12:45:40Z","file_id":"4739","creator":"system","relation":"main_file","file_name":"IST-2018-939-v1+1_2010_Kupczok_Accuracy_of.pdf","file_size":723929,"checksum":"e2497285388bc4da629bafb46662eb43","date_created":"2018-12-12T10:09:16Z","access_level":"open_access","content_type":"application/pdf"}]},{"year":"2010","oa_version":"Published Version","type":"research_data_reference","publisher":"Public Library of Science","author":[{"first_name":"Ulises","full_name":"Rosas, Ulises","last_name":"Rosas"},{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"last_name":"Copsey","full_name":"Copsey, Lucy","first_name":"Lucy"},{"full_name":"Barbier De Reuille, Pierre","last_name":"Barbier De Reuille","first_name":"Pierre"},{"last_name":"Coen","full_name":"Coen, Enrico","first_name":"Enrico"}],"month":"07","date_published":"2010-07-20T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","article_processing_charge":"No","date_updated":"2025-09-30T09:42:52Z","department":[{"_id":"NiBa"}],"title":"Heterosis and the drift load","doi":"10.1371/journal.pbio.1000429.s003","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"3779"}]},"_id":"9764","day":"20","date_created":"2021-08-02T09:45:39Z","citation":{"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>.","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>.","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>.","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).","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>"}},{"author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"full_name":"Kelleher, Jerome","last_name":"Kelleher","first_name":"Jerome"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"}],"external_id":{"isi":["000281636400017"]},"publist_id":"2780","volume":64,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2010-09-01T00:00:00Z","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.","status":"public","year":"2010","issue":"9","page":"2701 - 2715","language":[{"iso":"eng"}],"publication":"Evolution","doi":"10.1111/j.1558-5646.2010.01019.x","intvolume":"        64","corr_author":"1","day":"01","scopus_import":"1","date_created":"2018-12-11T11:46:40Z","quality_controlled":"1","citation":{"short":"N.H. Barton, J. Kelleher, A. Etheridge, Evolution 64 (2010) 2701–2715.","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.","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>","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.","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>.","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>","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>."},"article_processing_charge":"No","abstract":[{"lang":"eng","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."}],"month":"09","oa_version":"None","publisher":"Wiley-Blackwell","publication_status":"published","type":"journal_article","_id":"474","isi":1,"date_updated":"2025-09-30T09:50:22Z","title":"A new model for extinction and recolonization in two dimensions: Quantifying phylogeography","department":[{"_id":"NiBa"}]},{"oa":1,"file_date_updated":"2020-07-14T12:46:35Z","ddc":["005"],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","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. "}],"has_accepted_license":"1","conference":{"name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","location":"Chennai, India","end_date":"2010-12-18","start_date":"2010-12-15"},"article_processing_charge":"No","day":"01","corr_author":"1","alternative_title":["LIPIcs"],"quality_controlled":"1","citation":{"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>.","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>.","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>","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.","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>","short":"R. Alur, P. Cerny, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12.","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."},"date_created":"2018-12-11T11:46:45Z","scopus_import":"1","doi":"10.4230/LIPIcs.FSTTCS.2010.1","intvolume":"         8","language":[{"iso":"eng"}],"page":"1 - 12","year":"2010","status":"public","volume":8,"publist_id":"7331","external_id":{"isi":["000310361000001"]},"author":[{"first_name":"Rajeev","last_name":"Alur","full_name":"Alur, Rajeev"},{"last_name":"Cerny","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","full_name":"Cerny, Pavol","first_name":"Pavol"}],"pubrep_id":"948","file":[{"checksum":"5845be5aa19791830f7407d8853f2df0","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:08:29Z","file_name":"IST-2018-948-v1+1_2011_Cerny_Expressiveness_of.pdf","file_size":492344,"creator":"system","file_id":"4690","relation":"main_file","date_updated":"2020-07-14T12:46:35Z"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2010-01-01T00:00:00Z","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"department":[{"_id":"ToHe"}],"title":"Expressiveness of streaming string transducers","date_updated":"2025-09-30T09:49:32Z","isi":1,"_id":"488","oa_version":"Published