[{"publication_identifier":{"issn":["0022-1236"]},"article_type":"original","date_updated":"2021-01-12T08:19:49Z","date_published":"2005-12-01T00:00:00Z","volume":229,"keyword":["Analysis"],"article_processing_charge":"No","_id":"8516","author":[{"first_name":"Jean","full_name":"Bourgain, Jean","last_name":"Bourgain"},{"orcid":"0000-0002-6051-2628","last_name":"Kaloshin","first_name":"Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim"}],"intvolume":"       229","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","title":"On diffusion in high-dimensional Hamiltonian systems","issue":"1","doi":"10.1016/j.jfa.2004.09.006","year":"2005","day":"01","date_created":"2020-09-18T10:49:06Z","publication_status":"published","language":[{"iso":"eng"}],"status":"public","extern":"1","quality_controlled":"1","type":"journal_article","month":"12","page":"1-61","oa_version":"None","abstract":[{"text":"The purpose of this paper is to construct examples of diffusion for E-Hamiltonian perturbations\r\nof completely integrable Hamiltonian systems in 2d-dimensional phase space, with d large.\r\nIn the first part of the paper, simple and explicit examples are constructed illustrating absence\r\nof ‘long-time’ stability for size E Hamiltonian perturbations of quasi-convex integrable systems\r\nalready when the dimension 2d of phase space becomes as large as log 1/E . We first produce\r\nthe example in Gevrey class and then a real analytic one, with some additional work.\r\nIn the second part, we consider again E-Hamiltonian perturbations of completely integrable\r\nHamiltonian system in 2d-dimensional space with E-small but not too small, |E| > exp(−d), with\r\nd the number of degrees of freedom assumed large. It is shown that for a class of analytic\r\ntime-periodic perturbations, there exist linearly diffusing trajectories. The underlying idea for\r\nboth examples is similar and consists in coupling a fixed degree of freedom with a large\r\nnumber of them. The procedure and analytical details are however significantly different. As\r\nmentioned, the construction in Part I is totally elementary while Part II is more involved, relying\r\nin particular on the theory of normally hyperbolic invariant manifolds, methods of generating\r\nfunctions, Aubry–Mather theory, and Mather’s variational methods.","lang":"eng"}],"citation":{"ama":"Bourgain J, Kaloshin V. On diffusion in high-dimensional Hamiltonian systems. <i>Journal of Functional Analysis</i>. 2005;229(1):1-61. doi:<a href=\"https://doi.org/10.1016/j.jfa.2004.09.006\">10.1016/j.jfa.2004.09.006</a>","ieee":"J. Bourgain and V. Kaloshin, “On diffusion in high-dimensional Hamiltonian systems,” <i>Journal of Functional Analysis</i>, vol. 229, no. 1. Elsevier, pp. 1–61, 2005.","chicago":"Bourgain, Jean, and Vadim Kaloshin. “On Diffusion in High-Dimensional Hamiltonian Systems.” <i>Journal of Functional Analysis</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.jfa.2004.09.006\">https://doi.org/10.1016/j.jfa.2004.09.006</a>.","apa":"Bourgain, J., &#38; Kaloshin, V. (2005). On diffusion in high-dimensional Hamiltonian systems. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2004.09.006\">https://doi.org/10.1016/j.jfa.2004.09.006</a>","mla":"Bourgain, Jean, and Vadim Kaloshin. “On Diffusion in High-Dimensional Hamiltonian Systems.” <i>Journal of Functional Analysis</i>, vol. 229, no. 1, Elsevier, 2005, pp. 1–61, doi:<a href=\"https://doi.org/10.1016/j.jfa.2004.09.006\">10.1016/j.jfa.2004.09.006</a>.","ista":"Bourgain J, Kaloshin V. 2005. On diffusion in high-dimensional Hamiltonian systems. Journal of Functional Analysis. 229(1), 1–61.","short":"J. Bourgain, V. Kaloshin, Journal of Functional Analysis 229 (2005) 1–61."},"publication":"Journal of Functional Analysis"},{"publisher":"Pleiades Publishing","title":"The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6769","intvolume":"        50","pmid":1,"article_processing_charge":"No","date_updated":"2021-01-12T08:21:01Z","article_type":"original","publication":"Biofizika","page":"389 - 395","type":"journal_article","publication_status":"published","status":"public","day":"01","_id":"877","author":[{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694"}],"volume":50,"external_id":{"pmid":["15977826"]},"date_published":"2005-05-01T00:00:00Z","citation":{"apa":"Kondrashov, F. (2005). The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. <i>Biofizika</i>. Pleiades Publishing.","mla":"Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.” <i>Biofizika</i>, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 389–95.","ista":"Kondrashov F. 2005. The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. Biofizika. 50(3), 389–395.","chicago":"Kondrashov, Fyodor. “The Analysis of Monomer Sequences in Protein and TRNA and the Manifestation of the Compensation of Pathogenic Deviations in Their Evolution.” <i>Biofizika</i>. Pleiades Publishing, 2005.","short":"F. Kondrashov, Biofizika 50 (2005) 389–395.","ama":"Kondrashov F. The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution. <i>Biofizika</i>. 2005;50(3):389-395.","ieee":"F. Kondrashov, “The analysis of monomer sequences in protein and tRNA and the manifestation of the compensation of pathogenic deviations in their evolution,” <i>Biofizika</i>, vol. 50, no. 3. Pleiades Publishing, pp. 389–395, 2005."},"abstract":[{"lang":"eng","text":"Sequence analysis of protein and mitochondrially encoded tRNA genes shows that substitutions\r\nproducing pathogenic effects in humans are often found in normal, healthy individuals from other species.\r\nAnalysis of stability of protein and tRNA structures shows that the disease-causing effects of pathogenic\r\nmutations can be neutralized by other, compensatory substitutions that restore the structural stability of the\r\nmolecule. Further study of such substitutions will, hopefully, lead to new methods for curing genetic dis-\r\neases that may be based on the correction of molecule stability as a whole instead of reversing an individual\r\npathogenic mutation."}],"oa_version":"None","month":"05","main_file_link":[{"url":"http://pleiades.online/abstract/biophys/5/biophys0349_abstract.pdf"}],"quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:48:58Z","extern":"1","year":"2005","issue":"3"},{"_id":"878","author":[{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","full_name":"Fyodor Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        37","publisher":"Nature Publishing Group","title":"In search of the limits of evolution","publist_id":"6770","date_published":"2005-01-01T00:00:00Z","date_updated":"2021-01-12T08:21:02Z","volume":37,"month":"01","type":"journal_article","citation":{"short":"F. Kondrashov, Nature Genetics 37 (2005) 9–10.","mla":"Kondrashov, Fyodor. “In Search of the Limits of Evolution.” <i>Nature Genetics</i>, vol. 37, no. 1, Nature Publishing Group, 2005, pp. 9–10, doi:<a href=\"https://doi.org/10.1038/ng0105-9\">10.1038/ng0105-9</a>.","ista":"Kondrashov F. 2005. In search of the limits of evolution. Nature Genetics. 