{"id":"https://openalex.org/W2883795150","doi":"https://doi.org/10.1093/bib/bby045","title":"Physiological RNA dynamics in RNA-Seq analysis","display_name":"Physiological RNA dynamics in RNA-Seq analysis","publication_year":2018,"publication_date":"2018-06-26","ids":{"openalex":"https://openalex.org/W2883795150","doi":"https://doi.org/10.1093/bib/bby045","mag":"2883795150","pmid":"https://pubmed.ncbi.nlm.nih.gov/30010714"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bby045","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bby045","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103047684","display_name":"Zhongneng Xu","orcid":"https://orcid.org/0000-0002-2503-478X"},"institutions":[{"id":"https://openalex.org/I159948400","display_name":"Jinan University","ror":"https://ror.org/02xe5ns62","country_code":"CN","type":"education","lineage":["https://openalex.org/I159948400"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhongneng Xu","raw_affiliation_strings":["Department of Ecology, Jinan University, Guangzhou 510632, China"],"affiliations":[{"raw_affiliation_string":"Department of Ecology, Jinan University, Guangzhou 510632, China","institution_ids":["https://openalex.org/I159948400"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077439573","display_name":"Shuichi Asakawa","orcid":"https://orcid.org/0000-0002-7599-0825"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Shuichi Asakawa","raw_affiliation_strings":["Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Aquatic Bioscience, Graduate School of Agricultural and Life Science, The University of Tokyo, Tokyo 113-8657, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5077439573","https://openalex.org/A5103047684"],"corresponding_institution_ids":["https://openalex.org/I159948400","https://openalex.org/I74801974"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.4596,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.6273948,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"20","issue":"5","first_page":"1725","last_page":"1733"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9997000098228455,"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":0.9994000196456909,"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","display_name":"RNA","score":0.7884763479232788},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.7501295804977417},{"id":"https://openalex.org/keywords/intron","display_name":"Intron","score":0.5893261432647705},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5580339431762695},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.5521438121795654},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5301012992858887},{"id":"https://openalex.org/keywords/transcription","display_name":"Transcription (linguistics)","score":0.5232964158058167},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4732414186000824},{"id":"https://openalex.org/keywords/post-transcriptional-modification","display_name":"Post-transcriptional modification","score":0.44998759031295776},{"id":"https://openalex.org/keywords/rna-editing","display_name":"RNA editing","score":0.449216365814209},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.44112205505371094},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4411190152168274},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3465847373008728}],"concepts":[{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.7884763479232788},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.7501295804977417},{"id":"https://openalex.org/C94671646","wikidata":"https://www.wikidata.org/wiki/Q207551","display_name":"Intron","level":3,"score":0.5893261432647705},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5580339431762695},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.5521438121795654},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5301012992858887},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.5232964158058167},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4732414186000824},{"id":"https://openalex.org/C22232683","wikidata":"https://www.wikidata.org/wiki/Q417379","display_name":"Post-transcriptional modification","level":5,"score":0.44998759031295776},{"id":"https://openalex.org/C21786251","wikidata":"https://www.wikidata.org/wiki/Q14886350","display_name":"RNA editing","level":4,"score":0.449216365814209},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.44112205505371094},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4411190152168274},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3465847373008728},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bby045","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bby045","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30010714","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30010714","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":134,"referenced_works":["https://openalex.org/W144423133","https://openalex.org/W637806132","https://openalex.org/W1466315383","https://openalex.org/W1544910494","https://openalex.org/W1564698930","https://openalex.org/W1810761522","https://openalex.org/W1816176398","https://openalex.org/W1913071848","https://openalex.org/W1939689156","https://openalex.org/W1956454952","https://openalex.org/W1960424936","https://openalex.org/W1965175512","https://openalex.org/W1966116114","https://openalex.org/W1966327575","https://openalex.org/W1971584645","https://openalex.org/W1981509058","https://openalex.org/W1984708728","https://openalex.org/W1989996002","https://openalex.org/W1993023683","https://openalex.org/W1994414793","https://openalex.org/W2005361347","https://openalex.org/W2007058060","https://openalex