{"id":"https://openalex.org/W4416195815","doi":"https://doi.org/10.1093/bib/bbaf592","title":"FGeneBERT: function-driven pre-trained gene language model for metagenomics","display_name":"FGeneBERT: function-driven pre-trained gene language model for metagenomics","publication_year":2025,"publication_date":"2025-11-01","ids":{"openalex":"https://openalex.org/W4416195815","doi":"https://doi.org/10.1093/bib/bbaf592","pmid":"https://pubmed.ncbi.nlm.nih.gov/41211880"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf592","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf592","pdf_url":null,"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":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":"gold","oa_url":"https://doi.org/10.1093/bib/bbaf592","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5113129984","display_name":"Chenrui Duan","orcid":"https://orcid.org/0009-0000-5480-4272"},"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/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]},{"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":false,"raw_author_name":"Chenrui Duan","raw_affiliation_strings":["College of Computer Science and Technology, Zhejiang University , No. 866, Yuhangtang Road, 310058 Zhejiang ,","School of Engineering, Westlake University , No. 600 Dunyu Road, 310030 Zhejiang ,","College of Computer Science and Technology, Zhejiang University, No. 866, Yuhangtang Road, 310058 Zhejiang, P. R. China","School of Engineering, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P. R. China"],"raw_orcid":"https://orcid.org/0009-0000-5480-4272","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Zhejiang University , No. 866, Yuhangtang Road, 310058 Zhejiang ,","institution_ids":["https://openalex.org/I55712492"]},{"raw_affiliation_string":"School of Engineering, Westlake University , No. 600 Dunyu Road, 310030 Zhejiang ,","institution_ids":["https://openalex.org/I3133055985"]},{"raw_affiliation_string":"College of Computer Science and Technology, Zhejiang University, No. 866, Yuhangtang Road, 310058 Zhejiang, P. R. China","institution_ids":["https://openalex.org/I55712492","https://openalex.org/I76130692"]},{"raw_affiliation_string":"School of Engineering, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P. R. China","institution_ids":["https://openalex.org/I3133055985"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007012841","display_name":"Zelin Zang","orcid":"https://orcid.org/0000-0003-2831-5437"},"institutions":[{"id":"https://openalex.org/I4210121405","display_name":"Centre for Artificial Intelligence and Robotics","ror":"https://ror.org/01xnbq218","country_code":"IN","type":"facility","lineage":["https://openalex.org/I1340206300","https://openalex.org/I4210121405","https://openalex.org/I4210150591"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Zelin Zang","raw_affiliation_strings":["Centre for Artificial Intelligence and Robotics (CAIR), HKISI-CAS Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences , Hong Kong 310000 ,","Centre for Artificial Intelligence and Robotics (CAIR), HKISI-CAS Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong 310000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Artificial Intelligence and Robotics (CAIR), HKISI-CAS Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences , Hong Kong 310000 ,","institution_ids":["https://openalex.org/I4210121405"]},{"raw_affiliation_string":"Centre for Artificial Intelligence and Robotics (CAIR), HKISI-CAS Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong 310000, China","institution_ids":["https://openalex.org/I4210121405"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013753881","display_name":"Yongjie Xu","orcid":"https://orcid.org/0000-0002-6045-1626"},"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/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]},{"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":false,"raw_author_name":"Yongjie Xu","raw_affiliation_strings":["College of Computer Science and Technology, Zhejiang University , No. 866, Yuhangtang Road, 310058 Zhejiang ,","School of Engineering, Westlake University , No. 600 Dunyu Road, 310030 Zhejiang ,","School of Engineering, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P. R. China","College of Computer Science and Technology, Zhejiang University, No. 866, Yuhangtang Road, 310058 Zhejiang, P. R. China"],"raw_orcid":"https://orcid.org/0000-0002-6045-1626","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Zhejiang University , No. 866, Yuhangtang Road, 310058 Zhejiang ,","institution_ids":["https://openalex.org/I55712492"]},{"raw_affiliation_string":"School of Engineering, Westlake University , No. 600 Dunyu Road, 310030 Zhejiang ,","institution_ids":["https://openalex.org/I3133055985"]},{"raw_affiliation_string":"School of Engineering, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P. R. China","institution_ids":["https://openalex.org/I3133055985"]},{"raw_affiliation_string":"College of Computer Science and Technology, Zhejiang University, No. 866, Yuhangtang Road, 310058 Zhejiang, P. R. China","institution_ids":["https://openalex.org/I55712492","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030322451","display_name":"Hang He","orcid":"https://orcid.org/0000-0003-3165-283X"},"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":"Hang He","raw_affiliation_strings":["School of Medicine and School of Life Sciences, Westlake University , No. 600 Dunyu Road, 310030 Zhejiang ,","School of Medicine and School of Life Sciences, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Medicine and School of Life Sciences, Westlake University , No. 600 Dunyu Road, 310030 Zhejiang ,","institution_ids":["https://openalex.org/I3133055985"]},{"raw_affiliation_string":"School of Medicine and School of Life Sciences, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P. R. China","institution_ids":["https://openalex.org/I3133055985"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100406609","display_name":"Siyuan Li","orcid":"https://orcid.org/0000-0001-6806-2468"},"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/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]},{"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":false,"raw_author_name":"Siyuan Li","raw_affiliation_strings":["College of Computer Science and Technology, Zhejiang University , No. 866, Yuhangtang Road, 310058 Zhejiang ,","School of Engineering, Westlake University , No. 600 Dunyu Road, 310030 Zhejiang ,","School of Engineering, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P. R. China","College of Computer Science and Technology, Zhejiang University, No. 866, Yuhangtang Road, 310058 Zhejiang, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Zhejiang University , No. 866, Yuhangtang Road, 310058 Zhejiang ,","institution_ids":["https://openalex.org/I55712492"]},{"raw_affiliation_string":"School of Engineering, Westlake University , No. 600 Dunyu Road, 310030 Zhejiang ,","institution_ids":["https://openalex.org/I3133055985"]},{"raw_affiliation_string":"School of Engineering, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P. R. China","institution_ids":["https://openalex.org/I3133055985"]},{"raw_affiliation_string":"College of Computer Science and Technology, Zhejiang University, No. 866, Yuhangtang Road, 310058 Zhejiang, P. R. China","institution_ids":["https://openalex.org/I55712492","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046708535","display_name":"Zihan Liu","orcid":"https://orcid.org/0000-0001-6224-3823"},"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/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]},{"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":false,"raw_author_name":"Zihan Liu","raw_affiliation_strings":["College of Computer Science and Technology, Zhejiang University , No. 866, Yuhangtang Road, 310058 Zhejiang ,","School of Engineering, Westlake University , No. 600 Dunyu Road, 310030 Zhejiang ,","School of Engineering, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P. R. China","College of Computer Science and Technology, Zhejiang University, No. 866, Yuhangtang Road, 310058 Zhejiang, P. R. China"],"raw_orcid":"https://orcid.org/0000-0001-6224-3823","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Zhejiang University , No. 866, Yuhangtang Road, 310058 Zhejiang ,","institution_ids":["https://openalex.org/I55712492"]},{"raw_affiliation_string":"School of Engineering, Westlake University , No. 600 Dunyu Road, 310030 Zhejiang ,","institution_ids":["https://openalex.org/I3133055985"]},{"raw_affiliation_string":"School of Engineering, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P. R. China","institution_ids":["https://openalex.org/I3133055985"]},{"raw_affiliation_string":"College of Computer Science and Technology, Zhejiang University, No. 866, Yuhangtang Road, 310058 Zhejiang, P. R. China","institution_ids":["https://openalex.org/I55712492","https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101629247","display_name":"Zhen Lei","orcid":"https://orcid.org/0000-0002-0450-0913"},"institutions":[{"id":"https://openalex.org/I4210094879","display_name":"Shandong