{"id":"https://openalex.org/W4386554478","doi":"https://doi.org/10.1093/bioinformatics/btad556","title":"aenmd: annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants","display_name":"aenmd: annotating escape from nonsense-mediated decay for transcripts with protein-truncating variants","publication_year":2023,"publication_date":"2023-09-01","ids":{"openalex":"https://openalex.org/W4386554478","doi":"https://doi.org/10.1093/bioinformatics/btad556","pmid":"https://pubmed.ncbi.nlm.nih.gov/37688563"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad556","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad556","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad556/51472757/btad556.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad556/51472757/btad556.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081933174","display_name":"Jonathan Klonowski","orcid":"https://orcid.org/0000-0003-0776-5658"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jonathan Klonowski","raw_affiliation_strings":["Department of Developmental Biology, University of Pittsburgh School of Medicine , Pittsburgh, PA 15201, United States"],"affiliations":[{"raw_affiliation_string":"Department of Developmental Biology, University of Pittsburgh School of Medicine , Pittsburgh, PA 15201, United States","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024761367","display_name":"Qianqian Liang","orcid":"https://orcid.org/0000-0001-8797-7778"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qianqian Liang","raw_affiliation_strings":["Department of Developmental Biology, University of Pittsburgh School of Medicine , Pittsburgh, PA 15201, United States"],"affiliations":[{"raw_affiliation_string":"Department of Developmental Biology, University of Pittsburgh School of Medicine , Pittsburgh, PA 15201, United States","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058116898","display_name":"Zeynep Coban\u2010Akdemir","orcid":"https://orcid.org/0000-0001-9928-9032"},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zeynep Coban-Akdemir","raw_affiliation_strings":["Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health , Houston, TX 77030, United States"],"affiliations":[{"raw_affiliation_string":"Department of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health , Houston, TX 77030, United States","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022595874","display_name":"Cecilia Lo","orcid":"https://orcid.org/0000-0003-4314-3434"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cecilia Lo","raw_affiliation_strings":["Department of Developmental Biology, University of Pittsburgh School of Medicine , Pittsburgh, PA 15201, United States"],"affiliations":[{"raw_affiliation_string":"Department of Developmental Biology, University of Pittsburgh School of Medicine , Pittsburgh, PA 15201, United States","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010346419","display_name":"Dennis Kostka","orcid":"https://orcid.org/0000-0002-1460-5487"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dennis Kostka","raw_affiliation_strings":["Department of Computational & Systems Biology and Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine , Pittsburgh, PA 15260, United States","Department of Developmental Biology, University of Pittsburgh School of Medicine , Pittsburgh, PA 15201, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computational & Systems Biology and Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine , Pittsburgh, PA 15260, United States","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Department of Developmental Biology, University of Pittsburgh School of Medicine , Pittsburgh, PA 15201, United States","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5081933174"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.3703,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.81268215,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"39","issue":"9","first_page":null,"last_page":null},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994999766349792,"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":0.9994999766349792,"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/nonsense-mediated-decay","display_name":"Nonsense-mediated decay","score":0.8439174890518188},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5243585109710693},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5231983661651611},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5170548558235168},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.4585977792739868},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.45720794796943665},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.451094388961792},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.41811349987983704},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.1692695915699005},{"id":"https://openalex.org/keywords/rna-splicing","display_name":"RNA splicing","score":0.07241860032081604}],"concepts":[{"id":"https://openalex.org/C70219777","wikidata":"https://www.wikidata.org/wiki/Q14911527","display_name":"Nonsense-mediated decay","level":5,"score":0.8439174890518188},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5243585109710693},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5231983661651611},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5170548558235168},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.4585977792739868},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.45720794796943665},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.451094388961792},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.41811349987983704},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.1692695915699005},{"id":"https://openalex.org/C54458228","wikidata":"https://www.wikidata.org/wiki/Q237218","display_name":"RNA splicing","level":4,"score":0.07241860032081604}],"mesh":[{"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":"D018389","descriptor_name":"Codon, Nonsense","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018389","descriptor_name":"Codon, Nonsense","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018389","descriptor_name":"Codon, Nonsense","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059365","descriptor_name":"Nonsense Mediated mRNA Decay","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059365","descriptor_name":"Nonsense Mediated mRNA Decay","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059365","descriptor_name":"Nonsense Mediated mRNA Decay","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad556","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad556","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad556/51472757/btad556.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:37688563","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37688563","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:pubmedcentral.nih.gov:10534055","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10534055","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10534055/pdf/btad556.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad556","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad556","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad556/51472757/btad556.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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/G209257364","display_name":null,"funder_award_id":"HL142788","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G2400632270","display_name":null,"funder_award_id":"U01 HL131003","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G355382496","display_name":null,"funder_award_id":"HL14278","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4386554478.pdf"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1820845817","https://openalex.org/W1843990841","https://openalex.org/W1974578353","https://openalex.org/W1990481833","https://openalex.org/W2002564042","https://openalex.org/W2003419284","https://openalex.org/W2011239877","https://openalex.org/W2014349878","https://openalex.org/W2018914487","https://openalex.org/W2025943989","https://openalex.org/W2049891438","https://openalex.org/W2051524933","https://openalex.org/W2066841033","https://openalex.org/W2076622465","https://openalex.org/W2106578986","https://openalex.org/W2108996658","https://openalex.org/W2109276727","https://openalex.org/W2112001822","https://openalex.org/W2113619872","https://openalex.org/W2115103369","https://openalex.org/W2127534226","https://openalex.org/W2131478115","https://openalex.org/W2136939537","https://openalex.org/W2139548637","https://openalex.org/W2145322004","https://openalex.org/W2157854512","https://openalex.org/W2164735945","https://openalex.org/W2168765940","https://openalex.org/W2286680367","https://openalex.org/W2409690503","https://openalex.org/W2473818600","https://openalex.org/W2520188071","https://openalex.org/W2599546856","https://openalex.org/W2731570147","https://openalex.org/W2748225400","https://openalex.org/W2770026599","https://openalex.org/W2804469527","https://openalex.org/W2884715896","https://openalex.org/W2947234859","https://openalex.org/W2981514644","https://openalex.org/W2995263698","https://openalex.org/W3010792510","https://openalex.org/W3029661147","https://openalex.org/W3108579746","https://openalex.org/W3157711773","https://openalex.org/W3175980491","https://openalex.org/W3177303035","https://openalex.org/W4223623159","https://openalex.org/W4225148402","https://openalex.org/W4229030223","https://openalex.org/W4242521331","https://openalex.org/W4284881539","https://openalex.org/W4289110186","https://openalex.org/W4308616307","https://openalex.org/W6824788513"],"related_works":["https://openalex.org/W2612778081","https://openalex.org/W4206766185","https://openalex.org/W2939923831","https://openalex.org/W2904625576","https://openalex.org/W2564018796","https://openalex.org/W3108579746","https://openalex.org/W3040363657","https://openalex.org/W3177373917","https://openalex.org/W2288337573","https://openalex.org/W2464653720"],"abstract_inverted_index":{"aenmd":[0],"is":[1,9],"implemented":[2],"in":[3],"the":[4],"R":[5],"programming":[6],"language.":[7],"Code":[8],"available":[10],"on":[11],"GitHub":[12],"as":[13,18],"an":[14],"R-package":[15],"(github.com/kostkalab/aenmd.git),":[16],"and":[17],"a":[19],"containerized":[20],"command-line":[21],"interface":[22],"(github.com/kostkalab/aenmd_cli.git).":[23]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
