[{"status":"public","date_created":"2018-12-11T12:06:10Z","publisher":"Springer","volume":5903,"ddc":["000"],"language":[{"iso":"eng"}],"day":"17","scopus_import":1,"conference":{"start_date":"2009-11-29","location":"Zermatt, Switzerland","name":"3DPH: Modelling the Physiological Human","end_date":"2009-12-02"},"pubrep_id":"535","corr_author":"1","file":[{"creator":"system","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:46:21Z","checksum":"11fc85bcc19bab1f020e706a4b8a4660","relation":"main_file","date_created":"2018-12-12T10:08:33Z","file_id":"4694","file_size":165090,"file_name":"IST-2016-535-v1+1_2009-P-04-3ManifoldSegmentation.pdf"}],"department":[{"_id":"HeEd"}],"citation":{"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>.","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.","short":"H. Edelsbrunner, J. Harer, in:, Springer, 2009, pp. 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.","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>"},"intvolume":"      5903","alternative_title":["LNCS"],"file_date_updated":"2020-07-14T12:46:21Z","title":"The persistent Morse complex segmentation of a 3-manifold","date_updated":"2024-10-09T20:53:56Z","doi":"10.1007/978-3-642-10470-1_4","publication_status":"published","month":"11","oa_version":"Submitted Version","type":"conference","quality_controlled":"1","date_published":"2009-11-17T00:00:00Z","has_accepted_license":"1","_id":"3968","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2009","publist_id":"2160","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.","oa":1,"page":"36 - 50","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Harer, John","last_name":"Harer","first_name":"John"}],"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"}]},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"4136","date_published":"2009-11-05T00:00:00Z","type":"journal_article","quality_controlled":"1","oa_version":"Published Version","publication_status":"published","month":"11","author":[{"id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","last_name":"Polechova","first_name":"Jitka","full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"last_name":"Marion","first_name":"Glenn","full_name":"Marion, Glenn"}],"page":"E186 - E204","abstract":[{"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.","lang":"eng"}],"issue":"5","publist_id":"1986","year":"2009","oa":1,"isi":1,"main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.1086/605958"}],"article_processing_charge":"No","scopus_import":"1","pmid":1,"article_type":"original","language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1086/659642"}]},"day":"05","ddc":["570"],"publisher":"University of Chicago Press","volume":174,"status":"public","date_created":"2018-12-11T12:07:09Z","doi":"10.1086/605958","date_updated":"2025-09-30T09:53:09Z","title":"Species' range: Adaptation in space and time","intvolume":"       174","external_id":{"pmid":[" 19788353"],"isi":["000271021900002"]},"publication":"American Naturalist","department":[{"_id":"NiBa"}],"citation":{"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>","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>.","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>","ista":"Polechova J, Barton NH, Marion G. 2009. Species’ range: Adaptation in space and time. American Naturalist. 174(5), E186–E204.","short":"J. Polechova, N.H. Barton, G. Marion, American Naturalist 174 (2009) E186–E204.","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>.","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."},"pubrep_id":"552","corr_author":"1"},{"oa_version":"None","publication_status":"published","month":"03","quality_controlled":"1","type":"journal_article","_id":"4231","date_published":"2009-03-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_processing_charge":"No","isi":1,"publist_id":"1882","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.” ","year":"2009","issue":"3","abstract":[{"lang":"eng","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."}],"author":[{"full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"Harold","last_name":"De Vladar","full_name":"De Vladar, Harold"}],"page":"997 - 1011","date_created":"2018-12-11T12:07:44Z","status":"public","volume":181,"publisher":"Genetics Society of America","language":[{"iso":"eng"}],"day":"01","scopus_import":"1","corr_author":"1","citation":{"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.","ista":"Barton NH, De Vladar H. 2009. Statistical mechanics and the evolution of polygenic quantitative traits. Genetics. 181(3), 997–1011.","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>.","short":"N.H. Barton, H. De Vladar, Genetics 181 (2009) 997–1011.","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>.","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>","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>"},"department":[{"_id":"NiBa"}],"publication":"Genetics","intvolume":"       181","external_id":{"isi":["000270213500018"]},"doi":"10.1534/genetics.108.099309","title":"Statistical mechanics and the evolution of polygenic quantitative traits","date_updated":"2025-09-30T09:52:35Z"},{"file":[{"content_type":"application/pdf","access_level":"open_access","creator":"system","date_updated":"2020-07-14T12:46:25Z","checksum":"1920d2e25ef335833764256c1a47bbfb","date_created":"2018-12-12T10:11:46Z","relation":"main_file","file_name":"IST-2016-551-v1+1_BartonDeCaraRevNew.pdf","file_id":"4903","file_size":720913},{"file_id":"4904","file_size":290160,"file_name":"IST-2016-551-v1+2_BartonDeCaraRevNewSI.pdf","relation":"main_file","date_created":"2018-12-12T10:11:47Z","checksum":"c1c51bbc10d4f328fc96fc5b0e5dc25d","date_updated":"2020-07-14T12:46:25Z","creator":"system","access_level":"open_access","content_type":"application/pdf"}],"corr_author":"1","pubrep_id":"551","citation":{"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.","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>.","short":"N.H. Barton, M. De Cara, Evolution; International Journal of Organic Evolution 63 (2009) 1171–1190.","ista":"Barton NH, De Cara M. 2009. The evolution of strong reproductive isolation. Evolution; International Journal of Organic Evolution. 