{"id":"https://openalex.org/W4400687787","doi":"https://doi.org/10.1093/bib/bbae319","title":"Highly accurate classification and discovery of microbial protein-coding gene functions using FunGeneTyper: an extensible deep learning framework","display_name":"Highly accurate classification and discovery of microbial protein-coding gene functions using FunGeneTyper: an extensible deep learning framework","publication_year":2024,"publication_date":"2024-05-23","ids":{"openalex":"https://openalex.org/W4400687787","doi":"https://doi.org/10.1093/bib/bbae319"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae319","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae319","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae319/58544246/bbae319.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae319/58544246/bbae319.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100419064","display_name":"Guoqing Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I3133055985","display_name":"Westlake University","ror":"https://ror.org/05hfa4n20","country_code":"CN","type":"education","lineage":["https://openalex.org/I3133055985"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guoqing Zhang","raw_affiliation_strings":["Center of Synthetic Biology and Integrated Bioengineering, Westlake University , Hangzhou, Zhejiang 310030 , China","College of Environmental and Resource Sciences, Zhejiang University , Hangzhou, Zhejiang 310058 , China","Key Laboratory of Coastal Environment and Resources of Zhejiang Province , School of Engineering, , Hangzhou, Zhejiang 310030 , China","Westlake University , School of Engineering, , Hangzhou, Zhejiang 310030 , China"],"affiliations":[{"raw_affiliation_string":"Center of Synthetic Biology and Integrated Bioengineering, Westlake University , Hangzhou, Zhejiang 310030 , China","institution_ids":["https://openalex.org/I3133055985"]},{"raw_affiliation_string":"College of Environmental and Resource Sciences, Zhejiang University , Hangzhou, Zhejiang 310058 , China","institution_ids":["https://openalex.org/I76130692"]},{"raw_affiliation_string":"Key Laboratory of Coastal Environment and Resources of Zhejiang Province , School of Engineering, , Hangzhou, Zhejiang 310030 , China","institution_ids":[]},{"raw_affiliation_string":"Westlake University , School of Engineering, , Hangzhou, Zhejiang 310030 , China","institution_ids":["https://openalex.org/I3133055985"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100460768","display_name":"Hui Wang","orcid":"https://orcid.org/0000-0002-3394-1531"},"institutions":[{"id":"https://openalex.org/I3133055985","display_name":"Westlake University","ror":"https://ror.org/05hfa4n20","country_code":"CN","type":"education","lineage":["https://openalex.org/I3133055985"]},{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui Wang","raw_affiliation_strings":["Representation Learning Laboratory , School of Engineering, , Hangzhou, Zhejiang 310030 , China","Westlake University , School of Engineering, , Hangzhou, Zhejiang 310030 , China"],"affiliations":[{"raw_affiliation_string":"Representation Learning Laboratory , School of Engineering, , Hangzhou, Zhejiang 310030 , China","institution_ids":["https://openalex.org/I4210123185"]},{"raw_affiliation_string":"Westlake University , School of Engineering, , Hangzhou, Zhejiang 310030 , China","institution_ids":["https://openalex.org/I3133055985"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100363351","display_name":"Zhiguo Zhang","orcid":"https://orcid.org/0000-0002-3265-4936"},"institutions":[{"id":"https://openalex.org/I3133055985","display_name":"Westlake University","ror":"https://ror.org/05hfa4n20","country_code":"CN","type":"education","lineage":["https://openalex.org/I3133055985"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiguo Zhang","raw_affiliation_strings":["Key Laboratory of Coastal Environment and Resources of Zhejiang Province , School of Engineering, , Hangzhou, Zhejiang 310030 , China","Westlake University , School of Engineering, , Hangzhou, Zhejiang 310030 , China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Coastal Environment and Resources of Zhejiang Province , School of Engineering, , Hangzhou, Zhejiang 310030 , China","institution_ids":[]},{"raw_affiliation_string":"Westlake University , School of Engineering, , Hangzhou, Zhejiang 310030 , China","institution_ids":["https://openalex.org/I3133055985"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100388600","display_name":"Lu Zhang","orcid":"https://orcid.org/0000-0002-0446-7885"},"institutions":[{"id":"https://openalex.org/I3133055985","display_name":"Westlake University","ror":"https://ror.org/05hfa4n20","country_code":"CN","type":"education","lineage":["https://openalex.org/I3133055985"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lu Zhang","raw_affiliation_strings":["Key Laboratory of Coastal Environment and Resources of Zhejiang Province , School of Engineering, , Hangzhou, Zhejiang 310030 , China","Westlake University , School of