{"id":"https://openalex.org/W2144938907","doi":"https://doi.org/10.1093/bioinformatics/btr712","title":"PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data","display_name":"PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data","publication_year":2012,"publication_date":"2012-01-04","ids":{"openalex":"https://openalex.org/W2144938907","doi":"https://doi.org/10.1093/bioinformatics/btr712","mag":"2144938907","pmid":"https://pubmed.ncbi.nlm.nih.gov/22219203"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr712","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr712","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/4/479/48875929/bioinformatics_28_4_479.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/4/479/48875929/bioinformatics_28_4_479.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101575637","display_name":"Yanju Zhang","orcid":"https://orcid.org/0000-0002-8629-258X"},"institutions":[{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210131551","display_name":"Netherlands Consortium for Healthy Ageing","ror":"https://ror.org/03wnqyy64","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I4210131551"]}],"countries":["GB","NL"],"is_corresponding":true,"raw_author_name":"Yanju Zhang","raw_affiliation_strings":["1 Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, 2Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands, 3The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 4Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, 2Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands, 3The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 4Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands","institution_ids":["https://openalex.org/I2800006345","https://openalex.org/I2802476451","https://openalex.org/I4210131551"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047891732","display_name":"Eric-Wubbo Lameijer","orcid":"https://orcid.org/0000-0002-0397-0710"},"institutions":[{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210131551","display_name":"Netherlands Consortium for Healthy Ageing","ror":"https://ror.org/03wnqyy64","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I4210131551"]}],"countries":["GB","NL"],"is_corresponding":false,"raw_author_name":"Eric-Wubbo Lameijer","raw_affiliation_strings":["1 Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, 2Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands, 3The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 4Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, 2Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands, 3The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 4Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands","institution_ids":["https://openalex.org/I2800006345","https://openalex.org/I2802476451","https://openalex.org/I4210131551"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021033668","display_name":"Peter A.C. \u2019t Hoen","orcid":"https://orcid.org/0000-0003-4450-3112"},"institutions":[{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210131551","display_name":"Netherlands Consortium for Healthy Ageing","ror":"https://ror.org/03wnqyy64","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I4210131551"]}],"countries":["GB","NL"],"is_corresponding":false,"raw_author_name":"Peter A. C. 't Hoen","raw_affiliation_strings":["1 Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, 2Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands, 3The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 4Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, 2Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands, 3The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 4Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands","institution_ids":["https://openalex.org/I2800006345","https://openalex.org/I2802476451","https://openalex.org/I4210131551"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087942382","display_name":"Zemin Ning","orcid":"https://orcid.org/0000-0003-4359-776X"},"institutions":[{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210131551","display_name":"Netherlands Consortium for Healthy Ageing","ror":"https://ror.org/03wnqyy64","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I4210131551"]}],"countries":["GB","NL"],"is_corresponding":false,"raw_author_name":"Zemin Ning","raw_affiliation_strings":["1 Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, 2Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands, 3The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 4Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, 2Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands, 3The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 4Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands","institution_ids":["https://openalex.org/I2800006345","https://openalex.org/I2802476451","https://openalex.org/I4210131551"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071478025","display_name":"P. Eline Slagboom","orcid":"https://orcid.org/0000-0002-2875-4723"},"institutions":[{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210131551","display_name":"Netherlands Consortium for Healthy Ageing","ror":"https://ror.org/03wnqyy64","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I4210131551"]}],"countries":["GB","NL"],"is_corresponding":false,"raw_author_name":"P. Eline Slagboom","raw_affiliation_strings":["1 Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, 2Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands, 3The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 4Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, 2Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands, 3The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 4Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands","institution_ids":["https://openalex.org/I2800006345","https://openalex.org/I2802476451","https://openalex.org/I4210131551"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032548139","display_name":"Kai Ye","orcid":"https://orcid.org/0000-0002-2851-6741"},"institutions":[{"id":"https://openalex.org/I2800006345","display_name":"Leiden University Medical Center","ror":"https://ror.org/05xvt9f17","country_code":"NL","type":"funder","lineage":["https://openalex.org/I2800006345"]},{"id":"https://openalex.org/I2802476451","display_name":"Wellcome Sanger Institute","ror":"https://ror.org/05cy4wa09","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I2802476451","https://openalex.org/I87048295"]},{"id":"https://openalex.org/I4210131551","display_name":"Netherlands