{"id":"https://openalex.org/W4413017597","doi":"https://doi.org/10.1109/jbhi.2025.3548463","title":"Advanced Heterogeneous Network-Based Graph Neural Network Framework for Predicting Anti-CRISPR Protein Sequences","display_name":"Advanced Heterogeneous Network-Based Graph Neural Network Framework for Predicting Anti-CRISPR Protein Sequences","publication_year":2025,"publication_date":"2025-08-01","ids":{"openalex":"https://openalex.org/W4413017597","doi":"https://doi.org/10.1109/jbhi.2025.3548463","pmid":"https://pubmed.ncbi.nlm.nih.gov/40768438"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2025.3548463","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3548463","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112542713","display_name":"Yousong Wang","orcid":"https://orcid.org/0000-0001-6707-2584"},"institutions":[{"id":"https://openalex.org/I4210132539","display_name":"Northwest Institute of Mechanical and Electrical Engineering","ror":"https://ror.org/03pz37k82","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210132539"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yeqiang Wang","raw_affiliation_strings":["College of Information Engineering, Northwest A&amp;F University, Xianyang, China"],"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Northwest A&amp;F University, Xianyang, China","institution_ids":["https://openalex.org/I4210132539"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101465050","display_name":"Wenxiao Zhao","orcid":"https://orcid.org/0000-0001-7865-6251"},"institutions":[{"id":"https://openalex.org/I4210132539","display_name":"Northwest Institute of Mechanical and Electrical Engineering","ror":"https://ror.org/03pz37k82","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210132539"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenxiao Zhao","raw_affiliation_strings":["College of Animal Science and Technology, Northwest A&amp;F University, Xianyang, China"],"affiliations":[{"raw_affiliation_string":"College of Animal Science and Technology, Northwest A&amp;F University, Xianyang, China","institution_ids":["https://openalex.org/I4210132539"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020960138","display_name":"Yijun He","orcid":null},"institutions":[{"id":"https://openalex.org/I4210132539","display_name":"Northwest Institute of Mechanical and Electrical Engineering","ror":"https://ror.org/03pz37k82","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210132539"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yijun He","raw_affiliation_strings":["College of Information Engineering, Northwest A&amp;F University, Xianyang, China"],"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Northwest A&amp;F University, Xianyang, China","institution_ids":["https://openalex.org/I4210132539"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021580821","display_name":"Jiale Li","orcid":"https://orcid.org/0000-0002-4769-3647"},"institutions":[{"id":"https://openalex.org/I4210132539","display_name":"Northwest Institute of Mechanical and Electrical Engineering","ror":"https://ror.org/03pz37k82","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210132539"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiale Li","raw_affiliation_strings":["College of Information Engineering, Northwest A&amp;F University, Xianyang, China"],"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Northwest A&amp;F University, Xianyang, China","institution_ids":["https://openalex.org/I4210132539"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081284290","display_name":"Rui Mao","orcid":"https://orcid.org/0000-0001-5345-8128"},"institutions":[{"id":"https://openalex.org/I4210132539","display_name":"Northwest Institute of Mechanical and Electrical Engineering","ror":"https://ror.org/03pz37k82","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210132539"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui Mao","raw_affiliation_strings":["College of Information Engineering, Northwest A&amp;F University, Xianyang, China"],"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Northwest A&amp;F University, Xianyang, China","institution_ids":["https://openalex.org/I4210132539"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5112542713"],"corresponding_institution_ids":["https://openalex.org/I4210132539"],"apc_list":null,"apc_paid":null,"fwci":0.8249,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.75440839,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"29","issue":"8","first_page":"6092","last_page":"6104"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9984999895095825,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9984999895095825,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9955000281333923,"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":0.9868999719619751,"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/computer-science","display_name":"Computer science","score":0.7482231259346008},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5111163258552551},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5097844004631042},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4443264603614807},{"id":"https://openalex.org/keywords/crispr","display_name":"CRISPR","score":0.44155800342559814},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32338660955429077},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.28067147731781006},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.13115373253822327},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12352332472801208}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7482231259346008},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5111163258552551},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5097844004631042},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4443264603614807},{"id":"https://openalex.org/C98108389","wikidata":"https://www.wikidata.org/wiki/Q412563","display_name":"CRISPR","level":3,"score":0.44155800342559814},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32338660955429077},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.28067147731781006},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.13115373253822327},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12352332472801208},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","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":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064113","descriptor_name":"CRISPR-Cas