{"id":"https://openalex.org/W4288384163","doi":"https://doi.org/10.1093/bib/bbac310","title":"EVAtool: an optimized reads assignment tool for small ncRNA quantification and its application in extracellular vesicle datasets","display_name":"EVAtool: an optimized reads assignment tool for small ncRNA quantification and its application in extracellular vesicle datasets","publication_year":2022,"publication_date":"2022-07-28","ids":{"openalex":"https://openalex.org/W4288384163","doi":"https://doi.org/10.1093/bib/bbac310","pmid":"https://pubmed.ncbi.nlm.nih.gov/35901462"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac310","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac310","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001641983","display_name":"Gui\u2010Yan Xie","orcid":"https://orcid.org/0000-0002-2924-5306"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gui-Yan Xie","raw_affiliation_strings":["Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology ; Wuhan, 430074, China","Wuhan, 430074, China"],"raw_orcid":"https://orcid.org/0000-0002-2924-5306","affiliations":[{"raw_affiliation_string":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology ; Wuhan, 430074, China","institution_ids":["https://openalex.org/I47720641"]},{"raw_affiliation_string":"Wuhan, 430074, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086401733","display_name":"Chunjie Liu","orcid":"https://orcid.org/0000-0002-3008-3375"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chun-Jie Liu","raw_affiliation_strings":["Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology ; Wuhan, 430074, China","Wuhan, 430074, China"],"raw_orcid":"https://orcid.org/0000-0002-3008-3375","affiliations":[{"raw_affiliation_string":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology ; Wuhan, 430074, China","institution_ids":["https://openalex.org/I47720641"]},{"raw_affiliation_string":"Wuhan, 430074, China","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009558607","display_name":"An\u2010Yuan Guo","orcid":"https://orcid.org/0000-0002-5099-7465"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"An-Yuan Guo","raw_affiliation_strings":["Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology ; Wuhan, 430074, China","Shenzhen Huazhong University of Science and Technology Research Institute , Shenzhen, China","Wuhan, 430074, China"],"raw_orcid":"https://orcid.org/0000-0002-5099-7465","affiliations":[{"raw_affiliation_string":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology ; Wuhan, 430074, China","institution_ids":["https://openalex.org/I47720641"]},{"raw_affiliation_string":"Shenzhen Huazhong University of Science and Technology Research Institute , Shenzhen, China","institution_ids":["https://openalex.org/I47720641"]},{"raw_affiliation_string":"Wuhan, 430074, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5009558607","https://openalex.org/A5086401733"],"corresponding_institution_ids":["https://openalex.org/I47720641"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.4744,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.57479255,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"23","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":1.0,"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"}},"topics":[{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":1.0,"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/T10773","display_name":"Extracellular vesicles in disease","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/T11482","display_name":"RNA modifications and cancer","score":0.9990000128746033,"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/computational-biology","display_name":"Computational biology","score":0.6561753749847412},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.6432625651359558},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6250841617584229},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6140301823616028},{"id":"https://openalex.org/keywords/small-rna","display_name":"Small RNA","score":0.5926440358161926},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.4243104159832001},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.41561487317085266},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35650312900543213},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2517457604408264},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15216922760009766},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1323244571685791}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6561753749847412},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.6432625651359558},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6250841617584229},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6140301823616028},{"id":"https://openalex.org/C2779341050","wikidata":"https://www.wikidata.org/wiki/Q24287527","display_name":"Small RNA","level":4,"score":0.5926440358161926},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.4243104159832001},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.41561487317085266},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35650312900543213},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2517457604408264},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15216922760009766},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1323244571685791}],"mesh":[{"descriptor_ui":"D000067128","descriptor_name":"Extracellular Vesicles","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000067128","descriptor_name":"Extracellular Vesicles","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000067128","descriptor_name":"Extracellular Vesicles","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000067128","descriptor_name":"Extracellular