{"id":"https://openalex.org/W2883239502","doi":"https://doi.org/10.1186/s12859-018-2266-3","title":"trumpet: transcriptome-guided quality assessment of m6A-seq data","display_name":"trumpet: transcriptome-guided quality assessment of m6A-seq data","publication_year":2018,"publication_date":"2018-07-13","ids":{"openalex":"https://openalex.org/W2883239502","doi":"https://doi.org/10.1186/s12859-018-2266-3","mag":"2883239502","pmid":"https://pubmed.ncbi.nlm.nih.gov/30001693"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2266-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2266-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2266-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2266-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100372521","display_name":"Teng Zhang","orcid":"https://orcid.org/0000-0003-2495-6368"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Teng Zhang","raw_affiliation_strings":["Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an, 710027, Shaanxi, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an, 710027, Shaanxi, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061712236","display_name":"Shao\u2010Wu Zhang","orcid":"https://orcid.org/0000-0003-1305-7447"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shao-Wu Zhang","raw_affiliation_strings":["Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an, 710027, Shaanxi, China. zhangsw@nwpu.edu.cn","Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an, 710027, Shaanxi, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an, 710027, Shaanxi, China. zhangsw@nwpu.edu.cn","institution_ids":[]},{"raw_affiliation_string":"Key Laboratory of Information Fusion Technology of Ministry of Education, School of Automation, Northwestern Polytechnical University, Xi'an, 710027, Shaanxi, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100351875","display_name":"Lin Zhang","orcid":"https://orcid.org/0000-0002-7404-5231"},"institutions":[{"id":"https://openalex.org/I25757504","display_name":"China University of Mining and Technology","ror":"https://ror.org/01xt2dr21","country_code":"CN","type":"education","lineage":["https://openalex.org/I25757504"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Zhang","raw_affiliation_strings":["School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, Jiangsu, China"],"affiliations":[{"raw_affiliation_string":"School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, Jiangsu, China","institution_ids":["https://openalex.org/I25757504"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062986831","display_name":"Jia Meng","orcid":"https://orcid.org/0000-0003-3455-205X"},"institutions":[{"id":"https://openalex.org/I69356397","display_name":"Xi\u2019an Jiaotong-Liverpool University","ror":"https://ror.org/03zmrmn05","country_code":"CN","type":"education","lineage":["https://openalex.org/I69356397"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jia Meng","raw_affiliation_strings":["Department of Biological Sciences, Research Center for Precision Medicine, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, Jiangsu, China. jia.meng@xjtlu.edu.cn","Institute of Integrative Biology, University of Liverpool, L7 8TX, Liverpool, UK. jia.meng@xjtlu.edu.cn","Department of Biological Sciences, Research Center for Precision Medicine, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, Jiangsu, China"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, Research Center for Precision Medicine, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, Jiangsu, China. jia.meng@xjtlu.edu.cn","institution_ids":[]},{"raw_affiliation_string":"Institute of Integrative Biology, University of Liverpool, L7 8TX, Liverpool, UK. jia.meng@xjtlu.edu.cn","institution_ids":[]},{"raw_affiliation_string":"Department of Biological Sciences, Research Center for Precision Medicine, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, Jiangsu, China","institution_ids":["https://openalex.org/I69356397"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5062986831"],"corresponding_institution_ids":["https://openalex.org/I69356397"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.7447,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.70554249,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"19","issue":"1","first_page":"260","last_page":"260"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":1.0,"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/T11482","display_name":"RNA modifications and cancer","score":1.0,"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":0.9843999743461609,"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"}},{"id":"https://openalex.org/T13157","display_name":"Cancer-related gene regulation","score":0.9733999967575073,"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/rna-seq","display_name":"RNA-Seq","score":0.6995851993560791},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.6424915790557861},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5822980403900146},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.555708110332489},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.4851280152797699},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4622502028942108},{"id":"https://openalex.org/keywords/data-quality","display_name":"Data quality","score":0.43252891302108765},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.43051719665527344},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4304746389389038},{"id":"https://openalex.org/keywords/quality-assessment","display_name":"Quality assessment","score":0.4297887980937958},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37608885765075684},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3082577586174011},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17173582315444946},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15996503829956055},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.13487368822097778},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08433124423027039},{"id":"https://openalex.org/keywords/evaluation-methods","display_name":"Evaluation