{"id":"https://openalex.org/W2155486554","doi":"https://doi.org/10.1093/bioinformatics/btv001","title":"PVAAS: identify variants associated with aberrant splicing from RNA-seq","display_name":"PVAAS: identify variants associated with aberrant splicing from RNA-seq","publication_year":2015,"publication_date":"2015-01-07","ids":{"openalex":"https://openalex.org/W2155486554","doi":"https://doi.org/10.1093/bioinformatics/btv001","mag":"2155486554","pmid":"https://pubmed.ncbi.nlm.nih.gov/25573917"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv001","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv001","pdf_url":null,"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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4807355","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100636419","display_name":"Liguo Wang","orcid":"https://orcid.org/0000-0003-2072-4826"},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Liguo Wang","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110360116","display_name":"Jinfu Nie","orcid":null},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jinfu J. Nie","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071782757","display_name":"Jean\u2010Pierre Kocher","orcid":"https://orcid.org/0000-0002-0260-6773"},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jean-Pierre A. Kocher","raw_affiliation_strings":["Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN 55905, USA","institution_ids":["https://openalex.org/I1330342723"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5071782757","https://openalex.org/A5100636419"],"corresponding_institution_ids":["https://openalex.org/I1330342723"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1378,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.54025232,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"31","issue":"10","first_page":"1668","last_page":"1670"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9998000264167786,"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/T12610","display_name":"RNA regulation and disease","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"}}],"keywords":[{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.7773561477661133},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.7676182389259338},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6186785101890564},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5108672976493835},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5016627311706543},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.48533526062965393},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.28020918369293213},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2778146266937256},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.10826972126960754}],"concepts":[{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.7773561477661133},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.7676182389259338},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6186785101890564},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5108672976493835},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5016627311706543},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.48533526062965393},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.28020918369293213},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2778146266937256},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.10826972126960754}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","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":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv001","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv001","pdf_url":null,"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:25573917","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25573917","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:open-archive.highwire.org:bioinfo:31/10/1668","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/10/1668","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:4807355","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4807355","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:4807355","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4807355","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306143","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":8,"referenced_works":["https://openalex.org/W1983924599","https://openalex.org/W2012284471","https://openalex.org/W2045131720","https://openalex.org/W2063318299","https://openalex.org/W2089465951","https://openalex.org/W2098894238","https://openalex.org/W2108234281","https://openalex.org/W2155804510"],"related_works":["https://openalex.org/W4224241862","https://openalex.org/W4200033037","https://openalex.org/W2889547007","https://openalex.org/W1510729279","https://openalex.org/W3213655218","https://openalex.org/W2971615643","https://openalex.org/W2076384244","https://openalex.org/W4365452989","https://openalex.org/W2587969176","https://openalex.org/W1971332228"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"RNA-seq":[2,15,83],"has":[3,50],"been":[4,51],"widely":[5],"used":[6],"to":[7,12,18,34,53,57,71],"study":[8],"the":[9,43,104],"transcriptome.":[10],"Comparing":[11],"microarray,":[13],"sequencing-based":[14],"is":[16,118],"able":[17],"identify":[19,58,72,91],"splicing":[20,81,112],"variants":[21,25,36,59,75,97,109],"and":[22,110,115,122,126],"single":[23,73],"nucleotide":[24,74],"in":[26,87,120],"one":[27],"experiment":[28],"simultaneously.":[29],"This":[30],"provides":[31],"unique":[32],"opportunity":[33],"detect":[35],"that":[37,76],"associated":[38,60,77],"with":[39,61,78],"aberrant":[40,62,79,92,111],"splicing.":[41,63],"Despite":[42],"popularity":[44],"of":[45,106],"RNA-seq,":[46],"no":[47],"bioinformatics":[48],"tool":[49,70],"developed":[52,67],"leverage":[54],"this":[55],"advantage":[56],"Results:":[64],"We":[65],"have":[66],"PVAAS,":[68],"a":[69,127],"alternative":[80],"from":[82],"data.":[84],"PVAAS":[85,117],"works":[86],"three":[88],"steps:":[89],"(i)":[90],"splicings;":[93],"(ii)":[94],"use":[95],"user-provided":[96],"or":[98,138],"perform":[99],"variant":[100],"calling;":[101],"(iii)":[102],"assess":[103],"significance":[105],"association":[107],"between":[108],"events.":[113],"Availability":[114],"implementation:":[116],"written":[119],"Python":[121],"C.":[123],"Source":[124],"code":[125],"comprehensive":[128],"user\u2019s":[129],"manual":[130],"are":[131,144],"freely":[132],"available":[133,145],"at:":[134],"http://pvaas.sourceforge.net/.":[135],"Contact:":[136],"wang.liguo@mayo.edu":[137],"kocher.jeanpierre@mayo.edu":[139],"Supplementary":[140,142],"information:":[141],"data":[143],"at":[146],"Bioinformatics":[147],"online.":[148]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}