63(5), 1171–1190.","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>","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>"},"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:46:25Z","publication":"Evolution; International Journal of Organic Evolution","intvolume":"        63","external_id":{"isi":["000265145800006"]},"doi":"10.1111/j.1558-5646.2009.00622.x","date_updated":"2025-09-30T09:52:11Z","title":"The evolution of strong reproductive isolation","date_created":"2018-12-11T12:07:48Z","status":"public","volume":63,"publisher":"Wiley","language":[{"iso":"eng"}],"day":"01","ddc":["570"],"scopus_import":"1","article_processing_charge":"No","isi":1,"oa":1,"publist_id":"1866","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.","year":"2009","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."}],"issue":"5","author":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"},{"first_name":"Maria","last_name":"De Cara","full_name":"De Cara, Maria"}],"page":"1171 - 1190","oa_version":"Submitted Version","month":"05","publication_status":"published","quality_controlled":"1","type":"journal_article","has_accepted_license":"1","_id":"4242","date_published":"2009-05-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"date_created":"2021-06-04T08:55:41Z","status":"public","volume":324,"extern":"1","publisher":"American Association for the Advancement of Science","language":[{"iso":"eng"}],"day":"12","article_type":"original","pmid":1,"scopus_import":"1","citation":{"ama":"Hsieh T-F, Ibarra CA, Silva P, et al. Genome-wide demethylation of Arabidopsis endosperm. <i>Science</i>. 2009;324(5933):1451-1454. doi:<a href=\"https://doi.org/10.1126/science.1172417\">10.1126/science.1172417</a>","mla":"Hsieh, Tzung-Fu, et al. “Genome-Wide Demethylation of Arabidopsis Endosperm.” <i>Science</i>, vol. 324, no. 5933, American Association for the Advancement of Science, 2009, pp. 1451–54, doi:<a href=\"https://doi.org/10.1126/science.1172417\">10.1126/science.1172417</a>.","apa":"Hsieh, T.-F., Ibarra, C. A., Silva, P., Zemach, A., Eshed-Williams, L., Fischer, R. L., &#38; Zilberman, D. (2009). Genome-wide demethylation of Arabidopsis endosperm. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1172417\">https://doi.org/10.1126/science.1172417</a>","short":"T.-F. Hsieh, C.A. Ibarra, P. Silva, A. Zemach, L. Eshed-Williams, R.L. Fischer, D. Zilberman, Science 324 (2009) 1451–1454.","chicago":"Hsieh, Tzung-Fu, Christian A. Ibarra, Pedro Silva, Assaf Zemach, Leor Eshed-Williams, Robert L. Fischer, and Daniel Zilberman. “Genome-Wide Demethylation of Arabidopsis Endosperm.” <i>Science</i>. American Association for the Advancement of Science, 2009. <a href=\"https://doi.org/10.1126/science.1172417\">https://doi.org/10.1126/science.1172417</a>.","ista":"Hsieh T-F, Ibarra CA, Silva P, Zemach A, Eshed-Williams L, Fischer RL, Zilberman D. 2009. Genome-wide demethylation of Arabidopsis endosperm. Science. 324(5933), 1451–1454.","ieee":"T.-F. Hsieh <i>et al.</i>, “Genome-wide demethylation of Arabidopsis endosperm,” <i>Science</i>, vol. 324, no. 5933. American Association for the Advancement of Science, pp. 1451–1454, 2009."},"department":[{"_id":"DaZi"}],"publication":"Science","external_id":{"pmid":["19520962"]},"intvolume":"       324","title":"Genome-wide demethylation of Arabidopsis endosperm","date_updated":"2021-12-14T08:53:26Z","doi":"10.1126/science.1172417","publication_status":"published","month":"06","oa_version":"Submitted Version","quality_controlled":"1","type":"journal_article","date_published":"2009-06-12T00:00:00Z","_id":"9453","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4044190/"}],"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"oa":1,"year":"2009","keyword":["Multidisciplinary"],"abstract":[{"text":"Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here, we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo.","lang":"eng"}],"issue":"5933","author":[{"full_name":"Hsieh, Tzung-Fu","last_name":"Hsieh","first_name":"Tzung-Fu"},{"full_name":"Ibarra, Christian A.","first_name":"Christian A.","last_name":"Ibarra"},{"full_name":"Silva, Pedro","first_name":"Pedro","last_name":"Silva"},{"first_name":"Assaf","last_name":"Zemach","full_name":"Zemach, Assaf"},{"full_name":"Eshed-Williams, Leor","last_name":"Eshed-Williams","first_name":"Leor"},{"last_name":"Fischer","first_name":"Robert L.","full_name":"Fischer, Robert L."},{"last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"page":"1451-1454"},{"oa":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.","publist_id":"2309","year":"2009","abstract":[{"lang":"eng","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."}],"issue":"1","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"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":"Horn, Florian","first_name":"Florian","last_name":"Horn","id":"37327ACE-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","isi":1,"has_accepted_license":"1","_id":"3870","date_published":"2009-10-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","month":"10","publication_status":"published","quality_controlled":"1","type":"journal_article","file_date_updated":"2020-07-14T12:46:20Z","publication":"ACM Transactions on Computational Logic","intvolume":"        11","external_id":{"isi":["000272039900001"]},"das_tickbox":"1","doi":"10.1145/1614431.1614432","title":"Finitary winning in omega-regular games","date_updated":"2026-07-07T14:02:53Z","file":[{"file_name":"IST-2012-53-v1+1_Finitary_winning_in_omega-regular_games.pdf","file_id":"5125","file_size":180082,"checksum":"139c4586d24f11e5da31fb3a0cf96ef4","date_created":"2018-12-12T10:15:08Z","relation":"main_file","date_updated":"2020-07-14T12:46:20Z","content_type":"application/pdf","creator":"system","access_level":"open_access"}],"pubrep_id":"53","corr_author":"1","citation":{"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>","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>.","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>","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>.","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)."