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Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","mla":"Pavlogiannis, Andreas, et al. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">10.15479/AT:IST-2017-749-v3-1</a>.","ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">10.15479/AT:IST-2017-749-v3-1</a>","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 34p.","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2017-749-v3-1\">https://doi.org/10.15479/AT:IST-2017-749-v3-1</a>","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria, 2016."},"title":"Arbitrarily strong amplifiers of natural selection","date_published":"2016-12-30T00:00:00Z","oa":1,"has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"ddc":["000"],"type":"technical_report","fulldoi":"https://doi.org/10.15479/AT:IST-2017-749-v3-1","doi":"10.15479/AT:IST-2017-749-v3-1","alternative_title":["IST Austria Technical Report"],"date_updated":"2025-04-15T07:55:37Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:46:59Z","author":[{"first_name":"Andreas","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas"},{"orcid":"0000-0002-1097-9684","first_name":"Josef","full_name":"Tkadlec, Josef","last_name":"Tkadlec","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}]},{"publisher":"Institute of Science and Technology Austria","license":"https://creativecommons.org/publicdomain/zero/1.0/","citation":{"ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016.","apa":"Ellis, T., &#38; Field, D. (2016). Flower colour data and phylogeny (NEXUS) files. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>","ama":"Ellis T, Field D. Flower colour data and phylogeny (NEXUS) files. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>","ista":"Ellis T, Field D. 2016. Flower colour data and phylogeny (NEXUS) files, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","short":"T. Ellis, D. Field, (2016).","mla":"Ellis, Thomas, and David Field. <i>Flower Colour Data and Phylogeny (NEXUS) Files</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:34\">10.15479/AT:ISTA:34</a>.","chicago":"Ellis, Thomas, and David Field. “Flower Colour Data and Phylogeny (NEXUS) Files.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:34\">https://doi.org/10.15479/AT:ISTA:34</a>."},"year":"2016","month":"02","day":"19","oa_version":"Published Version","department":[{"_id":"NiBa"}],"status":"public","_id":"5550","file":[{"checksum":"950f85b80427d357bfeff09608ba02e9","access_level":"open_access","relation":"main_file","content_type":"application/zip","date_updated":"2020-07-14T12:47:00Z","creator":"system","file_id":"5594","file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","date_created":"2018-12-12T13:02:27Z","file_size":4468543}],"related_material":{"record":[{"id":"1382","relation":"research_paper","status":"public"}]},"article_processing_charge":"No","date_created":"2018-12-12T12:31:29Z","datarep_id":"34","abstract":[{"text":"We collected flower colour information on species in the tribe Antirrhineae from taxonomic literature. We also retreived molecular data from GenBank for as many of these species as possible to estimate phylogenetic relationships among these taxa. We then used the R package 'diversitree' to examine patterns of evolutionary transitions between anthocyanin and yellow pigmentation across the phylogeny.\r\n\r\nFor full details of the methods see:\r\nEllis TJ and Field DL \"Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae”, Annals of Botany (in press)","lang":"eng"}],"author":[{"orcid":"0000-0002-8511-0254","first_name":"Thomas","id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","last_name":"Ellis","full_name":"Ellis, Thomas"},{"full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478"}],"file_date_updated":"2020-07-14T12:47:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-09-22T07:32:43Z","publist_id":"5828","type":"research_data","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"doi":"10.15479/AT:ISTA:34","fulldoi":"https://doi.org/10.15479/AT:ISTA:34","has_accepted_license":"1","oa":1,"title":"Flower colour data and phylogeny (NEXUS) files","date_published":"2016-02-19T00:00:00Z","ddc":["576"]},{"file":[{"relation":"main_file","checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","access_level":"open_access","date_updated":"2020-07-14T12:47:02Z","content_type":"application/zip","creator":"system","file_id":"5616","file_name":"IST-2016-45-v1+1_PaperCode.zip","file_size":296722548,"date_created":"2018-12-12T13:02:58Z"}],"related_material":{"record":[{"relation":"used_in_publication","id":"8431","status":"deleted"},{"id":"1029","relation":"research_paper","status":"public"}]},"article_processing_charge":"No","datarep_id":"45","date_created":"2018-12-12T12:31:31Z","publisher":"Institute of Science and Technology Austria","license":"https://creativecommons.org/licenses/by-sa/4.0/","citation":{"ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016.","apa":"Lukacisin, M., Landon, M., &#38; Jajoo, R. (2016). MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:45\">https://doi.org/10.15479/AT:ISTA:45</a>","ama":"Lukacisin M, Landon M, Jajoo R. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>","ista":"Lukacisin M, Landon M, Jajoo R. 2016. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>.","short":"M. Lukacisin, M. Landon, R. Jajoo, (2016).","mla":"Lukacisin, Martin, et al. <i>MATLAB Analysis Code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.”</i> Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>.","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:45\">https://doi.org/10.15479/AT:ISTA:45</a>."},"year":"2016","month":"08","day":"25","oa_version":"Published Version","department":[{"_id":"ToBo"}],"_id":"5556","status":"public","tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png"},"type":"research_data","keyword":["transcription","pausing","backtracking","polymerase","RNA","NET-seq","nucleosome","basepairing"],"fulldoi":"https://doi.org/10.15479/AT:ISTA:45","doi":"10.15479/AT:ISTA:45","date_published":"2016-08-25T00:00:00Z","has_accepted_license":"1","oa":1,"title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","ddc":["571"],"abstract":[{"lang":"eng","text":"MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions"}],"file_date_updated":"2020-07-14T12:47:02Z","author":[{"id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisin","full_name":"Lukacisin, Martin","orcid":"0000-0001-6549-4177","first_name":"Martin"},{"full_name":"Landon, Matthieu","last_name":"Landon","first_name":"Matthieu"},{"full_name":"Jajoo, Rishi","last_name":"Jajoo","first_name":"Rishi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-07-10T11:49:51Z"},{"file":[{"access_level":"open_access","checksum":"aa5a16a0dc888da7186fb8fc45e88439","relation":"main_file","creator":"system","content_type":"application/zip","date_updated":"2020-07-14T12:47:02Z","file_id":"5645","file_size":36058401,"date_created":"2018-12-12T13:05:19Z","file_name":"IST-2016-46-v1+1_discrete_tomography_synthetic.zip"}],"article_processing_charge":"No","datarep_id":"46","date_created":"2018-12-12T12:31:31Z","publisher":"Institute of Science and Technology Austria","citation":{"ista":"Swoboda P. 2016. Synthetic discrete tomography problems, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>.","ama":"Swoboda P. Synthetic discrete tomography problems. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>","ieee":"P. Swoboda, “Synthetic discrete tomography problems.” Institute of Science and Technology Austria, 2016.","apa":"Swoboda, P. (2016). Synthetic discrete tomography problems. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:46\">https://doi.org/10.15479/AT:ISTA:46</a>","chicago":"Swoboda, Paul. “Synthetic Discrete Tomography Problems.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:46\">https://doi.org/10.15479/AT:ISTA:46</a>.","short":"P. Swoboda, (2016).","mla":"Swoboda, Paul. <i>Synthetic Discrete Tomography Problems</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>."},"year":"2016","month":"09","day":"20","oa_version":"Published Version","department":[{"_id":"VlKo"}],"_id":"5557","status":"public","contributor":[{"first_name":"Jan","contributor_type":"data_collector","last_name":"Kuske"}],"type":"research_data","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png"},"keyword":["discrete tomography"],"fulldoi":"https://doi.org/10.15479/AT:ISTA:46","doi":"10.15479/AT:ISTA:46","oa":1,"date_published":"2016-09-20T00:00:00Z","has_accepted_license":"1","title":"Synthetic discrete tomography problems","ddc":["006"],"abstract":[{"lang":"eng","text":"Small synthetic discrete tomography problems.\r\nSizes are 32x32, 64z64 and 256x256.\r\nProjection angles are 2, 4, and 6.\r\nNumber of labels are 3 and 5."}],"author":[{"first_name":"Paul","full_name":"Swoboda, Paul","last_name":"Swoboda","id":"446560C6-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:02Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-21T13:50:21Z"},{"license":"https://creativecommons.org/licenses/by-nc/4.0/","month":"03","pubrep_id":"587","publication_status":"published","volume":33,"department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"page":"770-782","quality_controlled":"1","related_material":{"record":[{"status":"public","id":"9719","relation":"research_data"}]},"article_processing_charge":"No","date_created":"2018-12-18T13:18:10Z","author":[{"full_name":"Wielgoss, Sébastien","last_name":"Wielgoss","first_name":"Sébastien"},{"first_name":"Tobias","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","last_name":"Bergmiller"},{"last_name":"Bischofberger","full_name":"Bischofberger, Anna M.","first_name":"Anna M."