Engineering, , Hangzhou, Zhejiang 310030 , China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Coastal Environment and Resources of Zhejiang Province , School of Engineering, , Hangzhou, Zhejiang 310030 , China","institution_ids":[]},{"raw_affiliation_string":"Westlake University , School of Engineering, , Hangzhou, Zhejiang 310030 , China","institution_ids":["https://openalex.org/I3133055985"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089326607","display_name":"Guibing Guo","orcid":null},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guibing Guo","raw_affiliation_strings":["Software College, Northeastern University , Shenyang, Liaoning 110169 , China"],"affiliations":[{"raw_affiliation_string":"Software College, Northeastern University , Shenyang, Liaoning 110169 , China","institution_ids":["https://openalex.org/I9224756"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100604690","display_name":"Jian Yang","orcid":"https://orcid.org/0000-0003-2001-2474"},"institutions":[{"id":"https://openalex.org/I3133055985","display_name":"Westlake University","ror":"https://ror.org/05hfa4n20","country_code":"CN","type":"education","lineage":["https://openalex.org/I3133055985"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Yang","raw_affiliation_strings":["Westlake Laboratory of Life Sciences and Biomedicine , School of Life Sciences, , Hangzhou, Zhejiang 310024 , China","Westlake University , School of Life Sciences, , Hangzhou, Zhejiang 310024 , China"],"affiliations":[{"raw_affiliation_string":"Westlake Laboratory of Life Sciences and Biomedicine , School of Life Sciences, , Hangzhou, Zhejiang 310024 , China","institution_ids":["https://openalex.org/I3133055985"]},{"raw_affiliation_string":"Westlake University , School of Life Sciences, , Hangzhou, Zhejiang 310024 , China","institution_ids":["https://openalex.org/I3133055985"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081665927","display_name":"Fajie Yuan","orcid":"https://orcid.org/0000-0001-8452-9929"},"institutions":[{"id":"https://openalex.org/I3133055985","display_name":"Westlake University","ror":"https://ror.org/05hfa4n20","country_code":"CN","type":"education","lineage":["https://openalex.org/I3133055985"]},{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fajie Yuan","raw_affiliation_strings":["Representation Learning Laboratory , School of Engineering, , Hangzhou, Zhejiang 310030 , China","Westlake University , School of Engineering, , Hangzhou, Zhejiang 310030 , China"],"affiliations":[{"raw_affiliation_string":"Representation Learning Laboratory , School of Engineering, , Hangzhou, Zhejiang 310030 , China","institution_ids":["https://openalex.org/I4210123185"]},{"raw_affiliation_string":"Westlake University , School of Engineering, , Hangzhou, Zhejiang 310030 , China","institution_ids":["https://openalex.org/I3133055985"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086548536","display_name":"Feng Ju","orcid":"https://orcid.org/0000-0003-4137-5928"},"institutions":[{"id":"https://openalex.org/I3133055985","display_name":"Westlake University","ror":"https://ror.org/05hfa4n20","country_code":"CN","type":"education","lineage":["https://openalex.org/I3133055985"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feng Ju","raw_affiliation_strings":["Center of Synthetic Biology and Integrated Bioengineering, Westlake University , Hangzhou, Zhejiang 310030 , China","Key Laboratory of Coastal Environment and Resources of Zhejiang Province , School of Engineering, , Hangzhou, Zhejiang 310030 , China","Westlake Laboratory of Life Sciences and Biomedicine , School of Life Sciences, , Hangzhou, Zhejiang 310024 , China","Westlake University , School of Engineering, , Hangzhou, Zhejiang 310030 , China","Westlake University , School of Life Sciences, , Hangzhou, Zhejiang 310024 , China"],"affiliations":[{"raw_affiliation_string":"Center of Synthetic Biology and Integrated Bioengineering, Westlake University , Hangzhou, Zhejiang 310030 , China","institution_ids":["https://openalex.org/I3133055985"]},{"raw_affiliation_string":"Key Laboratory of Coastal Environment and Resources of Zhejiang Province , School of Engineering, , Hangzhou, Zhejiang 310030 , China","institution_ids":[]},{"raw_affiliation_string":"Westlake Laboratory of Life Sciences and Biomedicine , School of Life Sciences, , Hangzhou, Zhejiang 310024 , China","institution_ids":["https://openalex.org/I3133055985"]},{"raw_affiliation_string":"Westlake University , School of Engineering, , Hangzhou, Zhejiang 310030 , China","institution_ids":["https://openalex.org/I3133055985"]},{"raw_affiliation_string":"Westlake University , School of Life Sciences, , Hangzhou, Zhejiang 310024 , China","institution_ids":["https://openalex.org/I3133055985"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5100419064"],"corresponding_institution_ids":["https://openalex.org/I3133055985","https://openalex.org/I76130692"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.9446,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.74217107,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"25","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9979000091552734,"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/T10141","display_name":"Probiotics