37(1), 9–10.","apa":"Kondrashov, F. (2005). In search of the limits of evolution. <i>Nature Genetics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ng0105-9\">https://doi.org/10.1038/ng0105-9</a>","chicago":"Kondrashov, Fyodor. “In Search of the Limits of Evolution.” <i>Nature Genetics</i>. Nature Publishing Group, 2005. <a href=\"https://doi.org/10.1038/ng0105-9\">https://doi.org/10.1038/ng0105-9</a>.","ieee":"F. Kondrashov, “In search of the limits of evolution,” <i>Nature Genetics</i>, vol. 37, no. 1. Nature Publishing Group, pp. 9–10, 2005.","ama":"Kondrashov F. In search of the limits of evolution. <i>Nature Genetics</i>. 2005;37(1):9-10. doi:<a href=\"https://doi.org/10.1038/ng0105-9\">10.1038/ng0105-9</a>"},"abstract":[{"text":"Negative trade-offs are thought to be a pervasive phenomenon and to inhibit evolution at all levels. New evidence shows that at the molecular level, there may be no trade-offs preventing the emergence of an enzyme with multiple functions.\n","lang":"eng"}],"publication":"Nature Genetics","page":"9 - 10","year":"2005","issue":"1","doi":"10.1038/ng0105-9","quality_controlled":0,"day":"01","status":"public","date_created":"2018-12-11T11:48:59Z","publication_status":"published","extern":1},{"issue":"3","year":"2005","extern":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:48:59Z","day":"01","status":"public","publication_status":"published","quality_controlled":"1","main_file_link":[{"url":"http://pleiades.online/abstract/biophys/5/biophys0356_abstract.pdf"}],"type":"journal_article","month":"05","oa_version":"None","page":"396 - 403","publication":"Biofizika","citation":{"chicago":"Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure of Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.” <i>Biofizika</i>. Pleiades Publishing, 2005.","ista":"Kondrashov F. 2005. The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. Biofizika. 50(3), 396–403.","mla":"Kondrashov, Fyodor. “The Convergent Evolution of the Secondary Structure of Mitochondrial Cysteine TRNA in the Nine-Banded Armadillo Dasypus Novemcinctus.” <i>Biofizika</i>, vol. 50, no. 3, Pleiades Publishing, 2005, pp. 396–403.","apa":"Kondrashov, F. (2005). The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. <i>Biofizika</i>. Pleiades Publishing.","short":"F. Kondrashov, Biofizika 50 (2005) 396–403.","ama":"Kondrashov F. The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus. <i>Biofizika</i>. 2005;50(3):396-403.","ieee":"F. Kondrashov, “The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus,” <i>Biofizika</i>, vol. 50, no. 3. Pleiades Publishing, pp. 396–403, 2005."},"abstract":[{"lang":"eng","text":"Here, I describe a case of loss of the D-arm by mitochondrial cysteine tRNA in the nine-banded armadillo (Dasypus novemcinctus) convergent with mt tRNASer(AGY). Such evolution sheds light on the relationship between structure and function of tRNA molecules and its impact on the patterns of molecular evolution."}],"date_updated":"2021-01-12T08:21:07Z","date_published":"2005-05-01T00:00:00Z","external_id":{"pmid":["15977827"]},"volume":50,"article_processing_charge":"No","intvolume":"        50","pmid":1,"_id":"880","author":[{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","full_name":"Kondrashov, Fyodor","last_name":"Kondrashov","orcid":"0000-0001-8243-4694"}],"publist_id":"6768","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The convergent evolution of the secondary structure of mitochondrial cysteine tRNA in the nine-banded armadillo Dasypus novemcinctus","publisher":"Pleiades Publishing"},{"type":"journal_article","month":"08","acknowledgement":"The author thanks P. Andolfatto, D. Bachtrog, N. Esipova, S. Makeev, A. Kondrashov, V. Ramensky, V. Tumanyan and P. Vlasov for a critical reading of the manuscript. The author is an NSF Graduate Research Fellow. This work was supported by a Contract of the Russian Ministry of Science and Education (02.434.11.1008) and a grant on Molecular and Cellular Biology from RAS.\n","page":"2415 - 2419","publication":"Human Molecular Genetics","abstract":[{"lang":"eng","text":"Some mutations in human mitochondrial tRNAs are severely pathogenic. The available computational methods have a poor record of predicting the impact of a tRNA mutation on the phenotype and fitness. Here patterns of evolution at tRNA sites that harbor pathogenic mutations and at sites that harbor phenotypically cryptic polymorphisms were compared. Mutations that are pathogenic to humans occupy more conservative sites, are only rarely fixed in closely related species, and, when located in stem structures, often disrupt Watson-Crick pairing and display signs of compensatory evolution. These observations make it possible to classify ∼90% of all known pathogenic mutations as deleterious together with only ∼30% of polymorphisms. These polymorphisms segregate at frequencies that are more than two times lower than frequencies of polymorphisms classified as benign, indicating that at least ∼30% of known polymorphisms in mitochondrial tRNAs affect fitness negatively."}],"citation":{"ieee":"F. Kondrashov, “Prediction of pathogenic mutations in mitochondrially encoded human tRNAs,” <i>Human Molecular Genetics</i>, vol. 14, no. 16. Oxford University Press, pp. 2415–2419, 2005.","ama":"Kondrashov F. Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. <i>Human Molecular Genetics</i>. 2005;14(16):2415-2419. doi:<a href=\"https://doi.org/10.1093/hmg/ddi243\">10.1093/hmg/ddi243</a>","short":"F. Kondrashov, Human Molecular Genetics 14 (2005) 2415–2419.","chicago":"Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” <i>Human Molecular Genetics</i>. Oxford University Press, 2005. <a href=\"https://doi.org/10.1093/hmg/ddi243\">https://doi.org/10.1093/hmg/ddi243</a>.","apa":"Kondrashov, F. (2005). Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. <i>Human Molecular Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/hmg/ddi243\">https://doi.org/10.1093/hmg/ddi243</a>","ista":"Kondrashov F. 2005. Prediction of pathogenic mutations in mitochondrially encoded human tRNAs. Human Molecular Genetics. 14(16), 2415–2419.","mla":"Kondrashov, Fyodor. “Prediction of Pathogenic Mutations in Mitochondrially Encoded Human TRNAs.” <i>Human Molecular Genetics</i>, vol. 14, no. 16, Oxford University Press, 2005, pp. 2415–19, doi:<a href=\"https://doi.org/10.1093/hmg/ddi243\">10.1093/hmg/ddi243</a>."},"doi":"10.1093/hmg/ddi243","issue":"16","year":"2005","extern":1,"publication_status":"published","date_created":"2018-12-11T11:49:00Z","status":"public","day":"15","quality_controlled":0,"intvolume":"        14","_id":"882","author":[{"orcid":"0000-0001-8243-4694","last_name":"Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Fyodor Kondrashov"}],"publist_id":"6767","title":"Prediction of pathogenic mutations in mitochondrially encoded human tRNAs","publisher":"Oxford University Press","date_updated":"2021-01-12T08:21:10Z","date_published":"2005-08-15T00:00:00Z","volume":14},{"quality_controlled":0,"extern":1,"date_created":"2018-12-11T11:49:03Z","status":"public","day":"10","publication_status":"published","year":"2005","doi":"10.1038/nature03306","issue":"7026","publication":"Nature","citation":{"ieee":"I. Jordan <i>et al.</i>, “A universal trend of amino acid gain and loss in protein evolution,” <i>Nature</i>, vol. 433, no. 7026. Nature Publishing Group, pp. 633–638, 2005.","ama":"Jordan I, Kondrashov F, Adzhubeǐ I, et al. A universal trend of amino acid gain and loss in protein evolution. <i>Nature</i>. 