Vesicles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000067128","descriptor_name":"Extracellular Vesicles","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000067128","descriptor_name":"Extracellular Vesicles","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D009103","descriptor_name":"Multiple Sclerosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009103","descriptor_name":"Multiple Sclerosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009103","descriptor_name":"Multiple Sclerosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012335","descriptor_name":"RNA, Ribosomal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012335","descriptor_name":"RNA, Ribosomal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012335","descriptor_name":"RNA, Ribosomal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012342","descriptor_name":"RNA, Small Nuclear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012342","descriptor_name":"RNA, Small Nuclear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012342","descriptor_name":"RNA, Small Nuclear","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012343","descriptor_name":"RNA, Transfer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","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":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D034741","descriptor_name":"RNA, Small Interfering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D058727","descriptor_name":"RNA, Small Untranslated","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac310","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac310","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35901462","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35901462","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G387474504","display_name":null,"funder_award_id":"JCYJ20210324141814037","funder_id":"https://openalex.org/F4320326705","funder_display_name":"Science, Technology and Innovation Commission of Shenzhen Municipality"}],"funders":[{"id":"https://openalex.org/F4320326705","display_name":"Science, Technology and Innovation Commission of Shenzhen Municipality","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W1486010693","https://openalex.org/W1990820461","https://openalex.org/W2013210832","https://openalex.org/W2053342030","https://openalex.org/W2070777085","https://openalex.org/W2102619694","https://openalex.org/W2131271579","https://openalex.org/W2134809456","https://openalex.org/W2170551349","https://openalex.org/W2170852633","https://openalex.org/W2172932999","https://openalex.org/W2311489434","https://openalex.org/W2763782267","https://openalex.org/W2768096340","https://openalex.org/W2797673761","https://openalex.org/W2904267251","https://openalex.org/W2904802348","https://openalex.org/W2928729781","https://openalex.org/W2956588751","https://openalex.org/W2988725512","https://openalex.org/W3011296395","https://openalex.org/W3011689356","https://openalex.org/W3119681197","https://openalex.org/W3192067290"],"related_works":["https://openalex.org/W2144339761","https://openalex.org/W4382982721","https://openalex.org/W2058984380","https://openalex.org/W1988125422","https://openalex.org/W1504075687","https://openalex.org/W2900182103","https://openalex.org/W4365136234","https://openalex.org/W2100652475","https://openalex.org/W3183769948","https://openalex.org/W2285854411"],"abstract_inverted_index":{"Extracellular":[0],"vesicles":[1],"(EVs)":[2],"carrying":[3],"various":[4],"small":[5,106,111],"non-coding":[6],"RNAs":[7],"(sncRNAs)":[8],"play":[9],"a":[10,28,66,179],"vital":[11],"roles":[12],"in":[13,25,97,159,194],"cell":[14],"communication":[15],"and":[16,118,139,181,191],"diseases.":[17],"Correct":[18],"quantification":[19],"of":[20,125,148,167],"multiple":[21,41,140,156,160],"sncRNA":[22,42,63,95,130,157,175],"biotypes":[23,158],"simultaneously":[24],"EVs":[26],"is":[27,170,178],"challenge":[29],"due":[30],"to":[31,40,56,61,80,92,155,187],"the":[32,62,123,129,165],"short":[33,149],"reads":[34,52,60,73,150],"(<30":[35],"bp)":[36],"could":[37],"be":[38],"mapped":[39,154],"types.":[43,176],"To":[44,121],"address":[45],"this":[46],"question,":[47],"we":[48,127],"developed":[49],"an":[50],"optimized":[51],"assignment":[53],"algorithm":[54],"(ORAA)":[55],"dynamically":[57],"map":[58],"multi-mapping":[59],"type":[64],"with":[65,72],"higher":[67,172],"proportion.":[68],"We":[69,142],"integrated":[70],"ORAA":[71],"processing":[74],"steps":[75],"into":[76],"EVAtool":[77,89,177],"Python-package":[78],"(http://bioinfo.life.hust.edu.cn/EVAtool)":[79],"quantify":[81],"sncRNAs,":[82],"especially":[83],"for":[84,133],"sncRNA-seq":[85],"from":[86,136],"EV":[87],"samples.":[88],"allows":[90],"users":[91],"specify":[93],"interested":[94],"types":[96],"advanced":[98],"mode":[99],"or":[100],"use":[101],"default":[102],"seven":[103],"sncRNAs":[104],"(microRNA,":[105],"nucleolar":[107],"RNA,":[108,113,115],"PIWI-interacting":[109],"RNAs,":[110],"nuclear":[112],"ribosomal":[114],"transfer":[116],"RNA":[117,169],"Y":[119,168],"RNA).":[120],"prove":[122],"utilities":[124],"EVAtool,":[126],"quantified":[128],"expression":[131],"profiles":[132],"200":[134],"samples":[135],"cognitive":[137,163],"decline":[138],"sclerosis.":[141,161],"found":[143],"that":[144,184],"more":[145],"than":[146,173],"20%":[147],"on":[151],"average":[152],"were":[153],"In":[162],"decline,":[164],"proportion":[166],"significantly":[171],"other":[174],"flexible":[180],"extensible":[182],"tool":[183],"would":[185],"benefit":[186],"mine":[188],"potential":[189],"biomarkers":[190],"functional":[192],"molecules":[193],"EVs.":[195]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