},"project":[{"_id":"25EFB36C-B435-11E9-9278-68D0E5697425","name":"COMponent-Based Embedded Systems design Techniques","call_identifier":"FP7","grant_number":"215543"}],"ec_funded":1,"department":[{"_id":"KrCh"}],"day":"01","language":[{"iso":"eng"}],"article_number":"1","ddc":["004"],"scopus_import":"1","date_created":"2018-12-11T12:05:37Z","status":"public","volume":11,"publisher":"ACM"},{"author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"page":"475 - 477","issue":"5-6","publist_id":"7302","year":"2008","isi":1,"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"517","date_published":"2008-10-29T00:00:00Z","type":"journal_article","quality_controlled":"1","oa_version":"None","publication_status":"published","month":"10","doi":"10.1017/S0016672308009683","date_updated":"2026-04-29T07:15:43Z","title":"Identity and coalescence in structured populations: A commentary on 'Inbreeding coefficients and coalescence times' by Montgomery Slatkin","intvolume":"        89","external_id":{"isi":["000207048900023"]},"publication":"Genetics Research","department":[{"_id":"NiBa"}],"citation":{"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.","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>.","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.","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>","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>.","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>"},"scopus_import":"1","article_type":"comment","day":"29","language":[{"iso":"eng"}],"publisher":"Cambridge University Press","volume":89,"status":"public","date_created":"2018-12-11T11:46:55Z"},{"external_id":{"pmid":["18815594"]},"intvolume":"       456","publication":"Nature","date_updated":"2021-12-14T08:54:36Z","title":"Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks","doi":"10.1038/nature07324","department":[{"_id":"DaZi"}],"citation":{"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.","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>.","short":"D. Zilberman, D. Coleman-Derr, T. Ballinger, S. Henikoff, Nature 456 (2008) 125–129.","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.","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>","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>.","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>"},"article_type":"letter_note","language":[{"iso":"eng"}],"day":"06","scopus_import":"1","pmid":1,"status":"public","date_created":"2021-06-04T11:49:32Z","extern":"1","publisher":"Springer Nature","volume":456,"year":"2008","keyword":["Multidisciplinary"],"oa":1,"author":[{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"},{"full_name":"Coleman-Derr, Devin","last_name":"Coleman-Derr","first_name":"Devin"},{"full_name":"Ballinger, Tracy","first_name":"Tracy","last_name":"Ballinger"},{"full_name":"Henikoff, Steven","last_name":"Henikoff","first_name":"Steven"}],"page":"125-129","issue":"7218","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."}],"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877514/","open_access":"1"}],"article_processing_charge":"No","publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"date_published":"2008-11-06T00:00:00Z","_id":"9457","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"11","publication_status":"published","oa_version":"Submitted Version","type":"journal_article","quality_controlled":"1"},{"author":[{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"page":"554-559","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"}],"issue":"5","year":"2008","publication_identifier":{"issn":["1369-5266"]},"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9537","date_published":"2008-10-01T00:00:00Z","type":"journal_article","quality_controlled":"1","oa_version":"None","month":"10","publication_status":"published","doi":"10.1016/j.pbi.2008.07.004","title":"The evolving functions of DNA methylation","date_updated":"2021-12-14T08:54:07Z","intvolume":"        11","external_id":{"pmid":["18774331"]},"publication":"Current Opinion in Plant Biology","department":[{"_id":"DaZi"}],"citation":{"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>","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>.","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>.","short":"D. Zilberman, Current Opinion in Plant Biology 11 (2008) 554–559.","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."},"scopus_import":"1","pmid":1,"article_type":"review","language":[{"iso":"eng"}],"publisher":"Elsevier ","extern":"1","volume":11,"status":"public","date_created":"2021-06-08T13:13:37Z"},{"publication_identifier":{"issn":["0168-9525"]},"article_processing_charge":"No","issue":"10","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."}],"author":[{"full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"first_name":"Hugh G.","last_name":"Dickinson","full_name":"Dickinson, Hugh G."}],"page":"503-510","year":"2007","acknowledgement":"X.F. holds a Clarendon Scholarship from the University of Oxford. We thank Angela Hay and Jill Harrison for helpful advice and discussion.","keyword":["Genetics"],"quality_controlled":"1","type":"journal_article","month":"10","publication_status":"published","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2007-10-01T00:00:00Z","_id":"12201","citation":{"ista":"Feng X, Dickinson HG. 2007. Packaging the male germline in plants. Trends in Genetics. 23(10), 503–510.","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>.","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.","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>","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>.","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>"},"department":[{"_id":"XiFe"}],"title":"Packaging the male germline in plants","date_updated":"2023-05-08T10:58:47Z","doi":"10.1016/j.tig.2007.08.005","publication":"Trends in Genetics","external_id":{"pmid":["17825943"]},"intvolume":"        23","volume":23,"publisher":"Elsevier BV","extern":"1","date_created":"2023-01-16T09:22:44Z","status":"public","pmid":1,"scopus_import":"1","language":[{"iso":"eng"}],"article_type":"original"},{"department":[{"_id":"DaZi"}],"citation":{"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>","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>.","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>","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.","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>.","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."