Version","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","type":"conference","publication_status":"published","month":"01"},{"oa_version":"None","type":"journal_article","publication_status":"published","publisher":"Springer","month":"12","department":[{"_id":"ToHe"}],"title":"Doomed program points","date_updated":"2025-09-30T09:48:58Z","isi":1,"_id":"533","issue":"2-3","page":"171 - 199","publication":"Formal Methods in System Design","language":[{"iso":"eng"}],"year":"2010","status":"public","external_id":{"isi":["000286631700004"]},"author":[{"full_name":"Hoenicke, Jochen","last_name":"Hoenicke","first_name":"Jochen"},{"last_name":"Leino","full_name":"Leino, Kari","first_name":"Kari"},{"first_name":"Andreas","last_name":"Podelski","full_name":"Podelski, Andreas"},{"last_name":"Schäf","full_name":"Schäf, Martin","first_name":"Martin"},{"first_name":"Thomas","full_name":"Wies, Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","last_name":"Wies"}],"volume":37,"publist_id":"7284","date_published":"2010-12-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"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.","lang":"eng"}],"article_processing_charge":"No","day":"01","corr_author":"1","scopus_import":"1","citation":{"short":"J. Hoenicke, K. Leino, A. Podelski, M. Schäf, T. Wies, Formal Methods in System Design 37 (2010) 171–199.","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.","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>","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>","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>.","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>.","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."},"quality_controlled":"1","date_created":"2018-12-11T11:47:01Z","doi":"10.1007/s10703-010-0102-0","intvolume":"        37"},{"status":"public","month":"10","file":[{"date_updated":"2020-07-14T12:46:42Z","creator":"system","file_id":"5515","relation":"main_file","file_name":"IST-2010-0004_IST-2010-0004.pdf","file_size":429101,"checksum":"da38782d2388a6fa32109d10bb9bad67","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T11:53:53Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"24","date_published":"2010-10-07T00:00:00Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny","full_name":"Cerny, Pavol"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","first_name":"Arjun"},{"last_name":"Singh","full_name":"Singh, Rohit","first_name":"Rohit"}],"page":"17","language":[{"iso":"eng"}],"type":"technical_report","publication_status":"published","publisher":"IST Austria","oa_version":"Published Version","year":"2010","date_created":"2018-12-12T11:39:03Z","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>","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>.","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>.","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>","short":"K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative Synthesis for Concurrent Programs, IST Austria, 2010.","ieee":"K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, <i>Quantitative synthesis for concurrent programs</i>. IST Austria, 2010."},"alternative_title":["IST Austria Technical Report"],"publication_identifier":{"issn":["2664-1690"]},"day":"07","related_material":{"record":[{"id":"3366","status":"public","relation":"later_version"}]},"_id":"5388","doi":"10.15479/AT:IST-2010-0004","abstract":[{"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.","lang":"eng"}],"title":"Quantitative synthesis for concurrent programs","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"ddc":["000","005"],"file_date_updated":"2020-07-14T12:46:42Z","oa":1,"date_updated":"2025-04-15T08:12:00Z","has_accepted_license":"1"},{"oa_version":"Published Version","year":"2010","publisher":"IST Austria","publication_status":"published","type":"technical_report","page":"21","language":[{"iso":"eng"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu"},{"full_name":"Fijalkow, Nathanaël","last_name":"Fijalkow","first_name":"Nathanaël"}],"month":"06","date_published":"2010-06-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"26","file":[{"date_created":"2018-12-12T11:54:10Z","content_type":"application/pdf","access_level":"open_access","checksum":"283d3604d76dd4d5161585d4c8625fbe","file_size":395662,"file_name":"IST-2010-0002_IST-2010-0002.pdf","relation":"main_file","file_id":"5532","creator":"system","date_updated":"2020-07-14T12:46:43Z"}],"status":"public","has_accepted_license":"1","date_updated":"2020-07-14T23:04:41Z","file_date_updated":"2020-07-14T12:46:43Z","oa":1,"title":"Topological, automata-theoretic and logical characterization of finitary languages","department":[{"_id":"KrCh"}],"ddc":["000"],"abstract":[{"lang":"eng","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."