{"id":"https://openalex.org/W2072467292","doi":"https://doi.org/10.1371/journal.pcbi.1004236","title":"Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism","display_name":"Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism","publication_year":2015,"publication_date":"2015-04-24","ids":{"openalex":"https://openalex.org/W2072467292","doi":"https://doi.org/10.1371/journal.pcbi.1004236","mag":"2072467292","pmid":"https://pubmed.ncbi.nlm.nih.gov/25909187"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004236","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004236","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004236&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004236&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108529198","display_name":"Katja N. Rybakova","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Katja N. Rybakova","raw_affiliation_strings":["Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047855050","display_name":"Frank J. Bruggeman","orcid":"https://orcid.org/0000-0002-0255-4766"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Frank J. Bruggeman","raw_affiliation_strings":["Systems Bioinformatics, VU University Amsterdam, Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Systems Bioinformatics, VU University Amsterdam, Amsterdam, The Netherlands","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102066885","display_name":"Aleksandra Tomaszewska","orcid":null},"institutions":[{"id":"https://openalex.org/I175532246","display_name":"University of Eastern Finland","ror":"https://ror.org/00cyydd11","country_code":"FI","type":"education","lineage":["https://openalex.org/I175532246"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Aleksandra Tomaszewska","raw_affiliation_strings":["School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland"],"affiliations":[{"raw_affiliation_string":"School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland","institution_ids":["https://openalex.org/I175532246"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084879409","display_name":"Martijn J. Mon\u00e9","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Martijn J. Mon\u00e9","raw_affiliation_strings":["Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035613777","display_name":"Carsten Carlberg","orcid":"https://orcid.org/0000-0003-2633-0684"},"institutions":[{"id":"https://openalex.org/I175532246","display_name":"University of Eastern Finland","ror":"https://ror.org/00cyydd11","country_code":"FI","type":"education","lineage":["https://openalex.org/I175532246"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Carsten Carlberg","raw_affiliation_strings":["School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland"],"affiliations":[{"raw_affiliation_string":"School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland","institution_ids":["https://openalex.org/I175532246"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043470360","display_name":"Hans V. Westerhoff","orcid":"https://orcid.org/0000-0002-0443-6114"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["GB","NL"],"is_corresponding":true,"raw_author_name":"Hans V. Westerhoff","raw_affiliation_strings":["Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands; Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, United Kingdom; Synthetic Systems Biology, Netherlands Institute for Systems Biology, University of Amsterdam, Amsterdam, The Netherlands","Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, United Kingdom","Synthetic Systems Biology, Netherlands Institute for Systems Biology, University of Amsterdam, Amsterdam, The Netherlands","Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands; Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, United Kingdom; Synthetic Systems Biology, Netherlands Institute for Systems Biology, University of Amsterdam, Amsterdam, The Netherlands","institution_ids":[]},{"raw_affiliation_string":"Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, United Kingdom","institution_ids":["https://openalex.org/I28407311"]},{"raw_affiliation_string":"Synthetic Systems Biology, Netherlands Institute for Systems Biology, University of Amsterdam, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I887064364"]},{"raw_affiliation_string":"Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5043470360"],"corresponding_institution_ids":["https://openalex.org/I28407311","https://openalex.org/I887064364"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.3343,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.80239785,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"11","issue":"4","first_page":"e1004236","last_page":"e1004236"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.7827353477478027},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.5814330577850342},{"id":"https://openalex.org/keywords/transcription-coregulator","display_name":"Transcription coregulator","score":0.5526694059371948},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5481708645820618},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5142940878868103},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.5110639333724976},{"id":"https://openalex.org/keywords/transcription-preinitiation-complex","display_name":"Transcription preinitiation complex","score":0.49938488006591797},{"id":"https://openalex.org/keywords/eukaryotic-transcription","display_name":"Eukaryotic