},"doi":"10.1073/pnas.0701861104","title":"DNA demethylation in the Arabidopsis genome","date_updated":"2021-12-14T08:55:12Z","intvolume":"       104","external_id":{"pmid":["17409185"]},"publication":"Proceedings of the National Academy of Sciences","publisher":"National Academy of Sciences","extern":"1","volume":104,"status":"public","date_created":"2021-06-07T09:38:21Z","scopus_import":"1","pmid":1,"article_type":"original","language":[{"iso":"eng"}],"day":"17","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.0701861104"}],"article_processing_charge":"No","page":"6752-6757","author":[{"last_name":"Penterman","first_name":"Jon","full_name":"Penterman, Jon"},{"first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"},{"last_name":"Huh","first_name":"Jin Hoe","full_name":"Huh, Jin Hoe"},{"last_name":"Ballinger","first_name":"Tracy","full_name":"Ballinger, Tracy"},{"last_name":"Henikoff","first_name":"Steven","full_name":"Henikoff, Steven"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."}],"issue":"16","abstract":[{"lang":"eng","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."}],"year":"2007","oa":1,"type":"journal_article","quality_controlled":"1","oa_version":"Published Version","publication_status":"published","month":"04","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9487","date_published":"2007-04-17T00:00:00Z"},{"type":"other_academic_publication","extern":"1","publisher":"Nature Publishing Group","quality_controlled":"1","volume":39,"oa_version":"None","publication_status":"published","status":"public","month":"04","date_created":"2021-06-07T12:08:24Z","pmid":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9504","date_published":"2007-04-01T00:00:00Z","day":"01","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"department":[{"_id":"DaZi"}],"citation":{"ieee":"D. Zilberman, <i>The human promoter methylome</i>, vol. 39, no. 4. Nature Publishing Group, 2007, pp. 442–443.","ista":"Zilberman D. 2007. The human promoter methylome, Nature Publishing Group,p.","short":"D. Zilberman, The Human Promoter Methylome, Nature Publishing Group, 2007.","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>.","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>"},"article_processing_charge":"No","doi":"10.1038/ng0407-442","author":[{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman"}],"title":"The human promoter methylome","page":"442-443","date_updated":"2021-12-14T08:55:46Z","issue":"4","intvolume":"        39","external_id":{"pmid":["17392803"]},"year":"2007","publication":"Nature Genetics"},{"status":"public","date_created":"2021-06-08T06:29:50Z","publisher":"The Company of Biologists","extern":"1","volume":134,"article_type":"review","language":[{"iso":"eng"}],"day":"15","scopus_import":"1","pmid":1,"department":[{"_id":"DaZi"}],"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>","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>","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.","short":"D. Zilberman, S. Henikoff, Development 134 (2007) 3959–3965.","ista":"Zilberman D, Henikoff S. 2007. Genome-wide analysis of DNA methylation patterns. Development. 134(22), 3959–3965.","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>."},"external_id":{"pmid":["17928417"]},"intvolume":"       134","publication":"Development","date_updated":"2021-12-14T08:57:58Z","title":"Genome-wide analysis of DNA methylation patterns","doi":"10.1242/dev.001131","publication_status":"published","month":"11","oa_version":"Published Version","type":"journal_article","quality_controlled":"1","date_published":"2007-11-15T00:00:00Z","_id":"9524","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1242/dev.001131"}],"article_processing_charge":"No","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"year":"2007","oa":1,"author":[{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"last_name":"Henikoff","first_name":"Steven","full_name":"Henikoff, Steven"}],"page":"3959-3965","abstract":[{"lang":"eng","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."}],"issue":"22"},{"date_published":"2006-11-26T00:00:00Z","_id":"9505","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","month":"11","oa_version":"None","type":"journal_article","quality_controlled":"1","year":"2006","author":[{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"full_name":"Gehring, Mary","last_name":"Gehring","first_name":"Mary"},{"full_name":"Tran, Robert K.","first_name":"Robert K.","last_name":"Tran"},{"last_name":"Ballinger","first_name":"Tracy","full_name":"Ballinger, Tracy"},{"last_name":"Henikoff","first_name":"Steven","full_name":"Henikoff, Steven"}],"page":"61-69","issue":"1","abstract":[{"lang":"eng","text":"Cytosine methylation, a common form of DNA modification that antagonizes transcription, is found at transposons and repeats in vertebrates, plants and fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana genome at high resolution. DNA methylation covers transposons and is present within a large fraction of A. thaliana genes. Methylation within genes is conspicuously biased away from gene ends, suggesting a dependence on RNA polymerase transit. Genic methylation is strongly influenced by transcription: moderately transcribed genes are most likely to be methylated, whereas genes at either extreme are least likely. In turn, transcription is influenced by methylation: short methylated genes are poorly expressed, and loss of methylation in the body of a gene leads to enhanced transcription. Our results indicate that genic transcription and DNA methylation are closely interwoven processes."}],"article_processing_charge":"No","publication_identifier":{"eissn":["1546-1718"],"issn":["1061-4036"]},"article_type":"original","language":[{"iso":"eng"}],"day":"26","scopus_import":"1","pmid":1,"status":"public","date_created":"2021-06-07T12:19:31Z","publisher":"Nature Publishing Group","extern":"1","volume":39,"external_id":{"pmid":["17128275"]},"intvolume":"        39","publication":"Nature Genetics","title":"Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription","date_updated":"2021-12-14T09:02:51Z","doi":"10.1038/ng1929","department":[{"_id":"DaZi"}],"citation":{"short":"D. Zilberman, M. Gehring, R.K. Tran, T. Ballinger, S. Henikoff, Nature Genetics 39 (2006) 61–69.","ista":"Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2006. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genetics. 39(1), 61–69.","chicago":"Zilberman, Daniel, Mary Gehring, Robert K. Tran, Tracy Ballinger, and Steven Henikoff. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers an Interdependence between Methylation and Transcription.” <i>Nature Genetics</i>. Nature Publishing Group, 2006. <a href=\"https://doi.org/10.1038/ng1929\">https://doi.org/10.1038/ng1929</a>.","ieee":"D. Zilberman, M. Gehring, R. K. Tran, T. Ballinger, and S. Henikoff, “Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription,” <i>Nature Genetics</i>, vol. 39, no. 1. Nature Publishing Group, pp. 61–69, 2006.","apa":"Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T., &#38; Henikoff, S. (2006). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. <i>Nature Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng1929\">https://doi.org/10.1038/ng1929</a>","ama":"Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. <i>Nature Genetics</i>. 2006;39(1):61-69. doi:<a href=\"https://doi.org/10.1038/ng1929\">10.1038/ng1929</a>","mla":"Zilberman, Daniel, et al. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers an Interdependence between Methylation and Transcription.” <i>Nature Genetics</i>, vol. 39, no. 1, Nature Publishing Group, 2006, pp. 61–69, doi:<a href=\"https://doi.org/10.1038/ng1929\">10.1038/ng1929</a>."}},{"pmid":1,"scopus_import":"1","language":[{"iso":"eng"}],"day":"26","article_type":"original","volume":15,"extern":"1","publisher":"Elsevier","date_created":"2021-06-07T10:24:30Z","status":"public","doi":"10.1016/j.cub.2005.01.008","date_updated":"2021-12-14T09:12:26Z","title":"DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes","publication":"Current Biology","intvolume":"        15","external_id":{"pmid":["15668172 "]},"citation":{"ieee":"R. K. Tran, J. G. Henikoff, D. Zilberman, R. F. Ditt, S. E. Jacobsen, and S. Henikoff, “DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes,” <i>Current Biology</i>, vol. 15, no. 2. Elsevier, pp. 154–159, 2005.","short":"R.K. Tran, J.G. Henikoff, D. Zilberman, R.F. Ditt, S.E. Jacobsen, S. Henikoff, Current Biology 15 (2005) 154–159.","chicago":"Tran, Robert K., Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven E. Jacobsen, and Steven Henikoff. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.” <i>Current Biology</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.cub.2005.01.008\">https://doi.org/10.1016/j.cub.2005.01.008</a>.","ista":"Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. 2005. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Current Biology. 15(2), 154–159.","apa":"Tran, R. K., Henikoff, J. G., Zilberman, D., Ditt, R. F., Jacobsen, S. E., &#38; Henikoff, S. (2005). DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2005.01.008\">https://doi.org/10.1016/j.cub.2005.01.008</a>","mla":"Tran, Robert K., et al. “DNA Methylation Profiling Identifies CG Methylation Clusters in Arabidopsis Genes.” <i>Current Biology</i>, vol. 15, no. 2, Elsevier, 2005, pp. 154–59, doi:<a href=\"https://doi.org/10.1016/j.cub.2005.01.008\">10.1016/j.cub.2005.01.008</a>.","ama":"Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. <i>Current Biology</i>. 2005;15(2):154-159. doi:<a href=\"https://doi.org/10.1016/j.cub.2005.01.008\">10.1016/j.cub.2005.01.008</a>"},"department":[{"_id":"DaZi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9491","date_published":"2005-01-26T00:00:00Z","quality_controlled":"1","type":"journal_article","oa_version":"Published Version","month":"01","publication_status":"published","abstract":[{"text":"Cytosine DNA methylation in vertebrates is widespread, but methylation in plants is found almost exclusively at transposable elements and repetitive DNA [1]. Within regions of methylation, methylcytosines are typically found in CG, CNG, and asymmetric contexts. CG sites are maintained by a plant homolog of mammalian Dnmt1 acting on hemi-methylated DNA after replication. Methylation of CNG and asymmetric sites appears to be maintained at each cell cycle by other mechanisms. We report a new type of DNA methylation in Arabidopsis, dense CG methylation clusters found at scattered sites throughout the genome. These clusters lack non-CG methylation and are preferentially found in genes, although they are relatively deficient toward the 5′ end. CG methylation clusters are present in lines derived from different accessions and in mutants that eliminate de novo methylation, indicating that CG methylation clusters are stably maintained at specific sites. Because 5-methylcytosine is mutagenic, the appearance of CG methylation clusters over evolutionary time predicts a genome-wide deficiency of CG dinucleotides and an excess of C(A/T)G trinucleotides within transcribed regions. This is exactly what we find, implying that CG methylation clusters have contributed profoundly to plant gene evolution. We suggest that CG methylation clusters silence cryptic promoters that arise sporadically within transcription units.","lang":"eng"}],"issue":"2","page":"154-159","author":[{"first_name":"Robert K.","last_name":"Tran","full_name":"Tran, Robert K."},{"full_name":"Henikoff, Jorja G.","first_name":"Jorja G.","last_name":"Henikoff"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"},{"first_name":"Renata F.","last_name":"Ditt","full_name":"Ditt, Renata F."},{"first_name":"Steven E.","last_name":"Jacobsen","full_name":"Jacobsen, Steven E."},{"full_name":"Henikoff, Steven","first_name":"Steven","last_name":"Henikoff"}],"oa":1,"year":"2005","publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2005.01.008"}]},{"oa":1,"year":"2005","abstract":[{"text":"Background:\r\nDNA methylation occurs at preferred sites in eukaryotes. In Arabidopsis, DNA cytosine methylation is maintained by three subfamilies of methyltransferases with distinct substrate specificities and different modes of action. Targeting of cytosine methylation at selected loci has been found to sometimes involve histone H3 methylation and small interfering (si)RNAs. However, the relationship between different cytosine methylation pathways and their preferred targets is not known.\r\nResults:\r\nWe used a microarray-based profiling method to explore the involvement of Arabidopsis CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP) and an Argonaute-related siRNA silencing component (AGO4) in methylating target loci. We found that KYP targets are also CMT3 targets, suggesting that histone methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar proximal distributions that correspond to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome. We find an inverse relationship between element size and loss of methylation in ago4 and drm mutants.