{"id":"https://openalex.org/W4367317956","doi":"https://doi.org/10.3389/fbinf.2023.1127661","title":"Application of annotation-agnostic RNA sequencing data analysis tools for biomarker discovery in liquid biopsy","display_name":"Application of annotation-agnostic RNA sequencing data analysis tools for biomarker discovery in liquid biopsy","publication_year":2023,"publication_date":"2023-04-28","ids":{"openalex":"https://openalex.org/W4367317956","doi":"https://doi.org/10.3389/fbinf.2023.1127661","pmid":"https://pubmed.ncbi.nlm.nih.gov/37252342"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2023.1127661","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1127661","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.3389/fbinf.2023.1127661","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017570701","display_name":"Gabriel Wajnberg","orcid":"https://orcid.org/0000-0002-4479-4063"},"institutions":[{"id":"https://openalex.org/I4210137444","display_name":"Atlantic Cancer Research Institute","ror":"https://ror.org/04neva792","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210137444"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Gabriel Wajnberg","raw_affiliation_strings":["Atlantic Cancer Research Institute, Moncton, NB, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Atlantic Cancer Research Institute, Moncton, NB, Canada","institution_ids":["https://openalex.org/I4210137444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062481709","display_name":"\u00c9ric P. Allain","orcid":"https://orcid.org/0000-0003-4283-6060"},"institutions":[{"id":"https://openalex.org/I154799132","display_name":"Universit\u00e9 de Moncton","ror":"https://ror.org/029tnqt29","country_code":"CA","type":"education","lineage":["https://openalex.org/I154799132"]},{"id":"https://openalex.org/I4210087543","display_name":"Beatrice Hunter Cancer Research Institute","ror":"https://ror.org/0052qq196","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210087543"]},{"id":"https://openalex.org/I4210137444","display_name":"Atlantic Cancer Research Institute","ror":"https://ror.org/04neva792","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210137444"]},{"id":"https://openalex.org/I4210153374","display_name":"Dr. Georges-L.-Dumont University Hospital Centre","ror":"https://ror.org/04gqmrb58","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I4210153374","https://openalex.org/I4210153458"]},{"id":"https://openalex.org/I4210153458","display_name":"Vitalit\u00e9 Health Network","ror":"https://ror.org/05j242h88","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I4210153458"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Eric P. Allain","raw_affiliation_strings":["Atlantic Cancer Research Institute, Moncton, NB, Canada","Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada","Department of Chemistry and Biochemistry, Universit\u00e9 de Moncton, Moncton, NB, Canada","Department of Clinical Genetics, Vitalit\u00e9 Health Network, Dr. Georges-L.-Dumont University Hospital Centre, Moncton, NB, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Atlantic Cancer Research Institute, Moncton, NB, Canada","institution_ids":["https://openalex.org/I4210137444"]},{"raw_affiliation_string":"Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada","institution_ids":["https://openalex.org/I4210087543"]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry, Universit\u00e9 de Moncton, Moncton, NB, Canada","institution_ids":["https://openalex.org/I154799132"]},{"raw_affiliation_string":"Department of Clinical Genetics, Vitalit\u00e9 Health Network, Dr. Georges-L.-Dumont University Hospital Centre, Moncton, NB, Canada","institution_ids":["https://openalex.org/I4210153374","https://openalex.org/I4210153458"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070568182","display_name":"Jeremy Roy","orcid":"https://orcid.org/0000-0003-0126-1248"},"institutions":[{"id":"https://openalex.org/I4210087543","display_name":"Beatrice Hunter Cancer Research Institute","ror":"https://ror.org/0052qq196","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210087543"]},{"id":"https://openalex.org/I4210137444","display_name":"Atlantic Cancer Research Institute","ror":"https://ror.org/04neva792","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210137444"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jeremy W. Roy","raw_affiliation_strings":["Atlantic Cancer Research Institute, Moncton, NB, Canada","Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Atlantic Cancer Research Institute, Moncton, NB, Canada","institution_ids":["https://openalex.org/I4210137444"]},{"raw_affiliation_string":"Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada","institution_ids":["https://openalex.org/I4210087543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087192207","display_name":"Shruti Srivastava","orcid":"https://orcid.org/0000-0003-3472-7665"},"institutions":[{"id":"https://openalex.org/I4210137444","display_name":"Atlantic Cancer Research Institute","ror":"https://ror.org/04neva792","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210137444"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Shruti Srivastava","raw_affiliation_strings":["Atlantic