{"id":"https://openalex.org/W2125847752","doi":"https://doi.org/10.1371/journal.pcbi.1003598","title":"Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data","display_name":"Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data","publication_year":2014,"publication_date":"2014-05-15","ids":{"openalex":"https://openalex.org/W2125847752","doi":"https://doi.org/10.1371/journal.pcbi.1003598","mag":"2125847752"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003598","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003598","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003598&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","datacite","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003598&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088432815","display_name":"Ciira wa Maina","orcid":"https://orcid.org/0000-0003-4203-3129"},"institutions":[{"id":"https://openalex.org/I344018163","display_name":"Dedan Kimathi University of Technology","ror":"https://ror.org/05jg5ty85","country_code":"KE","type":"education","lineage":["https://openalex.org/I344018163"]}],"countries":["KE"],"is_corresponding":true,"raw_author_name":"Ciira wa Maina","raw_affiliation_strings":["Department of Electrical and Electronic Engineering, Dedan Kimathi University of Technology, Nyeri, Kenya","dedan kimathi university of technology"],"affiliations":[{"raw_affiliation_string":"Department of Electrical and Electronic Engineering, Dedan Kimathi University of Technology, Nyeri, Kenya","institution_ids":["https://openalex.org/I344018163"]},{"raw_affiliation_string":"dedan kimathi university of technology","institution_ids":["https://openalex.org/I344018163"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071329195","display_name":"Antti Honkela","orcid":"https://orcid.org/0000-0001-9193-8093"},"institutions":[{"id":"https://openalex.org/I32943570","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940","country_code":"FI","type":"facility","lineage":["https://openalex.org/I133731052","https://openalex.org/I32943570","https://openalex.org/I9927081"]},{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Antti Honkela","raw_affiliation_strings":["Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland","#N##TAB##TAB##TAB##TAB# University of Helsinki#N##TAB##TAB##TAB#"],"affiliations":[{"raw_affiliation_string":"Helsinki Institute for Information Technology HIIT, Department of Computer Science, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I32943570","https://openalex.org/I133731052"]},{"raw_affiliation_string":"#N##TAB##TAB##TAB##TAB# University of Helsinki#N##TAB##TAB##TAB#","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079581490","display_name":"Filomena Matarese","orcid":null},"institutions":[{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Filomena Matarese","raw_affiliation_strings":["Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands","institution_ids":["https://openalex.org/I145872427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020626165","display_name":"Korbinian Grote","orcid":"https://orcid.org/0000-0002-4481-6584"},"institutions":[{"id":"https://openalex.org/I4210087817","display_name":"Software (Germany)","ror":"https://ror.org/004g36n56","country_code":"DE","type":"company","lineage":["https://openalex.org/I4210087817"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Korbinian Grote","raw_affiliation_strings":["Genomatix Software GmbH, Muenchen, Germany"],"affiliations":[{"raw_affiliation_string":"Genomatix Software GmbH, Muenchen, Germany","institution_ids":["https://openalex.org/I4210087817"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036095832","display_name":"Hendrik G. Stunnenberg","orcid":"https://orcid.org/0000-0002-0066-1576"},"institutions":[{"id":"https://openalex.org/I145872427","display_name":"Radboud University Nijmegen","ror":"https://ror.org/016xsfp80","country_code":"NL","type":"education","lineage":["https://openalex.org/I145872427"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Hendrik G. Stunnenberg","raw_affiliation_strings":["Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands"],"affiliations":[{"raw_affiliation_string":"Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands","institution_ids":["https://openalex.org/I145872427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047230260","display_name":"George Reid","orcid":"https://orcid.org/0000-0002-0298-693X"},"institutions":[{"id":"https://openalex.org/I4210165538","display_name":"Institute of Molecular Biology","ror":"https://ror.org/05kxtq558","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210165538"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"George Reid","raw_affiliation_strings":["Institute for Molecular Biology, Mainz, Germany"],"affiliations":[{"raw_affiliation_string":"Institute for Molecular