--- _id: '4393' abstract: - lang: eng 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 implementation 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. acknowledgement: This work was partially supported by the European Union project COMBEST and the European Network of Excellence ArtistDesign. alternative_title: - LNCS author: - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna citation: ama: 'Cerny P, Henzinger TA, Radhakrishna A. Simulation distances. In: Vol 6269. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:235-268. doi:10.1007/978-3-642-15375-4_18' apa: 'Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2010). Simulation distances (Vol. 6269, pp. 235–268). Presented at the CONCUR: Concurrency Theory, Paris, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-642-15375-4_18' chicago: Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. “Simulation Distances,” 6269:235–68. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. https://doi.org/10.1007/978-3-642-15375-4_18. ieee: 'P. Cerny, T. A. Henzinger, and A. Radhakrishna, “Simulation distances,” presented at the CONCUR: Concurrency Theory, Paris, France, 2010, vol. 6269, pp. 235–268.' ista: 'Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances. CONCUR: Concurrency Theory, LNCS, vol. 6269, 235–268.' mla: Cerny, Pavol, et al. Simulation Distances. Vol. 6269, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 235–68, doi:10.1007/978-3-642-15375-4_18. short: P. Cerny, T.A. Henzinger, A. Radhakrishna, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 235–268. conference: end_date: 2010-09-03 location: Paris, France name: 'CONCUR: Concurrency Theory' start_date: 2010-08-31 corr_author: '1' date_created: 2018-12-11T12:08:37Z date_published: 2010-11-01T00:00:00Z date_updated: 2026-06-18T18:41:23Z day: '01' ddc: - '005' department: - _id: ToHe doi: 10.1007/978-3-642-15375-4_18 ec_funded: 1 file: - access_level: open_access checksum: ea567903676ba8afe0507ee11313dce5 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:12Z date_updated: 2020-07-14T12:46:28Z file_id: '5130' file_name: IST-2012-42-v1+1_Simulation_distances.pdf file_size: 198913 relation: main_file file_date_updated: 2020-07-14T12:46:28Z has_accepted_license: '1' intvolume: ' 6269' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 235 - 268 project: - _id: 25EFB36C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '215543' name: COMponent-Based Embedded Systems design Techniques - _id: 25F1337C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '214373' name: Design for Embedded Systems publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '1065' pubrep_id: '42' quality_controlled: '1' related_material: record: - id: '5389' relation: earlier_version status: public - id: '3249' relation: later_version status: public scopus_import: 1 status: public title: Simulation distances type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 6269 year: '2010' ... --- _id: '4396' abstract: - lang: eng text: 'Shape analysis is a promising technique to prove program properties about recursive data structures. The challenge is to automatically determine the data-structure type, and to supply the shape analysis with the necessary information about the data structure. We present a stepwise approach to the selection of instrumentation predicates for a TVLA-based shape analysis, which takes us a step closer towards the fully automatic verification of data structures. The approach uses two techniques to guide the refinement of shape abstractions: (1) during program exploration, an explicit heap analysis collects sample instances of the heap structures, which are used to identify the data structures that are manipulated by the program; and (2) during abstraction refinement along an infeasible error path, we consider different possible heap abstractions and choose the coarsest one that eliminates the infeasible path. We have implemented this combined approach for automatic shape refinement as an extension of the software model checker BLAST. Example programs from a data-structure library that manipulate doubly-linked lists and trees were successfully verified by our tool.' alternative_title: - LNCS author: - first_name: Dirk full_name: Beyer, Dirk last_name: Beyer - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Grégory full_name: Théoduloz, Grégory last_name: Théoduloz - first_name: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 citation: ama: 'Beyer D, Henzinger TA, Théoduloz G, Zufferey D. Shape refinement through explicit heap analysis. In: Rosenblum D, Taenzer G, eds. Vol 6013. Springer; 2010:263-277. doi:10.1007/978-3-642-12029-9_19' apa: 'Beyer, D., Henzinger, T. A., Théoduloz, G., & Zufferey, D. (2010). Shape refinement through explicit heap analysis. In D. Rosenblum & G. Taenzer (Eds.) (Vol. 6013, pp. 263–277). Presented at the FASE: Fundamental Approaches To Software Engineering, Paphos, Cyprus: Springer. https://doi.org/10.1007/978-3-642-12029-9_19' chicago: Beyer, Dirk, Thomas A Henzinger, Grégory Théoduloz, and Damien Zufferey. “Shape Refinement through Explicit Heap Analysis.” edited by David Rosenblum and Gabriele Taenzer, 6013:263–77. Springer, 2010. https://doi.org/10.1007/978-3-642-12029-9_19. ieee: 'D. Beyer, T. A. Henzinger, G. Théoduloz, and D. Zufferey, “Shape refinement through explicit heap analysis,” presented at the FASE: Fundamental Approaches To Software Engineering, Paphos, Cyprus, 2010, vol. 6013, pp. 263–277.' ista: 'Beyer D, Henzinger TA, Théoduloz G, Zufferey D. 2010. Shape refinement through explicit heap analysis. FASE: Fundamental Approaches To Software Engineering, LNCS, vol. 6013, 263–277.' mla: Beyer, Dirk, et al. Shape Refinement through Explicit Heap Analysis. Edited by David Rosenblum and Gabriele Taenzer, vol. 6013, Springer, 2010, pp. 