{"id":"https://openalex.org/W4392861050","doi":"https://doi.org/10.1093/bioinformatics/btae099","title":"vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data","display_name":"vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data","publication_year":2024,"publication_date":"2024-03-01","ids":{"openalex":"https://openalex.org/W4392861050","doi":"https://doi.org/10.1093/bioinformatics/btae099","pmid":"https://pubmed.ncbi.nlm.nih.gov/38485700"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae099","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae099","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae099/56975843/btae099.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae099/56975843/btae099.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110364646","display_name":"Xingyu Bi","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":"Xingyu Bi","raw_affiliation_strings":["Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China","Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou, 215000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China","institution_ids":["https://openalex.org/I3923682"]},{"raw_affiliation_string":"Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou, 215000, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062005196","display_name":"Wenbin Ye","orcid":"https://orcid.org/0000-0002-7811-2710"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenbin Ye","raw_affiliation_strings":["Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California , Irvine, CA 92697, United States"],"raw_orcid":"https://orcid.org/0000-0002-7811-2710","affiliations":[{"raw_affiliation_string":"Division of Computational Biomedicine, Department of Biological Chemistry, School of Medicine, University of California , Irvine, CA 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102325307","display_name":"Xin Cheng","orcid":"https://orcid.org/0009-0001-7581-8662"},"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":"Xin Cheng","raw_affiliation_strings":["Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China","Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou, 215000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China","institution_ids":["https://openalex.org/I3923682"]},{"raw_affiliation_string":"Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou, 215000, China","institution_ids":["https://openalex.org/I3923682"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074516400","display_name":"Ning Yang","orcid":"https://orcid.org/0000-0001-5772-3320"},"institutions":[{"id":"https://openalex.org/I8991828","display_name":"Pukyong National University","ror":"https://ror.org/0433kqc49","country_code":"KR","type":"education","lineage":["https://openalex.org/I8991828"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Ning Yang","raw_affiliation_strings":["College of Industrial Design, Pukyong National University , Busan 48513, Korea","College of Industrial Design, Pukyong National University, Busan, 48513, Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Industrial Design, Pukyong National University , Busan 48513, Korea","institution_ids":["https://openalex.org/I8991828"]},{"raw_affiliation_string":"College of Industrial Design, Pukyong National University, Busan, 48513, Korea","institution_ids":["https://openalex.org/I8991828"]}]},{"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, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China","Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou, 215000, China"],"raw_orcid":"https://orcid.org/0000-0003-0356-7785","affiliations":[{"raw_affiliation_string":"Pasteurien College, Suzhou Medical College of Soochow University, Soochow University , Suzhou 215000, China","institution_ids":["https://openalex.org/I3923682"]},{"raw_affiliation_string":"Pasteurien College, Suzhou Medical College of Soochow University, Soochow University, Suzhou, 215000, China","institution_ids":["https://openalex.org/I3923682"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5091165765"],"corresponding_institution_ids":["https://openalex.org/I3923682"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4032,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.6003504,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"40","issue":"3","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":0.9819999933242798,"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":0.9819999933242798,"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/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.002899999963119626,"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/T10949","display_name":"Genetic Neurodegenerative Diseases","score":0.0012000000569969416,"subfield":{"id":"https://openalex.org/subfields/2804","display_name":"Cellular and Molecular Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6943789720535278},{"id":"https://openalex.org/keywords/polyadenylation","display_name":"Polyadenylation","score":0.668928861618042},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6549410820007324},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.5655112862586975},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5362396240234375},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4998321533203125},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4560941457748413},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.41319990158081055},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.25152328610420227},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22999614477157593},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15573915839195251},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15127083659172058},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12564504146575928}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6943789720535278},{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.668928861618042},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6549410820007324},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.5655112862586975},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5362396240234375},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4998321533203125},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4560941457748413},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.41319990158081055},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.25152328610420227},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22999614477157593},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15573915839195251},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15127083659172058},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12564504146575928},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020413","descriptor_name":"3' Untranslated Regions","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":"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":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056890","descriptor_name":"Eukaryota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btae099","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae099","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae099/56975843/btae099.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38485700","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38485700","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.org:ark:/13030/qt55w23703","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/55w23703","pdf_url":"https://escholarship.org/content/qt55w23703/qt55w23703.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Bioinformatics, vol 40, iss 3","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10950478","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10950478","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10950478/pdf/btae099.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,"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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:ark:/13030/qt55w23703","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae099","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae099","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae099/56975843/btae099.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4156249640","display_name":null,"funder_award_id":"T2222007","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":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4392861050.pdf"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W2971962973","https://openalex.org/W2973045249","https://openalex.org/W3012204315","https://openalex.org/W3084187150","https://openalex.org/W3096575107","https://openalex.org/W3109174802","https://openalex.org/W3217246491","https://openalex.org/W4284675316","https://openalex.org/W4297180053","https://openalex.org/W4297493876","https://openalex.org/W4391563323","https://openalex.org/W6804065736"],"related_works":["https://openalex.org/W47352601","https://openalex.org/W2981957539","https://openalex.org/W4287378204","https://openalex.org/W1976007281","https://openalex.org/W2545422590","https://openalex.org/W4240705470","https://openalex.org/W2945311252","https://openalex.org/W195216885","https://openalex.org/W1968152888","https://openalex.org/W631546281"],"abstract_inverted_index":{"MOTIVATION:":[0],"Alternative":[1],"polyadenylation":[2],"(APA)":[3],"is":[4,26],"a":[5,103],"widespread":[6],"post-transcriptional":[7],"regulatory":[8],"mechanism":[9],"across":[10,75,91],"all":[11],"eukaryotes.":[12],"With":[13],"the":[14,96],"accumulation":[15],"of":[16,69],"genome-wide":[17],"APA":[18,35,47,60,73,89,108,115],"sites,":[19],"especially":[20],"those":[21],"with":[22,71],"single-cell":[23,52,97],"resolution,":[24],"it":[25],"imperative":[27],"to":[28,33,111],"develop":[29],"easy-to-use":[30],"visualization":[31],"tools":[32],"guide":[34],"analysis.":[36],"RESULTS:":[37],"We":[38],"developed":[39],"an":[40],"R":[41],"package":[42],"called":[43],"vizAPA":[44,54,65,81,99],"for":[45,59,86,114],"visualizing":[46,88],"dynamics":[48,90],"from":[49],"bulk":[50],"and":[51,62,94],"data.":[53],"implements":[55],"unified":[56],"data":[57,61],"structures":[58],"genome":[63],"annotations.":[64],"also":[66],"enables":[67],"identification":[68],"genes":[70],"differential":[72],"usage":[74],"biological":[76,92],"samples":[77,93],"and/or":[78],"cell":[79],"types.":[80],"provides":[82],"four":[83],"unique":[84],"modules":[85],"extensively":[87],"at":[95],"level.":[98],"could":[100],"serve":[101],"as":[102],"plugin":[104],"in":[105],"many":[106],"routine":[107],"analysis":[109],"pipelines":[110],"augment":[112],"studies":[113],"dynamics.":[116],"AVAILABILITY":[117],"AND":[118],"IMPLEMENTATION:":[119],"https://github.com/BMILAB/vizAPA.":[120]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}