and Fermented Foods","score":0.9853000044822693,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food 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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9764999747276306,"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/metagenomics","display_name":"Metagenomics","score":0.6492220759391785},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5985592603683472},{"id":"https://openalex.org/keywords/gene-prediction","display_name":"Gene prediction","score":0.5669206976890564},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5589040517807007},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5565940141677856},{"id":"https://openalex.org/keywords/gene-annotation","display_name":"Gene Annotation","score":0.5389268398284912},{"id":"https://openalex.org/keywords/human-microbiome-project","display_name":"Human Microbiome Project","score":0.5356903076171875},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5230560898780823},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4989621639251709},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.48931023478507996},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4495198428630829},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.4426640272140503},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.4345315992832184},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3843449354171753},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.35150712728500366},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3495754599571228},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3350769281387329},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3120008111000061},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19361981749534607},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.16874158382415771}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.6492220759391785},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5985592603683472},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.5669206976890564},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5589040517807007},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5565940141677856},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.5389268398284912},{"id":"https://openalex.org/C190944805","wikidata":"https://www.wikidata.org/wiki/Q3922751","display_name":"Human Microbiome Project","level":4,"score":0.5356903076171875},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5230560898780823},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4989621639251709},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.48931023478507996},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4495198428630829},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.4426640272140503},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.4345315992832184},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3843449354171753},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.35150712728500366},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3495754599571228},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3350769281387329},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3120008111000061},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19361981749534607},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.16874158382415771},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbae319","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae319","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae319/58544246/bbae319.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11247404","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11247404","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11247404/pdf/bbae319.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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae319","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae319","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae319/58544246/bbae319.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8399999737739563,"id":"https://metadata.un.org/sdg/6","display_name":"Clean water and sanitation"}],"awards":[{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3085993365","display_name":null,"funder_award_id":"(Grant No.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7726157001","display_name":null,"funder_award_id":"Grant No.