{"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"],"raw_orcid":null,"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"],"raw_orcid":null,"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"],"raw_orcid":null,"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"],"raw_orcid":null,"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"],"raw_orcid":null,"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/I2898155008","display_name":"Academic Center for Dentistry Amsterdam","ror":"https://ror.org/04x5wnb75","country_code":"NL","type":"education","lineage":["https://openalex.org/I2898155008"]},{"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","Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands","Synthetic Systems Biology, Netherlands Institute for Systems Biology, University of Amsterdam, Amsterdam, The Netherlands"],"raw_orcid":null,"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":["https://openalex.org/I2898155008"]},{"raw_affiliation_string":"Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, United Kingdom","institution_ids":["https://openalex.org/I28407311"]},{"raw_affiliation_string":"Molecular Cell Physiology, VU University Amsterdam, Amsterdam, The Netherlands","institution_ids":[]},{"raw_affiliation_string":"Synthetic Systems Biology, Netherlands Institute for Systems Biology, University of Amsterdam, Amsterdam, The Netherlands","institution_ids":["https://openalex.org/I887064364"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5043470360"],"corresponding_institution_ids":["https://openalex.org/I28407311","https://openalex.org/I2898155008","https://openalex.org/I887064364"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.2382,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.78684766,"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":10,"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: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/article"},{"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":"info:eu-repo/semantics/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: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":false,"landing_page_url":"https://doaj.org/article/7a423745c54b4acf83b02400e4a836f8","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"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: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/S4306402621","display_name":"INDIGO (University of Illinois at Chicago)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39422238","host_organization_name":"University of Illinois Chicago","host_organization_lineage":["https://openalex.org/I39422238"],"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:research.vu.nl:openaire/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":"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"},{"id":"pmh:uvapub:oai:dare.uva.nl: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/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"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":"PLoS Computational Biology, 11(4). Public Library of Science","raw_type":"info:eu-repo/semantics/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/G106104336","display_name":"The systems biology of network stress based on data generated from in vitro differentiated hepatocytes from individual-specific human iPS cells","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/G1629171480","display_name":"Establishing the hierarchies in regulation .... in time","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/G2225772532","display_name":null,"funder_award_id":"BB/C008219/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G3631366965","display_name":"Biopolymers from syngas fermentation","funder_award_id":"311815","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"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/G4385601720","display_name":null,"funder_award_id":"311815","funder_id":"https://openalex.org/F4320338366","funder_display_name":"FP7 Food, Agriculture and Fisheries, Biotechnology"},{"id":"https://openalex.org/G4937468798","display_name":null,"funder_award_id":"H2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"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":"2026-08-14T07:06:38.338062","created_date":"2025-10-10T00:00:00"}