{"id":"https://openalex.org/W4404644013","doi":"https://doi.org/10.1093/bioinformatics/btae704","title":"ViraLM: empowering virus discovery through the genome foundation model","display_name":"ViraLM: empowering virus discovery through the genome foundation model","publication_year":2024,"publication_date":"2024-11-19","ids":{"openalex":"https://openalex.org/W4404644013","doi":"https://doi.org/10.1093/bioinformatics/btae704","pmid":"https://pubmed.ncbi.nlm.nih.gov/39579086"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae704","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae704","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae704/60797056/btae704.pdf","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://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae704/60797056/btae704.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100346437","display_name":"Cheng Peng","orcid":"https://orcid.org/0000-0002-8566-0707"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Cheng Peng","raw_affiliation_strings":["Department of Electrical Engineering, City University of Hong Kong , Hong Kong (SAR),","Department of Electrical Engineering, City University of Hong Kong, Hong Kong (SAR), China"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, City University of Hong Kong , Hong Kong (SAR),","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Department of Electrical Engineering, City University of Hong Kong, Hong Kong (SAR), China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083607843","display_name":"Jiayu Shang","orcid":"https://orcid.org/0000-0001-5974-4985"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jiayu Shang","raw_affiliation_strings":["Department of Information Engineering, The Chinese University of Hong Kong , Hong Kong (SAR),","Department of Information Engineering, The Chinese University of Hong Kong, Hong Kong (SAR), China"],"affiliations":[{"raw_affiliation_string":"Department of Information Engineering, The Chinese University of Hong Kong , Hong Kong (SAR),","institution_ids":["https://openalex.org/I177725633"]},{"raw_affiliation_string":"Department of Information Engineering, The Chinese University of Hong Kong, Hong Kong (SAR), China","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057508867","display_name":"Jiaojiao Guan","orcid":"https://orcid.org/0009-0005-9200-4862"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jiaojiao Guan","raw_affiliation_strings":["Department of Electrical Engineering, City University of Hong Kong , Hong Kong (SAR),","Department of Electrical Engineering, City University of Hong Kong, Hong Kong (SAR), China"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, City University of Hong Kong , Hong Kong (SAR),","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Department of Electrical Engineering, City University of Hong Kong, Hong Kong (SAR), China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115695428","display_name":"Donglin Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Donglin Wang","raw_affiliation_strings":["School of Environmental Science and Engineering, Shandong University , Qingdao 266200,"],"affiliations":[{"raw_affiliation_string":"School of Environmental Science and Engineering, Shandong University , Qingdao 266200,","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081855118","display_name":"Yanni Sun","orcid":"https://orcid.org/0000-0003-1373-8023"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yanni Sun","raw_affiliation_strings":["Department of Electrical Engineering, City University of Hong Kong , Hong Kong (SAR),","Department of Electrical Engineering, City University of Hong Kong, Hong Kong (SAR), China"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, City University of Hong Kong , Hong Kong (SAR),","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Department of Electrical Engineering, City University of Hong Kong, Hong Kong (SAR), China","institution_ids":["https://openalex.org/I168719708"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100346437"],"corresponding_institution_ids":["https://openalex.org/I168719708"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":9.0476,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.98239497,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"40","issue":"12","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9998000264167786,"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":0.9998000264167786,"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/T10494","display_name":"Plant Virus Research Studies","score":0.9937999844551086,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9894999861717224,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/foundation","display_name":"Foundation (evidence)","score":0.7185459733009338},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5531861186027527},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.499500036239624},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4737352132797241},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4228464961051941},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.4163680970668793},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40616574883461},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.40180906653404236},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2562808394432068},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.15809953212738037},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15534594655036926},{"id":"https://openalex.org/keywords/archaeology","display_name":"Archaeology","score":0.096981942653656}],"concepts":[{"id":"https://openalex.org/C2780966255","wikidata":"https://www.wikidata.org/wiki/Q5474306","display_name":"Foundation (evidence)","level":2,"score":0.7185459733009338},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5531861186027527},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.499500036239624},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4737352132797241},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4228464961051941},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.4163680970668793},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40616574883461},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.40180906653404236},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2562808394432068},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.15809953212738037},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15534594655036926},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.096981942653656}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btae704","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae704","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae704/60797056/btae704.pdf","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:39579086","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39579086","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:pure.atira.dk:publications/e1cf228d-efbb-4e68-add7-d873dac15783","is_oa":true,"landing_page_url":"https://hdl.handle.net/2031/e1cf228d-efbb-4e68-add7-d873dac15783","pdf_url":"https://scholars.cityu.edu.hk/files/269637251/263696498.pdf","source":{"id":"https://openalex.org/S7407055387","display_name":"CityU Scholars","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Peng, C, Shang, J, Guan, J, Wang, D & Sun, Y 2024, 'ViraLM : empowering virus discovery through the genome foundation model', Bioinformatics, vol. 40, no. 12, btae704. https://doi.org/10.1093/bioinformatics/btae704","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11631183","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11631183","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11631183/pdf/btae704.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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/btae704","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae704","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae704/60797056/btae704.pdf","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":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.6499999761581421}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309893","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23"},{"id":"https://openalex.org/F4320324196","display_name":"Innovation and Technology Commission - Hong Kong","ror":"https://ror.org/04vf9tr09"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4404644013.pdf","grobid_xml":"https://content.openalex.org/works/W4404644013.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W2055043387","https://openalex.org/W3003110834","https://openalex.org/W3018845879","https://openalex.org/W3033129278","https://openalex.org/W3127656915","https://openalex.org/W4226147938","https://openalex.org/W4283123905","https://openalex.org/W4289519938","https://openalex.org/W4295426379","https://openalex.org/W4386212812","https://openalex.org/W4386923826","https://openalex.org/W4387907269","https://openalex.org/W4390899026","https://openalex.org/W4400320667","https://openalex.org/W4404821554","https://openalex.org/W6857103676"],"related_works":["https://openalex.org/W2381393187","https://openalex.org/W2332779545","https://openalex.org/W2358060160","https://openalex.org/W2035483685","https://openalex.org/W1969764885","https://openalex.org/W596947562","https://openalex.org/W2793937822","https://openalex.org/W2790817834","https://openalex.org/W2777605427","https://openalex.org/W2501983714"],"abstract_inverted_index":{"The":[0],"source":[1],"code":[2],"of":[3],"ViraLM":[4],"is":[5],"available":[6],"via:":[7],"https://github.com/ChengPENG-wolf/ViraLM.":[8]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-07T14:57:38.498316","created_date":"2025-10-10T00:00:00"}