.org/W2009988114","https://openalex.org/W2011920499","https://openalex.org/W2021583109","https://openalex.org/W2021880506","https://openalex.org/W2026141529","https://openalex.org/W2027828573","https://openalex.org/W2028145262","https://openalex.org/W2033152634","https://openalex.org/W2034323007","https://openalex.org/W2039357236","https://openalex.org/W2041241597","https://openalex.org/W2047765648","https://openalex.org/W2048120844","https://openalex.org/W2048286155","https://openalex.org/W2057895365","https://openalex.org/W2060842569","https://openalex.org/W2062896692","https://openalex.org/W2064210252","https://openalex.org/W2067151470","https://openalex.org/W2069208087","https://openalex.org/W2073380432","https://openalex.org/W2074414424","https://openalex.org/W2074871118","https://openalex.org/W2077046573","https://openalex.org/W2087846512","https://openalex.org/W2090042982","https://openalex.org/W2094492214","https://openalex.org/W2097117811","https://openalex.org/W2097401587","https://openalex.org/W2104724027","https://openalex.org/W2105776281","https://openalex.org/W2107018762","https://openalex.org/W2107602656","https://openalex.org/W2110846454","https://openalex.org/W2112456256","https://openalex.org/W2117688129","https://openalex.org/W2117706451","https://openalex.org/W2117719890","https://openalex.org/W2121211805","https://openalex.org/W2122347842","https://openalex.org/W2123579165","https://openalex.org/W2124503920","https://openalex.org/W2126938291","https://openalex.org/W2127372456","https://openalex.org/W2129296076","https://openalex.org/W2133237718","https://openalex.org/W2135899392","https://openalex.org/W2137334937","https://openalex.org/W2137390416","https://openalex.org/W2141458291","https://openalex.org/W2145819283","https://openalex.org/W2149993795","https://openalex.org/W2150926065","https://openalex.org/W2152060958","https://openalex.org/W2152239989","https://openalex.org/W2152571160","https://openalex.org/W2153116581","https://openalex.org/W2154431984","https://openalex.org/W2156631105","https://openalex.org/W2157035703","https://openalex.org/W2161106528","https://openalex.org/W2162142896","https://openalex.org/W2162157385","https://openalex.org/W2165909549","https://openalex.org/W2166820820","https://openalex.org/W2168154998","https://openalex.org/W2178294617","https://openalex.org/W2187281001","https://openalex.org/W2259938310","https://openalex.org/W2268486506","https://openalex.org/W2276748084","https://openalex.org/W2287064828","https://openalex.org/W2289627053","https://openalex.org/W2308074142","https://openalex.org/W2313540090","https://openalex.org/W2321872593","https://openalex.org/W2323326409","https://openalex.org/W2340210804","https://openalex.org/W2395783098","https://openalex.org/W2396849069","https://openalex.org/W2413043813","https://openalex.org/W2416703957","https://openalex.org/W2502274642","https://openalex.org/W2510875395","https://openalex.org/W2522085729","https://openalex.org/W2524794421","https://openalex.org/W2525469791","https://openalex.org/W2528511699","https://openalex.org/W2528936845","https://openalex.org/W2532037152","https://openalex.org/W2546514099","https://openalex.org/W2554777987","https://openalex.org/W2561508962","https://openalex.org/W2562211106","https://openalex.org/W2571745526","https://openalex.org/W2572662684","https://openalex.org/W2583057870","https://openalex.org/W2603523955","https://openalex.org/W2604831109","https://openalex.org/W2605090810","https://openalex.org/W2605810679","https://openalex.org/W2606575226","https://openalex.org/W2610451542","https://openalex.org/W2630377436","https://openalex.org/W2760342316","https://openalex.org/W2899794439","https://openalex.org/W3191661929","https://openalex.org/W4233994749","https://openalex.org/W6685492720","https://openalex.org/W6696779977","https://openalex.org/W6724529465","https://openalex.org/W6736049595"],"related_works":["https://openalex.org/W2036825900","https://openalex.org/W2053217774","https://openalex.org/W4247273247","https://openalex.org/W2146323391","https://openalex.org/W2080039255","https://openalex.org/W3146618441","https://openalex.org/W2051643759","https://openalex.org/W2513916811","https://openalex.org/W3131196013","https://openalex.org/W2089788811"],"abstract_inverted_index":{"Physiological":[0,8,53],"RNA":[1,9,15,19,26,47,50,54,72],"dynamics":[2],"cause":[3],"problems":[4],"in":[5,114],"transcriptome":[6,115],"analysis.":[7],"accumulation":[10,45,55],"affects":[11,21],"the":[12,22,25,34,39,91],"analysis":[13,23],"of":[14,24,41,46,66,78],"quantification,":[16,68],"and":[17,31,44,56,87,102,105],"physiological":[18,42],"degradation":[20,43,57],"sequence":[27],"length,":[28],"feature":[29],"site":[30],"quantification.":[32],"In":[33],"present":[35],"article,":[36],"we":[37],"review":[38],"effects":[40],"on":[48],"analysing":[49],"sequencing":[51],"data.":[52],"probably":[58],"led":[59],"to":[60,96,110],"such":[61],"phenomena":[62],"as":[63],"incorrect":[64],"estimations":[65],"transcription":[67],"differential":[69],"expressions,":[70],"co-expressions,":[71],"decay":[73],"rates,":[74],"alternative":[75],"splicing,":[76],"boundaries":[77],"transcription,":[79],"novel":[80],"genes,":[81],"new":[82],"single-nucleotide":[83],"polymorphisms,":[84],"small":[85],"RNAs":[86],"gene":[88],"fusion.":[89],"Thus,":[90],"transcriptomic":[92],"data":[93,113],"obtained":[94],"up":[95],"date":[97],"warrant":[98],"further":[99],"scrutiny.":[100],"New":[101],"improved":[103],"techniques":[104],"bioinformatics":[106],"software":[107],"are":[108],"needed":[109],"produce":[111],"accurate":[112],"research.":[116]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}