}],"doi":"10.15479/AT:IST-2010-0002","_id":"5390","alternative_title":["IST Austria Technical Report"],"publication_identifier":{"issn":["2664-1690"]},"day":"04","date_created":"2018-12-12T11:39:03Z","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.","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>","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>.","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>","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>.","ista":"Chatterjee K, Fijalkow N. 2010. Topological, automata-theoretic and logical characterization of finitary languages, IST Austria, 21p."}},{"oa":1,"file_date_updated":"2020-07-14T12:46:43Z","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"}],"ddc":["004"],"department":[{"_id":"ToHe"}],"title":"Model checking of linearizability of concurrent list implementations","has_accepted_license":"1","date_updated":"2024-10-21T06:03:05Z","day":"19","publication_identifier":{"issn":["2664-1690"]},"alternative_title":["IST Austria 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.","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>.","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>","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>."},"date_created":"2018-12-12T11:39:04Z","doi":"10.15479/AT:IST-2010-0001","related_material":{"record":[{"relation":"later_version","status":"public","id":"4390"}]},"_id":"5391","language":[{"iso":"eng"}],"page":"27","year":"2010","oa_version":"Published Version","type":"technical_report","publication_status":"published","publisher":"IST Austria","status":"public","author":[{"first_name":"Pavol","full_name":"Cerny, Pavol","id":"4DCBEFFE-F248-11E8-B48F-1D18A9856A87","last_name":"Cerny"},{"first_name":"Arjun","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","last_name":"Radhakrishna"},{"id":"4397AC76-F248-11E8-B48F-1D18A9856A87","last_name":"Zufferey","orcid":"0000-0002-3197-8736","full_name":"Zufferey, Damien","first_name":"Damien"},{"first_name":"Swarat","last_name":"Chaudhuri","full_name":"Chaudhuri, Swarat"},{"first_name":"Rajeev","full_name":"Alur, Rajeev","last_name":"Alur"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2010-04-19T00:00:00Z","pubrep_id":"27","file":[{"file_name":"IST-2010-0001_IST-2010-0001.pdf","file_size":372286,"checksum":"986645caad7dd85a6a091488f6c646dc","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T11:53:44Z","date_updated":"2020-07-14T12:46:43Z","creator":"system","file_id":"5505","relation":"main_file"}],"month":"04"},{"publication":"Knee Surgery, Sports Traumatology, Arthroscopy","language":[{"iso":"eng"}],"page":"1792 - 1794","issue":"12","publication_status":"published","publisher":"Springer","type":"journal_article","year":"2010","oa_version":"None","status":"public","month":"08","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2010-08-20T00:00:00Z","external_id":{"isi":["000284375000028"]},"author":[{"first_name":"M.","last_name":"Sabeti Aschraf","full_name":"Sabeti Aschraf, M."},{"last_name":"Gonano","full_name":"Gonano, C.","first_name":"C."},{"full_name":"Nemecek, E.","last_name":"Nemecek","first_name":"E."},{"id":"3BC78B60-F248-11E8-B48F-1D18A9856A87","last_name":"Cichocki","full_name":"Cichocki, Lisa","first_name":"Lisa"},{"first_name":"C.","last_name":"Schueller Weidekamm","full_name":"Schueller Weidekamm, C."}],"publist_id":"2889","volume":18,"abstract":[{"text":"Purpose\r\nCalcifying tendinitis is a common condition of the shoulder. In many cases, arthroscopic reduction in the deposit is indicated. The localization of the deposit is sometimes challenging and time-consuming. Pre-operative ultrasound (US)-guided needle placement in the deposit and pre-operative US marking of the deposit at the skin with a ballpoint are described and recommended methods to alleviate the procedure without using ionizing radiation by fluoroscopy.\r\nMethods\r\nIntra-operative sonography of the shoulder is introduced as a new method to localize the calcific deposit with high accuracy. After standard arthroscopic buresectomy, the surgeon performs an ultrasound examination under sterile conditions to localize the deposits. A ventral longitudinal US section is recommended, and the upper arm is rotated until the deposit is visible. Subsequently, perpendicular to the skin at the position of the transducer, a needle is introduced under arthroscopic and ultrasound visualization to puncture the deposit.\r\nResults\r\nThe presence of snow-white crystals at the tip of the needle proves the exact localization. Consecutively, the curettage can be accomplished. Another intra-operative sonography evaluates possible calcific remnants and the tendon structure.\r\nConclusion\r\nThis new technique may alleviate arthroscopic calcific deposit curettage by visualizing the deposit without using ionizing radiation. Additionally, soft tissue damage due to decreased number of punctures to detect the deposit may be achieved. Both factors may contribute to reduced operation time.","lang":"eng"}],"title":"Intra-operative ultrasound facilitates the localization of the calcific deposit during arthroscopic treatment of calcifying tendinitis","article_processing_charge":"No","date_updated":"2025-09-30T09:47:29Z","scopus_import":"1","isi":1,"citation":{"ama":"Sabeti Aschraf M, Gonano C, Nemecek E, Cichocki L, Schueller Weidekamm C. Intra-operative ultrasound facilitates the localization of the calcific deposit during arthroscopic treatment of calcifying tendinitis. <i>Knee Surgery, Sports Traumatology, Arthroscopy</i>. 