{"id":"https://openalex.org/W4386306370","doi":"https://doi.org/10.1093/bib/bbad311","title":"HiFun: homology independent protein function prediction by a novel protein-language self-attention model","display_name":"HiFun: homology independent protein function prediction by a novel protein-language self-attention model","publication_year":2023,"publication_date":"2023-08-30","ids":{"openalex":"https://openalex.org/W4386306370","doi":"https://doi.org/10.1093/bib/bbad311","pmid":"https://pubmed.ncbi.nlm.nih.gov/37649370"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad311","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad311","pdf_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad311/51711254/bbad311.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad311/51711254/bbad311.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101712306","display_name":"Jun Wu","orcid":"https://orcid.org/0000-0002-3381-2561"},"institutions":[{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]},{"id":"https://openalex.org/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Wu","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","East China Normal University , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","Center for Bioinformatics and Computational Biology, the Institute of Biomedical Sciences and The School of Life Sciences, East China Normal University, Shanghai , 200241, China"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","institution_ids":["https://openalex.org/I4210162648"]},{"raw_affiliation_string":"East China Normal University , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","institution_ids":["https://openalex.org/I66867065"]},{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, the Institute of Biomedical Sciences and The School of Life Sciences, East China Normal University, Shanghai , 200241, China","institution_ids":["https://openalex.org/I66867065"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101239430","display_name":"Haipeng Qing","orcid":null},"institutions":[{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]},{"id":"https://openalex.org/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haipeng Qing","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","East China Normal University , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","Center for Bioinformatics and Computational Biology, the Institute of Biomedical Sciences and The School of Life Sciences, East China Normal University, Shanghai , 200241, China"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","institution_ids":["https://openalex.org/I4210162648"]},{"raw_affiliation_string":"East China Normal University , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","institution_ids":["https://openalex.org/I66867065"]},{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, the Institute of Biomedical Sciences and The School of Life Sciences, East China Normal University, Shanghai , 200241, China","institution_ids":["https://openalex.org/I66867065"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101796254","display_name":"Jian Ouyang","orcid":"https://orcid.org/0000-0002-7851-7064"},"institutions":[{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]},{"id":"https://openalex.org/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Ouyang","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","East China Normal University , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","Center for Bioinformatics and Computational Biology, the Institute of Biomedical Sciences and The School of Life Sciences, East China Normal University, Shanghai , 200241, China"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","institution_ids":["https://openalex.org/I4210162648"]},{"raw_affiliation_string":"East China Normal University , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","institution_ids":["https://openalex.org/I66867065"]},{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, the Institute of Biomedical Sciences and The School of Life Sciences, East China Normal University, Shanghai , 200241, China","institution_ids":["https://openalex.org/I66867065"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100417645","display_name":"Jiajia Zhou","orcid":"https://orcid.org/0000-0003-2696-2809"},"institutions":[{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]},{"id":"https://openalex.org/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiajia Zhou","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","East China Normal University , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","Center for Bioinformatics and Computational Biology, the Institute of Biomedical Sciences and The School of Life Sciences, East China Normal University, Shanghai , 200241, China"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","institution_ids":["https://openalex.org/I4210162648"]},{"raw_affiliation_string":"East China Normal University , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","institution_ids":["https://openalex.org/I66867065"]},{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, the Institute of Biomedical Sciences and The School of Life Sciences, East China Normal University, Shanghai , 200241, China","institution_ids":["https://openalex.org/I66867065"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102727411","display_name":"Zihao Gao","orcid":"https://orcid.org/0009-0005-2709-3870"},"institutions":[{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]},{"id":"https://openalex.org/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zihao Gao","raw_affiliation_strings":["Center for Bioinformatics and Computational Biology , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","East China Normal University , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","Center for Bioinformatics and Computational Biology, the Institute of Biomedical Sciences and The School of Life Sciences, East China Normal University, Shanghai , 200241, China"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","institution_ids":["https://openalex.org/I4210162648"]},{"raw_affiliation_string":"East China Normal University , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","institution_ids":["https://openalex.org/I66867065"]},{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, the Institute of Biomedical Sciences and The School of Life Sciences, East China Normal University, Shanghai , 200241, China","institution_ids":["https://openalex.org/I66867065"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085435765","display_name":"Christopher