methods","score":0.0665421187877655}],"concepts":[{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.6995851993560791},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.6424915790557861},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5822980403900146},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.555708110332489},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.4851280152797699},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4622502028942108},{"id":"https://openalex.org/C24756922","wikidata":"https://www.wikidata.org/wiki/Q1757694","display_name":"Data quality","level":3,"score":0.43252891302108765},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.43051719665527344},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4304746389389038},{"id":"https://openalex.org/C3020001037","wikidata":"https://www.wikidata.org/wiki/Q836575","display_name":"Quality assessment","level":3,"score":0.4297887980937958},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37608885765075684},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3082577586174011},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17173582315444946},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15996503829956055},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.13487368822097778},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08433124423027039},{"id":"https://openalex.org/C3018395757","wikidata":"https://www.wikidata.org/wiki/Q1379672","display_name":"Evaluation methods","level":2,"score":0.0665421187877655},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C200601418","wikidata":"https://www.wikidata.org/wiki/Q2193887","display_name":"Reliability engineering","level":1,"score":0.0},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0}],"mesh":[{"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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-018-2266-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2266-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2266-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30001693","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30001693","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:ab37ae7bcf6c4d6086299b5d35ccc3c6","is_oa":true,"landing_page_url":"https://doaj.org/article/ab37ae7bcf6c4d6086299b5d35ccc3c6","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 19, Iss 1, Pp 1-11 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4997400","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6044007","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:10.1186/s12859-018-2266-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2266-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2266-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1427182054","display_name":null,"funder_award_id":"16KJB180027","funder_id":"https://openalex.org/F4320321410","funder_display_name":"Jiangsu University"},{"id":"https://openalex.org/G2763083788","display_name":null,"funder_award_id":"31671373","funder_id":"https://openalex.org/F4320321410","funder_display_name":"Jiangsu University"}],"funders":[{"id":"https://openalex.org/F4320310677","display_name":"University of Texas at San Antonio","ror":"https://ror.org/01kd65564"},{"id":"https://openalex.org/F4320321410","display_name":"Jiangsu University","ror":"https://ror.org/03jc41j30"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2883239502.pdf","grobid_xml":"https://content.openalex.org/works/W2883239502.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1820614038","https://openalex.org/W1981509058","https://openalex.org/W1991807334","https://openalex.org/W2007429249","https://openalex.org/W2009002761","https://openalex.org/W2015696149","https://openalex.org/W2065847836","https://openalex.org/W2071930821","https://openalex.org/W2078964320","https://openalex.org/W2085928743","https://openalex.org/W2102872651","https://openalex.org/W2111281047","https://openalex.org/W2127653962","https://openalex.org/W2127779221","https://openalex.org/W2131478115","https://openalex.org/W2132762486","https://openalex.org/W2137586531","https://openalex.org/W2160443244","https://openalex.org/W2161890613","https://openalex.org/W2166153887","https://openalex.org/W2271549028","https://openalex.org/W2271995006","https://openalex.org/W2335010255","https://openalex.org/W2546967042","https://openalex.org/W2566386603","https://openalex.org/W2572064190","https://openalex.org/W2584435361","https://openalex.org/W2752930292","https://openalex.org/W2767731367","https://openalex.org/W2768833223","https://openalex.org/W2806565274","https://openalex.org/W2808337257","https://openalex.org/W2808441339","https://openalex.org/W4230831850"],"related_works":["https://openalex.org/W2589019771","https://openalex.org/W2985540061","https://openalex.org/W4200033037","https://openalex.org/W4287867321","https://openalex.org/W1596854558","https://openalex.org/W2902823524","https://openalex.org/W4245815800","https://openalex.org/W2499364091","https://openalex.org/W4244016743","https://openalex.org/W4214700692"],"abstract_inverted_index":{"The":[0],"trumpet":[1],"R":[2],"package":[3],"makes":[4],"a":[5],"valuable":[6],"tool":[7],"for":[8],"assessing":[9],"the":[10],"data":[11],"quality":[12],"of":[13],"m<sup>6</sup>A-seq,":[14],"and":[15],"it":[16],"is":[17],"also":[18],"applicable":[19],"to":[20],"other":[21],"fragmented":[22],"RNA":[23],"immunoprecipitation":[24],"sequencing":[25],"techniques,":[26],"including":[27],"m<sup>1</sup>A-seq,":[28],"CeU-Seq,":[29],"\u03a8-seq,":[30],"etc.":[31]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2018-08-03T00:00:00"}