2010;18(12):1792-1794. doi:<a href=\"https://doi.org/10.1007/s00167-010-1227-9\">10.1007/s00167-010-1227-9</a>","ieee":"M. Sabeti Aschraf, C. Gonano, E. Nemecek, L. Cichocki, and C. Schueller Weidekamm, “Intra-operative ultrasound facilitates the localization of the calcific deposit during arthroscopic treatment of calcifying tendinitis,” <i>Knee Surgery, Sports Traumatology, Arthroscopy</i>, vol. 18, no. 12. Springer, pp. 1792–1794, 2010.","short":"M. Sabeti Aschraf, C. Gonano, E. Nemecek, L. Cichocki, C. Schueller Weidekamm, Knee Surgery, Sports Traumatology, Arthroscopy 18 (2010) 1792–1794.","ista":"Sabeti Aschraf M, Gonano C, Nemecek E, Cichocki L, Schueller Weidekamm C. 2010. Intra-operative ultrasound facilitates the localization of the calcific deposit during arthroscopic treatment of calcifying tendinitis. Knee Surgery, Sports Traumatology, Arthroscopy. 18(12), 1792–1794.","apa":"Sabeti Aschraf, M., Gonano, C., Nemecek, E., Cichocki, L., &#38; Schueller Weidekamm, C. (2010). Intra-operative ultrasound facilitates the localization of the calcific deposit during arthroscopic treatment of calcifying tendinitis. <i>Knee Surgery, Sports Traumatology, Arthroscopy</i>. Springer. <a href=\"https://doi.org/10.1007/s00167-010-1227-9\">https://doi.org/10.1007/s00167-010-1227-9</a>","chicago":"Sabeti Aschraf, M., C. Gonano, E. Nemecek, Lisa Cichocki, and C. Schueller Weidekamm. “Intra-Operative Ultrasound Facilitates the Localization of the Calcific Deposit during Arthroscopic Treatment of Calcifying Tendinitis.” <i>Knee Surgery, Sports Traumatology, Arthroscopy</i>. Springer, 2010. <a href=\"https://doi.org/10.1007/s00167-010-1227-9\">https://doi.org/10.1007/s00167-010-1227-9</a>.","mla":"Sabeti Aschraf, M., et al. “Intra-Operative Ultrasound Facilitates the Localization of the Calcific Deposit during Arthroscopic Treatment of Calcifying Tendinitis.” <i>Knee Surgery, Sports Traumatology, Arthroscopy</i>, vol. 18, no. 12, Springer, 2010, pp. 1792–94, doi:<a href=\"https://doi.org/10.1007/s00167-010-1227-9\">10.1007/s00167-010-1227-9</a>."},"quality_controlled":"1","date_created":"2018-12-11T12:03:39Z","day":"20","intvolume":"        18","_id":"3498","doi":"10.1007/s00167-010-1227-9"},{"isi":1,"_id":"3604","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","date_updated":"2025-09-30T09:47:00Z","month":"03","publication_status":"published","publisher":"Wiley-Blackwell","type":"journal_article","oa_version":"None","scopus_import":"1","date_created":"2018-12-11T12:04:12Z","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>","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.","short":"H. Senn, S. Goodman, G. Swanson, N.H. Barton, J. Pemberton, Molecular Ecology 19 (2010) 910–924.","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.","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>","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>.","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>."},"quality_controlled":"1","day":"01","intvolume":"        19","doi":"10.1111/j.1365-294X.2009.04497.x","abstract":[{"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.","lang":"eng"}],"article_processing_charge":"No","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2010-03-01T00:00:00Z","external_id":{"isi":["000274550100008"]},"author":[{"last_name":"Senn","full_name":"Senn, Helen","first_name":"Helen"},{"first_name":"Simon","last_name":"Goodman","full_name":"Goodman, Simon"},{"last_name":"Swanson","full_name":"Swanson, Graeme","first_name":"Graeme"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"},{"first_name":"Josephine","full_name":"Pemberton, Josephine","last_name":"Pemberton"}],"publist_id":"2779","volume":19,"publication":"Molecular Ecology","language":[{"iso":"eng"}],"page":"910 - 924","issue":"5","year":"2010"},{"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."}],"article_processing_charge":"No","day":"01","corr_author":"1","scopus_import":"1","quality_controlled":"1","date_created":"2018-12-11T12:04:47Z","citation":{"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.","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>","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.","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>.","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>","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>."