2005;433(7026):633-638. doi:<a href=\"https://doi.org/10.1038/nature03306\">10.1038/nature03306</a>","short":"I. Jordan, F. Kondrashov, I. Adzhubeǐ, Y. Wolf, E. Koonin, A. Kondrashov, S. Sunyaev, Nature 433 (2005) 633–638.","chicago":"Jordan, Ingo, Fyodor Kondrashov, Ivan Adzhubeǐ, Yuri Wolf, Eugene Koonin, Alexey Kondrashov, and Shamil Sunyaev. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” <i>Nature</i>. Nature Publishing Group, 2005. <a href=\"https://doi.org/10.1038/nature03306\">https://doi.org/10.1038/nature03306</a>.","ista":"Jordan I, Kondrashov F, Adzhubeǐ I, Wolf Y, Koonin E, Kondrashov A, Sunyaev S. 2005. A universal trend of amino acid gain and loss in protein evolution. Nature. 433(7026), 633–638.","apa":"Jordan, I., Kondrashov, F., Adzhubeǐ, I., Wolf, Y., Koonin, E., Kondrashov, A., &#38; Sunyaev, S. (2005). A universal trend of amino acid gain and loss in protein evolution. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature03306\">https://doi.org/10.1038/nature03306</a>","mla":"Jordan, Ingo, et al. “A Universal Trend of Amino Acid Gain and Loss in Protein Evolution.” <i>Nature</i>, vol. 433, no. 7026, Nature Publishing Group, 2005, pp. 633–38, doi:<a href=\"https://doi.org/10.1038/nature03306\">10.1038/nature03306</a>."},"abstract":[{"text":"Amino acid composition of proteins varies substantially between taxa and, thus, can evolve. For example, proteins from organisms with (G+C)-rich (or (A+T)-rich) genomes contain more (or fewer) amino acids encoded by (G+C)-rich codons. However, no universal trends in ongoing changes of amino acid frequencies have been reported. We compared sets of orthologous proteins encoded by triplets of closely related genomes from 15 taxa representing all three domains of life (Bacteria, Archaea and Eukaryota), and used phylogenies to polarize amino acid substitutions. Cys, Met, His, Ser and Phe accrue in at least 14 taxa, whereas Pro, Ala, Glu and Gly are consistently lost. The same nine amino acids are currently accrued or lost in human proteins, as shown by analysis of non-synonymous single-nucleotide polymorphisms. All amino acids with declining frequencies are thought to be among the first incorporated into the genetic code; conversely, all amino acids with increasing frequencies, except Ser, were probably recruited late. Thus, expansion of initially under-represented amino acids, which began over 3,400 million years ago, apparently continues to this day.","lang":"eng"}],"page":"633 - 638","acknowledgement":"S.S. and I.A.A. were supported by the Genome Canada Foundation.","month":"02","type":"journal_article","volume":433,"date_published":"2005-02-10T00:00:00Z","date_updated":"2021-01-12T08:21:23Z","title":"A universal trend of amino acid gain and loss in protein evolution","publisher":"Nature Publishing Group","publist_id":"6757","intvolume":"       433","_id":"893","author":[{"first_name":"Ingo","full_name":"Jordan, Ingo K","last_name":"Jordan"},{"full_name":"Fyodor Kondrashov","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","last_name":"Kondrashov"},{"last_name":"Adzhubeǐ","full_name":"Adzhubeǐ, Ivan A","first_name":"Ivan"},{"full_name":"Wolf, Yuri I","first_name":"Yuri","last_name":"Wolf"},{"last_name":"Koonin","full_name":"Koonin, Eugene V","first_name":"Eugene"},{"last_name":"Kondrashov","first_name":"Alexey","full_name":"Kondrashov, Alexey S"},{"last_name":"Sunyaev","full_name":"Sunyaev, Shamil R","first_name":"Shamil"}]},{"volume":15,"external_id":{"pmid":["15668172 "]},"date_published":"2005-01-26T00:00:00Z","department":[{"_id":"DaZi"}],"publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"_id":"9491","author":[{"first_name":"Robert K.","full_name":"Tran, Robert K.","last_name":"Tran"},{"first_name":"Jorja G.","full_name":"Henikoff, Jorja G.","last_name":"Henikoff"},{"orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel"},{"last_name":"Ditt","first_name":"Renata F.","full_name":"Ditt, Renata F."},{"first_name":"Steven E.","full_name":"Jacobsen, Steven E.","last_name":"Jacobsen"},{"last_name":"Henikoff","full_name":"Henikoff, Steven","first_name":"Steven"}],"quality_controlled":"1","date_created":"2021-06-07T10:24:30Z","language":[{"iso":"eng"}],"extern":"1","year":"2005","oa":1,"issue":"2","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.","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>","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>.","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>.","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>"},"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"}],"oa_version":"Published Version","month":"01","main_file_link":[{"url":"https://doi.org/10.1016/j.cub.2005.01.008","open_access":"1"}],"article_type":"original","date_updated":"2021-12-14T09:12:26Z","publisher":"Elsevier","title":"DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","pmid":1,"intvolume":"        15","article_processing_charge":"No","status":"public","day":"26","publication_status":"published","doi":"10.1016/j.cub.2005.01.008","publication":"Current Biology","page":"154-159","scopus_import":"1","type":"journal_article"},{"date_published":"2005-10-19T00:00:00Z","department":[{"_id":"DaZi"}],"publication_identifier":{"issn":["1474-760X"],"eissn":["1465-6906"]},"external_id":{"pmid":["16277745"]},"volume":6,"article_number":"R90","_id":"9514","author":[{"full_name":"Tran, Robert K.","first_name":"Robert K.","last_name":"Tran"},{"last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"full_name":"de Bustos, Cecilia","first_name":"Cecilia","last_name":"de Bustos"},{"last_name":"Ditt","full_name":"Ditt, Renata F.","first_name":"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"},{"last_name":"Boyle","full_name":"Boyle, Tom","first_name":"Tom"},{"full_name":"Kwong, Samson","first_name":"Samson","last_name":"Kwong"},{"last_name":"Bryson","full_name":"Bryson, Terri D.","first_name":"Terri D."},{"full_name":"Jacobsen, Steven E.","first_name":"Steven E.","last_name":"Jacobsen"},{"last_name":"Henikoff","full_name":"Henikoff, Steven","first_name":"Steven"}],"oa":1,"year":"2005","issue":"11","quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2021-06-07T13:12:41Z","extern":"1","month":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/gb-2005-6-11-r90"}],"abstract":[{"lang":"eng","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."}],"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.","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>","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).","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>.","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>.","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.","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>"},"oa_version":"Published Version","article_type":"original","date_updated":"2021-12-14T09:09:41Z","intvolume":"         6","pmid":1,"article_processing_charge":"No","publisher":"Springer Nature","title":"Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1186/gb-2005-6-11-r90","publication_status":"published","status":"public","day":"19","scopus_import":"1","type":"journal_article","publication":"Genome Biology"},{"date_updated":"2021-12-14T09:13:13Z","article_type":"review","publisher":"Elsevier","title":"Epigenetic inheritance in Arabidopsis: Selective silence","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"        15","pmid":1,"article_processing_charge":"No","publication_status":"published","status":"public","doi":"10.1016/j.gde.2005.07.002","publication":"Current Opinion in Genetics and Development","page":"557-562","scopus_import":"1","type":"journal_article","volume":15,"external_id":{"pmid":["16085410"]},"date_published":"2005-10-01T00:00:00Z","department":[{"_id":"DaZi"}],"publication_identifier":{"issn":["0959-437X"]},"_id":"9529","author":[{"full_name":"Zilberman, Daniel","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","last_name":"Zilberman"},{"first_name":"Steven","full_name":"Henikoff, Steven","last_name":"Henikoff"}],"quality_controlled":"1","date_created":"2021-06-08T09:05:56Z","language":[{"iso":"eng"}],"extern":"1","year":"2005","issue":"5","citation":{"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>","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.","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>","ista":"Zilberman D, Henikoff S. 2005. Epigenetic inheritance in Arabidopsis: Selective silence. Current Opinion in Genetics and Development. 