},{"last_name":"Hall","full_name":"Hall, Alex R.","first_name":"Alex R."}],"publication":"Molecular Biology and Evolution","scopus_import":"1","type":"journal_article","doi":"10.1093/molbev/msv270","oa":1,"title":"Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria","pmid":1,"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"publisher":"Oxford University Press","citation":{"chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>.","mla":"Wielgoss, Sébastien, et al. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3, Oxford University Press, 2016, pp. 770–82, doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>.","short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology and Evolution 33 (2016) 770–782.","ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. 2016;33(3):770-782. doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>","ista":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2016. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. Molecular Biology and Evolution. 33(3), 770–782.","apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &#38; Hall, A. R. (2016). Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria,” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3. Oxford University Press, pp. 770–782, 2016."},"year":"2016","acknowledgement":"The authors thank three anonymous reviewers and the editor for helpful comments on the manuscript, as well as Dominique Schneider for feedback on an earlier draft, Jenna Gallie for lytic λ and Julien Capelle for T5 and T6. This work was supported by the Swiss National Science Foundation (PZ00P3_148255 to A.H.) and an EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development (FP7-PEOPLE-2012-IEF-331824 to S.W.).","isi":1,"day":"01","oa_version":"Published Version","status":"public","_id":"5749","intvolume":"        33","file":[{"file_id":"5750","date_created":"2018-12-18T13:21:45Z","file_size":634037,"file_name":"2016_MolBiolEvol_Wielgoss.pdf","relation":"main_file","access_level":"open_access","checksum":"47d9010690b6c5c17f2ac830cc63ac5c","creator":"dernst","date_updated":"2020-07-14T12:47:10Z","content_type":"application/pdf"}],"issue":"3","external_id":{"isi":["000371219500015"],"pmid":["26609077"]},"file_date_updated":"2020-07-14T12:47:10Z","abstract":[{"lang":"eng","text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-04-29T05:57:02Z","DOAJ_listed":"1","OA_place":"publisher","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"fulldoi":"https://doi.org/10.1093/molbev/msv270","article_type":"original","date_published":"2016-03-01T00:00:00Z","has_accepted_license":"1","OA_type":"gold","ddc":["576"]},{"type":"book_chapter","doi":"10.1007/978-3-319-39441-1_23","title":"On some local topological properties of naive discrete sphere","publication_identifier":{"isbn":["978-3-319-39440-4"],"eissn":["1611-3349"],"eisbn":["978-3-319-39441-1"],"issn":["0302-9743"]},"extern":"1","conference":{"start_date":"2016-06-15","location":"Marseille, France","end_date":"2016-06-17","name":"CTIC: Computational Topology in Image Context"},"author":[{"last_name":"Sen","full_name":"Sen, Nabhasmita","first_name":"Nabhasmita"},{"orcid":"0000-0002-5372-7890","first_name":"Ranita","full_name":"Biswas, Ranita","last_name":"Biswas","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Partha","last_name":"Bhowmick","full_name":"Bhowmick, Partha"}],"publication":"Computational Topology in Image Context","article_processing_charge":"No","date_created":"2019-01-08T20:44:24Z","quality_controlled":"1","place":"Cham","publication_status":"published","language":[{"iso":"eng"}],"volume":9667,"department":[{"_id":"HeEd"}],"page":"253-264","month":"06","fulldoi":"https://doi.org/10.1007/978-3-319-39441-1_23","date_published":"2016-06-02T00:00:00Z","alternative_title":["LNCS"],"date_updated":"2022-01-28T08:01:22Z","abstract":[{"text":"Discretization of sphere in the integer space follows a particular discretization scheme, which, in principle, conforms to some topological model. This eventually gives rise to interesting topological properties of a discrete spherical surface, which need to be investigated for its analytical characterization. This paper presents some novel results on the local topological properties of the naive model of discrete sphere. They follow from the bijection of each quadraginta octant of naive sphere with its projection map called f -map on the corresponding functional plane and from the characterization of certain jumps in the f-map. As an application, we have shown how these properties can be used in designing an efficient reconstruction algorithm for a naive spherical surface from an input voxel set when it is sparse or noisy.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"      9667","oa_version":"None","_id":"5805","status":"public","publisher":"Springer Nature","citation":{"ista":"Sen N, Biswas R, Bhowmick P. 2016.On some local topological properties of naive discrete sphere. In: Computational Topology in Image Context. LNCS, vol. 9667, 253–264.","ama":"Sen N, Biswas R, Bhowmick P. On some local topological properties of naive discrete sphere. In: <i>Computational Topology in Image Context</i>. Vol 9667. Cham: Springer Nature; 2016:253-264. doi:<a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">10.1007/978-3-319-39441-1_23</a>","apa":"Sen, N., Biswas, R., &#38; Bhowmick, P. (2016). On some local topological properties of naive discrete sphere. In <i>Computational Topology in Image Context</i> (Vol. 9667, pp. 253–264). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">https://doi.org/10.1007/978-3-319-39441-1_23</a>","ieee":"N. Sen, R. Biswas, and P. Bhowmick, “On some local topological properties of naive discrete sphere,” in <i>Computational Topology in Image Context</i>, vol. 9667, Cham: Springer Nature, 2016, pp. 253–264.","chicago":"Sen, Nabhasmita, Ranita Biswas, and Partha Bhowmick. “On Some Local Topological Properties of Naive Discrete Sphere.” In <i>Computational Topology in Image Context</i>, 9667:253–64. Cham: Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">https://doi.org/10.1007/978-3-319-39441-1_23</a>.","mla":"Sen, Nabhasmita, et al. “On Some Local Topological Properties of Naive Discrete Sphere.” <i>Computational Topology in Image Context</i>, vol. 9667, Springer Nature, 2016, pp. 253–64, doi:<a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">10.1007/978-3-319-39441-1_23</a>.","short":"N. Sen, R. Biswas, P. Bhowmick, in:, Computational Topology in Image Context, Springer Nature, Cham, 2016, pp. 253–264."},"year":"2016","day":"02"},{"abstract":[{"lang":"eng","text":"Although the concept of functional plane for naive plane is studied and reported in the literature in great detail, no similar study is yet found for naive sphere. This article exposes the first study in this line, opening up further prospects of analyzing the topological properties of sphere in the discrete space. We show that each quadraginta octant Q of a naive sphere forms a bijection with its projected pixel set on a unique coordinate plane, which thereby serves as the functional plane of Q, and hence gives rise to merely mono-jumps during back projection. The other two coordinate planes serve as para-functional and dia-functional planes for Q, as the former is ‘mono-jumping’ but not bijective, whereas the latter holds neither of the two. Owing to this, the quadraginta octants form symmetry groups and subgroups with equivalent jump conditions. We also show a potential application in generating a special class of discrete 3D circles based on back projection and jump bridging by Steiner voxels. A circle in this class possesses 4-symmetry, uniqueness, and bounded distance from the underlying real sphere and real plane."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["LNCS"],"date_updated":"2022-01-28T08:10:11Z","fulldoi":"https://doi.org/10.1007/978-3-319-32360-2_20","date_published":"2016-04-09T00:00:00Z","publisher":"Springer Nature","year":"2016","citation":{"short":"R. Biswas, P. Bhowmick, in:, Discrete Geometry for Computer Imagery, Springer Nature, Cham, 2016, pp. 256–267.","mla":"Biswas, Ranita, and Partha Bhowmick. “On Functionality of Quadraginta Octants of Naive Sphere with Application to Circle Drawing.” <i>Discrete Geometry for Computer Imagery</i>, vol. 9647, Springer Nature, 2016, pp. 256–67, doi:<a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">10.1007/978-3-319-32360-2_20</a>.","chicago":"Biswas, Ranita, and Partha Bhowmick. “On Functionality of Quadraginta Octants of Naive Sphere with Application to Circle Drawing.” In <i>Discrete Geometry for Computer Imagery</i>, 9647:256–67. Cham: Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">https://doi.org/10.1007/978-3-319-32360-2_20</a>.","ieee":"R. Biswas and P. Bhowmick, “On functionality of quadraginta octants of naive sphere with application to circle drawing,” in <i>Discrete Geometry for Computer Imagery</i>, Nantes, France, 2016, vol. 9647, pp. 256–267.","apa":"Biswas, R., &#38; Bhowmick, P. (2016). On functionality of quadraginta octants of naive sphere with application to circle drawing. In <i>Discrete Geometry for Computer Imagery</i> (Vol. 9647, pp. 256–267). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">https://doi.org/10.1007/978-3-319-32360-2_20</a>","ista":"Biswas R, Bhowmick P. 2016. On functionality of quadraginta octants of naive sphere with application to circle drawing. Discrete Geometry for Computer Imagery. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 9647, 256–267.","ama":"Biswas R, Bhowmick P. On functionality of quadraginta octants of naive sphere with application to circle drawing. In: <i>Discrete Geometry for Computer Imagery</i>. Vol 9647. Cham: Springer Nature; 2016:256-267. doi:<a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">10.1007/978-3-319-32360-2_20</a>"},"day":"09","oa_version":"None","_id":"5806","status":"public","intvolume":"      9647","author":[{"orcid":"0000-0002-5372-7890","first_name":"Ranita","full_name":"Biswas, Ranita","last_name":"Biswas","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Partha","last_name":"Bhowmick","full_name":"Bhowmick, Partha"}],"publication":"Discrete Geometry for Computer Imagery","conference":{"start_date":"2016-04-18","name":"DGCI: International Conference on Discrete Geometry for Computer Imagery","end_date":"2016-04-20","location":"Nantes, France"},"extern":"1","type":"conference","doi":"10.1007/978-3-319-32360-2_20","title":"On functionality of quadraginta octants of naive sphere with application to circle drawing","publication_identifier":{"issn":["0302-9743","1611-3349"],"isbn":["978-3-319-32359-6"],"eisbn":["978-3-319-32360-2"]},"month":"04","publication_status":"published","volume":9647,"department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"page":"256-267","quality_controlled":"1","place":"Cham","article_processing_charge":"No","date_created":"2019-01-08T20:44:37Z"},{"author":[{"first_name":"Ranita","orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas"},{"last_name":"Bhowmick","full_name":"Bhowmick, Partha","first_name":"Partha"},{"first_name":"Valentin E.","last_name":"Brimkov","full_name":"Brimkov, Valentin E."}],"publication":"Combinatorial image analysis","conference":{"location":"Kolkata, India","end_date":"2015-11-27","name":"IWCIA: International Workshop on Combinatorial Image Analysis","start_date":"2015-11-24"},"extern":"1","type":"book_chapter","doi":"10.1007/978-3-319-26145-4_7","title":"On the connectivity and smoothness of discrete spherical circles","publication_identifier":{"eisbn":["978-3-319-26145-4"],"eissn":["1611-3349"],"isbn":["978-3-319-26144-7"],"issn":["0302-9743"]},"month":"01","publication_status":"published","department":[{"_id":"HeEd"}],"volume":9448,"language":[{"iso":"eng"}],"page":"86-100","quality_controlled":"1","place":"Cham","article_processing_charge":"No","date_created":"2019-01-08T20:45:19Z","abstract":[{"text":"A discrete spherical circle is a topologically well-connected 3D circle in the integer space, which belongs to a discrete sphere as well as a discrete plane. It is one of the most important 3D geometric primitives, but has not possibly yet been studied up to its merit. This paper is a maiden exposition of some of its elementary properties, which indicates a sense of its profound theoretical prospects in the framework of digital geometry. We have shown how different types of discretization can lead to forbidden and admissible classes, when one attempts to define the discretization of a spherical circle in terms of intersection between a discrete sphere and a discrete plane. Several fundamental theoretical results have been presented, the algorithm for construction of discrete spherical circles has been discussed, and some test results have been furnished to demonstrate its practicality and usefulness.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2022-01-28T08:13:03Z","fulldoi":"https://doi.org/10.1007/978-3-319-26145-4_7","date_published":"2016-01-06T00:00:00Z","publisher":"Springer Nature","citation":{"short":"R. Biswas, P. Bhowmick, V.E. Brimkov, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2016, pp. 86–100.","mla":"Biswas, Ranita, et al. “On the Connectivity and Smoothness of Discrete Spherical Circles.” <i>Combinatorial Image Analysis</i>, vol. 9448, Springer Nature, 2016, pp. 86–100, doi:<a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">10.1007/978-3-319-26145-4_7</a>.","chicago":"Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Connectivity and Smoothness of Discrete Spherical Circles.” In <i>Combinatorial Image Analysis</i>, 9448:86–100. Cham: Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">https://doi.org/10.1007/978-3-319-26145-4_7</a>.","apa":"Biswas, R., Bhowmick, P., &#38; Brimkov, V. E. (2016). On the connectivity and smoothness of discrete spherical circles. In <i>Combinatorial image analysis</i> (Vol. 9448, pp. 86–100). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">https://doi.org/10.1007/978-3-319-26145-4_7</a>","ieee":"R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the connectivity and smoothness of discrete spherical circles,” in <i>Combinatorial image analysis</i>, vol. 9448, Cham: Springer Nature, 2016, pp. 86–100.","ista":"Biswas R, Bhowmick P, Brimkov VE. 2016.On the connectivity and smoothness of discrete spherical circles. In: Combinatorial image analysis. vol. 9448, 86–100.","ama":"Biswas R, Bhowmick P, Brimkov VE. On the connectivity and smoothness of discrete spherical circles. In: <i>Combinatorial Image Analysis</i>. Vol 9448. Cham: Springer Nature; 2016:86-100. doi:<a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">10.1007/978-3-319-26145-4_7</a>"},"year":"2016","day":"06","oa_version":"None","_id":"5809","status":"public","intvolume":"      9448"},{"date_updated":"2026-04-07T08:32:03Z","corr_author":"1","author":[{"full_name":"Harada, Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","first_name":"Harumi","orcid":"0000-0001-7429-7896"},{"full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"}],"abstract":[{"text":"Visualizing molecular localization at high resolution contributes to understanding of their functions and roles in physiological and pathological conditions. Sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) is a powerful electron microscopy method to study high-resolution two-dimensional distribution of transmembrane proteins and their tightly associated proteins on platinum-carbon replica. During treatment with SDS, unfixed proteins and intracellular organelle are dissolved and integral membrane proteins captured and stabilized by carbon and platinum deposition are denatured, retaining most of their antigenicity, and exposed on exoplasmic and protoplasmic surfaces of lipid monolayers. The exposure of these antigens on the surface of replica facilitates the accessibility of antibodies and therefore provides higher labeling efficiency than those obtained with other immunoelectron microscopy techniques. In this chapter, we describe the protocols of SDS-FRL adapted for mammalian brain samples and an additional procedure for fluorescence-guided electron microscopy for replica immunolabeling.","lang":"eng"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication":"Receptor and Ion Channel Detection in the Brain","type":"book_chapter","fulldoi":"https://doi.org/10.1007/978-1-4939-3064-7_17","doi":"10.1007/978-1-4939-3064-7_17","title":"High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL)","date_published":"2016-02-02T00:00:00Z","OA_type":"closed access","publication_identifier":{"issn":["0893-2336"],"eissn":["1940-6045"],"eisbn":["9781493930647"],"isbn":["9781493930630"]},"oa_version":"None","publication_status":"published","department":[{"_id":"RySh"}],"language":[{"iso":"eng"}],"_id":"19990","series_title":"Neuromethods","status":"public","page":"233-245","publisher":"Springer Nature","acknowledgement":"We thank Mitsuru Ikeda for preparing replica images used in Fig. 2.","year":"2016","citation":{"chicago":"Harada, Harumi, and Ryuichi Shigemoto. “High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” In <i>Receptor and Ion Channel Detection in the Brain</i>, 233–45. Neuromethods. Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">https://doi.org/10.1007/978-1-4939-3064-7_17</a>.","short":"H. Harada, R. Shigemoto, in:, Receptor and Ion Channel Detection in the Brain, Springer Nature, 2016, pp. 233–245.","mla":"Harada, Harumi, and Ryuichi Shigemoto. “High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL).” <i>Receptor and Ion Channel Detection in the Brain</i>, Springer Nature, 2016, pp. 233–45, doi:<a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">10.1007/978-1-4939-3064-7_17</a>.","ista":"Harada H, Shigemoto R. 2016.High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In: Receptor and Ion Channel Detection in the Brain. , 233–245.","ama":"Harada H, Shigemoto R. High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In: <i>Receptor and Ion Channel Detection in the Brain</i>. Neuromethods. Springer Nature; 2016:233-245. doi:<a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">10.1007/978-1-4939-3064-7_17</a>","apa":"Harada, H., &#38; Shigemoto, R. (2016). High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL). In <i>Receptor and Ion Channel Detection in the Brain</i> (pp. 233–245). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4939-3064-7_17\">https://doi.org/10.1007/978-1-4939-3064-7_17</a>","ieee":"H. Harada and R. Shigemoto, “High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL),” in <i>Receptor and Ion Channel Detection in the Brain</i>, Springer Nature, 2016, pp. 233–245."},"month":"02","day":"02","article_processing_charge":"No","date_created":"2025-07-10T13:56:06Z","quality_controlled":"1"},{"_id":"19991","page":"1-4","status":"public","language":[{"iso":"eng"}],"department":[{"_id":"ChLa"}],"oa_version":"None","publication_status":"published","day":"06","month":"07","year":"2016","citation":{"chicago":"Sharmanska, Viktoriia, and Novi Quadrianto. “Learning Using Privileged Information.” In <i>Encyclopedia of Machine Learning and Data Mining</i>, 1–4. Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-1-4899-7502-7_892-1\">https://doi.org/10.1007/978-1-4899-7502-7_892-1</a>.","mla":"Sharmanska, Viktoriia, and Novi Quadrianto. “Learning Using Privileged Information.” <i>Encyclopedia of Machine Learning and Data Mining</i>, Springer Nature, 2016, pp. 1–4, doi:<a href=\"https://doi.org/10.1007/978-1-4899-7502-7_892-1\">10.1007/978-1-4899-7502-7_892-1</a>.","short":"V. Sharmanska, N. Quadrianto, in:, Encyclopedia of Machine Learning and Data Mining, Springer Nature, 2016, pp. 1–4.","ama":"Sharmanska V, Quadrianto N. Learning Using Privileged Information. In: <i>Encyclopedia of Machine Learning and Data Mining</i>. Springer Nature; 2016:1-4. doi:<a href=\"https://doi.org/10.1007/978-1-4899-7502-7_892-1\">10.1007/978-1-4899-7502-7_892-1</a>","ista":"Sharmanska V, Quadrianto N. 2016.Learning Using Privileged Information. In: Encyclopedia of Machine Learning and Data Mining. , 1–4.","ieee":"V. Sharmanska and N. Quadrianto, “Learning Using Privileged Information,” in <i>Encyclopedia of Machine Learning and Data Mining</i>, Springer Nature, 2016, pp. 1–4.","apa":"Sharmanska, V., &#38; Quadrianto, N. (2016). Learning Using Privileged Information. In <i>Encyclopedia of Machine Learning and Data Mining</i> (pp. 1–4). Springer Nature. <a href=\"https://doi.org/10.1007/978-1-4899-7502-7_892-1\">https://doi.org/10.1007/978-1-4899-7502-7_892-1</a>"},"publisher":"Springer Nature","date_created":"2025-07-10T13:57:52Z","article_processing_charge":"No","quality_controlled":"1","corr_author":"1","date_updated":"2025-09-23T10:53:13Z","publication":"Encyclopedia of Machine Learning and Data Mining","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"When applying machine learning techniques to real-world problems, prior knowledge plays a crucial role in enriching the learning system. This prior knowledge is typically defined by domain experts and can be integrated into machine learning algorithms in a variety of ways: as a preference of certain prediction functions over others, as a Bayesian prior over parameters, or as additional information about the samples in the training set used for learning a prediction function. The latter setup is called learning using privileged information (LUPI) and was adopted by Vapnik and Vashist in (Neural Netw, 2009). Formally, LUPI refers to the setting when, in addition to the main data modality, the learning system has access to an extra source of information about the training examples. The additional source of information is only available during training and therefore is called privileged. The main goal of LUPI is to utilize privileged information and to learn a better model in the main data modality than one would learn without the privileged source. As an illustration, for protein classification based on amino-acid sequences, the protein tertiary structure can be considered additional information. Another example is recognizing objects in images; the textual information in the form of image tags contains additional object descriptions and can be used as privileged.","lang":"eng"}],"author":[{"last_name":"Sharmanska","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","full_name":"Sharmanska, Viktoriia","first_name":"Viktoriia","orcid":"0000-0003-0192-9308"},{"first_name":"Novi","full_name":"Quadrianto, Novi","last_name":"Quadrianto"}],"publication_identifier":{"eisbn":["9781489975027"]},"date_published":"2016-07-06T00:00:00Z","OA_type":"closed access","title":"Learning Using Privileged Information","fulldoi":"https://doi.org/10.1007/978-1-4899-7502-7_892-1","doi":"10.1007/978-1-4899-7502-7_892-1","type":"book_chapter"},{"doi":"10.1021/acssynbio.6b00013","type":"journal_article","title":"An orthogonal permease–inducer–repressor feedback loop shows bistability","author":[{"first_name":"Robert","last_name":"Gnügge","full_name":"Gnügge, Robert"},{"last_name":"Dharmarajan","full_name":"Dharmarajan, Lekshmi","first_name":"Lekshmi"},{"full_name":"Lang, Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","last_name":"Lang","first_name":"Moritz"},{"first_name":"Jörg","last_name":"Stelling","full_name":"Stelling, Jörg"}],"publication":"ACS Synthetic Biology","date_created":"2018-12-11T11:49:40Z","article_processing_charge":"No","quality_controlled":"1","volume":5,"language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"publication_status":"published","page":"1098 - 1107","month":"05","fulldoi":"https://doi.org/10.1021/acssynbio.6b00013","date_published":"2016-05-05T00:00:00Z","date_updated":"2025-09-22T14:20:45Z","publist_id":"6390","abstract":[{"lang":"eng","text":"Feedback loops in biological networks, among others, enable differentiation and cell cycle progression, and increase robustness in signal transduction. In natural networks, feedback loops are often complex and intertwined, making it challenging to identify which loops are mainly responsible for an observed behavior. However, minimal synthetic replicas could allow for such identification. Here, we engineered a synthetic permease-inducer-repressor system in Saccharomyces cerevisiae to analyze if a transport-mediated positive feedback loop could be a core mechanism for the switch-like behavior in the regulation of metabolic gene networks such as the S. cerevisiae GAL system or the Escherichia coli lac operon. We characterized the synthetic circuit using deterministic and stochastic mathematical models. Similar to its natural counterparts, our synthetic system shows bistable and hysteretic behavior, and the inducer concentration range for bistability as well as the switching rates between the two stable states depend on the repressor concentration. Our results indicate that a generic permease–inducer–repressor circuit with a single feedback loop is sufficient to explain the experimentally observed bistable behavior of the natural systems. We anticipate that the approach of reimplementing natural systems with orthogonal parts to identify crucial network components is applicable to other natural systems such as signaling pathways."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"         5","external_id":{"isi":["000386196100008"]},"issue":"10","oa_version":"None","_id":"1008","status":"public","citation":{"chicago":"Gnügge, Robert, Lekshmi Dharmarajan, Moritz Lang, and Jörg Stelling. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” <i>ACS Synthetic Biology</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acssynbio.6b00013\">https://doi.org/10.1021/acssynbio.6b00013</a>.","mla":"Gnügge, Robert, et al. “An Orthogonal Permease–Inducer–Repressor Feedback Loop Shows Bistability.” <i>ACS Synthetic Biology</i>, vol. 5, no. 10, American Chemical Society, 2016, pp. 1098–107, doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00013\">10.1021/acssynbio.6b00013</a>.","short":"R. Gnügge, L. Dharmarajan, M. Lang, J. Stelling, ACS Synthetic Biology 5 (2016) 1098–1107.","ama":"Gnügge R, Dharmarajan L, Lang M, Stelling J. An orthogonal permease–inducer–repressor feedback loop shows bistability. <i>ACS Synthetic Biology</i>. 2016;5(10):1098-1107. doi:<a href=\"https://doi.org/10.1021/acssynbio.6b00013\">10.1021/acssynbio.6b00013</a>","ista":"Gnügge R, Dharmarajan L, Lang M, Stelling J. 2016. An orthogonal permease–inducer–repressor feedback loop shows bistability. ACS Synthetic Biology. 5(10), 1098–1107.","apa":"Gnügge, R., Dharmarajan, L., Lang, M., &#38; Stelling, J. (2016). An orthogonal permease–inducer–repressor feedback loop shows bistability. <i>ACS Synthetic Biology</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssynbio.6b00013\">https://doi.org/10.1021/acssynbio.6b00013</a>","ieee":"R. Gnügge, L. Dharmarajan, M. Lang, and J. Stelling, “An orthogonal permease–inducer–repressor feedback loop shows bistability,” <i>ACS Synthetic Biology</i>, vol. 5, no. 10. American Chemical Society, pp. 1098–1107, 2016."},"year":"2016","acknowledgement":"We thank Julio Polaina (Instituto de Agroqu ı ́ mica y Tecnolog ı ́ a de Alimentos, C.S.I.C., Paterna, Spain) for the gift of plasmid pMR4, Gregor W. Schmidt for provision of and support with the micro fl uidic device, Markus Du ̈ rr for the cell tracking R script, and Lukas Widmer for the script for MEIGO using “ parfor ” in MATLAB. We acknowledge the members of the Stelling group for discussions, comments, and support.","publisher":"American Chemical Society","day":"05","isi":1},{"oa":1,"title":"Conditionally optimal algorithms for generalized Büchi Games","type":"conference","doi":"10.4230/LIPIcs.MFCS.2016.25","article_number":"25","conference":{"location":"Krakow, Poland","name":"MFCS: Mathematical Foundations of Computer Science","end_date":"2016-08-26","start_date":"2016-08-22"},"scopus_import":"1","author":[{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Wolfgang","full_name":"Dvorák, Wolfgang","last_name":"Dvorák"},{"full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"}],"article_processing_charge":"No","date_created":"2018-12-11T11:49:58Z","project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}],"quality_controlled":"1","pubrep_id":"779","publication_status":"published","department":[{"_id":"KrCh"}],"volume":58,"language":[{"iso":"eng"}],"month":"08","license":"https://creativecommons.org/licenses/by/3.0/","has_accepted_license":"1","date_published":"2016-08-01T00:00:00Z","ddc":["000","004","006"],"tmp":{"short":"CC BY (3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","image":"/images/cc_by.png"},"fulldoi":"https://doi.org/10.4230/LIPIcs.MFCS.2016.25","alternative_title":["LIPIcs"],"date_updated":"2025-07-10T11:49:55Z","publist_id":"6317","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Games on graphs provide the appropriate framework to study several central problems in computer science, such as verification and synthesis of reactive systems. One of the most basic objectives for games on graphs is the liveness (or Büchi) objective that given a target set of vertices requires that some vertex in the target set is visited infinitely often. We study generalized Büchi objectives (i.e., conjunction of liveness objectives), and implications between two generalized Büchi objectives (known as GR(1) objectives), that arise in numerous applications in computer-aided verification. We present improved algorithms and conditional super-linear lower bounds based on widely believed assumptions about the complexity of (A1) combinatorial Boolean matrix multiplication and (A2) CNF-SAT. We consider graph games with n vertices, m edges, and generalized Büchi objectives with k conjunctions. First, we present an algorithm with running time O(k*n^2), improving the previously known O(k*n*m) and O(k^2*n^2) worst-case bounds. Our algorithm is optimal for dense graphs under (A1). Second, we show that the basic algorithm for the problem is optimal for sparse graphs when the target sets have constant size under (A2). Finally, we consider GR(1) objectives, with k_1 conjunctions in the antecedent and k_2 conjunctions in the consequent, and present an O(k_1 k_2 n^{2.5})-time algorithm, improving the previously known O(k_1*k_2*n*m)-time algorithm for m &gt; n^{1.5}. ","lang":"eng"}],"ec_funded":1,"file_date_updated":"2018-12-12T10:16:02Z","intvolume":"        58","file":[{"file_size":632786,"date_created":"2018-12-12T10:16:02Z","file_name":"IST-2017-779-v1+1_LIPIcs-MFCS-2016-25.pdf","file_id":"5187","creator":"system","content_type":"application/pdf","date_updated":"2018-12-12T10:16:02Z","access_level":"open_access","relation":"main_file"}],"status":"public","_id":"1068","oa_version":"Published Version","day":"01","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2016","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Conditionally Optimal Algorithms for Generalized Büchi Games</i>. Vol. 58, 25, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">10.4230/LIPIcs.MFCS.2016.25</a>.","short":"K. Chatterjee, W. Dvorák, M. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvorák, Monika Henzinger, and Veronika Loitzenbauer. “Conditionally Optimal Algorithms for Generalized Büchi Games,” Vol. 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">https://doi.org/10.4230/LIPIcs.MFCS.2016.25</a>.","ieee":"K. Chatterjee, W. Dvorák, M. Henzinger, and V. Loitzenbauer, “Conditionally optimal algorithms for generalized Büchi Games,” presented at the MFCS: Mathematical Foundations of Computer Science, Krakow, Poland, 2016, vol. 58.","apa":"Chatterjee, K., Dvorák, W., Henzinger, M., &#38; Loitzenbauer, V. (2016). Conditionally optimal algorithms for generalized Büchi Games (Vol. 58). Presented at the MFCS: Mathematical Foundations of Computer Science, Krakow, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">https://doi.org/10.4230/LIPIcs.MFCS.2016.25</a>","ista":"Chatterjee K, Dvorák W, Henzinger M, Loitzenbauer V. 2016. Conditionally optimal algorithms for generalized Büchi Games. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 58, 25.","ama":"Chatterjee K, Dvorák W, Henzinger M, Loitzenbauer V. Conditionally optimal algorithms for generalized Büchi Games. In: Vol 58. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2016.25\">10.4230/LIPIcs.MFCS.2016.25</a>"},"acknowledgement":"K. C., M. H., and W. D. are partially supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Start grant (279307"},{"pubrep_id":"778","publication_status":"published","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"volume":55,"license":"https://creativecommons.org/licenses/by/4.0/","month":"08","article_processing_charge":"No","date_created":"2018-12-11T11:49:59Z","quality_controlled":"1","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307"},{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989"}],"scopus_import":"1","conference":{"start_date":"2016-07-12","end_date":"2016-07-15","name":"ICALP: Automata, Languages and Programming","location":"Rome, Italy"},"author":[{"id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","last_name":"Chonev","full_name":"Chonev, Ventsislav K","first_name":"Ventsislav K"},{"first_name":"Joël","full_name":"Ouaknine, Joël","last_name":"Ouaknine"},{"first_name":"James","last_name":"Worrell","full_name":"Worrell, James"}],"type":"conference","doi":"10.4230/LIPIcs.ICALP.2016.100","oa":1,"title":"On the skolem problem for continuous linear dynamical systems","article_number":"100","oa_version":"Published Version","_id":"1069","status":"public","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","citation":{"ista":"Chonev VK, Ouaknine J, Worrell J. 2016. On the skolem problem for continuous linear dynamical systems. ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 100.","ama":"Chonev VK, Ouaknine J, Worrell J. On the skolem problem for continuous linear dynamical systems. In: Vol 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">10.4230/LIPIcs.ICALP.2016.100</a>","ieee":"V. K. Chonev, J. Ouaknine, and J. Worrell, “On the skolem problem for continuous linear dynamical systems,” presented at the ICALP: Automata, Languages and Programming, Rome, Italy, 2016, vol. 55.","apa":"Chonev, V. K., Ouaknine, J., &#38; Worrell, J. (2016). On the skolem problem for continuous linear dynamical systems (Vol. 55). Presented at the ICALP: Automata, Languages and Programming, Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">https://doi.org/10.4230/LIPIcs.ICALP.2016.100</a>","chicago":"Chonev, Ventsislav K, Joël Ouaknine, and James Worrell. “On the Skolem Problem for Continuous Linear Dynamical Systems,” Vol. 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">https://doi.org/10.4230/LIPIcs.ICALP.2016.100</a>.","mla":"Chonev, Ventsislav K., et al. <i>On the Skolem Problem for Continuous Linear Dynamical Systems</i>. Vol. 55, 100, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.100\">10.4230/LIPIcs.ICALP.2016.100</a>.","short":"V.K. Chonev, J. Ouaknine, J. Worrell, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016."},"acknowledgement":"Ventsislav Chonev is supported by Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307:  Graph Games), and ERC Advanced Grant (267989: QUAREM).","year":"2016","day":"01","intvolume":"        55","file":[{"file_id":"5213","file_name":"IST-2017-778-v1+1_LIPIcs-ICALP-2016-100.pdf","file_size":521415,"date_created":"2018-12-12T10:16:26Z","relation":"main_file","access_level":"open_access","date_updated":"2018-12-12T10:16:26Z","content_type":"application/pdf","creator":"system"}],"alternative_title":["LIPIcs"],"publist_id":"6314","date_updated":"2025-06-03T11:32:08Z","abstract":[{"lang":"eng","text":"The Continuous Skolem Problem asks whether a real-valued function satisfying a linear differen-\r\ntial equation has a zero in a given interval of real numbers. This is a fundamental reachability\r\nproblem for continuous linear dynamical systems, such as linear hybrid automata and continuous-\r\ntime Markov chains. Decidability of the problem is currently open – indeed decidability is open\r\neven for the sub-problem in which a zero is sought in a bounded interval. In this paper we show\r\ndecidability of the bounded problem subject to Schanuel’s Conjecture, a unifying conjecture in\r\ntranscendental number theory. We furthermore analyse the unbounded problem in terms of the\r\nfrequencies of the differential equation, that is, the imaginary parts of the characteristic roots.\r\nWe show that the unbounded problem can be reduced to the bounded problem if there is at most\r\none rationally linearly independent frequency, or if there are two rationally linearly independent\r\nfrequencies and all characteristic roots are simple. We complete the picture by showing that de-\r\ncidability of the unbounded problem in the case of two (or more) rationally linearly independent\r\nfrequencies would entail a major new effectiveness result in Diophantine approximation, namely\r\ncomputability of the Diophantine-approximation types of all real algebraic numbers."}],"ec_funded":1,"file_date_updated":"2018-12-12T10:16:26Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"image":"/images/cc_by.png","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)"},"fulldoi":"https://doi.org/10.4230/LIPIcs.ICALP.2016.100","date_published":"2016-08-01T00:00:00Z","has_accepted_license":"1","ddc":["004","006"]},{"file":[{"file_id":"4714","file_size":546133,"date_created":"2018-12-12T10:08:52Z","file_name":"IST-2017-812-v1+1_LIPIcs-ICALP-2016-98.pdf","access_level":"open_access","relation":"main_file","creator":"system","content_type":"application/pdf","date_updated":"2018-12-12T10:08:52Z"}],"intvolume":"        55","status":"public","_id":"1070","oa_version":"Published Version","day":"01","year":"2016","citation":{"ieee":"K. Chatterjee and L. Doyen, “Computation tree logic for synchronization properties,” presented at the ICALP: Automata, Languages and Programming, Rome, Italy, 2016, vol. 55.","apa":"Chatterjee, K., &#38; Doyen, L. (2016). Computation tree logic for synchronization properties (Vol. 55). Presented at the ICALP: Automata, Languages and Programming, Rome, Italy: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">https://doi.org/10.4230/LIPIcs.ICALP.2016.98</a>","ista":"Chatterjee K, Doyen L. 2016. Computation tree logic for synchronization properties. ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 98.","ama":"Chatterjee K, Doyen L. Computation tree logic for synchronization properties. In: Vol 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">10.4230/LIPIcs.ICALP.2016.98</a>","mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Computation Tree Logic for Synchronization Properties</i>. Vol. 55, 98, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">10.4230/LIPIcs.ICALP.2016.98</a>.","short":"K. Chatterjee, L. Doyen, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Computation Tree Logic for Synchronization Properties,” Vol. 55. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2016.98\">https://doi.org/10.4230/LIPIcs.ICALP.2016.98</a>."},"acknowledgement":"This research was partially supported by Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003, and European project Cassting (FP7-601148).\r\n\r\nWe thank Stefan Göller and anonymous reviewers for their insightful\r\ncomments and suggestions.\r\n","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","ddc":["005"],"date_published":"2016-01-01T00:00:00Z","has_accepted_license":"1","fulldoi":"https://doi.org/10.4230/LIPIcs.ICALP.2016.98","tmp":{"image":"/images/cc_by.png","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)"},"date_updated":"2025-06-03T11:18:54Z","publist_id":"6313","alternative_title":["LIPIcs"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2018-12-12T10:08:52Z","abstract":[{"lang":"eng","text":"We present a logic that extends CTL (Computation Tree Logic) with operators that express synchronization properties. A property is synchronized in a system if it holds in all paths of a certain length. The new logic is obtained by using the same path quantifiers and temporal operators as in CTL, but allowing a different order of the quantifiers. This small syntactic variation induces a logic that can express non-regular properties for which known extensions of MSO with equality of path length are undecidable. We show that our variant of CTL is decidable and that the model-checking problem is in Delta_3^P = P^{NP^NP}, and is DP-hard. We analogously consider quantifier exchange in extensions of CTL, and we present operators defined using basic operators of CTL* that express the occurrence of infinitely many synchronization points. We show that the model-checking problem remains in Delta_3^P. The distinguishing power of CTL and of our new logic coincide if the Next operator is allowed in the logics, thus the classical bisimulation quotient can be used for state-space reduction before model checking. "}],"ec_funded":1,"date_created":"2018-12-11T11:49:59Z","article_processing_charge":"No","project":[{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","language":[{"iso":"eng"}],"volume":55,"department":[{"_id":"KrCh"}],"pubrep_id":"812","publication_status":"published","month":"01","oa":1,"title":"Computation tree logic for synchronization properties","doi":"10.4230/LIPIcs.ICALP.2016.98","type":"conference","article_number":"98","conference":{"start_date":"2016-07-12","end_date":"2016-07-15","name":"ICALP: Automata, Languages and Programming","location":"Rome, Italy"},"scopus_import":"1","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"}]},{"intvolume":"        57","file":[{"access_level":"open_access","relation":"main_file","creator":"system","content_type":"application/pdf","date_updated":"2018-12-12T10:14:31Z","file_id":"5084","file_size":579225,"date_created":"2018-12-12T10:14:31Z","file_name":"IST-2017-777-v1+1_LIPIcs-ESA-2016-28.pdf"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE) and ERC Start grant (279307: Graph Games).","year":"2016","citation":{"short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","mla":"Chatterjee, Krishnendu, et al. <i>Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant Treewidth Graphs</i>. Vol. 57, 28, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">10.4230/LIPIcs.ESA.2016.28</a>.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Optimal Reachability and a Space Time Tradeoff for Distance Queries in Constant Treewidth Graphs,” Vol. 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">https://doi.org/10.4230/LIPIcs.ESA.2016.28</a>.","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2016). Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs (Vol. 57). Presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">https://doi.org/10.4230/LIPIcs.ESA.2016.28</a>","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, “Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs,” presented at the ESA: European Symposium on Algorithms, Aarhus, Denmark, 2016, vol. 57.","ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs. In: Vol 57. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ESA.2016.28\">10.4230/LIPIcs.ESA.2016.28</a>","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2016. Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs. ESA: European Symposium on Algorithms, LIPIcs, vol. 57, 28."},"day":"01","oa_version":"Published Version","_id":"1071","status":"public","tmp":{"image":"/images/cc_by.png","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)"},"fulldoi":"https://doi.org/10.4230/LIPIcs.ESA.2016.28","has_accepted_license":"1","date_published":"2016-08-01T00:00:00Z","ddc":["004","006"],"abstract":[{"text":"We consider data-structures for answering reachability and distance queries on constant-treewidth graphs with n nodes, on the standard RAM computational model with wordsize W=Theta(log n). Our first contribution is a data-structure that after O(n) preprocessing time, allows (1) pair reachability queries in O(1) time; and (2) single-source reachability queries in O(n/log n) time. This is (asymptotically) optimal and is faster than DFS/BFS when answering more than a constant number of single-source queries. The data-structure uses at all times O(n) space. Our second contribution is a space-time tradeoff data-structure for distance queries. For any epsilon in [1/2,1], we provide a data-structure with polynomial preprocessing time that allows pair queries in O(n^{1-\\epsilon} alpha(n)) time, where alpha is the inverse of the Ackermann function, and at all times uses O(n^epsilon) space. The input graph G is not considered in the space complexity. ","lang":"eng"}],"ec_funded":1,"file_date_updated":"2018-12-12T10:14:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-04-08T14:22:16Z","publist_id":"6312","alternative_title":["LIPIcs"],"quality_controlled":"1","related_material":{"record":[{"status":"public","id":"821","relation":"dissertation_contains"}]},"project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"article_processing_charge":"No","date_created":"2018-12-11T11:49:59Z","month":"08","publication_status":"published","pubrep_id":"777","language":[{"iso":"eng"}],"volume":57,"department":[{"_id":"KrCh"}],"article_number":"28","type":"conference","doi":"10.4230/LIPIcs.ESA.2016.28","oa":1,"title":"Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","last_name":"Ibsen-Jensen","full_name":"Ibsen-Jensen, Rasmus","first_name":"Rasmus","orcid":"0000-0003-4783-0389"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","orcid":"0000-0002-8943-0722"}],"scopus_import":"1","conference":{"start_date":"2016-08-22","location":"Aarhus, Denmark","end_date":"2016-08-24","name":"ESA: European Symposium on Algorithms"}},{"article_number":"16018","oa":1,"title":"Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells","type":"journal_article","doi":"10.1038/celldisc.2016.18","publication":"Cell Discovery","author":[{"first_name":"Łukasz","full_name":"Łangowski, Łukasz","last_name":"Łangowski"},{"full_name":"Wabnik, Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","last_name":"Wabnik","first_name":"Krzysztof T","orcid":"0000-0001-7263-0560"},{"orcid":"0000-0001-5039-9660","first_name":"Hongjiang","full_name":"Li, Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","last_name":"Li"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"last_name":"Naramoto","full_name":"Naramoto, Satoshi","first_name":"Satoshi"},{"first_name":"Hirokazu","last_name":"Tanaka","full_name":"Tanaka, Hirokazu"},{"orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","project":[{"grant_number":"282300","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","article_processing_charge":"No","date_created":"2018-12-11T11:50:02Z","month":"07","publication_status":"published","pubrep_id":"757","volume":2,"language":[{"iso":"eng"}],"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"date_published":"2016-07-19T00:00:00Z","has_accepted_license":"1","ddc":["580"],"tmp":{"image":"/images/cc_by.png","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)"},"fulldoi":"https://doi.org/10.1038/celldisc.2016.18","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"lang":"eng","text":"The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells."}],"ec_funded":1,"file_date_updated":"2018-12-12T10:13:33Z","date_updated":"2025-09-22T14:19:46Z","publist_id":"6299","external_id":{"isi":["000414797400001"]},"intvolume":"         2","file":[{"relation":"main_file","access_level":"open_access","date_updated":"2018-12-12T10:13:33Z","content_type":"application/pdf","creator":"system","file_id":"5017","file_name":"IST-2017-757-v1+1_celldisc201618.pdf","date_created":"2018-12-12T10:13:33Z","file_size":5261671}],"isi":1,"day":"19","publisher":"Nature Publishing Group","citation":{"ista":"Łangowski Ł, Wabnik KT, Li H, Vanneste S, Naramoto S, Tanaka H, Friml J. 2016. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. Cell Discovery. 2, 16018.","ama":"Łangowski Ł, Wabnik KT, Li H, et al. Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. <i>Cell Discovery</i>. 2016;2. doi:<a href=\"https://doi.org/10.1038/celldisc.2016.18\">10.1038/celldisc.2016.18</a>","apa":"Łangowski, Ł., Wabnik, K. T., Li, H., Vanneste, S., Naramoto, S., Tanaka, H., &#38; Friml, J. (2016). Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells. <i>Cell Discovery</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/celldisc.2016.18\">https://doi.org/10.1038/celldisc.2016.18</a>","ieee":"Ł. Łangowski <i>et al.</i>, “Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells,” <i>Cell Discovery</i>, vol. 2. Nature Publishing Group, 2016.","chicago":"Łangowski, Łukasz, Krzysztof T Wabnik, Hongjiang Li, Steffen Vanneste, Satoshi Naramoto, Hirokazu Tanaka, and Jiří Friml. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” <i>Cell Discovery</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/celldisc.2016.18\">https://doi.org/10.1038/celldisc.2016.18</a>.","mla":"Łangowski, Łukasz, et al. “Cellular Mechanisms for Cargo Delivery and Polarity Maintenance at Different Polar Domains in Plant Cells.” <i>Cell Discovery</i>, vol. 2, 16018, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/celldisc.2016.18\">10.1038/celldisc.2016.18</a>.","short":"Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J. Friml, Cell Discovery 2 (2016)."},"acknowledgement":"We thank Bonnie Bartel, Jenny Russinova and Niko Geldner\r\nfor sharing published material, Martine de Cock and Annick\r\nBleys for help in preparing the manuscript. This work was\r\nsupported by the European Research Council (project\r\nERC-2011-StG-20101109-PSDP); Czech Science Foundation\r\nGAČR (GA13-40637S); project CEITEC—Central European\r\nInstitute of Technology (CZ.1.05/1.1.00/02.0068). SV is a\r\npostdoctoral fellow of the Research Foundation-Flanders.\r\nSN is a Project Assistant Professor supported by the Japanese\r\nSociety for the Promotion of Science (JSPS; 30612022 to SN),\r\nthe NC-CARP project of the Ministry of Education, Culture,\r\nSports, Science and Technology in Japan to SN.","year":"2016","status":"public","_id":"1081","oa_version":"Published Version"},{"title":"Self-organized control of an tendon driven arm by differential extrinsic plasticity","oa":1,"publication_identifier":{"isbn":["9780262339360"]},"type":"conference","doi":"10.7551/978-0-262-33936-0-ch029","publication":"15th International Conference on the Synthesis and Simulation of Living Systems","author":[{"last_name":"Martius","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","full_name":"Martius, Georg S","first_name":"Georg S"},{"last_name":"Hostettler","full_name":"Hostettler, Rafael","first_name":"Rafael"},{"first_name":"Alois","last_name":"Knoll","full_name":"Knoll, Alois"},{"first_name":"Ralf","last_name":"Der","full_name":"Der, Ralf"}],"conference":{"start_date":"2016-07-04","name":"ALIFE 2016: Conference on the Synthesis and Simulation of Living Systems","end_date":"2016-07-08","location":"Cancun, Mexico"},"corr_author":"1","scopus_import":"1","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"quality_controlled":"1","article_processing_charge":"No","date_created":"2020-07-05T22:00:47Z","month":"09","page":"142-143","publication_status":"published","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"volume":28,"language":[{"iso":"eng"}],"date_published":"2016-09-01T00:00:00Z","has_accepted_license":"1","ddc":["610"],"tmp":{"image":"/images/cc_by.png","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)"},"fulldoi":"https://doi.org/10.7551/978-0-262-33936-0-ch029","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2020-07-14T12:48:09Z","abstract":[{"text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.","lang":"eng"}],"ec_funded":1,"date_updated":"2025-07-10T11:55:05Z","intvolume":"        28","file":[{"file_name":"2016_ProcALIFE_Martius.pdf","file_size":678670,"date_created":"2020-07-06T12:59:09Z","file_id":"8096","date_updated":"2020-07-14T12:48:09Z","content_type":"application/pdf","creator":"cziletti","checksum":"cff63e7a4b8ac466ba51a9c84153a940","access_level":"open_access","relation":"main_file"}],"day":"01","publisher":"MIT Press","citation":{"ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>, Cancun, Mexico, 2016, vol. 28, pp. 142–143.","apa":"Martius, G. S., Hostettler, R., Knoll, A., &#38; Der, R. (2016). Self-organized control of an tendon driven arm by differential extrinsic plasticity. In <i>15th International Conference on the Synthesis and Simulation of Living Systems</i> (Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>","ama":"Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon driven arm by differential extrinsic plasticity. In: <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>. Vol 28. MIT Press; 2016:142-143. doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. 15th International Conference on the Synthesis and Simulation of Living Systems. ALIFE 2016: Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.","mla":"Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>, vol. 28, MIT Press, 2016, pp. 142–43, doi:<a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">10.7551/978-0-262-33936-0-ch029</a>.","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, 15th International Conference on the Synthesis and Simulation of Living Systems, MIT Press, 2016, pp. 142–143.","chicago":"Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In <i>15th International Conference on the Synthesis and Simulation of Living Systems</i>, 28:142–43. MIT Press, 2016. <a href=\"https://doi.org/10.7551/978-0-262-33936-0-ch029\">https://doi.org/10.7551/978-0-262-33936-0-ch029</a>."},"year":"2016","_id":"8094","status":"public","oa_version":"Published Version"},{"date_created":"2021-06-04T11:34:55Z","article_processing_charge":"No","quality_controlled":"1","volume":538,"language":[{"iso":"eng"}],"department":[{"_id":"DaZi"}],"publication_status":"published","page":"533-536","month":"10","doi":"10.1038/nature20110","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5684705/"}],"type":"journal_article","pmid":1,"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"oa":1,"title":"Mechanism for DNA transposons to generate introns on genomic scales","extern":"1","scopus_import":"1","author":[{"last_name":"Huff","full_name":"Huff, Jason T.","first_name":"Jason T."},{"first_name":"Daniel","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"},{"first_name":"Scott W.","last_name":"Roy","full_name":"Roy, Scott W."}],"publication":"Nature","intvolume":"       538","external_id":{"pmid":["27760113"]},"issue":"7626","oa_version":"Submitted Version","status":"public","_id":"9456","year":"2016","citation":{"mla":"Huff, Jason T., et al. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>, vol. 538, no. 7626, Springer Nature , 2016, pp. 533–36, doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>.","short":"J.T. Huff, D. Zilberman, S.W. Roy, Nature 538 (2016) 533–536.","chicago":"Huff, Jason T., Daniel Zilberman, and Scott W. Roy. “Mechanism for DNA Transposons to Generate Introns on Genomic Scales.” <i>Nature</i>. Springer Nature , 2016. <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>.","apa":"Huff, J. T., Zilberman, D., &#38; Roy, S. W. (2016). Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. Springer Nature . <a href=\"https://doi.org/10.1038/nature20110\">https://doi.org/10.1038/nature20110</a>","ieee":"J. T. Huff, D. Zilberman, and S. W. Roy, “Mechanism for DNA transposons to generate introns on genomic scales,” <i>Nature</i>, vol. 538, no. 7626. Springer Nature , pp. 533–536, 2016.","ama":"Huff JT, Zilberman D, Roy SW. Mechanism for DNA transposons to generate introns on genomic scales. <i>Nature</i>. 2016;538(7626):533-536. doi:<a href=\"https://doi.org/10.1038/nature20110\">10.1038/nature20110</a>","ista":"Huff JT, Zilberman D, Roy SW. 2016. Mechanism for DNA transposons to generate introns on genomic scales. Nature. 538(7626), 533–536."},"publisher":"Springer Nature ","day":"27","fulldoi":"https://doi.org/10.1038/nature20110","article_type":"letter_note","date_published":"2016-10-27T00:00:00Z","date_updated":"2021-12-14T07:55:30Z","abstract":[{"lang":"eng","text":"The discovery of introns four decades ago was one of the most unexpected findings in molecular biology. Introns are sequences interrupting genes that must be removed as part of messenger RNA production. Genome sequencing projects have shown that most eukaryotic genes contain at least one intron, and frequently many. Comparison of these genomes reveals a history of long evolutionary periods during which few introns were gained, punctuated by episodes of rapid, extensive gain. However, although several detailed mechanisms for such episodic intron generation have been proposed, none has been empirically supported on a genomic scale. Here we show how short, non-autonomous DNA transposons independently generated hundreds to thousands of introns in the prasinophyte Micromonas pusilla and the pelagophyte Aureococcus anophagefferens. Each transposon carries one splice site. The other splice site is co-opted from the gene sequence that is duplicated upon transposon insertion, allowing perfect splicing out of the RNA. The distributions of sequences that can be co-opted are biased with respect to codons, and phasing of transposon-generated introns is similarly biased. These transposons insert between pre-existing nucleosomes, so that multiple nearby insertions generate nucleosome-sized intervening segments. Thus, transposon insertion and sequence co-option may explain the intron phase biases and prevalence of nucleosome-sized exons observed in eukaryotes. Overall, the two independent examples of proliferating elements illustrate a general DNA transposon mechanism that can plausibly account for episodes of rapid, extensive intron gain during eukaryotic evolution."