[{"abstract":[{"text":"The fixation probability is the probability that a new mutant introduced in a homogeneous population eventually takes over the entire population.\r\nThe fixation probability is a fundamental quantity of natural selection, and known to depend on the population structure.\r\nAmplifiers of natural selection are population structures which increase the fixation probability of advantageous mutants, as compared to the baseline case of well-mixed populations. In this work we focus on symmetric population structures represented as undirected graphs. In the regime of undirected graphs, the strongest amplifier known has been the Star graph, and the existence of undirected graphs with stronger amplification properties has remained open for over a decade.\r\nIn this work we present the Comet and Comet-swarm families of undirected graphs. We show that for a range of fitness values of the mutants, the Comet and Comet-swarm graphs have fixation probability strictly larger than the fixation probability of the Star graph, for fixed population size and at the limit of large populations, respectively.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"09","type":"technical_report","publication_status":"published","ddc":["519"],"date_published":"2016-11-09T00:00:00Z","status":"public","doi":"10.15479/AT:IST-2016-648-v1-1","has_accepted_license":"1","date_updated":"2025-09-18T09:50:09Z","publisher":"IST Austria","oa":1,"month":"11","oa_version":"Updated Version","_id":"5449","language":[{"iso":"eng"}],"date_created":"2018-12-12T11:39:24Z","related_material":{"record":[{"relation":"later_version","id":"512","status":"public"}]},"department":[{"_id":"KrCh"}],"author":[{"first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722"},{"orcid":"0000-0002-1097-9684","last_name":"Tkadlec","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Nowak, Martin","last_name":"Nowak","first_name":"Martin"}],"citation":{"ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">10.15479/AT:IST-2016-648-v1-1</a>","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Amplification on Undirected Population Structures: Comets Beat Stars, IST Austria, 2016.","mla":"Pavlogiannis, Andreas, et al. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">10.15479/AT:IST-2016-648-v1-1</a>.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Amplification on undirected population structures: Comets beat stars</i>. IST Austria, 2016.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Amplification on Undirected Population Structures: Comets Beat Stars</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-648-v1-1\">https://doi.org/10.15479/AT:IST-2016-648-v1-1</a>.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Amplification on undirected population structures: Comets beat stars, IST Austria, 22p."},"file":[{"date_updated":"2020-07-14T12:46:58Z","access_level":"open_access","file_id":"5529","relation":"main_file","file_name":"IST-2016-648-v1+1_tr.pdf","creator":"system","checksum":"8345a8c1e7d7f0cd92516d182b7fc59e","date_created":"2018-12-12T11:54:07Z","content_type":"application/pdf","file_size":1264221}],"page":"22","pubrep_id":"648","year":"2016","publication_identifier":{"issn":["2664-1690"]},"title":"Amplification on undirected population structures: Comets beat stars","alternative_title":["IST Austria Technical Report"],"file_date_updated":"2020-07-14T12:46:58Z"},{"doi":"10.15479/AT:IST-2016-728-v1-1","has_accepted_license":"1","status":"public","oa":1,"publisher":"IST Austria","date_updated":"2023-02-23T12:27:05Z","date_published":"2016-12-30T00:00:00Z","type":"technical_report","ddc":["000"],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"30","alternative_title":["IST Austria Technical Report"],"title":"Strong amplifiers of natural selection","publication_identifier":{"issn":["2664-1690"]},"file_date_updated":"2020-07-14T12:46:59Z","pubrep_id":"728","year":"2016","author":[{"full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","first_name":"Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1097-9684","last_name":"Tkadlec","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"citation":{"ama":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. <i>Strong Amplifiers of Natural Selection</i>. IST Austria; 2016. doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">10.15479/AT:IST-2016-728-v1-1</a>","apa":"Pavlogiannis, A., Tkadlec, J., Chatterjee, K., &#38; Nowak, M. (2016). <i>Strong amplifiers of natural selection</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">https://doi.org/10.15479/AT:IST-2016-728-v1-1</a>","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Strong Amplifiers of Natural Selection, IST Austria, 2016.","mla":"Pavlogiannis, Andreas, et al. <i>Strong Amplifiers of Natural Selection</i>. IST Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">10.15479/AT:IST-2016-728-v1-1</a>.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Strong amplifiers of natural selection, IST Austria, 34p.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Strong amplifiers of natural selection</i>. IST Austria, 2016.