{"id":"https://openalex.org/W7213643107","doi":"https://doi.org/10.64898/2026.09.15.751837","title":"DeepVir: A reproducible workflow for large-scale viral dark matter discovery","display_name":"DeepVir: A reproducible workflow for large-scale viral dark matter discovery","publication_year":2026,"publication_date":"2026-09-18","ids":{"openalex":"https://openalex.org/W7213643107","doi":"https://doi.org/10.64898/2026.09.15.751837"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.15.751837","doi":"https://doi.org/10.64898/2026.09.15.751837","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.15.751837","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/18/2026.09.15.751837.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/18/2026.09.15.751837.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031668990","display_name":"Matheus Augusto Calvano Cosentino","orcid":"https://orcid.org/0000-0001-9372-6561","observed_orcids":["https://orcid.org/0000-0001-9372-6561"]},"institutions":[{"id":"https://openalex.org/I122140584","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77","country_code":"BR","type":"education","lineage":["https://openalex.org/I122140584"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I2802818602","https://openalex.org/I4210090127","https://openalex.org/I4210131494","https://openalex.org/I4210166444"]},{"id":"https://openalex.org/I4387153971","display_name":"Recherches Translationnelles sur le VIH et les Maladies Infectieuses","ror":"https://ror.org/014sj8802","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I19894307","https://openalex.org/I2802818602","https://openalex.org/I4210090127","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4387153971"]}],"countries":["BR","FR"],"is_corresponding":false,"raw_author_name":"Matheus Augusto Calvano Cosentino","raw_affiliation_strings":["Laborat\u00f3rio de Diversidade e Doen\u00e7as Virais, Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil","TransVIHMI, University of Montpellier, Institut de Recherche pour le D\u00e9veloppement, Montpellier, France"],"raw_orcid":"https://orcid.org/0000-0001-9372-6561","affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio de Diversidade e Doen\u00e7as Virais, Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil","institution_ids":["https://openalex.org/I122140584"]},{"raw_affiliation_string":"TransVIHMI, University of Montpellier, Institut de Recherche pour le D\u00e9veloppement, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I4210166444","https://openalex.org/I4387153971"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033538139","display_name":"Nicolas Fernandez","orcid":"https://orcid.org/0000-0001-8490-3714","observed_orcids":["https://orcid.org/0000-0001-8490-3714"]},"institutions":[{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I2802818602","https://openalex.org/I4210090127","https://openalex.org/I4210131494","https://openalex.org/I4210166444"]},{"id":"https://openalex.org/I4387153971","display_name":"Recherches Translationnelles sur le VIH et les Maladies Infectieuses","ror":"https://ror.org/014sj8802","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I19894307","https://openalex.org/I2802818602","https://openalex.org/I4210090127","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4387153971"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Nicolas Fernandez","raw_affiliation_strings":["TransVIHMI, University of Montpellier, Institut de Recherche pour le D\u00e9veloppement, Montpellier, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TransVIHMI, University of Montpellier, Institut de Recherche pour le D\u00e9veloppement, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I4210166444","https://openalex.org/I4387153971"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000173153","display_name":"Marcelo Alves Soares","orcid":"https://orcid.org/0000-0002-9013-2570","observed_orcids":["https://orcid.org/0000-0002-9013-2570"]},"institutions":[{"id":"https://openalex.org/I122140584","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77","country_code":"BR","type":"education","lineage":["https://openalex.org/I122140584"]},{"id":"https://openalex.org/I4210142683","display_name":"Instituto Nacional de C\u00e2ncer - INCA","ror":"https://ror.org/055n68305","country_code":"BR","type":"healthcare","lineage":["https://openalex.org/I4210142683"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Marcelo A. Soares","raw_affiliation_strings":["Laborat\u00f3rio de Diversidade e Doen\u00e7as Virais, Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil","Programa de Gen\u00e9tica e Virologia Tumoral, Instituto Nacional de C\u00e2ncer, Rio de Janeiro, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio de Diversidade e Doen\u00e7as Virais, Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil","institution_ids":["https://openalex.org/I122140584"]},{"raw_affiliation_string":"Programa de Gen\u00e9tica e Virologia Tumoral, Instituto Nacional de C\u00e2ncer, Rio de Janeiro, Brazil","institution_ids":["https://openalex.org/I4210142683"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087573541","display_name":"Ahidjo Ayouba","orcid":"https://orcid.org/0000-0002-5081-1632","observed_orcids":["https://orcid.org/0000-0002-5081-1632"]},"institutions":[{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I2802818602","https://openalex.org/I4210090127","https://openalex.org/I4210131494","https://openalex.org/I4210166444"]},{"id":"https://openalex.org/I4387153971","display_name":"Recherches Translationnelles sur le VIH et les Maladies Infectieuses","ror":"https://ror.org/014sj8802","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I19894307","https://openalex.org/I2802818602","https://openalex.org/I4210090127","https://openalex.org/I4210131494","https://openalex.org/I4210166444","https://openalex.org/I4387153971"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Ahidjo