{"id":"https://openalex.org/W2990049185","doi":"https://doi.org/10.1093/bioinformatics/btz438","title":"PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis","display_name":"PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis","publication_year":2019,"publication_date":"2019-05-22","ids":{"openalex":"https://openalex.org/W2990049185","doi":"https://doi.org/10.1093/bioinformatics/btz438","mag":"2990049185","pmid":"https://pubmed.ncbi.nlm.nih.gov/31135034"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz438","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz438","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/6901072","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002057869","display_name":"Kuan\u2010Ting Lin","orcid":"https://orcid.org/0000-0003-1294-1142"},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kuan-Ting Lin","raw_affiliation_strings":["Cold Spring Harbor Laboratory, Cold Spring Harbor , NY, USA"],"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory, Cold Spring Harbor , NY, USA","institution_ids":["https://openalex.org/I2750212522"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113482239","display_name":"Adrian R. Krainer","orcid":null},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Adrian R Krainer","raw_affiliation_strings":["Cold Spring Harbor Laboratory, Cold Spring Harbor , NY, USA"],"affiliations":[{"raw_affiliation_string":"Cold Spring Harbor Laboratory, Cold Spring Harbor , NY, USA","institution_ids":["https://openalex.org/I2750212522"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5113482239"],"corresponding_institution_ids":["https://openalex.org/I2750212522"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.2353,"has_fulltext":false,"cited_by_count":62,"citation_normalized_percentile":{"value":0.88895818,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"35","issue":"23","first_page":"5048","last_page":"5054"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/intron","display_name":"Intron","score":0.6535654067993164},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6419025659561157},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6119795441627502},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.560779333114624},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.559935450553894},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5332742929458618},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5312081575393677},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.527584433555603},{"id":"https://openalex.org/keywords/false-discovery-rate","display_name":"False discovery rate","score":0.502980649471283},{"id":"https://openalex.org/keywords/nanopore-sequencing","display_name":"Nanopore sequencing","score":0.42773354053497314},{"id":"https://openalex.org/keywords/exon","display_name":"Exon","score":0.4133444130420685},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.31895896792411804},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28053146600723267},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2506064176559448},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.20944109559059143},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.16621679067611694},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.15099415183067322}],"concepts":[{"id":"https://openalex.org/C94671646","wikidata":"https://www.wikidata.org/wiki/Q207551","display_name":"Intron","level":3,"score":0.6535654067993164},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6419025659561157},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6119795441627502},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.560779333114624},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.559935450553894},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5332742929458618},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5312081575393677},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.527584433555603},{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.502980649471283},{"id":"https://openalex.org/C126513998","wikidata":"https://www.wikidata.org/wiki/Q8973627","display_name":"Nanopore sequencing","level":4,"score":0.42773354053497314},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.4133444130420685},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.31895896792411804},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28053146600723267},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2506064176559448},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.20944109559059143},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.16621679067611694},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.15099415183067322},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"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":"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":"D017398","descriptor_name":"Alternative Splicing","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":false},{"descriptor_ui":"D017398","descriptor_name":"Alternative Splicing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":4,"locations":[{"id":"doi:10.1093/bioinformatics/btz438","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz438","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:31135034","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31135034","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:repository.cshl.edu:37982","is_oa":false,"landing_page_url":"https://repository.cshl.edu/id/eprint/37982/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402288","display_name":"Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Paper"},{"id":"pmh:oai:pubmedcentral.nih.gov:6901072","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6901072","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:6901072","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6901072","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1200689522","display_name":null,"funder_award_id":"CA13106","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W2012098861","https://openalex.org/W2012827002","https://openalex.org/W2018838463","https://openalex.org/W2037164009","https://openalex.org/W2066231767","https://openalex.org/W2106678197","https://openalex.org/W2117131162","https://openalex.org/W2159730169","https://openalex.org/W2169456326","https://openalex.org/W2170480204","https://openalex.org/W2223556930","https://openalex.org/W2255131131","https://openalex.org/W2487518698","https://openalex.org/W2771247031","https://openalex.org/W2781977790","https://openalex.org/W2887104804","https://openalex.org/W2891885918","https://openalex.org/W2949317881","https://openalex.org/W2949619425","https://openalex.org/W2950063384","https://openalex.org/W2953020124","https://openalex.org/W6754068987"],"related_works":["https://openalex.org/W3090446747","https://openalex.org/W2083872838","https://openalex.org/W2056412942","https://openalex.org/W2087463521","https://openalex.org/W2045666137","https://openalex.org/W2093797995","https://openalex.org/W4211196276","https://openalex.org/W2171581216","https://openalex.org/W4240704896","https://openalex.org/W2162713462"],"abstract_inverted_index":{"PSI-Sigma":[0],"is":[1,3],"implemented":[2],"available":[4],"at":[5],"https://github.com/wososa/PSI-Sigma.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":2}],"updated_date":"2026-03-06T13:50:29.536080","created_date":"2025-10-10T00:00:00"}