{"id":"https://openalex.org/W7163545796","doi":"https://doi.org/10.64898/2026.06.01.729264","title":"A comparative analysis of promoter-proximal pausing reveals kinetic and distributional dimensions of variation","display_name":"A comparative analysis of promoter-proximal pausing reveals kinetic and distributional dimensions of variation","publication_year":2026,"publication_date":"2026-06-04","ids":{"openalex":"https://openalex.org/W7163545796","doi":"https://doi.org/10.64898/2026.06.01.729264","pmid":"https://pubmed.ncbi.nlm.nih.gov/42282755","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13251929"},"language":"en","primary_location":{"id":"doi:10.64898/2026.06.01.729264","doi":"https://doi.org/10.64898/2026.06.01.729264","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.06.01.729264","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.64898/2026.06.01.729264","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5133688483","display_name":"Xin Zeng","orcid":"https://orcid.org/0009-0007-9525-1468","observed_orcids":["https://orcid.org/0009-0007-9525-1468"]},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xin Zeng","raw_affiliation_strings":["Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA"],"raw_orcid":"https://orcid.org/0009-0007-9525-1468","affiliations":[{"raw_affiliation_string":"Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025034792","display_name":"Gilad Barshad","orcid":"https://orcid.org/0000-0001-7845-7658","observed_orcids":["https://orcid.org/0000-0001-7845-7658"]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I4210151139","display_name":"New York State College of Veterinary Medicine","ror":"https://ror.org/04r17kf39","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4210151139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gilad Barshad","raw_affiliation_strings":["Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4210151139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5121307253","display_name":"Rebecca Hassett","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rebecca Hassett","raw_affiliation_strings":["Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110693706","display_name":"Edward J. Rice","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I4210151139","display_name":"New York State College of Veterinary Medicine","ror":"https://ror.org/04r17kf39","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4210151139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edward J Rice","raw_affiliation_strings":["Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4210151139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024923108","display_name":"Charles G. Danko","orcid":"https://orcid.org/0000-0002-1999-7125","observed_orcids":["https://orcid.org/0000-0002-1999-7125"]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I4210151139","display_name":"New York State College of Veterinary Medicine","ror":"https://ror.org/04r17kf39","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4210151139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charles G Danko","raw_affiliation_strings":["Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA"],"raw_orcid":"https://orcid.org/0000-0002-1999-7125","affiliations":[{"raw_affiliation_string":"Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4210151139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137821949","display_name":"Adam Siepel","orcid":"https://orcid.org/0000-0002-3557-7219","observed_orcids":["https://orcid.org/0000-0002-3557-7219"]},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Adam Siepel","raw_affiliation_strings":["Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA"],"raw_orcid":"https://orcid.org/0000-0002-3557-7219","affiliations":[{"raw_affiliation_string":"Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070348247","display_name":"Yixin Zhao","orcid":"https://orcid.org/0000-0002-7856-2818","observed_orcids":["https://orcid.org/0000-0002-7856-2818"]},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yixin Zhao","raw_affiliation_strings":["Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA","Yazhouwan National Laboratory, Sanya, Hainan 572025, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA","institution_ids":["https://openalex.org/I2750212522"]},{"raw_affiliation_string":"Yazhouwan National Laboratory, Sanya, Hainan 572025, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5137821949"],"corresponding_institution_ids":["https://openalex.org/I2750212522"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9984999895095825,"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":0.9984999895095825,"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/T12820","display_name":"Chromatin