[{"volume":74,"doi":"10.1101/sqb.2009.74.030","isi":1,"external_id":{"isi":["000578380600022"]},"month":"11","department":[{"_id":"NiBa"}],"publisher":"Cold Spring Harbor Laboratory Press","day":"10","corr_author":"1","fulldoi":"https://doi.org/10.1101/sqb.2009.74.030","date_published":"2009-11-10T00:00:00Z","article_processing_charge":"No","quality_controlled":"1","year":"2009","publication_status":"published","intvolume":"        74","publist_id":"2708","language":[{"iso":"eng"}],"acknowledgement":"Royal Society and the Engineering and Physical Sciences for support (GR/ T11753/01)","publication":"Cold Spring Harbor Symposia on Quantitative Biology","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-30T09:56:29Z","citation":{"apa":"Barton, N. H. (2009). Why sex and recombination? In <i>Cold Spring Harbor Symposia on Quantitative Biology</i> (Vol. 74, pp. 187–195). Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/sqb.2009.74.030\">https://doi.org/10.1101/sqb.2009.74.030</a>","chicago":"Barton, Nicholas H. “Why Sex and Recombination?” In <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, 74:187–95. Cold Spring Harbor Laboratory Press, 2009. <a href=\"https://doi.org/10.1101/sqb.2009.74.030\">https://doi.org/10.1101/sqb.2009.74.030</a>.","short":"N.H. Barton, in:, Cold Spring Harbor Symposia on Quantitative Biology, Cold Spring Harbor Laboratory Press, 2009, pp. 187–195.","ista":"Barton NH. 2009.Why sex and recombination? In: Cold Spring Harbor Symposia on Quantitative Biology. vol. 74, 187–195.","ieee":"N. H. Barton, “Why sex and recombination?,” in <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 74, Cold Spring Harbor Laboratory Press, 2009, pp. 187–195.","ama":"Barton NH. Why sex and recombination? In: <i>Cold Spring Harbor Symposia on Quantitative Biology</i>. Vol 74. Cold Spring Harbor Laboratory Press; 2009:187-195. doi:<a href=\"https://doi.org/10.1101/sqb.2009.74.030\">10.1101/sqb.2009.74.030</a>","mla":"Barton, Nicholas H. “Why Sex and Recombination?” <i>Cold Spring Harbor Symposia on Quantitative Biology</i>, vol. 74, Cold Spring Harbor Laboratory Press, 2009, pp. 187–95, doi:<a href=\"https://doi.org/10.1101/sqb.2009.74.030\">10.1101/sqb.2009.74.030</a>."},"page":"187 - 195","oa_version":"None","type":"book_chapter","abstract":[{"lang":"eng","text":"Sex and recombination have long been seen as adaptations that facilitate natural selection by generating favorable variations. If recombination is to aid selection, there must be negative linkage disequilibria—favorable alleles must be found together less often than expected by chance. These negative linkage disequilibria can be generated directly by selection, but this must involve negative epistasis of just the right strength, which is not expected, from either experiment or theory. Random drift provides a more general source of negative associations: Favorable mutations almost always arise on different genomes, and negative associations tend to persist, precisely because they shield variation from selection.\r\n\r\nWe can understand how recombination aids adaptation by determining the maximum possible rate of adaptation. With unlinked loci, this rate increases only logarithmically with the influx of favorable mutations. With a linear genome, a scaling argument shows that in a large population, the rate of adaptive substitution depends only on the expected rate in the absence of interference, divided by the total rate of recombination. A two-locus approximation predicts an upper bound on the rate of substitution, proportional to recombination rate.\r\n\r\nIf associations between linked loci do impede adaptation, there can be substantial selection for modifiers that increase recombination. Whether this can account for the maintenance of high rates of sex and recombination depends on the extent of selection. It is clear that the rate of species-wide substitutions is typically far too low to generate appreciable selection for recombination. However, local sweeps within a subdivided population may be effective."}],"_id":"3675","title":"Why sex and recombination?","author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T12:04:33Z","status":"public"},{"publist_id":"2452","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by a Royal Society/Wolfson Award, and by grants EP/T11753/01, EP/C546318/01 from the EPSRC.\r\nWe are grateful to M. Cates, H.P. de Vladar and G. Sella, and to two anonymous referees, for their helpful comments.","publication":"Journal of Theoretical Biology","scopus_import":"1","issue":"2","date_updated":"2025-09-30T09:56:01Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"apa":"Barton, N. H., &#38; Coe, J. (2009). On the application of statistical physics to evolutionary biology. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">https://doi.org/10.1016/j.jtbi.2009.03.019</a>","chicago":"Barton, Nicholas H, and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” <i>Journal of Theoretical Biology</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">https://doi.org/10.1016/j.jtbi.2009.03.019</a>.","short":"N.H. Barton, J. Coe, Journal of Theoretical Biology 259 (2009) 317–324.","ista":"Barton NH, Coe J. 2009. On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. 259(2), 317–324.","ieee":"N. H. Barton and J. Coe, “On the application of statistical physics to evolutionary biology,” <i>Journal of Theoretical Biology</i>, vol. 259, no. 2. Elsevier, pp. 317–324, 2009.","ama":"Barton NH, Coe J. On the application of statistical physics to evolutionary biology. <i>Journal of Theoretical Biology</i>. 2009;259(2):317-324. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">10.1016/j.jtbi.2009.03.019</a>","mla":"Barton, Nicholas H., and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” <i>Journal of Theoretical Biology</i>, vol. 259, no. 2, Elsevier, 2009, pp. 317–24, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">10.1016/j.jtbi.2009.03.019</a>."},"page":"317 - 324","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"There is a close analogy between statistical thermodynamics and the evolution of allele frequencies under mutation, selection and random drift. Wright's formula for the stationary distribution of allele frequencies is analogous to the Boltzmann distribution in statistical physics. Population size, 2N, plays the role of the inverse temperature, 1/kT, and determines the magnitude of random fluctuations. Log mean fitness, View the MathML source, tends to increase under selection, and is analogous to a (negative) energy; a potential function, U, increases under mutation in a similar way. An entropy, SH, can be defined which measures the deviation from the distribution of allele frequencies expected under random drift alone; the sum View the MathML source gives a free fitness that increases as the population evolves towards its stationary distribution. Usually, we observe the distribution of a few quantitative traits that depend on the frequencies of very many alleles. The mean and variance of such traits are analogous to observable quantities in statistical thermodynamics. Thus, we can define an entropy, SΩ, which measures the volume of allele frequency space that is consistent with the observed trait distribution. The stationary distribution of the traits is View the MathML source; this applies with arbitrary epistasis and dominance. The entropies SΩ, SH are distinct, but converge when there are so many alleles that traits fluctuate close to their expectations. Populations tend to evolve towards states that can be realised in many ways (i.e., large SΩ), which may lead to a substantial drop below the adaptive peak; we illustrate this point with a simple model of genetic redundancy. This analogy with statistical thermodynamics brings together previous ideas in a general framework, and justifies a maximum entropy approximation to the dynamics of quantitative traits."}],"title":"On the application of statistical physics to evolutionary biology","_id":"3775","date_created":"2018-12-11T12:05:06Z","author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Coe, Jason","first_name":"Jason","last_name":"Coe"}],"status":"public","volume":259,"doi":"10.1016/j.jtbi.2009.03.019","isi":1,"external_id":{"isi":["000267176100013"]},"publisher":"Elsevier","month":"07","department":[{"_id":"NiBa"}],"day":"21","oa":1,"corr_author":"1","fulldoi":"https://doi.org/10.1016/j.jtbi.2009.03.019","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-00554594/document","open_access":"1"}],"date_published":"2009-07-21T00:00:00Z","article_processing_charge":"No","publication_status":"published","quality_controlled":"1","year":"2009","intvolume":"       259"},{"pubrep_id":"553","oa":1,"day":"01","department":[{"_id":"NiBa"}],"month":"08","publisher":"Wiley","external_id":{"isi":["000268029800006"]},"isi":1,"file":[{"file_id":"6044","file_size":2583812,"file_name":"Davison_JEB_v31_2009.pdf","date_updated":"2020-07-14T12:46:15Z","content_type":"application/pdf","date_created":"2019-02-22T09:21:44Z","checksum":"f70c15c6ab9306121d4153a3be0d2346","creator":"dernst","relation":"main_file","access_level":"open_access"}],"doi":"10.1111/j.1420-9101.2009.01770.x","volume":22,"ddc":["570"],"intvolume":"        22","year":"2009","quality_controlled":"1","publication_status":"published","article_processing_charge":"No","file_date_updated":"2020-07-14T12:46:15Z","date_published":"2009-08-01T00:00:00Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.1111/j.1420-9101.2009.01770.x","issue":"8","scopus_import":"1","publication":"Journal of Evolutionary Biology","acknowledgement":"We owe a great debt to Jim Murray for his many contributions to the study of Partula, in the field, in the laboratory, in the interpretation of data, and in generating new ideas