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2016-728-v1-1\">https://doi.org/10.15479/AT:IST-2016-728-v1-1</a>."},"date_created":"2018-12-12T11:39:24Z","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"page":"34","file":[{"date_created":"2018-12-12T11:53:04Z","creator":"system","checksum":"7b8bb17c322c0556acba6ac169fa71c1","file_size":1014732,"content_type":"application/pdf","access_level":"open_access","file_id":"5465","date_updated":"2020-07-14T12:46:59Z","relation":"main_file","file_name":"IST-2016-728-v1+1_main.pdf"}],"month":"12","oa_version":"Published Version","_id":"5451"},{"type":"technical_report","ddc":["000"],"ec_funded":1,"doi":"10.15479/AT:IST-2017-728-v2-1","oa":1,"date_updated":"2025-04-15T07:55:39Z","article_processing_charge":"No","date_published":"2016-12-30T00:00:00Z","author":[{"orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"full_name":"Tkadlec, Josef","last_name":"Tkadlec","orcid":"0000-0002-1097-9684","first_name":"Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"date_created":"2018-12-12T11:39:25Z","page":"32","file":[{"file_size":811558,"content_type":"application/pdf","checksum":"58e895f26c82f560c0f0989bf8b08599","creator":"system","date_created":"2018-12-12T11:52:59Z","file_name":"IST-2017-728-v2+1_main.pdf","relation":"main_file","date_updated":"2020-07-14T12:46:59Z","file_id":"5460","access_level":"open_access"}],"month":"12","alternative_title":["IST Austria Technical Report"],"publication_identifier":{"issn":["2664-1690"]},"pubrep_id":"750","year":"2016","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"30","has_accepted_license":"1","status":"public","publisher":"IST Austria","citation":{"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-2017-728-v2-1\">https://doi.org/10.15479/AT:IST-2017-728-v2-1</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-2017-728-v2-1\">10.15479/AT:IST-2017-728-v2-1</a>","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <a href=\"https://doi.org/10.15479/AT:IST-2017-728-v2-1\">https://doi.org/10.15479/AT:IST-2017-728-v2-1</a>.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria, 2016.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 32p.","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-2017-728-v2-1\">10.15479/AT:IST-2017-728-v2-1</a>.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016."},"related_material":{"record":[{"relation":"later_version","id":"5453","status":"public"},{"relation":"popular_science","status":"public","id":"5559"}]},"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"oa_version":"Published Version","_id":"5452","title":"Arbitrarily strong amplifiers of natural selection","file_date_updated":"2020-07-14T12:46:59Z"},{"file_date_updated":"2020-07-14T12:46:59Z","alternative_title":["IST Austria Technical Report"],"publication_identifier":{"issn":["2664-1690"]},"title":"Arbitrarily strong amplifiers of natural selection","year":"2016","pubrep_id":"755","page":"34","file":[{"date_updated":"2020-07-14T12:46:59Z","access_level":"open_access","file_id":"5474","relation":"main_file","file_name":"IST-2017-749-v3+1_main.pdf","creator":"system","checksum":"83b0313dab3bff4bdb6ac38695026fda","date_created":"2018-12-12T11:53:13Z","file_size":1015647,"content_type":"application/pdf"}],"author":[{"orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"},{"orcid":"0000-0002-1097-9684","last_name":"Tkadlec","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"citation":{"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>","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>","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>.","short":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, M. Nowak, Arbitrarily Strong Amplifiers of Natural Selection, IST Austria, 2016.","ieee":"A. Pavlogiannis, J. Tkadlec, K. Chatterjee, and M. Nowak, <i>Arbitrarily strong amplifiers of natural selection</i>. IST Austria, 2016.","chicago":"Pavlogiannis, Andreas, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. <i>Arbitrarily Strong Amplifiers of Natural Selection</i>. IST Austria, 2016. <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>.","ista":"Pavlogiannis A, Tkadlec J, Chatterjee K, Nowak M. 2016. Arbitrarily strong amplifiers of natural selection, IST Austria, 34p."},"date_created":"2018-12-12T11:39:25Z","related_material":{"record":[{"status":"public","id":"5452","relation":"earlier_version"}]},"department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"_id":"5453","oa_version":"Published Version","month":"12","oa":1,"publisher":"IST Austria","date_updated":"2025-04-15T07:55:37Z","doi":"10.15479/AT:IST-2017-749-v3-1","status":"public","has_accepted_license":"1","date_published":"2016-12-30T00:00:00Z","publication_status":"published","ddc":["000"],"type":"technical_report","day":"30","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_updated":"2025-09-22T07:32:43Z","oa":1,"publisher":"Institute of Science and Technology