Consortium for Healthy Ageing","ror":"https://ror.org/03wnqyy64","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I4210131551"]}],"countries":["GB","NL"],"is_corresponding":true,"raw_author_name":"Kai Ye","raw_affiliation_strings":["1 Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, 2Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands, 3The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 4Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Molecular Epidemiology, Medical Statistics and Bioinformatics, 2Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands, 3The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK and 4Netherlands Consortium for Healthy Ageing, Leiden, The Netherlands","institution_ids":["https://openalex.org/I2800006345","https://openalex.org/I2802476451","https://openalex.org/I4210131551"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5032548139","https://openalex.org/A5101575637"],"corresponding_institution_ids":["https://openalex.org/I2800006345","https://openalex.org/I2802476451","https://openalex.org/I4210131551"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":{"value":3989,"currency":"USD","value_usd":3989},"fwci":2.4955,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.89916723,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"28","issue":"4","first_page":"479","last_page":"486"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9797999858856201,"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":0.9797999858856201,"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":0.005100000184029341,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0034000000450760126,"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/passion","display_name":"Passion","score":0.8414125442504883},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.7412926554679871},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.6167412996292114},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5941944122314453},{"id":"https://openalex.org/keywords/exon","display_name":"Exon","score":0.577346682548523},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5204896330833435},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5006015300750732},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.451647013425827},{"id":"https://openalex.org/keywords/ensembl","display_name":"Ensembl","score":0.43813806772232056},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4173716604709625},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3980848789215088},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3936736285686493},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.3213052749633789},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3130449652671814},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.25819557905197144},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.256947785615921},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.21731901168823242},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1706094741821289},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.07702744007110596}],"concepts":[{"id":"https://openalex.org/C2780310893","wikidata":"https://www.wikidata.org/wiki/Q335046","display_name":"Passion","level":2,"score":0.8414125442504883},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.7412926554679871},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6167412996292114},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5941944122314453},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.577346682548523},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5204896330833435},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5006015300750732},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.451647013425827},{"id":"https://openalex.org/C141674004","wikidata":"https://www.wikidata.org/wiki/Q1344256","display_name":"Ensembl","level":5,"score":0.43813806772232056},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4173716604709625},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3980848789215088},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3936736285686493},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.3213052749633789},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3130449652671814},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.25819557905197144},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.256947785615921},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.21731901168823242},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1706094741821289},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.07702744007110596},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002886","descriptor_name":"Chromosomes, Human, Pair 17","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002886","descriptor_name":"Chromosomes, Human, Pair 17","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002886","descriptor_name":"Chromosomes, Human, Pair 17","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005091","descriptor_name":"Exons","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012326","descriptor_name":"RNA Splicing","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":"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":"D022821","descriptor_name":"RNA Splice Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022821","descriptor_name":"RNA Splice Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D022821","descriptor_name":"RNA Splice Sites","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},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1093/bioinformatics/btr712","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr712","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/4/479/48875929/bioinformatics_28_4_479.