transcription","score":0.4608248472213745},{"id":"https://openalex.org/keywords/chia-pet","display_name":"ChIA-PET","score":0.4522765278816223},{"id":"https://openalex.org/keywords/bursting","display_name":"Bursting","score":0.4331793189048767},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.38797858357429504},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3439788818359375},{"id":"https://openalex.org/keywords/chromatin-remodeling","display_name":"Chromatin remodeling","score":0.312896728515625},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3103942275047302},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.22225356101989746},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.19613799452781677},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.08054578304290771}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.7827353477478027},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.5814330577850342},{"id":"https://openalex.org/C137365298","wikidata":"https://www.wikidata.org/wiki/Q7833928","display_name":"Transcription coregulator","level":5,"score":0.5526694059371948},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5481708645820618},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5142940878868103},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.5110639333724976},{"id":"https://openalex.org/C188740287","wikidata":"https://www.wikidata.org/wiki/Q423333","display_name":"Transcription preinitiation complex","level":5,"score":0.49938488006591797},{"id":"https://openalex.org/C100733574","wikidata":"https://www.wikidata.org/wiki/Q5408694","display_name":"Eukaryotic transcription","level":5,"score":0.4608248472213745},{"id":"https://openalex.org/C67258246","wikidata":"https://www.wikidata.org/wiki/Q5065897","display_name":"ChIA-PET","level":5,"score":0.4522765278816223},{"id":"https://openalex.org/C195221683","wikidata":"https://www.wikidata.org/wiki/Q5000649","display_name":"Bursting","level":2,"score":0.4331793189048767},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.38797858357429504},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3439788818359375},{"id":"https://openalex.org/C167227067","wikidata":"https://www.wikidata.org/wiki/Q5113739","display_name":"Chromatin remodeling","level":4,"score":0.312896728515625},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3103942275047302},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.22225356101989746},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.19613799452781677},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.08054578304290771},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001683","descriptor_name":"Biological Clocks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001683","descriptor_name":"Biological Clocks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001683","descriptor_name":"Biological Clocks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001683","descriptor_name":"Biological Clocks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015533","descriptor_name":"Transcriptional Activation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":13,"locations":[{"id":"doi:10.1371/journal.pcbi.1004236","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004236","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004236&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:25909187","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25909187","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:dare.uva.nl:openaire_cris_publications/2cc47dde-f41f-4b14-8f96-63a07965e28a","is_oa":true,"landing_page_url":"https://dare.uva.nl/personal/pure/en/publications/multiplex-eukaryotic-transcription-inactivation-timing-bursting-and-cycling-of-a-ratchet-clock-mechanism(2cc47dde-f41f-4b14-8f96-63a07965e28a).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400088","display_name":"UvA-DARE (University of Amsterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887064364","host_organization_name":"University of Amsterdam","host_organization_lineage":["https://openalex.org/I887064364"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Rybakova, K N, Bruggeman, F J, Tomaszewska, A, Mon\u00e9, M J, Carlberg, C & Westerhoff, H V 2015, 'Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism', PLoS Computational Biology, vol. 11, no. 4, pp. e1004236. https://doi.org/10.1371/journal.pcbi.1004236","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/787d8b28-e4d7-45eb-980a-c05bb986ab4c","is_oa":false,"landing_page_url":"https://research.manchester.ac.uk/en/publications/787d8b28-e4d7-45eb-980a-c05bb986ab4c","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Rybakova, K N, Bruggeman, F J, Tomaszewska, A, Mon\u00e9, M J, Carlberg, C & Westerhoff, H V 2015, 'Multiplex Eukaryotic Transcription (In) activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism', PL o S Computational Biology, vol. 11, no. 4, e1004236. https://doi.org/10.1371/journal.pcbi.1004236","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:research.vu.nl:openaire_cris_publications/2962e375-c036-418b-a216-2f0d394a0289","is_oa":true,"landing_page_url":"https://research.vu.nl/en/publications/2962e375-c036-418b-a216-2f0d394a0289","pdf_url":null,"source":{"id":"https://openalex.org/S4306401107","display_name":"VU Research Portal","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I865915315","host_organization_name":"Vrije Universiteit Amsterdam","host_organization_lineage":["https://openalex.org/I865915315"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Rybakova, E