about evolution. With pleasure and respect we dedicate this paper to him. Jim Murray played a leading role in making the collections used here. We are very grateful also to Ann Clarke and Elizabeth Murray for help with collecting, to Lorna Stewart for snail dissections, to Joris Koene for the gift of snails, to Natasha Constant for entering the data, and Takahiro Asami, Edmund Gittenberger and Gerhard Falkner for establishing the sinistral stock of L. stagnalis. Comments from an anonymous referee, A. Richard Palmer and the editorial board improved the manuscript. Work in the field was supported by the Royal Society, The Carnegie Trust, the Percy Sladen Trust and the National Science Foundation. The Science Research Council (B/SR/4144), the National Science Foundation (GB-4188), the Royal Society and the University of Nottingham supported work in the laboratory.","publist_id":"2447","language":[{"iso":"eng"}],"date_created":"2018-12-11T12:05:08Z","author":[{"full_name":"Davison, Angus","last_name":"Davison","first_name":"Angus"},{"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":"Clarke, Bryan","last_name":"Clarke","first_name":"Bryan"}],"status":"public","_id":"3780","title":"The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails","abstract":[{"lang":"eng","text":"Why are sinistral snails so rare? Two main hypotheses are that selection acts against the establishment of new coiling morphs, because dextral and sinistral snails have trouble mating, or else a developmental constraint prevents the establishment of sinistrals. We therefore used an isolate of the snail Lymnaea stagnalis, in which sinistrals are rare, and populations of Partula suturalis, in which sinistrals are common, as well as a mathematical model, to understand the circumstances by which new morphs evolve. The main finding is that the sinistral genotype is associated with reduced egg viability in L. stagnalis, but in P. suturalis individuals of sinistral and dextral genotype appear equally fecund, implying a lack of a constraint. As positive frequency-dependent selection against the rare chiral morph in P. suturalis also operates over a narrow range (&lt; 3%), the results suggest a model for chiral evolution in snails in which weak positive frequency-dependent selection may be overcome by a negative frequency-dependent selection, such as reproductive character displacement. In snails, there is not always a developmental constraint. As the direction of cleavage, and thus the directional asymmetry of the entire body, does not generally vary in other Spiralia (annelids, echiurans, vestimentiferans, sipunculids and nemerteans), it remains an open question as to whether this is because of a constraint and/or because most taxa do not have a conspicuous external asymmetry (like a shell) upon which selection can act."}],"oa_version":"Submitted Version","type":"journal_article","citation":{"ieee":"A. Davison, N. H. Barton, and B. Clarke, “The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails,” <i>Journal of Evolutionary Biology</i>, vol. 22, no. 8. Wiley, pp. 1624–1635, 2009.","short":"A. Davison, N.H. Barton, B. Clarke, Journal of Evolutionary Biology 22 (2009) 1624–1635.","ista":"Davison A, Barton NH, Clarke B. 2009. The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal of Evolutionary Biology. 22(8), 1624–1635.","ama":"Davison A, Barton NH, Clarke B. The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. <i>Journal of Evolutionary Biology</i>. 2009;22(8):1624-1635. doi:<a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">10.1111/j.1420-9101.2009.01770.x</a>","mla":"Davison, Angus, et al. “The Effect of Chirality Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” <i>Journal of Evolutionary Biology</i>, vol. 22, no. 8, Wiley, 2009, pp. 1624–35, doi:<a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">10.1111/j.1420-9101.2009.01770.x</a>.","apa":"Davison, A., Barton, N. H., &#38; Clarke, B. (2009). The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">https://doi.org/10.1111/j.1420-9101.2009.01770.x</a>","chicago":"Davison, Angus, Nicholas H Barton, and Bryan Clarke. “The Effect of Chirality Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” <i>Journal of Evolutionary Biology</i>. Wiley, 2009. <a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">https://doi.org/10.1111/j.1420-9101.2009.01770.x</a>."},"page":"1624 - 1635","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-30T09:55:32Z"},{"publication":"EMSOFT '09 Proceedings of the seventh ACM international conference on Embedded software","scopus_import":"1","acknowledgement":"This work is supported by the Center for Hybrid and Embedded Software Systems (CHESS) at UC Berkeley, which receives support from the National Science Foundation (NSF awards #0720882 (CSR-EHS: PRET) and #0720841 (CSR-CPS)), the U.S. Army Research Office (ARO #W911NF-07-2-0019), the U.S. Air Force Office of Scientific Research (MURI #FA9550-06-0312), the Air Force Research Lab (AFRL), the State of California Micro Program, and the following companies: Agilent, Bosch, Lockheed-Martin, National Instruments, Thales and Toyota. This work is also supported by the COMBEST and ArtistDesign projects of the European Union, and the Swiss National Science Foundation. ","ec_funded":1,"language":[{"iso":"eng"}],"publist_id":"2360","title":"On relational interfaces","_id":"3837","status":"public","author":[{"full_name":"Tripakis, Stavros","last_name":"Tripakis","first_name":"Stavros"},{"full_name":"Lickly, Ben","first_name":"Ben","last_name":"Lickly"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lee, Edward","first_name":"Edward","last_name":"Lee"}],"date_created":"2018-12-11T12:05:26Z","type":"conference","oa_version":"Submitted Version","abstract":[{"text":"In this paper we extend the work of Alfaro, Henzinger et al. on interface theories for component-based design. Existing interface theories often fail to capture functional relations between the inputs and outputs of an interface. For example, a simple synchronous interface that takes as input a number n ≥ 0 and returns, at the same time, as output n + 1, cannot be expressed in existing theories. In this paper we provide a theory of relational interfaces, where such input-output relations can be captured. Our theory supports synchronous interfaces, both stateless and stateful. It includes explicit notions of environments and pluggability, and satisfies fundamental properties such as preservation of refinement by composition, and characterization of pluggability by refinement. We achieve these properties by making reasonable restrictions on feedback loops in interface compositions.","lang":"eng"}],"citation":{"chicago":"Tripakis, Stavros, Ben Lickly, Thomas A Henzinger, and Edward Lee. “On Relational Interfaces.” In <i>EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software</i>, 67–76. ACM, 2009. <a href=\"https://doi.org/10.1145/1629335.1629346\">https://doi.org/10.1145/1629335.1629346</a>.","apa":"Tripakis, S., Lickly, B., Henzinger, T. A., &#38; Lee, E. (2009). On relational interfaces. In <i>EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software</i> (pp. 67–76). Grenoble, France: ACM. <a href=\"https://doi.org/10.1145/1629335.1629346\">https://doi.org/10.1145/1629335.1629346</a>","ama":"Tripakis S, Lickly B, Henzinger TA, Lee E. On relational interfaces. In: <i>EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software</i>. ACM; 2009:67-76. doi:<a href=\"https://doi.org/10.1145/1629335.1629346\">10.1145/1629335.1629346</a>","mla":"Tripakis, Stavros, et al. “On Relational Interfaces.” <i>EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software</i>, ACM, 2009, pp. 67–76, doi:<a href=\"https://doi.org/10.1145/1629335.1629346\">10.1145/1629335.1629346</a>.","short":"S. Tripakis, B. Lickly, T.A. Henzinger, E. Lee, in:, EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software, ACM, 2009, pp. 67–76.","ieee":"S. Tripakis, B. Lickly, T. A. Henzinger, and E. Lee, “On relational interfaces,” in <i>EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software</i>, Grenoble, France, 2009, pp. 67–76.","ista":"Tripakis S, Lickly B, Henzinger TA, Lee E. 2009. On relational interfaces. EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software. EMSOFT: Embedded Software , 67–76."},"page":"67 - 76","project":[{"name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543"},{"call_identifier":"FP7","name":"Design for Embedded Systems","_id":"25F1337C-B435-11E9-9278-68D0E5697425","grant_number":"214373"}],"date_updated":"2024-10-21T06:03:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","oa":1,"pubrep_id":"70","publisher":"ACM","month":"01","department":[{"_id":"ToHe"}],"doi":"10.1145/1629335.1629346","file":[{"date_created":"2018-12-12T10:13:57Z","checksum":"3a70e21527dfaad2f198549ae5710786","access_level":"open_access","relation":"main_file","creator":"system","file_id":"5045","date_updated":"2020-07-14T12:46:16Z","content_type":"application/pdf","file_name":"IST-2012-70-v1+1_On_Relational_Interfaces.pdf","file_size":310902}],"ddc":["004"],"publication_status":"published","year":"2009","quality_controlled":"1","conference":{"end_date":"2009-10-16","start_date":"2009-10-12","name":"EMSOFT: Embedded Software ","location":"Grenoble, France"},"has_accepted_license":"1","file_date_updated":"2020-07-14T12:46:16Z","date_published":"2009-01-01T00:00:00Z","fulldoi":"https://doi.org/10.1145/1629335.1629346"},{"publist_id":"2352","language":[{"iso":"eng"}],"scopus_import":1,"acknowledgement":"This research was supported in part by the Excellence Cluster on Multimodal Computing and Interaction and the Swiss National Science Foundation.","related_material":{"record":[{"id":"3381","relation":"later_version","status":"public"}]},"citation":{"apa":"Henzinger, T. A., Jobstmann, B., &#38; Wolf, V. (2009). Formalisms for specifying Markovian population models (Vol. 5797, pp. 3–23). Presented at the RP: Reachability Problems, Palaiseau, France: Springer. <a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">https://doi.org/10.1007/978-3-642-04420-5_2</a>","chicago":"Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for Specifying Markovian Population Models,” 5797:3–23. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">https://doi.org/10.1007/978-3-642-04420-5_2</a>.","ieee":"T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian population models,” presented at the RP: Reachability Problems, Palaiseau, France, 2009, vol. 5797, pp. 3–23.","ista":"Henzinger TA, Jobstmann B, Wolf V. 2009. Formalisms for specifying Markovian population models. RP: Reachability Problems, LNCS, vol. 5797, 3–23.","short":"T.A. Henzinger, B. Jobstmann, V. Wolf, in:, Springer, 2009, pp. 3–23.","mla":"Henzinger, Thomas A., et al. <i>Formalisms for Specifying Markovian Population Models</i>. Vol. 5797, Springer, 2009, pp. 3–23, doi:<a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">10.1007/978-3-642-04420-5_2</a>.","ama":"Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population models. In: Vol 5797. Springer; 2009:3-23. doi:<a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">10.1007/978-3-642-04420-5_2</a>"},"page":"3 - 23","date_updated":"2025-09-30T08:49:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Formalisms for specifying Markovian population models","_id":"3841","author":[{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jobstmann, Barbara","first_name":"Barbara","last_name":"Jobstmann"},{"full_name":"Wolf, Verena","first_name":"Verena","last_name":"Wolf"}],"date_created":"2018-12-11T12:05:28Z","status":"public","type":"conference","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"We compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. These languages —matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models— all describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, ease of use, and the support they provide for checking the well-formedness of a model and for analyzing a model. "}],"volume":5797,"doi":"10.1007/978-3-642-04420-5_2","file":[{"file_name":"IST-2012-67-v1+1_Formalisms_for_specifying_Markovian_population_models.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:16Z","file_size":222840,"file_id":"4702","access_level":"open_access","creator":"system","relation":"main_file","date_created":"2018-12-12T10:08:41Z","checksum":"df88431872586c773fbcfea37d7b36a2"}],"day":"07","oa":1,"pubrep_id":"67","publisher":"Springer","month":"09","department":[{"_id":"ToHe"}],"has_accepted_license":"1","conference":{"location":"Palaiseau, France","name":"RP: Reachability Problems","end_date":"2009-09-25","start_date":"2009-09-23"},"alternative_title":["LNCS"],"file_date_updated":"2020-07-14T12:46:16Z","date_published":"2009-09-07T00:00:00Z","fulldoi":"https://doi.org/10.1007/978-3-642-04420-5_2","ddc":["005"],"publication_status":"published","quality_controlled":"1","year":"2009","intvolume":"      5797"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-30T09:54:51Z","page":"118 - 127","citation":{"apa":"Didier, F., Henzinger, T. A., Mateescu, M., &#38; Wolf, V. (2009). Fast adaptive uniformization of the chemical master equation (Vol. 4, pp. 118–127). Presented at the HIBI: High-Performance Computational Systems Biology, Trento, Italy: IEEE. <a href=\"https://doi.org/10.1109/HiBi.2009.23\">https://doi.org/10.1109/HiBi.2009.23</a>","chicago":"Didier, Frédéric, Thomas A Henzinger, Maria Mateescu, and Verena Wolf. “Fast Adaptive Uniformization of the Chemical Master Equation,” 4:118–27. IEEE, 2009. <a href=\"https://doi.org/10.1109/HiBi.2009.23\">https://doi.org/10.1109/HiBi.2009.23</a>.","short":"F. Didier, T.A. Henzinger, M. Mateescu, V. Wolf, in:, IEEE, 2009, pp. 118–127.","ista":"Didier F, Henzinger TA, Mateescu M, Wolf V. 2009. Fast adaptive uniformization of the chemical master equation. HIBI: High-Performance Computational Systems Biology vol. 4, 118–127.","ieee":"F. Didier, T. A. Henzinger, M. Mateescu, and V. Wolf, “Fast adaptive uniformization of the chemical master equation,” presented at the HIBI: High-Performance Computational Systems Biology, Trento, Italy, 2009, vol. 4, no. 6, pp. 118–127.","mla":"Didier, Frédéric, et al. <i>Fast Adaptive Uniformization of the Chemical Master Equation</i>. Vol. 4, no. 6, IEEE, 2009, pp. 118–27, doi:<a href=\"https://doi.org/10.1109/HiBi.2009.23\">10.1109/HiBi.2009.23</a>.","ama":"Didier F, Henzinger TA, Mateescu M, Wolf V. Fast adaptive uniformization of the chemical master equation. In: Vol 4. IEEE; 2009:118-127. doi:<a href=\"https://doi.org/10.1109/HiBi.2009.23\">10.1109/HiBi.2009.23</a>"},"related_material":{"record":[{"status":"public","id":"3842","relation":"later_version"}]},"abstract":[{"text":"Within systems biology there is an increasing interest in the stochastic behavior of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous- time Markov chain (CTMC).\r\nStandard Uniformization (SU) is an efficient method for the transient analysis of CTMCs. For systems with very different time scales, such as biochemical reaction networks, SU is computationally expensive. In these cases, a variant of SU, called adaptive uniformization (AU), is known to reduce the large number of iterations needed by SU. The additional difficulty of AU is that it requires the solution of a birth process.\r\nIn this paper we present an on-the-fly variant of AU, where we improve the original algorithm for AU at the cost of a small approximation error. By means of several examples, we show that our approach is particularly well-suited for biochemical reaction networks.","lang":"eng"}],"type":"conference","oa_version":"Submitted Version","status":"public","author":[{"last_name":"Didier","first_name":"Frédéric","full_name":"Didier, Frédéric"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Mateescu, Maria","id":"3B43276C-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","last_name":"Mateescu"},{"first_name":"Verena","last_name":"Wolf","full_name":"Wolf, Verena"}],"date_created":"2018-12-11T12:05:28Z","_id":"3843","title":"Fast adaptive uniformization of the chemical master equation","publist_id":"2348","language":[{"iso":"eng"}],"acknowledgement":"This research has been partially funded by the Swiss National Science Foundation under grant 205321-111840 and by the Cluster of Excellence on Multimodal Computing and Interaction at Saarland University.","issue":"6","scopus_import":"1","fulldoi":"https://doi.org/10.1109/HiBi.2009.23","article_processing_charge":"No","file_date_updated":"2020-07-14T12:46:17Z","date_published":"2009-10-30T00:00:00Z","conference":{"name":"HIBI: High-Performance Computational Systems Biology","start_date":"2009-10-14","end_date":"2009-10-16","location":"Trento, Italy"},"has_accepted_license":"1","intvolume":"         4","year":"2009","quality_controlled":"1","publication_status":"published","ddc":["000"],"file":[{"checksum":"9a3bde48f43203991a0b3c6a277c2f5b","date_created":"2020-05-19T16:33:55Z","creator":"dernst","relation":"main_file","access_level":"open_access","file_id":"7874","file_size":222890,"file_name":"2009_HIBI_Didier.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:17Z"}],"doi":"10.1109/HiBi.2009.23","volume":4,"isi":1,"month":"10","department":[{"_id":"ToHe"},{"_id":"CaGu"}],"publisher":"IEEE","external_id":{"isi":["000275038300017"]},"oa":1,"day":"30"},{"doi":"10.1109/RTSS.2009.9","file":[{"creator":"system","relation":"main_file","access_level":"open_access","date_created":"2018-12-12T10:07:56Z","checksum":"b2b15a5ef71eb50d62eaa5aea7efd8c4","file_size":526458,"file_name":"IST-2012-65-v1+1_Distributed_modular_Htl.pdf","date_updated":"2020-07-14T12:46:17Z","content_type":"application/pdf","file_id":"4655"}],"isi":1,"external_id":{"isi":["000277465500016"]},"publisher":"IEEE","month":"01","department":[{"_id":"ToHe"}],"day":"01","oa":1,"pubrep_id":"65","fulldoi":"https://doi.org/10.1109/RTSS.2009.9","has_accepted_license":"1","conference":{"location":"Washington, DC, United States","end_date":"2009-12-04","start_date":"2009-12-01","name":"RTSS: Real-Time Systems Symposium"},"file_date_updated":"2020-07-14T12:46:17Z","date_published":"2009-01-01T00:00:00Z","article_processing_charge":"No","publication_status":"published","year":"2009","quality_controlled":"1","ddc":["000"],"publist_id":"2346","language":[{"iso":"eng"}],"ec_funded":1,"acknowledgement":"Supported by the EU ArtistDesign Network of Excellence on Embedded Systems Design, the EU project COMBEST, the Austrian Science Funds P18913-N15 and V00125, and Fundacao para a Ciencia e Tecnologia funds SFRH/BD/29461/2006 and PTDC/EIA/71462/2006","scopus_import":"1","date_updated":"2025-09-30T09:54:22Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"apa":"Henzinger, T. A., Kirsch, C., Marques, E., &#38; Sokolova, A. (2009). Distributed, modular HTL (pp. 171–180). Presented at the RTSS: Real-Time Systems Symposium, Washington, DC, United States: IEEE. <a href=\"https://doi.org/10.1109/RTSS.2009.9\">https://doi.org/10.1109/RTSS.2009.9</a>","chicago":"Henzinger, Thomas A, Christoph Kirsch, Eduardo Marques, and Ana Sokolova. “Distributed, Modular HTL,” 171–80. IEEE, 2009. <a href=\"https://doi.org/10.1109/RTSS.2009.9\">https://doi.org/10.1109/RTSS.2009.9</a>.","ieee":"T. A. Henzinger, C. Kirsch, E. Marques, and A. Sokolova, “Distributed, modular HTL,” presented at the RTSS: Real-Time Systems Symposium, Washington, DC, United States, 2009, pp. 171–180.","short":"T.A. Henzinger, C. Kirsch, E. Marques, A. Sokolova, in:, IEEE, 2009, pp. 171–180.","ista":"Henzinger TA, Kirsch C, Marques E, Sokolova A. 2009. Distributed, modular HTL. RTSS: Real-Time Systems Symposium, 171–180.","mla":"Henzinger, Thomas A., et al. <i>Distributed, Modular HTL</i>. IEEE, 2009, pp. 171–80, doi:<a href=\"https://doi.org/10.1109/RTSS.2009.9\">10.1109/RTSS.2009.9</a>.","ama":"Henzinger TA, Kirsch C, Marques E, Sokolova A. Distributed, modular HTL. In: IEEE; 2009:171-180. doi:<a href=\"https://doi.org/10.1109/RTSS.2009.9\">10.1109/RTSS.2009.9</a>"},"page":"171 - 180","project":[{"grant_number":"214373","call_identifier":"FP7","name":"Design for Embedded Systems","_id":"25F1337C-B435-11E9-9278-68D0E5697425"},{"name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","grant_number":"215543"}],"type":"conference","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"The Hierarchical Timing Language (HTL) is a real-time coordination language for distributed control systems. HTL programs must be checked for well-formedness, race freedom, transmission safety (schedulability of inter-host communication), and time safety (schedulability of host computation). We present a modular abstract syntax and semantics for HTL, modular checks of well-formedness, race freedom, and transmission safety, and modular code distribution. Our contributions here complement previous results on HTL time safety and modular code generation. Modularity in HTL can be utilized in easy program composition as well as fast program analysis and code generation, but also in so-called runtime patching, where program components may be modified at runtime."}],"title":"Distributed, modular HTL","_id":"3844","date_created":"2018-12-11T12:05:28Z","status":"public","author":[{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"full_name":"Kirsch, Christoph","last_name":"Kirsch","first_name":"Christoph"},{"full_name":"Marques, Eduardo","last_name":"Marques","first_name":"Eduardo"},{"first_name":"Ana","last_name":"Sokolova","full_name":"Sokolova, Ana"}]},{"publist_id":"2304","language":[{"iso":"eng"}],"scopus_import":1,"ec_funded":1,"acknowledgement":"This research was supported in part by the Swiss National Science Foundation under the Indo-Swiss Joint Research Programme, by the European Network of Excellence on Embedded Systems Design (ArtistDesign), by the European projects Combest, Quasimodo, and Gasics, by the PAI program Moves funded by the Belgian Federal Government, and by the CFV (Federated Center in Verification ) funded by the F.R.S.-FNRS.","page":"244 - 258","citation":{"ista":"Chatterjee K, Doyen L, Henzinger TA. 2009. Probabilistic weighted automata. CONCUR: Concurrency Theory, LNCS, vol. 5710, 244–258.","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “Probabilistic weighted automata,” presented at the CONCUR: Concurrency Theory, Bologna, Italy, 2009, vol. 5710, pp. 244–258.","short":"K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2009, pp. 244–258.","ama":"Chatterjee K, Doyen L, Henzinger TA. Probabilistic weighted automata. In: Vol 5710. Springer; 2009:244-258. doi:<a href=\"https://doi.org/10.1007/978-3-642-04081-8_17\">10.1007/978-3-642-04081-8_17</a>","mla":"Chatterjee, Krishnendu, et al. <i>Probabilistic Weighted Automata</i>. Vol. 5710, Springer, 2009, pp. 244–58, doi:<a href=\"https://doi.org/10.1007/978-3-642-04081-8_17\">10.1007/978-3-642-04081-8_17</a>.","apa":"Chatterjee, K., Doyen, L., &#38; Henzinger, T. A. (2009). Probabilistic weighted automata (Vol. 5710, pp. 244–258). Presented at the CONCUR: Concurrency Theory, Bologna, Italy: Springer. <a href=\"https://doi.org/10.1007/978-3-642-04081-8_17\">https://doi.org/10.1007/978-3-642-04081-8_17</a>","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Probabilistic Weighted Automata,” 5710:244–58. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-04081-8_17\">https://doi.org/10.1007/978-3-642-04081-8_17</a>."},"project":[{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Design for Embedded Systems","grant_number":"214373"},{"grant_number":"215543","_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7"}],"date_updated":"2024-10-09T20:53:56Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T12:05:37Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"last_name":"Doyen","first_name":"Laurent","full_name":"Doyen, Laurent"},{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"}],"status":"public","title":"Probabilistic weighted automata","_id":"3871","abstract":[{"text":"Nondeterministic weighted automata are finite automata with numerical weights oil transitions. They define quantitative languages 1, that assign to each word v; a real number L(w). The value of ail infinite word w is computed as the maximal value of all runs over w, and the value of a run as the supremum, limsup liminf, limit average, or discounted sum of the transition weights. We introduce probabilistic weighted antomata, in which the transitions are chosen in a randomized (rather than nondeterministic) fashion. Under almost-sure semantics (resp. positive semantics), the value of a word v) is the largest real v such that the runs over w have value at least v with probability I (resp. positive probability). We study the classical questions of automata theory for probabilistic weighted automata: emptiness and universality, expressiveness, and closure under various operations oil languages. For quantitative languages, emptiness university axe defined as whether the value of some (resp. every) word exceeds a given threshold. We prove some, of these questions to he decidable, and others undecidable. Regarding expressive power, we show that probabilities allow its to define a wide variety of new classes of quantitative languages except for discounted-sum automata, where probabilistic choice is no more expressive than nondeterminism. Finally we live ail almost complete picture of the closure of various classes of probabilistic weighted automata for the following, provide, is operations oil quantitative languages: maximum, sum. and numerical complement.","lang":"eng"}],"oa_version":"Submitted Version","type":"conference","doi":"10.1007/978-3-642-04081-8_17","file":[{"relation":"main_file","creator":"system","access_level":"open_access","date_created":"2018-12-12T10:09:46Z","checksum":"af973ddbcf131b8810c6bff2c055ff56","file_size":200161,"file_name":"IST-2012-52-v1+1_Probabilistic_Weighted_Automata.pdf","date_updated":"2020-07-14T12:46:20Z","content_type":"application/pdf","file_id":"4771"}],"volume":5710,"corr_author":"1","oa":1,"pubrep_id":"52","day":"01","publisher":"Springer","month":"09","department":[{"_id":"KrCh"}],"has_accepted_license":"1","conference":{"name":"CONCUR: Concurrency Theory","start_date":"2009-09-01","end_date":"2009-09-04","location":"Bologna, Italy"},"alternative_title":["LNCS"],"date_published":"2009-09-01T00:00:00Z","file_date_updated":"2020-07-14T12:46:20Z","fulldoi":"https://doi.org/10.1007/978-3-642-04081-8_17","ddc":["000","005"],"intvolume":"      5710","publication_status":"published","year":"2009","quality_controlled":"1"},{"publist_id":"2160","language":[{"iso":"eng"}],"scopus_import":1,"acknowledgement":"This research was partially supported by Geomagic, Inc., and by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057.","citation":{"ista":"Edelsbrunner H, Harer J. 2009. The persistent Morse complex segmentation of a 3-manifold. 3DPH: Modelling the Physiological Human, LNCS, vol. 5903, 36–50.","ieee":"H. Edelsbrunner and J. Harer, “The persistent Morse complex segmentation of a 3-manifold,” presented at the 3DPH: Modelling the Physiological Human, Zermatt, Switzerland, 2009, vol. 5903, pp. 36–50.","short":"H. Edelsbrunner, J. Harer, in:, Springer, 2009, pp. 36–50.","ama":"Edelsbrunner H, Harer J. The persistent Morse complex segmentation of a 3-manifold. In: Vol 5903. Springer; 2009:36-50. doi:<a href=\"https://doi.org/10.1007/978-3-642-10470-1_4\">10.1007/978-3-642-10470-1_4</a>","mla":"Edelsbrunner, Herbert, and John Harer. <i>The Persistent Morse Complex Segmentation of a 3-Manifold</i>. Vol. 5903, Springer, 2009, pp. 36–50, doi:<a href=\"https://doi.org/10.1007/978-3-642-10470-1_4\">10.1007/978-3-642-10470-1_4</a>.","apa":"Edelsbrunner, H., &#38; Harer, J. (2009). The persistent Morse complex segmentation of a 3-manifold (Vol. 5903, pp. 36–50). Presented at the 3DPH: Modelling the Physiological Human, Zermatt, Switzerland: Springer. <a href=\"https://doi.org/10.1007/978-3-642-10470-1_4\">https://doi.org/10.1007/978-3-642-10470-1_4</a>","chicago":"Edelsbrunner, Herbert, and John Harer. “The Persistent Morse Complex Segmentation of a 3-Manifold,” 5903:36–50. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-10470-1_4\">https://doi.org/10.1007/978-3-642-10470-1_4</a>."