}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"date_updated":"2023-05-08T11:00:40Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Cytosine DNA methylation regulates the expression of eukaryotic genes and transposons. Methylation is copied by methyltransferases after DNA replication, which results in faithful transmission of methylation patterns during cell division and, at least in flowering plants, across generations. Transgenerational inheritance is mediated by a small group of cells that includes gametes and their progenitors. However, methylation is usually analyzed in somatic tissues that do not contribute to the next generation, and the mechanisms of transgenerational inheritance are inferred from such studies. To gain a better understanding of how DNA methylation is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases. We find that DNA methylation dependency on these enzymes is similar in sperm, vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin in vegetative cells, likely reflecting transcription of heterochromatic transposons in this cell type. We also show that lack of histone H1, which elevates heterochromatic DNA methylation in somatic tissues, does not have this effect in pollen. Instead, levels of CG methylation in wild-type sperm and vegetative cells, as well as in wild-type microspores from which both pollen cell types originate, are substantially higher than in wild-type somatic tissues and similar to those of H1-depleted roots. Our results demonstrate that the mechanisms of methylation maintenance are similar between pollen and somatic cells, but the efficiency of CG methylation is higher in pollen, allowing methylation patterns to be accurately inherited across generations.","lang":"eng"}],"date_published":"2016-12-27T00:00:00Z","fulldoi":"https://doi.org/10.1073/pnas.1619074114","article_type":"original","_id":"9473","status":"public","oa_version":"Published Version","day":"27","citation":{"chicago":"Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman, Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>.","mla":"Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15132–37, doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>.","short":"P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman, X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.","ama":"Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15132-15137. doi:<a href=\"https://doi.org/10.1073/pnas.1619074114\">10.1073/pnas.1619074114</a>","ista":"Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. Proceedings of the National Academy of Sciences. 113(52), 15132–15137.","apa":"Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L., … Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619074114\">https://doi.org/10.1073/pnas.1619074114</a>","ieee":"P.-H. Hsieh <i>et al.</i>, “Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15132–15137, 2016."},"year":"2016","publisher":"National Academy of Sciences","external_id":{"pmid":["27956643"]},"issue":"52","intvolume":"       113","scopus_import":"1","publication":"Proceedings of the National Academy of Sciences","author":[{"last_name":"Hsieh","full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung"},{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"first_name":"Toby","last_name":"Buttress","full_name":"Buttress, Toby"},{"full_name":"Gao, Hongbo","last_name":"Gao","first_name":"Hongbo"},{"first_name":"Matthew","full_name":"Couchman, Matthew","last_name":"Couchman"},{"first_name":"Robert L.","last_name":"Fischer","full_name":"Fischer, Robert L."},{"orcid":"0000-0002-0123-8649","first_name":"Daniel","full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman"},{"full_name":"Feng, Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","orcid":"0000-0002-4008-1234","first_name":"Xiaoqi"}],"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"pmid":1,"title":"Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation than somatic tissues","oa":1,"doi":"10.1073/pnas.1619074114","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1619074114","open_access":"1"}],"type":"journal_article","extern":"1","page":"15132-15137","language":[{"iso":"eng"}],"volume":113,"department":[{"_id":"DaZi"},{"_id":"XiFe"}],"publication_status":"published","month":"12","date_created":"2021-06-07T06:21:39Z","article_processing_charge":"No","quality_controlled":"1"},{"oa_version":"Published Version","status":"public","_id":"9477","year":"2016","citation":{"short":"K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman, R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy of Sciences 113 (2016) 15138–15143.","mla":"Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>.","chicago":"Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun, Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the Central Cells of Arabidopsis and Rice.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2016. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>.","apa":"Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten, S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1619047114\">https://doi.org/10.1073/pnas.1619047114</a>","ieee":"K. Park <i>et al.</i>, “DNA demethylation is initiated in the central cells of Arabidopsis and rice,” <i>Proceedings of the National Academy of Sciences</i>, vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.","ama":"Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central cells of Arabidopsis and rice. <i>Proceedings of the National Academy of Sciences</i>. 2016;113(52):15138-15143. doi:<a href=\"https://doi.org/10.1073/pnas.1619047114\">10.1073/pnas.1619047114</a>","ista":"Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences. 113(52), 15138–15143."},"publisher":"National Academy of Sciences","day":"27","intvolume":"       113","external_id":{"pmid":["27956642"]},"issue":"52","date_updated":"2023-05-08T11:00:07Z","abstract":[{"text":"Cytosine methylation is a DNA modification with important regulatory functions in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive DNA demethylation, which is required for proper gene expression in the endosperm, a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm cell carried in the pollen and a female central cell. Endosperm DNA demethylation is observed specifically on the chromosomes inherited from the central cell in Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase in Arabidopsis. DEMETER is expressed in the central cell before fertilization, suggesting that endosperm demethylation patterns are inherited from the central cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed to contribute to central cell demethylation. However, with the exception of three maize genes, central cell DNA methylation has not been directly measured, leaving the origin and mechanism of endosperm demethylation uncertain. Here, we report genome-wide analysis of DNA methylation in the central cells of Arabidopsis and rice—species that diverged 150 million years ago—as well as in rice egg cells. We find that DNA demethylation in both species is initiated in central cells, which requires DEMETER in Arabidopsis. However, we do not observe a global reduction of CG methylation that would be indicative of lowered MET1 activity; on the contrary, CG methylation efficiency is elevated in female gametes compared with nonsexual tissues. Our results demonstrate that locus-specific, active DNA demethylation in the central cell is the origin of maternal chromosome hypomethylation in the endosperm.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","fulldoi":"https://doi.org/10.1073/pnas.1619047114","keyword":["Multidisciplinary"],"date_published":"2016-12-27T00:00:00Z","department":[{"_id":"DaZi"},{"_id":"XiFe"}],"volume":113,"language":[{"iso":"eng"}],"publication_status":"published","page":"15138-15143","month":"12","date_created":"2021-06-07T07:10:59Z","article_processing_charge":"No","quality_controlled":"1","scopus_import":"1","author":[{"last_name":"Park","full_name":"Park, Kyunghyuk","first_name":"Kyunghyuk"},{"last_name":"Kim","full_name":"Kim, M. Yvonne","first_name":"M. Yvonne"},{"first_name":"Martin","full_name":"Vickers, Martin","last_name":"Vickers"},{"first_name":"Jin-Sup","last_name":"Park","full_name":"Park, Jin-Sup"},{"full_name":"Hyun, Youbong","last_name":"Hyun","first_name":"Youbong"},{"full_name":"Okamoto, Takashi","last_name":"Okamoto","first_name":"Takashi"},{"full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","orcid":"0000-0002-0123-8649"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng"},{"full_name":"Choi, Yeonhee","last_name":"Choi","first_name":"Yeonhee"},{"first_name":"Stefan","full_name":"Scholten, Stefan","last_name":"Scholten"}],"publication":"Proceedings of the National Academy of Sciences","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1619047114","open_access":"1"}],"doi":"10.1073/pnas.1619047114","type":"journal_article","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"pmid":1,"oa":1,"title":"DNA demethylation is initiated in the central cells of Arabidopsis and rice","extern":"1"}]