Ayouba","raw_affiliation_strings":["TransVIHMI, University of Montpellier, Institut de Recherche pour le D\u00e9veloppement, Montpellier, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TransVIHMI, University of Montpellier, Institut de Recherche pour le D\u00e9veloppement, Montpellier, France","institution_ids":["https://openalex.org/I19894307","https://openalex.org/I4210166444","https://openalex.org/I4387153971"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103960025","display_name":"Andr\u00e9 dos Santos","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I122140584","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77","country_code":"BR","type":"education","lineage":["https://openalex.org/I122140584"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Andr\u00e9 Felipe Andrade dos Santos","raw_affiliation_strings":["Laborat\u00f3rio de Diversidade e Doen\u00e7as Virais, Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio de Diversidade e Doen\u00e7as Virais, Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil","institution_ids":["https://openalex.org/I122140584"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052851170","display_name":"Mirela D\u2019arc","orcid":"https://orcid.org/0000-0003-3644-0246","observed_orcids":["https://orcid.org/0000-0003-3644-0246"]},"institutions":[{"id":"https://openalex.org/I122140584","display_name":"Universidade Federal do Rio de Janeiro","ror":"https://ror.org/03490as77","country_code":"BR","type":"education","lineage":["https://openalex.org/I122140584"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Mirela D\u2019arc","raw_affiliation_strings":["Laborat\u00f3rio de Diversidade e Doen\u00e7as Virais, Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laborat\u00f3rio de Diversidade e Doen\u00e7as Virais, Genetics Department, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil","institution_ids":["https://openalex.org/I122140584"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9429000020027161,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9429000020027161,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.01209999993443489,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11135","display_name":"Virology and Viral Diseases","score":0.011500000022351742,"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/viral-dark-matter","display_name":"viral dark matter","score":0.9860000014305115},{"id":"https://openalex.org/keywords/virus-discovery","display_name":"virus discovery","score":0.6899999976158142},{"id":"https://openalex.org/keywords/snakemake-workflow","display_name":"Snakemake workflow","score":0.7630000114440918},{"id":"https://openalex.org/keywords/rna-dependent-rna-polymerase","display_name":"RNA-dependent RNA polymerase","score":0.8479999899864197},{"id":"https://openalex.org/keywords/profile-hmm","display_name":"HMM profiles","score":0.6579999923706055},{"id":"https://openalex.org/keywords/viral-metagenomics","display_name":"viral metagenomics","score":0.5270000100135803},{"id":"https://openalex.org/keywords/bat-virome","display_name":"bat virome","score":0.7860000133514404},{"id":"https://openalex.org/keywords/novel-viral-lineages","display_name":"novel viral lineages","score":0.75},{"id":"https://openalex.org/keywords/mononegavirales","display_name":"Mononegavirales","score":0.7620000243186951},{"id":"https://openalex.org/keywords/bunyaviridae","display_name":"Bunyaviridae","score":0.996999979019165},{"id":"https://openalex.org/keywords/viral-evolution","display_name":"viral evolution","score":0.4950000047683716},{"id":"https://openalex.org/keywords/viral-surveillance","display_name":"viral surveillance","score":0.37400001287460327}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6541000008583069},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.5996999740600586},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.5932999849319458},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5893999934196472},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5507000088691711},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4722999930381775},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43790000677108765},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.43689998984336853},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.42320001125335693},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.3637000024318695},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.35350000858306885},{"id":"https://openalex.org/C164614171","wikidata":"https://www.wikidata.org/wiki/Q5204775","display_name":"DECIPHER","level":2,"score":0.32710000872612},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3228999972343445},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.3188000023365021},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.31630000472068787},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.29919999837875366},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2962000072002411},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.2915000021457672},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2863999903202057},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.27239999175071716},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2653000056743622},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.26339998841285706},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.2605000138282776},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2590999901294708},{"id":"https://openalex.org/C59582021","wikidata":"https://www.wikidata.org/wiki/Q1128751","display_name":"Contig","level":4,"score":0.25450000166893005},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25220000743865967}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.15.751837","doi":"https://doi.org/10.64898/2026.09.15.751837","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.15.751837","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/18/2026.09.15.751837.