[{"year":"2014","publication_identifier":{"eissn":["1869-7135"],"issn":["0012-0456"]},"month":"03","keyword":["General Medicine"],"page":"21-41","department":[{"_id":"RoSe"}],"date_created":"2022-03-04T07:54:39Z","language":[{"iso":"eng"}],"author":[{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521"}],"date_published":"2014-03-01T00:00:00Z","article_processing_charge":"No","date_updated":"2024-10-09T21:01:45Z","doi":"10.1365/s13291-014-0083-9","volume":116,"article_type":"original","quality_controlled":"1","abstract":[{"lang":"eng","text":"We review recent progress towards a rigorous understanding of the excitation spectrum of bosonic quantum many-body systems. In particular, we explain how one can rigorously establish the predictions resulting from the Bogoliubov approximation in the mean field limit. The latter predicts that the spectrum is made up of elementary excitations, whose energy behaves linearly in the momentum for small momentum. This property is crucial for the superfluid behavior of the system. We also discuss a list of open problems in this field."}],"intvolume":"       116","corr_author":"1","publication":"Jahresbericht der Deutschen Mathematiker-Vereinigung","scopus_import":"1","type":"journal_article","title":"The excitation spectrum for Bose fluids with weak interactions","oa_version":"None","_id":"10814","citation":{"ama":"Seiringer R. The excitation spectrum for Bose fluids with weak interactions. <i>Jahresbericht der Deutschen Mathematiker-Vereinigung</i>. 2014;116:21-41. doi:<a href=\"https://doi.org/10.1365/s13291-014-0083-9\">10.1365/s13291-014-0083-9</a>","apa":"Seiringer, R. (2014). The excitation spectrum for Bose fluids with weak interactions. <i>Jahresbericht Der Deutschen Mathematiker-Vereinigung</i>. Springer Nature. <a href=\"https://doi.org/10.1365/s13291-014-0083-9\">https://doi.org/10.1365/s13291-014-0083-9</a>","short":"R. Seiringer, Jahresbericht Der Deutschen Mathematiker-Vereinigung 116 (2014) 21–41.","mla":"Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.” <i>Jahresbericht Der Deutschen Mathematiker-Vereinigung</i>, vol. 116, Springer Nature, 2014, pp. 21–41, doi:<a href=\"https://doi.org/10.1365/s13291-014-0083-9\">10.1365/s13291-014-0083-9</a>.","chicago":"Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.” <i>Jahresbericht Der Deutschen Mathematiker-Vereinigung</i>. Springer Nature, 2014. <a href=\"https://doi.org/10.1365/s13291-014-0083-9\">https://doi.org/10.1365/s13291-014-0083-9</a>.","ista":"Seiringer R. 2014. The excitation spectrum for Bose fluids with weak interactions. Jahresbericht der Deutschen Mathematiker-Vereinigung. 116, 21–41.","ieee":"R. Seiringer, “The excitation spectrum for Bose fluids with weak interactions,” <i>Jahresbericht der Deutschen Mathematiker-Vereinigung</i>, vol. 116. Springer Nature, pp. 21–41, 2014."},"publisher":"Springer Nature","status":"public","day":"01","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published"},{"publication_status":"published","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"01","acknowledgement":"The authors thank all the members of the Division of Morphogenesis, National Institute for Basic Biology, for their contributions to the research, their encouragement, and helpful discussions, particularly Dr M. Suzuki for his critical reading of the manuscript. We also thank the Model Animal Research and Spectrography and Bioimaging Facilities, NIBB Core Research Facilities, for technical support. M.H. was supported by a research fellowship from the Japan Society for the Promotion of Science (JSPS). Our work introduced in this review was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan, to N.U.","status":"public","publisher":"Wiley","external_id":{"isi":["000331769200001"],"pmid":["24666178"]},"isi":1,"citation":{"ieee":"M. Hashimoto, H. Morita, and N. Ueno, “Molecular and cellular mechanisms of development underlying congenital diseases,” <i>Congenital Anomalies</i>, vol. 54, no. 1. Wiley, pp. 1–7, 2014.","chicago":"Hashimoto, Masakazu, Hitoshi Morita, and Naoto Ueno. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” <i>Congenital Anomalies</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/cga.12039\">https://doi.org/10.1111/cga.12039</a>.","ista":"Hashimoto M, Morita H, Ueno N. 2014. Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. 54(1), 1–7.","short":"M. Hashimoto, H. Morita, N. Ueno, Congenital Anomalies 54 (2014) 1–7.","mla":"Hashimoto, Masakazu, et al. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” <i>Congenital Anomalies</i>, vol. 54, no. 1, Wiley, 2014, pp. 1–7, doi:<a href=\"https://doi.org/10.1111/cga.12039\">10.1111/cga.12039</a>.","apa":"Hashimoto, M., Morita, H., &#38; Ueno, N. (2014). Molecular and cellular mechanisms of development underlying congenital diseases. <i>Congenital Anomalies</i>. Wiley. <a href=\"https://doi.org/10.1111/cga.12039\">https://doi.org/10.1111/cga.12039</a>","ama":"Hashimoto M, Morita H, Ueno N. Molecular and cellular mechanisms of development underlying congenital diseases. <i>Congenital Anomalies</i>. 2014;54(1):1-7. doi:<a href=\"https://doi.org/10.1111/cga.12039\">10.1111/cga.12039</a>"},"pmid":1,"oa_version":"None","_id":"10815","title":"Molecular and cellular mechanisms of development underlying congenital diseases","scopus_import":"1","type":"journal_article","intvolume":"        54","publication":"Congenital Anomalies","quality_controlled":"1","abstract":[{"lang":"eng","text":"In the last several decades, developmental biology has clarified the molecular mechanisms of embryogenesis and organogenesis. In particular, it has demonstrated that the “tool-kit genes” essential for regulating developmental processes are not only highly conserved among species, but are also used as systems at various times and places in an organism to control distinct developmental events. Therefore, mutations in many of these tool-kit genes may cause congenital diseases involving morphological abnormalities. This link between genes and abnormal morphological phenotypes underscores the importance of understanding how cells behave and contribute to morphogenesis as a result of gene function. Recent improvements in live imaging and in quantitative analyses of cellular dynamics will advance our understanding of the cellular pathogenesis of congenital diseases associated with aberrant morphologies. In these studies, it is critical to select an appropriate model organism for the particular phenomenon of interest."