{"id":"https://openalex.org/W4384388016","doi":"https://doi.org/10.1093/genetics/iyad128","title":"Somatic mutations inferred from RNA-seq data highlight the contribution of replication timing to mutation rate variation in a model plant","display_name":"Somatic mutations inferred from RNA-seq data highlight the contribution of replication timing to mutation rate variation in a model plant","publication_year":2023,"publication_date":"2023-07-14","ids":{"openalex":"https://openalex.org/W4384388016","doi":"https://doi.org/10.1093/genetics/iyad128","pmid":"https://pubmed.ncbi.nlm.nih.gov/37450609","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/10550316"},"language":"en","primary_location":{"id":"doi:10.1093/genetics/iyad128","doi":"https://doi.org/10.1093/genetics/iyad128","is_oa":true,"landing_page_url":"https://doi.org/10.1093/genetics/iyad128","pdf_url":"https://academic.oup.com/genetics/advance-article-pdf/doi/10.1093/genetics/iyad128/51277512/iyad128.pdf","source":{"id":"https://openalex.org/S65932378","display_name":"Genetics","issn_l":"0016-6731","issn":["0016-6731","1943-2631"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"GENETICS","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/genetics/advance-article-pdf/doi/10.1093/genetics/iyad128/51277512/iyad128.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5129398115","display_name":"Patrick M. Staunton","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Patrick M Staunton","raw_affiliation_strings":["School of Mathematical and Statistical Sciences, University of Galway , Galway H91 TK33 ,","School of Mathematical and Statistical Sciences, University of Galway, Galway H91 TK33, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical and Statistical Sciences, University of Galway , Galway H91 TK33 ,","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"School of Mathematical and Statistical Sciences, University of Galway, Galway H91 TK33, Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Andrew J Peters","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Andrew J Peters","raw_affiliation_strings":["School of Mathematical and Statistical Sciences, University of Galway , Galway H91 TK33 ,","School of Mathematical and Statistical Sciences, University of Galway, Galway H91 TK33, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical and Statistical Sciences, University of Galway , Galway H91 TK33 ,","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"School of Mathematical and Statistical Sciences, University of Galway, Galway H91 TK33, Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004762593","display_name":"Cathal Seoighe","orcid":"https://orcid.org/0000-0003-0496-4029","observed_orcids":["https://orcid.org/0000-0003-0496-4029"]},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":true,"raw_author_name":"Cathal Seoighe","raw_affiliation_strings":["School of Mathematical and Statistical Sciences, University of Galway , Galway H91 TK33 ,","School of Mathematical and Statistical Sciences, University of Galway, Galway H91 TK33, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical and Statistical Sciences, University of Galway , Galway H91 TK33 ,","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"School of Mathematical and Statistical Sciences, University of Galway, Galway H91 TK33, Ireland","institution_ids":["https://openalex.org/I188760350"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5004762593"],"corresponding_institution_ids":["https://openalex.org/I188760350"],"apc_list":{"value":4264,"currency":"USD","value_usd":4264},"apc_paid":{"value":4264,"currency":"USD","value_usd":4264},"fwci":1.2358,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.77675536,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"225","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3837999999523163,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.3837999999523163,"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/T12828","display_name":"Plant Genetic and Mutation Studies","score":0.2433999925851822,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.21310000121593475,"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/somatic-mutations","display_name":"somatic mutations","score":0.9240000247955322},{"id":"https://openalex.org/keywords/replication-timing","display_name":"DNA replication