{"id":"https://openalex.org/W4404022077","doi":"https://doi.org/10.1093/bioinformatics/btae651","title":"Quantifying defective and wild-type viruses from high-throughput RNA sequencing","display_name":"Quantifying defective and wild-type viruses from high-throughput RNA sequencing","publication_year":2024,"publication_date":"2024-10-29","ids":{"openalex":"https://openalex.org/W4404022077","doi":"https://doi.org/10.1093/bioinformatics/btae651","pmid":"https://pubmed.ncbi.nlm.nih.gov/39495116"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae651","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae651","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btae651","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054164179","display_name":"Juan C. Mu\u00f1oz-S\u00e1nchez","orcid":"https://orcid.org/0000-0002-5570-4983"},"institutions":[{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]},{"id":"https://openalex.org/I4210152685","display_name":"Institute for Integrative Systems Biology","ror":"https://ror.org/05jw4kp39","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I16097986","https://openalex.org/I4210152685"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Juan C Mu\u00f1oz-S\u00e1nchez","raw_affiliation_strings":["Departament de F\u00edsica Te\u00f2rica, Universitat de Val\u00e8ncia , Burjassot, Val\u00e8ncia 46100,","Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de Val\u00e8ncia , Paterna, Val\u00e8ncia 46980,"],"raw_orcid":"https://orcid.org/0000-0002-5570-4983","affiliations":[{"raw_affiliation_string":"Departament de F\u00edsica Te\u00f2rica, Universitat de Val\u00e8ncia , Burjassot, Val\u00e8ncia 46100,","institution_ids":["https://openalex.org/I16097986"]},{"raw_affiliation_string":"Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de Val\u00e8ncia , Paterna, Val\u00e8ncia 46980,","institution_ids":["https://openalex.org/I4210152685","https://openalex.org/I16097986"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005813023","display_name":"Mar\u00eda J. Olmo-Uceda","orcid":"https://orcid.org/0000-0001-8570-424X"},"institutions":[{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]},{"id":"https://openalex.org/I4210152685","display_name":"Institute for Integrative Systems Biology","ror":"https://ror.org/05jw4kp39","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I16097986","https://openalex.org/I4210152685"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Mar\u00eda J Olmo-Uceda","raw_affiliation_strings":["Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de Val\u00e8ncia , Paterna, Val\u00e8ncia 46980,"],"raw_orcid":"https://orcid.org/0000-0001-8570-424X","affiliations":[{"raw_affiliation_string":"Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de Val\u00e8ncia , Paterna, Val\u00e8ncia 46980,","institution_ids":["https://openalex.org/I4210152685","https://openalex.org/I16097986"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076329468","display_name":"J A Oteo","orcid":"https://orcid.org/0000-0003-1682-5798"},"institutions":[{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]},{"id":"https://openalex.org/I4210152685","display_name":"Institute for Integrative Systems Biology","ror":"https://ror.org/05jw4kp39","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I16097986","https://openalex.org/I4210152685"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Jos\u00e9-\u00c1ngel Oteo","raw_affiliation_strings":["Departament de F\u00edsica Te\u00f2rica, Universitat de Val\u00e8ncia , Burjassot, Val\u00e8ncia 46100,","Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de Val\u00e8ncia , Paterna, Val\u00e8ncia 46980,"],"raw_orcid":"https://orcid.org/0000-0003-1682-5798","affiliations":[{"raw_affiliation_string":"Departament de F\u00edsica Te\u00f2rica, Universitat de Val\u00e8ncia , Burjassot, Val\u00e8ncia 46100,","institution_ids":["https://openalex.org/I16097986"]},{"raw_affiliation_string":"Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de Val\u00e8ncia , Paterna, Val\u00e8ncia 46980,","institution_ids":["https://openalex.org/I4210152685","https://openalex.org/I16097986"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5001395924","display_name":"Santiago F. Elena","orcid":"https://orcid.org/0000-0001-8249-5593"},"institutions":[{"id":"https://openalex.org/I1308548392","display_name":"Santa Fe Institute","ror":"https://ror.org/01arysc35","country_code":"US","type":"funder","lineage":["https://openalex.org/I1308548392"]},{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]},{"id":"https://openalex.org/I4210152685","display_name":"Institute for Integrative Systems Biology","ror":"https://ror.org/05jw4kp39","country_code":"ES","type":"facility","lineage":["https://openalex.org/I134820265","https://openalex.org/I16097986","https://openalex.org/I4210152685"]}],"countries":["ES","US"],"is_corresponding":false,"raw_author_name":"Santiago F Elena","raw_affiliation_strings":["Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de Val\u00e8ncia , Paterna, Val\u00e8ncia 46980,","Santa Fe Institute , Santa Fe, NM 87501,"],"raw_orcid":"https://orcid.org/0000-0001-8249-5593","affiliations":[{"raw_affiliation_string":"Institute for Integrative Systems Biology (I2SysBio), CSIC-Universitat de Val\u00e8ncia , Paterna, Val\u00e8ncia 46980,","institution_ids":["https://openalex.org/I4210152685","https://openalex.org/I16097986"]},{"raw_affiliation_string":"Santa Fe Institute , Santa Fe, NM 