},"doi":"10.1016/j.neuropharm.2010.05.013","intvolume":"        59","issue":"6","publication":"Neuropharmacology","language":[{"iso":"eng"}],"page":"406 - 415","year":"2010","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","author":[{"first_name":"José","last_name":"Guzmán","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2209-5242","full_name":"Guzmán, José"},{"last_name":"Schmidt","full_name":"Schmidt, Hartmut","first_name":"Hartmut"},{"first_name":"Heike","full_name":"Franke, Heike","last_name":"Franke"},{"full_name":"Krügel, Ute","last_name":"Krügel","first_name":"Ute"},{"full_name":"Eilers, Jens","last_name":"Eilers","first_name":"Jens"},{"first_name":"Peter","last_name":"Illes","full_name":"Illes, Peter"},{"full_name":"Gerevich, Zoltan","last_name":"Gerevich","first_name":"Zoltan"}],"external_id":{"isi":["000283453300006"]},"publist_id":"2512","volume":59,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2010-11-01T00:00:00Z","department":[{"_id":"PeJo"}],"title":"P2Y1 receptors inhibit long-term depression in the prefrontal cortex.","date_updated":"2025-09-30T09:46:27Z","isi":1,"_id":"3718","oa_version":"None","publisher":"Elsevier","type":"journal_article","publication_status":"published","month":"11"},{"month":"06","publisher":"Public Library of Science","publication_status":"published","type":"journal_article","oa_version":"Published Version","isi":1,"_id":"3772","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Understanding adaptation in large populations","department":[{"_id":"NiBa"}],"date_updated":"2025-09-30T09:45:21Z","status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pubrep_id":"524","date_published":"2010-06-17T00:00:00Z","file":[{"date_updated":"2020-07-14T12:46:15Z","creator":"system","file_id":"5075","relation":"main_file","file_name":"IST-2016-524-v1+1_journal.pgen.1000987.PDF","file_size":349965,"checksum":"5c14de2680ab483cb835096c99ee734d","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:14:24Z"}],"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"}],"external_id":{"isi":["000279805200002"]},"volume":6,"publist_id":"2454","publication":"PLoS Genetics","language":[{"iso":"eng"}],"issue":"6","year":"2010","scopus_import":"1","quality_controlled":"1","citation":{"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>","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>.","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>","ieee":"N. H. Barton, “Understanding adaptation in large populations,” <i>PLoS Genetics</i>, vol. 6, no. 6. Public Library of Science, 2010.","short":"N.H. Barton, PLoS Genetics 6 (2010)."},"date_created":"2018-12-11T12:05:05Z","day":"17","corr_author":"1","intvolume":"         6","doi":"10.1371/journal.pgen.1000987","ddc":["570","576"],"file_date_updated":"2020-07-14T12:46:15Z","oa":1,"article_processing_charge":"No","article_number":"e1000987","has_accepted_license":"1"},{"oa_version":"Submitted Version","type":"journal_article","publication_status":"published","publisher":"Royal Society","month":"06","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pubmed/20439284","open_access":"1"}],"date_updated":"2025-09-30T09:45:54Z","title":"What role does natural selection play in speciation?","department":[{"_id":"NiBa"}],"pmid":1,"_id":"3773","isi":1,"year":"2010","issue":"1547","page":"1825 - 1840","publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","language":[{"iso":"eng"}],"publist_id":"2455","volume":365,"author":[{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["20439284"],"isi":["000277208600009"]},"date_published":"2010-06-12T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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","status":"public","article_processing_charge":"No","oa":1,"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"}],"doi":"10.1098/rstb.2010.0001","intvolume":"       365","corr_author":"1","day":"12","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>","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>.","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>.","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.","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>"},"date_created":"2018-12-11T12:05:05Z","quality_controlled":"1","scopus_import":"1"},{"year":"2010","page":"414 - 425","language":[{"iso":"eng"}],"publication":"Journal of Animal Ecology","issue":"2","date_published":"2010-03-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Senn, Helen","last_name":"Senn","first_name":"Helen"},{"full_name":"Swanson, Graeme","last_name":"Swanson","first_name":"Graeme"},{"full_name":"Goodman, Simon","last_name":"Goodman","first_name":"Simon"},{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"full_name":"Pemberton, Josephine","last_name":"Pemberton","first_name":"Josephine"}],"external_id":{"pmid":["20002231"],"isi":["000274321200014"]},"volume":79,"publist_id":"2453","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.","status":"public","article_processing_charge":"No","abstract":[{"lang":"eng","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."}],"intvolume":"        79","doi":"10.1111/j.1365-2656.2009.01633.x","scopus_import":"1","date_created":"2018-12-11T12:05:06Z","citation":{"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.","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>.","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>","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."