timing","score":0.9139999747276306},{"id":"https://openalex.org/keywords/mutation-rate-variation","display_name":"mutation rate variation","score":0.9309999942779541},{"id":"https://openalex.org/keywords/arabidopsis-thaliana","display_name":"Arabidopsis thaliana","score":0.8949999809265137},{"id":"https://openalex.org/keywords/bulk-rna-sequencing","display_name":"bulk RNA-seq","score":0.7260000109672546},{"id":"https://openalex.org/keywords/h3k36me3","display_name":"H3K36me3","score":0.8420000076293945},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.8399999737739563},{"id":"https://openalex.org/keywords/gc-content","display_name":"GC content","score":0.9179999828338623},{"id":"https://openalex.org/keywords/histone-modifications","display_name":"histone modifications","score":0.6549999713897705},{"id":"https://openalex.org/keywords/dna-damage-and-repair","display_name":"DNA damage and repair","score":0.6499999761581421},{"id":"https://openalex.org/keywords/germline-mutations","display_name":"germline mutations","score":0.765999972820282}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8666257858276367},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.7491228580474854},{"id":"https://openalex.org/C134305767","wikidata":"https://www.wikidata.org/wiki/Q725508","display_name":"Somatic cell","level":3,"score":0.6890175342559814},{"id":"https://openalex.org/C13514818","wikidata":"https://www.wikidata.org/wiki/Q5552256","display_name":"Germline mutation","level":4,"score":0.5799652934074402},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.5544424057006836},{"id":"https://openalex.org/C98638677","wikidata":"https://www.wikidata.org/wiki/Q2067051","display_name":"Mutation rate","level":3,"score":0.5363368391990662},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5051060318946838},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4596092700958252},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3407878577709198},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07952520251274109}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003596","descriptor_name":"Cytosine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D042522","descriptor_name":"DNA Replication Timing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059645","descriptor_name":"Mutation Rate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/genetics/iyad128","doi":"https://doi.org/10.1093/genetics/iyad128","is_oa":true,"landing_page_url":"https://doi.org/10.1093/genetics/iyad128","pdf_url":"https://academic.oup.com/genetics/advance-article-pdf/doi/10.1093/genetics/iyad128/51277512/iyad128.pdf","source":{"id":"https://openalex.org/S65932378","display_name":"Genetics","issn_l":"0016-6731","issn":["0016-6731","1943-2631"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"GENETICS","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10550316","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10550316","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10550316/pdf/iyad128.pdf","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genetics","raw_type":"Text"},{"id":"pmid:37450609","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37450609","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":"Genetics","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/genetics/iyad128","doi":"https://doi.org/10.1093/genetics/iyad128","is_oa":true,"landing_page_url":"https://doi.org/10.1093/genetics/iyad128","pdf_url":"https://academic.oup.com/genetics/advance-article-pdf/doi/10.1093/genetics/iyad128/51277512/iyad128.pdf","source":{"id":"https://openalex.org/S65932378","display_name":"Genetics","issn_l":"0016-6731","issn":["0016-6731","1943-2631"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","doyens","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"GENETICS","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G5594609917","display_name":"Inference of somatic mutation rates from high-throughput sequencing data: models and applications","funder_award_id":"16/IA/4612","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"}],"funders":[{"id":"https://openalex.org/F4320320847","display_name":"Science Foundation Ireland","ror":"https://ror.org/0271asj38"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4384388016.pdf","grobid_xml":"https://content.openalex.org/works/W4384388016.