Biology, Mainz, Germany","institution_ids":["https://openalex.org/I4210165538"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023849469","display_name":"Neil D. Lawrence","orcid":"https://orcid.org/0000-0001-9258-1030"},"institutions":[{"id":"https://openalex.org/I91136226","display_name":"University of Sheffield","ror":"https://ror.org/05krs5044","country_code":"GB","type":"education","lineage":["https://openalex.org/I91136226"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Neil D. Lawrence","raw_affiliation_strings":["Department of Computer Science, University of Sheffield, Sheffield, United Kingdom","University of  Sheffield"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Sheffield, Sheffield, United Kingdom","institution_ids":["https://openalex.org/I91136226"]},{"raw_affiliation_string":"University of  Sheffield","institution_ids":["https://openalex.org/I91136226"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023995814","display_name":"Magnus Rattray","orcid":"https://orcid.org/0000-0001-8196-5565"},"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"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Magnus Rattray","raw_affiliation_strings":["Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom","University of Manchester\u00a0"],"affiliations":[{"raw_affiliation_string":"Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom","institution_ids":["https://openalex.org/I28407311"]},{"raw_affiliation_string":"University of Manchester\u00a0","institution_ids":["https://openalex.org/I28407311"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5023849469","https://openalex.org/A5023995814","https://openalex.org/A5088432815"],"corresponding_institution_ids":["https://openalex.org/I28407311","https://openalex.org/I344018163","https://openalex.org/I91136226"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.854,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.85540294,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"10","issue":"5","first_page":"e1003598","last_page":"e1003598"},"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/T10604","display_name":"RNA Research and Splicing","score":0.9988999962806702,"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/T10885","display_name":"Gene expression and cancer classification","score":0.993399977684021,"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/rna-polymerase-ii","display_name":"RNA polymerase II","score":0.641043484210968},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.561398446559906},{"id":"https://openalex.org/keywords/chromatin-immunoprecipitation","display_name":"Chromatin immunoprecipitation","score":0.5483707189559937},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5450322031974792},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5343842506408691},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.49607953429222107},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.44013717770576477},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.43816766142845154},{"id":"https://openalex.org/keywords/markov-chain-monte-carlo","display_name":"Markov chain Monte Carlo","score":0.42712879180908203},{"id":"https://openalex.org/keywords/bayesian-inference","display_name":"Bayesian inference","score":0.4239952564239502},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3880424499511719},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.326696515083313},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.29527121782302856},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.11434686183929443}],"concepts":[{"id":"https://openalex.org/C64350747","wikidata":"https://www.wikidata.org/wiki/Q15334993","display_name":"RNA polymerase II","level":5,"score":0.641043484210968},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.561398446559906},{"id":"https://openalex.org/C134320426","wikidata":"https://www.wikidata.org/wiki/Q901026","display_name":"Chromatin immunoprecipitation","level":5,"score":0.5483707189559937},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5450322031974792},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5343842506408691},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.49607953429222107},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.44013717770576477},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.43816766142845154},{"id":"https://openalex.org/C111350023","wikidata":"https://www.wikidata.org/wiki/Q1191869","display_name":"Markov chain Monte