}],"article_type":"original","doi":"10.1111/cga.12039","volume":54,"date_updated":"2025-09-29T13:21:58Z","oa":1,"date_published":"2014-02-01T00:00:00Z","article_processing_charge":"No","date_created":"2022-03-04T08:17:25Z","department":[{"_id":"CaHe"}],"language":[{"iso":"eng"}],"author":[{"first_name":"Masakazu","last_name":"Hashimoto","full_name":"Hashimoto, Masakazu"},{"last_name":"Morita","full_name":"Morita, Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","first_name":"Hitoshi"},{"last_name":"Ueno","full_name":"Ueno, Naoto","first_name":"Naoto"}],"page":"1-7","keyword":["Developmental Biology","Embryology","General Medicine","Pediatrics","Perinatology","and Child Health"],"month":"02","main_file_link":[{"url":"https://doi.org/10.1111/cga.12039","open_access":"1"}],"issue":"1","publication_identifier":{"issn":["0914-3505"]},"year":"2014"},{"corr_author":"1","intvolume":"         3","ddc":["500"],"publication":"Proceeding of the International Congress of Mathematicans","type":"conference","scopus_import":"1","OA_type":"free access","conference":{"name":"ICM: International Congress of Mathematicans","end_date":"2014-08-21","location":"Seoul, South Korea","start_date":"2014-08-13"},"quality_controlled":"1","abstract":[{"text":"Many questions concerning models in quantum mechanics require a detailed analysis of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable Hilbert space. Of particular relevance for an understanding of the low-temperature properties of a system is the structure of the excitation spectrum, which is the part of the spectrum close to the spectral bottom. We present recent progress on this question for bosonic many-body quantum systems with weak two-body interactions. Such system are currently of great interest, due to their experimental realization in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations, which predicts that the low-energy spectrum is made up of sums of elementary excitations, with linear dispersion law at low momentum. The latter property is crucial for the superfluid behavior the system.","lang":"eng"}],"date_updated":"2026-06-18T19:30:06Z","oa":1,"volume":3,"date_published":"2014-08-01T00:00:00Z","article_processing_charge":"No","page":"1175-1194","department":[{"_id":"RoSe"}],"date_created":"2020-06-29T07:59:35Z","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-6781-0521","last_name":"Seiringer","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"}],"month":"08","main_file_link":[{"open_access":"1","url":"http://www.icm2014.org/en/vod/proceedings.html"}],"publication_identifier":{"isbn":["9788961058063"]},"year":"2014","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","publisher":"International Congress of Mathematicians","status":"public","citation":{"ama":"Seiringer R. Structure of the excitation spectrum for many-body quantum systems. In: <i>Proceeding of the International Congress of Mathematicans</i>. Vol 3. International Congress of Mathematicians; 2014:1175-1194.","apa":"Seiringer, R. (2014). Structure of the excitation spectrum for many-body quantum systems. In <i>Proceeding of the International Congress of Mathematicans</i> (Vol. 3, pp. 1175–1194). Seoul, South Korea: International Congress of Mathematicians.","mla":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” <i>Proceeding of the International Congress of Mathematicans</i>, vol. 3, International Congress of Mathematicians, 2014, pp. 1175–94.","short":"R. Seiringer, in:, Proceeding of the International Congress of Mathematicans, International Congress of Mathematicians, 2014, pp. 1175–1194.","chicago":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” In <i>Proceeding of the International Congress of Mathematicans</i>, 3:1175–94. International Congress of Mathematicians, 2014.","ieee":"R. Seiringer, “Structure of the excitation spectrum for many-body quantum systems,” in <i>Proceeding of the International Congress of Mathematicans</i>, Seoul, South Korea, 2014, vol. 3, pp. 1175–1194.","ista":"Seiringer R. 2014. Structure of the excitation spectrum for many-body quantum systems. Proceeding of the International Congress of Mathematicans. ICM: International Congress of Mathematicans vol. 3, 1175–1194."},"oa_version":"Published Version","_id":"8044","OA_place":"publisher","title":"Structure of the excitation spectrum for many-body quantum systems"},{"intvolume":"       156","publication":"Cell","type":"journal_article","scopus_import":"1","article_type":"original","quality_controlled":"1","abstract":[{"lang":"eng","text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints."}],"date_updated":"2021-12-14T08:22:36Z","oa":1,"volume":156,"doi":"10.1016/j.cell.2014.01.029","date_published":"2014-03-13T00:00:00Z","article_processing_charge":"No","page":"1286-1297","department":[{"_id":"DaZi"}],"language":[{"iso":"eng"}],"date_created":"2021-06-04T12:00:16Z","author":[{"first_name":"Jason T.","last_name":"Huff","full_name":"Huff, Jason T."},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"issue":"6","month":"03","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2014.01.029"}],"publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"year":"2014","extern":"1","publication_status":"published","day":"13","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Elsevier","status":"public","external_id":{"pmid":["24630728"]},"pmid":1,"citation":{"apa":"Huff, J. T., &#38; Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. 2014;156(6):1286-1297. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” <i>Cell</i>, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014.","chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>.","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.","mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>.","short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297."},"oa_version":"Published Version","_id":"9458","title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes"},{"title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","pmid":1,"citation":{"ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171.","ieee":"Z. Mérai <i>et al.</i>, “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>.","mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>.","short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171.","apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>","ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(45):16166-16171. doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>"},"oa_version":"Published Version","_id":"9479","publisher":"National Academy of Sciences","status":"public","external_id":{"pmid":["25344531"]},"publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"11","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"extern":"1","year":"2014","page":"16166-16171","language":[{"iso":"eng"}],"date_created":"2021-06-07T07:23:43Z","department":[{"_id":"DaZi"}],"author":[{"full_name":"Mérai, Zsuzsanna","last_name":"Mérai","first_name":"Zsuzsanna"},{"first_name":"Nina","last_name":"Chumak","full_name":"Chumak, Nina"},{"last_name":"García-Aguilar","full_name":"García-Aguilar, Marcelina","first_name":"Marcelina"},{"first_name":"Tzung-Fu","last_name":"Hsieh","full_name":"Hsieh, Tzung-Fu"},{"full_name":"Nishimura, Toshiro","last_name":"Nishimura","first_name":"Toshiro"},{"first_name":"Vera K.","last_name":"Schoft","full_name":"Schoft, Vera K."