{"id":"https://openalex.org/W3006336422","doi":"https://doi.org/10.1371/journal.pcbi.1007618","title":"A stochastic model for simulating ribosome kinetics in vivo","display_name":"A stochastic model for simulating ribosome kinetics in vivo","publication_year":2020,"publication_date":"2020-02-12","ids":{"openalex":"https://openalex.org/W3006336422","doi":"https://doi.org/10.1371/journal.pcbi.1007618","mag":"3006336422","pmid":"https://pubmed.ncbi.nlm.nih.gov/32049979"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007618","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007618","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1007618","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028462860","display_name":"Eric C. Dykeman","orcid":"https://orcid.org/0000-0002-8344-8446"},"institutions":[{"id":"https://openalex.org/I52099693","display_name":"University of York","ror":"https://ror.org/04m01e293","country_code":"GB","type":"education","lineage":["https://openalex.org/I52099693"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Eric Charles Dykeman","raw_affiliation_strings":["Department of Mathematics, University of York, York, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-8344-8446","affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of York, York, United Kingdom","institution_ids":["https://openalex.org/I52099693"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5028462860"],"corresponding_institution_ids":["https://openalex.org/I52099693"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.3376,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.79769257,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"16","issue":"2","first_page":"e1007618","last_page":"e1007618"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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/T11482","display_name":"RNA modifications and cancer","score":0.9994999766349792,"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":0.9988999962806702,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/ribosome","display_name":"Ribosome","score":0.7013376355171204},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.6627975106239319},{"id":"https://openalex.org/keywords/protein-biosynthesis","display_name":"Protein biosynthesis","score":0.5845375061035156},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.5617489814758301},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5135822296142578},{"id":"https://openalex.org/keywords/stochastic-modelling","display_name":"Stochastic modelling","score":0.5001657009124756},{"id":"https://openalex.org/keywords/ribosomal-rna","display_name":"Ribosomal RNA","score":0.4866986572742462},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46725839376449585},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.38620808720588684},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.36659595370292664},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.270956814289093},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.16158699989318848},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14769607782363892},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09700417518615723}],"concepts":[{"id":"https://openalex.org/C88478588","wikidata":"https://www.wikidata.org/wiki/Q42244","display_name":"Ribosome","level":4,"score":0.7013376355171204},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.6627975106239319},{"id":"https://openalex.org/C3675279","wikidata":"https://www.wikidata.org/wiki/Q211935","display_name":"Protein biosynthesis","level":2,"score":0.5845375061035156},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.5617489814758301},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5135822296142578},{"id":"https://openalex.org/C127491075","wikidata":"https://www.wikidata.org/wiki/Q7617825","display_name":"Stochastic modelling","level":2,"score":0.5001657009124756},{"id":"https://openalex.org/C67905577","wikidata":"https://www.wikidata.org/wiki/Q215980","display_name":"Ribosomal RNA","level":3,"score":0.4866986572742462},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46725839376449585},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38620808720588684},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.36659595370292664},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.270956814289093},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.16158699989318848},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14769607782363892},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09700417518615723},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010441","descriptor_name":"Peptide Chain Elongation, Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010441","descriptor_name":"Peptide Chain Elongation, Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010441","descriptor_name":"Peptide Chain Elongation, Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012270","descriptor_name":"Ribosomes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1007618","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007618","pdf_url":null,"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:32049979","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32049979","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:eprints.whiterose.ac.uk:156267","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400854","display_name":"White