Carlo","level":3,"score":0.42712879180908203},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.4239952564239502},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3880424499511719},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.326696515083313},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.29527121782302856},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11434686183929443},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":13,"locations":[{"id":"doi:10.1371/journal.pcbi.1003598","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003598","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003598&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":"pmh:oai:pure.atira.dk:openaire/942963a3-63e2-482d-8644-94411d492461","is_oa":true,"landing_page_url":"https://research.manchester.ac.uk/en/publications/942963a3-63e2-482d-8644-94411d492461","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"wa Maina, C, Honkela, A, Matarese, F, Grote, K, Stunnenberg, H G, Reid, G, Lawrence, N D & Rattray, M 2014, 'Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.', PL o S Computational Biology, vol. 10, no. 5, e1003598. https://doi.org/10.1371/journal.pcbi.1003598","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:RePEc:plo:pcbi00:1003598","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003598","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:27e2faf94bcd43ada12ff2123fb158a3","is_oa":true,"landing_page_url":"https://doaj.org/article/27e2faf94bcd43ada12ff2123fb158a3","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 10, Iss 5, p e1003598 (2014)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:3003061","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC4022483","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":"","raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/1028031","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Inference_of_RNA_Polymerase_II_Transcription_Dynamics_from_Chromatin_Immunoprecipitation_Time_Course_Data_/1028031","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:helda.helsinki.fi:10138/144483","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/144483","pdf_url":null,"source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4022483","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4022483","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:publications/942963a3-63e2-482d-8644-94411d492461","is_oa":true,"landing_page_url":"https://www.research.manchester.ac.uk/portal/en/publications/inference-of-rna-polymerase-ii-transcription-dynamics-from-chromatin-immunoprecipitation-time-course-data(942963a3-63e2-482d-8644-94411d492461).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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"wa Maina, C, Honkela, A, Matarese, F, Grote, K, Stunnenberg, H G, Reid, G, Lawrence, N D & Rattray, M 2014, 'Inference of RNA polymerase II transcription dynamics from chromatin immunoprecipitation time course data.', PL o S Computational Biology, vol. 10, no. 5, e1003598. https://doi.org/10.1371/journal.pcbi.1003598","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:repository.ubn.ru.nl:2066/128086","is_oa":false,"landing_page_url":"http://repository.ubn.ru.nl/handle/2066/128086","pdf_url":null,"source":{"id":"https://openalex.org/S4306401067","display_name":"Radboud Repository (Radboud University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I145872427","host_organization_name":"Radboud University Nijmegen","host_organization_lineage":["https://openalex.org/I145872427"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article / Letter to editor"},{"id":"pmh:oai:www.repository.cam.ac.uk:1810/300881","is_oa":true,"landing_page_url":"https://www.repository.cam.ac.uk/handle/1810/300881","pdf_url":null,"source":{"id":"https://openalex.org/S4306401777","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"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":"Article"},{"id":"pmh:ru:oai:repository.ubn.ru.nl:2066/128086","is_oa":true,"landing_page_url":"http://hdl.handle.net/2066/128086","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, 10, e1003598","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.17863/cam.47956","is_oa":true,"landing_page_url":"https://doi.org/10.17863/cam.47956","pdf_url":null,"source":{"id":"https://openalex.org/S7407050737","display_name":"Apollo","issn_l":null,"issn":[],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003598","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003598","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003598&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":[{"id":"https://metadata.un.org/sdg/3","score":0.7099999785423279,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G4801751224","display_name":null,"funder_award_id":"BB/I004769/2","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2125847752.pdf","grobid_xml":"https://content.openalex.org/works/W2125847752.