263–77, doi:10.1007/978-3-642-12029-9_19. short: D. Beyer, T.A. Henzinger, G. Théoduloz, D. Zufferey, in:, D. Rosenblum, G. Taenzer (Eds.), Springer, 2010, pp. 263–277. conference: end_date: 2010-03-28 location: Paphos, Cyprus name: 'FASE: Fundamental Approaches To Software Engineering' start_date: 2010-03-20 date_created: 2018-12-11T12:08:38Z date_published: 2010-04-21T00:00:00Z date_updated: 2021-01-12T07:56:40Z day: '21' ddc: - '004' department: - _id: ToHe doi: 10.1007/978-3-642-12029-9_19 editor: - first_name: David full_name: Rosenblum, David last_name: Rosenblum - first_name: Gabriele full_name: Taenzer, Gabriele last_name: Taenzer file: - access_level: open_access checksum: 7d26e59a9681487d7283eba337292b2c content_type: application/pdf creator: system date_created: 2018-12-12T10:18:13Z date_updated: 2020-07-14T12:46:29Z file_id: '5332' file_name: IST-2012-41-v1+1_Shape_refinement_through_explicit_heap_analysis.pdf file_size: 312147 relation: main_file file_date_updated: 2020-07-14T12:46:29Z has_accepted_license: '1' intvolume: ' 6013' language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 263 - 277 project: - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: Springer publist_id: '1061' pubrep_id: '41' quality_controlled: '1' scopus_import: 1 status: public title: Shape refinement through explicit heap analysis type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 6013 year: '2010' ... --- _id: '474' 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.' 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. article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Jerome full_name: Kelleher, Jerome last_name: Kelleher - first_name: Alison full_name: Etheridge, Alison last_name: Etheridge citation: ama: 'Barton NH, Kelleher J, Etheridge A. A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. 2010;64(9):2701-2715. doi:10.1111/j.1558-5646.2010.01019.x' apa: 'Barton, N. H., Kelleher, J., & Etheridge, A. (2010). A new model for extinction and recolonization in two dimensions: Quantifying phylogeography. Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.2010.01019.x' chicago: 'Barton, Nicholas H, Jerome Kelleher, and Alison Etheridge. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” Evolution. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1558-5646.2010.01019.x.' ieee: 'N. H. Barton, J. Kelleher, and A. Etheridge, “A new model for extinction and recolonization in two dimensions: Quantifying phylogeography,” Evolution, vol. 64, no. 9. Wiley-Blackwell, pp. 2701–2715, 2010.' 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.' mla: 'Barton, Nicholas H., et al. “A New Model for Extinction and Recolonization in Two Dimensions: Quantifying Phylogeography.” Evolution, vol. 64, no. 9, Wiley-Blackwell, 2010, pp. 2701–15, doi:10.1111/j.1558-5646.2010.01019.x.' short: N.H. Barton, J. Kelleher, A. Etheridge, Evolution 64 (2010) 2701–2715. corr_author: '1' date_created: 2018-12-11T11:46:40Z date_published: 2010-09-01T00:00:00Z date_updated: 2025-09-30T09:50:22Z day: '01' department: - _id: NiBa doi: 10.1111/j.1558-5646.2010.01019.x external_id: isi: - '000281636400017' intvolume: ' 64' isi: 1 issue: '9' language: - iso: eng month: '09' oa_version: None page: 2701 - 2715 publication: Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '2780' quality_controlled: '1' scopus_import: '1' status: public title: 'A new model for extinction and recolonization in two dimensions: Quantifying phylogeography' type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 64 year: '2010' ... --- _id: '488' 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 "regular" 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. ' alternative_title: - LIPIcs article_processing_charge: No author: - first_name: Rajeev full_name: Alur, Rajeev last_name: Alur - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny citation: ama: 'Alur R, Cerny P. Expressiveness of streaming string transducers. In: Vol 8. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2010:1-12. doi:10.4230/LIPIcs.FSTTCS.2010.1' apa: 'Alur, R., & 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. https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1' chicago: Alur, Rajeev, and Pavol Cerny. “Expressiveness of Streaming String Transducers,” 8:1–12. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010. https://doi.org/10.4230/LIPIcs.FSTTCS.2010.1. 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.' 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.' mla: Alur, Rajeev, and Pavol Cerny. Expressiveness of Streaming String Transducers. Vol. 8, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12, doi:10.4230/LIPIcs.FSTTCS.2010.1. short: R. Alur, P. Cerny, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2010, pp. 1–12. conference: end_date: 2010-12-18 location: Chennai, India name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science' start_date: 2010-12-15 corr_author: '1' date_created: 2018-12-11T11:46:45Z date_published: 2010-01-01T00:00:00Z date_updated: 2025-09-30T09:49:32Z day: '01' ddc: - '005' department: - _id: ToHe doi: 10.4230/LIPIcs.FSTTCS.2010.1 external_id: isi: - '000310361000001' file: - access_level: open_access checksum: 5845be5aa19791830f7407d8853f2df0 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:29Z date_updated: 2020-07-14T12:46:35Z file_id: '4690' file_name: IST-2018-948-v1+1_2011_Cerny_Expressiveness_of.pdf file_size: 492344 relation: main_file file_date_updated: 2020-07-14T12:46:35Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 1 - 12 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '7331' pubrep_id: '948' quality_controlled: '1' scopus_import: '1' status: public title: Expressiveness of streaming string transducers tmp: 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) short: CC BY-NC-ND (4.0) type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 8 year: '2010' ... --- _id: '489' abstract: - lang: eng 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.' alternative_title: - EPTCS article_processing_charge: No arxiv: 1 author: - first_name: Julien full_name: Cristau, Julien last_name: Cristau - first_name: Claire full_name: David, Claire last_name: David - first_name: Florian full_name: Horn, Florian id: 37327ACE-F248-11E8-B48F-1D18A9856A87 last_name: Horn citation: ama: 'Cristau J, David C, Horn F. How do we remember the past in randomised strategies? In: Proceedings of GandALF 2010. Vol 25. Open Publishing Association; 2010:30-39. doi:10.4204/EPTCS.25.7' apa: 'Cristau, J., David, C., & Horn, F. (2010). How do we remember the past in randomised strategies? In Proceedings of GandALF 2010 (Vol. 25, pp. 30–39). Minori, Amalfi Coast, Italy: Open Publishing Association. https://doi.org/10.4204/EPTCS.25.7' chicago: Cristau, Julien, Claire David, and Florian Horn. “How Do We Remember the Past in Randomised Strategies?” In Proceedings of GandALF 2010, 25:30–39. Open Publishing Association, 2010. https://doi.org/10.4204/EPTCS.25.7. ieee: J. Cristau, C. David, and F. Horn, “How do we remember the past in randomised strategies?,” in Proceedings of GandALF 2010, Minori, Amalfi Coast, Italy, 2010, vol. 25, pp. 30–39. 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.' mla: Cristau, Julien, et al. “How Do We Remember the Past in Randomised Strategies?” Proceedings of GandALF 2010, vol. 25, Open Publishing Association, 2010, pp. 30–39, doi:10.4204/EPTCS.25.7. short: J. Cristau, C. David, F. Horn, in:, Proceedings of GandALF 2010, Open Publishing Association, 2010, pp. 30–39. conference: end_date: 2010-06-18 location: Minori, Amalfi Coast, Italy name: 'GandALF: Games, Automata, Logic, and Formal Verification' start_date: 2010-06-17 corr_author: '1' date_created: 2018-12-11T11:46:45Z date_published: 2010-06-09T00:00:00Z date_updated: 2026-06-18T18:51:53Z day: '09' ddc: - '000' department: - _id: KrCh doi: 10.4204/EPTCS.25.7 external_id: arxiv: - '1006.1404' intvolume: ' 25' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1006.1404 month: '06' oa: 1 oa_version: Published Version page: 30 - 39 publication: Proceedings of GandALF 2010 publication_status: published publisher: Open Publishing Association publist_id: '7332' quality_controlled: '1' scopus_import: '1' status: public title: How do we remember the past in randomised strategies? type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2010' ... --- _id: '533' 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 ("noise") 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. article_processing_charge: No author: - first_name: Jochen full_name: Hoenicke, Jochen last_name: Hoenicke - first_name: Kari full_name: Leino, Kari last_name: Leino - first_name: Andreas full_name: Podelski, Andreas last_name: Podelski - first_name: Martin full_name: Schäf, Martin last_name: Schäf - first_name: Thomas full_name: Wies, Thomas id: 447BFB88-F248-11E8-B48F-1D18A9856A87 last_name: Wies citation: ama: Hoenicke J, Leino K, Podelski A, Schäf M, Wies T. Doomed program points. Formal Methods in System Design. 2010;37(2-3):171-199. doi:10.1007/s10703-010-0102-0 apa: Hoenicke, J., Leino, K., Podelski, A., Schäf, M., & Wies, T. (2010). Doomed program points. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-010-0102-0 chicago: Hoenicke, Jochen, Kari Leino, Andreas Podelski, Martin Schäf, and Thomas Wies. “Doomed Program Points.” Formal Methods in System Design. Springer, 2010. https://doi.org/10.1007/s10703-010-0102-0. ieee: J. Hoenicke, K. Leino, A. Podelski, M. Schäf, and T. Wies, “Doomed program points,” Formal Methods in System Design, vol. 37, no. 2–3. Springer, pp. 171–199, 2010. 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. mla: Hoenicke, Jochen, et al. “Doomed Program Points.” Formal Methods in System Design, vol. 37, no. 2–3, Springer, 2010, pp. 171–99, doi:10.1007/s10703-010-0102-0. short: J. Hoenicke, K. Leino, A. Podelski, M. Schäf, T. Wies, Formal Methods in System Design 37 (2010) 171–199. corr_author: '1' date_created: 2018-12-11T11:47:01Z date_published: 2010-12-01T00:00:00Z date_updated: 2025-09-30T09:48:58Z day: '01' department: - _id: ToHe doi: 10.1007/s10703-010-0102-0 external_id: isi: - '000286631700004' intvolume: ' 37' isi: 1 issue: 2-3 language: - iso: eng month: '12' oa_version: None page: 171 - 199 publication: Formal Methods in System Design publication_status: published publisher: Springer publist_id: '7284' quality_controlled: '1' scopus_import: '1' status: public title: Doomed program points type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 37 year: '2010' ... --- _id: '5388' 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." alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna - first_name: Rohit full_name: Singh, Rohit last_name: Singh citation: ama: Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. Quantitative Synthesis for Concurrent Programs. IST Austria; 2010. doi:10.15479/AT:IST-2010-0004 apa: Chatterjee, K., Cerny, P., Henzinger, T. A., Radhakrishna, A., & Singh, R. (2010). Quantitative synthesis for concurrent programs. IST Austria. https://doi.org/10.15479/AT:IST-2010-0004 chicago: Chatterjee, Krishnendu, Pavol Cerny, Thomas A Henzinger, Arjun Radhakrishna, and Rohit Singh. Quantitative Synthesis for Concurrent Programs. IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0004. ieee: K. Chatterjee, P. Cerny, T. A. Henzinger, A. Radhakrishna, and R. Singh, Quantitative synthesis for concurrent programs. IST Austria, 2010. ista: Chatterjee K, Cerny P, Henzinger TA, Radhakrishna A, Singh R. 2010. Quantitative synthesis for concurrent programs, IST Austria, 17p. mla: Chatterjee, Krishnendu, et al. Quantitative Synthesis for Concurrent