E. Mason","orcid":"https://orcid.org/0000-0002-1850-1642"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher E Mason","raw_affiliation_strings":["Weill Cornell Medicine"],"affiliations":[{"raw_affiliation_string":"Weill Cornell Medicine","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100459811","display_name":"Zhichao Liu","orcid":"https://orcid.org/0000-0003-3542-0905"},"institutions":[{"id":"https://openalex.org/I4210160255","display_name":"Boehringer Ingelheim (United States)","ror":"https://ror.org/05kffp613","country_code":"US","type":"company","lineage":["https://openalex.org/I1330995197","https://openalex.org/I4210160255"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhichao Liu","raw_affiliation_strings":["Nonclinical Drug Safety, Boehringer Ingelheim Pharmaceuticals, Inc. , Ridgefield, Connecticut 06877 , United States"],"affiliations":[{"raw_affiliation_string":"Nonclinical Drug Safety, Boehringer Ingelheim Pharmaceuticals, Inc. , Ridgefield, Connecticut 06877 , United States","institution_ids":["https://openalex.org/I4210160255"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048591018","display_name":"Tieliu Shi","orcid":"https://orcid.org/0000-0001-5592-2836"},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]},{"id":"https://openalex.org/I183519381","display_name":"Capital Medical University","ror":"https://ror.org/013xs5b60","country_code":"CN","type":"education","lineage":["https://openalex.org/I183519381"]},{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]},{"id":"https://openalex.org/I4210165198","display_name":"Beijing Advanced Sciences and Innovation Center","ror":"https://ror.org/05qm21180","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165198"]},{"id":"https://openalex.org/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]},{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tieliu Shi","raw_affiliation_strings":["Beihang University & Capital Medical University , for Big Data-Based Precision Medicine, , Beijing 100083 , China","Beijing Advanced Innovation Center , for Big Data-Based Precision Medicine, , Beijing 100083 , China","Center for Bioinformatics and Computational Biology , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","East China Normal University , Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, , Shanghai 200062 , China","East China Normal University , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","School of Statistics , Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, , Shanghai 200062 , China","School of Statistics, Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, East China Normal University, Shanghai 200062, China","Center for Bioinformatics and Computational Biology, the Institute of Biomedical Sciences and The School of Life Sciences, East China Normal University, Shanghai , 200241, China","Beijing Advanced Innovation Center, for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing 100083, China"],"affiliations":[{"raw_affiliation_string":"Beihang University & Capital Medical University , for Big Data-Based Precision Medicine, , Beijing 100083 , China","institution_ids":["https://openalex.org/I183519381","https://openalex.org/I82880672"]},{"raw_affiliation_string":"Beijing Advanced Innovation Center , for Big Data-Based Precision Medicine, , Beijing 100083 , China","institution_ids":["https://openalex.org/I4210165198"]},{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","institution_ids":["https://openalex.org/I4210162648"]},{"raw_affiliation_string":"East China Normal University , Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, , Shanghai 200062 , China","institution_ids":["https://openalex.org/I66867065"]},{"raw_affiliation_string":"East China Normal University , the Institute of Biomedical Sciences and The School of Life Sciences, , Shanghai , 200241 , China","institution_ids":["https://openalex.org/I66867065"]},{"raw_affiliation_string":"School of Statistics , Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, , Shanghai 200062 , China","institution_ids":["https://openalex.org/I143593769"]},{"raw_affiliation_string":"School of Statistics, Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, East China Normal University, Shanghai 200062, China","institution_ids":["https://openalex.org/I66867065"]},{"raw_affiliation_string":"Center for Bioinformatics and Computational Biology, the Institute of Biomedical Sciences and The School of Life Sciences, East China Normal University, Shanghai , 200241, China","institution_ids":["https://openalex.org/I66867065"]},{"raw_affiliation_string":"Beijing Advanced Innovation Center, for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing 100083, China","institution_ids":["https://openalex.org/I183519381","https://openalex.org/I82880672"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5048591018","https://openalex.org/A5100459811"],"corresponding_institution_ids":["https://openalex.org/I143593769","https://openalex.org/I183519381","https://openalex.org/I4210160255","https://openalex.org/I4210162648","https://openalex.org/I4210165198","https://openalex.org/I66867065","https://openalex.org/I82880672"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.5884,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.89926387,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"24","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9983000159263611,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9983000159263611,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9965000152587891,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9962999820709229,"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/protein-function","display_name":"Protein function","score":0.5784765481948853},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5212574601173401},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5024967193603516},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.4928162395954132},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.48682111501693726},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4795684218406677},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2370832860469818},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18867582082748413},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10444071888923645}],"concepts":[{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.5784765481948853},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5212574601173401},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5024967193603516},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.4928162395954132},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.48682111501693726},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4795684218406677},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2370832860469818},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18867582082748413},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10444071888923645}],"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":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad311","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad311","pdf_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad311/51711254/bbad311.