Austria","doi":"10.15479/AT:ISTA:34","status":"public","has_accepted_license":"1","date_published":"2016-02-19T00:00:00Z","tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"article_processing_charge":"No","license":"https://creativecommons.org/publicdomain/zero/1.0/","ddc":["576"],"type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"19","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"}],"publist_id":"5828","file_date_updated":"2020-07-14T12:47:00Z","title":"Flower colour data and phylogeny (NEXUS) files","year":"2016","file":[{"file_name":"IST-2016-34-v1+1_tellis_flower_colour_data.zip","relation":"main_file","date_updated":"2020-07-14T12:47:00Z","file_id":"5594","access_level":"open_access","file_size":4468543,"content_type":"application/zip","checksum":"950f85b80427d357bfeff09608ba02e9","creator":"system","date_created":"2018-12-12T13:02:27Z"}],"datarep_id":"34","related_material":{"record":[{"relation":"research_paper","status":"public","id":"1382"}]},"department":[{"_id":"NiBa"}],"date_created":"2018-12-12T12:31:29Z","author":[{"id":"3153D6D4-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ellis","orcid":"0000-0002-8511-0254","full_name":"Ellis, Thomas"},{"full_name":"Field, David","last_name":"Field","orcid":"0000-0002-4014-8478","first_name":"David","id":"419049E2-F248-11E8-B48F-1D18A9856A87"}],"citation":{"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>","ieee":"T. Ellis and D. Field, “Flower colour data and phylogeny (NEXUS) files.” Institute of Science and Technology Austria, 2016.","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>.","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>.","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>."},"oa_version":"Published Version","_id":"5550","month":"02"},{"_id":"5555","oa_version":"Published Version","keyword":["cell migration","wide field microscopy","FIJI"],"month":"07","datarep_id":"44","file":[{"content_type":"application/zip","file_size":20692,"checksum":"9f96cddbcd4ed689f48712ffe234d5e5","creator":"system","date_created":"2018-12-12T13:03:03Z","file_name":"IST-2016-44-v1+1_migrationAnalyzer.zip","relation":"main_file","date_updated":"2020-07-14T12:47:02Z","file_id":"5621","access_level":"open_access"}],"author":[{"full_name":"Hauschild, Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"}],"citation":{"mla":"Hauschild, Robert. <i>Fiji Script to Determine Average Speed and Direction of Migration of Cells</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:44\">10.15479/AT:ISTA:44</a>.","short":"R. Hauschild, (2016).","ieee":"R. Hauschild, “Fiji script to determine average speed and direction of migration of cells.” Institute of Science and Technology Austria, 2016.","chicago":"Hauschild, Robert. “Fiji Script to Determine Average Speed and Direction of Migration of Cells.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:44\">https://doi.org/10.15479/AT:ISTA:44</a>.","ista":"Hauschild R. 2016. Fiji script to determine average speed and direction of migration of cells, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:44\">10.15479/AT:ISTA:44</a>.","ama":"Hauschild R. Fiji script to determine average speed and direction of migration of cells. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:44\">10.15479/AT:ISTA:44</a>","apa":"Hauschild, R. (2016). Fiji script to determine average speed and direction of migration of cells. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:44\">https://doi.org/10.15479/AT:ISTA:44</a>"},"department":[{"_id":"Bio"}],"date_created":"2018-12-12T12:31:31Z","year":"2016","file_date_updated":"2020-07-14T12:47:02Z","title":"Fiji script to determine average speed and direction of migration of cells","day":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"This FIJI script calculates the population average of the migration speed as a function of time of all cells from wide field microscopy movies.","lang":"eng"}],"ddc":["570"],"type":"research_data","article_processing_charge":"No","date_published":"2016-07-08T00:00:00Z","tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"publisher":"Institute of Science and Technology Austria","oa":1,"date_updated":"2024-02-21T13:50:06Z","status":"public","has_accepted_license":"1","doi":"10.15479/AT:ISTA:44"},{"license":"https://creativecommons.org/licenses/by-sa/4.0/","article_processing_charge":"No","date_published":"2016-08-25T00:00:00Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"status":"public","has_accepted_license":"1","doi":"10.15479/AT:ISTA:45","publisher":"Institute of Science and Technology Austria","oa":1,"date_updated":"2025-07-10T11:49:51Z","abstract":[{"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","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"25","type":"research_data","ddc":["571"],"year":"2016","title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","file_date_updated":"2020-07-14T12:47:02Z","keyword":["transcription","pausing","backtracking","polymerase","RNA","NET-seq","nucleosome","basepairing"],"month":"08","oa_version":"Published