{"doi":"10.1093/nar/gkq343","title":"Mathematical modelling of whole chromosome replication","abstract":null,"journal":"Nucleic Acids Research","year":2010,"id":667341,"datarank":0.6995158641168101,"base_score":4.663439094112067,"endowment":4.663439094112067,"self_citation_contribution":0.6995158641168101,"citation_network_contribution":0.0,"self_endowment_contribution":0.6995158641168101,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":105,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1742746,"name":"Renata Retkute","orcid":null,"position":1,"is_corresponding":false},{"id":1742747,"name":"Michelle Hawkins","orcid":null,"position":2,"is_corresponding":false},{"id":34445,"name":"Conrad A. Nieduszynski","orcid":"0000-0003-2001-076X","position":3,"is_corresponding":false},{"id":1742745,"name":"Alessandro P. S. de Moura","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Mathematical modelling of whole chromosome replication","abstract":"All chromosomes must be completely replicated prior to cell division, a requirement that demands the activation of a sufficient number of appropriately distributed DNA replication origins. Here we investigate how the activity of multiple origins on each chromosome is coordinated to ensure successful replication. We present a stochastic model for whole chromosome replication where the dynamics are based upon the parameters of individual origins. Using this model we demonstrate that mean replication time at any given chromosome position is determined collectively by the parameters of all origins. Combining parameter estimation with extensive simulations we show that there is a range of model parameters consistent with mean replication data, emphasising the need for caution in interpreting such data. In contrast, the replicated-fraction at time points through S phase contains more information than mean replication time data and allowed us to use our model to uniquely estimate many origin parameters. These estimated parameters enable us to make a number of predictions that showed agreement with independent experimental data, confirming that our model has predictive power. In summary, we demonstrate that a stochastic model can recapitulate experimental observations, including those that might be interpreted as deterministic such as ordered origin activation times.","is_dataset_classified":null,"base_score":4.663439094112067,"endowment":4.663439094112067,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"20457753","pmcid":"PMC2943597","openalex_id":"https://openalex.org/W2109176256","authors":[],"funders":[{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"BB/G001596/1","title":null},{"funder_name":"Biotechnology and Biological Sciences Research Council","grant_id":"BB/E023754/1","title":"What regulates replication origin activation?"}],"total_grants":2,"fwci":4.8572,"citation_percentile":0.96097297,"influential_citations":0,"citation_trend":[{"year":2012,"count":14},{"year":2013,"count":18},{"year":2014,"count":9},{"year":2015,"count":3},{"year":2016,"count":4},{"year":2017,"count":3},{"year":2018,"count":5},{"year":2019,"count":9},{"year":2020,"count":8},{"year":2021,"count":8},{"year":2022,"count":3},{"year":2023,"count":3},{"year":2024,"count":5},{"year":2025,"count":5},{"year":2026,"count":1}],"oa_status":"gold","license":"cc-by-nc","oa_locations":[{"url":"https://academic.oup.com/nar/article-pdf/38/17/5623/16766173/gkq343.pdf","host_type":"journal"},{"url":"https://academic.oup.com/nar/article-pdf/38/17/5623/16766173/gkq343.pdf","host_type":"publisher"},{"url":"http://academic.oup.com/nar/article-pdf/38/17/5623/16766173/gkq343.pdf","host_type":"publisher"},{"url":"https://doi.org/10.1093/nar/gkq343","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/20457753","host_type":"repository"},{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2943597","host_type":"repository"},{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.709.1432","host_type":""},{"url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.812.6592","host_type":""},{"url":"http://hdl.handle.net/2164/2638","host_type":"repository"},{"url":"http://nar.oxfordjournals.org/content/38/17/5623.full","host_type":"repository"},{"url":"https://nottingham-repository.worktribe.com/output/706502","host_type":"repository"},{"url":"http://nar.oxfordjournals.org/cgi/content/short/38/17/5623","host_type":"repository"},{"url":"https://ueaeprints.uea.ac.uk/id/eprint/87891/","host_type":"repository"},{"url":"https://europepmc.org/articles/PMC2943597","host_type":"Europe_PMC"},{"url":"https://europepmc.org/articles/PMC2943597?pdf=render","host_type":"Europe_PMC"},{"url":"http://dx.doi.org/10.1093/nar/gkq343","host_type":""},{"url":"https://nottingham-repository.worktribe.com/file/706502/1/de_Moura,2010,Mathematical_modelling_of_whole_chromosome.pdf","host_type":""},{"url":"https://dx.doi.org/10.1093/nar/gkq343","host_type":""},{"url":"https://doi.org/https://doi.org/10.1093/nar/gkq343","host_type":""}],"fields_of_study":["DNA Repair Mechanisms","Microtubule and mitosis dynamics","DNA and Nucleic Acid Chemistry","0301 basic medicine","0303 health sciences","03 medical and health sciences","Algorithms","Chromosomes","Chromosomes, Fungal","Computer Simulation","DNA Replication","DNA Replication Timing","Kinetics","Models, Genetic","Replication Origin","Saccharomyces cerevisiae","Stochastic Processes"],"mesh_terms":["Algorithms","Chromosomes","Computer Simulation","DNA Replication","Kinetics","Models, Genetic","Saccharomyces cerevisiae","Stochastic Processes","Chromosomes, Fungal","Replication Origin","DNA Replication Timing"],"keywords":["Replication (statistics)","Biology","Replication timing","Origin of replication","DNA replication","Chromosome","Genetics","Computational biology","Stochastic modelling","Range (aeronautics)","DNA","Gene","Statistics","Mathematics","570","Stochastic Processes","Models, Genetic","DNA Replication Timing","610","Q Science (General)","Replication Origin","Saccharomyces cerevisiae","Q1","Chromosomes","Kinetics","Computer Simulation","Chromosomes, Fungal","Algorithms"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-13T17:33:29.350141Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}