},{"full_name":"Bindics, János","last_name":"Bindics","first_name":"János"},{"first_name":"Lucyna","full_name":"Ślusarz, Lucyna","last_name":"Ślusarz"},{"last_name":"Arnoux","full_name":"Arnoux, Stéphanie","first_name":"Stéphanie"},{"first_name":"Susanne","full_name":"Opravil, Susanne","last_name":"Opravil"},{"first_name":"Karl","full_name":"Mechtler, Karl","last_name":"Mechtler"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","full_name":"Zilberman, Daniel"},{"first_name":"Robert L.","full_name":"Fischer, Robert L.","last_name":"Fischer"},{"full_name":"Tamaru, Hisashi","last_name":"Tamaru","first_name":"Hisashi"}],"issue":"45","month":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1418564111"}],"date_updated":"2021-12-14T08:23:26Z","oa":1,"volume":111,"doi":"10.1073/pnas.1418564111","date_published":"2014-11-11T00:00:00Z","article_processing_charge":"No","intvolume":"       111","publication":"Proceedings of the National Academy of Sciences","scopus_import":"1","type":"journal_article","article_type":"original","quality_controlled":"1","abstract":[{"lang":"eng","text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction."}]},{"publication_identifier":{"issn":["1360-1385"],"eissn":["1878-4372"]},"year":"2014","extern":"1","date_created":"2021-06-07T14:38:09Z","language":[{"iso":"eng"}],"department":[{"_id":"DaZi"}],"author":[{"first_name":"M. Yvonne","full_name":"Kim, M. Yvonne","last_name":"Kim"},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"page":"320-326","month":"05","issue":"5","doi":"10.1016/j.tplants.2014.01.014","volume":19,"date_updated":"2021-12-14T08:24:48Z","date_published":"2014-05-04T00:00:00Z","article_processing_charge":"No","type":"journal_article","scopus_import":"1","intvolume":"        19","publication":"Trends in Plant Science","quality_controlled":"1","abstract":[{"lang":"eng","text":"Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression."}],"article_type":"review","title":"DNA methylation as a system of plant genomic immunity","citation":{"apa":"Kim, M. Y., &#38; Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>","ama":"Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. 2014;19(5):320-326. doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>","ieee":"M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic immunity,” <i>Trends in Plant Science</i>, vol. 19, no. 5. Elsevier, pp. 320–326, 2014.","ista":"Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 19(5), 320–326.","chicago":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>.","short":"M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.","mla":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>, vol. 19, no. 5, Elsevier, 2014, pp. 320–26, doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>."},"pmid":1,"oa_version":"None","_id":"9519","status":"public","publisher":"Elsevier","external_id":{"pmid":["24618094 "]},"publication_status":"published","day":"04","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"title":"Transition probability between TF expression states when Dbx2 inhibits Nkx2.2","year":"2014","department":[{"_id":"JoCs"}],"date_created":"2021-07-26T14:35:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2004"}]},"author":[{"last_name":"Lovrics","full_name":"Lovrics, Anna","first_name":"Anna"},{"first_name":"Yu","full_name":"Gao, Yu","last_name":"Gao"},{"full_name":"Juhász, Bianka","last_name":"Juhász","first_name":"Bianka"},{"last_name":"Bock","full_name":"Bock, István","first_name":"István"},{"first_name":"Helen M.","full_name":"Byrne, Helen M.","last_name":"Byrne"},{"first_name":"András","full_name":"Dinnyés, András","last_name":"Dinnyés"},{"full_name":"Kovács, Krisztián","last_name":"Kovács","first_name":"Krisztián","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ieee":"A. Lovrics <i>et al.</i>, “Transition probability between TF expression states when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.","chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>.","ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács, (2014).","mla":"Lovrics, Anna, et al. <i>Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2</i>. Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., &#38; Kovács, K. (2014). Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>","ama":"Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. 2014. doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>"},"oa_version":"Published Version","_id":"9722","month":"11","date_updated":"2025-09-29T12:02:47Z","publisher":"Public Library of Science","status":"public","doi":"10.1371/journal.pone.0111430.s006","date_published":"2014-11-14T00:00:00Z","article_processing_charge":"No","type":"research_data_reference","day":"14","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf"},{"year":"2014","title":"Detailed proofs for “The time scale of evolutionary innovation”","month":"09","oa_version":"Published Version","_id":"9739","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Detailed Proofs for “The Time Scale of Evolutionary Innovation.”</i> Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014).","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for ‘The time scale of evolutionary innovation.’” Public Library of Science, 2014.","ista":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for “The time scale of evolutionary innovation”, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak. “Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>.","ama":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time scale of evolutionary innovation.” 2014. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>","apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., &#38; Novak, M. (2014). Detailed proofs for “The time scale of evolutionary innovation.” Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>"},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722"},{"full_name":"Adlam, Ben","last_name":"Adlam","first_name":"Ben"},{"first_name":"Martin","last_name":"Novak","full_name":"Novak, Martin"}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2039"}]},"date_created":"2021-07-28T08:13:57Z","department":[{"_id":"KrCh"}],"article_processing_charge":"No","date_published":"2014-09-11T00:00:00Z","status":"public","doi":"10.1371/journal.pcbi.1003818.s001","publisher":"Public Library of Science","date_updated":"2025-09-29T11:53:46Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"11","type":"research_data_reference"},{"article_processing_charge":"No","date_published":"2014-11-13T00:00:00Z","doi":"10.5061/dryad.vm0vc","status":"public","publisher":"Dryad","oa":1,"date_updated":"2025-09-23T07:55:02Z","abstract":[{"text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens.","lang":"eng"}],"day":"13","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","corr_author":"1","year":"2014","title":"Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.vm0vc"}],"month":"11","oa_version":"Published Version","_id":"9740","author":[{"last_name":"Konrad","full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias"},{"last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Tragust","full_name":"Tragust, Simon"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","full_name":"Cremer, Sylvia"}],"citation":{"apa":"Konrad, M., Grasse, A. V., Tragust, S., &#38; Cremer, S. (2014). Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Dryad. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>","ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad, <a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host.” Dryad, 2014.","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>.","mla":"Konrad, Matthias, et al. <i>Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014)."},"related_material":{"record":[{"status":"public","id":"1993","relation":"used_in_publication"}]},"department":[{"_id":"SyCr"}],"date_created":"2021-07-28T08:38:40Z"},{"title":"Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses","year":"2014","date_created":"2021-07-28T08:48:06Z","department":[{"_id":"CaGu"}],"related_material":{"record":[{"relation":"used_in_publication","id":"2036","status":"public"}]},"citation":{"ama":"Lagator M, Colegrave N, Neve P. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>","apa":"Lagator, M., Colegrave, N., &#38; Neve, P. (2014). Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses. Dryad. <a href=\"https://doi.org/10.5061/dryad.85dn7\">https://doi.org/10.5061/dryad.85dn7</a>","mla":"Lagator, Mato, et al. <i>Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>.","short":"M. Lagator, N. Colegrave, P. Neve, (2014).","ieee":"M. Lagator, N. Colegrave, and P. Neve, “Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses.” Dryad, 2014.","ista":"Lagator M, Colegrave N, Neve P. 2014. Data from: Selection history and epistatic interactions impact dynamics of adaptation to novel environmental stresses, Dryad, <a href=\"https://doi.org/10.5061/dryad.85dn7\">10.5061/dryad.85dn7</a>.","chicago":"Lagator, Mato, Nick Colegrave, and Paul Neve. “Data from: Selection History and Epistatic Interactions Impact Dynamics of Adaptation to Novel Environmental Stresses.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.85dn7\">https://doi.org/10.5061/dryad.85dn7</a>."},"author":[{"first_name":"Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","last_name":"Lagator"},{"first_name":"Nick","last_name":"Colegrave","full_name":"Colegrave, Nick"},{"first_name":"Paul","last_name":"Neve","full_name":"Neve, Paul"}],"month":"08","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.85dn7"}],"_id":"9741","oa_version":"Published Version","doi":"10.5061/dryad.85dn7","status":"public","date_updated":"2025-09-29T11:54:45Z","oa":1,"publisher":"Dryad","date_published":"2014-08-21T00:00:00Z","article_processing_charge":"No","type":"research_data_reference","abstract":[{"text":"In rapidly changing environments, selection history may impact the dynamics of adaptation. Mutations selected in one environment may result in pleiotropic fitness trade-offs in subsequent novel environments, slowing the rates of adaptation. Epistatic interactions between mutations selected in sequential stressful environments may slow or accelerate subsequent rates of adaptation, depending on the nature of that interaction. We explored the dynamics of adaptation during sequential exposure to herbicides with different modes of action in Chlamydomonas reinhardtii. Evolution of resistance to two of the herbicides was largely independent of selection history. For carbetamide, previous adaptation to other herbicide modes of action positively impacted the likelihood of adaptation to this herbicide. Furthermore, while adaptation to all individual herbicides was associated with pleiotropic fitness costs in stress-free environments, we observed that accumulation of resistance mechanisms was accompanied by a reduction in overall fitness costs. We suggest that antagonistic epistasis may be a driving mechanism that enables populations to more readily adapt in novel environments. These findings highlight the potential for sequences of xenobiotics to facilitate the rapid evolution of multiple-drug and -pesticide resistance, as well as the potential for epistatic interactions between adaptive mutations to facilitate evolutionary rescue in rapidly changing environments.","lang":"eng"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"21"},{"author":[{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","first_name":"Mato","last_name":"Lagator","full_name":"Lagator, Mato"},{"last_name":"Morgan","full_name":"Morgan, Andrew","first_name":"Andrew"},{"first_name":"Paul","last_name":"Neve","full_name":"Neve, Paul"},{"first_name":"Nick","last_name":"Colegrave","full_name":"Colegrave, Nick"}],"citation":{"chicago":"Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from: Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>.","ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex and migration in adaptation to sink environments.” Dryad, 2014.","ista":"Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and migration in adaptation to sink environments, Dryad, <a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>.","mla":"Lagator, Mato, et al. <i>Data from: Role of Sex and Migration in Adaptation to Sink Environments</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>.","short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014).","apa":"Lagator, M., Morgan, A., Neve, P., &#38; Colegrave, N. (2014). Data from: Role of sex and migration in adaptation to sink environments. Dryad. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>","ama":"Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration in adaptation to sink environments. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>"},"date_created":"2021-07-28T15:32:55Z","related_material":{"record":[{"status":"public","id":"2083","relation":"used_in_publication"}]},"department":[{"_id":"CaGu"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s42n1"}],"month":"04","_id":"9747","oa_version":"Published Version","title":"Data from: Role of sex and migration in adaptation to sink environments","year":"2014","type":"research_data_reference","abstract":[{"text":"Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.","lang":"eng"}],"day":"17","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","doi":"10.5061/dryad.s42n1","oa":1,"publisher":"Dryad","date_updated":"2025-09-29T11:46:47Z","article_processing_charge":"No","date_published":"2014-04-17T00:00:00Z"},{"type":"research_data_reference","abstract":[{"lang":"eng","text":"Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible."}],"day":"07","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","doi":"10.5061/dryad.246qg","date_updated":"2025-09-29T14:27:23Z","publisher":"Dryad","oa":1,"date_published":"2014-11-07T00:00:00Z","article_processing_charge":"No","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"2277"}]},"date_created":"2021-07-30T08:13:52Z","department":[{"_id":"GaTk"}],"citation":{"mla":"Simmons, Kristina, et al. <i>Data from: Transformation of Stimulus Correlations by the Retina</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>.","short":"K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).","ieee":"K. Simmons <i>et al.</i>, “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.","chicago":"Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation of Stimulus Correlations by the Retina.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>.","ista":"Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad, <a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>.","ama":"Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus correlations by the retina. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>","apa":"Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations by the retina. Dryad. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>"},"author":[{"full_name":"Simmons, Kristina","last_name":"Simmons","first_name":"Kristina"},{"first_name":"Jason","last_name":"Prentice","full_name":"Prentice, Jason"},{"last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"},{"first_name":"Jan","full_name":"Homann, Jan","last_name":"Homann"},{"full_name":"Yee, Heather","last_name":"Yee","first_name":"Heather"},{"first_name":"Stephanie","full_name":"Palmer, Stephanie","last_name":"Palmer"},{"full_name":"Nelson, Philip","last_name":"Nelson","first_name":"Philip"},{"first_name":"Vijay","last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay"}],"month":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.246qg"}],"_id":"9752","oa_version":"Published Version","title":"Data from: Transformation of stimulus correlations by the retina","year":"2014"},{"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"This monograph presents a short course in computational geometry and topology. In the first part the book covers Voronoi diagrams and Delaunay triangulations, then it presents the theory of alpha complexes which play a crucial role in biology. The central part of the book is the homology theory and their computation, including the theory of persistence which is indispensable for applications, e.g. shape reconstruction. The target audience comprises researchers and practitioners in mathematics, biology, neuroscience and computer science, but the book may also be beneficial to graduate students of these fields.","lang":"eng"}],"quality_controlled":"1","publication_status":"published","scopus_import":"1","type":"book","series_title":"SpringerBriefs in Applied Sciences and Technology","article_processing_charge":"No","date_published":"2014-01-01T00:00:00Z","publisher":"Springer Nature","date_updated":"2022-03-04T07:47:54Z","doi":"10.1007/978-3-319-05957-0","status":"public","oa_version":"None","_id":"6853","month":"01","page":"IX, 110","citation":{"ama":"Edelsbrunner H. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed. Cham: Springer Nature; 2014. doi:<a href=\"https://doi.org/10.1007/978-3-319-05957-0\">10.1007/978-3-319-05957-0</a>","apa":"Edelsbrunner, H. (2014). <i>A Short Course in Computational Geometry and Topology</i> (1st ed.). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-05957-0\">https://doi.org/10.1007/978-3-319-05957-0</a>","short":"H. Edelsbrunner, A Short Course in Computational Geometry and Topology, 1st ed., Springer Nature, Cham, 2014.","mla":"Edelsbrunner, Herbert. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed., Springer Nature, 2014, doi:<a href=\"https://doi.org/10.1007/978-3-319-05957-0\">10.1007/978-3-319-05957-0</a>.","chicago":"Edelsbrunner, Herbert. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed. SpringerBriefs in Applied Sciences and Technology. Cham: Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-319-05957-0\">https://doi.org/10.1007/978-3-319-05957-0</a>.","ieee":"H. Edelsbrunner, <i>A Short Course in Computational Geometry and Topology</i>, 1st ed. Cham: Springer Nature, 2014.","ista":"Edelsbrunner H. 2014. A Short Course in Computational Geometry and Topology 1st ed., Cham: Springer Nature, IX, 110p."},"author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"description":"available as eBook via catalog IST BookList","relation":"other","url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=356106"},{"url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=373842","relation":"other","description":"available via catalog IST BookList"}]},"date_created":"2019-09-06T09:22:33Z","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"place":"Cham","year":"2014","edition":"1","alternative_title":["SpringerBriefs in Applied Sciences and Technology"],"publication_identifier":{"isbn":["9-783-3190-5956-3"],"eisbn":["9-783-3190-5957-0"],"eissn":["2191-5318"],"issn":["2191-530X"]},"title":"A Short Course in Computational Geometry and Topology"},{"title":"Playful Math - An introduction to mathematical games","file_date_updated":"2020-07-14T12:47:48Z","year":"2014","author":[{"full_name":"Huszár, Kristóf","orcid":"0000-0002-5445-5057","last_name":"Huszár","first_name":"Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rolinek, Michal","last_name":"Rolinek","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87"}],"citation":{"apa":"Huszár, K., &#38; Rolinek, M. 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Rolinek, Playful Math - An Introduction to Mathematical Games, IST Austria, n.d."},"department":[{"_id":"VlKo"},{"_id":"UlWa"}],"language":[{"iso":"eng"}],"date_created":"2019-11-18T15:57:05Z","page":"5","file":[{"content_type":"application/pdf","file_size":511233,"checksum":"2b94e5e1f4c3fe8ab89b12806276fb09","creator":"dernst","date_created":"2019-11-18T15:57:51Z","file_name":"2014_Playful_Math_Huszar.pdf","relation":"main_file","date_updated":"2020-07-14T12:47:48Z","file_id":"7039","access_level":"open_access"}],"month":"06","oa_version":"Published Version","_id":"7038","status":"public","has_accepted_license":"1","oa":1,"publisher":"IST Austria","date_updated":"2025-06-26T12:38:53Z","article_processing_charge":"No","date_published":"2014-06-30T00:00:00Z","type":"working_paper","publication_status":"draft","ddc":["510"],"corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"30"},{"article_processing_charge":"No","date_updated":"2025-09-29T11:45:40Z","publisher":"Public Library of Science","status":"public","doi":"10.1371/journal.pone.0103989.s003","day":"06","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","abstract":[{"lang":"eng","text":"Detailed description of the experimental prodedures, data analyses and additional statistical analyses of the results."