Version","_id":"5556","citation":{"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>.","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.","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>.","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>.","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>","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>"},"author":[{"first_name":"Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","full_name":"Lukacisin, Martin","last_name":"Lukacisin","orcid":"0000-0001-6549-4177"},{"first_name":"Matthieu","last_name":"Landon","full_name":"Landon, Matthieu"},{"first_name":"Rishi","full_name":"Jajoo, Rishi","last_name":"Jajoo"}],"department":[{"_id":"ToBo"}],"date_created":"2018-12-12T12:31:31Z","related_material":{"record":[{"relation":"used_in_publication","id":"8431","status":"deleted"},{"id":"1029","status":"public","relation":"research_paper"}]},"datarep_id":"45","file":[{"file_size":296722548,"content_type":"application/zip","date_created":"2018-12-12T13:02:58Z","creator":"system","checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","relation":"main_file","file_name":"IST-2016-45-v1+1_PaperCode.zip","access_level":"open_access","file_id":"5616","date_updated":"2020-07-14T12:47:02Z"}]},{"keyword":["discrete tomography"],"month":"09","_id":"5557","oa_version":"Published Version","author":[{"full_name":"Swoboda, Paul","last_name":"Swoboda","first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87"}],"citation":{"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>","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>","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>.","ieee":"P. Swoboda, “Synthetic discrete tomography problems.” Institute of Science and Technology Austria, 2016.","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>.","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>."},"department":[{"_id":"VlKo"}],"date_created":"2018-12-12T12:31:31Z","datarep_id":"46","file":[{"file_id":"5645","access_level":"open_access","date_updated":"2020-07-14T12:47:02Z","file_name":"IST-2016-46-v1+1_discrete_tomography_synthetic.zip","relation":"main_file","date_created":"2018-12-12T13:05:19Z","checksum":"aa5a16a0dc888da7186fb8fc45e88439","creator":"system","file_size":36058401,"content_type":"application/zip"}],"year":"2016","contributor":[{"first_name":"Jan","contributor_type":"data_collector","last_name":"Kuske"}],"title":"Synthetic discrete tomography problems","file_date_updated":"2020-07-14T12:47:02Z","abstract":[{"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.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"20","type":"research_data","ddc":["006"],"article_processing_charge":"No","date_published":"2016-09-20T00:00:00Z","tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"status":"public","has_accepted_license":"1","doi":"10.15479/AT:ISTA:46","publisher":"Institute of Science and Technology Austria","oa":1,"date_updated":"2024-02-21T13:50:21Z"},{"article_processing_charge":"No","date_published":"2016-03-01T00:00:00Z","doi":"10.1093/molbev/msv270","volume":33,"oa":1,"date_updated":"2026-04-29T05:57:02Z","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."}],"quality_controlled":"1","article_type":"original","scopus_import":"1","DOAJ_listed":"1","OA_type":"gold","type":"journal_article","publication":"Molecular Biology and Evolution","ddc":["576"],"intvolume":"        33","pubrep_id":"587","year":"2016","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"month":"03","issue":"3","author":[{"last_name":"Wielgoss","full_name":"Wielgoss, Sébastien","first_name":"Sébastien"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias","last_name":"Bergmiller","orcid":"0000-0001-5396-4346","full_name":"Bergmiller, Tobias"},{"last_name":"Bischofberger","full_name":"Bischofberger, Anna M.","first_name":"Anna M."},{"first_name":"Alex R.","full_name":"Hall, Alex R.","last_name":"Hall"}],"date_created":"2018-12-18T13:18:10Z","department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"page":"770-782","file":[{"file_size":634037,"content_type":"application/pdf","date_created":"2018-12-18T13:21:45Z","creator":"dernst","checksum":"47d9010690b6c5c17f2ac830cc63ac5c","relation":"main_file","file_name":"2016_MolBiolEvol_Wielgoss.pdf","access_level":"open_access","file_id":"5750","date_updated":"2020-07-14T12:47:10Z"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","external_id":{"isi":["000371219500015"],"pmid":["26609077"]},"tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"isi":1,"status":"public","has_accepted_license":"1","publisher":"Oxford University Press","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.).","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","title":"Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria","file_date_updated":"2020-07-14T12:47:10Z","OA_place":"publisher","_id":"5749","oa_version":"Published Version","citation":{"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>","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>","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>.","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.","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.","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."