87501,","institution_ids":["https://openalex.org/I1308548392"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5054164179"],"corresponding_institution_ids":["https://openalex.org/I16097986","https://openalex.org/I4210152685"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.8124,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.70461783,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"40","issue":"11","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11495","display_name":"Animal Virus Infections Studies","score":0.6539999842643738,"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"}},"topics":[{"id":"https://openalex.org/T11495","display_name":"Animal Virus Infections Studies","score":0.6539999842643738,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.0737999975681305,"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/T11135","display_name":"Virology and Viral Diseases","score":0.05829999968409538,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"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/genome","display_name":"Genome","score":0.7787610292434692},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7244558334350586},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.6325501799583435},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5962928533554077},{"id":"https://openalex.org/keywords/helper-virus","display_name":"Helper virus","score":0.5812218189239502},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5609021782875061},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5308887362480164},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.47466304898262024},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3930145800113678},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.39154180884361267}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7787610292434692},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7244558334350586},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6325501799583435},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5962928533554077},{"id":"https://openalex.org/C144001008","wikidata":"https://www.wikidata.org/wiki/Q458226","display_name":"Helper virus","level":4,"score":0.5812218189239502},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5609021782875061},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5308887362480164},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.47466304898262024},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3930145800113678},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.39154180884361267}],"mesh":[{"descriptor_ui":"D003673","descriptor_name":"Defective Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D003673","descriptor_name":"Defective Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D003673","descriptor_name":"Defective Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D003673","descriptor_name":"Defective Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D003673","descriptor_name":"Defective Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae651","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae651","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39495116","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39495116","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:11583936","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11583936","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11583936/pdf/btae651.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae651","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae651","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1422035950","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320321864","funder_display_name":"Generalitat Valenciana"},{"id":"https://openalex.org/G1599646647","display_name":null,"funder_award_id":"PID2019","funder_id":"https://openalex.org/F4320338080","funder_display_name":"European Social Fund"},{"id":"https://openalex.org/G1622782223","display_name":null,"funder_award_id":"MCIN/AEI/10","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G2262748287","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G2745972340","display_name":null,"funder_award_id":"2020/2094","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G276391773","display_name":null,"funder_award_id":"ACIF/2021","funder_id":"https://openalex.org/F4320321864","funder_display_name":"Generalitat Valenciana"},{"id":"https://openalex.org/G3480869486","display_name":null,"funder_award_id":"13039","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G3681454997","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G3722519122","display_name":null,"funder_award_id":"FPU19","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"},{"id":"https://openalex.org/G4042783231","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G451917667","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G5080475149","display_name":null,"funder_award_id":"10.13039","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G5555131222","display_name":null,"funder_award_id":"PID2019","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"},{"id":"https://openalex.org/G5967599077","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G6218905885","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320338080","funder_display_name":"European Social Fund"},{"id":"https://openalex.org/G7084143925","display_name":null,"funder_award_id":"AEI/10","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7266728691","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7535663061","display_name":null,"funder_award_id":"AEI/10.","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"},{"id":"https://openalex.org/G7689916216","display_name":null,"funder_award_id":"CIAICO/2021/180","funder_id":"https://openalex.org/F4320321864","funder_display_name":"Generalitat