15(5), 557–562.","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>.","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>.","short":"D. Zilberman, S. Henikoff, Current Opinion in Genetics and Development 15 (2005) 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"}],"oa_version":"None","month":"10"},{"publisher":"Springer","title":"Interface-based design","publist_id":"85","author":[{"last_name":"De Alfaro","full_name":"de Alfaro, Luca","first_name":"Luca"},{"last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Thomas Henzinger"}],"_id":"4624","intvolume":"       195","volume":195,"date_published":"2005-07-15T00:00:00Z","date_updated":"2021-01-12T08:00:36Z","alternative_title":["NATO Science Series: Mathematics, Physics, and Chemistry"],"citation":{"ieee":"L. De Alfaro and T. A. Henzinger, “Interface-based design,” presented at the Engineering Theories of Software Intensive Systems, 2005, vol. 195, pp. 83–104.","ama":"De Alfaro L, Henzinger TA. Interface-based design. In: Vol 195. Springer; 2005:83-104. doi:<a href=\"https://doi.org/10.1007/1-4020-3532-2_3\">10.1007/1-4020-3532-2_3</a>","short":"L. De Alfaro, T.A. Henzinger, in:, Springer, 2005, pp. 83–104.","apa":"De Alfaro, L., &#38; Henzinger, T. A. (2005). Interface-based design (Vol. 195, pp. 83–104). Presented at the Engineering Theories of Software Intensive Systems, Springer. <a href=\"https://doi.org/10.1007/1-4020-3532-2_3\">https://doi.org/10.1007/1-4020-3532-2_3</a>","ista":"De Alfaro L, Henzinger TA. 2005. Interface-based design. Engineering Theories of Software Intensive Systems, NATO Science Series: Mathematics, Physics, and Chemistry, vol. 195, 83–104.","mla":"De Alfaro, Luca, and Thomas A. Henzinger. <i>Interface-Based Design</i>. Vol. 195, Springer, 2005, pp. 83–104, doi:<a href=\"https://doi.org/10.1007/1-4020-3532-2_3\">10.1007/1-4020-3532-2_3</a>.","chicago":"De Alfaro, Luca, and Thomas A Henzinger. “Interface-Based Design,” 195:83–104. Springer, 2005. <a href=\"https://doi.org/10.1007/1-4020-3532-2_3\">https://doi.org/10.1007/1-4020-3532-2_3</a>."},"abstract":[{"text":"Surveying results from [5] and [6], we motivate and introduce the theory behind formalizing rich interfaces for software and hardware components. Rich interfaces specify the protocol aspects of component interaction. Their formalization, called interface automata, permits a compiler to check the compatibility of component interaction protocols. Interface automata support incremental design and independent implementability. Incremental design means that the compatibility checking of interfaces can proceed for partial system descriptions, without knowing the interfaces of all components. Independent implementability means that compatible interfaces can be refined separately, while still maintaining compatibility.","lang":"eng"}],"page":"83 - 104","month":"07","type":"conference","quality_controlled":0,"day":"15","date_created":"2018-12-11T12:09:49Z","publication_status":"published","status":"public","conference":{"name":"Engineering Theories of Software Intensive Systems"},"extern":1,"year":"2005","doi":"10.1007/1-4020-3532-2_3"},{"volume":345,"date_published":"2005-11-21T00:00:00Z","date_updated":"2021-01-12T08:00:37Z","title":"Model checking discounted temporal properties","publisher":"Elsevier","publist_id":"80","intvolume":"       345","_id":"4625","author":[{"full_name":"de Alfaro, Luca","first_name":"Luca","last_name":"De Alfaro"},{"full_name":"Faella, Marco","first_name":"Marco","last_name":"Faella"},{"full_name":"Thomas Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"last_name":"Majumdar","first_name":"Ritankar","full_name":"Majumdar, Ritankar S"},{"full_name":"Stoelinga, Mariëlle","first_name":"Mariëlle","last_name":"Stoelinga"}],"quality_controlled":0,"extern":1,"day":"21","publication_status":"published","status":"public","date_created":"2018-12-11T12:09:49Z","year":"2005","doi":"10.1016/j.tcs.2005.07.033","issue":"1","publication":"Theoretical Computer Science","citation":{"ieee":"L. De Alfaro, M. Faella, T. A. Henzinger, R. Majumdar, and M. Stoelinga, “Model checking discounted temporal properties,” <i>Theoretical Computer Science</i>, vol. 345, no. 1. Elsevier, pp. 139–170, 2005.","ama":"De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. Model checking discounted temporal properties. <i>Theoretical Computer Science</i>. 2005;345(1):139-170. doi:<a href=\"https://doi.org/10.1016/j.tcs.2005.07.033\">10.1016/j.tcs.2005.07.033</a>","short":"L. De Alfaro, M. Faella, T.A. Henzinger, R. Majumdar, M. Stoelinga, Theoretical Computer Science 345 (2005) 139–170.","chicago":"De Alfaro, Luca, Marco Faella, Thomas A Henzinger, Ritankar Majumdar, and Mariëlle Stoelinga. “Model Checking Discounted Temporal Properties.” <i>Theoretical Computer Science</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.tcs.2005.07.033\">https://doi.org/10.1016/j.tcs.2005.07.033</a>.","apa":"De Alfaro, L., Faella, M., Henzinger, T. A., Majumdar, R., &#38; Stoelinga, M. (2005). Model checking discounted temporal properties. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2005.07.033\">https://doi.org/10.1016/j.tcs.2005.07.033</a>","ista":"De Alfaro L, Faella M, Henzinger TA, Majumdar R, Stoelinga M. 2005. Model checking discounted temporal properties. Theoretical Computer Science. 345(1), 139–170.","mla":"De Alfaro, Luca, et al. “Model Checking Discounted Temporal Properties.” <i>Theoretical Computer Science</i>, vol. 345, no. 1, Elsevier, 2005, pp. 139–70, doi:<a href=\"https://doi.org/10.1016/j.tcs.2005.07.033\">10.1016/j.tcs.2005.07.033</a>."},"abstract":[{"text":"Temporal logic is two-valued: formulas are interpreted as either true or false. When applied to the analysis of stochastic systems, or systems with imprecise formal models, temporal logic is therefore fragile: even small changes in the model can lead to opposite truth values for a specification. We present a generalization of the branching-time logic CTL which achieves robustness with respect to model perturbations by giving a quantitative interpretation to predicates and logical operators, and by discounting the importance of events according to how late they occur. In every state, the value of a formula is a real number in the interval [0,1], where 1 corresponds to truth and 0 to falsehood. The boolean operators and and or are replaced by min and max, the path quantifiers ∃ and ∀ determine sup and inf over all paths from a given state, and the temporal operators ⋄ and □ specify sup and inf over a given path; a new operator averages all values along a path. Furthermore, all path operators are discounted by a parameter that can be chosen to give more weight to states that are closer to the beginning of the path.