},"page":"36 - 50","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-10-09T20:53:56Z","_id":"3968","title":"The persistent Morse complex segmentation of a 3-manifold","date_created":"2018-12-11T12:06:10Z","status":"public","author":[{"last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"full_name":"Harer, John","first_name":"John","last_name":"Harer"}],"type":"conference","oa_version":"Submitted Version","abstract":[{"text":"We describe an algorithm for segmenting three-dimensional medical imaging data modeled as a continuous function on a 3-manifold. It is related to watershed algorithms developed in image processing but is closer to its mathematical roots, which are Morse theory and homological algebra. It allows for the implicit treatment of an underlying mesh, thus combining the structural integrity of its mathematical foundations with the computational efficiency of image processing.","lang":"eng"}],"volume":5903,"file":[{"checksum":"11fc85bcc19bab1f020e706a4b8a4660","date_created":"2018-12-12T10:08:33Z","access_level":"open_access","relation":"main_file","creator":"system","file_id":"4694","file_name":"IST-2016-535-v1+1_2009-P-04-3ManifoldSegmentation.pdf","date_updated":"2020-07-14T12:46:21Z","content_type":"application/pdf","file_size":165090}],"doi":"10.1007/978-3-642-10470-1_4","day":"17","pubrep_id":"535","corr_author":"1","oa":1,"month":"11","department":[{"_id":"HeEd"}],"publisher":"Springer","alternative_title":["LNCS"],"date_published":"2009-11-17T00:00:00Z","file_date_updated":"2020-07-14T12:46:21Z","has_accepted_license":"1","conference":{"location":"Zermatt, Switzerland","name":"3DPH: Modelling the Physiological Human","end_date":"2009-12-02","start_date":"2009-11-29"},"fulldoi":"https://doi.org/10.1007/978-3-642-10470-1_4","ddc":["000"],"year":"2009","quality_controlled":"1","publication_status":"published","intvolume":"      5903"},{"isi":1,"volume":174,"doi":"10.1086/605958","day":"05","oa":1,"corr_author":"1","pubrep_id":"552","external_id":{"isi":["000271021900002"],"pmid":[" 19788353"]},"publisher":"University of Chicago Press","month":"11","department":[{"_id":"NiBa"}],"date_published":"2009-11-05T00:00:00Z","article_processing_charge":"No","fulldoi":"https://doi.org/10.1086/605958","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.1086/605958"}],"ddc":["570"],"publication_status":"published","pmid":1,"year":"2009","quality_controlled":"1","intvolume":"       174","publist_id":"1986","language":[{"iso":"eng"}],"publication":"American Naturalist","scopus_import":"1","issue":"5","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1086/659642"}]},"citation":{"short":"J. Polechova, N.H. Barton, G. Marion, American Naturalist 174 (2009) E186–E204.","ista":"Polechova J, Barton NH, Marion G. 2009. Species’ range: Adaptation in space and time. American Naturalist. 174(5), E186–E204.","ieee":"J. Polechova, N. H. Barton, and G. Marion, “Species’ range: Adaptation in space and time,” <i>American Naturalist</i>, vol. 174, no. 5. University of Chicago Press, pp. E186–E204, 2009.","mla":"Polechova, Jitka, et al. “Species’ Range: Adaptation in Space and Time.” <i>American Naturalist</i>, vol. 174, no. 5, University of Chicago Press, 2009, pp. E186–204, doi:<a href=\"https://doi.org/10.1086/605958\">10.1086/605958</a>.","ama":"Polechova J, Barton NH, Marion G. Species’ range: Adaptation in space and time. <i>American Naturalist</i>. 2009;174(5):E186-E204. doi:<a href=\"https://doi.org/10.1086/605958\">10.1086/605958</a>","apa":"Polechova, J., Barton, N. H., &#38; Marion, G. (2009). Species’ range: Adaptation in space and time. <i>American Naturalist</i>. University of Chicago Press. <a href=\"https://doi.org/10.1086/605958\">https://doi.org/10.1086/605958</a>","chicago":"Polechova, Jitka, Nicholas H Barton, and Glenn Marion. “Species’ Range: Adaptation in Space and Time.” <i>American Naturalist</i>. University of Chicago Press, 2009. <a href=\"https://doi.org/10.1086/605958\">https://doi.org/10.1086/605958</a>."},"page":"E186 - E204","date_updated":"2025-09-30T09:53:09Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","title":"Species' range: Adaptation in space and time","_id":"4136","date_created":"2018-12-11T12:07:09Z","status":"public","author":[{"full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","last_name":"Polechova","first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton"},{"full_name":"Marion, Glenn","first_name":"Glenn","last_name":"Marion"}],"type":"journal_article","oa_version":"Published Version","article_type":"original","abstract":[{"lang":"eng","text":"Populations living in a spatially and temporally changing environment can adapt to the changing optimum and/or migrate toward favorable habitats. Here we extend previous analyses with a static optimum to allow the environment to vary in time as well as in space. The model follows both population dynamics and the trait mean under stabilizing selection, and the outcomes can be understood by comparing the loads due to genetic variance, dispersal, and temporal change. With fixed genetic variance, we obtain two regimes: (1) adaptation that is uniform along the environmental gradient and that responds to the moving optimum as expected for panmictic populations and when the spatial gradient is sufficiently steep, and (2) a population with limited range that adapts more slowly than the environmental optimum changes in both time and space; the population therefore becomes locally extinct and migrates toward suitable habitat. We also use a population‐genetic model with many loci to allow genetic variance to evolve, and we show that the only solution now has uniform adaptation."}]},{"publisher":"Genetics Society of America","month":"03","department":[{"_id":"NiBa"}],"external_id":{"isi":["000270213500018"]},"corr_author":"1","day":"01","doi":"10.1534/genetics.108.099309","volume":181,"isi":1,"intvolume":"       181","publication_status":"published","year":"2009","quality_controlled":"1","fulldoi":"https://doi.org/10.1534/genetics.108.099309","article_processing_charge":"No","date_published":"2009-03-01T00:00:00Z","acknowledgement":"N.B. was supported by the Engineering and Physical Sciences Research Council (GR/T11753 and GR/T19537) and by the Royal Society.\r\nWe are grateful to Ellen Baake for helping to initiate this project and for her comments on this manuscript. We also thank Michael Turelli for his comments on the manuscript and I. Pen for discussions and support in this project. This project was a result of a collaboration supported by the European Science Foundation grant “Integrating population genetics and conservation biology.” ","scopus_import":"1","issue":"3","publication":"Genetics","language":[{"iso":"eng"}],"publist_id":"1882","abstract":[{"text":"The evolution of quantitative characters depends on the frequencies of the alleles involved, yet these frequencies cannot usually be measured. Previous groups have proposed an approximation to the dynamics of quantitative traits, based on an analogy with statistical mechanics. We present a modified version of that approach, which makes the analogy more precise and applies quite generally to describe the evolution of allele frequencies. We calculate explicitly how the macroscopic quantities (i.e., quantities that depend on the quantitative trait) depend on evolutionary forces, in a way that is independent of the microscopic details. We first show that the stationary distribution of allele frequencies under drift, selection, and mutation maximizes a certain measure of entropy, subject to constraints on the expectation of observable quantities. We then approximate the dynamical changes in these expectations, assuming that the distribution of allele frequencies always maximizes entropy, conditional on the expected values. When applied to directional selection on an additive trait, this gives a very good approximation to the evolution of the trait mean and the genetic variance, when the number of mutations per generation is sufficiently high (4Nμ &gt; 1). We show how the method can be modified for small mutation rates (4Nμ → 0). We outline how this method describes epistatic interactions as, for example, with stabilizing selection.","lang":"eng"}],"type":"journal_article","oa_version":"None","status":"public","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"full_name":"De Vladar, Harold","last_name":"De Vladar","first_name":"Harold"}],"date_created":"2018-12-11T12:07:44Z","title":"Statistical mechanics and the evolution of polygenic quantitative traits","_id":"4231","date_updated":"2025-09-30T09:52:35Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"ama":"Barton NH, De Vladar H. Statistical mechanics and the evolution of polygenic quantitative traits. <i>Genetics</i>. 2009;181(3):997-1011. doi:<a href=\"https://doi.org/10.1534/genetics.108.099309\">10.1534/genetics.108.099309</a>","mla":"Barton, Nicholas H., and Harold De Vladar. “Statistical Mechanics and the Evolution of Polygenic Quantitative Traits.” <i>Genetics</i>, vol. 181, no. 3, Genetics Society of America, 2009, pp. 997–1011, doi:<a href=\"https://doi.org/10.1534/genetics.108.099309\">10.1534/genetics.108.099309</a>.","short":"N.H. Barton, H. De Vladar, Genetics 181 (2009) 997–1011.","ista":"Barton NH, De Vladar H. 2009. Statistical mechanics and the evolution of polygenic quantitative traits. Genetics. 181(3), 997–1011.","ieee":"N. H. Barton and H. De Vladar, “Statistical mechanics and the evolution of polygenic quantitative traits,” <i>Genetics</i>, vol. 181, no. 3. Genetics Society of America, pp. 997–1011, 2009.","chicago":"Barton, Nicholas H, and Harold De Vladar. “Statistical Mechanics and the Evolution of Polygenic Quantitative Traits.” <i>Genetics</i>. Genetics Society of America, 2009. <a href=\"https://doi.org/10.1534/genetics.108.099309\">https://doi.org/10.1534/genetics.108.099309</a>.","apa":"Barton, N. H., &#38; De Vladar, H. (2009). Statistical mechanics and the evolution of polygenic quantitative traits. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.108.099309\">https://doi.org/10.1534/genetics.108.099309</a>"},"page":"997 - 1011"},{"year":"2009","quality_controlled":"1","publication_status":"published","intvolume":"        63","ddc":["570"],"fulldoi":"https://doi.org/10.1111/j.1558-5646.2009.00622.x","date_published":"2009-05-01T00:00:00Z","file_date_updated":"2020-07-14T12:46:25Z","has_accepted_license":"1","article_processing_charge":"No","external_id":{"isi":["000265145800006"]},"department":[{"_id":"NiBa"}],"month":"05","publisher":"Wiley","day":"01","pubrep_id":"551","corr_author":"1","oa":1,"volume":63,"file":[{"checksum":"1920d2e25ef335833764256c1a47bbfb","date_created":"2018-12-12T10:11:46Z","access_level":"open_access","relation":"main_file","creator":"system","file_id":"4903","file_name":"IST-2016-551-v1+1_BartonDeCaraRevNew.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:25Z","file_size":720913},{"file_id":"4904","file_name":"IST-2016-551-v1+2_BartonDeCaraRevNewSI.