Cancer Research Institute, Moncton, NB, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Atlantic Cancer Research Institute, Moncton, NB, Canada","institution_ids":["https://openalex.org/I4210137444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111321201","display_name":"D. Saucier","orcid":null},"institutions":[{"id":"https://openalex.org/I154799132","display_name":"Universit\u00e9 de Moncton","ror":"https://ror.org/029tnqt29","country_code":"CA","type":"education","lineage":["https://openalex.org/I154799132"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Daniel Saucier","raw_affiliation_strings":["Department of Chemistry and Biochemistry, Universit\u00e9 de Moncton, Moncton, NB, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, Universit\u00e9 de Moncton, Moncton, NB, Canada","institution_ids":["https://openalex.org/I154799132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008659188","display_name":"Pier Morin","orcid":"https://orcid.org/0000-0001-8117-0236"},"institutions":[{"id":"https://openalex.org/I154799132","display_name":"Universit\u00e9 de Moncton","ror":"https://ror.org/029tnqt29","country_code":"CA","type":"education","lineage":["https://openalex.org/I154799132"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Pier Morin","raw_affiliation_strings":["Department of Chemistry and Biochemistry, Universit\u00e9 de Moncton, Moncton, NB, Canada","Department of Chemistry and Biochemistry, Universit\u00e9 de Moncton, Moncton, NB, Canada,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, Universit\u00e9 de Moncton, Moncton, NB, Canada","institution_ids":["https://openalex.org/I154799132"]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry, Universit\u00e9 de Moncton, Moncton, NB, Canada,","institution_ids":["https://openalex.org/I154799132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111723353","display_name":"Alier Marrero","orcid":null},"institutions":[{"id":"https://openalex.org/I4210153374","display_name":"Dr. Georges-L.-Dumont University Hospital Centre","ror":"https://ror.org/04gqmrb58","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I4210153374","https://openalex.org/I4210153458"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Alier Marrero","raw_affiliation_strings":["Dr. Georges-L.-Dumont University Hospital Centre, Moncton, NB, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dr. Georges-L.-Dumont University Hospital Centre, Moncton, NB, Canada","institution_ids":["https://openalex.org/I4210153374"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020349857","display_name":"Colleen O\u2019Connell","orcid":"https://orcid.org/0000-0002-4760-4093"},"institutions":[{"id":"https://openalex.org/I4210148947","display_name":"Stan Cassidy Foundation","ror":"https://ror.org/055zm4v44","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210148947"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Colleen O\u2019Connell","raw_affiliation_strings":["Stan Cassidy Centre for Rehabilitation, Fredericton, NB, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Stan Cassidy Centre for Rehabilitation, Fredericton, NB, Canada","institution_ids":["https://openalex.org/I4210148947"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101912134","display_name":"Anirban Ghosh","orcid":"https://orcid.org/0000-0002-8735-1780"},"institutions":[{"id":"https://openalex.org/I4210137444","display_name":"Atlantic Cancer Research Institute","ror":"https://ror.org/04neva792","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210137444"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Anirban Ghosh","raw_affiliation_strings":["Atlantic Cancer Research Institute, Moncton, NB, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Atlantic Cancer Research Institute, Moncton, NB, Canada","institution_ids":["https://openalex.org/I4210137444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069233341","display_name":"Stephen M. Lewis","orcid":"https://orcid.org/0000-0001-9537-5822"},"institutions":[{"id":"https://openalex.org/I154799132","display_name":"Universit\u00e9 de Moncton","ror":"https://ror.org/029tnqt29","country_code":"CA","type":"education","lineage":["https://openalex.org/I154799132"]},{"id":"https://openalex.org/I4210087543","display_name":"Beatrice Hunter Cancer Research Institute","ror":"https://ror.org/0052qq196","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210087543"]},{"id":"https://openalex.org/I4210137444","display_name":"Atlantic Cancer Research Institute","ror":"https://ror.org/04neva792","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210137444"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Stephen M. Lewis","raw_affiliation_strings":["Atlantic Cancer Research Institute, Moncton, NB, Canada","Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada","Department of Chemistry and Biochemistry, Universit\u00e9 de Moncton, Moncton, NB, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Atlantic Cancer Research Institute, Moncton, NB, Canada","institution_ids":["https://openalex.org/I4210137444"]},{"raw_affiliation_string":"Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada","institution_ids":["https://openalex.org/I4210087543"]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry, Universit\u00e9 