\n\nWe interpret the resulting logic DCTL over transition systems, Markov chains, and Markov decision processes. We present two semantics for DCTL: a path semantics, inspired by the standard interpretation of state and path formulas in CTL, and a fixpoint semantics, inspired by the μ-calculus evaluation of CTL formulas. We show that, while these semantics coincide for CTL, they differ for DCTL, and we provide model-checking algorithms for both semantics.","lang":"eng"}],"page":"139 - 170","month":"11","type":"journal_article"},{"doi":" 10.1109/QELS.2005.1548783","year":"2005","extern":1,"date_created":"2018-12-11T11:47:16Z","conference":{"name":"QELS: Quantum Electronics and Laser Science"},"day":"01","publication_status":"published","status":"public","quality_controlled":0,"type":"conference","month":"01","page":"365 - 367","abstract":[{"lang":"eng","text":"We present the first demonstration of Jozsa's &quot;counterfactual computation&quot;, using an optical Grover's search algorithm. We put the algorithm in a superposition of 'running' and 'not-running', obtaining information even though the algorithm does not run."}],"alternative_title":["QELS"],"citation":{"short":"O. Hosten, M. Rakher, J. Barreiro, N. Peters, P. Kwiat, in:, IEEE, 2005, pp. 365–367.","ista":"Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. 2005. Counterfactual quantum computation. QELS: Quantum Electronics and Laser Science, QELS, vol. 1, 365–367.","mla":"Hosten, Onur, et al. <i>Counterfactual Quantum Computation</i>. Vol. 1, IEEE, 2005, pp. 365–67, doi:<a href=\"https://doi.org/ 10.1109/QELS.2005.1548783\"> 10.1109/QELS.2005.1548783</a>.","apa":"Hosten, O., Rakher, M., Barreiro, J., Peters, N., &#38; Kwiat, P. (2005). Counterfactual quantum computation (Vol. 1, pp. 365–367). Presented at the QELS: Quantum Electronics and Laser Science, IEEE. <a href=\"https://doi.org/ 10.1109/QELS.2005.1548783\">https://doi.org/ 10.1109/QELS.2005.1548783</a>","chicago":"Hosten, Onur, Matthew Rakher, Julio Barreiro, Nicholas Peters, and Paul Kwiat. “Counterfactual Quantum Computation,” 1:365–67. IEEE, 2005. <a href=\"https://doi.org/ 10.1109/QELS.2005.1548783\">https://doi.org/ 10.1109/QELS.2005.1548783</a>.","ieee":"O. Hosten, M. Rakher, J. Barreiro, N. Peters, and P. Kwiat, “Counterfactual quantum computation,” presented at the QELS: Quantum Electronics and Laser Science, 2005, vol. 1, pp. 365–367.","ama":"Hosten O, Rakher M, Barreiro J, Peters N, Kwiat P. Counterfactual quantum computation. In: Vol 1. IEEE; 2005:365-367. doi:<a href=\"https://doi.org/ 10.1109/QELS.2005.1548783\"> 10.1109/QELS.2005.1548783</a>"},"date_updated":"2021-01-12T08:03:18Z","date_published":"2005-01-01T00:00:00Z","volume":1,"intvolume":"         1","_id":"575","author":[{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur","full_name":"Onur Hosten","orcid":"0000-0002-2031-204X","last_name":"Hosten"},{"full_name":"Rakher, Matthew T","first_name":"Matthew","last_name":"Rakher"},{"last_name":"Barreiro","full_name":"Barreiro, Julio T","first_name":"Julio"},{"full_name":"Peters, Nicholas A","first_name":"Nicholas","last_name":"Peters"},{"last_name":"Kwiat","full_name":"Kwiat, Paul G","first_name":"Paul"}],"publist_id":"7237","title":"Counterfactual quantum computation","publisher":"IEEE"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Annual Reviews","title":"Neuronal substrates of complex behaviors in C. elegans","article_processing_charge":"No","_id":"6153","author":[{"full_name":"de Bono, Mario","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","orcid":"0000-0001-8347-0443"},{"last_name":"Villu Maricq","first_name":"Andres","full_name":"Villu Maricq, Andres"}],"intvolume":"        28","pmid":1,"external_id":{"pmid":["16022603"]},"volume":28,"article_type":"original","publication_identifier":{"issn":["0147-006X"],"eissn":["1545-4126"]},"date_updated":"2025-07-01T06:45:21Z","date_published":"2005-07-21T00:00:00Z","oa_version":"None","page":"451-501","citation":{"ieee":"M. de Bono and A. Villu Maricq, “Neuronal substrates of complex behaviors in C. elegans,” <i>Annual Review of Neuroscience</i>, vol. 28. Annual Reviews, pp. 451–501, 2005.","ama":"de Bono M, Villu Maricq A. Neuronal substrates of complex behaviors in C. elegans. <i>Annual Review of Neuroscience</i>. 2005;28:451-501. doi:<a href=\"https://doi.org/10.1146/annurev.neuro.27.070203.144259\">10.1146/annurev.neuro.27.070203.144259</a>","short":"M. de Bono, A. Villu Maricq, Annual Review of Neuroscience 28 (2005) 451–501.","chicago":"Bono, Mario de, and Andres Villu Maricq. “Neuronal Substrates of Complex Behaviors in C. Elegans.” <i>Annual Review of Neuroscience</i>. Annual Reviews, 2005. <a href=\"https://doi.org/10.1146/annurev.neuro.27.070203.144259\">https://doi.org/10.1146/annurev.neuro.27.070203.144259</a>.","apa":"de Bono, M., &#38; Villu Maricq, A. (2005). Neuronal substrates of complex behaviors in C. elegans. <i>Annual Review of Neuroscience</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev.neuro.27.070203.144259\">https://doi.org/10.1146/annurev.neuro.27.070203.144259</a>","ista":"de Bono M, Villu Maricq A. 2005. Neuronal substrates of complex behaviors in C. elegans. Annual Review of Neuroscience. 28, 451–501.","mla":"de Bono, Mario, and Andres Villu Maricq. “Neuronal Substrates of Complex Behaviors in C. Elegans.” <i>Annual Review of Neuroscience</i>, vol. 28, Annual Reviews, 2005, pp. 451–501, doi:<a href=\"https://doi.org/10.1146/annurev.neuro.27.070203.144259\">10.1146/annurev.neuro.27.070203.144259</a>."},"abstract":[{"text":"A current challenge in neuroscience is to bridge the gaps between genes, proteins, neurons, neural circuits, and behavior in a single animal model. The nematode Caenorhabditis elegans has unique features that facilitate this synthesis. Its nervous system includes exactly 302 neurons, and their pattern of synaptic connectivity is known. With only five olfactory neurons, C. elegans can dynamically respond to dozens of attractive and repellant odors. Thermosensory neurons enable the nematode to remember its cultivation temperature and to track narrow isotherms. Polymodal sensory neurons detect a wide range of nociceptive cues and signal robust escape responses. Pairing of sensory stimuli leads to long-lived changes in behavior consistent with associative learning. Worms exhibit social behaviors and complex ultradian rhythms driven by Ca2+ oscillators with clock-like properties. Genetic analysis has identified gene products required for nervous system function and elucidated the molecular and neural bases of behaviors.","lang":"eng"}],"publication":"Annual Review of Neuroscience","type":"journal_article","month":"07","day":"21","language":[{"iso":"eng"}],"publication_status":"published","status":"public","date_created":"2019-03-21T09:31:29Z","extern":"1","quality_controlled":"1","doi":"10.1146/annurev.neuro.27.070203.144259","year":"2005"},{"external_id":{"pmid":["15916947"]},"volume":15,"date_published":"2005-05-24T00:00:00Z","publication_identifier":{"issn":["0960-9822"]},"date_updated":"2021-01-12T08:06:24Z","title":"Experience-dependent