{"id":"https://openalex.org/W3089953766","doi":"https://doi.org/10.1093/bioinformatics/btaa859","title":"VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data","display_name":"VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data","publication_year":2020,"publication_date":"2020-09-21","ids":{"openalex":"https://openalex.org/W3089953766","doi":"https://doi.org/10.1093/bioinformatics/btaa859","mag":"3089953766","pmid":"https://pubmed.ncbi.nlm.nih.gov/33017003"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa859","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa859","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/10/1465/38663701/btaa859.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/10/1465/38663701/btaa859.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022153955","display_name":"Yoshiaki Yasumizu","orcid":"https://orcid.org/0000-0002-9872-4909"},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshiaki Yasumizu","raw_affiliation_strings":["Osaka University Department of Experimental Immunology, Immunology Frontier Research Center, , Osaka 565-0871, Japan"],"affiliations":[{"raw_affiliation_string":"Osaka University Department of Experimental Immunology, Immunology Frontier Research Center, , Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108944564","display_name":"Atsushi Hara","orcid":null},"institutions":[{"id":"https://openalex.org/I64926303","display_name":"Nara Medical University","ror":"https://ror.org/045ysha14","country_code":"JP","type":"education","lineage":["https://openalex.org/I64926303"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Atsushi Hara","raw_affiliation_strings":["Nara Medical University Department of Immunology, , Kashihara, Nara 634-8521, Japan"],"affiliations":[{"raw_affiliation_string":"Nara Medical University Department of Immunology, , Kashihara, Nara 634-8521, Japan","institution_ids":["https://openalex.org/I64926303"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025764166","display_name":"Shimon Sakaguchi","orcid":"https://orcid.org/0000-0001-8265-6094"},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Shimon Sakaguchi","raw_affiliation_strings":["Osaka University Department of Experimental Immunology, Immunology Frontier Research Center, , Osaka 565-0871, Japan"],"affiliations":[{"raw_affiliation_string":"Osaka University Department of Experimental Immunology, Immunology Frontier Research Center, , Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042599703","display_name":"Naganari Ohkura","orcid":null},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Naganari Ohkura","raw_affiliation_strings":["Osaka University Department of Experimental Immunology, Immunology Frontier Research Center, , Osaka 565-0871, Japan"],"affiliations":[{"raw_affiliation_string":"Osaka University Department of Experimental Immunology, Immunology Frontier Research Center, , Osaka 565-0871, Japan","institution_ids":["https://openalex.org/I98285908"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5025764166","https://openalex.org/A5042599703"],"corresponding_institution_ids":["https://openalex.org/I98285908"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.769,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.84064194,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"37","issue":"10","first_page":"1465","last_page":"1467"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9937000274658203,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9937000274658203,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11495","display_name":"Animal Virus Infections Studies","score":0.9912999868392944,"subfield":{"id":"https://openalex.org/subfields/1103","display_name":"Animal Science and Zoology"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10976","display_name":"Viral gastroenteritis research and epidemiology","score":0.974399983882904,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.741113007068634},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.558927059173584},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5484732389450073},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4899443984031677},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4217666983604431},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.306807279586792},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.22927692532539368},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19010114669799805},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1572650969028473},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.14110425114631653},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1074848473072052}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.741113007068634},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.558927059173584},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5484732389450073},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4899443984031677},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4217666983604431},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.306807279586792},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.22927692532539368},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19010114669799805},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1572650969028473},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.14110425114631653},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1074848473072052}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa859","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa859","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/10/1465/38663701/btaa859.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33017003","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33017003","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:7745649","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7745649","pdf_url":null,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa859","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa859","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/10/1465/38663701/btaa859.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.4300000071525574,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G1307691974","display_name":null,"funder_award_id":"B 15H04744","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G1369108393","display_name":null,"funder_award_id":"15H04744","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G1735162682","display_name":null,"funder_award_id":"17 gm0410016h0006","funder_id":"https://openalex.org/F4320338075","funder_display_name":"Core Research for Evolutional Science and Technology"},{"id":"https://openalex.org/G1755812565","display_name":null,"funder_award_id":"Japan Science and Technology Agency","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G179417612","display_name":null,"funder_award_id":"Scientific Research B","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G1993181957","display_name":"\u4eba\u683c\u7814\u7a76\u306b\u304a\u3051\u308b\u7d75\u753b\u523a\u6fc0\u6761\u4ef6\u306e\u57fa\u790e\u7684\u7814\u7a76","funder_award_id":"10016","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G2178869851","display_name":"\u8ee2\u63db\u671f\u306b\u304a\u3051\u308b\u793e\u5bfa\u3068\u793e\u4f1a\u306e\u7dcf\u5408\u7684\u6bd4\u8f03\u7814\u7a76","funder_award_id":"041001","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G2521286739","display_name":null,"funder_award_id":"CREST","funder_id":"https://openalex.org/F4320334789","funder_display_name":"Japan Science and Technology Agency"},{"id":"https://openalex.org/G2576085165","display_name":null,"funder_award_id":"CREST","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G2972834904","display_name":null,"funder_award_id":"gm0010005h0001","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G3017254386","display_name":null,"funder_award_id":"16H06295","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G3708579941","display_name":null,"funder_award_id":"16H0629","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4381687251","display_name":null,"funder_award_id":"h0001","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G5706980351","display_name":null,"funder_award_id":"Japanese Society for the Promotion of Science","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5731184981","display_name":null,"funder_award_id":"18 gm0010005h0001","funder_id":"https://openalex.org/F4320334789","funder_display_name":"Japan Science and Technology Agency"},{"id":"https://openalex.org/G664615684","display_name":"\u30ab\u30a6\u30f3\u30bb\u30ea\u30f3\u30b0\u904e\u7a0b\u306e\u30d7\u30ed\u30b0\u30e9\u30df\u30f3\u30b0\u306b\u95a2\u3059\u308b\u57fa\u790e\u7814\u7a76(\u7279\u306b\u9032\u8def\u76f8\u8ac7)","funder_award_id":"10005","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G6718509927","display_name":null,"funder_award_id":"CREST","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8345629862","display_name":null,"funder_award_id":"06295","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8512173905","display_name":null,"funder_award_id":"17 gm0410016h0006","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320334789","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19"},{"id":"https://openalex.org/F4320338075","display_name":"Core Research for Evolutional Science and Technology","ror":"https://ror.org/00097mb19"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3089953766.pdf","grobid_xml":"https://content.openalex.org/works/W3089953766.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W2169456326","https://openalex.org/W2556559016","https://openalex.org/W2592811885","https://openalex.org/W2603488895","https://openalex.org/W2803062674","https://openalex.org/W2906848853","https://openalex.org/W2919861422","https://openalex.org/W2944073176","https://openalex.org/W2951912016","https://openalex.org/W2963954504","https://openalex.org/W2981445981","https://openalex.org/W2990618091","https://openalex.org/W3005400930","https://openalex.org/W3005510968"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