Institute of Automation","ror":"https://ror.org/00qdtba35","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210094879","https://openalex.org/I4210142748"]},{"id":"https://openalex.org/I4210100255","display_name":"Beijing Academy of Artificial Intelligence","ror":"https://ror.org/016a74861","country_code":"CN","type":"other","lineage":["https://openalex.org/I4210100255"]},{"id":"https://openalex.org/I4210112150","display_name":"Institute of Automation","ror":"https://ror.org/022c3hy66","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210112150"]},{"id":"https://openalex.org/I4210121405","display_name":"Centre for Artificial Intelligence and Robotics","ror":"https://ror.org/01xnbq218","country_code":"IN","type":"facility","lineage":["https://openalex.org/I1340206300","https://openalex.org/I4210121405","https://openalex.org/I4210150591"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN","IN"],"is_corresponding":false,"raw_author_name":"Zhen Lei","raw_affiliation_strings":["Centre for Artificial Intelligence and Robotics (CAIR), HKISI-CAS Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences , Hong Kong 310000 ,","School of Artificial Intelligence, University of Chinese Academy of Sciences (UCAS) , Beijing 100049 ,","State Key Laboratory of Multimodal Artificial Intelligence Systems (MAIS), Institute of Automation, Chinese Academy of Sciences (CASIA) , Beijing 100190 ,","State Key Laboratory of Multimodal Artificial Intelligence Systems (MAIS), Institute of Automation, Chinese Academy of Sciences (CASIA), Beijing 100190, China","School of Artificial Intelligence, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China","Centre for Artificial Intelligence and Robotics (CAIR), HKISI-CAS Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong 310000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Artificial Intelligence and Robotics (CAIR), HKISI-CAS Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences , Hong Kong 310000 ,","institution_ids":["https://openalex.org/I4210121405"]},{"raw_affiliation_string":"School of Artificial Intelligence, University of Chinese Academy of Sciences (UCAS) , Beijing 100049 ,","institution_ids":["https://openalex.org/I4210100255"]},{"raw_affiliation_string":"State Key Laboratory of Multimodal Artificial Intelligence Systems (MAIS), Institute of Automation, Chinese Academy of Sciences (CASIA) , Beijing 100190 ,","institution_ids":["https://openalex.org/I4210094879","https://openalex.org/I4210112150"]},{"raw_affiliation_string":"State Key Laboratory of Multimodal Artificial Intelligence Systems (MAIS), Institute of Automation, Chinese Academy of Sciences (CASIA), Beijing 100190, China","institution_ids":["https://openalex.org/I4210094879","https://openalex.org/I4210112150"]},{"raw_affiliation_string":"School of Artificial Intelligence, University of Chinese Academy of Sciences (UCAS), Beijing 100049, China","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"Centre for Artificial Intelligence and Robotics (CAIR), HKISI-CAS Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong 310000, China","institution_ids":["https://openalex.org/I4210121405"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078567214","display_name":"Ju\u2010Sheng Zheng","orcid":"https://orcid.org/0000-0001-6560-4890"},"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":"Ju-Sheng Zheng","raw_affiliation_strings":["School of Medicine and School of Life Sciences, Westlake University , No. 600 Dunyu Road, 310030 Zhejiang ,","School of Medicine and School of Life Sciences, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P. R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Medicine and School of Life Sciences, Westlake University , No. 600 Dunyu Road, 310030 Zhejiang ,","institution_ids":["https://openalex.org/I3133055985"]},{"raw_affiliation_string":"School of Medicine and School of Life Sciences, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P. R. China","institution_ids":["https://openalex.org/I3133055985"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082786719","display_name":"Stan Z. Li","orcid":"https://orcid.org/0000-0002-2961-8096"},"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/I55712492","display_name":"Zhejiang University of Technology","ror":"https://ror.org/02djqfd08","country_code":"CN","type":"education","lineage":["https://openalex.org/I55712492"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Stan Z Li","raw_affiliation_strings":["College of Computer Science and Technology, Zhejiang University , No. 