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:25Z","file_size":290160,"date_created":"2018-12-12T10:11:47Z","checksum":"c1c51bbc10d4f328fc96fc5b0e5dc25d","access_level":"open_access","relation":"main_file","creator":"system"}],"doi":"10.1111/j.1558-5646.2009.00622.x","isi":1,"type":"journal_article","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Felsenstein distinguished two ways by which selection can directly strengthen isolation. First, a modifier that strengthens prezygotic isolation can be favored everywhere. This fits with the traditional view of reinforcement as an adaptation to reduce deleterious hybridization by strengthening assortative mating. Second, selection can favor association between different incompatibilities, despite recombination. We generalize this “two allele” model to follow associations among any number of incompatibilities, which may include both assortment and hybrid inviability. Our key argument is that this process, of coupling between incompatibilities, may be quite different from the usual view of reinforcement: strong isolation can evolve through the coupling of any kind of incompatibility, whether prezygotic or postzygotic. Single locus incompatibilities become coupled because associations between them increase the variance in compatibility, which in turn increases mean fitness if there is positive epistasis. Multiple incompatibilities, each maintained by epistasis, can become coupled in the same way. In contrast, a single-locus incompatibility can become coupled with loci that reduce the viability of haploid hybrids because this reduces harmful recombination. We obtain simple approximations for the limits of tight linkage, and strong assortment, and show how assortment alleles can invade through associations with other components of reproductive isolation."}],"_id":"4242","title":"The evolution of strong reproductive isolation","date_created":"2018-12-11T12:07:48Z","author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria","last_name":"De Cara","full_name":"De Cara, Maria"}],"status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-30T09:52:11Z","page":"1171 - 1190","citation":{"mla":"Barton, Nicholas H., and Maria De Cara. “The Evolution of Strong Reproductive Isolation.” <i>Evolution; International Journal of Organic Evolution</i>, vol. 63, no. 5, Wiley, 2009, pp. 1171–90, doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">10.1111/j.1558-5646.2009.00622.x</a>.","ama":"Barton NH, De Cara M. The evolution of strong reproductive isolation. <i>Evolution; International Journal of Organic Evolution</i>. 2009;63(5):1171-1190. doi:<a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">10.1111/j.1558-5646.2009.00622.x</a>","ista":"Barton NH, De Cara M. 2009. The evolution of strong reproductive isolation. Evolution; International Journal of Organic Evolution. 63(5), 1171–1190.","ieee":"N. H. Barton and M. De Cara, “The evolution of strong reproductive isolation,” <i>Evolution; International Journal of Organic Evolution</i>, vol. 63, no. 5. Wiley, pp. 1171–1190, 2009.","short":"N.H. Barton, M. De Cara, Evolution; International Journal of Organic Evolution 63 (2009) 1171–1190.","chicago":"Barton, Nicholas H, and Maria De Cara. “The Evolution of Strong Reproductive Isolation.” <i>Evolution; International Journal of Organic Evolution</i>. Wiley, 2009. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">https://doi.org/10.1111/j.1558-5646.2009.00622.x</a>.","apa":"Barton, N. H., &#38; De Cara, M. (2009). The evolution of strong reproductive isolation. <i>Evolution; International Journal of Organic Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/j.1558-5646.2009.00622.x\">https://doi.org/10.1111/j.1558-5646.2009.00622.x</a>"},"acknowledgement":"This work was supported by a Royal Society/Wolfson Research Merit award, and by a grant from the Natural Environment Research Council.\r\nWe are very grateful for insightful comments from S. P. Otto, and for helpful suggestions from the referees and the Associate Editor, Maria Servedio.","publication":"Evolution; International Journal of Organic Evolution","issue":"5","scopus_import":"1","publist_id":"1866","language":[{"iso":"eng"}]},{"external_id":{"isi":["000272039900001"]},"publisher":"ACM","month":"10","department":[{"_id":"KrCh"}],"day":"01","corr_author":"1","oa":1,"pubrep_id":"53","volume":11,"doi":"10.1145/1614431.1614432","file":[{"checksum":"139c4586d24f11e5da31fb3a0cf96ef4","date_created":"2018-12-12T10:15:08Z","creator":"system","relation":"main_file","access_level":"open_access","file_id":"5125","file_size":180082,"file_name":"IST-2012-53-v1+1_Finitary_winning_in_omega-regular_games.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:46:20Z"}],"isi":1,"article_number":"1","publication_status":"published","quality_controlled":"1","year":"2009","intvolume":"        11","ddc":["004"],"das_tickbox":"1","fulldoi":"https://doi.org/10.1145/1614431.1614432","has_accepted_license":"1","file_date_updated":"2020-07-14T12:46:20Z","date_published":"2009-10-01T00:00:00Z","article_processing_charge":"No","ec_funded":1,"acknowledgement":"This research was supported in part by the AFOSR MURI grant F49620-00-1-0327, the NSF grants CCR-0132780, CNS-0720884, and CCR- 225610, by the Swiss National Science Foundation, by the COMBEST project of the European Union, and EU-TMR network Games.\r\nWe thank anonymous reviewers for useful comments.","publication":"ACM Transactions on Computational Logic","scopus_import":"1","issue":"1","publist_id":"2309","language":[{"iso":"eng"}],"oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"Games on graphs with omega-regular objectives provide a model for the control and synthesis of reactive systems. Every omega-regular objective 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. While for one-shot liveness (reachability) objectives, classical and finitary liveness coincide, for repeated liveness (Buchi) objectives, the finitary formulation is strictly stronger. In this work we study games with finitary parity and Streett objectives. We prove the determinacy of these games, present algorithms for solving these games, and characterize the memory requirements of winning strategies. We show that finitary parity games can be solved in polynomial time, which is not known for infinitary parity games. For finitary Streett games, we give an EXPTIME algorithm and show that the problem is NP-hard. Our algorithms can be used, for example, for synthesizing controllers that do not let the response time of a system increase without bound.","lang":"eng"}],"title":"Finitary winning in omega-regular games","_id":"3870","date_created":"2018-12-11T12:05:37Z","status":"public","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"},{"id":"37327ACE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Horn","full_name":"Horn, Florian"}],"date_updated":"2026-07-07T14:02:53Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Chatterjee K, Henzinger TA, Horn F. Finitary winning in omega-regular games. <i>ACM Transactions on Computational Logic</i>. 2009;11(1). doi:<a href=\"https://doi.org/10.1145/1614431.1614432\">10.1145/1614431.1614432</a>","mla":"Chatterjee, Krishnendu, et al. “Finitary Winning in Omega-Regular Games.” <i>ACM Transactions on Computational Logic</i>, vol. 11, no. 1, 1, ACM, 2009, doi:<a href=\"https://doi.org/10.1145/1614431.1614432\">10.1145/1614431.1614432</a>.","ista":"Chatterjee K, Henzinger TA, Horn F. 2009. Finitary winning in omega-regular games. ACM Transactions on Computational Logic. 11(1), 1.","short":"K. Chatterjee, T.A. Henzinger, F. Horn, ACM Transactions on Computational Logic 11 (2009).","ieee":"K. Chatterjee, T. A. Henzinger, and F. Horn, “Finitary winning in omega-regular games,” <i>ACM Transactions on Computational Logic</i>, vol. 11, no. 1. ACM, 2009.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “Finitary Winning in Omega-Regular Games.” <i>ACM Transactions on Computational Logic</i>. ACM, 2009. <a href=\"https://doi.org/10.1145/1614431.1614432\">https://doi.org/10.1145/1614431.1614432</a>.","apa":"Chatterjee, K., Henzinger, T. A., &#38; Horn, F. (2009). Finitary winning in omega-regular games. <i>ACM Transactions on Computational Logic</i>. ACM. <a href=\"https://doi.org/10.1145/1614431.1614432\">https://doi.org/10.1145/1614431.1614432</a>"},"project":[{"grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"}]},{"language":[{"iso":"eng"}],"publist_id":"7302","publication":"Genetics Research","issue":"5-6","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-04-29T07:15:43Z","citation":{"ista":"Barton NH. 2008. Identity and coalescence in structured populations: A commentary on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin. Genetics Research. 89(5–6), 475–477.","short":"N.H. Barton, Genetics Research 89 (2008) 475–477.","ieee":"N. H. Barton, “Identity and coalescence in structured populations: A commentary on ‘Inbreeding coefficients and coalescence times’ by Montgomery Slatkin,” <i>Genetics Research</i>, vol. 89, no. 5–6. Cambridge University Press, pp. 475–477, 2008.","ama":"Barton NH. Identity and coalescence in structured populations: A commentary on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. <i>Genetics Research</i>. 2008;89(5-6):475-477. doi:<a href=\"https://doi.org/10.1017/S0016672308009683\">10.1017/S0016672308009683</a>","mla":"Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.” <i>Genetics Research</i>, vol. 89, no. 5–6, Cambridge University Press, 2008, pp. 475–77, doi:<a href=\"https://doi.org/10.1017/S0016672308009683\">10.1017/S0016672308009683</a>.","apa":"Barton, N. H. (2008). Identity and coalescence in structured populations: A commentary on “Inbreeding coefficients and coalescence times” by Montgomery Slatkin. <i>Genetics Research</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/S0016672308009683\">https://doi.org/10.1017/S0016672308009683</a>","chicago":"Barton, Nicholas H. “Identity and Coalescence in Structured Populations: A Commentary on ‘Inbreeding Coefficients and Coalescence Times’ by Montgomery Slatkin.” <i>Genetics Research</i>. Cambridge University Press, 2008. <a href=\"https://doi.org/10.1017/S0016672308009683\">https://doi.org/10.1017/S0016672308009683</a>."