}],"type":"research_data_reference","year":"2014","title":"Supporting information","oa_version":"Published Version","_id":"9888","month":"08","date_created":"2021-08-11T14:17:53Z","department":[{"_id":"SyCr"}],"related_material":{"record":[{"id":"2086","status":"public","relation":"used_in_publication"}]},"author":[{"first_name":"Stephan","last_name":"Wolf","full_name":"Wolf, Stephan"},{"first_name":"Dino","full_name":"Mcmahon, Dino","last_name":"Mcmahon"},{"full_name":"Lim, Ka","last_name":"Lim","first_name":"Ka"},{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher","orcid":"0000-0003-1122-3982","last_name":"Pull","full_name":"Pull, Christopher"},{"last_name":"Clark","full_name":"Clark, Suzanne","first_name":"Suzanne"},{"full_name":"Paxton, Robert","last_name":"Paxton","first_name":"Robert"},{"last_name":"Osborne","full_name":"Osborne, Juliet","first_name":"Juliet"}],"citation":{"ieee":"S. Wolf <i>et al.</i>, “Supporting information.” Public Library of Science, 2014.","chicago":"Wolf, Stephan, Dino Mcmahon, Ka Lim, Christopher Pull, Suzanne Clark, Robert Paxton, and Juliet Osborne. “Supporting Information.” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">https://doi.org/10.1371/journal.pone.0103989.s003</a>.","ista":"Wolf S, Mcmahon D, Lim K, Pull C, Clark S, Paxton R, Osborne J. 2014. Supporting information, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">10.1371/journal.pone.0103989.s003</a>.","mla":"Wolf, Stephan, et al. <i>Supporting Information</i>. Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">10.1371/journal.pone.0103989.s003</a>.","short":"S. Wolf, D. Mcmahon, K. Lim, C. Pull, S. Clark, R. Paxton, J. Osborne, (2014).","apa":"Wolf, S., Mcmahon, D., Lim, K., Pull, C., Clark, S., Paxton, R., &#38; Osborne, J. (2014). Supporting information. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">https://doi.org/10.1371/journal.pone.0103989.s003</a>","ama":"Wolf S, Mcmahon D, Lim K, et al. Supporting information. 2014. doi:<a href=\"https://doi.org/10.1371/journal.pone.0103989.s003\">10.1371/journal.pone.0103989.s003</a>"}},{"month":"06","issue":"6","date_created":"2021-08-17T09:03:09Z","department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"author":[{"full_name":"Dhar, Riddhiman","last_name":"Dhar","first_name":"Riddhiman"},{"full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","last_name":"Wagner","full_name":"Wagner, Andreas"}],"page":"1775-1791","year":"2014","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"quality_controlled":"1","abstract":[{"lang":"eng","text":"Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, subfunctionalization, and neofunctionalization. Little experimental data exist on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in Escherichia coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region."}],"article_type":"original","type":"journal_article","scopus_import":"1","intvolume":"        68","publication":"Evolution","date_published":"2014-06-03T00:00:00Z","article_processing_charge":"No","volume":68,"doi":"10.1111/evo.12373","date_updated":"2025-09-29T13:20:48Z","_id":"9931","oa_version":"None","related_material":{"record":[{"relation":"research_data","status":"public","id":"9932"}]},"citation":{"ista":"Dhar R, Bergmiller T, Wagner A. 2014. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution. 68(6), 1775–1791.","ieee":"R. Dhar, T. Bergmiller, and A. Wagner, “Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes,” <i>Evolution</i>, vol. 68, no. 6. Wiley, pp. 1775–1791, 2014.","chicago":"Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” <i>Evolution</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/evo.12373\">https://doi.org/10.1111/evo.12373</a>.","short":"R. Dhar, T. Bergmiller, A. Wagner, Evolution 68 (2014) 1775–1791.","mla":"Dhar, Riddhiman, et al. “Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” <i>Evolution</i>, vol. 68, no. 6, Wiley, 2014, pp. 1775–91, doi:<a href=\"https://doi.org/10.1111/evo.12373\">10.1111/evo.12373</a>.","apa":"Dhar, R., Bergmiller, T., &#38; Wagner, A. (2014). Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.12373\">https://doi.org/10.1111/evo.12373</a>","ama":"Dhar R, Bergmiller T, Wagner A. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. <i>Evolution</i>. 2014;68(6):1775-1791. doi:<a href=\"https://doi.org/10.1111/evo.12373\">10.1111/evo.12373</a>"},"pmid":1,"title":"Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes","day":"03","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"We thank the Functional Genomics Center Zurich for its service in generating sequencing data, M. Ackermann and E. Hayden for helpful discussions, A. de Visser for comments on earlier versions of this manuscript, and M. Moser for help with quantitative PCR. This work was supported by Swiss National Science Foundation (grant 315230–129708), as well as through the YeastX project of SystemsX.ch, and the University Priority Research Program in Systems Biology at the University of Zurich. RD acknowledges support from the Forschungskredit program of the University of Zurich. The authors declare no conflict of interest.","publication_status":"published","external_id":{"isi":["000337558900019"],"pmid":["24495000"]},"isi":1,"status":"public","publisher":"Wiley"},{"abstract":[{"lang":"eng","text":"Gene duplication is important in evolution, because it provides new raw material for evolutionary adaptations. Several existing hypotheses about the causes of duplicate retention and diversification differ in their emphasis on gene dosage, sub-functionalization, and neo-functionalization. Little experimental data exists on the relative importance of gene expression changes and changes in coding regions for the evolution of duplicate genes. Furthermore, we do not know how strongly the environment could affect this importance. To address these questions, we performed evolution experiments with the TEM-1 beta lactamase gene in E. coli to study the initial stages of duplicate gene evolution in the laboratory. We mimicked tandem duplication by inserting two copies of the TEM-1 gene on the same plasmid. We then subjected these copies to repeated cycles of mutagenesis and selection in various environments that contained antibiotics in different combinations and concentrations. Our experiments showed that gene dosage is the most important factor in the initial stages of duplicate gene evolution, and overshadows the importance of point mutations in the coding region."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"27","type":"research_data_reference","article_processing_charge":"No","date_published":"2014-01-27T00:00:00Z","status":"public","doi":"10.5061/dryad.jc402","publisher":"Dryad","oa":1,"date_updated":"2025-09-29T13:20:47Z","main_file_link":[{"url":"https://doi.org/10.5061/dryad.jc402","open_access":"1"}],"month":"01","oa_version":"Published Version","_id":"9932","author":[{"full_name":"Dhar, Riddhiman","last_name":"Dhar","first_name":"Riddhiman"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","full_name":"Bergmiller, Tobias"},{"full_name":"Wagner, Andreas","last_name":"Wagner","first_name":"Andreas"}],"citation":{"apa":"Dhar, R., Bergmiller, T., &#38; Wagner, A. (2014). Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Dryad. <a href=\"https://doi.org/10.5061/dryad.jc402\">https://doi.org/10.5061/dryad.jc402</a>","ama":"Dhar R, Bergmiller T, Wagner A. Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.jc402\">10.5061/dryad.jc402</a>","ista":"Dhar R, Bergmiller T, Wagner A. 2014. Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes, Dryad, <a href=\"https://doi.org/10.5061/dryad.jc402\">10.5061/dryad.jc402</a>.","chicago":"Dhar, Riddhiman, Tobias Bergmiller, and Andreas Wagner. “Data from: Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.jc402\">https://doi.org/10.5061/dryad.jc402</a>.","ieee":"R. Dhar, T. Bergmiller, and A. Wagner, “Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes.” Dryad, 2014.","short":"R. Dhar, T. Bergmiller, A. Wagner, (2014).","mla":"Dhar, Riddhiman, et al. <i>Data from: Increased Gene Dosage Plays a Predominant Role in the Initial Stages of Evolution of Duplicate TEM-1 Beta Lactamase Genes</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.jc402\">10.5061/dryad.jc402</a>."},"department":[{"_id":"CaGu"}],"related_material":{"record":[{"status":"public","id":"9931","relation":"used_in_publication"}]},"date_created":"2021-08-17T09:11:40Z","year":"2014","title":"Data from: Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes"},{"title":"Adaptation to changes in higher-order stimulus statistics in the salamander retina","file_date_updated":"2020-07-14T12:46:06Z","citation":{"mla":"Tkačik, Gašper, et al. “Adaptation to Changes in Higher-Order Stimulus Statistics in the Salamander Retina.” <i>PLoS One</i>, vol. 9, no. 1, e85841, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0085841\">10.1371/journal.pone.0085841</a>.","short":"G. Tkačik, A. Ghosh, E. Schneidman, R. Segev, PLoS One 9 (2014).","ieee":"G. Tkačik, A. Ghosh, E. Schneidman, and R. Segev, “Adaptation to changes in higher-order stimulus statistics in the salamander retina,” <i>PLoS One</i>, vol. 9, no. 1. Public Library of Science, 2014.","ista":"Tkačik G, Ghosh A, Schneidman E, Segev R. 2014. Adaptation to changes in higher-order stimulus statistics in the salamander retina. PLoS One. 9(1), e85841.","chicago":"Tkačik, Gašper, Anandamohan Ghosh, Elad Schneidman, and Ronen Segev. “Adaptation to Changes in Higher-Order Stimulus Statistics in the Salamander Retina.” <i>PLoS One</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0085841\">https://doi.org/10.1371/journal.pone.0085841</a>.","ama":"Tkačik G, Ghosh A, Schneidman E, Segev R. Adaptation to changes in higher-order stimulus statistics in the salamander retina. <i>PLoS One</i>. 2014;9(1). doi:<a href=\"https://doi.org/10.1371/journal.pone.0085841\">10.1371/journal.pone.0085841</a>","apa":"Tkačik, G., Ghosh, A., Schneidman, E., &#38; Segev, R. (2014). Adaptation to changes in higher-order stimulus statistics in the salamander retina. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0085841\">https://doi.org/10.1371/journal.pone.0085841</a>"},"_id":"3263","oa_version":"Published Version","status":"public","has_accepted_license":"1","article_number":"e85841","publisher":"Public Library of Science","external_id":{"isi":["000330244500130"]},"isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_status":"published","publist_id":"3385","day":"21","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","acknowledgement":"This work was supported by The Israel Science Foundation and The Human Frontiers Science Program.\r\nWe thank the referees for helping significantly improve this paper. We also thank Vijay Balasubramanian, Kristina Simmons, and Jason Prentice for stimulating discussions. GT wishes to thank the faculty and students of the “Methods in Computational Neuroscience” course at Marine Biological Laboratory, Woods Hole.\r\n","pubrep_id":"432","year":"2014","date_created":"2018-12-11T12:02:20Z","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"author":[{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"},{"first_name":"Anandamohan","full_name":"Ghosh, Anandamohan","last_name":"Ghosh"},{"first_name":"Elad","last_name":"Schneidman","full_name":"Schneidman, Elad"},{"first_name":"Ronen","full_name":"Segev, Ronen","last_name":"Segev"}],"file":[{"date_created":"2018-12-12T10:13:28Z","creator":"system","checksum":"1d5816b343abe5eadc3eb419bcece971","content_type":"application/pdf","file_size":1568524,"access_level":"open_access","file_id":"5011","date_updated":"2020-07-14T12:46:06Z","relation":"main_file","file_name":"IST-2016-432-v1+1_journal.pone.0085841.pdf"}],"month":"01","issue":"1","doi":"10.1371/journal.pone.0085841","volume":9,"date_updated":"2025-09-29T11:09:18Z","oa":1,"date_published":"2014-01-21T00:00:00Z","article_processing_charge":"No","scopus_import":"1","type":"journal_article","intvolume":"         9","corr_author":"1","publication":"PLoS One","ddc":["570"],"quality_controlled":"1","abstract":[{"lang":"eng","text":"Adaptation in the retina is thought to optimize the encoding of natural light signals into sequences of spikes sent to the brain. While adaptive changes in retinal processing to the variations of the mean luminance level and second-order stimulus statistics have been documented before, no such measurements have been performed when higher-order moments of the light distribution change. We therefore measured the ganglion cell responses in the tiger salamander retina to controlled changes in the second (contrast), third (skew) and fourth (kurtosis) moments of the light intensity distribution of spatially uniform temporally independent stimuli. The skew and kurtosis of the stimuli were chosen to cover the range observed in natural scenes. We quantified adaptation in ganglion cells by studying linear-nonlinear models that capture well the retinal encoding properties across all stimuli. We found that the encoding properties of retinal ganglion cells change only marginally when higher-order statistics change, compared to the changes observed in response to the variation in contrast. By analyzing optimal coding in LN-type models, we showed that neurons can maintain a high information rate without large dynamic adaptation to changes in skew or kurtosis. This is because, for uncorrelated stimuli, spatio-temporal summation within the receptive field averages away non-gaussian aspects of the light intensity distribution."}]},{"publist_id":"5392","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"04","publication_status":"published","external_id":{"isi":["000347601300009"],"arxiv":["1210.2450"]},"isi":1,"status":"public","publisher":"Elsevier","project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"_id":"1733","oa_version":"Submitted Version","citation":{"short":"P. Cerny, M. Chmelik, T.A. Henzinger, A. Radhakrishna, Theoretical Computer Science 560 (2014) 348–363.","mla":"Cerny, Pavol, et al. “Interface Simulation Distances.” <i>Theoretical Computer Science</i>, vol. 560, no. 3, Elsevier, 2014, pp. 348–63, doi:<a href=\"https://doi.org/10.1016/j.tcs.2014.08.019\">10.1016/j.tcs.2014.08.019</a>.","ista":"Cerny P, Chmelik M, Henzinger TA, Radhakrishna A. 2014. Interface simulation distances. Theoretical Computer Science. 