Programs. IST Austria, 2010, doi:10.15479/AT:IST-2010-0004. short: K. Chatterjee, P. Cerny, T.A. Henzinger, A. Radhakrishna, R. Singh, Quantitative Synthesis for Concurrent Programs, IST Austria, 2010. date_created: 2018-12-12T11:39:03Z date_published: 2010-10-07T00:00:00Z date_updated: 2025-04-15T08:12:00Z day: '07' ddc: - '000' - '005' department: - _id: KrCh - _id: ToHe doi: 10.15479/AT:IST-2010-0004 file: - access_level: open_access checksum: da38782d2388a6fa32109d10bb9bad67 content_type: application/pdf creator: system date_created: 2018-12-12T11:53:53Z date_updated: 2020-07-14T12:46:42Z file_id: '5515' file_name: IST-2010-0004_IST-2010-0004.pdf file_size: 429101 relation: main_file file_date_updated: 2020-07-14T12:46:42Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '17' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '24' related_material: record: - id: '3366' relation: later_version status: public status: public title: Quantitative synthesis for concurrent programs type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2010' ... --- _id: '5389' abstract: - lang: eng 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. alternative_title: - IST Austria Technical Report author: - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Arjun full_name: Radhakrishna, Arjun id: 3B51CAC4-F248-11E8-B48F-1D18A9856A87 last_name: Radhakrishna citation: ama: Cerny P, Henzinger TA, Radhakrishna A. Simulation Distances. IST Austria; 2010. doi:10.15479/AT:IST-2010-0003 apa: Cerny, P., Henzinger, T. A., & Radhakrishna, A. (2010). Simulation distances. IST Austria. https://doi.org/10.15479/AT:IST-2010-0003 chicago: Cerny, Pavol, Thomas A Henzinger, and Arjun Radhakrishna. Simulation Distances. IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0003. ieee: P. Cerny, T. A. Henzinger, and A. Radhakrishna, Simulation distances. IST Austria, 2010. ista: Cerny P, Henzinger TA, Radhakrishna A. 2010. Simulation distances, IST Austria, 24p. mla: Cerny, Pavol, et al. Simulation Distances. IST Austria, 2010, doi:10.15479/AT:IST-2010-0003. short: P. Cerny, T.A. Henzinger, A. Radhakrishna, Simulation Distances, IST Austria, 2010. date_created: 2018-12-12T11:39:03Z date_published: 2010-06-04T00:00:00Z date_updated: 2026-06-18T18:41:23Z day: '04' ddc: - '005' department: - _id: ToHe doi: 10.15479/AT:IST-2010-0003 file: - access_level: open_access checksum: 284ded99764e32a583a8ea83fcea254b content_type: application/pdf creator: system date_created: 2018-12-12T11:54:25Z date_updated: 2020-07-14T12:46:42Z file_id: '5547' file_name: IST-2010-0003_IST-2010-0003.pdf file_size: 367246 relation: main_file file_date_updated: 2020-07-14T12:46:42Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '24' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '25' related_material: record: - id: '4393' relation: later_version status: public - id: '3249' relation: later_version status: public status: public title: Simulation distances type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2010' ... --- _id: '5390' 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. alternative_title: - IST Austria Technical Report author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Nathanaël full_name: Fijalkow, Nathanaël last_name: Fijalkow citation: ama: Chatterjee K, Fijalkow N. Topological, Automata-Theoretic and Logical Characterization of Finitary Languages. IST Austria; 2010. doi:10.15479/AT:IST-2010-0002 apa: Chatterjee, K., & Fijalkow, N. (2010). Topological, automata-theoretic and logical characterization of finitary languages. IST Austria. https://doi.org/10.15479/AT:IST-2010-0002 chicago: Chatterjee, Krishnendu, and Nathanaël Fijalkow. Topological, Automata-Theoretic and Logical Characterization of Finitary Languages. IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0002. ieee: K. Chatterjee and N. Fijalkow, Topological, automata-theoretic and logical characterization of finitary languages. IST Austria, 2010. ista: Chatterjee K, Fijalkow N. 2010. Topological, automata-theoretic and logical characterization of finitary languages, IST Austria, 21p. mla: Chatterjee, Krishnendu, and Nathanaël Fijalkow. Topological, Automata-Theoretic and Logical Characterization of Finitary Languages. IST Austria, 2010, doi:10.15479/AT:IST-2010-0002. short: K. Chatterjee, N. Fijalkow, Topological, Automata-Theoretic and Logical Characterization of Finitary Languages, IST Austria, 2010. date_created: 2018-12-12T11:39:03Z date_published: 2010-06-04T00:00:00Z date_updated: 2020-07-14T23:04:41Z day: '04' ddc: - '000' department: - _id: KrCh doi: 10.15479/AT:IST-2010-0002 file: - access_level: open_access checksum: 283d3604d76dd4d5161585d4c8625fbe content_type: application/pdf creator: system date_created: 2018-12-12T11:54:10Z date_updated: 2020-07-14T12:46:43Z file_id: '5532' file_name: IST-2010-0002_IST-2010-0002.pdf file_size: 395662 relation: main_file file_date_updated: 2020-07-14T12:46:43Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '21' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '26' status: public title: Topological, automata-theoretic and logical characterization of finitary languages type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2010' ... --- _id: '5391' abstract: - lang: eng text: Concurrent data structures with fine-grained synchronization are notoriously difficult to implement correctly. The difficulty of reasoning about these implementations does not stem from the number of variables or the program size, but rather from the large number of possible interleavings. These implementations are therefore prime candidates for model checking. We introduce an algorithm for verifying linearizability of singly-linked heap-based concurrent data structures. We consider a model consisting of an unbounded heap where each node consists an element from