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.15.751837","doi":"https://doi.org/10.64898/2026.09.15.751837","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.15.751837","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/18/2026.09.15.751837.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2823776494","display_name":null,"funder_award_id":"88887","funder_id":"https://openalex.org/F4320321091","funder_display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior"},{"id":"https://openalex.org/G4374289430","display_name":null,"funder_award_id":"2023-00","funder_id":"https://openalex.org/F4320321091","funder_display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior"}],"funders":[{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320321178","display_name":"Governo Brasil","ror":"https://ror.org/00n0s9w57"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"},{"id":"https://openalex.org/F4320322749","display_name":"Funda\u00e7\u00e3o Carlos Chagas Filho de Amparo \u00e0 Pesquisa do Estado do Rio de Janeiro","ror":"https://ror.org/03kk0s825"},{"id":"https://openalex.org/F4320323807","display_name":"Institut National Du Cancer","ror":"https://ror.org/03m8vkq32"},{"id":"https://openalex.org/F4320337157","display_name":"Instituto Nacional do C\u00e2ncer, Minist\u00e9rio da Sa\u00fade","ror":"https://ror.org/055n68305"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7213643107.pdf","grobid_xml":"https://content.openalex.org/works/W7213643107.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W2900249913","https://openalex.org/W4407127599","https://openalex.org/W4412848788","https://openalex.org/W7129273518"],"related_works":["https://openalex.org/W4414484211","https://openalex.org/W7125942832","https://openalex.org/W6927074279","https://openalex.org/W4306756223","https://openalex.org/W2596392831","https://openalex.org/W7126014918","https://openalex.org/W4294253063","https://openalex.org/W7167786131","https://openalex.org/W4403245162","https://openalex.org/W2546602325"],"abstract_inverted_index":{"Abstract":[0],"High-throughput":[1],"sequencing":[2],"(HTS)":[3],"has":[4],"revolutionized":[5],"virosphere":[6],"exploration.":[7],"However,":[8],"characterizing":[9],"highly":[10,181],"divergent":[11,182],"viral":[12,65,121,130],"sequences":[13],"remains":[14],"a":[15,42,70],"bottleneck":[16,44],"known":[17,129],"as":[18],"Viral":[19],"Dark":[20],"Matter":[21],"(VDM).":[22],"Numerous":[23],"tools":[24],"were":[25],"developed":[26,68],"to":[27,45,230],"unravel":[28],"such":[29],"diversity,":[30],"but":[31],"they":[32],"usually":[33],"require":[34],"complex":[35,54,220],"prior":[36],"HTS":[37],"data":[38,105],"analysis":[39],"processes.":[40],"Consequently,":[41],"common":[43],"VDM":[46,165,183],"exploration":[47],"is":[48],"the":[49,59,87,94,133,159,190,200,205,209,215,232,241],"manual,":[50],"chained":[51],"execution":[52],"of":[53,86,101,135,199,208,237,243],"command-line":[55],"applications.":[56],"To":[57,92],"address":[58],"need":[60],"for":[61,204],"automated":[62],"and":[63,155,172,193,234,246],"scalable":[64,224],"discovery,":[66],"we":[67,97,178],"DeepVir,":[69],"reproducible":[71],"Snakemake":[72],"pipeline":[73,160],"that":[74],"integrates":[75],"classical":[76],"homology-based":[77],"alignments":[78],"with":[79,189],"profile":[80],"Hidden":[81],"Markov":[82],"Model":[83],"(HMM)":[84],"mining":[85],"RNA-dependent":[88],"RNA":[89],"polymerase":[90],"(RdRp).":[91],"validate":[93],"pipeline\u2019s":[95,201],"efficacy,":[96],"analyzed":[98],"385.23":[99],"GB":[100],"publicly":[102],"available":[103],"transcriptomic":[104],"(203":[106],"Sequence":[107,173],"Read":[108],"Archive":[109],"libraries)":[110],"from":[111],"49":[112],"American":[113],"bat":[114],"species.":[115],"DeepVir":[116,227],"successfully":[117],"identified":[118],"179":[119],"distinct":[120],"groups.":[122],"This":[123],"included":[124],"903":[125],"contigs":[126],"spanning":[127],"nine":[128],"families,":[131],"enabling":[132],"characterization":[134,242],"novel":[136,164],"genomes":[137],"within":[138],"Orthomyxoviridae":[139],"(Influenza":[140],"A":[141],"H7N9),":[142],"Picornaviridae":[143],",":[144,146,152,154],"Alphaflexiviridae":[145],"Retroviridae":[147],"(":[148],"Spumaretrovirinae":[149],"),":[150],"Papillomaviridae":[151],"Herpesviridae":[153],"Adenoviridae":[156],".":[157,195],"Furthermore,":[158],"uncovered":[161],"170":[162],"putative":[163,211],"lineages.":[166],"By":[167],"employing":[168],"deep":[169],"homology":[170],"searches":[171],"Similarity":[174],"Network":[175],"(SSN)":[176],"visualization,":[177],"contextualized":[179],"these":[180],"sequences,":[184],"revealing":[185],"significant":[186],"evolutionary":[187],"relationships":[188],"orders":[191],"Mononegavirales":[192],"Bunyavirales":[194],"Notably,":[196],"human-driven":[197],"curation":[198],"outputs":[202],"allowed":[203],"cross-library":[206],"assembly":[207],"first":[210],"exogenous":[212],"Spumavirus":[213],"in":[214],"Americas.":[216],"Ultimately,":[217],"by":[218],"automating":[219],"bioinformatic":[221],"processing":[222],"steps,":[223],"pipelines":[225],"like":[226],"empower":[228],"researchers":[229],"prioritize":[231],"biological":[233],"epidemiological":[235],"interpretation":[236],"their":[238],"findings,":[239],"accelerating":[240],"wildlife":[244],"virospheres":[245],"enhancing":[247],"pathogen":[248],"genomic":[249],"surveillance.":[250]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2026-09-20T00:00:00"}