Systems","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2025.3548463","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3548463","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:40768438","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40768438","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":"IEEE journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":60,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1987219048","https://openalex.org/W1998566510","https://openalex.org/W2019197162","https://openalex.org/W2087064593","https://openalex.org/W2095705004","https://openalex.org/W2102245393","https://openalex.org/W2102461176","https://openalex.org/W2114850508","https://openalex.org/W2116341502","https://openalex.org/W2138122982","https://openalex.org/W2143210482","https://openalex.org/W2151831732","https://openalex.org/W2156125289","https://openalex.org/W2161151688","https://openalex.org/W2163241233","https://openalex.org/W2430331709","https://openalex.org/W2503461883","https://openalex.org/W2564226239","https://openalex.org/W2612935389","https://openalex.org/W2621720225","https://openalex.org/W2757079914","https://openalex.org/W2760870410","https://openalex.org/W2765323781","https://openalex.org/W2766653916","https://openalex.org/W2896457183","https://openalex.org/W2897791282","https://openalex.org/W2917873126","https://openalex.org/W2963263347","https://openalex.org/W2978726884","https://openalex.org/W3004490498","https://openalex.org/W3011910186","https://openalex.org/W3015370321","https://openalex.org/W3029055906","https://openalex.org/W3043299403","https://openalex.org/W3097237310","https://openalex.org/W3146944767","https://openalex.org/W3164208486","https://openalex.org/W3187966659","https://openalex.org/W4255900881","https://openalex.org/W4281963872","https://openalex.org/W4289745080","https://openalex.org/W4293173766","https://openalex.org/W4297733535","https://openalex.org/W4306697720","https://openalex.org/W4307583934","https://openalex.org/W4313334552","https://openalex.org/W4318978985","https://openalex.org/W4327550249","https://openalex.org/W4366603469","https://openalex.org/W4375955768","https://openalex.org/W4400491933","https://openalex.org/W4402475181","https://openalex.org/W4404035653","https://openalex.org/W6631190155","https://openalex.org/W6674330103","https://openalex.org/W6726497184","https://openalex.org/W6738964360","https://openalex.org/W6745316256","https://openalex.org/W6847365274"],"related_works":["https://openalex.org/W4293199045","https://openalex.org/W2405656580","https://openalex.org/W3162049976","https://openalex.org/W2642604616","https://openalex.org/W4401091785","https://openalex.org/W4381712632","https://openalex.org/W3011910186","https://openalex.org/W4365936098","https://openalex.org/W4213036952","https://openalex.org/W4377030018"],"abstract_inverted_index":{"Anti-CRISPR":[0],"proteins":[1,22,39,77],"play":[2],"a":[3,57,64,124],"crucial":[4],"role":[5],"in":[6],"bacterial-phage":[7],"interactions":[8,29],"by":[9,68],"inhibiting":[10],"the":[11,44,129,141],"CRISPR/Cas":[12],"system":[13],"and":[14,30,47,71,78,88,91,99,123],"thus":[15],"enhancing":[16],"phage":[17],"survival.":[18],"Accurately":[19],"predicting":[20],"these":[21],"is":[23],"essential":[24],"for":[25],"understanding":[26],"phage-host":[27],"immune":[28],"progressing":[31],"CRISPR/":[32],"Cas-based":[33],"technologies.":[34],"Current":[35],"approaches":[36],"primarily":[37],"analyze":[38],"individually,":[40],"which":[41],"may":[42],"overlook":[43],"intrinsic":[45],"similarities":[46],"potential":[48],"connections":[49],"among":[50],"protein":[51,66,106],"sequences.":[52],"This":[53],"study":[54],"introduces":[55],"PACRGNN,":[56],"graph":[58],"neural":[59],"network":[60,67],"framework":[61],"that":[62],"creates":[63],"heterogeneous":[65],"integrating":[69],"sequence":[70],"structural":[72],"similarities,":[73],"wherein":[74],"nodes":[75],"represent":[76],"edges":[79],"signify":[80],"their":[81],"relationships.":[82],"By":[83],"combining":[84],"Graph":[85,89],"Attention":[86],"(GAT)":[87],"Sample":[90],"Aggregation":[92],"(GraphSAGE)":[93],"layers,":[94],"PACRGNN":[95,113],"captures":[96],"both":[97],"local":[98],"global":[100],"topological":[101],"dependencies,":[102],"while":[103],"incorporating":[104],"six":[105],"feature":[107],"categories":[108],"to":[109,137],"enrich":[110],"node":[111],"representations.":[112],"achieves":[114],"an":[115,119],"accuracy":[116],"of":[117,121,126],"0.9577,":[118],"F1-Score":[120],"0.9572,":[122],"PRAUC":[125],"0.9876":[127],"on":[128,140],"validation":[130],"set.":[131],"The":[132],"model":[133],"demonstrated":[134],"superior":[135],"performance":[136],"existing":[138],"methods":[139],"independent":[142],"test":[143],"set":[144],"derived":[145],"from":[146],"NCBI":[147],"database":[148],"(Jan.-Oct.":[149],"2024).":[150]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-25T14:56:36.534964","created_date":"2025-10-10T00:00:00"}