\r\nConclusion:\r\nWe conclude that the targets of both DNA methylation and histone H3K9 methylation pathways are transposable elements genome-wide, irrespective of element type and position. Our findings also suggest that RNA-directed DNA methylation is required to silence isolated elements that may be too small to be maintained in a silent state by a chromatin-based mechanism alone. Thus, parallel pathways would be needed to maintain silencing of transposable elements.","lang":"eng"}],"issue":"11","author":[{"full_name":"Tran, Robert K.","first_name":"Robert K.","last_name":"Tran"},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman"},{"full_name":"de Bustos, Cecilia","last_name":"de Bustos","first_name":"Cecilia"},{"last_name":"Ditt","first_name":"Renata F.","full_name":"Ditt, Renata F."},{"last_name":"Henikoff","first_name":"Jorja G.","full_name":"Henikoff, Jorja G."},{"last_name":"Lindroth","first_name":"Anders M.","full_name":"Lindroth, Anders M."},{"full_name":"Delrow, Jeffrey","first_name":"Jeffrey","last_name":"Delrow"},{"full_name":"Boyle, Tom","last_name":"Boyle","first_name":"Tom"},{"full_name":"Kwong, Samson","first_name":"Samson","last_name":"Kwong"},{"last_name":"Bryson","first_name":"Terri D.","full_name":"Bryson, Terri D."},{"first_name":"Steven E.","last_name":"Jacobsen","full_name":"Jacobsen, Steven E."},{"full_name":"Henikoff, Steven","last_name":"Henikoff","first_name":"Steven"}],"article_processing_charge":"No","main_file_link":[{"url":"https://doi.org/10.1186/gb-2005-6-11-r90","open_access":"1"}],"publication_identifier":{"issn":["1474-760X"],"eissn":["1465-6906"]},"_id":"9514","date_published":"2005-10-19T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","publication_status":"published","month":"10","quality_controlled":"1","type":"journal_article","publication":"Genome Biology","intvolume":"         6","external_id":{"pmid":["16277745"]},"doi":"10.1186/gb-2005-6-11-r90","date_updated":"2021-12-14T09:09:41Z","title":"Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis","citation":{"ieee":"R. K. Tran <i>et al.</i>, “Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis,” <i>Genome Biology</i>, vol. 6, no. 11. Springer Nature, 2005.","chicago":"Tran, Robert K., Daniel Zilberman, Cecilia de Bustos, Renata F. Ditt, Jorja G. Henikoff, Anders M. Lindroth, Jeffrey Delrow, et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.” <i>Genome Biology</i>. Springer Nature, 2005. <a href=\"https://doi.org/10.1186/gb-2005-6-11-r90\">https://doi.org/10.1186/gb-2005-6-11-r90</a>.","ista":"Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S. 2005. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. Genome Biology. 6(11), R90.","short":"R.K. Tran, D. Zilberman, C. de Bustos, R.F. Ditt, J.G. Henikoff, A.M. Lindroth, J. Delrow, T. Boyle, S. Kwong, T.D. Bryson, S.E. Jacobsen, S. Henikoff, Genome Biology 6 (2005).","mla":"Tran, Robert K., et al. “Chromatin and SiRNA Pathways Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.” <i>Genome Biology</i>, vol. 6, no. 11, R90, Springer Nature, 2005, doi:<a href=\"https://doi.org/10.1186/gb-2005-6-11-r90\">10.1186/gb-2005-6-11-r90</a>.","ama":"Tran RK, Zilberman D, de Bustos C, et al. Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. <i>Genome Biology</i>. 2005;6(11). doi:<a href=\"https://doi.org/10.1186/gb-2005-6-11-r90\">10.1186/gb-2005-6-11-r90</a>","apa":"Tran, R. K., Zilberman, D., de Bustos, C., Ditt, R. F., Henikoff, J. G., Lindroth, A. M., … Henikoff, S. (2005). Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. <i>Genome Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1186/gb-2005-6-11-r90\">https://doi.org/10.1186/gb-2005-6-11-r90</a>"},"department":[{"_id":"DaZi"}],"language":[{"iso":"eng"}],"article_number":"R90","day":"19","article_type":"original","pmid":1,"scopus_import":"1","date_created":"2021-06-07T13:12:41Z","status":"public","volume":6,"publisher":"Springer Nature","extern":"1"},{"type":"journal_article","quality_controlled":"1","oa_version":"None","month":"10","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9529","date_published":"2005-10-01T00:00:00Z","publication_identifier":{"issn":["0959-437X"]},"article_processing_charge":"No","author":[{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"full_name":"Henikoff, Steven","last_name":"Henikoff","first_name":"Steven"}],"page":"557-562","abstract":[{"text":"Eukaryotic organisms have the remarkable ability to inherit states of gene activity without altering the underlying DNA sequence. This epigenetic inheritance can persist over thousands of years, providing an alternative to genetic mutations as a substrate for natural selection. Epigenetic inheritance might be propagated by differences in DNA methylation, post-translational histone modifications, and deposition of histone variants. Mounting evidence also indicates that small interfering RNA (siRNA)-mediated mechanisms play central roles in setting up and maintaining states of gene activity. Much of the epigenetic machinery of many organisms, including Arabidopsis, appears to be directed at silencing viruses and transposable elements, with epigenetic regulation of endogenous genes being mostly derived from such processes.","lang":"eng"}],"issue":"5","year":"2005","publisher":"Elsevier","extern":"1","volume":15,"status":"public","date_created":"2021-06-08T09:05:56Z","scopus_import":"1","pmid":1,"article_type":"review","language":[{"iso":"eng"}],"department":[{"_id":"DaZi"}],"citation":{"short":"D. Zilberman, S. Henikoff, Current Opinion in Genetics and Development 15 (2005) 557–562.","chicago":"Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis: Selective Silence.” <i>Current Opinion in Genetics and Development</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.gde.2005.07.002\">https://doi.org/10.1016/j.gde.2005.07.002</a>.","ista":"Zilberman D, Henikoff S. 2005. Epigenetic inheritance in Arabidopsis: Selective silence. Current Opinion in Genetics and Development. 