},"related_material":{"record":[{"relation":"research_data","id":"9719","status":"public"}]},"pmid":1},{"type":"book_chapter","intvolume":"      9667","publication":"Computational Topology in Image Context","quality_controlled":"1","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"}],"conference":{"location":"Marseille, France","start_date":"2016-06-15","name":"CTIC: Computational Topology in Image Context","end_date":"2016-06-17"},"volume":9667,"doi":"10.1007/978-3-319-39441-1_23","date_updated":"2022-01-28T08:01:22Z","date_published":"2016-06-02T00:00:00Z","article_processing_charge":"No","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"date_created":"2019-01-08T20:44:24Z","author":[{"last_name":"Sen","full_name":"Sen, Nabhasmita","first_name":"Nabhasmita"},{"first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita","orcid":"0000-0002-5372-7890","last_name":"Biswas"},{"full_name":"Bhowmick, Partha","last_name":"Bhowmick","first_name":"Partha"}],"page":"253-264","month":"06","publication_identifier":{"eisbn":["978-3-319-39441-1"],"isbn":["978-3-319-39440-4"],"issn":["0302-9743"],"eissn":["1611-3349"]},"alternative_title":["LNCS"],"year":"2016","extern":"1","publication_status":"published","day":"02","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","publisher":"Springer Nature","citation":{"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>.","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.","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.","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.","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>","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>"},"oa_version":"None","_id":"5805","title":"On some local topological properties of naive discrete sphere","place":"Cham"},{"place":"Cham","title":"On functionality of quadraginta octants of naive sphere with application to circle drawing","oa_version":"None","_id":"5806","citation":{"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>","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>","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.","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>.","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.","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>.","short":"R. Biswas, P. Bhowmick, in:, Discrete Geometry for Computer Imagery, Springer Nature, Cham, 2016, pp. 256–267."},"publisher":"Springer Nature","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","day":"09","publication_status":"published","extern":"1","year":"2016","alternative_title":["LNCS"],"publication_identifier":{"eisbn":["978-3-319-32360-2"],"isbn":["978-3-319-32359-6"],"issn":["0302-9743","1611-3349"]},"month":"04","page":"256-267","author":[{"last_name":"Biswas","orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita"},{"last_name":"Bhowmick","full_name":"Bhowmick, Partha","first_name":"Partha"}],"language":[{"iso":"eng"}],"date_created":"2019-01-08T20:44:37Z","department":[{"_id":"HeEd"}],"article_processing_charge":"No","date_published":"2016-04-09T00:00:00Z","date_updated":"2022-01-28T08:10:11Z","volume":9647,"doi":"10.1007/978-3-319-32360-2_20","conference":{"location":"Nantes, France","start_date":"2016-04-18","name":"DGCI: International Conference on Discrete Geometry for Computer Imagery","end_date":"2016-04-20"},"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."}],"quality_controlled":"1","publication":"Discrete Geometry for Computer Imagery","intvolume":"      9647","type":"conference"},{"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"eisbn":["978-3-319-26145-4"],"isbn":["978-3-319-26144-7"]},"title":"On the connectivity and smoothness of discrete spherical circles","year":"2016","extern":"1","place":"Cham","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"date_created":"2019-01-08T20:45:19Z","author":[{"last_name":"Biswas","orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita"},{"first_name":"Partha","last_name":"Bhowmick","full_name":"Bhowmick, Partha"},{"last_name":"Brimkov","full_name":"Brimkov, Valentin E.","first_name":"Valentin E."}],"citation":{"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>","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>","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>.","short":"R. Biswas, P. Bhowmick, V.E. Brimkov, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2016, pp. 86–100.","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.","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>."