{"id":"https://openalex.org/W2135835936","doi":"https://doi.org/10.1093/bioinformatics/btt446","title":"Accurate identification of polyadenylation sites from 3\u2032 end deep sequencing using a na\u00efve Bayes classifier","display_name":"Accurate identification of polyadenylation sites from 3\u2032 end deep sequencing using a na\u00efve Bayes classifier","publication_year":2013,"publication_date":"2013-08-20","ids":{"openalex":"https://openalex.org/W2135835936","doi":"https://doi.org/10.1093/bioinformatics/btt446","mag":"2135835936","pmid":"https://pubmed.ncbi.nlm.nih.gov/23962617"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt446","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt446","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/20/2564/16918414/btt446.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/20/2564/16918414/btt446.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047941457","display_name":"Sarah E. Sheppard","orcid":"https://orcid.org/0000-0003-3480-8123"},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sarah Sheppard","raw_affiliation_strings":["1 Program in Gene Function and Expression and 2Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, USA"],"affiliations":[{"raw_affiliation_string":"1 Program in Gene Function and Expression and 2Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, USA","institution_ids":["https://openalex.org/I166722992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055322887","display_name":"Nathan D. Lawson","orcid":"https://orcid.org/0000-0001-7788-9619"},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathan D. Lawson","raw_affiliation_strings":["1 Program in Gene Function and Expression and 2Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, USA"],"affiliations":[{"raw_affiliation_string":"1 Program in Gene Function and Expression and 2Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, USA","institution_ids":["https://openalex.org/I166722992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070760688","display_name":"Lihua Julie Zhu","orcid":"https://orcid.org/0000-0001-7416-0590"},"institutions":[{"id":"https://openalex.org/I166722992","display_name":"University of Massachusetts Chan Medical School","ror":"https://ror.org/0464eyp60","country_code":"US","type":"education","lineage":["https://openalex.org/I166722992"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lihua Julie Zhu","raw_affiliation_strings":["1 Program in Gene Function and Expression and 2Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, USA"],"affiliations":[{"raw_affiliation_string":"1 Program in Gene Function and Expression and 2Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 364 Plantation St, Worcester, MA 01605, USA","institution_ids":["https://openalex.org/I166722992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5047941457"],"corresponding_institution_ids":["https://openalex.org/I166722992"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5959,"has_fulltext":false,"cited_by_count":36,"citation_normalized_percentile":{"value":0.6953163,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"29","issue":"20","first_page":"2564","last_page":"2571"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9991000294685364,"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":0.9991000294685364,"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":0.9983000159263611,"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":0.9969000220298767,"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/polyadenylation","display_name":"Polyadenylation","score":0.8200702667236328},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.5886884927749634},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5651213526725769},{"id":"https://openalex.org/keywords/bayes-theorem","display_name":"Bayes' theorem","score":0.5409913659095764},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5266932249069214},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.48020896315574646},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4209863543510437},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.38030102849006653},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3774803876876831},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3603219985961914},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.28322580456733704},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.19784024357795715},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1545095145702362}],"concepts":[{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.8200702667236328},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.5886884927749634},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5651213526725769},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.5409913659095764},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5266932249069214},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48020896315574646},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4209863543510437},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.38030102849006653},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3774803876876831},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3603219985961914},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.28322580456733704},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.19784024357795715},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1545095145702362},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D024509","descriptor_name":"3' Flanking Region","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D024509","descriptor_name":"3' Flanking Region","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D024509","descriptor_name":"3' Flanking Region","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":"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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btt446","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt446","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/20/2564/16918414/btt446.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23962617","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23962617","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:escholarship.umassmed.edu:pgfe_pp-1229","is_oa":false,"landing_page_url":"https://escholarship.umassmed.edu/pgfe_pp/229","pdf_url":null,"source":{"id":"https://openalex.org/S4306400883","display_name":"The Journal of the American Medical Association (JAMA) Network (American Medical Association)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I173654999","host_organization_name":"American Medical Association","host_organization_lineage":["https://openalex.org/I173654999"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Program in Gene Function and Expression Publications","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3789547","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3789547","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt446","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt446","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/20/2564/16918414/btt446.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/14","score":0.6200000047683716,"display_name":"Life below water"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332606","display_name":"University of Massachusetts Medical School","ror":"https://ror.org/0464eyp60"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2135835936.pdf","grobid_xml":"https://content.openalex.org/works/W2135835936.grobid-xml"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W203942436","https://openalex.org/W1549887922","https://openalex.org/W1556198965","https://openalex.org/W1583837637","https://openalex.org/W1590648220","https://openalex.org/W1592870802","https://openalex.org/W1979764753","https://openalex.org/W1981239255","https://openalex.org/W1996831533","https://openalex.org/W2000875411","https://openalex.org/W2044648543","https://openalex.org/W2049211478","https://openalex.org/W2053295196","https://openalex.org/W2063443647","https://openalex.org/W2083196263","https://openalex.org/W2095930993","https://openalex.org/W2096352448","https://openalex.org/W2097065948","https://openalex.org/W2101815618","https://openalex.org/W2105060337","https://openalex.org/W2105545925","https://openalex.org/W2105879579","https://openalex.org/W2106774938","https://openalex.org/W2109553965","https://openalex.org/W2112326496","https://openalex.org/W2114672936","https://openalex.org/W2118031210","https://openalex.org/W2118834857","https://openalex.org/W2119560696","https://openalex.org/W2124985265","https://openalex.org/W2125349610","https://openalex.org/W2125546320","https://openalex.org/W2129078669","https://openalex.org/W2131446214","https://openalex.org/W2140006817","https://openalex.org/W2141458291","https://openalex.org/W2143852617","https://openalex.org/W2151562469","https://openalex.org/W2156880688","https://openalex.org/W2170669858","https://openalex.org/W2171791048","https://openalex.org/W2172203661","https://openalex.org/W2325343629","https://openalex.org/W2582743722","https://openalex.org/W3197051897","https://openalex.org/W4298018660","https://openalex.org/W6632852417","https://openalex.org/W6635200387","https://openalex.org/W6678093492"],"related_works":["https://openalex.org/W1976007281","https://openalex.org/W1968152888","https://openalex.org/W195216885","https://openalex.org/W2081082232","https://openalex.org/W4205787488","https://openalex.org/W2065213545","https://openalex.org/W2414745490","https://openalex.org/W2124120782","https://openalex.org/W2074164095","https://openalex.org/W2049864679"],"abstract_inverted_index":{"By":[0],"analyzing":[1],"sequence":[2],"features":[3],"flanking":[4],"3'":[5],"ends":[6],"derived":[7],"from":[8],"oligo-dT-based":[9],"sequencing,":[10],"we":[11],"developed":[12],"a":[13],"na\u00efve":[14],"Bayes":[15],"classifier":[16],"to":[17],"classify":[18],"them":[19],"as":[20],"true":[21],"or":[22],"false/internally":[23],"primed.":[24],"The":[25],"resulting":[26],"algorithm":[27],"is":[28],"highly":[29],"accurate,":[30],"outperforms":[31],"previous":[32],"heuristic":[33],"filters":[34],"and":[35],"facilitates":[36],"identification":[37],"of":[38],"novel":[39],"polyadenylation":[40],"sites.":[41]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}