Rose Research Online (University of Leeds, The University of Sheffield, University of York)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2800616092","host_organization_name":"White Rose University Consortium","host_organization_lineage":["https://openalex.org/I2800616092"],"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":"PeerReviewed"},{"id":"pmh:oai:doaj.org/article:4716bff860a2433ca50eeeb565a553b5","is_oa":true,"landing_page_url":"https://doaj.org/article/4716bff860a2433ca50eeeb565a553b5","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 16, Iss 2, p e1007618 (2020)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/11843502","is_oa":true,"landing_page_url":"https://figshare.com/articles/A_stochastic_model_for_simulating_ribosome_kinetics_i_in_vivo_i_/11843502","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":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7015319","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7015319","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"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007618","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007618","pdf_url":null,"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/G5797131149","display_name":null,"funder_award_id":"EP/R023204/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W208046272","https://openalex.org/W1733413688","https://openalex.org/W1787838197","https://openalex.org/W1828556185","https://openalex.org/W1897486837","https://openalex.org/W1976515682","https://openalex.org/W1989714452","https://openalex.org/W2000840693","https://openalex.org/W2019404346","https://openalex.org/W2019472515","https://openalex.org/W2020138003","https://openalex.org/W2026384929","https://openalex.org/W2036505177","https://openalex.org/W2042700625","https://openalex.org/W2044859335","https://openalex.org/W2057969996","https://openalex.org/W2086665421","https://openalex.org/W2090535199","https://openalex.org/W2102038046","https://openalex.org/W2113934702","https://openalex.org/W2118333970","https://openalex.org/W2131881387","https://openalex.org/W2148627082","https://openalex.org/W2149124745","https://openalex.org/W2152671698","https://openalex.org/W2155418451","https://openalex.org/W2168765510","https://openalex.org/W2387558558","https://openalex.org/W2513858144","https://openalex.org/W2586128695","https://openalex.org/W2966297016"],"related_works":["https://openalex.org/W961542009","https://openalex.org/W1995458469","https://openalex.org/W4318955118","https://openalex.org/W2021902173","https://openalex.org/W2008993245","https://openalex.org/W1572513090","https://openalex.org/W2469568055","https://openalex.org/W2330892220","https://openalex.org/W133826215","https://openalex.org/W202078529"],"abstract_inverted_index":{"Computational":[0],"modelling":[1],"of":[2,15,26,34,47,57,62,88,96,108,148,159,167,177],"in":[3,63,67,126,184],"vivo":[4,64],"protein":[5,39,52,65,122],"synthesis":[6,66,123],"is":[7,55],"highly":[8],"complicated,":[9],"as":[10,22,24,133,145],"it":[11],"requires":[12],"the":[13,19,27,45,59,94,105,134,149,157,161],"simulation":[14],"ribosomal":[16],"movement":[17],"over":[18],"entire":[20],"transcriptome,":[21],"well":[23],"consideration":[25],"concentration":[28,109],"effects":[29],"from":[30],"40+":[31],"different":[32],"types":[33],"tRNAs":[35],"and":[36,83,117,169],"numerous":[37],"other":[38,118],"factors.":[40],"Here":[41],"I":[42,101],"report":[43,84],"on":[44,85],"development":[46],"a":[48,68,86,171],"stochastic":[49,152],"model":[50,153],"for":[51,81,121],"translation":[53,178],"that":[54,179],"capable":[56],"simulating":[58],"dynamical":[60],"process":[61,163],"prokaryotic":[69],"cell":[70],"containing":[71],"several":[72,129],"thousand":[73],"unique":[74],"mRNA":[75],"sequences,":[76],"with":[77,139],"explicit":[78],"nucleotide":[79],"information":[80],"each,":[82],"number":[87],"biological":[89,130],"predictions":[90],"which":[91],"are":[92,124,143,180],"beyond":[93],"scope":[95],"existing":[97],"models.":[98,187],"In":[99],"particular,":[100],"show":[102],"that,":[103],"when":[104],"complex":[106],"network":[107],"dependent":[110],"interactions":[111],"between":[112],"elongation":[113,137],"factors,":[114],"tRNAs,":[115],"ribosomes,":[116],"factors":[119],"required":[120],"included":[125],"full":[127],"detail,":[128,168],"phenomena,":[131],"such":[132],"increasing":[135],"peptide":[136],"rate":[138],"bacterial":[140],"growth":[141],"rate,":[142],"predicted":[144],"emergent":[146],"properties":[147],"model.":[150],"The":[151],"presented":[154],"here":[155],"demonstrates":[156],"importance":[158],"considering":[160],"translational":[162],"at":[164],"this":[165],"level":[166],"provides":[170],"platform":[172],"to":[173,182],"interrogate":[174],"various":[175],"aspects":[176],"difficult":[181],"study":[183],"more":[185],"coarse-grained":[186]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":1}],"updated_date":"2026-04-25T08:17:42.794288","created_date":"2025-10-10T00:00:00"}