an unbounded data domain, with a restricted set of operations for testing and updating pointers and data elements. Our main result is that linearizability is decidable for programs that invoke a fixed number of methods, possibly in parallel. This decidable fragment covers many of the common implementation techniques — fine-grained locking, lazy synchronization, and lock-free synchronization. We also show how the technique can be used to verify optimistic implementations with the help of programmer annotations. We developed a verification tool CoLT and evaluated it on a representative sample of Java implementations of the concurrent set data structure. The tool verified linearizability of a number of implementations, found a known error in a lock-free imple- mentation and proved that the corrected version is linearizable. alternative_title: - IST Austria Technical Report 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 - first_name: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 - first_name: Swarat full_name: Chaudhuri, Swarat last_name: Chaudhuri - first_name: Rajeev full_name: Alur, Rajeev last_name: Alur citation: ama: Cerny P, Radhakrishna A, Zufferey D, Chaudhuri S, Alur R. Model Checking of Linearizability of Concurrent List Implementations. IST Austria; 2010. doi:10.15479/AT:IST-2010-0001 apa: Cerny, P., Radhakrishna, A., Zufferey, D., Chaudhuri, S., & Alur, R. (2010). Model checking of linearizability of concurrent list implementations. IST Austria. https://doi.org/10.15479/AT:IST-2010-0001 chicago: Cerny, Pavol, Arjun Radhakrishna, Damien Zufferey, Swarat Chaudhuri, and Rajeev Alur. Model Checking of Linearizability of Concurrent List Implementations. IST Austria, 2010. https://doi.org/10.15479/AT:IST-2010-0001. ieee: P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, and R. Alur, Model checking of linearizability of concurrent list implementations. IST Austria, 2010. 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. Model Checking of Linearizability of Concurrent List Implementations. IST Austria, 2010, doi:10.15479/AT:IST-2010-0001. short: P. Cerny, A. Radhakrishna, D. Zufferey, S. Chaudhuri, R. Alur, Model Checking of Linearizability of Concurrent List Implementations, IST Austria, 2010. date_created: 2018-12-12T11:39:04Z date_published: 2010-04-19T00:00:00Z date_updated: 2024-10-21T06:03:05Z day: '19' ddc: - '004' department: - _id: ToHe doi: 10.15479/AT:IST-2010-0001 file: - access_level: open_access checksum: 986645caad7dd85a6a091488f6c646dc content_type: application/pdf creator: system date_created: 2018-12-12T11:53:44Z date_updated: 2020-07-14T12:46:43Z file_id: '5505' file_name: IST-2010-0001_IST-2010-0001.pdf file_size: 372286 relation: main_file file_date_updated: 2020-07-14T12:46:43Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: '27' publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria pubrep_id: '27' related_material: record: - id: '4390' relation: later_version status: public status: public title: Model checking of linearizability of concurrent list implementations type: technical_report user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2010' ... --- _id: '9452' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: 'Assaf ' full_name: 'Zemach, Assaf ' last_name: Zemach - first_name: Ivy E. full_name: McDaniel, Ivy E. last_name: McDaniel - first_name: Pedro full_name: Silva, Pedro last_name: Silva - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Zemach A, McDaniel IE, Silva P, Zilberman D. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 2010;328(5980):916-919. doi:10.1126/science.1186366 apa: Zemach, A., McDaniel, I. E., Silva, P., & Zilberman, D. (2010). Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1186366 chicago: Zemach, Assaf , Ivy E. McDaniel, Pedro Silva, and Daniel Zilberman. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” Science. American Association for the Advancement of Science, 2010. https://doi.org/10.1126/science.1186366. ieee: A. Zemach, I. E. McDaniel, P. Silva, and D. Zilberman, “Genome-wide evolutionary analysis of eukaryotic DNA methylation,” Science, vol. 328, no. 5980. American Association for the Advancement of Science, pp. 916–919, 2010. ista: Zemach A, McDaniel IE, Silva P, Zilberman D. 2010. Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science. 328(5980), 916–919. mla: Zemach, Assaf, et al. “Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation.” Science, vol. 328, no. 5980, American Association for the Advancement of Science, 2010, pp. 916–19, doi:10.1126/science.1186366. short: A. Zemach, I.E. McDaniel, P. Silva, D. Zilberman, Science 328 (2010) 916–919. date_created: 2021-06-04T08:26:08Z date_published: 2010-05-14T00:00:00Z date_updated: 2021-12-14T08:35:37Z day: '14' department: - _id: DaZi doi: 10.1126/science.1186366 extern: '1' external_id: pmid: - '20395474 ' intvolume: ' 328' issue: '5980' keyword: - Multidisciplinary language: - iso: eng month: '05' oa_version: None page: 916-919 pmid: 1 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Genome-wide evolutionary analysis of eukaryotic DNA methylation type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 328 year: '2010' ... --- _id: '9485' 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.' article_processing_charge: No article_type: original author: - first_name: Assaf full_name: Zemach, Assaf last_name: Zemach - first_name: M. Yvonne full_name: Kim, M. Yvonne last_name: Kim - first_name: Pedro full_name: Silva, Pedro last_name: Silva - first_name: Jessica A. full_name: Rodrigues, Jessica A. last_name: Rodrigues - first_name: Bradley full_name: Dotson, Bradley last_name: Dotson - first_name: Matthew D. full_name: Brooks, Matthew D. last_name: Brooks - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Zemach A, Kim MY, Silva P, et al. Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. 2010;107(43):18729-18734. doi:10.1073/pnas.1009695107 apa: Zemach, A., Kim, M. Y., Silva, P., Rodrigues, J. A., Dotson, B., Brooks, M. D., & Zilberman, D. (2010). Local DNA hypomethylation activates genes in rice endosperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1009695107 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.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2010. https://doi.org/10.1073/pnas.1009695107. ieee: A. Zemach et al., “Local DNA hypomethylation activates genes in rice endosperm,” Proceedings of the National Academy of Sciences, vol. 107, no. 43. National Academy of Sciences, pp. 18729–18734, 2010. 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.” Proceedings of the National Academy of Sciences, vol. 107, no. 43, National Academy of Sciences, 2010, pp. 18729–34, doi:10.1073/pnas.1009695107. 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. date_created: 2021-06-07T09:31:01Z date_published: 2010-10-26T00:00:00Z date_updated: 2021-12-14T08:40:02Z day: '26' department: - _id: DaZi doi: 10.1073/pnas.1009695107 extern: '1' external_id: pmid: - '20937895' intvolume: ' 107' issue: '43' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1009695107 month: '10' oa: 1 oa_version: Published Version page: 18729-18734 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Local DNA hypomethylation activates genes in rice endosperm type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 107 year: '2010' ... --- _id: '9489' 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. article_processing_charge: No article_type: review author: - first_name: Assaf full_name: Zemach, Assaf last_name: Zemach - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Zemach A, Zilberman D. Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. 2010;20(17):R780-R785. doi:10.1016/j.cub.2010.07.007 apa: Zemach, A., & Zilberman, D. (2010). Evolution of eukaryotic DNA methylation and the pursuit of safer sex. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2010.07.007 chicago: Zemach, Assaf, and Daniel Zilberman. “Evolution of Eukaryotic DNA Methylation and the Pursuit of Safer Sex.” Current Biology. Elsevier, 2010. https://doi.org/10.1016/j.cub.2010.07.007. ieee: A. Zemach and D. Zilberman, “Evolution of eukaryotic DNA methylation and the pursuit of safer sex,” Current Biology, vol. 20, no. 17. Elsevier, pp. R780–R785, 2010. 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.” Current Biology, vol. 20, no. 17, Elsevier, 2010, pp. R780–85, doi:10.1016/j.cub.2010.07.007. short: A. Zemach, D. Zilberman, Current Biology 20 (2010) R780–R785. date_created: 2021-06-07T09:45:27Z date_published: 2010-09-14T00:00:00Z date_updated: 2021-12-14T08:52:34Z day: '14' department: - _id: DaZi doi: 10.1016/j.cub.2010.07.007 extern: '1' external_id: pmid: - '20833323' intvolume: ' 20' issue: '17' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cub.2010.07.007 month: '09' oa: 1 oa_version: Published Version page: R780-R785 pmid: 1 publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Evolution of eukaryotic DNA methylation and the pursuit of safer sex type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 20 year: '2010' ... --- _id: '9764' article_processing_charge: No author: - first_name: Ulises full_name: Rosas, Ulises last_name: Rosas - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Lucy full_name: Copsey, Lucy last_name: Copsey - first_name: Pierre full_name: Barbier De Reuille, Pierre last_name: Barbier De Reuille - first_name: Enrico full_name: Coen, Enrico last_name: Coen citation: ama: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. Heterosis and the drift load. 2010. doi:10.1371/journal.pbio.1000429.s003 apa: Rosas, U., Barton, N. H., Copsey, L., Barbier De Reuille, P., & Coen, E. (2010). Heterosis and the drift load. Public Library of Science. https://doi.org/10.1371/journal.pbio.1000429.s003 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. https://doi.org/10.1371/journal.pbio.1000429.s003. 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. ista: Rosas U, Barton NH, Copsey L, Barbier De Reuille P, Coen E. 2010. Heterosis and the drift load, Public Library of Science, 10.1371/journal.pbio.1000429.s003. mla: Rosas, Ulises, et al. Heterosis and the Drift Load. Public Library of Science, 2010, doi:10.1371/journal.pbio.1000429.s003. short: U. Rosas, N.H. Barton, L. Copsey, P. Barbier De Reuille, E. Coen, (2010). date_created: 2021-08-02T09:45:39Z date_published: 2010-07-20T00:00:00Z date_updated: 2025-09-30T09:42:52Z day: '20' department: - _id: NiBa doi: 10.1371/journal.pbio.1000429.s003 month: '07' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '3779' relation: used_in_publication status: public status: public title: Heterosis and the drift load type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2010' ... --- _id: '3303' abstract: - lang: eng text: 'Biological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population. ' acknowledgement: "This work was supported in part by a Robert N. Noyce Stanford Graduate Fellowship and European Research Council grant 250152 (to D.B.W.) and by National Institutes of Health grant GM 28016 (to M.W.F.).\r\nWe thank Michael Desai for many ideas and discussions and are grateful to Joanna Masel and an anonymous reviewer for their helpful suggestions. " article_processing_charge: No author: - first_name: Daniel full_name: Weissman, Daniel id: 2D0CE020-F248-11E8-B48F-1D18A9856A87 last_name: Weissman - first_name: Marcus full_name: Feldman, Marcus last_name: Feldman - first_name: Daniel full_name: Fisher, Daniel last_name: Fisher citation: ama: Weissman D, Feldman M, Fisher D. The rate of fitness-valley crossing in sexual populations. Genetics. 