},"page":"86-100","month":"01","oa_version":"None","_id":"5809","status":"public","volume":9448,"doi":"10.1007/978-3-319-26145-4_7","date_updated":"2022-01-28T08:13:03Z","publisher":"Springer Nature","date_published":"2016-01-06T00:00:00Z","article_processing_charge":"No","type":"book_chapter","intvolume":"      9448","publication":"Combinatorial image analysis","publication_status":"published","quality_controlled":"1","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"}],"day":"06","conference":{"location":"Kolkata, India","start_date":"2015-11-24","name":"IWCIA: International Workshop on Combinatorial Image Analysis","end_date":"2015-11-27"},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"article_processing_charge":"No","date_published":"2016-02-02T00:00:00Z","publisher":"Springer Nature","date_updated":"2026-04-07T08:32:03Z","doi":"10.1007/978-1-4939-3064-7_17","status":"public","acknowledgement":"We thank Mitsuru Ikeda for preparing replica images used in Fig. 2.","day":"02","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","publication_status":"published","publication":"Receptor and Ion Channel Detection in the Brain","corr_author":"1","OA_type":"closed access","type":"book_chapter","series_title":"Neuromethods","year":"2016","publication_identifier":{"issn":["0893-2336"],"eissn":["1940-6045"],"isbn":["9781493930630"],"eisbn":["9781493930647"]},"title":"High-Resolution Localization of Membrane Proteins by SDS-Digested Freeze-Fracture Replica Labeling (SDS-FRL)","_id":"19990","oa_version":"None","month":"02","page":"233-245","author":[{"full_name":"Harada, Harumi","last_name":"Harada","orcid":"0000-0001-7429-7896","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","orcid":"0000-0001-8761-9444"}],"citation":{"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>.","short":"H. Harada, R. Shigemoto, in:, Receptor and Ion Channel Detection in the Brain, Springer Nature, 2016, pp. 233–245.","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.","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.","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>.","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>"},"language":[{"iso":"eng"}],"department":[{"_id":"RySh"}],"date_created":"2025-07-10T13:56:06Z"},{"corr_author":"1","publication_status":"published","publication":"Encyclopedia of Machine Learning and Data Mining","OA_type":"closed access","type":"book_chapter","day":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","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"}],"date_updated":"2025-09-23T10:53:13Z","publisher":"Springer Nature","doi":"10.1007/978-1-4899-7502-7_892-1","status":"public","date_published":"2016-07-06T00:00:00Z","article_processing_charge":"No","page":"1-4","language":[{"iso":"eng"}],"date_created":"2025-07-10T13:57:52Z","department":[{"_id":"ChLa"}],"citation":{"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.","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.","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>.","ista":"Sharmanska V, Quadrianto N. 2016.Learning Using Privileged Information. In: Encyclopedia of Machine Learning and Data Mining. , 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>","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>"},"author":[{"id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","first_name":"Viktoriia","orcid":"0000-0003-0192-9308","last_name":"Sharmanska","full_name":"Sharmanska, Viktoriia"},{"first_name":"Novi","last_name":"Quadrianto","full_name":"Quadrianto, Novi"}],"_id":"19991","oa_version":"None","month":"07","title":"Learning Using Privileged Information","publication_identifier":{"eisbn":["9781489975027"]},"year":"2016"},{"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."}],"quality_controlled":"1","publication":"ACS Synthetic Biology","intvolume":"         5","type":"journal_article","article_processing_charge":"No","date_published":"2016-05-05T00:00:00Z","date_updated":"2025-09-22T14:20:45Z","doi":"10.1021/acssynbio.6b00013","volume":5,"issue":"10","month":"05","page":"1098 - 1107","author":[{"full_name":"Gnügge, Robert","last_name":"Gnügge","first_name":"Robert"},{"full_name":"Dharmarajan, Lekshmi","last_name":"Dharmarajan","first_name":"Lekshmi"},{"full_name":"Lang, Moritz","last_name":"Lang","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stelling","full_name":"Stelling, Jörg","first_name":"Jörg"}],"department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:49:40Z","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.","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"05","publist_id":"6390","publication_status":"published","isi":1,"external_id":{"isi":["000386196100008"]},"publisher":"American Chemical Society","status":"public","oa_version":"None","_id":"1008","citation":{"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.","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>.","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.","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.","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>","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>"},"title":"An orthogonal permease–inducer–repressor feedback loop shows bistability"},{"date_updated":"2025-07-10T11:49:55Z","oa":1,"volume":58,"doi":"10.4230/LIPIcs.MFCS.2016.25","date_published":"2016-08-01T00:00:00Z","article_processing_charge":"No","intvolume":"        58","ddc":["000","004","006"],"type":"conference","scopus_import":"1","conference":{"name":"MFCS: Mathematical Foundations of Computer