866, Yuhangtang Road, 310058 Zhejiang ,","School of Engineering, Westlake University , No. 600 Dunyu Road, 310030 Zhejiang ,","School of Engineering, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P. R. China"],"raw_orcid":"https://orcid.org/0000-0002-2961-8096","affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Zhejiang University , No. 866, Yuhangtang Road, 310058 Zhejiang ,","institution_ids":["https://openalex.org/I55712492"]},{"raw_affiliation_string":"School of Engineering, Westlake University , No. 600 Dunyu Road, 310030 Zhejiang ,","institution_ids":["https://openalex.org/I3133055985"]},{"raw_affiliation_string":"School of Engineering, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P. R. China","institution_ids":["https://openalex.org/I3133055985"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.20802755,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"6","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":0.334199994802475,"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":0.334199994802475,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.30489999055862427,"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":0.14640000462532043,"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":0.9718000292778015},{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.5404000282287598},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5166000127792358},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5151000022888184},{"id":"https://openalex.org/keywords/gene-prediction","display_name":"Gene prediction","score":0.35040000081062317},{"id":"https://openalex.org/keywords/human-microbiome-project","display_name":"Human Microbiome Project","score":0.3424000144004822}],"concepts":[{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.9718000292778015},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6640999913215637},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.5404000282287598},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5166000127792358},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5151000022888184},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47749999165534973},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46869999170303345},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.35040000081062317},{"id":"https://openalex.org/C190944805","wikidata":"https://www.wikidata.org/wiki/Q3922751","display_name":"Human Microbiome Project","level":4,"score":0.3424000144004822},{"id":"https://openalex.org/C203075996","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operon","level":4,"score":0.3249000012874603},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.32010000944137573},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2957000136375427},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.28200000524520874},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2766000032424927},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.2662000060081482},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.26249998807907104},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.25699999928474426},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25360000133514404}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf592","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf592","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41211880","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41211880","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},{"id":"pmh:oai:europepmc.org:11432629","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12624452","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf592","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf592","pdf_url":null,"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":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/G2112497919","display_name":null,"funder_award_id":"WU2022A009","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2543416449","display_name":null,"funder_award_id":"U21A20427","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G324441156","display_name":null,"funder_award_id":"2022ZD0115101","funder_id":"https://openalex.org/F4320329860","funder_display_name":"National Science and Technology Major Project"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320329860","display_name":"National Science and Technology Major