},"page":"475 - 477","article_type":"comment","type":"journal_article","oa_version":"None","_id":"517","title":"Identity and coalescence in structured populations: A commentary on 'Inbreeding coefficients and coalescence times' by Montgomery Slatkin","date_created":"2018-12-11T11:46:55Z","author":[{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"status":"public","volume":89,"doi":"10.1017/S0016672308009683","isi":1,"external_id":{"isi":["000207048900023"]},"month":"10","department":[{"_id":"NiBa"}],"publisher":"Cambridge University Press","day":"29","fulldoi":"https://doi.org/10.1017/S0016672308009683","date_published":"2008-10-29T00:00:00Z","article_processing_charge":"No","quality_controlled":"1","year":"2008","publication_status":"published","intvolume":"        89"},{"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"issue":"7218","scopus_import":"1","publication":"Nature","language":[{"iso":"eng"}],"extern":"1","abstract":[{"lang":"eng","text":"Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation1–6. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development4,5, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer7. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation."}],"article_type":"letter_note","type":"journal_article","oa_version":"Submitted Version","date_created":"2021-06-04T11:49:32Z","status":"public","author":[{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman"},{"first_name":"Devin","last_name":"Coleman-Derr","full_name":"Coleman-Derr, Devin"},{"first_name":"Tracy","last_name":"Ballinger","full_name":"Ballinger, Tracy"},{"full_name":"Henikoff, Steven","last_name":"Henikoff","first_name":"Steven"}],"_id":"9457","title":"Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-12-14T08:54:36Z","page":"125-129","citation":{"chicago":"Zilberman, Daniel, Devin Coleman-Derr, Tracy Ballinger, and Steven Henikoff. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” <i>Nature</i>. Springer Nature, 2008. <a href=\"https://doi.org/10.1038/nature07324\">https://doi.org/10.1038/nature07324</a>.","apa":"Zilberman, D., Coleman-Derr, D., Ballinger, T., &#38; Henikoff, S. (2008). Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nature07324\">https://doi.org/10.1038/nature07324</a>","ama":"Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. <i>Nature</i>. 2008;456(7218):125-129. doi:<a href=\"https://doi.org/10.1038/nature07324\">10.1038/nature07324</a>","mla":"Zilberman, Daniel, et al. “Histone H2A.Z and DNA Methylation Are Mutually Antagonistic Chromatin Marks.” <i>Nature</i>, vol. 456, no. 7218, Springer Nature, 2008, pp. 125–29, doi:<a href=\"https://doi.org/10.1038/nature07324\">10.1038/nature07324</a>.","ieee":"D. Zilberman, D. Coleman-Derr, T. Ballinger, and S. Henikoff, “Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks,” <i>Nature</i>, vol. 456, no. 7218. Springer Nature, pp. 125–129, 2008.","ista":"Zilberman D, Coleman-Derr D, Ballinger T, Henikoff S. 2008. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature. 456(7218), 125–129.","short":"D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008) 125–129."},"month":"11","department":[{"_id":"DaZi"}],"publisher":"Springer Nature","external_id":{"pmid":["18815594"]},"oa":1,"day":"06","doi":"10.1038/nature07324","volume":456,"intvolume":"       456","pmid":1,"year":"2008","quality_controlled":"1","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877514/"}],"fulldoi":"https://doi.org/10.1038/nature07324","keyword":["Multidisciplinary"],"article_processing_charge":"No","date_published":"2008-11-06T00:00:00Z"},{"intvolume":"        11","pmid":1,"year":"2008","quality_controlled":"1","publication_status":"published","article_processing_charge":"No","date_published":"2008-10-01T00:00:00Z","fulldoi":"https://doi.org/10.1016/j.pbi.2008.07.004","month":"10","department":[{"_id":"DaZi"}],"publisher":"Elsevier ","external_id":{"pmid":["18774331"]},"doi":"10.1016/j.pbi.2008.07.004","volume":11,"author":[{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel"}],"date_created":"2021-06-08T13:13:37Z","status":"public","_id":"9537","title":"The evolving functions of DNA methylation","abstract":[{"text":"DNA methylation is an ancient process found in all domains of life. Although the enzymes that mediate methylation have remained highly conserved, DNA methylation has been adapted for a variety of uses throughout evolution, including defense against transposable elements and control of gene expression. Defects in DNA methylation are linked to human diseases, including cancer. Methylation has been lost several times in the course of animal and fungal evolution, thus limiting the opportunity for study in common model organisms. In the past decade, plants have emerged as a premier model system for genetic dissection of DNA methylation. A recent combination of plant genetics with powerful genomic approaches has led to a number of exciting discoveries and promises many more.","lang":"eng"}],"extern":"1","article_type":"review","type":"journal_article","oa_version":"None","citation":{"ama":"Zilberman D. The evolving functions of DNA methylation. <i>Current Opinion in Plant Biology</i>. 2008;11(5):554-559. doi:<a href=\"https://doi.org/10.1016/j.pbi.2008.07.004\">10.1016/j.pbi.2008.07.004</a>","mla":"Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” <i>Current Opinion in Plant Biology</i>, vol. 11, no. 5, Elsevier , 2008, pp. 554–59, doi:<a href=\"https://doi.org/10.1016/j.pbi.2008.07.004\">10.1016/j.pbi.2008.07.004</a>.","ieee":"D. Zilberman, “The evolving functions of DNA methylation,” <i>Current Opinion in Plant Biology</i>, vol. 11, no. 5. Elsevier , pp. 554–559, 2008.","short":"D. Zilberman, Current Opinion in Plant Biology 11 (2008) 554–559.","ista":"Zilberman D. 2008. The evolving functions of DNA methylation. Current Opinion in Plant Biology. 11(5), 554–559.","chicago":"Zilberman, Daniel. “The Evolving Functions of DNA Methylation.” <i>Current Opinion in Plant Biology</i>. Elsevier , 2008. <a href=\"https://doi.org/10.1016/j.pbi.2008.07.004\">https://doi.org/10.1016/j.pbi.2008.07.004</a>.","apa":"Zilberman, D. (2008). The evolving functions of DNA methylation. <i>Current Opinion in Plant Biology</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.pbi.2008.07.004\">https://doi.org/10.1016/j.pbi.2008.07.004</a>"},"page":"554-559","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-12-14T08:54:07Z","issue":"5","scopus_import":"1","publication":"Current Opinion in Plant Biology","publication_identifier":{"issn":["1369-5266"]},"language":[{"iso":"eng"}]},{"intvolume":"        23","publication_status":"published","pmid":1,"quality_controlled":"1","year":"2007","fulldoi":"https://doi.org/10.1016/j.tig.2007.08.005","article_processing_charge":"No","keyword":["Genetics"],"date_published":"2007-10-01T00:00:00Z","publisher":"Elsevier BV","department":[{"_id":"XiFe"}],"month":"10","external_id":{"pmid":["17825943"]},"doi":"10.1016/j.tig.2007.08.005","volume":23,"abstract":[{"lang":"eng","text":"The development of plant lateral organs is interesting because, although many of the same genes seem to be involved in the early growth of primordia, completely different gene combinations are required for the complete development of organs such as leaves and stamens. Thus, the genes common to the development of most organs, which generally form and polarize the primordial ‘envelope’, must at some stage interact with those that ‘install’ the functional content of the organ – in the case of the stamen, the four microsporangia. Although distinct genetic pathways of organ initiation, polarity establishment and setting up the reproductive cell line can readily be recognized, they do not occur sequentially. Rather, they are activated early and run in parallel. There is evidence for continuing crosstalk between these pathways."}],"extern":"1","type":"journal_article","oa_version":"None","article_type":"original","status":"public","author":[{"orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","last_name":"Feng","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"first_name":"Hugh G.","last_name":"Dickinson","full_name":"Dickinson, Hugh G."}],"date_created":"2023-01-16T09:22:44Z","title":"Packaging the male germline in plants","_id":"12201","date_updated":"2023-05-08T10:58:47Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.” <i>Trends in Genetics</i>, vol. 23, no. 10, Elsevier BV, 2007, pp. 503–10, doi:<a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">10.1016/j.tig.2007.08.005</a>.","ama":"Feng X, Dickinson HG. Packaging the male germline in plants. <i>Trends in Genetics</i>. 2007;23(10):503-510. doi:<a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">10.1016/j.tig.2007.08.005</a>","ista":"Feng X, Dickinson HG. 2007. Packaging the male germline in plants. Trends in Genetics. 