15(5), 557–562.","ieee":"D. Zilberman and S. Henikoff, “Epigenetic inheritance in Arabidopsis: Selective silence,” <i>Current Opinion in Genetics and Development</i>, vol. 15, no. 5. Elsevier, pp. 557–562, 2005.","ama":"Zilberman D, Henikoff S. Epigenetic inheritance in Arabidopsis: Selective silence. <i>Current Opinion in Genetics and Development</i>. 2005;15(5):557-562. doi:<a href=\"https://doi.org/10.1016/j.gde.2005.07.002\">10.1016/j.gde.2005.07.002</a>","mla":"Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis: Selective Silence.” <i>Current Opinion in Genetics and Development</i>, vol. 15, no. 5, Elsevier, 2005, pp. 557–62, doi:<a href=\"https://doi.org/10.1016/j.gde.2005.07.002\">10.1016/j.gde.2005.07.002</a>.","apa":"Zilberman, D., &#38; Henikoff, S. (2005). Epigenetic inheritance in Arabidopsis: Selective silence. <i>Current Opinion in Genetics and Development</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.gde.2005.07.002\">https://doi.org/10.1016/j.gde.2005.07.002</a>"},"doi":"10.1016/j.gde.2005.07.002","title":"Epigenetic inheritance in Arabidopsis: Selective silence","date_updated":"2021-12-14T09:13:13Z","intvolume":"        15","external_id":{"pmid":["16085410"]},"publication":"Current Opinion in Genetics and Development"},{"keyword":["Endocrinology","Genetics","Molecular Biology","Biochemistry"],"acknowledgement":"This study was financially supported by China National High-Tech “863” Program. The authors are very thankful to Dr Li Wang (School of Life Sciences, Fudan University, Shanghai, China) for her kind help with constructing the phylogenetic tree.","year":"2004","author":[{"first_name":"Zhihua","last_name":"Liao","full_name":"Liao, Zhihua"},{"last_name":"Chen","first_name":"Min","full_name":"Chen, Min"},{"first_name":"Yifu","last_name":"Gong","full_name":"Gong, Yifu"},{"last_name":"Guo","first_name":"Liang","full_name":"Guo, Liang"},{"last_name":"Tan","first_name":"Qiumin","full_name":"Tan, Qiumin"},{"orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"last_name":"Sun","first_name":"Xiaofen","full_name":"Sun, Xiaofen"},{"last_name":"Tan","first_name":"Feng","full_name":"Tan, Feng"},{"last_name":"Tang","first_name":"Kexuan","full_name":"Tang, Kexuan"}],"page":"153-158","issue":"2","abstract":[{"text":"Geranylgeranyl diphosphate synthase (GGPPS, EC: 2.5.1.29) catalyzes the biosynthesis of geranylgeranyl diphosphate (GGPP), which is a key precursor for ginkgolide biosynthesis. Here we reported for the first time the cloning of a new full-length cDNA encoding GGPPS from the living fossil plant Ginkgo biloba. The full-length cDNA encoding G. biloba GGPPS (designated as GbGGPPS) was 1657bp long and contained a 1176bp open reading frame encoding a 391 amino acid protein. Comparative analysis showed that GbGGPPS possessed a 79 amino acid transit peptide at its N-terminal, which directed GbGGPPS to target to the plastids. Bioinformatic analysis revealed that GbGGPPS was a member of polyprenyltransferases with two highly conserved aspartate-rich motifs like other plant GGPPSs. Phylogenetic tree analysis indicated that plant GGPPSs could be classified into two groups, angiosperm and gymnosperm GGPPSs, while GbGGPPS had closer relationship with gymnosperm plant GGPPSs.","lang":"eng"}],"article_processing_charge":"No","publication_identifier":{"issn":["1042-5179"]},"_id":"12203","date_published":"2004-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","publication_status":"published","type":"journal_article","quality_controlled":"1","intvolume":"        15","external_id":{"pmid":["15352294"]},"publication":"DNA Sequence","doi":"10.1080/10425170410001667348","date_updated":"2023-05-08T10:58:29Z","title":"A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides","department":[{"_id":"XiFe"}],"citation":{"ieee":"Z. Liao <i>et al.</i>, “A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides,” <i>DNA Sequence</i>, vol. 15, no. 2. Informa UK Limited, pp. 153–158, 2004.","chicago":"Liao, Zhihua, Min Chen, Yifu Gong, Liang Guo, Qiumin Tan, Xiaoqi Feng, Xiaofen Sun, Feng Tan, and Kexuan Tang. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” <i>DNA Sequence</i>. Informa UK Limited, 2004. <a href=\"https://doi.org/10.1080/10425170410001667348\">https://doi.org/10.1080/10425170410001667348</a>.","short":"Z. Liao, M. Chen, Y. Gong, L. Guo, Q. Tan, X. Feng, X. Sun, F. Tan, K. Tang, DNA Sequence 15 (2004) 153–158.","ista":"Liao Z, Chen M, Gong Y, Guo L, Tan Q, Feng X, Sun X, Tan F, Tang K. 2004. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. DNA Sequence. 15(2), 153–158.","mla":"Liao, Zhihua, et al. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.” <i>DNA Sequence</i>, vol. 15, no. 2, Informa UK Limited, 2004, pp. 153–58, doi:<a href=\"https://doi.org/10.1080/10425170410001667348\">10.1080/10425170410001667348</a>.","ama":"Liao Z, Chen M, Gong Y, et al. A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. <i>DNA Sequence</i>. 2004;15(2):153-158. doi:<a href=\"https://doi.org/10.1080/10425170410001667348\">10.1080/10425170410001667348</a>","apa":"Liao, Z., Chen, M., Gong, Y., Guo, L., Tan, Q., Feng, X., … Tang, K. (2004). A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides. <i>DNA Sequence</i>. Informa UK Limited. <a href=\"https://doi.org/10.1080/10425170410001667348\">https://doi.org/10.1080/10425170410001667348</a>"},"article_type":"original","language":[{"iso":"eng"}],"scopus_import":"1","pmid":1,"status":"public","date_created":"2023-01-16T09:24:50Z","extern":"1","publisher":"Informa UK Limited","volume":15},{"issue":"5662","page":"1336","author":[{"full_name":"Chan, Simon W.-L.","last_name":"Chan","first_name":"Simon W.-L."},{"last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"last_name":"Xie","first_name":" Zhixin","full_name":"Xie,  Zhixin"},{"first_name":" Lisa K.","last_name":"Johansen","full_name":"Johansen,  Lisa K."},{"first_name":"James C.","last_name":"Carrington","full_name":"Carrington, James C."},{"last_name":"Jacobsen","first_name":"Steven E.","full_name":"Jacobsen, Steven E."}],"year":"2004","keyword":["Multidisciplinary"],"publication_identifier":{"eissn":["1095-9203"],"issn":["0036-8075"]},"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2004-02-27T00:00:00Z","_id":"9454","quality_controlled":"1","type":"journal_article","month":"02","publication_status":"published","oa_version":"None","date_updated":"2021-12-14T09:13:53Z","title":"RNA silencing genes control de novo DNA methylation","doi":"10.1126/science.1095989","publication":"Science","external_id":{"pmid":["14988555"]},"intvolume":"       303","citation":{"ieee":"S. W.