modulation of C. elegans behavior by ambient oxygen","publisher":"Elsevier","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","pmid":1,"intvolume":"        15","_id":"6154","author":[{"full_name":"Cheung, Benny H.H.","first_name":"Benny H.H.","last_name":"Cheung"},{"full_name":"Cohen, Merav","first_name":"Merav","last_name":"Cohen"},{"last_name":"Rogers","first_name":"Candida","full_name":"Rogers, Candida"},{"last_name":"Albayram","first_name":"Onder","full_name":"Albayram, Onder"},{"full_name":"de Bono, Mario","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","last_name":"de Bono"}],"quality_controlled":"1","extern":"1","day":"24","publication_status":"published","language":[{"iso":"eng"}],"date_created":"2019-03-21T09:37:48Z","status":"public","year":"2005","doi":"10.1016/j.cub.2005.04.017","issue":"10","publication":"Current Biology","citation":{"ieee":"B. H. H. Cheung, M. Cohen, C. Rogers, O. Albayram, and M. de Bono, “Experience-dependent modulation of C. elegans behavior by ambient oxygen,” <i>Current Biology</i>, vol. 15, no. 10. Elsevier, pp. 905–917, 2005.","ama":"Cheung BHH, Cohen M, Rogers C, Albayram O, de Bono M. Experience-dependent modulation of C. elegans behavior by ambient oxygen. <i>Current Biology</i>. 2005;15(10):905-917. doi:<a href=\"https://doi.org/10.1016/j.cub.2005.04.017\">10.1016/j.cub.2005.04.017</a>","short":"B.H.H. Cheung, M. Cohen, C. Rogers, O. Albayram, M. de Bono, Current Biology 15 (2005) 905–917.","ista":"Cheung BHH, Cohen M, Rogers C, Albayram O, de Bono M. 2005. Experience-dependent modulation of C. elegans behavior by ambient oxygen. Current Biology. 15(10), 905–917.","apa":"Cheung, B. H. H., Cohen, M., Rogers, C., Albayram, O., &#38; de Bono, M. (2005). Experience-dependent modulation of C. elegans behavior by ambient oxygen. <i>Current Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cub.2005.04.017\">https://doi.org/10.1016/j.cub.2005.04.017</a>","mla":"Cheung, Benny H. H., et al. “Experience-Dependent Modulation of C. Elegans Behavior by Ambient Oxygen.” <i>Current Biology</i>, vol. 15, no. 10, Elsevier, 2005, pp. 905–17, doi:<a href=\"https://doi.org/10.1016/j.cub.2005.04.017\">10.1016/j.cub.2005.04.017</a>.","chicago":"Cheung, Benny H.H., Merav Cohen, Candida Rogers, Onder Albayram, and Mario de Bono. “Experience-Dependent Modulation of C. Elegans Behavior by Ambient Oxygen.” <i>Current Biology</i>. Elsevier, 2005. <a href=\"https://doi.org/10.1016/j.cub.2005.04.017\">https://doi.org/10.1016/j.cub.2005.04.017</a>."},"page":"905-917","oa_version":"None","month":"05","type":"journal_article"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"2975","publisher":"American Physical Society","title":"Robust formation of morphogen gradients","article_processing_charge":"No","author":[{"full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","last_name":"Bollenbach"},{"last_name":"Kruse","first_name":"Karsten","full_name":"Kruse, Karsten"},{"last_name":"Pantazis","first_name":"Periklis","full_name":"Pantazis, Periklis"},{"last_name":"González Gaitán","first_name":"Marcos","full_name":"González Gaitán, Marcos"},{"first_name":"Frank","full_name":"Jülicher, Frank","last_name":"Jülicher"}],"_id":"3426","intvolume":"        94","external_id":{"arxiv":["q-bio/0412014"]},"volume":94,"arxiv":1,"date_updated":"2021-01-12T07:43:23Z","date_published":"2005-01-01T00:00:00Z","oa_version":"Preprint","abstract":[{"text":"We discuss the formation of graded morphogen profiles in a cell layer by nonlinear transport phenomena, important for patterning developing organisms. We focus on a process termed transcytosis, where morphogen transport results from the binding of ligands to receptors on the cell surface, incorporation into the cell, and subsequent externalization. Starting from a microscopic model, we derive effective transport equations. We show that, in contrast to morphogen transport by extracellular diffusion, transcytosis leads to robust ligand profiles which are insensitive to the rate of ligand production.","lang":"eng"}],"citation":{"ama":"Bollenbach MT, Kruse K, Pantazis P, González Gaitán M, Jülicher F. Robust formation of morphogen gradients. <i>Physical Review Letters</i>. 2005;94(1). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.94.018103\">10.1103/PhysRevLett.94.018103</a>","ieee":"M. T. Bollenbach, K. Kruse, P. Pantazis, M. González Gaitán, and F. Jülicher, “Robust formation of morphogen gradients,” <i>Physical Review Letters</i>, vol. 94, no. 1. American Physical Society, 2005.","apa":"Bollenbach, M. T., Kruse, K., Pantazis, P., González Gaitán, M., &#38; Jülicher, F. (2005). Robust formation of morphogen gradients. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.94.018103\">https://doi.org/10.1103/PhysRevLett.94.018103</a>","ista":"Bollenbach MT, Kruse K, Pantazis P, González Gaitán M, Jülicher F. 2005. Robust formation of morphogen gradients. Physical Review Letters. 94(1).","mla":"Bollenbach, Mark Tobias, et al. “Robust Formation of Morphogen Gradients.” <i>Physical Review Letters</i>, vol. 94, no. 1, American Physical Society, 2005, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.94.018103\">10.1103/PhysRevLett.94.018103</a>.","chicago":"Bollenbach, Mark Tobias, Karsten Kruse, Periklis Pantazis, Marcos González Gaitán, and Frank Jülicher. “Robust Formation of Morphogen Gradients.” <i>Physical Review Letters</i>. American Physical Society, 2005. <a href=\"https://doi.org/10.1103/PhysRevLett.94.018103\">https://doi.org/10.1103/PhysRevLett.94.018103</a>.","short":"M.T. Bollenbach, K. Kruse, P. Pantazis, M. González Gaitán, F. Jülicher, Physical Review Letters 94 (2005)."},"publication":"Physical Review Letters","type":"journal_article","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/q-bio/0412014"}],"month":"01","publication_status":"published","day":"01","date_created":"2018-12-11T12:03:16Z","status":"public","language":[{"iso":"eng"}],"extern":"1","issue":"1","doi":"10.1103/PhysRevLett.94.018103","oa":1,"year":"2005"},{"date_updated":"2021-01-12T07:43:26Z","date_published":"2005-04-21T00:00:00Z","author":[{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","full_name":"Jonathan Bollback","last_name":"Bollback","orcid":"0000-0002-4624-4612"}],"_id":"3433","editor":[{"last_name":"Nielsen","full_name":"Nielsen, Rasmus","first_name":"Rasmus"}],"publist_id":"2967","publisher":"Springer","title":"Posterior mapping and posterior predictive distributions","doi":"10.1007/0-387-27733-1","year":"2005","status":"public","day":"21","date_created":"2018-12-11T12:03:18Z","publication_status":"published","extern":1,"quality_controlled":0,"type":"book_chapter","month":"04","page":"439 - 462","citation":{"chicago":"Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.” In <i>Statistical Methods in Molecular Evolution</i>, edited by Rasmus Nielsen, 439–62. Springer, 2005. <a href=\"https://doi.org/10.1007/0-387-27733-1\">https://doi.org/10.1007/0-387-27733-1</a>.","mla":"Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.” <i>Statistical Methods in Molecular Evolution</i>, edited by Rasmus Nielsen, Springer, 2005, pp. 439–62, doi:<a href=\"https://doi.org/10.1007/0-387-27733-1\">10.1007/0-387-27733-1</a>.","ista":"Bollback JP. 2005.Posterior mapping and posterior predictive distributions. In: Statistical methods in Molecular Evolution. , 439–462.","apa":"Bollback, J. P. (2005). Posterior mapping and posterior predictive distributions. In R. Nielsen (Ed.), <i>Statistical methods in Molecular Evolution</i> (pp. 439–462). Springer. <a href=\"https://doi.org/10.1007/0-387-27733-1\">https://doi.org/10.1007/0-387-27733-1</a>","short":"J.P. Bollback, in:, R. Nielsen (Ed.), Statistical Methods in Molecular Evolution, Springer, 2005, pp. 439–462.","ama":"Bollback JP. Posterior mapping and posterior predictive distributions. In: Nielsen R, ed. <i>Statistical Methods in Molecular Evolution</i>. Springer; 2005:439-462. doi:<a href=\"https://doi.org/10.1007/0-387-27733-1\">10.1007/0-387-27733-1</a>","ieee":"J. P. Bollback, “Posterior mapping and posterior predictive distributions,” in <i>Statistical methods in Molecular Evolution</i>, R. Nielsen, Ed. Springer, 2005, pp. 439–462."