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22219203","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22219203","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:2290181","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3278765","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:lumc:oai:scholarlypublications.universiteitleiden.nl:item_3015954","is_oa":false,"landing_page_url":"http://hdl.handle.net/1887/99115","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"VOLUME=28;ISSUE=4;STARTPAGE=479;ENDPAGE=486;TITLE=None","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:lumc:oai:scholarlypublications.universiteitleiden.nl:item_3016045","is_oa":false,"landing_page_url":"http://hdl.handle.net/1887/99223","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"VOLUME=28;ISSUE=4;STARTPAGE=479;ENDPAGE=486;TITLE=None","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:lumc:oai:scholarlypublications.universiteitleiden.nl:item_3017491","is_oa":false,"landing_page_url":"http://hdl.handle.net/1887/119073","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 28(4), 479 - 86","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:openaccess.leidenuniv.nl:1887/137579","is_oa":false,"landing_page_url":"http://hdl.handle.net/1887/137579","pdf_url":null,"source":{"id":"https://openalex.org/S4306400850","display_name":"Leiden Repository (Leiden University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I121797337","host_organization_name":"Leiden University","host_organization_lineage":["https://openalex.org/I121797337"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"28","raw_type":"Article / Letter to editor"},{"id":"pmh:oai:scholarlypublications.universiteitleiden.nl:item_3015954","is_oa":false,"landing_page_url":"https://hdl.handle.net/1887/99115","pdf_url":null,"source":{"id":"https://openalex.org/S4306400850","display_name":"Leiden Repository (Leiden University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I121797337","host_organization_name":"Leiden University","host_organization_lineage":["https://openalex.org/I121797337"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article / Letter to editor"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr712","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr712","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/4/479/48875929/bioinformatics_28_4_479.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2476663878","display_name":null,"funder_award_id":"FP7/2007-2011","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4121974843","display_name":"Sharing capacity across Europe in high-throughput sequencing technology to explore genetic variation in health and disease","funder_award_id":"261123","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5702163051","display_name":null,"funder_award_id":"FP7/2007","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5984585972","display_name":"Integrated research on DEvelopmental determinants of Aging and Longevity","funder_award_id":"259679","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"},{"id":"https://openalex.org/F4320328608","display_name":"Centre for Medical Systems Biology","ror":"https://ror.org/00e7dfm13"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2144938907.pdf","grobid_xml":"https://content.openalex.org/works/W2144938907.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1987590932","https://openalex.org/W2011920499","https://openalex.org/W2083871583","https://openalex.org/W2097065948","https://openalex.org/W2098824600","https://openalex.org/W2103441770","https://openalex.org/W2108234281","https://openalex.org/W2111054661","https://openalex.org/W2112067162","https://openalex.org/W2116166762","https://openalex.org/W2124985265","https://openalex.org/W2126144698","https://openalex.org/W2142619120","https://openalex.org/W2148399176","https://openalex.org/W2154397429","https://openalex.org/W2155804510","https://openalex.org/W2160164696","https://openalex.org/W2168196587"],"related_works":["https://openalex.org/W4388377433","https://openalex.org/W2156564520","https://openalex.org/W2130439870","https://openalex.org/W2151954452","https://openalex.org/W178291922","https://openalex.org/W2000278701","https://openalex.org/W2055681276","https://openalex.org/W2160947509","https://openalex.org/W2235368041","https://openalex.org/W2001406627"],"abstract_inverted_index":{"MOTIVATION:":[0],"RNA-seq":[1],"is":[2,44,65,104,114],"a":[3,66,73],"powerful":[4],"technology":[5],"for":[6,21,78],"the":[7,27,38,47,62,87,110,126,139,156,160,183],"study":[8],"of":[9,29,41,58,89,112,173],"transcriptome":[10],"profiles":[11],"that":[12,49,102,144],"uses":[13],"deep-sequencing":[14],"technologies.":[15],"Moreover,":[16,109],"it":[17],"may":[18],"be":[19,153,211],"used":[20],"cellular":[22],"phenotyping":[23],"and":[24,55,99,120,169,187,198,208,216],"help":[25],"establishing":[26],"etiology":[28],"diseases":[30],"characterized":[31],"by":[32,117,155],"abnormal":[33],"splicing":[34,42,149,171,200],"patterns.":[35],"In":[36,191],"RNA-Seq,":[37],"exact":[39],"nature":[40],"events":[43],"buried":[45],"in":[46,82,133,182],"reads":[48,60],"span":[50],"exon-exon":[51],"boundaries.":[52],"The":[53,206],"accurate":[54],"efficient":[56],"mapping":[57],"these":[59,107],"to":[61,91,141],"reference":[63],"genome":[64],"major":[67],"challenge.":[68],"RESULTS:":[69],"We":[70],"developed":[71],"PASSion,":[72],"pattern":[74],"growth":[75],"algorithm-based":[76],"pipeline":[77],"splice":[79],"site":[80],"detection":[81],"paired-end":[83],"RNA-Seq":[84,94,163],"reads.":[85],"Comparing":[86],"performance":[88,111],"PASSion":[90,103,113,137,165],"three":[92,128],"existing":[93],"analysis":[95],"pipelines,":[96],"TopHat,":[97],"MapSplice":[98],"HMMSplicer,":[100],"revealed":[101],"competitive":[105],"with":[106],"packages.":[108],"not":[115,146],"affected":[116],"read":[118],"length":[119],"coverage.":[121],"It":[122],"performs":[123],"better":[124],"than":[125],"other":[127,157],"approaches":[129],"when":[130],"detecting":[131],"junctions":[132,143,180],"highly":[134],"abundant":[135],"transcripts.":[136],"has":[138],"ability":[140],"detect":[142],"do":[145],"have":[147],"known":[148,179],"motifs,":[150],"which":[151,174],"cannot":[152],"found":[154],"tools.":[158],"Of":[159],"two":[161],"public":[162],"datasets,":[164],"predicted":[166],"\u2248":[167],"137,000":[168],"173,000":[170],"events,":[172],"on":[175],"average":[176],"82":[177],"are":[178,189],"annotated":[181],"Ensembl":[184],"transcript":[185],"database":[186],"18%":[188],"novel.":[190],"addition,":[192],"our":[193],"package":[194],"can":[195,210],"discover":[196],"differential":[197],"shared":[199],"patterns":[201],"among":[202],"multiple":[203],"samples.":[204],"AVAILABILITY:":[205],"code":[207],"utilities":[209],"freely":[212],"downloaded":[213],"from":[214],"https://trac.nbic.nl/passion":[215],"ftp://ftp.sanger.ac.uk/pub/zn1/passion.":[217]},"counts_by_year":[{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":3},{"year":2021,"cited_by_count":5},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":4}],"updated_date":"2026-09-02T18:50:13.731487","created_date":"2025-10-10T00:00:00"}