Science","end_date":"2016-08-26","location":"Krakow, Poland","start_date":"2016-08-22"},"quality_controlled":"1","ec_funded":1,"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"}],"alternative_title":["LIPIcs"],"year":"2016","pubrep_id":"779","file":[{"creator":"system","date_created":"2018-12-12T10:16:02Z","content_type":"application/pdf","file_size":632786,"date_updated":"2018-12-12T10:16:02Z","file_id":"5187","access_level":"open_access","file_name":"IST-2017-779-v1+1_LIPIcs-MFCS-2016-25.pdf","relation":"main_file"}],"department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:49:58Z","language":[{"iso":"eng"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Dvorák, Wolfgang","last_name":"Dvorák","first_name":"Wolfgang"},{"id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika","first_name":"Veronika"}],"month":"08","article_number":"25","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","status":"public","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)"},"license":"https://creativecommons.org/licenses/by/3.0/","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","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","publist_id":"6317","file_date_updated":"2018-12-12T10:16:02Z","title":"Conditionally optimal algorithms for generalized Büchi Games","citation":{"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>","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>","short":"K. Chatterjee, W. Dvorák, M. Henzinger, V. Loitzenbauer, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","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>.","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.","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.","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>."},"_id":"1068","oa_version":"Published Version","project":[{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}]},{"oa":1,"date_updated":"2025-06-03T11:32:08Z","doi":"10.4230/LIPIcs.ICALP.2016.100","volume":55,"article_processing_charge":"No","date_published":"2016-08-01T00:00:00Z","ddc":["004","006"],"intvolume":"        55","scopus_import":"1","type":"conference","conference":{"location":"Rome, Italy","start_date":"2016-07-12","name":"ICALP: Automata, Languages and Programming","end_date":"2016-07-15"},"ec_funded":1,"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."}],"quality_controlled":"1","alternative_title":["LIPIcs"],"year":"2016","pubrep_id":"778","file":[{"creator":"system","date_created":"2018-12-12T10:16:26Z","content_type":"application/pdf","file_size":521415,"date_updated":"2018-12-12T10:16:26Z","access_level":"open_access","file_id":"5213","relation":"main_file","file_name":"IST-2017-778-v1+1_LIPIcs-ICALP-2016-100.pdf"}],"author":[{"first_name":"Ventsislav K","id":"36CBE2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Chonev, Ventsislav K","last_name":"Chonev"},{"first_name":"Joël","full_name":"Ouaknine, Joël","last_name":"Ouaknine"},{"full_name":"Worrell, James","last_name":"Worrell","first_name":"James"}],"date_created":"2018-12-11T11:49:59Z","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"month":"08","article_number":"100","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","has_accepted_license":"1","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_status":"published","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).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","publist_id":"6314","file_date_updated":"2018-12-12T10:16:26Z","title":"On the skolem problem for continuous linear dynamical systems","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.","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.","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>.","short":"V.K. Chonev, J. Ouaknine, J. Worrell, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","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>.","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>","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>"},"oa_version":"Published Version","_id":"1069","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"}]},{"publist_id":"6313","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","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","publication_status":"published","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"status":"public","has_accepted_license":"1","article_number":"98","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"oa_version":"Published Version","_id":"1070","citation":{"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>","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>","ista":"Chatterjee K, Doyen L. 2016. Computation tree logic for synchronization properties. ICALP: Automata, Languages and Programming, LIPIcs, vol. 55, 98.","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.","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>.","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."