N, Bruggeman, F J, Tomaszewska, A, Mone, M J, Carlberg, C & Westerhoff, H V 2015, 'Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism', PLoS Computational Biology, vol. 11, no. 4. https://doi.org/10.1371/journal.pcbi.1004236","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:erepo.uef.fi:123456789/37","is_oa":true,"landing_page_url":"https://erepo.uef.fi/handle/123456789/37","pdf_url":null,"source":{"id":"https://openalex.org/S4306402418","display_name":"UEF eRepo (University of Eastern Finland)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I175532246","host_organization_name":"University of Eastern Finland","host_organization_lineage":["https://openalex.org/I175532246"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"","raw_type":"http://purl.org/eprint/type/JournalArticle"},{"id":"pmh:oai:dare.uva.nl:publications/2cc47dde-f41f-4b14-8f96-63a07965e28a","is_oa":false,"landing_page_url":"http://dare.uva.nl/personal/pure/en/publications/multiplex-eukaryotic-transcription-inactivation-timing-bursting-and-cycling-of-a-ratchet-clock-mechanism(2cc47dde-f41f-4b14-8f96-63a07965e28a).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400088","display_name":"UvA-DARE (University of Amsterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887064364","host_organization_name":"University of Amsterdam","host_organization_lineage":["https://openalex.org/I887064364"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:doaj.org/article:7a423745c54b4acf83b02400e4a836f8","is_oa":true,"landing_page_url":"https://doaj.org/article/7a423745c54b4acf83b02400e4a836f8","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 11, Iss 4, p e1004236 (2015)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3388689","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4409292","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/1393993","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Multiplex_Eukaryotic_Transcription_In_activation_Timing_Bursting_and_Cycling_of_a_Ratchet_Clock_Mechanism_/1393993","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:4409292","is_oa":true,"landing_page_url":"http://doi.org/10.1371/journal.pcbi.1004236","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:publications/787d8b28-e4d7-45eb-980a-c05bb986ab4c","is_oa":false,"landing_page_url":"https://www.research.manchester.ac.uk/portal/en/publications/multiplex-eukaryotic-transcription-in-activation-timing-bursting-and-cycling-of-a-ratchet-clock-mechanism(787d8b28-e4d7-45eb-980a-c05bb986ab4c).html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Rybakova, K N, Bruggeman, F J, Tomaszewska, A, Mon\u00e9, M J, Carlberg, C & Westerhoff, H V 2015, 'Multiplex Eukaryotic Transcription (In) activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism', PL o S Computational Biology, vol. 11, no. 4, e1004236. https://doi.org/10.1371/journal.pcbi.1004236","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:research.vu.nl:publications/2962e375-c036-418b-a216-2f0d394a0289","is_oa":true,"landing_page_url":"https://hdl.handle.net/1871.1/2962e375-c036-418b-a216-2f0d394a0289","pdf_url":null,"source":{"id":"https://openalex.org/S4306400546","display_name":"Digital Academic REpository of VU University Amsterdam (Vrije Universiteit Amsterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I865915315","host_organization_name":"Vrije Universiteit Amsterdam","host_organization_lineage":["https://openalex.org/I865915315"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Rybakova, E N, Bruggeman, F J, Tomaszewska, A, Mone, M J, Carlberg, C & Westerhoff, H V 2015, 'Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism', PLoS Computational Biology, vol. 11, no. 4. https://doi.org/10.1371/journal.pcbi.1004236","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004236","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004236","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004236&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G365880270","display_name":null,"funder_award_id":"BB/I004688/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G4125866353","display_name":null,"funder_award_id":"BB/D019079/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G5045220161","display_name":null,"funder_award_id":"H2020","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"},{"id":"https://openalex.org/F4320332999","display_name":"Horizon 2020 Framework Programme","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"},{"id":"https://openalex.org/F4320338366","display_name":"FP7 Food, Agriculture and Fisheries, Biotechnology","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2072467292.pdf","grobid_xml":"https://content.openalex.org/works/W2072467292.grobid-xml"},"referenced_works_count":82,"referenced_works":["https://openalex.org/W614012683","https://openalex.org/W1518531052","https://openalex.org/W1598957092","https://openalex.org/W1601315441","https://openalex.org/W1951165114","https://openalex.org/W1964318436","https://openalex.org/W1967339738","https://openalex.org/W1971236504","https://openalex.org/W1977281942","https://openalex.org/W1978182054","https://openalex.org/W1978657111","https://openalex.org/W1986463324","https://openalex.org/W1992927069","https://openalex.org/W1993009001","https://openalex.org/W1997581297","https://openalex.org/W1999777663","https://openalex.org/W2001188520","https://openalex.org/W2002583673","https://openalex.org/W2003499939","https://openalex.org/W2015416439","https://openalex.org