Project","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":68,"referenced_works":["https://openalex.org/W1989075680","https://openalex.org/W2048816826","https://openalex.org/W2073848363","https://openalex.org/W2099837668","https://openalex.org/W2111973517","https://openalex.org/W2119497560","https://openalex.org/W2131026689","https://openalex.org/W2131847331","https://openalex.org/W2145514756","https://openalex.org/W2146256775","https://openalex.org/W2163365522","https://openalex.org/W2419548415","https://openalex.org/W2601746657","https://openalex.org/W2749464300","https://openalex.org/W2797911275","https://openalex.org/W2855293443","https://openalex.org/W2888863429","https://openalex.org/W2906991531","https://openalex.org/W2908510526","https://openalex.org/W2963341956","https://openalex.org/W2965656510","https://openalex.org/W2979826702","https://openalex.org/W3003110834","https://openalex.org/W3008594856","https://openalex.org/W3013532204","https://openalex.org/W3025472913","https://openalex.org/W3127238141","https://openalex.org/W3177828909","https://openalex.org/W3203588026","https://openalex.org/W3205657162","https://openalex.org/W3209378281","https://openalex.org/W3212385379","https://openalex.org/W3217463608","https://openalex.org/W4200505767","https://openalex.org/W4205304950","https://openalex.org/W4220680270","https://openalex.org/W4224988655","https://openalex.org/W4280524269","https://openalex.org/W4280578513","https://openalex.org/W4280594315","https://openalex.org/W4282926623","https://openalex.org/W4298006192","https://openalex.org/W4304187617","https://openalex.org/W4309506674","https://openalex.org/W4310075481","https://openalex.org/W4315707368","https://openalex.org/W4327550249","https://openalex.org/W4367846784","https://openalex.org/W4386690951","https://openalex.org/W4387541035","https://openalex.org/W4387994442","https://openalex.org/W4390718970","https://openalex.org/W4395679582","https://openalex.org/W4396553387","https://openalex.org/W4396615120","https://openalex.org/W4396622387","https://openalex.org/W4402696041","https://openalex.org/W4403118713","https://openalex.org/W4403817591","https://openalex.org/W4404821554","https://openalex.org/W4405702281","https://openalex.org/W4406164158","https://openalex.org/W4406275792","https://openalex.org/W4406419344","https://openalex.org/W4406497704","https://openalex.org/W4407684107","https://openalex.org/W4407697397","https://openalex.org/W4415795191"],"related_works":[],"abstract_inverted_index":{"Metagenomic":[0],"data,":[1],"comprising":[2],"mixed":[3],"multi-species":[4],"genomes,":[5],"are":[6],"prevalent":[7],"in":[8,58,160],"diverse":[9],"environments":[10],"like":[11],"oceans":[12],"and":[13,19,34,48,54,82,98,130,133,147,156],"soils,":[14],"significantly":[15],"impacting":[16],"human":[17],"health":[18],"ecological":[20],"functions.":[21],"However,":[22],"current":[23],"research":[24],"relies":[25],"on":[26,110,120],"K-mer,":[27],"which":[28],"limits":[29],"the":[30,52,92],"capture":[31],"of":[32,94,144],"structurally":[33],"functionally":[35],"relevant":[36],"gene":[37,77,88,106,148],"contexts.":[38],"Moreover,":[39],"these":[40,63],"approaches":[41],"struggle":[42],"with":[43],"encoding":[44],"biologically":[45],"meaningful":[46],"genes":[47],"fail":[49],"to":[50,90,104,137],"address":[51],"one-to-many":[53],"many-to-one":[55],"relationships":[56,97],"inherent":[57],"metagenomic":[59,70,101,114,121,161],"data.":[60],"To":[61],"overcome":[62],"challenges,":[64],"we":[65],"introduce":[66],"FGeneBERT,":[67],"a":[68,75,80],"novel":[69],"pre-trained":[71],"model":[72],"that":[73],"employs":[74],"protein-based":[76],"representation":[78],"as":[79],"context-aware":[81],"structure-relevant":[83],"tokenizer.":[84],"FGeneBERT":[85,116],"incorporates":[86],"masked":[87],"modeling":[89],"enhance":[91],"understanding":[93],"inter-gene":[95],"contextual":[96],"triplet":[99],"enhanced":[100],"contrastive":[102],"learning":[103],"elucidate":[105],"sequence-function":[107],"relationships.":[108],"Pre-trained":[109],"over":[111],"100":[112],"million":[113],"sequences,":[115],"demonstrates":[117],"superior":[118],"performance":[119],"datasets":[122],"at":[123],"four":[124],"levels,":[125],"spanning":[126],"gene,":[127],"functional,":[128],"bacterial,":[129],"environmental":[131],"levels":[132],"ranging":[134],"from":[135],"1":[136],"213":[138],"k":[139],"input":[140],"sequences.":[141],"Case":[142],"studies":[143],"ATP":[145],"synthase":[146],"operons":[149],"highlight":[150],"FGeneBERT's":[151],"capability":[152],"for":[153],"functional":[154],"recognition":[155],"its":[157],"biological":[158],"relevance":[159],"research.":[162]},"counts_by_year":[],"updated_date":"2026-07-25T09:21:30.201066","created_date":"2025-11-10T00:00:00"}