560(3), 348–363.","ieee":"P. Cerny, M. Chmelik, T. A. Henzinger, and A. Radhakrishna, “Interface simulation distances,” <i>Theoretical Computer Science</i>, vol. 560, no. 3. Elsevier, pp. 348–363, 2014.","chicago":"Cerny, Pavol, Martin Chmelik, Thomas A Henzinger, and Arjun Radhakrishna. “Interface Simulation Distances.” <i>Theoretical Computer Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tcs.2014.08.019\">https://doi.org/10.1016/j.tcs.2014.08.019</a>.","ama":"Cerny P, Chmelik M, Henzinger TA, Radhakrishna A. Interface simulation distances. <i>Theoretical Computer Science</i>. 2014;560(3):348-363. doi:<a href=\"https://doi.org/10.1016/j.tcs.2014.08.019\">10.1016/j.tcs.2014.08.019</a>","apa":"Cerny, P., Chmelik, M., Henzinger, T. A., &#38; Radhakrishna, A. (2014). Interface simulation distances. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2014.08.019\">https://doi.org/10.1016/j.tcs.2014.08.019</a>"},"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"2916"}]},"title":"Interface simulation distances","abstract":[{"lang":"eng","text":"The classical (boolean) notion of refinement for behavioral interfaces of system components is the alternating refinement preorder. In this paper, we define a distance for interfaces, called interface simulation distance. It makes the alternating refinement preorder quantitative by, intuitively, tolerating errors (while counting them) in the alternating simulation game. We show that the interface simulation distance satisfies the triangle inequality, that the distance between two interfaces does not increase under parallel composition with a third interface, that the distance between two interfaces can be bounded from above and below by distances between abstractions of the two interfaces, and how to synthesize an interface from incompatible requirements. We illustrate the framework, and the properties of the distances under composition of interfaces, with two case studies."}],"ec_funded":1,"quality_controlled":"1","scopus_import":"1","type":"journal_article","arxiv":1,"publication":"Theoretical Computer Science","corr_author":"1","intvolume":"       560","article_processing_charge":"No","date_published":"2014-12-04T00:00:00Z","doi":"10.1016/j.tcs.2014.08.019","volume":560,"oa":1,"date_updated":"2025-09-29T13:14:25Z","main_file_link":[{"url":"http://arxiv.org/abs/1210.2450","open_access":"1"}],"month":"12","issue":"3","author":[{"first_name":"Pavol","last_name":"Cerny","full_name":"Cerny, Pavol"},{"first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","full_name":"Chmelik, Martin","last_name":"Chmelik"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"first_name":"Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","full_name":"Radhakrishna, Arjun","last_name":"Radhakrishna"}],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"date_created":"2018-12-11T11:53:43Z","language":[{"iso":"eng"}],"page":"348 - 363","year":"2014"},{"date_updated":"2024-10-09T20:55:54Z","publisher":"Springer","status":"public","doi":"10.1007/978-3-7091-1526-8_8","date_published":"2014-04-01T00:00:00Z","corr_author":"1","publication_status":"published","publication":"Auxin and Its Role in Plant Development","type":"book_chapter","scopus_import":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","day":"01","quality_controlled":"1","publist_id":"5304","abstract":[{"lang":"eng","text":"The generation of asymmetry, at both cellular and tissue level, is one of the most essential capabilities of all eukaryotic organisms. It mediates basically all multicellular development ranging from embryogenesis and de novo organ formation till responses to various environmental stimuli. In plants, the awe-inspiring number of such processes is regulated by phytohormone auxin and its directional, cell-to-cell transport. The mediators of this transport, PIN auxin transporters, are asymmetrically localized at the plasma membrane, and this polar localization determines the directionality of intercellular auxin flow. Thus, auxin transport contributes crucially to the generation of local auxin gradients or maxima, which instruct given cell to change its developmental program. Here, we introduce and discuss the molecular components and cellular mechanisms regulating the generation and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity in plants."}],"title":"Auxin on the road navigated by cellular PIN polarity","year":"2014","editor":[{"last_name":"Zažímalová","full_name":"Zažímalová, Eva","first_name":"Eva"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková","orcid":"0000-0002-8510-9739"}],"page":"143 - 170","department":[{"_id":"JiFr"}],"date_created":"2018-12-11T11:54:07Z","language":[{"iso":"eng"}],"author":[{"first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87","full_name":"Baster, Pawel","last_name":"Baster"},{"full_name":"Friml, Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"citation":{"ama":"Baster P, Friml J. Auxin on the road navigated by cellular PIN polarity. In: Zažímalová E, Petrášek J, Benková E, eds. <i>Auxin and Its Role in Plant Development</i>. Springer; 2014:143-170. doi:<a href=\"https://doi.org/10.1007/978-3-7091-1526-8_8\">10.1007/978-3-7091-1526-8_8</a>","apa":"Baster, P., &#38; Friml, J. (2014). Auxin on the road navigated by cellular PIN polarity. In E. Zažímalová, J. Petrášek, &#38; E. Benková (Eds.), <i>Auxin and Its Role in Plant Development</i> (pp. 143–170). Springer. <a href=\"https://doi.org/10.1007/978-3-7091-1526-8_8\">https://doi.org/10.1007/978-3-7091-1526-8_8</a>","short":"P. Baster, J. Friml, in:, E. Zažímalová, J. Petrášek, E. Benková (Eds.), Auxin and Its Role in Plant Development, Springer, 2014, pp. 143–170.","mla":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” <i>Auxin and Its Role in Plant Development</i>, edited by Eva Zažímalová et al., Springer, 2014, pp. 143–70, doi:<a href=\"https://doi.org/10.1007/978-3-7091-1526-8_8\">10.1007/978-3-7091-1526-8_8</a>.","chicago":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” In <i>Auxin and Its Role in Plant Development</i>, edited by Eva Zažímalová, Jan Petrášek, and Eva Benková, 143–70. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-7091-1526-8_8\">https://doi.org/10.1007/978-3-7091-1526-8_8</a>.","ista":"Baster P, Friml J. 2014.Auxin on the road navigated by cellular PIN polarity. In: Auxin and Its Role in Plant Development. , 143–170.","ieee":"P. Baster and J. Friml, “Auxin on the road navigated by cellular PIN polarity,” in <i>Auxin and Its Role in Plant Development</i>, E. Zažímalová, J. Petrášek, and E. Benková, Eds. Springer, 2014, pp. 143–170."},"oa_version":"None","_id":"1806","month":"04"}]