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W34929345","https://openalex.org/W1520585082","https://openalex.org/W1534349507","https://openalex.org/W1746819321","https://openalex.org/W1964259728","https://openalex.org/W1968343445","https://openalex.org/W1968475238","https://openalex.org/W1981276685","https://openalex.org/W1985621639","https://openalex.org/W2002262418","https://openalex.org/W2012284471","https://openalex.org/W2016028169","https://openalex.org/W2017297735","https://openalex.org/W2023878500","https://openalex.org/W2028748300","https://openalex.org/W2033220168","https://openalex.org/W2034071085","https://openalex.org/W2040627562","https://openalex.org/W2046317813","https://openalex.org/W2074097219","https://openalex.org/W2080683349","https://openalex.org/W2083735573","https://openalex.org/W2092992881","https://openalex.org/W2102619694","https://openalex.org/W2103248242","https://openalex.org/W2105380177","https://openalex.org/W2117089877","https://openalex.org/W2118532317","https://openalex.org/W2125373697","https://openalex.org/W2132241624","https://openalex.org/W2133465414","https://openalex.org/W2143672530","https://openalex.org/W2144561939","https://openalex.org/W2146611938","https://openalex.org/W2154968323","https://openalex.org/W2156936974","https://openalex.org/W2158217645","https://openalex.org/W2166037178","https://openalex.org/W2167503371","https://openalex.org/W2167986580","https://openalex.org/W2206846202","https://openalex.org/W2478027467","https://openalex.org/W2954040150","https://openalex.org/W4206212643","https://openalex.org/W4211018930","https://openalex.org/W4211049957"],"related_works":["https://openalex.org/W2009966535","https://openalex.org/W2008301391","https://openalex.org/W1520612026","https://openalex.org/W1818003313","https://openalex.org/W2039269859","https://openalex.org/W2969657660","https://openalex.org/W2141454371","https://openalex.org/W2111182449","https://openalex.org/W2754342607","https://openalex.org/W2170014373"],"abstract_inverted_index":{"Gene":[0],"transcription":[1,41,62,119,208,246],"mediated":[2],"by":[3,243],"RNA":[4],"polymerase":[5],"II":[6],"(pol-II)":[7],"is":[8,44],"a":[9,37],"key":[10],"step":[11],"in":[12,272],"gene":[13,30,74,134],"expression.":[14,31],"The":[15,55,95,125,207],"dynamics":[16,42],"of":[17,29,40,108,118,130,144,220,237],"pol-II":[18,47,69,131,193,239],"moving":[19],"along":[20],"the":[21,25,67,73,106,115,128,133,142,152,223,234,238],"transcribed":[22],"region":[23],"influence":[24],"rate":[26],"and":[27,64,104,136,169,176,250,269],"timing":[28],"In":[32],"this":[33],"work,":[34],"we":[35,158,210],"present":[36],"probabilistic":[38],"model":[39,56,126],"which":[43,163],"fitted":[45],"to":[46,60,65,140,161,167,185,191],"occupancy":[48,194],"time":[49,143,156],"course":[50],"data":[51,187],"measured":[52],"using":[53,80,89,189],"ChIP-Seq.":[54],"can":[57,137,228],"be":[58,138,179,229],"used":[59,139],"estimate":[61],"speed":[63],"infer":[66],"temporal":[68],"activity":[70,155,174,241],"profile":[71],"at":[72],"promoter.":[75],"Model":[76],"parameters":[77],"are":[78,159,202,261],"estimated":[79],"either":[81],"maximum":[82],"likelihood":[83],"estimation":[84],"or":[85],"via":[86],"Bayesian":[87,96],"inference":[88],"Markov":[90],"chain":[91],"Monte":[92],"Carlo":[93],"sampling.":[94],"approach":[97,227],"provides":[98],"confidence":[99],"intervals":[100],"for":[101,146,217,263],"parameter":[102],"estimates":[103],"allows":[105],"use":[107],"priors":[109],"that":[110,172,225,257],"capture":[111],"domain":[112],"knowledge,":[113],"e.g.":[114],"expected":[116],"range":[117],"speeds,":[120],"based":[121],"on":[122],"previous":[123],"experiments.":[124],"describes":[127],"movement":[129],"down":[132],"body":[135],"identify":[141],"induction":[145],"transcriptionally":[147],"engaged":[148],"genes.":[149],"By":[150],"clustering":[151],"inferred":[153],"promoter":[154,240,275],"profiles,":[157],"able":[160],"determine":[162],"genes":[164,171,221,260],"respond":[165],"quickly":[166],"stimuli":[168],"group":[170],"share":[173],"profiles":[175],"may":[177],"therefore":[178],"co-regulated.":[180],"We":[181,232,255],"apply":[182],"our":[183,226],"methodology":[184],"biological":[186,235],"obtained":[188,215],"ChIP-seq":[190],"measure":[192],"genome-wide":[195],"when":[196],"MCF-7":[197],"human":[198],"breast":[199],"cancer":[200],"cells":[201],"treated":[203],"with":[204,213,222],"estradiol":[205],"(E2).":[206],"speeds":[209],"obtain":[211],"agree":[212],"those":[214],"previously":[216],"smaller":[218],"numbers":[219],"advantage":[224],"applied":[230],"genome-wide.":[231],"validate":[233],"significance":[236],"clusters":[242],"investigating":[244],"cluster-specific":[245],"factor":[247],"binding":[248,271],"patterns":[249],"determining":[251],"canonical":[252],"pathway":[253],"enrichment.":[254],"find":[256],"rapidly":[258],"induced":[259],"enriched":[262],"both":[264],"estrogen":[265],"receptor":[266],"alpha":[267],"(ERa)":[268],"FOXA1":[270],"their":[273],"proximal":[274],"regions.":[276]},"counts_by_year":[{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2016-06-24T00:00:00"}