2010;186(4):1389-1410. doi:10.1534/genetics.110.123240 apa: Weissman, D., Feldman, M., & Fisher, D. (2010). The rate of fitness-valley crossing in sexual populations. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.110.123240 chicago: Weissman, Daniel, Marcus Feldman, and Daniel Fisher. “The Rate of Fitness-Valley Crossing in Sexual Populations.” Genetics. Genetics Society of America, 2010. https://doi.org/10.1534/genetics.110.123240. ieee: D. Weissman, M. Feldman, and D. Fisher, “The rate of fitness-valley crossing in sexual populations,” Genetics, vol. 186, no. 4. Genetics Society of America, pp. 1389–1410, 2010. ista: Weissman D, Feldman M, Fisher D. 2010. The rate of fitness-valley crossing in sexual populations. Genetics. 186(4), 1389–1410. mla: Weissman, Daniel, et al. “The Rate of Fitness-Valley Crossing in Sexual Populations.” Genetics, vol. 186, no. 4, Genetics Society of America, 2010, pp. 1389–410, doi:10.1534/genetics.110.123240. short: D. Weissman, M. Feldman, D. Fisher, Genetics 186 (2010) 1389–1410. corr_author: '1' date_created: 2018-12-11T12:02:33Z date_published: 2010-12-01T00:00:00Z date_updated: 2025-09-30T09:47:59Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.110.123240 ec_funded: 1 external_id: isi: - '000285297000025' intvolume: ' 186' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998319/ month: '12' oa: 1 oa_version: Submitted Version page: 1389 - 1410 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '3337' quality_controlled: '1' scopus_import: '1' status: public title: The rate of fitness-valley crossing in sexual populations type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 186 year: '2010' ... --- _id: '3604' 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. article_processing_charge: No author: - first_name: Helen full_name: Senn, Helen last_name: Senn - first_name: Simon full_name: Goodman, Simon last_name: Goodman - first_name: Graeme full_name: Swanson, Graeme last_name: Swanson - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Josephine full_name: Pemberton, Josephine last_name: Pemberton 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. Molecular Ecology. 2010;19(5):910-924. doi:10.1111/j.1365-294X.2009.04497.x apa: Senn, H., Goodman, S., Swanson, G., Barton, N. H., & 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. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2009.04497.x 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.” Molecular Ecology. Wiley-Blackwell, 2010. https://doi.org/10.1111/j.1365-294X.2009.04497.x. 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,” Molecular Ecology, vol. 19, no. 5. Wiley-Blackwell, pp. 910–924, 2010. 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.” Molecular Ecology, vol. 19, no. 5, Wiley-Blackwell, 2010, pp. 910–24, doi:10.1111/j.1365-294X.2009.04497.x. short: H. Senn, S. Goodman, G. Swanson, N.H. Barton, J. Pemberton, Molecular Ecology 19 (2010) 910–924. date_created: 2018-12-11T12:04:12Z date_published: 2010-03-01T00:00:00Z date_updated: 2025-09-30T09:47:00Z day: '01' department: - _id: NiBa doi: 10.1111/j.1365-294X.2009.04497.x external_id: isi: - '000274550100008' intvolume: ' 19' isi: 1 issue: '5' language: - iso: eng month: '03' oa_version: None page: 910 - 924 publication: Molecular Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '2779' quality_controlled: '1' scopus_import: '1' status: public title: Investigating temporal changes in hybridisation and introgression between invasive sika (Cervus nippon) and native red deer (Cervus elaphus) on the Kintyre Peninsula, Scotland type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 19 year: '2010' ... --- _id: '3718' 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. 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." article_processing_charge: No author: - first_name: José full_name: Guzmán, José id: 30CC5506-F248-11E8-B48F-1D18A9856A87 last_name: Guzmán orcid: 0000-0003-2209-5242 - first_name: Hartmut full_name: Schmidt, Hartmut last_name: Schmidt - first_name: Heike full_name: Franke, Heike last_name: Franke - first_name: Ute full_name: Krügel, Ute last_name: Krügel - first_name: Jens full_name: Eilers, Jens last_name: Eilers - first_name: Peter full_name: Illes, Peter last_name: Illes - first_name: Zoltan full_name: Gerevich, Zoltan last_name: Gerevich citation: ama: Guzmán J, Schmidt H, Franke H, et al. P2Y1 receptors inhibit long-term depression in the prefrontal cortex. Neuropharmacology. 2010;59(6):406-415. doi:10.1016/j.neuropharm.2010.05.013 apa: 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. Elsevier. https://doi.org/10.1016/j.neuropharm.2010.05.013 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.” Neuropharmacology. Elsevier, 2010. https://doi.org/10.1016/j.neuropharm.2010.05.013. ieee: J. Guzmán et al., “P2Y1 receptors inhibit long-term depression in the prefrontal cortex.,” Neuropharmacology, vol. 59, no. 6. Elsevier, pp. 406–415, 2010. 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.” Neuropharmacology, vol. 59, no. 6, Elsevier, 2010, pp. 406–15, doi:10.1016/j.neuropharm.2010.05.013. short: J. Guzmán, H. Schmidt, H. Franke, U. Krügel, J. Eilers, P. Illes, Z. Gerevich, Neuropharmacology 59 (2010) 406–415. corr_author: '1' date_created: 2018-12-11T12:04:47Z date_published: 2010-11-01T00:00:00Z date_updated: 2025-09-30T09:46:27Z day: '01' department: - _id: PeJo doi: 10.1016/j.neuropharm.2010.05.013 external_id: isi: - '000283453300006' intvolume: ' 59' isi: 1 issue: '6' language: - iso: eng month: '11' oa_version: None page: 406 - 415 publication: Neuropharmacology publication_status: published publisher: Elsevier publist_id: '2512' quality_controlled: '1' scopus_import: '1' status: public title: P2Y1 receptors inhibit long-term depression in the prefrontal cortex. type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 59 year: '2010' ... --- _id: '3719' abstract: - lang: eng 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. 