},"title":"Computation tree logic for synchronization properties","file_date_updated":"2018-12-12T10:08:52Z","quality_controlled":"1","ec_funded":1,"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. "}],"conference":{"location":"Rome, Italy","start_date":"2016-07-12","name":"ICALP: Automata, Languages and Programming","end_date":"2016-07-15"},"type":"conference","scopus_import":"1","intvolume":"        55","ddc":["005"],"date_published":"2016-01-01T00:00:00Z","article_processing_charge":"No","doi":"10.4230/LIPIcs.ICALP.2016.98","volume":55,"date_updated":"2025-06-03T11:18:54Z","oa":1,"month":"01","date_created":"2018-12-11T11:49:59Z","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"first_name":"Laurent","full_name":"Doyen, Laurent","last_name":"Doyen"}],"file":[{"date_updated":"2018-12-12T10:08:52Z","file_id":"4714","access_level":"open_access","file_name":"IST-2017-812-v1+1_LIPIcs-ICALP-2016-98.pdf","relation":"main_file","creator":"system","date_created":"2018-12-12T10:08:52Z","content_type":"application/pdf","file_size":546133}],"pubrep_id":"812","year":"2016","alternative_title":["LIPIcs"]},{"title":"Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs","file_date_updated":"2018-12-12T10:14:31Z","citation":{"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>","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>","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>.","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.","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."},"related_material":{"record":[{"status":"public","id":"821","relation":"dissertation_contains"}]},"project":[{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"_id":"1071","oa_version":"Published Version","has_accepted_license":"1","status":"public","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","article_number":"28","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publication_status":"published","publist_id":"6312","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).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","alternative_title":["LIPIcs"],"pubrep_id":"777","year":"2016","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"}],"language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:49:59Z","file":[{"relation":"main_file","file_name":"IST-2017-777-v1+1_LIPIcs-ESA-2016-28.pdf","access_level":"open_access","file_id":"5084","date_updated":"2018-12-12T10:14:31Z","content_type":"application/pdf","file_size":579225,"date_created":"2018-12-12T10:14:31Z","creator":"system"}],"month":"08","doi":"10.4230/LIPIcs.ESA.2016.28","volume":57,"oa":1,"date_updated":"2026-04-08T14:22:16Z","article_processing_charge":"No","date_published":"2016-08-01T00:00:00Z","scopus_import":"1","type":"conference","ddc":["004","006"],"intvolume":"        57","abstract":[{"lang":"eng","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. "}],"ec_funded":1,"quality_controlled":"1","conference":{"name":"ESA: European Symposium on Algorithms","end_date":"2016-08-24","location":"Aarhus, Denmark","start_date":"2016-08-22"}},{"citation":{"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>","short":"Ł. Łangowski, K.T. Wabnik, H. Li, S. Vanneste, S. Naramoto, H. Tanaka, J. Friml, Cell Discovery 2 (2016).","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>.","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.","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>.","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."},"_id":"1081","oa_version":"Published Version","project":[{"call_identifier":"FP7","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"file_date_updated":"2018-12-12T10:13:33Z","title":"Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells","publication_status":"published","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.","day":"19","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publist_id":"6299","publisher":"Nature Publishing Group","article_number":"16018","status":"public","has_accepted_license":"1","isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000414797400001"]},"file":[{"access_level":"open_access","file_id":"5017","date_updated":"2018-12-12T10:13:33Z","relation":"main_file","file_name":"IST-2017-757-v1+1_celldisc201618.pdf","date_created":"2018-12-12T10:13:33Z","creator":"system","file_size":5261671,"content_type":"application/pdf"}],"author":[{"last_name":"Łangowski","full_name":"Łangowski, Łukasz","first_name":"Łukasz"},{"last_name":"Wabnik","orcid":"0000-0001-7263-0560","full_name":"Wabnik, Krzysztof T","id":"4DE369A4-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof T"},{"orcid":"0000-0001-5039-9660","last_name":"Li","full_name":"Li, Hongjiang","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"first_name":"Hirokazu","last_name":"Tanaka","full_name":"Tanaka, Hirokazu"},{"full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2018-12-11T11:50:02Z","language":[{"iso":"eng"}],"department":[{"_id":"EvBe"},{"_id":"JiFr"}],"month":"07","year":"2016","pubrep_id":"757","publication":"Cell Discovery","ddc":["580"],"intvolume":"         2","scopus_import":"1","type":"journal_article","ec_funded":1,"abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","oa":1,"date_updated":"2025-09-22T14:19:46Z","volume":2,"doi":"10.1038/celldisc.2016.18","article_processing_charge":"No","date_published":"2016-07-19T00:00:00Z"}]