},"publication":"Statistical methods in Molecular Evolution"},{"doi":"10.1523/JNEUROSCI.3269-05.2005","issue":"42","year":"2005","extern":1,"day":"19","status":"public","publication_status":"published","date_created":"2018-12-11T12:03:21Z","quality_controlled":0,"type":"journal_article","month":"10","page":"9782 - 9793","publication":"Journal of Neuroscience","citation":{"ieee":"T. Klausberger <i>et al.</i>, “Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations,” <i>Journal of Neuroscience</i>, vol. 25, no. 42. Society for Neuroscience, pp. 9782–9793, 2005.","ama":"Klausberger T, Marton L, O’Neill J, et al. Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations. <i>Journal of Neuroscience</i>. 2005;25(42):9782-9793. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.3269-05.2005\">10.1523/JNEUROSCI.3269-05.2005</a>","short":"T. Klausberger, L. Marton, J. O’Neill, J. Huck, Y. Dalezios, P. Fuentealba, W. Suen, E. Papp, T. Kaneko, M. Watanabe, J.L. Csicsvari, P. Somogyi, Journal of Neuroscience 25 (2005) 9782–9793.","chicago":"Klausberger, Thomas, Laszlo Marton, Joseph O’Neill, Jojanneke Huck, Yannis Dalezios, Pablo Fuentealba, Wai Suen, et al. “Complementary Roles of Cholecystokinin- and Parvalbumin-Expressing GABAergic Neurons in Hippocampal Network Oscillations.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2005. <a href=\"https://doi.org/10.1523/JNEUROSCI.3269-05.2005\">https://doi.org/10.1523/JNEUROSCI.3269-05.2005</a>.","apa":"Klausberger, T., Marton, L., O’Neill, J., Huck, J., Dalezios, Y., Fuentealba, P., … Somogyi, P. (2005). Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.3269-05.2005\">https://doi.org/10.1523/JNEUROSCI.3269-05.2005</a>","mla":"Klausberger, Thomas, et al. “Complementary Roles of Cholecystokinin- and Parvalbumin-Expressing GABAergic Neurons in Hippocampal Network Oscillations.” <i>Journal of Neuroscience</i>, vol. 25, no. 42, Society for Neuroscience, 2005, pp. 9782–93, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.3269-05.2005\">10.1523/JNEUROSCI.3269-05.2005</a>.","ista":"Klausberger T, Marton L, O’Neill J, Huck J, Dalezios Y, Fuentealba P, Suen W, Papp E, Kaneko T, Watanabe M, Csicsvari JL, Somogyi P. 2005. Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations. Journal of Neuroscience. 25(42), 9782–9793."},"abstract":[{"lang":"eng","text":"In the hippocampal CA1 area, a relatively homogenous population of pyramidal cells is accompanied by a diversity of GABAergic interneurons. Previously, we found that parvalbumin-expressing basket, axo-axonic, bistratified, and oriens-lacunosum moleculare cells, innervating different domains of pyramidal cells, have distinct firing patterns during network oscillations in vivo. A second family of interneurons, expressing cholecystokinin but not parvalbumin, is known to target the same domains of pyramidal cells as do the parvalbumin cells. To test the temporal activity of these independent and parallel GABAergic inputs, we recorded the precise spike timing of identified cholecystokinin interneurons during hippocampal network oscillations in anesthetized rats and determined their molecular expression profiles and synaptic targets. The cells were cannabinoid receptor type 1 immunopositive. Contrary to the stereotyped firing of parvalbumin interneurons, cholecystokinin-expressing basket and dendrite-innervating cells discharge, on average, with 1.7 ± 2.0 Hz during high-frequency ripple oscillations in an episode-dependent manner. During theta oscillations, cholecystokinin- expressing interneurons fire with 8.8 ± 3.3 Hz at a characteristic time on the ascending phase of theta waves (155 ± 81°), when place cells start firing in freely moving animals. The firing patterns of some interneurons recorded in drug-free behaving rats were similar to cholecystokinin cells in anesthetized animals. Our results demonstrate that cholecystokinin- and parvalbumin-expressing interneurons make different contributions to network oscillations and play distinct roles in different brain states. We suggest that the specific spike timing of cholecystokinin interneurons and their sensitivity to endocannabinoids might contribute to differentiate subgroups of pyramidal cells forming neuronal assemblies, whereas parvalbumin interneurons contribute to synchronizing the entire network. Copyright © 2005 Society for Neuroscience."}],"date_updated":"2021-01-12T07:43:30Z","date_published":"2005-10-19T00:00:00Z","volume":25,"intvolume":"        25","author":[{"full_name":"Klausberger,Thomas","first_name":"Thomas","last_name":"Klausberger"},{"last_name":"Marton","full_name":"Marton,Laszlo F","first_name":"Laszlo"},{"last_name":"O'Neill","full_name":"Joseph O'Neill","first_name":"Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Huck","full_name":"Huck, Jojanneke H","first_name":"Jojanneke"},{"last_name":"Dalezios","first_name":"Yannis","full_name":"Dalezios, Yannis"},{"first_name":"Pablo","full_name":"Fuentealba,Pablo","last_name":"Fuentealba"},{"full_name":"Suen, Wai Yee","first_name":"Wai","last_name":"Suen"},{"first_name":"Edit","full_name":"Papp, Edit Cs","last_name":"Papp"},{"full_name":"Kaneko, Takeshi","first_name":"Takeshi","last_name":"Kaneko"},{"last_name":"Watanabe","first_name":"Masahiko","full_name":"Watanabe, Masahiko"},{"orcid":"0000-0002-5193-4036","last_name":"Csicsvari","full_name":"Jozsef Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L"},{"last_name":"Somogyi","first_name":"Péter","full_name":"Somogyi, Péter"}],"_id":"3443","publist_id":"2944","title":"Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations","publisher":"Society for Neuroscience"},{"oa_version":"Published Version","abstract":[{"text":"Methods, apparatus and computer program products can generate light weight but highly realistic and accurate colored models of three-dimensional colored objects. The colored model may be generated from a second plurality of points that define a coarse digital representation of the surface and at least one texture map containing information derived from a first plurality of colored points that define a fine digital representation of the surface. This derivation is achieved by mapping points within the texture map to the fine digital representation of the three-dimensional surface. Colored scan data may be used to construct the fine digital representation as a triangulated surface (i.e., triangulation) using a wrapping operation.","lang":"eng"}],"citation":{"chicago":"Williams, Steven, Herbert Edelsbrunner, and Ping Fu. “Methods, Apparatus and Computer Program Products for Modeling Three-Dimensional Colored Objects,” 2005.","mla":"Williams, Steven, et al. <i>Methods, Apparatus and Computer Program Products for Modeling Three-Dimensional Colored Objects</i>. 