{"id":"https://openalex.org/W4283723390","doi":"https://doi.org/10.1093/bib/bbac271","title":"PolyAtailor: measuring poly(A) tail length from short-read and long-read sequencing data","display_name":"PolyAtailor: measuring poly(A) tail length from short-read and long-read sequencing data","publication_year":2022,"publication_date":"2022-06-30","ids":{"openalex":"https://openalex.org/W4283723390","doi":"https://doi.org/10.1093/bib/bbac271","pmid":"https://pubmed.ncbi.nlm.nih.gov/35769001"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac271","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac271","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":"article","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/A5017812451","display_name":"Mengfei Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]},{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mengfei Liu","raw_affiliation_strings":["Department of Automation, Xiamen University , Xiamen, Fujian 361005, China","Pasteurien College, Soochow University , Suzhou, Jiangsu 215000, China"],"affiliations":[{"raw_affiliation_string":"Department of Automation, Xiamen University , Xiamen, Fujian 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"Pasteurien College, Soochow University , Suzhou, Jiangsu 215000, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100765297","display_name":"Linlin Hao","orcid":"https://orcid.org/0000-0001-6518-6502"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Linlin Hao","raw_affiliation_strings":["Pasteurien College, Soochow University , Suzhou, Jiangsu 215000, China"],"affiliations":[{"raw_affiliation_string":"Pasteurien College, Soochow University , Suzhou, Jiangsu 215000, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011256892","display_name":"Sien Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sien Yang","raw_affiliation_strings":["Pasteurien College, Soochow University , Suzhou, Jiangsu 215000, China"],"affiliations":[{"raw_affiliation_string":"Pasteurien College, Soochow University , Suzhou, Jiangsu 215000, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091165765","display_name":"Xiaohui Wu","orcid":"https://orcid.org/0000-0003-0356-7785"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaohui Wu","raw_affiliation_strings":["Pasteurien College, Soochow University , Suzhou, Jiangsu 215000, China"],"affiliations":[{"raw_affiliation_string":"Pasteurien College, Soochow University , Suzhou, Jiangsu 215000, China","institution_ids":["https://openalex.org/I3923682"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5091165765"],"corresponding_institution_ids":["https://openalex.org/I3923682"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.5147,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.60940498,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"23","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9998999834060669,"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/T10604","display_name":"RNA Research and Splicing","score":0.9998999834060669,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9973999857902527,"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":0.9973000288009644,"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/computational-biology","display_name":"Computational biology","score":0.5136274695396423},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.46353912353515625},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.4485090672969818},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.4186370372772217},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4061742424964905},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24776199460029602},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24436551332473755}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5136274695396423},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.46353912353515625},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4485090672969818},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.4186370372772217},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4061742424964905},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24776199460029602},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24436551332473755}],"mesh":[{"descriptor_ui":"D011061","descriptor_name":"Poly A","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011061","descriptor_name":"Poly A","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011061","descriptor_name":"Poly A","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011061","descriptor_name":"Poly A","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011061","descriptor_name":"Poly A","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011061","descriptor_name":"Poly