{"id":"https://openalex.org/W4382631374","doi":"https://doi.org/10.1093/bioinformatics/btad229","title":"PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer","display_name":"PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer","publication_year":2023,"publication_date":"2023-06-01","ids":{"openalex":"https://openalex.org/W4382631374","doi":"https://doi.org/10.1093/bioinformatics/btad229","pmid":"https://pubmed.ncbi.nlm.nih.gov/37387136"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad229","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad229","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i30/50741407/btad229.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/article-pdf/39/Supplement_1/i30/50741407/btad229.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083607843","display_name":"Jiayu Shang","orcid":"https://orcid.org/0000-0001-5974-4985"},"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":"Jiayu Shang","raw_affiliation_strings":["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), China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","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":false,"raw_author_name":"Cheng Peng","raw_affiliation_strings":["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), China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076779212","display_name":"Xubo Tang","orcid":"https://orcid.org/0000-0003-1304-6983"},"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":"Xubo Tang","raw_affiliation_strings":["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), China","institution_ids":["https://openalex.org/I168719708"]}]},{"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), China"],"affiliations":[{"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":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5083607843"],"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":5.5869,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.96082705,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"39","issue":"Supplement_1","first_page":"i30","last_page":"i39"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9987000226974487,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9886000156402588,"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/computational-biology","display_name":"Computational biology","score":0.580912172794342},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5204832553863525},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.4900761842727661},{"id":"https://openalex.org/keywords/bacteriophage","display_name":"Bacteriophage","score":0.4895973801612854},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4648066759109497},{"id":"https://openalex.org/keywords/capsid","display_name":"Capsid","score":0.4646994471549988},{"id":"https://openalex.org/keywords/phage-display","display_name":"Phage display","score":0.45534855127334595},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4348594546318054},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.33442002534866333},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.32751768827438354},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23880130052566528},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.17177125811576843},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11118388175964355},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.1048453152179718},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.09786581993103027}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.580912172794342},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5204832553863525},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.4900761842727661},{"id":"https://openalex.org/C2776441376","wikidata":"https://www.wikidata.org/wiki/Q165028","display_name":"Bacteriophage","level":4,"score":0.4895973801612854},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4648066759109497},{"id":"https://openalex.org/C202878990","wikidata":"https://www.wikidata.org/wiki/Q830465","display_name":"Capsid","level":3,"score":0.4646994471549988},{"id":"https://openalex.org/C186268636","wikidata":"https://www.wikidata.org/wiki/Q896217","display_name":"Phage display","level":3,"score":0.45534855127334595},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4348594546318054},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33442002534866333},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32751768827438354},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23880130052566528},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.17177125811576843},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11118388175964355},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.1048453152179718},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.09786581993103027}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014771","descriptor_name":"Virion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014771","descriptor_name":"Virion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014771","descriptor_name":"Virion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad229","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad229","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i30/50741407/btad229.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:37387136","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37387136","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:10311294","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10311294","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10311294/pdf/btad229.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"},{"id":"pmh:oai:pure.atira.dk:publications/30719fd8-cdf4-4189-9973-ff1bfe743c59","is_oa":true,"landing_page_url":"https://hdl.handle.net/2031/30719fd8-cdf4-4189-9973-ff1bfe743c59","pdf_url":null,"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":"Shang, J, Peng, C, Tang, X & Sun, Y 2023, PhaVIP : Phage VIrion Protein classification based on chaos game representation and Vision Transformer. in ISMB/ECCB 2023 Proceedings. Bioinformatics, no. Supplement_1, vol. 39, Oxford University Press, pp. i30-i39, 31st International Conference on Intelligent Systems for Molecular Biology and 22nd European Conference on Computational Biology (ISMB/ECCB 2023), LYON, France, 23/07/23. https://doi.org/10.1093/bioinformatics/btad229","raw_type":"contributionToPeriodical"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad229","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad229","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i30/50741407/btad229.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":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.75}],"awards":[{"id":"https://openalex.org/G1859322275","display_name":null,"funder_award_id":"InnoHK","funder_id":"https://openalex.org/F4320321920","funder_display_name":"Innovation and Technology Commission"},{"id":"https://openalex.org/G2642563814","display_name":null,"funder_award_id":"CIMDA","funder_id":"https://openalex.org/F4320321920","funder_display_name":"Innovation and Technology Commission"},{"id":"https://openalex.org/G3501418804","display_name":null,"funder_award_id":"9667256","funder_id":"https://openalex.org/F4320309893","funder_display_name":"City University of Hong Kong"},{"id":"https://openalex.org/G3800229870","display_name":null,"funder_award_id":"7005453","funder_id":"https://openalex.org/F4320309893","funder_display_name":"City University of Hong Kong"},{"id":"https://openalex.org/G711425152","display_name":null,"funder_award_id":"9678241","funder_id":"https://openalex.org/F4320309893","funder_display_name":"City University of Hong Kong"}],"funders":[{"id":"https://openalex.org/F4320309893","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23"},{"id":"https://openalex.org/F4320321920","display_name":"Innovation and Technology Commission","ror":"https://ror.org/04vf9tr09"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4382631374.pdf"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W1970157853","https://openalex.org/W1976978745","https://openalex.org/W1980571326","https://openalex.org/W1999529515","https://openalex.org/W2028998981","https://openalex.org/W2064601533","https://openalex.org/W2083895686","https://openalex.org/W2095943622","https://openalex.org/W2119859604","https://openalex.org/W2129103781","https://openalex.org/W2131871423","https://openalex.org/W2143485490","https://openalex.org/W2145370398","https://openalex.org/W2156125289","https://openalex.org/W2159277024","https://openalex.org/W2320294474","https://openalex.org/W2512477880","https://openalex.org/W2610162525","https://openalex.org/W2765259403","https://openalex.org/W2791956910","https://openalex.org/W2792246829","https://openalex.org/W2807988699","https://openalex.org/W2885768951","https://openalex.org/W2924848383","https://openalex.org/W2950270741","https://openalex.org/W2963157085","https://openalex.org/W2972445543","https://openalex.org/W2973579020","https://openalex.org/W2982295165","https://openalex.org/W3002133731","https://openalex.org/W3003285614","https://openalex.org/W3009723183","https://openalex.org/W3035978132","https://openalex.org/W3096218861","https://openalex.org/W3122809531","https://openalex.org/W3128210660","https://openalex.org/W3158178572","https://openalex.org/W3173487238","https://openalex.org/W3195030397","https://openalex.org/W3203901993","https://openalex.org/W3213133098","https://openalex.org/W3215755691","https://openalex.org/W4211003308","https://openalex.org/W4211129290","https://openalex.org/W4220691725","https://openalex.org/W4226147938","https://openalex.org/W4287022992","https://openalex.org/W4291017722","https://openalex.org/W4313273216","https://openalex.org/W6800217721","https://openalex.org/W6808300544"],"related_works":["https://openalex.org/W2137572138","https://openalex.org/W2968050865","https://openalex.org/W2076921277","https://openalex.org/W2079290149","https://openalex.org/W4316495397","https://openalex.org/W2900897541","https://openalex.org/W1961120812","https://openalex.org/W2066862872","https://openalex.org/W1998773331","https://openalex.org/W1533264849"],"abstract_inverted_index":{"The":[0,9],"web":[1],"server":[2],"of":[3,12],"PhaVIP":[4,13],"is":[5,14],"available":[6,15],"via:":[7,16],"https://phage.ee.cityu.edu.hk/phavip.":[8],"source":[10],"code":[11],"https://github.com/KennthShang/PhaVIP.":[17]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":2}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