2005.","apa":"Williams, S., Edelsbrunner, H., &#38; Fu, P. (2005). Methods, apparatus and computer program products for modeling three-dimensional colored objects.","ista":"Williams S, Edelsbrunner H, Fu P. 2005. Methods, apparatus and computer program products for modeling three-dimensional colored objects.","short":"S. Williams, H. Edelsbrunner, P. Fu, (2005).","ama":"Williams S, Edelsbrunner H, Fu P. Methods, apparatus and computer program products for modeling three-dimensional colored objects. 2005.","ieee":"S. Williams, H. Edelsbrunner, and P. Fu, “Methods, apparatus and computer program products for modeling three-dimensional colored objects.” 2005."},"type":"patent","main_file_link":[{"open_access":"1","url":"https://patents.google.com/patent/US6853373B2/"}],"month":"02","date_created":"2018-12-11T12:03:42Z","status":"public","day":"08","extern":"1","year":"2005","oa":1,"ipc":"G06T17/20 ; G06T15/04","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publist_id":"2878","title":"Methods, apparatus and computer program products for modeling three-dimensional colored objects","publication_date":"2005-02-08","article_processing_charge":"No","_id":"3509","author":[{"last_name":"Williams","first_name":"Steven","full_name":"Williams, Steven"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert"},{"last_name":"Fu","full_name":"Fu, Ping","first_name":"Ping"}],"ipn":"US6853373B2","applicant":["Raindrop Geomagic, Inc."],"date_updated":"2022-01-05T13:59:09Z","date_published":"2005-02-08T00:00:00Z"},{"year":"2005","doi":"http://dx.doi.org/10.2312/SGP/SGP05/009-011","quality_controlled":0,"date_created":"2018-12-11T12:03:57Z","status":"public","publication_status":"published","day":"01","conference":{"name":"SGP: Eurographics Symposium on Geometry processing"},"extern":1,"month":"07","type":"conference","main_file_link":[{"open_access":"0","url":"http://www.cs.duke.edu/~edels/Papers/2005-P-03-SurfaceTiling.pdf"}],"citation":{"ieee":"H. Edelsbrunner, “Surface tiling with differential topology,” presented at the SGP: Eurographics Symposium on Geometry processing, 2005, pp. 9–11.","ama":"Edelsbrunner H. Surface tiling with differential topology. In: ACM; 2005:9-11. doi:<a href=\"http://dx.doi.org/10.2312/SGP/SGP05/009-011\">http://dx.doi.org/10.2312/SGP/SGP05/009-011</a>","short":"H. Edelsbrunner, in:, ACM, 2005, pp. 9–11.","ista":"Edelsbrunner H. 2005. Surface tiling with differential topology. SGP: Eurographics Symposium on Geometry processing, 9–11.","apa":"Edelsbrunner, H. (2005). Surface tiling with differential topology (pp. 9–11). Presented at the SGP: Eurographics Symposium on Geometry processing, ACM. <a href=\"http://dx.doi.org/10.2312/SGP/SGP05/009-011\">http://dx.doi.org/10.2312/SGP/SGP05/009-011</a>","mla":"Edelsbrunner, Herbert. <i>Surface Tiling with Differential Topology</i>. ACM, 2005, pp. 9–11, doi:<a href=\"http://dx.doi.org/10.2312/SGP/SGP05/009-011\">http://dx.doi.org/10.2312/SGP/SGP05/009-011</a>.","chicago":"Edelsbrunner, Herbert. “Surface Tiling with Differential Topology,” 9–11. ACM, 2005. <a href=\"http://dx.doi.org/10.2312/SGP/SGP05/009-011\">http://dx.doi.org/10.2312/SGP/SGP05/009-011</a>."},"abstract":[{"text":"A challenging problem in computer-aided geometric design is the decomposition of a surface into four-sided regions that are then represented by NURBS patches. There are various approaches published in the literature and implemented as commercially available software, but all fall short in either automation or quality of the result. At Raindrop Geomagic, we have recently taken a fresh approach based on concepts from Morse theory. This by itself is not a new idea, but we have some novel ingredients that make this work, one being a rational notion of hierarchy that guides the construction of a simplified decomposition sensitive to only the major critical points.","lang":"eng"}],"page":"9 - 11","date_published":"2005-07-01T00:00:00Z","date_updated":"2021-01-12T07:44:17Z","_id":"3557","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Herbert Edelsbrunner","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"}],"publisher":"ACM","title":"Surface tiling with differential topology","publist_id":"2828"},{"date_updated":"2021-01-12T07:44:18Z","date_published":"2005-01-01T00:00:00Z","publist_id":"2827","publisher":"ACM","title":"Extraction and simplification of iso-surfaces in tandem","author":[{"first_name":"Dominique","full_name":"Attali, Dominique","last_name":"Attali"},{"first_name":"David","full_name":"Cohen-Steiner, David","last_name":"Cohen Steiner"},{"full_name":"Herbert Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"}],"_id":"3558","publication_status":"published","status":"public","day":"01","date_created":"2018-12-11T12:03:57Z","conference":{"name":"SGP: Eurographics Symposium on Geometry processing"},"extern":1,"quality_controlled":0,"year":"2005","page":"139 - 148","citation":{"chicago":"Attali, Dominique, David Cohen Steiner, and Herbert Edelsbrunner. “Extraction and Simplification of Iso-Surfaces in Tandem,” 139–48. ACM, 2005.","mla":"Attali, Dominique, et al. <i>Extraction and Simplification of Iso-Surfaces in Tandem</i>. ACM, 2005, pp. 139–48.","ista":"Attali D, Cohen Steiner D, Edelsbrunner H. 2005. Extraction and simplification of iso-surfaces in tandem. SGP: Eurographics Symposium on Geometry processing, 139–148.","apa":"Attali, D., Cohen Steiner, D., &#38; Edelsbrunner, H. (2005). Extraction and simplification of iso-surfaces in tandem (pp. 139–148). Presented at the SGP: Eurographics Symposium on Geometry processing, ACM.","short":"D. Attali, D. Cohen Steiner, H. Edelsbrunner, in:, ACM, 2005, pp. 139–148.","ama":"Attali D, Cohen Steiner D, Edelsbrunner H. Extraction and simplification of iso-surfaces in tandem. In: ACM; 2005:139-148.","ieee":"D. Attali, D. Cohen Steiner, and H. Edelsbrunner, “Extraction and simplification of iso-surfaces in tandem,” presented at the SGP: Eurographics Symposium on Geometry processing, 2005, pp. 139–148."},"abstract":[{"lang":"eng","text":"The tandem algorithm combines the marching cube algorithm for surface extraction and the edge contraction algorithm for surface simplification in lock-step to avoid the costly intermediate step of storing the entire extracted surface triangulation. Beyond this basic strategy, we introduce refinements to prevent artifacts in the resulting triangulation, first, by carefully monitoring the amount of simplification during the process and, second, by driving the simplification toward a compromise between shape approximation and mesh quality. We have implemented the algorithm and used extensive computational experiments to document the effects of various design options and to further fine-tune the algorithm."}],"type":"conference","main_file_link":[{"url":"http://dl.acm.org/citation.cfm?id=1281943","open_access":"0"}],"acknowledgement":"Partially supported the generated triangulations. Two questions arise: “how do by NSF grant CCR-00-86013 (BioGeometry).","month":"01"}]