23(10), 503–510.","short":"X. Feng, H.G. Dickinson, Trends in Genetics 23 (2007) 503–510.","ieee":"X. Feng and H. G. Dickinson, “Packaging the male germline in plants,” <i>Trends in Genetics</i>, vol. 23, no. 10. Elsevier BV, pp. 503–510, 2007.","chicago":"Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.” <i>Trends in Genetics</i>. Elsevier BV, 2007. <a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">https://doi.org/10.1016/j.tig.2007.08.005</a>.","apa":"Feng, X., &#38; Dickinson, H. G. (2007). Packaging the male germline in plants. <i>Trends in Genetics</i>. Elsevier BV. <a href=\"https://doi.org/10.1016/j.tig.2007.08.005\">https://doi.org/10.1016/j.tig.2007.08.005</a>"},"page":"503-510","publication_identifier":{"issn":["0168-9525"]},"acknowledgement":"X.F. holds a Clarendon Scholarship from the University of Oxford. We thank Angela Hay and Jill Harrison for helpful advice and discussion.","scopus_import":"1","issue":"10","publication":"Trends in Genetics","language":[{"iso":"eng"}]},{"quality_controlled":"1","year":"2007","pmid":1,"publication_status":"published","intvolume":"       104","date_published":"2007-04-17T00:00:00Z","article_processing_charge":"No","fulldoi":"https://doi.org/10.1073/pnas.0701861104","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.0701861104"}],"day":"17","oa":1,"external_id":{"pmid":["17409185"]},"department":[{"_id":"DaZi"}],"month":"04","publisher":"National Academy of Sciences","volume":104,"doi":"10.1073/pnas.0701861104","_id":"9487","title":"DNA demethylation in the Arabidopsis genome","author":[{"full_name":"Penterman, Jon","last_name":"Penterman","first_name":"Jon"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"},{"last_name":"Huh","first_name":"Jin Hoe","full_name":"Huh, Jin Hoe"},{"full_name":"Ballinger, Tracy","first_name":"Tracy","last_name":"Ballinger"},{"full_name":"Henikoff, Steven","first_name":"Steven","last_name":"Henikoff"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."}],"date_created":"2021-06-07T09:38:21Z","status":"public","article_type":"original","type":"journal_article","oa_version":"Published Version","abstract":[{"text":"Cytosine DNA methylation is considered to be a stable epigenetic mark, but active demethylation has been observed in both plants and animals. In Arabidopsis thaliana, DNA glycosylases of the DEMETER (DME) family remove methylcytosines from DNA. Demethylation by DME is necessary for genomic imprinting, and demethylation by a related protein, REPRESSOR OF SILENCING1, prevents gene silencing in a transgenic background. However, the extent and function of demethylation by DEMETER-LIKE (DML) proteins in WT plants is not known. Using genome-tiling microarrays, we mapped DNA methylation in mutant and WT plants and identified 179 loci actively demethylated by DML enzymes. Mutations in DML genes lead to locus-specific DNA hypermethylation. Reintroducing WT DML genes restores most loci to the normal pattern of methylation, although at some loci, hypermethylated epialleles persist. Of loci demethylated by DML enzymes, >80% are near or overlap genes. Genic demethylation by DML enzymes primarily occurs at the 5′ and 3′ ends, a pattern opposite to the overall distribution of WT DNA methylation. Our results show that demethylation by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis genome to protect genes from potentially deleterious methylation.","lang":"eng"}],"extern":"1","citation":{"short":"J. Penterman, D. Zilberman, J.H. Huh, T. Ballinger, S. Henikoff, R.L. Fischer, Proceedings of the National Academy of Sciences 104 (2007) 6752–6757.","ista":"Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. 2007. DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy of Sciences. 104(16), 6752–6757.","ieee":"J. Penterman, D. Zilberman, J. H. Huh, T. Ballinger, S. Henikoff, and R. L. Fischer, “DNA demethylation in the Arabidopsis genome,” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 16. National Academy of Sciences, pp. 6752–6757, 2007.","mla":"Penterman, Jon, et al. “DNA Demethylation in the Arabidopsis Genome.” <i>Proceedings of the National Academy of Sciences</i>, vol. 104, no. 16, National Academy of Sciences, 2007, pp. 6752–57, doi:<a href=\"https://doi.org/10.1073/pnas.0701861104\">10.1073/pnas.0701861104</a>.","ama":"Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. DNA demethylation in the Arabidopsis genome. <i>Proceedings of the National Academy of Sciences</i>. 2007;104(16):6752-6757. doi:<a href=\"https://doi.org/10.1073/pnas.0701861104\">10.1073/pnas.0701861104</a>","apa":"Penterman, J., Zilberman, D., Huh, J. H., Ballinger, T., Henikoff, S., &#38; Fischer, R. L. (2007). DNA demethylation in the Arabidopsis genome. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0701861104\">https://doi.org/10.1073/pnas.0701861104</a>","chicago":"Penterman, Jon, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven Henikoff, and Robert L. Fischer. “DNA Demethylation in the Arabidopsis Genome.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2007. <a href=\"https://doi.org/10.1073/pnas.0701861104\">https://doi.org/10.1073/pnas.0701861104</a>."},"page":"6752-6757","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-12-14T08:55:12Z","publication":"Proceedings of the National Academy of Sciences","issue":"16","scopus_import":"1","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"publication":"Nature Genetics","issue":"4","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2021-12-14T08:55:46Z","page":"442-443","citation":{"ista":"Zilberman D. 2007. The human promoter methylome, Nature Publishing Group,p.","ieee":"D. Zilberman, <i>The human promoter methylome</i>, vol. 39, no. 4. Nature Publishing Group, 2007, pp. 442–443.","short":"D. Zilberman, The Human Promoter Methylome, Nature Publishing Group, 2007.","mla":"Zilberman, Daniel. “The Human Promoter Methylome.” <i>Nature Genetics</i>, vol. 39, no. 4, Nature Publishing Group, 2007, pp. 442–43, doi:<a href=\"https://doi.org/10.1038/ng0407-442\">10.1038/ng0407-442</a>.","ama":"Zilberman D. <i>The Human Promoter Methylome</i>. Vol 39. Nature Publishing Group; 2007:442-443. doi:<a href=\"https://doi.org/10.1038/ng0407-442\">10.1038/ng0407-442</a>","apa":"Zilberman, D. (2007). <i>The human promoter methylome</i>. <i>Nature Genetics</i> (Vol. 39, pp. 442–443). Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng0407-442\">https://doi.org/10.1038/ng0407-442</a>","chicago":"Zilberman, Daniel. <i>The Human Promoter Methylome</i>. <i>Nature Genetics</i>. Vol. 39. Nature Publishing Group, 2007. <a href=\"https://doi.org/10.1038/ng0407-442\">https://doi.org/10.1038/ng0407-442</a>."},"type":"other_academic_publication","oa_version":"None","extern":"1","_id":"9504","title":"The human promoter methylome","date_created":"2021-06-07T12:08:24Z","author":[{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"status":"public","volume":39,"doi":"10.1038/ng0407-442","external_id":{"pmid":["17392803"]},"month":"04","department":[{"_id":"DaZi"}],"publisher":"Nature Publishing Group","day":"01","fulldoi":"https://doi.org/10.1038/ng0407-442","date_published":"2007-04-01T00:00:00Z","article_processing_charge":"No","year":"2007","quality_controlled":"1","pmid":1,"publication_status":"published","intvolume":"        39"},{"doi":"10.1242/dev.001131","volume":134,"publisher":"The Company of Biologists","department":[{"_id":"DaZi"}],"month":"11","external_id":{"pmid":["17928417"]},"oa":1,"day":"15","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/dev.001131"}],"fulldoi":"https://doi.org/10.1242/dev.001131","article_processing_charge":"No","date_published":"2007-11-15T00:00:00Z","intvolume":"       134","publication_status":"published","pmid":1,"year":"2007","quality_controlled":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"scopus_import":"1","issue":"22","publication":"Development","date_updated":"2021-12-14T08:57:58Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Zilberman, D., &#38; Henikoff, S. (2007). Genome-wide analysis of DNA methylation patterns. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.001131\">https://doi.org/10.1242/dev.001131</a>","chicago":"Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation Patterns.” <i>Development</i>. The Company of Biologists, 2007. <a href=\"https://doi.org/10.1242/dev.001131\">https://doi.org/10.1242/dev.001131</a>.","short":"D. Zilberman, S. Henikoff, Development 134 (2007) 3959–3965.","ieee":"D. Zilberman and S. Henikoff, “Genome-wide analysis of DNA methylation patterns,” <i>Development</i>, vol. 134, no. 22. The Company of Biologists, pp. 3959–3965, 2007.","ista":"Zilberman D, Henikoff S. 2007. Genome-wide analysis of DNA methylation patterns. Development. 134(22), 3959–3965.","mla":"Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation Patterns.” <i>Development</i>, vol. 134, no. 22, The Company of Biologists, 2007, pp. 3959–65, doi:<a href=\"https://doi.org/10.1242/dev.001131\">10.1242/dev.001131</a>.","ama":"Zilberman D, Henikoff S. Genome-wide analysis of DNA methylation patterns. <i>Development</i>. 2007;134(22):3959-3965. doi:<a href=\"https://doi.org/10.1242/dev.001131\">10.1242/dev.001131</a>"},"page":"3959-3965","extern":"1","abstract":[{"text":"Cytosine methylation is the most common covalent modification of DNA in eukaryotes. DNA methylation has an important role in many aspects of biology, including development and disease. Methylation can be detected using bisulfite conversion, methylation-sensitive restriction enzymes, methyl-binding proteins and anti-methylcytosine antibodies. Combining these techniques with DNA microarrays and high-throughput sequencing has made the mapping of DNA methylation feasible on a genome-wide scale. Here we discuss recent developments and future directions for identifying and mapping methylation, in an effort to help colleagues to identify the approaches that best serve their research interests.","lang":"eng"}],"oa_version":"Published Version","type":"journal_article","article_type":"review","author":[{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"first_name":"Steven","last_name":"Henikoff","full_name":"Henikoff, Steven"}],"status":"public","date_created":"2021-06-08T06:29:50Z","title":"Genome-wide analysis of DNA methylation patterns","_id":"9524"}]