{"id":"https://openalex.org/W2971962973","doi":"https://doi.org/10.1093/bioinformatics/btz701","title":"scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data","display_name":"scDAPA: detection and visualization of dynamic alternative polyadenylation from single cell RNA-seq data","publication_year":2019,"publication_date":"2019-09-04","ids":{"openalex":"https://openalex.org/W2971962973","doi":"https://doi.org/10.1093/bioinformatics/btz701","mag":"2971962973","pmid":"https://pubmed.ncbi.nlm.nih.gov/31557285"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz701","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz701","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/4/1262/38712506/btz701.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/36/4/1262/38712506/btz701.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032396845","display_name":"Congting Ye","orcid":"https://orcid.org/0000-0003-4803-2098"},"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"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Congting Ye","raw_affiliation_strings":["Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University , Xiamen, Fujian 361102, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University , Xiamen, Fujian 361102, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055339874","display_name":"Qian Zhou","orcid":"https://orcid.org/0000-0002-6384-6535"},"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"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qian Zhou","raw_affiliation_strings":["Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University , Xiamen, Fujian 361102, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University , Xiamen, Fujian 361102, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091165765","display_name":"Xiaohui Wu","orcid":"https://orcid.org/0000-0003-0356-7785"},"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"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaohui Wu","raw_affiliation_strings":["Department of Automation, Xiamen University , Xiamen, Fujian 361005, China","National Institute for Data Science in Health and Medicine, Xiamen University , Xiamen, Fujian 361102, China"],"affiliations":[{"raw_affiliation_string":"Department of Automation, Xiamen University , Xiamen, Fujian 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"National Institute for Data Science in Health and Medicine, Xiamen University , Xiamen, Fujian 361102, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100656449","display_name":"Yu Chen","orcid":"https://orcid.org/0000-0001-9651-9875"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chen Yu","raw_affiliation_strings":["Department of Ophthalmology, Duke University , Durham, NC 27710, USA"],"affiliations":[{"raw_affiliation_string":"Department of Ophthalmology, Duke University , Durham, NC 27710, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111373172","display_name":"Guoli Ji","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"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guoli Ji","raw_affiliation_strings":["Department of Automation, Xiamen University , Xiamen, Fujian 361005, China","National Institute for Data Science in Health and Medicine, Xiamen University , Xiamen, Fujian 361102, China"],"affiliations":[{"raw_affiliation_string":"Department of Automation, Xiamen University , Xiamen, Fujian 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"National Institute for Data Science in Health and Medicine, Xiamen University , Xiamen, Fujian 361102, China","institution_ids":["https://openalex.org/I191208505"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039527047","display_name":"Daniel R. Saban","orcid":"https://orcid.org/0000-0003-4177-8065"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel R Saban","raw_affiliation_strings":["Department of Immunology, Duke University , Durham, NC 27710, USA","Department of Ophthalmology, Duke University , Durham, NC 27710, USA"],"affiliations":[{"raw_affiliation_string":"Department of Immunology, Duke University , Durham, NC 27710, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"Department of Ophthalmology, Duke University , Durham, NC 27710, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011758500","display_name":"Qingshun Quinn Li","orcid":"https://orcid.org/0000-0003-4105-1480"},"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/I93393672","display_name":"Western University of Health Sciences","ror":"https://ror.org/05167c961","country_code":"US","type":"education","lineage":["https://openalex.org/I93393672"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Qingshun Q Li","raw_affiliation_strings":["Graduate College of Biomedical Sciences, Western University of Health Sciences , Pomona, CA 91766, USA","Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University , Xiamen, Fujian 361102, China"],"affiliations":[{"raw_affiliation_string":"Graduate College of Biomedical Sciences, Western University of Health Sciences , Pomona, CA 91766, USA","institution_ids":["https://openalex.org/I93393672"]},{"raw_affiliation_string":"Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University , Xiamen, Fujian 361102, China","institution_ids":["https://openalex.org/I191208505"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5032396845"],"corresponding_institution_ids":["https://openalex.org/I191208505"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.8037,"has_fulltext":false,"cited_by_count":34,"citation_normalized_percentile":{"value":0.85713474,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"36","issue":"4","first_page":"1262","last_page":"1264"},"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994999766349792,"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":0.9984999895095825,"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":0.6555178165435791},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.59622722864151},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.542750358581543},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.46773561835289},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4238853454589844},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3503187298774719},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.25844329595565796},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22818639874458313},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.22646355628967285},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1797894537448883}],"concepts":[{"id":"https://openalex.org/C142575336","wikidata":"https://www.wikidata.org/wiki/Q412148","display_name":"Polyadenylation","level":4,"score":0.6555178165435791},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.59622722864151},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.542750358581543},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.46773561835289},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4238853454589844},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3503187298774719},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25844329595565796},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22818639874458313},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.22646355628967285},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1797894537448883},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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},{"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":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz701","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz701","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/4/1262/38712506/btz701.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:31557285","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31557285","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:pubmedcentral.nih.gov:8215916","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8215916","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/btz701","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz701","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/4/1262/38712506/btz701.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":[],"awards":[{"id":"https://openalex.org/G1188635553","display_name":null,"funder_award_id":"61802323","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3164098587","display_name":null,"funder_award_id":"20720190106","funder_id":"https://openalex.org/F4320325434","funder_display_name":"Xiamen University"},{"id":"https://openalex.org/G4485151630","display_name":null,"funder_award_id":"20720170076","funder_id":"https://openalex.org/F4320325434","funder_display_name":"Xiamen University"},{"id":"https://openalex.org/G7435240018","display_name":null,"funder_award_id":"61573296","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7443917920","display_name":null,"funder_award_id":"31801268","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"},{"id":"https://openalex.org/F4320325434","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2971962973.pdf","grobid_xml":"https://content.openalex.org/works/W2971962973.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W2069295116","https://openalex.org/W2122364231","https://openalex.org/W2755381547","https://openalex.org/W2763864472","https://openalex.org/W2766614445","https://openalex.org/W2807394374","https://openalex.org/W2916580767","https://openalex.org/W2919717197","https://openalex.org/W2944358912","https://openalex.org/W2951506174"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W1993948687","https://openalex.org/W2000169967","https://openalex.org/W2112883198"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":5}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
