{"id":"https://openalex.org/W2809526652","doi":"https://doi.org/10.1093/bioinformatics/bty483","title":"TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts","display_name":"TranscriptClean: variant-aware correction of indels, mismatches and splice junctions in long-read transcripts","publication_year":2018,"publication_date":"2018-06-13","ids":{"openalex":"https://openalex.org/W2809526652","doi":"https://doi.org/10.1093/bioinformatics/bty483","mag":"2809526652","pmid":"https://pubmed.ncbi.nlm.nih.gov/29912287"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty483","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty483","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/2/340/27496966/bty483.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","license_id":"https://openalex.org/licenses/cc-by","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/35/2/340/27496966/bty483.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063294163","display_name":"Dana Wyman","orcid":"https://orcid.org/0000-0002-1002-2188"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dana Wyman","raw_affiliation_strings":["Center for Complex Biological Systems, UC Irvine, Irvine, CA, USA","Department of Developmental and Cell Biology, UC Irvine, Irvine, CA, USA"],"affiliations":[{"raw_affiliation_string":"Center for Complex Biological Systems, UC Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Developmental and Cell Biology, UC Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074895828","display_name":"A Mortazavi","orcid":"https://orcid.org/0000-0002-4259-6362"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ali Mortazavi","raw_affiliation_strings":["Center for Complex Biological Systems, UC Irvine, Irvine, CA, USA","Department of Developmental and Cell Biology, UC Irvine, Irvine, CA, USA"],"affiliations":[{"raw_affiliation_string":"Center for Complex Biological Systems, UC Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Developmental and Cell Biology, UC Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074895828"],"corresponding_institution_ids":["https://openalex.org/I204250578"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.5129,"has_fulltext":true,"cited_by_count":95,"citation_normalized_percentile":{"value":0.90286739,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"35","issue":"2","first_page":"340","last_page":"342"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10015","display_name":"Genomics and Phylogenetic Studies","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/T10604","display_name":"RNA Research and Splicing","score":0.9994000196456909,"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":0.9993000030517578,"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/splice","display_name":"splice","score":0.8758487701416016},{"id":"https://openalex.org/keywords/indel","display_name":"Indel","score":0.741563081741333},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6960412263870239},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6657196283340454},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5941206216812134},{"id":"https://openalex.org/keywords/exon","display_name":"Exon","score":0.5385680198669434},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.5127606987953186},{"id":"https://openalex.org/keywords/gene-isoform","display_name":"Gene isoform","score":0.5062865018844604},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.4978184700012207},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.46050307154655457},{"id":"https://openalex.org/keywords/alternative-splicing","display_name":"Alternative splicing","score":0.45405417680740356},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.43597424030303955},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4280340075492859},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3441329896450043},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.16390588879585266},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10523545742034912},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.10141220688819885}],"concepts":[{"id":"https://openalex.org/C2780989783","wikidata":"https://www.wikidata.org/wiki/Q7578557","display_name":"splice","level":3,"score":0.8758487701416016},{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.741563081741333},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6960412263870239},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6657196283340454},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5941206216812134},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.5385680198669434},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.5127606987953186},{"id":"https://openalex.org/C53345823","wikidata":"https://www.wikidata.org/wiki/Q5531554","display_name":"Gene isoform","level":3,"score":0.5062865018844604},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.4978184700012207},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.46050307154655457},{"id":"https://openalex.org/C194583182","wikidata":"https://www.wikidata.org/wiki/Q21114084","display_name":"Alternative splicing","level":4,"score":0.45405417680740356},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43597424030303955},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4280340075492859},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3441329896450043},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.16390588879585266},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10523545742034912},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.10141220688819885},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020033","descriptor_name":"Protein Isoforms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bty483","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty483","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/2/340/27496966/bty483.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29912287","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29912287","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:ark:/13030/qt5tw6f3pz","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt5tw6f3pz","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/5tw6f3pz","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 35, iss 2","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5307529","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6329999","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty483","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty483","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/2/340/27496966/bty483.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4998422154","display_name":null,"funder_award_id":"UM1 HG009443","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2809526652.pdf","grobid_xml":"https://content.openalex.org/works/W2809526652.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W958219903","https://openalex.org/W2117476795","https://openalex.org/W2132341951","https://openalex.org/W2136899396","https://openalex.org/W2169456326","https://openalex.org/W2195724570","https://openalex.org/W2236822143","https://openalex.org/W2337011385","https://openalex.org/W2952666313","https://openalex.org/W2971373028"],"related_works":["https://openalex.org/W2156997304","https://openalex.org/W2733300197","https://openalex.org/W3177344798","https://openalex.org/W2104358039","https://openalex.org/W198662619","https://openalex.org/W3144511734","https://openalex.org/W2998711935","https://openalex.org/W2340062477","https://openalex.org/W2022601898","https://openalex.org/W1989438369"],"abstract_inverted_index":{"All":[0],"Python":[1],"and":[2],"R":[3],"scripts":[4],"used":[5],"in":[6],"this":[7],"paper":[8],"are":[9],"available":[10],"at":[11],"https://github.com/dewyman/TranscriptClean.":[12]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":31},{"year":2022,"cited_by_count":12},{"year":2021,"cited_by_count":13},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":7}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