},"quality_controlled":"1","day":"01","type":"journal_article","publication_status":"published","publisher":"Wiley-Blackwell","oa_version":"None","month":"03","date_updated":"2025-09-30T09:44:45Z","department":[{"_id":"NiBa"}],"title":"Phenotypic correlates of hybridisation between red and sika deer (genus Cervus)","_id":"3774","pmid":1,"isi":1},{"date_created":"2018-12-11T12:05:06Z","quality_controlled":"1","citation":{"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>","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>.","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>.","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.","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.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 2559–2569.","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>"},"scopus_import":"1","day":"27","corr_author":"1","intvolume":"       365","doi":"10.1098/rstb.2010.0106","abstract":[{"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.","lang":"eng"}],"ddc":["570"],"oa":1,"file_date_updated":"2020-07-14T12:46:15Z","article_processing_charge":"No","has_accepted_license":"1","acknowledgement":"Royal Society and Wolfson Foundation for their support\r\nWe would like to thank Brian Charlesworth and Sally Otto for their helpful comments.","status":"public","date_published":"2010-08-27T00:00:00Z","pubrep_id":"555","file":[{"file_name":"IST-2016-555-v1+1_RS2009_revised.pdf","file_size":250255,"checksum":"4d8aade10db030124ab158b622e337e0","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:14:40Z","date_updated":"2020-07-14T12:46:15Z","creator":"system","file_id":"5093","relation":"main_file"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":365,"publist_id":"2450","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"external_id":{"isi":["000280097000016"]},"language":[{"iso":"eng"}],"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","page":"2559 - 2569","issue":"1552","year":"2010","isi":1,"_id":"3776","title":"Genetic linkage and natural selection","department":[{"_id":"NiBa"}],"date_updated":"2025-09-30T09:43:27Z","month":"08","type":"journal_article","publisher":"Royal Society","publication_status":"published","oa_version":"Submitted Version"},{"publication":"Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences","language":[{"iso":"eng"}],"page":"1281 - 1294","issue":"1544","year":"2010","status":"public","acknowledgement":"I would like to thank W. G. Hill and L. Loewe for organizing this special issue, and the Royal Society and Wolfson Foundation for their support. Also, A. Kondrashov and L. Loewe gave very helpful comments that helped improve the manuscript.","date_published":"2010-04-27T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"2451","volume":365,"external_id":{"pmid":["20308104"],"isi":["000275811000015"]},"author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H"}],"abstract":[{"text":"Under the classical view, selection depends more or less directly on mutation: standing genetic variance is maintained by a balance between selection and mutation, and adaptation is fuelled by new favourable mutations. Recombination is favoured if it breaks negative associations among selected alleles, which interfere with adaptation. Such associations may be generated by negative epistasis, or by random drift (leading to the Hill-Robertson effect). Both deterministic and stochastic explanations depend primarily on the genomic mutation rate, U. This may be large enough to explain high recombination rates in some organisms, but seems unlikely to be so in general. Random drift is a more general source of negative linkage disequilibria, and can cause selection for recombination even in large populations, through the chance loss of new favourable mutations. The rate of species-wide substitutions is much too low to drive this mechanism, but local fluctuations in selection, combined with gene flow, may suffice. These arguments are illustrated by comparing the interaction between good and bad mutations at unlinked loci under the infinitesimal model.","lang":"eng"}],"oa":1,"article_processing_charge":"No","date_created":"2018-12-11T12:05:07Z","citation":{"ieee":"N. H. Barton, “Mutation and the evolution of recombination,” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1544. Royal Society, pp. 1281–1294, 2010.","short":"N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1281–1294.","ama":"Barton NH. Mutation and the evolution of recombination. <i>Philosophical Transactions of the Royal Society of London Series B, Biological Sciences</i>. 2010;365(1544):1281-1294. doi:<a href=\"https://doi.org/10.1098/rstb.2009.0320\">10.1098/rstb.2009.0320</a>","chicago":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” <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.2009.0320\">https://doi.org/10.1098/rstb.2009.0320</a>.","mla":"Barton, Nicholas H. “Mutation and the Evolution of Recombination.” <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>, vol. 365, no. 1544, Royal Society, 2010, pp. 1281–94, doi:<a href=\"https://doi.org/10.1098/rstb.2009.0320\">10.1098/rstb.2009.0320</a>.","apa":"Barton, N. H. (2010). Mutation and the evolution of recombination. <i>Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences</i>. Royal Society. <a href=\"https://doi.org/10.1098/rstb.2009.0320\">https://doi.org/10.1098/rstb.2009.0320</a>","ista":"Barton NH. 2010. Mutation and the evolution of recombination. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365(1544), 1281–1294."},"quality_controlled":"1","scopus_import":"1","day":"27","corr_author":"1","intvolume":"       365","doi":"10.1098/rstb.2009.0320","publication_status":"published","type":"journal_article","publisher":"Royal Society","oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pubmed/20308104"}],"month":"04","department":[{"_id":"NiBa"}],"title":"Mutation and the evolution of recombination","date_updated":"2025-09-30T09:44:03Z","isi":1,"_id":"3777","pmid":1},{"author":[{"first_name":"Ulises","last_name":"Rosas","full_name":"Rosas, Ulises"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H"},{"full_name":"Copsey, Lucy","last_name":"Copsey","first_name":"Lucy"},{"first_name":"Pierre","last_name":"Barbier De Reuille","full_name":"Barbier De Reuille, Pierre"},{"last_name":"Coen","full_name":"Coen, Enrico","first_name":"Enrico"}],"external_id":{"isi":["000280557100013"]},"volume":8,"publist_id":"2448","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pubrep_id":"366","file":[{"file_name":"IST-2015-366-v1+1_journal.pbio.1000429.pdf","file_size":1089530,"checksum":"ee1ce2fb283a6b4127544ae532d0b4a1","access_level":"open_access","content_type":"application/pdf","date_created":"2018-12-12T10:14:11Z","date_updated":"2020-07-14T12:46:15Z","creator":"system","file_id":"5060","relation":"main_file"}],"date_published":"2010-07-20T00:00:00Z","status":"public","acknowledgement":"This was supported by a Marie Curie grant for early stage training and the BBSRC-John Innes Centre PhD Rotation Program.\r\nWe would like to thank X. Feng and A. Hudson for assistance with introgressions and genotyping; A. Green, A. Bangham and J. Pateman for advice and assistance on shape model procedures; F. Alderson and S.Mitchell from JIC horticultural services; P.J. Wittkopp for protocols and advice on pyrosequencing; and R. Sablowski for discussions and comments.\r\n","year":"2010","issue":"7","language":[{"iso":"eng"}],"publication":"PLoS Biology","doi":"10.1371/journal.pbio.1000429","intvolume":"         8","related_material":{"record":[{"id":"9764","status":"public","relation":"research_data"}]},"day":"20","scopus_import":"1","quality_controlled":"1","citation":{"ama":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Cryptic variation between species and the basis of hybrid performance. <i>PLoS Biology</i>. 2010;8(7). doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429\">10.1371/journal.pbio.1000429</a>","ieee":"U. Rosas, N. H. Barton, L. Copsey, P. Barbier De Reuille, and E. Coen, “Cryptic variation between species and the basis of hybrid performance,” <i>PLoS Biology</i>, vol. 8, no. 7. Public Library of Science, 2010.","short":"U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, PLoS Biology 8 (2010).","apa":"Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., &#38; Coen, E. (2010). Cryptic variation between species and the basis of hybrid performance. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.1000429\">https://doi.org/10.1371/journal.pbio.1000429</a>","chicago":"Rosas, Ulises, Nicholas H Barton, Lucy Copsey, Pierre Barbier De Reuille, and Enrico Coen. “Cryptic Variation between Species and the Basis of Hybrid Performance.” <i>PLoS Biology</i>. Public Library of Science, 2010. <a href=\"https://doi.org/10.1371/journal.pbio.1000429\">https://doi.org/10.1371/journal.pbio.1000429</a>.","mla":"Rosas, Ulises, et al. “Cryptic Variation between Species and the Basis of Hybrid Performance.” <i>PLoS Biology</i>, vol. 8, no. 7, e1000429, Public Library of Science, 2010, doi:<a href=\"https://doi.org/10.1371/journal.pbio.1000429\">10.1371/journal.pbio.1000429</a>.","ista":"Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Cryptic variation between species and the basis of hybrid performance. PLoS Biology. 8(7), e1000429."},"date_created":"2018-12-11T12:05:07Z","has_accepted_license":"1","article_processing_charge":"No","article_number":"e1000429","file_date_updated":"2020-07-14T12:46:15Z","oa":1,"ddc":["576"],"abstract":[{"lang":"eng","text":"Crosses between closely related species give two contrasting results. One result is that species hybrids may be inferior to their parents, for example, being less fertile [1]. The other is that F1 hybrids may display superior performance (heterosis), for example with increased vigour [2]. Although various hypotheses have been proposed to account for these two aspects of hybridisation, their biological basis is still poorly understood [3]. To gain further insights into this issue, we analysed the role that variation in gene expression may play. We took a conserved trait, flower asymmetry in Antirrhinum, and determined the extent to which the underlying regulatory genes varied in expression among closely related species. We show that expression of both genes analysed, CYC and RAD, varies significantly between