A","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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},{"descriptor_ui":"D026723","descriptor_name":"Polyadenylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D026723","descriptor_name":"Polyadenylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D026723","descriptor_name":"Polyadenylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac271","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac271","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:35769001","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35769001","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":[{"id":"https://openalex.org/G3773187572","display_name":null,"funder_award_id":"61871463","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1585782442","https://openalex.org/W2012097856","https://openalex.org/W2021302019","https://openalex.org/W2039916525","https://openalex.org/W2072770570","https://openalex.org/W2091840213","https://openalex.org/W2106678197","https://openalex.org/W2116486533","https://openalex.org/W2117843359","https://openalex.org/W2132520315","https://openalex.org/W2141040548","https://openalex.org/W2161030070","https://openalex.org/W2167317609","https://openalex.org/W2295195360","https://openalex.org/W2337011385","https://openalex.org/W2462053388","https://openalex.org/W2487617124","https://openalex.org/W2493043445","https://openalex.org/W2525507785","https://openalex.org/W2743879473","https://openalex.org/W2766614445","https://openalex.org/W2767350841","https://openalex.org/W2798898815","https://openalex.org/W2894073648","https://openalex.org/W2903167102","https://openalex.org/W2907757318","https://openalex.org/W2910680408","https://openalex.org/W2953562574","https://openalex.org/W2953929685","https://openalex.org/W2955517832","https://openalex.org/W2966617337","https://openalex.org/W2969891778","https://openalex.org/W2971539337","https://openalex.org/W2978910436","https://openalex.org/W2980708325","https://openalex.org/W2989499631","https://openalex.org/W2989998760","https://openalex.org/W2991218662","https://openalex.org/W3035253480","https://openalex.org/W3090681822","https://openalex.org/W3184351134","https://openalex.org/W3186264726","https://openalex.org/W3191021353","https://openalex.org/W3198164668","https://openalex.org/W3203156997","https://openalex.org/W4220773262","https://openalex.org/W6751145073","https://openalex.org/W6769271699","https://openalex.org/W6801116008"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2082860237","https://openalex.org/W1990804418","https://openalex.org/W2130076355","https://openalex.org/W1993764875","https://openalex.org/W1641042124","https://openalex.org/W2013243191","https://openalex.org/W2151865869","https://openalex.org/W2117258802"],"abstract_inverted_index":{"The":[0],"poly(A)":[1,45,65,87,105,157,160,166,169,213,221],"tail":[2,46,142,144,146,149,158,214],"is":[3,56,209,234],"a":[4,78,122,133],"dynamic":[5],"addition":[6],"to":[7,39],"the":[8,12],"eukaryotic":[9],"mRNA":[10,29],"and":[11,31,52,60,80,85,109,148,159,172,174,176,192,203,216,228],"change":[13],"in":[14,21,48,67,132,181,200,211],"its":[15],"length":[16,47,167,215],"plays":[17],"an":[18],"essential":[19],"role":[20],"regulating":[22],"gene":[23],"expression":[24],"through":[25],"affecting":[26],"nuclear":[27],"export,":[28],"stability":[30],"translation.":[32],"Only":[33],"recently":[34],"high-throughput":[35],"sequencing":[36,68,72,198],"strategies":[37],"began":[38],"emerge":[40],"for":[41,63,83,103,115,156],"transcriptome-wide":[42],"profiling":[43,116],"of":[44,178,219],"diverse":[49],"developmental":[50],"stages":[51],"organisms.":[53],"However,":[54],"there":[55],"currently":[57],"no":[58],"easy-to-use":[59],"universal":[61],"tool":[62],"measuring":[64,104,212],"tails":[66,88,117,131],"data":[69,195],"from":[70,89,196],"different":[71],"protocols.":[73],"Here":[74],"we":[75],"established":[76],"PolyAtailor,":[77],"unified":[79],"efficient":[81],"framework,":[82],"identifying":[84],"analyzing":[86],"PacBio-based":[90],"long":[91],"reads":[92],"or":[93,119],"next":[94],"generation":[95],"short":[96],"reads.":[97],"PolyAtailor":[98,126,152,185,208,233],"provides":[99],"two":[100],"core":[101],"functions":[102,155],"tails,":[106],"namely":[107],"Tail_map":[108],"Tail_scan,":[110],"which":[111,223],"can":[112,127],"be":[113],"used":[114],"with":[118,137,186],"without":[120],"using":[121,194],"reference":[123],"genome.":[124],"Particularly,":[125],"identify":[128],"all":[129],"potential":[130],"read,":[134],"providing":[135],"users":[136],"detailed":[138],"information":[139],"such":[140,163],"as":[141,164],"position,":[143],"length,":[145,222],"sequence":[147],"type.":[150],"Moreover,":[151],"integrates":[153],"rich":[154],"site":[161,170],"analyses,":[162],"differential":[165,220],"analysis,":[168],"identification":[171],"annotation,":[173],"statistics":[175],"visualization":[177],"base":[179],"composition":[180],"tails.":[182],"We":[183],"compared":[184],"three":[187,197],"latest":[188],"methods,":[189],"FLAMAnalysis,":[190],"FLEPSeq":[191],"PAIsoSeqAnalysis,":[193],"protocols":[199],"HeLa":[201],"samples":[202],"Arabidopsis.":[204],"Results":[205],"show":[206],"that":[207],"effective":[210],"detecting":[217],"significance":[218],"achieves":[224],"much":[225],"higher":[226],"sensitivity":[227],"accuracy":[229],"than":[230],"competing":[231],"methods.":[232],"available":[235],"at":[236],"https://github.com/BMILAB/PolyAtailor.":[237]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