Remodeling and Cancer","score":0.00019999999494757503,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":9.999999747378752e-05,"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/promoter-proximal-pausing","display_name":"promoter-proximal pausing","score":0.9980000257492065},{"id":"https://openalex.org/keywords/rna-polymerase-ii","display_name":"RNA polymerase II","score":0.9929999709129333},{"id":"https://openalex.org/keywords/pro-seq","display_name":"PRO-seq","score":0.9390000104904175},{"id":"https://openalex.org/keywords/nucleosome-occupancy","display_name":"nucleosome occupancy","score":0.8769999742507935},{"id":"https://openalex.org/keywords/gc-skew","display_name":"GC skew","score":0.9649999737739563},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"transcriptional regulation","score":0.6349999904632568},{"id":"https://openalex.org/keywords/model-based-analysis","display_name":"model-based analysis","score":0.4620000123977661}],"concepts":[{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.6844000220298767},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4918999969959259},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.44920000433921814},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.44749999046325684},{"id":"https://openalex.org/C131584629","wikidata":"https://www.wikidata.org/wiki/Q4308705","display_name":"Coupling (piping)","level":2,"score":0.4090999960899353},{"id":"https://openalex.org/C177562468","wikidata":"https://www.wikidata.org/wiki/Q182893","display_name":"Dispersion (optics)","level":2,"score":0.3864000141620636},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3725999891757965},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.3560999929904938},{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.35199999809265137},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.34860000014305115},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3264000117778778},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.3158000111579895},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.30809998512268066},{"id":"https://openalex.org/C110121322","wikidata":"https://www.wikidata.org/wiki/Q865811","display_name":"Distribution (mathematics)","level":2,"score":0.2939999997615814},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.2775999903678894},{"id":"https://openalex.org/C182306322","wikidata":"https://www.wikidata.org/wiki/Q1779371","display_name":"Order (exchange)","level":2,"score":0.2612999975681305},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.25699999928474426}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.64898/2026.06.01.729264","doi":"https://doi.org/10.64898/2026.06.01.729264","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.06.01.729264","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:42282755","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42282755","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,"listed_in":[],"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":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13251929","doi":null,"is_oa":true,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42282755/","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,"listed_in":[],"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv","raw_type":"Text"},{"id":"pmh:oai:repository.cshl.edu:42229","doi":null,"is_oa":false,"landing_page_url":"https://repository.cshl.edu/id/eprint/42229/1/10.64898.2026.06.01.729264.pdf","pdf_url":"https://repository.cshl.edu/id/eprint/42229/1/10.64898.2026.06.01.729264.pdf","source":{"id":"https://openalex.org/S4306402288","display_name":"Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Paper"}],"best_oa_location":{"id":"doi:10.64898/2026.06.01.729264","doi":"https://doi.org/10.64898/2026.06.01.729264","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.06.01.729264","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1456250384","display_name":null,"funder_award_id":"R01-HG010346","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4083614489","display_name":null,"funder_award_id":"R01-HG012944","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G4110359441","display_name":"Evolution of Chromatin Architecture and Transcriptional Regulation in Mammals","funder_award_id":"5r01hg010346-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7502776515","display_name":"A unified probabilistic model and software implementation for analysis of nascent RNA