species because of cis-acting differences. By making a quantitative genotype-phenotype map, using a range of mutant alleles, we demonstrate that the species lie on a plateau in gene expression-morphology space, so that the variation has no detectable phenotypic effect. However, phenotypic differences can be revealed by shifting genotypes off the plateau through genetic crosses. Our results can be readily explained if genomes are free to evolve within an effectively neutral zone in gene expression space. The consequences of this drift will be negligible for individual loci, but when multiple loci across the genome are considered, we show that the variation may have significant effects on phenotype and fitness, causing a significant drift load. By considering these consequences for various gene-expression-fitness landscapes, we conclude that F1 hybrids might be expected to show increased performance with regard to conserved traits, such as basic physiology, but reduced performance with regard to others. Thus, our study provides a new way of explaining how various aspects of hybrid performance may arise through natural variation in gene activity."}],"month":"07","oa_version":"Published Version","type":"journal_article","publisher":"Public Library of Science","publication_status":"published","_id":"3779","isi":1,"date_updated":"2025-09-30T09:42:52Z","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Cryptic variation between species and the basis of hybrid performance","department":[{"_id":"NiBa"}]},{"volume":6533,"publist_id":"2445","author":[{"full_name":"Chen, Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao"},{"first_name":"Daniel","full_name":"Freedman, Daniel","last_name":"Freedman"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2010-12-31T00:00:00Z","month":"12","acknowledgement":"Partially supported by the Austri an Science Fund unde r grant P20134-N13.\r\nWe thank Helena Molina-Abril for very helpful discussion. We thank anonymous reviewers for helpful comments.","status":"public","year":"2010","oa_version":"None","type":"conference","publisher":"Springer","publication_status":"published","page":"31 - 42","publication":" Conference proceedings MCV 2010","language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-18421-5_4","_id":"3782","intvolume":"      6533","day":"31","alternative_title":["LNCS"],"citation":{"ama":"Chen C, Freedman D. Topology noise removal for curve  and surface evolution. In: <i> Conference Proceedings MCV 2010</i>. Vol 6533. Springer; 2010:31-42. doi:<a href=\"https://doi.org/10.1007/978-3-642-18421-5_4\">10.1007/978-3-642-18421-5_4</a>","short":"C. Chen, D. Freedman, in:,  Conference Proceedings MCV 2010, Springer, 2010, pp. 31–42.","ieee":"C. Chen and D. Freedman, “Topology noise removal for curve  and surface evolution,” in <i> Conference proceedings MCV 2010</i>, Beijing, China, 2010, vol. 6533, pp. 31–42.","apa":"Chen, C., &#38; Freedman, D. (2010). Topology noise removal for curve  and surface evolution. In <i> Conference proceedings MCV 2010</i> (Vol. 6533, pp. 31–42). Beijing, China: Springer. <a href=\"https://doi.org/10.1007/978-3-642-18421-5_4\">https://doi.org/10.1007/978-3-642-18421-5_4</a>","mla":"Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve  and Surface Evolution.” <i> Conference Proceedings MCV 2010</i>, vol. 6533, Springer, 2010, pp. 31–42, doi:<a href=\"https://doi.org/10.1007/978-3-642-18421-5_4\">10.1007/978-3-642-18421-5_4</a>.","chicago":"Chen, Chao, and Daniel Freedman. “Topology Noise Removal for Curve  and Surface Evolution.” In <i> Conference Proceedings MCV 2010</i>, 6533:31–42. Springer, 2010. <a href=\"https://doi.org/10.1007/978-3-642-18421-5_4\">https://doi.org/10.1007/978-3-642-18421-5_4</a>.","ista":"Chen C, Freedman D. 2010. Topology noise removal for curve  and surface evolution.  Conference proceedings MCV 2010. MCV: Medical Computer Vision, LNCS, vol. 6533, 31–42."},"quality_controlled":"1","date_created":"2018-12-11T12:05:08Z","scopus_import":1,"conference":{"end_date":"2010-09-20","name":"MCV: Medical Computer Vision","location":"Beijing, China","start_date":"2010-09-20"},"date_updated":"2021-01-12T07:52:10Z","abstract":[{"lang":"eng","text":"In cortex surface segmentation, the extracted surface is required to have a particular topology, namely, a two-sphere. We present a new method for removing topology noise of a curve or surface within the level set framework, and thus produce a cortical surface with correct topology. We define a new energy term which quantifies topology noise. We then show how to minimize this term by computing its functional derivative with respect to the level set function. This method differs from existing methods in that it is inherently continuous and not digital; and in the way that our energy directly relates to the topology of the underlying curve or surface, versus existing knot-based measures which are related in a more indirect fashion. The proposed flow is validated empirically."}],"title":"Topology noise removal for curve  and surface evolution","department":[{"_id":"HeEd"}]}]