/W2020767030","https://openalex.org/W2029059014","https://openalex.org/W2031720568","https://openalex.org/W2031822229","https://openalex.org/W2032015210","https://openalex.org/W2034119200","https://openalex.org/W2037768790","https://openalex.org/W2038208040","https://openalex.org/W2040249346","https://openalex.org/W2040321376","https://openalex.org/W2042321087","https://openalex.org/W2044729009","https://openalex.org/W2046566365","https://openalex.org/W2053460598","https://openalex.org/W2057182894","https://openalex.org/W2059506882","https://openalex.org/W2060584995","https://openalex.org/W2061851611","https://openalex.org/W2062669590","https://openalex.org/W2065310225","https://openalex.org/W2069281865","https://openalex.org/W2069678913","https://openalex.org/W2072391169","https://openalex.org/W2077046573","https://openalex.org/W2077249217","https://openalex.org/W2083245183","https://openalex.org/W2087177706","https://openalex.org/W2089689396","https://openalex.org/W2094997711","https://openalex.org/W2102818379","https://openalex.org/W2103018966","https://openalex.org/W2103354991","https://openalex.org/W2105512180","https://openalex.org/W2107578201","https://openalex.org/W2108958484","https://openalex.org/W2110823478","https://openalex.org/W2114040881","https://openalex.org/W2118274513","https://openalex.org/W2118623812","https://openalex.org/W2119038778","https://openalex.org/W2125937596","https://openalex.org/W2127013070","https://openalex.org/W2128551987","https://openalex.org/W2133452708","https://openalex.org/W2135185213","https://openalex.org/W2141688036","https://openalex.org/W2142362541","https://openalex.org/W2145787498","https://openalex.org/W2146689455","https://openalex.org/W2147372875","https://openalex.org/W2149824993","https://openalex.org/W2151715550","https://openalex.org/W2156852080","https://openalex.org/W2157118622","https://openalex.org/W2164542985","https://openalex.org/W2165962849","https://openalex.org/W2167241965","https://openalex.org/W2167244112","https://openalex.org/W2171327609","https://openalex.org/W2172102540","https://openalex.org/W2198199336","https://openalex.org/W4211018930"],"related_works":["https://openalex.org/W1883973295","https://openalex.org/W1996183389","https://openalex.org/W760758862","https://openalex.org/W2047605620","https://openalex.org/W3176680964","https://openalex.org/W1520448866","https://openalex.org/W2033325031","https://openalex.org/W407374352","https://openalex.org/W2064501897","https://openalex.org/W2039578001"],"abstract_inverted_index":{"Activation":[0],"of":[1,13,49,70,82,100,132,145,156,175,183,198,210,218,237],"eukaryotic":[2,50],"transcription":[3,51,75,84,185,192,220,224],"is":[4,92,111,160],"an":[5,215,235],"intricate":[6],"process":[7],"that":[8,52,79,107],"relies":[9],"on":[10,18,31,87,124,205,246],"a":[11,25,47,112,133,153,173,180],"multitude":[12],"regulatory":[14,102,202],"proteins":[15,203],"forming":[16],"complexes":[17,86,121],"chromatin.":[19,32],"Chromatin":[20,127],"modifications":[21,128],"appear":[22],"to":[23,38,54,65,97,179,229],"play":[24],"guiding":[26],"role":[27],"in":[28,171,231,242],"protein-complex":[29],"assembly":[30,81,144,166],"Together,":[33],"these":[34,109],"processes":[35],"give":[36],"rise":[37,178],"stochastic,":[39],"often":[40],"bursting,":[41],"transcriptional":[42,238],"activity.":[43],"Here":[44],"we":[45],"present":[46],"model":[48,106],"aims":[53],"integrate":[55],"those":[56],"mechanisms.":[57],"We":[58,77],"use":[59],"stochastic":[60,170],"and":[61,95,137,250],"ordinary-differential-equation":[62],"modeling":[63],"frameworks":[64],"examine":[66],"various":[67],"possible":[68],"mechanisms":[69,91],"gene":[71],"regulation":[72],"by":[73],"multiple":[74],"factors.":[76],"find":[78],"the":[80,125,130,139,143,146,164,184],"large":[83],"factor":[85],"chromatin":[88,141,206,248],"via":[89],"equilibrium-binding":[90],"highly":[93,169],"inefficient":[94],"insensitive":[96],"concentration":[98],"changes":[99],"single":[101],"proteins.":[103],"An":[104],"alternative":[105],"lacks":[108],"limitations":[110],"cyclic":[113],"ratchet":[114],"mechanism.":[115],"In":[116,150],"this":[117,151],"mechanism,":[118],"small":[119],"protein":[120,134,148,157],"assemble":[122],"sequentially":[123],"promoter.":[126],"mark":[129],"completion":[131],"complex":[135,158],"assembly,":[136],"sensitize":[138],"local":[140],"for":[142,196,207],"next":[147],"complex.":[149],"manner,":[152],"strict":[154],"order":[155],"assemblies":[159],"attained.":[161],"Even":[162],"though":[163],"individual":[165,227],"steps":[167],"are":[168,214],"duration,":[172],"sequence":[174],"them":[176],"gives":[177],"remarkable":[181],"precision":[182],"cycle":[186],"duration.":[187],"This":[188],"mechanism":[189],"explains":[190],"how":[191],"activation":[193,221],"cycles,":[194],"lasting":[195],"tens":[197,209],"minutes,":[199],"derive":[200],"from":[201],"residing":[204],"only":[208],"seconds.":[211],"Transcriptional":[212],"bursts":[213],"inherent":[216],"feature":[217],"such":[219],"cycles.":[222],"Bursting":[223],"can":[225],"cause":[226],"cells":[228],"remain":[230],"synchrony":[232],"transiently,":[233],"offering":[234],"explanation":[236],"cycling":[239],"as":[240],"observed":[241],"cell":[243],"populations,":[244],"both":[245],"promoter":[247],"status":[249],"mRNA":[251],"levels.":[252]},"counts_by_year":[{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2}],"updated_date":"2026-03-07T16:01:11.037858","created_date":"2016-06-24T00:00:00"}