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W1579768575","https://openalex.org/W1977249461","https://openalex.org/W1980602152","https://openalex.org/W1983660137","https://openalex.org/W2009096224","https://openalex.org/W2023568503","https://openalex.org/W2032320097","https://openalex.org/W2034525444","https://openalex.org/W2089855871","https://openalex.org/W2108234281","https://openalex.org/W2116041602","https://openalex.org/W2117277048","https://openalex.org/W2118683755","https://openalex.org/W2127604631","https://openalex.org/W2129785061","https://openalex.org/W2130308369","https://openalex.org/W2135046866","https://openalex.org/W2136384781","https://openalex.org/W2169456326","https://openalex.org/W2204695746","https://openalex.org/W2266041843","https://openalex.org/W2419574648","https://openalex.org/W2462490406","https://openalex.org/W2564919749","https://openalex.org/W2763009832","https://openalex.org/W2782019561","https://openalex.org/W2784876057","https://openalex.org/W2795600679","https://openalex.org/W2802201353","https://openalex.org/W2803430912","https://openalex.org/W2884704125","https://openalex.org/W2890764841","https://openalex.org/W2898789672","https://openalex.org/W2902284386","https://openalex.org/W2936580916","https://openalex.org/W2948188025","https://openalex.org/W2948371032","https://openalex.org/W2976201866","https://openalex.org/W2983766472","https://openalex.org/W2995831454","https://openalex.org/W2997414986","https://openalex.org/W3008360793","https://openalex.org/W3008946812","https://openalex.org/W3023937007","https://openalex.org/W3042141026","https://openalex.org/W3131055609","https://openalex.org/W3190854090","https://openalex.org/W4205215099","https://openalex.org/W4205790736","https://openalex.org/W4288826216","https://openalex.org/W4294541781","https://openalex.org/W4393230748"],"related_works":["https://openalex.org/W4416714785","https://openalex.org/W4403114050","https://openalex.org/W2953211079","https://openalex.org/W4391671404","https://openalex.org/W4205598186","https://openalex.org/W7133804389","https://openalex.org/W6969365020","https://openalex.org/W4395676972","https://openalex.org/W1995654069","https://openalex.org/W6925072445"],"abstract_inverted_index":{"Variation":[0],"in":[1,86,156],"the":[2,12,77,84,87,92,128,142,148,157],"rates":[3],"and":[4,8,22,25,35,51,147,180,194,200],"characteristics":[5],"of":[6,14,32,58,65,79,94,106,110,130,159,171],"germline":[7],"somatic":[9,45,88,111,144,177,191],"mutations":[10,46],"across":[11,91],"genome":[13,93],"an":[15,107,172],"organism":[16,33],"is":[17,153],"informative":[18],"about":[19],"DNA":[20,195],"damage":[21,132],"repair":[23],"processes":[24],"can":[26],"also":[27,136],"shed":[28],"light":[29],"on":[30],"aspects":[31],"physiology":[34],"evolution.":[36],"We":[37,98,121,135],"adapted":[38],"a":[39,55,138,186],"recently":[40],"developed":[41],"method":[42],"for":[43,70,197],"inferring":[44],"from":[47],"bulk":[48],"RNA-seq":[49],"data":[50,67],"applied":[52],"it":[53],"to":[54,75,114,167],"large":[56],"collection":[57],"Arabidopsis":[59],"thaliana":[60,72],"accessions.":[61],"The":[62],"wide":[63],"range":[64],"genomic":[66,81,115],"types":[68],"available":[69],"A.":[71],"enabled":[73],"us":[74],"investigate":[76],"relationships":[78],"multiple":[80],"features":[82],"with":[83,127],"variation":[85],"mutation":[89,112,145,178,192],"rate":[90,109],"this":[95],"model":[96],"plant.":[97],"observed":[99,137],"that":[100,117],"late":[101],"replicated":[102,119],"regions":[103,116],"showed":[104],"evidence":[105],"elevated":[108],"compared":[113],"are":[118],"early.":[120],"identified":[122],"transcriptional":[123],"strand":[124],"asymmetries,":[125],"consistent":[126],"effects":[129],"transcription-coupled":[131],"and/or":[133],"repair.":[134],"negative":[139],"relationship":[140,174,188],"between":[141,175,189],"inferred":[143,176,190],"count":[146,179,193],"H3K36me3":[149],"histone":[150],"mark":[151],"which":[152],"well":[154,184],"documented":[155],"literature":[158],"human":[160],"systems.":[161],"In":[162],"addition,":[163],"we":[164],"were":[165],"able":[166],"support":[168],"previous":[169],"reports":[170],"inverse":[173],"guanine-cytosine":[181],"content":[182],"as":[183,185],"positive":[187],"methylation":[196],"both":[198],"cytosine":[199],"noncytosine":[201],"mutations.":[202]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2023-07-15T00:00:00"}