Valenciana"},{"id":"https://openalex.org/G7693665080","display_name":null,"funder_award_id":"SGL2021-03-052","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7805626310","display_name":null,"funder_award_id":"10.13039","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"},{"id":"https://openalex.org/G8497050386","display_name":null,"funder_award_id":"501100011033","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"},{"id":"https://openalex.org/G8516412140","display_name":null,"funder_award_id":"13039/501100011033","funder_id":"https://openalex.org/F4320315062","funder_display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades"},{"id":"https://openalex.org/G8684520763","display_name":null,"funder_award_id":"PID2019","funder_id":"https://openalex.org/F4320335598","funder_display_name":"Agencia Estatal de Investigaci\u00f3n"}],"funders":[{"id":"https://openalex.org/F4320307502","display_name":"American Concrete Institute Foundation","ror":"https://ror.org/02a207p76"},{"id":"https://openalex.org/F4320312777","display_name":"Santa Fe Institute","ror":"https://ror.org/01arysc35"},{"id":"https://openalex.org/F4320315062","display_name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades","ror":null},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320321864","display_name":"Generalitat Valenciana","ror":"https://ror.org/0097mvx21"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320335598","display_name":"Agencia Estatal de Investigaci\u00f3n","ror":null},{"id":"https://openalex.org/F4320338080","display_name":"European Social Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W1964699038","https://openalex.org/W2105611306","https://openalex.org/W2236822143","https://openalex.org/W2603019565","https://openalex.org/W2883561599","https://openalex.org/W2945572186","https://openalex.org/W2948601199","https://openalex.org/W2963367647","https://openalex.org/W2996038594","https://openalex.org/W3013591402","https://openalex.org/W3125590130","https://openalex.org/W3133097471","https://openalex.org/W3154923640","https://openalex.org/W3156841087","https://openalex.org/W3160337431","https://openalex.org/W3196418044","https://openalex.org/W3214039811","https://openalex.org/W3214232062","https://openalex.org/W4281563772","https://openalex.org/W4295078876","https://openalex.org/W4315707395","https://openalex.org/W4322486339","https://openalex.org/W4366351736","https://openalex.org/W4385190940","https://openalex.org/W4387968960","https://openalex.org/W4388837454","https://openalex.org/W4394764018","https://openalex.org/W4395011156","https://openalex.org/W4399561702","https://openalex.org/W4402188522"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W3129816939","https://openalex.org/W2912862995","https://openalex.org/W2985427592","https://openalex.org/W2101501829","https://openalex.org/W2400569965","https://openalex.org/W2060263731","https://openalex.org/W1969270468","https://openalex.org/W1994127922","https://openalex.org/W2325088585"],"abstract_inverted_index":{"MOTIVATION:":[0],"Defective":[1],"viral":[2,51],"genomes":[3,136,176],"(DVGs)":[4],"are":[5,61,225],"variants":[6],"of":[7,26,41,132,163,169,172,177,205],"the":[8,14,24,36,56,99,119,130,148,156,170,188,197,203,222],"wild-type":[9],"(wt)":[10],"virus":[11],"that":[12,200],"lack":[13],"ability":[15],"to":[16,63,85,88,95,127],"complete":[17],"autonomously":[18],"an":[19,167],"infectious":[20],"cycle.":[21],"However,":[22],"in":[23,50,182],"presence":[25],"their":[27,86,114],"parental":[28],"(helper)":[29],"wt":[30,135,173,206],"virus,":[31,101],"DVGs":[32,53,73,81,133,208],"can":[33],"interfere":[34],"with":[35,118,144],"replication,":[37],"encapsidation,":[38],"and":[39,60,66,71,134,174,207,221],"spread":[40],"functional":[42],"genomes,":[43],"acting":[44],"as":[45],"a":[46,125,138,160],"significant":[47,145],"selective":[48],"force":[49],"evolution.":[52],"also":[54],"affect":[55],"host's":[57],"immune":[58],"responses":[59],"linked":[62],"chronic":[64],"infections":[65],"milder":[67],"symptoms.":[68],"Thus,":[69],"identifying":[70,141],"characterizing":[72],"is":[74,82,110,196],"crucial":[75],"for":[76,112,191],"understanding":[77,113],"infection":[78],"prognosis.":[79],"Quantifying":[80],"challenging":[83],"due":[84],"inability":[87],"sustain":[89],"themselves,":[90],"which":[91,165],"makes":[92],"it":[93],"difficult":[94],"distinguish":[96],"them":[97],"from":[98,147,211],"helper":[100,120],"especially":[102],"using":[103],"high-throughput":[104],"RNA":[105,213],"sequencing.":[106,214],"An":[107],"accurate":[108],"quantification":[109],"essential":[111],"very":[115],"dynamical":[116],"interactions":[117],"virus.":[121],"RESULTS:":[122],"We":[123],"present":[124],"method":[126,199],"simultaneously":[128,201],"estimate":[129,168],"abundances":[131],"within":[137],"sample":[139],"by":[140],"genomic":[142,193],"regions":[143],"deviations":[146],"expected":[149],"sequencing":[150],"depth.":[151],"Our":[152],"approach":[153],"involves":[154],"reconstructing":[155],"depth":[157],"profile":[158],"through":[159],"linear":[161],"system":[162],"equations,":[164],"provides":[166],"number":[171],"DVG":[175],"each":[178],"type.":[179],"Until":[180],"now,":[181],"silico":[183],"methods":[184],"have":[185],"only":[186],"estimated":[187],"DVG-to-wt":[189],"ratio":[190],"localized":[192],"regions.":[194],"This":[195],"first":[198],"estimates":[202],"proportions":[204],"genome":[209],"wide":[210],"short-reads":[212],"AVAILABILITY":[215],"AND":[216],"IMPLEMENTATION:":[217],"The":[218],"Matlab":[219],"code":[220],"synthetic":[223],"datasets":[224],"freely":[226],"available":[227],"at":[228],"https://github.com/jmusan/wtDVGquantific.":[229]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2025-10-10T00:00:00"}