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. alternative_title: - EPTCS arxiv: 1 author: - first_name: Jérôme full_name: Feret, Jérôme last_name: Feret - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Heinz full_name: Koeppl, Heinz last_name: Koeppl - first_name: Tatjana full_name: Petrov, Tatjana id: 3D5811FC-F248-11E8-B48F-1D18A9856A87 last_name: Petrov orcid: 0000-0002-9041-0905 citation: ama: 'Feret J, Henzinger TA, Koeppl H, Petrov T. Lumpability abstractions of rule-based systems. In: Vol 40. Open Publishing Association; 2010:142-161.' apa: 'Feret, J., Henzinger, T. A., Koeppl, H., & 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.' mla: Feret, Jérôme, et al. Lumpability Abstractions of Rule-Based Systems. Vol. 40, Open Publishing Association, 2010, pp. 142–61. short: J. Feret, T.A. Henzinger, H. Koeppl, T. Petrov, in:, Open Publishing Association, 2010, pp. 142–161. conference: end_date: 2010-08-23 location: Jena, Germany name: 'MECBIC: Membrane Computing and Biologically Inspired Process Calculi' start_date: 2010-08-23 date_created: 2018-12-11T12:04:47Z date_published: 2010-10-30T00:00:00Z date_updated: 2026-06-18T18:39:27Z day: '30' ddc: - '570' department: - _id: ToHe - _id: CaGu external_id: arxiv: - '1011.0496' file: - access_level: open_access checksum: eaaba991a86fff37606b0eb5196878e8 content_type: application/pdf creator: kschuh date_created: 2019-01-31T12:09:09Z date_updated: 2020-07-14T12:46:14Z file_id: '5904' file_name: Lumpability_abstractions_of_rule-based_systems.pdf file_size: 907155 relation: main_file file_date_updated: 2020-07-14T12:46:14Z has_accepted_license: '1' intvolume: ' 40' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 142-161 publication_status: published publisher: Open Publishing Association publist_id: '2511' quality_controlled: '1' related_material: record: - id: '3168' relation: later_version status: public scopus_import: 1 status: public title: Lumpability abstractions of rule-based systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 40 year: '2010' ... --- _id: '3772' article_number: e1000987 article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. Understanding adaptation in large populations. PLoS Genetics. 2010;6(6). doi:10.1371/journal.pgen.1000987 apa: Barton, N. H. (2010). Understanding adaptation in large populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1000987 chicago: Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS Genetics. Public Library of Science, 2010. https://doi.org/10.1371/journal.pgen.1000987. ieee: N. H. Barton, “Understanding adaptation in large populations,” PLoS Genetics, vol. 6, no. 6. Public Library of Science, 2010. ista: Barton NH. 2010. Understanding adaptation in large populations. PLoS Genetics. 6(6), e1000987. mla: Barton, Nicholas H. “Understanding Adaptation in Large Populations.” PLoS Genetics, vol. 6, no. 6, e1000987, Public Library of Science, 2010, doi:10.1371/journal.pgen.1000987. short: N.H. Barton, PLoS Genetics 6 (2010). corr_author: '1' date_created: 2018-12-11T12:05:05Z date_published: 2010-06-17T00:00:00Z date_updated: 2025-09-30T09:45:21Z day: '17' ddc: - '570' - '576' department: - _id: NiBa doi: 10.1371/journal.pgen.1000987 external_id: isi: - '000279805200002' file: - access_level: open_access checksum: 5c14de2680ab483cb835096c99ee734d content_type: application/pdf creator: system date_created: 2018-12-12T10:14:24Z date_updated: 2020-07-14T12:46:15Z file_id: '5075' file_name: IST-2016-524-v1+1_journal.pgen.1000987.PDF file_size: 349965 relation: main_file file_date_updated: 2020-07-14T12:46:15Z has_accepted_license: '1' intvolume: ' 6' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '2454' pubrep_id: '524' quality_controlled: '1' scopus_import: '1' status: public title: Understanding adaptation in large populations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 6 year: '2010' ... --- _id: '3773' abstract: - lang: eng 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. 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" article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2010;365(1547):1825-1840. doi:10.1098/rstb.2010.0001 apa: Barton, N. H. (2010). What role does natural selection play in speciation? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society. https://doi.org/10.1098/rstb.2010.0001 chicago: Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. Royal Society, 2010. https://doi.org/10.1098/rstb.2010.0001. ieee: N. H. Barton, “What role does natural selection play in speciation?,” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1547. Royal Society, pp. 1825–1840, 2010. 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. mla: Barton, Nicholas H. “What Role Does Natural Selection Play in Speciation?” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, vol. 365, no. 1547, Royal Society, 2010, pp. 1825–40, doi:10.1098/rstb.2010.0001. short: N.H. Barton, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 365 (2010) 1825–1840. corr_author: '1' date_created: 2018-12-11T12:05:05Z date_published: 2010-06-12T00:00:00Z date_updated: 2025-09-30T09:45:54Z day: '12' department: - _id: NiBa doi: 10.1098/rstb.2010.0001 external_id: isi: - '000277208600009' pmid: - '20439284' intvolume: ' 365' isi: 1 issue: '1547' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pubmed/20439284 month: '06' oa: 1 oa_version: Submitted Version page: 1825 - 1840 pmid: 1 publication: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences publication_status: published publisher: Royal Society publist_id: '2455' quality_controlled: '1' scopus_import: '1' status: public title: What role does natural selection play in speciation? type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 365 year: '2010' ...