{"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/I4210131551","display_name":"Netherlands Consortium for Healthy Ageing","ror":"https://ror.org/03wnqyy64","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I4210131551"]},{"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"]}],"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"],"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/I2802476451","https://openalex.org/I2800006345","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/I4210131551","display_name":"Netherlands Consortium for Healthy Ageing","ror":"https://ror.org/03wnqyy64","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I4210131551"]},{"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"]}],"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"],"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/I2802476451","https://openalex.org/I2800006345","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/I4210131551","display_name":"Netherlands Consortium for Healthy Ageing","ror":"https://ror.org/03wnqyy64","country_code":"NL","type":"healthcare","lineage":["https://openalex.org/I4210131551"]},{"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"]}],"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"],"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/I2802476451","https://openalex.org/I2800006345","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/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"]},{"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"]}],"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"],"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/I2802476451","https://openalex.org/I2800006345","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/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/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/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"],"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/I2802476451","https://openalex.org/I2800006345","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/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/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/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":"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"],"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/I2802476451","https://openalex.org/I2800006345","https://openalex.org/I4210131551"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5101575637"],"corresponding_institution_ids":["https://openalex.org/I2800006345","https://openalex.org/I2802476451","https://openalex.org/I4210131551"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.6893,"has_fulltext":true,"cited_by_count":35,"citation_normalized_percentile":{"value":0.9069698,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"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":0.9998999834060669,"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/T11482","display_name":"RNA modifications and cancer","score":0.9997000098228455,"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":0.9995999932289124,"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":11,"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":null},{"id":"pmh:lumc:oai:openaccess.leidenuniv.nl:1887/99115","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_3015537","is_oa":false,"landing_page_url":"http://hdl.handle.net/1887/137579","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 - 486","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: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:oai:scholarlypublications.universiteitleiden.nl:item_3015537","is_oa":false,"landing_page_url":"https://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":"Bioinformatics","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"},{"id":"pmh:oai:scholarlypublications.universiteitleiden.nl:item_3016045","is_oa":false,"landing_page_url":"https://hdl.handle.net/1887/99223","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"},{"id":"pmh:oai:scholarlypublications.universiteitleiden.nl:item_3017491","is_oa":false,"landing_page_url":"https://hdl.handle.net/1887/119073","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":"Bioinformatics","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/G3514550006","display_name":null,"funder_award_id":"Centre","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3981126665","display_name":null,"funder_award_id":"Seventh Framework Programme","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G4121974843","display_name":null,"funder_award_id":"261123","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5365867299","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"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":null,"funder_award_id":"259679","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G645663373","display_name":null,"funder_award_id":"7th Framework","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8051717526","display_name":null,"funder_award_id":"Grant","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":{"The":[0],"code":[1],"and":[2,10],"utilities":[3],"can":[4],"be":[5],"freely":[6],"downloaded":[7],"from":[8],"https://trac.nbic.nl/passion":[9],"ftp://ftp.sanger.ac.uk/pub/zn1/passion.":[11]},"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":"2026-04-19T08:26:33.389920","created_date":"2025-10-10T00:00:00"}