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8531903697","display_name":null,"funder_award_id":"LR22D010001","funder_id":"https://openalex.org/F4320338464","funder_display_name":"Natural Science Foundation of Zhejiang Province"}],"funders":[{"id":"https://openalex.org/F4320318567","display_name":"Westlake University","ror":null},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320338464","display_name":"Natural Science Foundation of Zhejiang Province","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4400687787.pdf"},"referenced_works_count":51,"referenced_works":["https://openalex.org/W1964640602","https://openalex.org/W2012365024","https://openalex.org/W2033002674","https://openalex.org/W2045204781","https://openalex.org/W2055043387","https://openalex.org/W2099249681","https://openalex.org/W2101220662","https://openalex.org/W2112586763","https://openalex.org/W2124351063","https://openalex.org/W2140477768","https://openalex.org/W2150842398","https://openalex.org/W2189978128","https://openalex.org/W2419548415","https://openalex.org/W2736751812","https://openalex.org/W2813910014","https://openalex.org/W2889713700","https://openalex.org/W2896457183","https://openalex.org/W2910615673","https://openalex.org/W2921872415","https://openalex.org/W2938011530","https://openalex.org/W2951274106","https://openalex.org/W2967125766","https://openalex.org/W2980789587","https://openalex.org/W2982531601","https://openalex.org/W3015124682","https://openalex.org/W3104596207","https://openalex.org/W3111174583","https://openalex.org/W3111227863","https://openalex.org/W3128120098","https://openalex.org/W3131565611","https://openalex.org/W3144239152","https://openalex.org/W3144701084","https://openalex.org/W3146514680","https://openalex.org/W3146881283","https://openalex.org/W3146944767","https://openalex.org/W3166142427","https://openalex.org/W3191207131","https://openalex.org/W3214432604","https://openalex.org/W4206677002","https://openalex.org/W4213112325","https://openalex.org/W4214943162","https://openalex.org/W4220991280","https://openalex.org/W4226250938","https://openalex.org/W4239019441","https://openalex.org/W4297153942","https://openalex.org/W4313423309","https://openalex.org/W4362471278","https://openalex.org/W6755207826","https://openalex.org/W6760517126","https://openalex.org/W6769556952","https://openalex.org/W6793326456"],"related_works":["https://openalex.org/W1222064643","https://openalex.org/W1543301402","https://openalex.org/W1604004112","https://openalex.org/W3023731925","https://openalex.org/W2786547608","https://openalex.org/W4283818647","https://openalex.org/W8235432","https://openalex.org/W2950883119","https://openalex.org/W2608221519","https://openalex.org/W1648007346"],"abstract_inverted_index":{"Abstract":[0],"High-throughput":[1],"DNA":[2],"sequencing":[3],"technologies":[4],"decode":[5],"tremendous":[6],"amounts":[7],"of":[8,62,76,94,152,158,165],"microbial":[9],"protein-coding":[10,159],"gene":[11,20,160],"sequences.":[12],"However,":[13],"accurately":[14],"assigning":[15],"protein":[16],"functions":[17,161],"to":[18,143],"novel":[19],"sequences":[21,81],"remain":[22],"a":[23,130,173],"challenge.":[24],"To":[25],"this":[26],"end,":[27],"we":[28],"developed":[29],"FunGeneTyper,":[30],"an":[31,72],"extensible":[32],"framework":[33,87,126],"with":[34],"two":[35],"new":[36,95],"deep":[37],"learning":[38],"models":[39],"(i.e.,":[40],"FunTrans":[41],"and":[42,46,59,67,104,113,118,133,141,145,162,184],"FunRep),":[43],"structured":[44],"databases,":[45],"supporting":[47],"resources":[48],"for":[49,155],"achieving":[50],"highly":[51],"accurate":[52],"(Accuracy":[53],">":[54,57],"0.99,":[55],"F1-score":[56],"0.97)":[58],"fine-grained":[60],"classification":[61,157],"antibiotic":[63],"resistance":[64],"genes":[65],"(ARGs)":[66],"virulence":[68],"factor":[69],"genes.":[70],"Using":[71],"experimentally":[73],"confirmed":[74],"dataset":[75],"ARGs":[77,96],"comprising":[78],"remote":[79],"homologous":[80],"as":[82,129],"the":[83,92,109,163],"test":[84],"set,":[85],"our":[86,125],"achieves":[88],"by-far-the-best":[89],"performance":[90],"in":[91],"discovery":[93,164],"from":[97],"human":[98],"gut":[99],"(F1-score:":[100,116,120],"0.6948),":[101],"wastewater":[102],"(0.6072),":[103],"soil":[105],"(0.5445)":[106],"microbiomes,":[107],"beating":[108],"state-of-the-art":[110],"bioinformatics":[111],"tools":[112],"sequence":[114],"alignment-based":[115],"0.0556\u20130.5065)":[117],"domain-based":[119],"0.2630\u20130.5224)":[121],"annotation":[122],"approaches.":[123],"Furthermore,":[124],"is":[127],"implemented":[128],"lightweight,":[131],"privacy-preserving,":[132],"plug-and-play":[134],"neural":[135],"network":[136],"module,":[137],"facilitating":[138],"its":[139],"versatility":[140],"accessibility":[142],"developers":[144],"users":[146],"worldwide.":[147],"We":[148],"anticipate":[149],"widespread":[150],"utilization":[151],"FunGeneTyper":[153],"(https://github.com/emblab-westlake/FunGeneTyper)":[154],"precise":[156],"numerous":[166],"valuable":[167],"enzymes.":[168],"This":[169],"advancement":[170],"will":[171],"have":[172],"significant":[174],"impact":[175],"on":[176],"various":[177],"fields,":[178],"including":[179],"microbiome":[180],"research,":[181],"biotechnology,":[182],"metagenomics,":[183],"bioinformatics.":[185]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-25T23:56:10.502304","created_date":"2025-10-10T00:00:00"}