de Moncton, Moncton, NB, Canada","institution_ids":["https://openalex.org/I154799132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086316706","display_name":"Rodney J. Ouellette","orcid":"https://orcid.org/0000-0002-2281-2769"},"institutions":[{"id":"https://openalex.org/I154799132","display_name":"Universit\u00e9 de Moncton","ror":"https://ror.org/029tnqt29","country_code":"CA","type":"education","lineage":["https://openalex.org/I154799132"]},{"id":"https://openalex.org/I4210087543","display_name":"Beatrice Hunter Cancer Research Institute","ror":"https://ror.org/0052qq196","country_code":"CA","type":"facility","lineage":["https://openalex.org/I4210087543"]},{"id":"https://openalex.org/I4210137444","display_name":"Atlantic Cancer Research Institute","ror":"https://ror.org/04neva792","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210137444"]},{"id":"https://openalex.org/I4210153374","display_name":"Dr. Georges-L.-Dumont University Hospital Centre","ror":"https://ror.org/04gqmrb58","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I4210153374","https://openalex.org/I4210153458"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Rodney J. Ouellette","raw_affiliation_strings":["Atlantic Cancer Research Institute, Moncton, NB, Canada","Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada","Department of Chemistry and Biochemistry, Universit\u00e9 de Moncton, Moncton, NB, Canada","Dr. Georges-L.-Dumont University Hospital Centre, Moncton, NB, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Atlantic Cancer Research Institute, Moncton, NB, Canada","institution_ids":["https://openalex.org/I4210137444"]},{"raw_affiliation_string":"Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada","institution_ids":["https://openalex.org/I4210087543"]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry, Universit\u00e9 de Moncton, Moncton, NB, Canada","institution_ids":["https://openalex.org/I154799132"]},{"raw_affiliation_string":"Dr. Georges-L.-Dumont University Hospital Centre, Moncton, NB, Canada","institution_ids":["https://openalex.org/I4210153374"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014390881","display_name":"Nicolas Crapoulet","orcid":"https://orcid.org/0000-0002-7832-6196"},"institutions":[{"id":"https://openalex.org/I4210137444","display_name":"Atlantic Cancer Research Institute","ror":"https://ror.org/04neva792","country_code":"CA","type":"nonprofit","lineage":["https://openalex.org/I4210137444"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Nicolas Crapoulet","raw_affiliation_strings":["Atlantic Cancer Research Institute, Moncton, NB, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Atlantic Cancer Research Institute, Moncton, NB, Canada","institution_ids":["https://openalex.org/I4210137444"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5014390881"],"corresponding_institution_ids":["https://openalex.org/I4210137444"],"apc_list":{"value":2550,"currency":"CHF","value_usd":3077},"apc_paid":{"value":2550,"currency":"CHF","value_usd":3077},"fwci":0.5528,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.60839731,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"3","issue":null,"first_page":"1127661","last_page":"1127661"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"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"}},"topics":[{"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/T10604","display_name":"RNA Research and Splicing","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"}},{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.9918000102043152,"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/computational-biology","display_name":"Computational biology","score":0.6442310214042664},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5376381278038025},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4986844062805176},{"id":"https://openalex.org/keywords/biomarker-discovery","display_name":"Biomarker discovery","score":0.4855460822582245},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4602438807487488},{"id":"https://openalex.org/keywords/sequence-analysis","display_name":"Sequence analysis","score":0.4435345232486725},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3899691104888916},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3465326726436615},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.25277581810951233},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.21921667456626892},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1272532045841217}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6442310214042664},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5376381278038025},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4986844062805176},{"id":"https://openalex.org/C124535831","wikidata":"https://www.wikidata.org/wiki/Q4915074","display_name":"Biomarker