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37649370","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37649370","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbad311","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad311","pdf_url":"https://academic.oup.com/bib/article-pdf/24/5/bbad311/51711254/bbad311.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2884910486","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320322724","funder_display_name":"Ministry of Education, India"},{"id":"https://openalex.org/G8111733239","display_name":null,"funder_award_id":"2021SHZDZX0100","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320322370","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67"},{"id":"https://openalex.org/F4320322724","display_name":"Ministry of Education, India","ror":"https://ror.org/048xjjh50"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386306370.pdf","grobid_xml":"https://content.openalex.org/works/W4386306370.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W1592870802","https://openalex.org/W2045204781","https://openalex.org/W2067964678","https://openalex.org/W2068361619","https://openalex.org/W2071841602","https://openalex.org/W2083184875","https://openalex.org/W2096358531","https://openalex.org/W2098127859","https://openalex.org/W2098432760","https://openalex.org/W2102245393","https://openalex.org/W2103777723","https://openalex.org/W2107158607","https://openalex.org/W2115540209","https://openalex.org/W2117486996","https://openalex.org/W2135621733","https://openalex.org/W2227395312","https://openalex.org/W2344155264","https://openalex.org/W2514866683","https://openalex.org/W2557496587","https://openalex.org/W2611792444","https://openalex.org/W2615066396","https://openalex.org/W2761688050","https://openalex.org/W2900629010","https://openalex.org/W2910615673","https://openalex.org/W2921815890","https://openalex.org/W2925298688","https://openalex.org/W2935275081","https://openalex.org/W2949841808","https://openalex.org/W2968334948","https://openalex.org/W2989608901","https://openalex.org/W3016001898","https://openalex.org/W3046574445","https://openalex.org/W3094053700","https://openalex.org/W3136918052","https://openalex.org/W3146944767","https://openalex.org/W3159719254","https://openalex.org/W3163965514","https://openalex.org/W3163970933","https://openalex.org/W3164046276","https://openalex.org/W3174167596","https://openalex.org/W3176037658","https://openalex.org/W3177828909","https://openalex.org/W3186179742","https://openalex.org/W3187251571","https://openalex.org/W4200166788","https://openalex.org/W4200338219","https://openalex.org/W4205126063","https://openalex.org/W4205827692","https://openalex.org/W4211238993","https://openalex.org/W4220991280","https://openalex.org/W4236358448","https://openalex.org/W4286251201","https://openalex.org/W4291994084","https://openalex.org/W4313453841","https://openalex.org/W6635200387","https://openalex.org/W6726025202","https://openalex.org/W6742348326","https://openalex.org/W6839066592"],"related_works":["https://openalex.org/W2094822546","https://openalex.org/W4388708026","https://openalex.org/W1969080446","https://openalex.org/W3108941781","https://openalex.org/W1578069856","https://openalex.org/W2084200259","https://openalex.org/W2134206588","https://openalex.org/W2065993463","https://openalex.org/W4400576356","https://openalex.org/W2401071219"],"abstract_inverted_index":{"Protein":[0],"function":[1,122,132],"prediction":[2],"based":[3,65],"on":[4,66],"amino":[5],"acid":[6],"sequence":[7,74],"alone":[8],"is":[9],"an":[10,173],"extremely":[11,35],"challenging":[12],"but":[13],"important":[14],"task,":[15],"especially":[16],"in":[17,20,90,111,151],"metagenomics/metatranscriptomics":[18],"field,":[19],"which":[21,126],"novel":[22,109],"proteins":[23,40,106,142],"have":[24],"been":[25],"uncovered":[26],"exponentially":[27],"from":[28],"new":[29],"microorganisms.":[30],"Many":[31],"of":[32,80,98,148],"them":[33],"are":[34],"low":[36],"homology":[37],"to":[38,130],"known":[39],"and":[41,88,107,144,160,175],"cannot":[42],"be":[43],"annotated":[44,101],"with":[45],"homology-based":[46],"or":[47],"information":[48],"integrative":[49],"methods.":[50],"To":[51,94],"overcome":[52],"this":[53],"problem,":[54],"we":[55,100,156],"proposed":[56],"a":[57,67,158],"Homology":[58],"Independent":[59],"protein":[60,76,167,180],"Function":[61],"annotation":[62,133,143],"method":[63],"(HiFun)":[64],"unified":[68],"deep-learning":[69],"model":[70],"by":[71],"reassembling":[72],"the":[73,85,91,96,112],"as":[75,169],"language.":[77],"The":[78],"robustness":[79],"HiFun":[81,118,137],"was":[82],"evaluated":[83],"using":[84],"benchmark":[86],"datasets":[87],"metrics":[89],"CAFA3":[92],"challenge.":[93],"navigate":[95],"utility":[97],"HiFun,":[99],"2":[102],"212":[103],"663":[104],"unknown":[105],"discovered":[108],"motifs":[110],"UHGP-50":[113],"catalog.":[114],"We":[115],"proved":[116],"that":[117],"can":[119,138],"extract":[120],"latent":[121],"related":[123],"structure":[124],"features":[125],"empowers":[127],"it":[128],"ability":[129],"achieve":[131],"for":[134,178],"non-homology":[135],"proteins.":[136],"substantially":[139],"improve":[140],"newly":[141],"expand":[145],"our":[146],"understanding":[147],"microorganisms'":[149],"adaptation":[150],"various":[152],"ecological":[153],"niches.":[154],"Moreover,":[155],"provided":[157],"free":[159],"accessible":[161],"webservice":[162],"at":[163],"http://www.unimd.org/HiFun,":[164],"requiring":[165],"only":[166],"sequences":[168],"input,":[170],"offering":[171],"researchers":[172],"efficient":[174],"practical":[176],"platform":[177],"predicting":[179],"functions.":[181]},"counts_by_year":[{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":9}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