sequencing data","funder_award_id":"1r01hg012944-01a1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000887997","display_name":"Evolutionary Human Genomics: Demography, Natural Selection, and Transcriptional Regulation","funder_award_id":"R35GM127070","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W1862136016","https://openalex.org/W1967052041","https://openalex.org/W1967706132","https://openalex.org/W1985567287","https://openalex.org/W1986388692","https://openalex.org/W1996813139","https://openalex.org/W2007844697","https://openalex.org/W2021397048","https://openalex.org/W2023491365","https://openalex.org/W2025836692","https://openalex.org/W2027585195","https://openalex.org/W2035618305","https://openalex.org/W2037429489","https://openalex.org/W2050913592","https://openalex.org/W2064210252","https://openalex.org/W2081567150","https://openalex.org/W2101654493","https://openalex.org/W2102136017","https://openalex.org/W2125761685","https://openalex.org/W2149301312","https://openalex.org/W2259938310","https://openalex.org/W2417661205","https://openalex.org/W2498392978","https://openalex.org/W2763578259","https://openalex.org/W2802479546","https://openalex.org/W2897250433","https://openalex.org/W2908497471","https://openalex.org/W2915985519","https://openalex.org/W2945278782","https://openalex.org/W2952444044","https://openalex.org/W2969118999","https://openalex.org/W2970073459","https://openalex.org/W2971605288","https://openalex.org/W2988396470","https://openalex.org/W2988641336","https://openalex.org/W2994069347","https://openalex.org/W3007825745","https://openalex.org/W3009422893","https://openalex.org/W3016861944","https://openalex.org/W3038060414","https://openalex.org/W3119936302","https://openalex.org/W3192788912","https://openalex.org/W3199510140","https://openalex.org/W3205724993","https://openalex.org/W4231356616","https://openalex.org/W4237403594","https://openalex.org/W4313530701","https://openalex.org/W4322738638","https://openalex.org/W4327677475","https://openalex.org/W4376612735","https://openalex.org/W4383868194","https://openalex.org/W4387965095","https://openalex.org/W4388298748","https://openalex.org/W4390701279","https://openalex.org/W4399107395","https://openalex.org/W4407705817","https://openalex.org/W4408220851","https://openalex.org/W4415660373","https://openalex.org/W4417482177","https://openalex.org/W7165537622"],"related_works":["https://openalex.org/W3164842640","https://openalex.org/W3133792336","https://openalex.org/W3202099260","https://openalex.org/W2417661205","https://openalex.org/W7136561762","https://openalex.org/W3148295382","https://openalex.org/W2064210252","https://openalex.org/W2751862591","https://openalex.org/W7154317421","https://openalex.org/W3174611515"],"abstract_inverted_index":{"Promoter-proximal":[0],"pausing":[1,24,136,144],"of":[2,17,42,77,134,143],"RNA":[3],"polymerase":[4],"II":[5],"is":[6],"a":[7,35,128],"key":[8],"regulatory":[9],"checkpoint":[10],"in":[11,79,112],"metazoan":[12],"transcription.":[13],"Despite":[14],"extensive":[15],"study":[16],"this":[18],"process,":[19],"quantitative":[20,129],"methods":[21],"for":[22,38,131],"comparing":[23],"dynamics":[25],"across":[26,49,64,69,146],"biological":[27,147],"contexts":[28],"have":[29],"been":[30],"lacking.":[31],"Here":[32],"we":[33],"introduce":[34],"model-based":[36],"framework":[37,130],"rigorous":[39],"comparative":[40,67,132],"analysis":[41,133],"both":[43,80],"pause-escape":[44,81,101],"kinetics":[45,82],"and":[46,53,66,72,83,95,137,140],"pause-site":[47,84,113],"distributions":[48],"genes,":[50],"cell":[51,70],"types,":[52],"species.":[54],"An":[55],"application":[56],"to":[57],"available":[58],"PRO-seq":[59],"datasets":[60],"revealed":[61],"striking":[62],"differences":[63],"perturbations,":[65],"analyses":[68],"types":[71],"species":[73],"highlighted":[74],"distinct":[75],"patterns":[76],"variation":[78,145],"distributions,":[85],"with":[86,93,105,117],"only":[87],"weak":[88],"coupling":[89],"between":[90],"them.":[91],"Integration":[92],"chromatin":[94],"sequence":[96,118],"features":[97,119],"showed":[98],"that":[99],"lower":[100],"rates":[102],"are":[103,115],"associated":[104,116],"stronger":[106],"promoter-proximal":[107,135],"nucleosome":[108],"occupancy,":[109],"whereas":[110],"changes":[111],"dispersion":[114],"such":[120],"as":[121],"GC":[122],"skew.":[123],"Together,":[124],"these":[125],"results":[126],"establish":[127],"reveal":[138],"kinetic":[139],"distributional":[141],"dimensions":[142],"contexts.":[148]},"counts_by_year":[],"updated_date":"2026-10-30T12:39:25.321706","created_date":"2026-06-05T00:00:00"}