discovery","level":4,"score":0.4855460822582245},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4602438807487488},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.4435345232486725},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3899691104888916},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3465326726436615},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.25277581810951233},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.21921667456626892},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1272532045841217}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2023.1127661","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1127661","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37252342","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37252342","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":"Frontiers in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10213969","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10213969","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10213969/pdf/fbinf-03-1127661.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"Front Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:25203c6510e94eb1b769c6c31a326ea8","is_oa":true,"landing_page_url":"https://doaj.org/article/25203c6510e94eb1b769c6c31a326ea8","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 3 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2023.1127661","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1127661","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W1600420628","https://openalex.org/W1954530082","https://openalex.org/W2052785172","https://openalex.org/W2069041912","https://openalex.org/W2104005232","https://openalex.org/W2108234281","https://openalex.org/W2109525082","https://openalex.org/W2112876600","https://openalex.org/W2114104545","https://openalex.org/W2124985265","https://openalex.org/W2130305733","https://openalex.org/W2130386995","https://openalex.org/W2134526812","https://openalex.org/W2138207763","https://openalex.org/W2140910902","https://openalex.org/W2147495091","https://openalex.org/W2151883199","https://openalex.org/W2523875478","https://openalex.org/W2735264627","https://openalex.org/W2765992771","https://openalex.org/W2769912973","https://openalex.org/W2777367343","https://openalex.org/W2786514708","https://openalex.org/W2801917323","https://openalex.org/W2887110521","https://openalex.org/W2887329987","https://openalex.org/W2898731714","https://openalex.org/W2899540665","https://openalex.org/W2900059354","https://openalex.org/W2900756811","https://openalex.org/W2904034429","https://openalex.org/W2919278937","https://openalex.org/W2928729781","https://openalex.org/W2945288061","https://openalex.org/W2952114411","https://openalex.org/W2952421891","https://openalex.org/W2952874835","https://openalex.org/W2983152401","https://openalex.org/W3185328556","https://openalex.org/W3196004732"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W1533177136","https://openalex.org/W4380994516","https://openalex.org/W2556260348"],"abstract_inverted_index":{"RNA":[0,21,96],"sequencing":[1,97],"analysis":[2,47,85,94,115,151,184],"is":[3],"an":[4],"important":[5],"field":[6],"in":[7,73,136,169],"the":[8,33,93,129,150],"study":[9],"of":[10,20,32,48,54,86,95,120,131,152,163],"extracellular":[11],"vesicles":[12],"(EVs),":[13],"as":[14,167,197],"these":[15,57,175],"particles":[16],"contain":[17],"a":[18,83,182],"variety":[19],"species":[22],"that":[23,141,174],"may":[24,58,67,192],"have":[25],"diagnostic,":[26],"prognostic":[27],"and":[28,88,110,116,127,155,191],"predictive":[29],"value.":[30],"Many":[31],"bioinformatics":[34],"tools":[35,91,148,176],"currently":[36],"used":[37,72,180],"to":[38,62,146],"analyze":[39],"EV":[40],"cargo":[41],"rely":[42],"on":[43],"third-party":[44],"annotations.":[45],"Recently,":[46],"unannotated":[49,121,159],"expressed":[50,160],"RNAs":[51,122],"has":[52],"become":[53],"interest,":[55],"since":[56],"provide":[59],"complementary":[60],"information":[61],"traditional":[63],"annotated":[64],"biomarkers":[65,135],"or":[66,185],"help":[68],"refine":[69],"biological":[70],"signatures":[71],"machine":[74],"learning":[75],"by":[76],"including":[77,132],"unknown":[78],"regions.":[79],"Here":[80],"we":[81],"perform":[82,144],"comparative":[84],"annotation-free":[87],"classical":[89],"read-summarization":[90],"for":[92,100,149,181,195],"data":[98],"generated":[99],"EVs":[101],"isolated":[102],"from":[103],"persons":[104],"with":[105],"amyotrophic":[106],"lateral":[107],"sclerosis":[108],"(ALS)":[109],"healthy":[111],"donors.":[112],"Differential":[113],"expression":[114],"digital-droplet":[117],"PCR":[118],"validation":[119],"also":[123,157],"confirmed":[124],"their":[125],"existence":[126],"demonstrates":[128],"usefulness":[130],"such":[133],"potential":[134],"transcriptome":[137],"analysis.":[138],"We":[139,172],"show":[140],"find-then-annotate":[142],"methods":[143],"similarly":[145],"standard":[147],"known":[153],"features,":[154],"can":[156,177,199],"identify":[158],"RNAs,":[161],"two":[162],"which":[164],"were":[165],"validated":[166],"overexpressed":[168],"ALS":[170],"samples.":[171],"demonstrate":[173],"therefore":[178],"be":[179,193,200],"stand-alone":[183],"easily":[186],"integrated":[187,201],"into":[188],"current":[189],"workflows":[190],"useful":[194],"re-analysis":[196],"annotations":[198],"post":[202],"hoc.":[203]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}