-L. Chan, D. Zilberman,  Zhixin Xie,  Lisa K. Johansen, J. C. Carrington, and S. E. Jacobsen, “RNA silencing genes control de novo DNA methylation,” <i>Science</i>, vol. 303, no. 5662. American Association for the Advancement of Science, p. 1336, 2004.","short":"S.W.-L. Chan, D. Zilberman,  Zhixin Xie,  Lisa K. Johansen, J.C. Carrington, S.E. Jacobsen, Science 303 (2004) 1336.","chicago":"Chan, Simon W.-L., Daniel Zilberman,  Zhixin Xie,  Lisa K. Johansen, James C. Carrington, and Steven E. Jacobsen. “RNA Silencing Genes Control de Novo DNA Methylation.” <i>Science</i>. American Association for the Advancement of Science, 2004. <a href=\"https://doi.org/10.1126/science.1095989\">https://doi.org/10.1126/science.1095989</a>.","ista":"Chan SW-L, Zilberman D, Xie  Zhixin, Johansen  Lisa K., Carrington JC, Jacobsen SE. 2004. RNA silencing genes control de novo DNA methylation. Science. 303(5662), 1336.","apa":"Chan, S. W.-L., Zilberman, D., Xie,  Zhixin, Johansen,  Lisa K., Carrington, J. C., &#38; Jacobsen, S. E. (2004). RNA silencing genes control de novo DNA methylation. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1095989\">https://doi.org/10.1126/science.1095989</a>","mla":"Chan, Simon W. L., et al. “RNA Silencing Genes Control de Novo DNA Methylation.” <i>Science</i>, vol. 303, no. 5662, American Association for the Advancement of Science, 2004, p. 1336, doi:<a href=\"https://doi.org/10.1126/science.1095989\">10.1126/science.1095989</a>.","ama":"Chan SW-L, Zilberman D, Xie  Zhixin, Johansen  Lisa K., Carrington JC, Jacobsen SE. RNA silencing genes control de novo DNA methylation. <i>Science</i>. 2004;303(5662):1336. doi:<a href=\"https://doi.org/10.1126/science.1095989\">10.1126/science.1095989</a>"},"department":[{"_id":"DaZi"}],"pmid":1,"scopus_import":"1","day":"27","language":[{"iso":"eng"}],"article_type":"original","volume":303,"extern":"1","publisher":"American Association for the Advancement of Science","date_created":"2021-06-04T11:12:35Z","status":"public"},{"author":[{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"full_name":"Cao, Xiaofeng","last_name":"Cao","first_name":"Xiaofeng"},{"first_name":"Lisa K.","last_name":"Johansen","full_name":"Johansen, Lisa K."},{"full_name":"Xie, Zhixin","first_name":"Zhixin","last_name":"Xie"},{"full_name":"Carrington, James C.","first_name":"James C.","last_name":"Carrington"},{"first_name":"Steven E.","last_name":"Jacobsen","full_name":"Jacobsen, Steven E."}],"page":"1214-1220","abstract":[{"text":"In a number of organisms, transgenes containing transcribed inverted repeats (IRs) that produce hairpin RNA can trigger RNA-mediated silencing, which is associated with 21-24 nucleotide small interfering RNAs (siRNAs). In plants, IR-driven RNA silencing also causes extensive cytosine methylation of homologous DNA in both the transgene \"trigger\" and any other homologous DNA sequences--\"targets\". Endogenous genomic sequences, including transposable elements and repeated elements, are also subject to RNA-mediated silencing. The RNA silencing gene ARGONAUTE4 (AGO4) is required for maintenance of DNA methylation at several endogenous loci and for the establishment of methylation at the FWA gene. Here, we show that mutation of AGO4 substantially reduces the maintenance of DNA methylation triggered by IR transgenes, but AGO4 loss-of-function does not block the initiation of DNA methylation by IRs. AGO4 primarily affects non-CG methylation of the target sequences, while the IR trigger sequences lose methylation in all sequence contexts. Finally, we find that AGO4 and the DRM methyltransferase genes are required for maintenance of siRNAs at a subset of endogenous sequences, but AGO4 is not required for the accumulation of IR-induced siRNAs or a number of endogenous siRNAs, suggesting that AGO4 may function downstream of siRNA production.","lang":"eng"}],"issue":"13","year":"2004","oa":1,"publication_identifier":{"issn":["0960-9822"],"eissn":["1879-0445"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2004.06.055"}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9493","date_published":"2004-07-13T00:00:00Z","type":"journal_article","quality_controlled":"1","oa_version":"Published Version","month":"07","publication_status":"published","doi":"10.1016/j.cub.2004.06.055","title":"Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats","date_updated":"2021-12-14T08:52:00Z","intvolume":"        14","external_id":{"pmid":["15242620 "]},"publication":"Current Biology","department":[{"_id":"DaZi"}],"citation":{"apa":"Zilberman, D., Cao, X., Johansen, L. K., Xie, Z., Carrington, J. C., &#38; Jacobsen, S. E. (2004). Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">https://doi.org/10.1016/j.cub.2004.06.055</a>","ama":"Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. <i>Current Biology</i>. 2004;14(13):1214-1220. doi:<a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">10.1016/j.cub.2004.06.055</a>","mla":"Zilberman, Daniel, et al. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” <i>Current Biology</i>, vol. 14, no. 13, Elsevier, 2004, pp. 1214–20, doi:<a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">10.1016/j.cub.2004.06.055</a>.","chicago":"Zilberman, Daniel, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C. Carrington, and Steven E. Jacobsen. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA Methylation Triggered by Inverted Repeats.” <i>Current Biology</i>. Elsevier, 2004. <a href=\"https://doi.org/10.1016/j.cub.2004.06.055\">https://doi.org/10.1016/j.cub.2004.06.055</a>.","ista":"Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. 2004. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Current Biology. 14(13), 1214–1220.","short":"D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen, Current Biology 14 (2004) 1214–1220.","ieee":"D. Zilberman, X. Cao, L. K. Johansen, Z. Xie, J. C. Carrington, and S. E. Jacobsen, “Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats,” <i>Current Biology</i>, vol. 14, no. 13. Elsevier, pp. 1214–1220, 2004."},"scopus_import":"1","pmid":1,"article_type":"original","language":[{"iso":"eng"}],"day":"13","publisher":"Elsevier","extern":"1","volume":14,"status":"public","date_created":"2021-06-07T10:33:00Z"}]