{"id":"https://openalex.org/W4392870889","doi":"https://doi.org/10.1093/bib/bbae085","title":"metaProbiotics: a tool for mining probiotic from metagenomic binning data based on a language model","display_name":"metaProbiotics: a tool for mining probiotic from metagenomic binning data based on a language model","publication_year":2024,"publication_date":"2024-01-22","ids":{"openalex":"https://openalex.org/W4392870889","doi":"https://doi.org/10.1093/bib/bbae085","pmid":"https://pubmed.ncbi.nlm.nih.gov/38487846"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae085","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae085","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae085/56968598/bbae085.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","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae085/56968598/bbae085.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060407179","display_name":"Shufang Wu","orcid":"https://orcid.org/0000-0001-7793-2509"},"institutions":[{"id":"https://openalex.org/I4210120929","display_name":"Zhujiang Hospital","ror":"https://ror.org/02mhxa927","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210120929"]},{"id":"https://openalex.org/I58200834","display_name":"Southern Medical University","ror":"https://ror.org/01vjw4z39","country_code":"CN","type":"education","lineage":["https://openalex.org/I58200834"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shufang Wu","raw_affiliation_strings":["Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929"]},{"raw_affiliation_string":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]},{"raw_affiliation_string":"Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075165869","display_name":"Tao Feng","orcid":"https://orcid.org/0000-0003-1984-4265"},"institutions":[{"id":"https://openalex.org/I4210120929","display_name":"Zhujiang Hospital","ror":"https://ror.org/02mhxa927","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210120929"]},{"id":"https://openalex.org/I58200834","display_name":"Southern Medical University","ror":"https://ror.org/01vjw4z39","country_code":"CN","type":"education","lineage":["https://openalex.org/I58200834"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tao Feng","raw_affiliation_strings":["Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929"]},{"raw_affiliation_string":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]},{"raw_affiliation_string":"Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074287374","display_name":"Waijiao Tang","orcid":"https://orcid.org/0000-0002-4993-5806"},"institutions":[{"id":"https://openalex.org/I4210120929","display_name":"Zhujiang Hospital","ror":"https://ror.org/02mhxa927","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210120929"]},{"id":"https://openalex.org/I58200834","display_name":"Southern Medical University","ror":"https://ror.org/01vjw4z39","country_code":"CN","type":"education","lineage":["https://openalex.org/I58200834"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Waijiao Tang","raw_affiliation_strings":["Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929"]},{"raw_affiliation_string":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]},{"raw_affiliation_string":"Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059079638","display_name":"Cancan Qi","orcid":"https://orcid.org/0000-0003-3825-5802"},"institutions":[{"id":"https://openalex.org/I4210120929","display_name":"Zhujiang Hospital","ror":"https://ror.org/02mhxa927","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210120929"]},{"id":"https://openalex.org/I58200834","display_name":"Southern Medical University","ror":"https://ror.org/01vjw4z39","country_code":"CN","type":"education","lineage":["https://openalex.org/I58200834"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cancan Qi","raw_affiliation_strings":["Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929"]},{"raw_affiliation_string":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]},{"raw_affiliation_string":"Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030389698","display_name":"Jie Gao","orcid":"https://orcid.org/0000-0002-3366-3156"},"institutions":[{"id":"https://openalex.org/I4210090868","display_name":"Second Affiliated Hospital of Guangzhou Medical University","ror":"https://ror.org/00a98yf63","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210090868"]},{"id":"https://openalex.org/I4210120929","display_name":"Zhujiang Hospital","ror":"https://ror.org/02mhxa927","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210120929"]},{"id":"https://openalex.org/I58200834","display_name":"Southern Medical University","ror":"https://ror.org/01vjw4z39","country_code":"CN","type":"education","lineage":["https://openalex.org/I58200834"]},{"id":"https://openalex.org/I92039509","display_name":"Guangzhou Medical University","ror":"https://ror.org/00zat6v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I92039509"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Gao","raw_affiliation_strings":["Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou Medical University , Guangzhou , China","Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China","Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou Medical University , Guangzhou , China","institution_ids":["https://openalex.org/I4210090868","https://openalex.org/I92039509"]},{"raw_affiliation_string":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929"]},{"raw_affiliation_string":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]},{"raw_affiliation_string":"Department of Gastroenterology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China","institution_ids":["https://openalex.org/I4210090868","https://openalex.org/I92039509"]},{"raw_affiliation_string":"Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100714225","display_name":"Xiaolong He","orcid":"https://orcid.org/0000-0002-1509-8739"},"institutions":[{"id":"https://openalex.org/I4210120929","display_name":"Zhujiang Hospital","ror":"https://ror.org/02mhxa927","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210120929"]},{"id":"https://openalex.org/I58200834","display_name":"Southern Medical University","ror":"https://ror.org/01vjw4z39","country_code":"CN","type":"education","lineage":["https://openalex.org/I58200834"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaolong He","raw_affiliation_strings":["Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929"]},{"raw_affiliation_string":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]},{"raw_affiliation_string":"Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100621285","display_name":"Jiaxuan Wang","orcid":"https://orcid.org/0000-0002-9311-1513"},"institutions":[{"id":"https://openalex.org/I4210120929","display_name":"Zhujiang Hospital","ror":"https://ror.org/02mhxa927","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210120929"]},{"id":"https://openalex.org/I58200834","display_name":"Southern Medical University","ror":"https://ror.org/01vjw4z39","country_code":"CN","type":"education","lineage":["https://openalex.org/I58200834"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiaxuan Wang","raw_affiliation_strings":["Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929"]},{"raw_affiliation_string":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]},{"raw_affiliation_string":"Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108467653","display_name":"Hongwei Zhou","orcid":"https://orcid.org/0000-0003-2472-8541"},"institutions":[{"id":"https://openalex.org/I4210120929","display_name":"Zhujiang Hospital","ror":"https://ror.org/02mhxa927","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210120929"]},{"id":"https://openalex.org/I58200834","display_name":"Southern Medical University","ror":"https://ror.org/01vjw4z39","country_code":"CN","type":"education","lineage":["https://openalex.org/I58200834"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hongwei Zhou","raw_affiliation_strings":["Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929"]},{"raw_affiliation_string":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]},{"raw_affiliation_string":"Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057137618","display_name":"Zhencheng Fang","orcid":"https://orcid.org/0000-0002-0137-4683"},"institutions":[{"id":"https://openalex.org/I4210120929","display_name":"Zhujiang Hospital","ror":"https://ror.org/02mhxa927","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210120929"]},{"id":"https://openalex.org/I58200834","display_name":"Southern Medical University","ror":"https://ror.org/01vjw4z39","country_code":"CN","type":"education","lineage":["https://openalex.org/I58200834"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhencheng Fang","raw_affiliation_strings":["Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"Microbiome Medicine Center , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929"]},{"raw_affiliation_string":"Southern Medical University , Department of Laboratory Medicine, Zhujiang Hospital, , Guangzhou , China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]},{"raw_affiliation_string":"Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China","institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5057137618","https://openalex.org/A5108467653"],"corresponding_institution_ids":["https://openalex.org/I4210120929","https://openalex.org/I58200834"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":7.4947,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":{"value":0.98073286,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"25","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9994000196456909,"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/T10066","display_name":"Gut microbiota and health","score":0.9994000196456909,"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":0.9976999759674072,"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/T10015","display_name":"Genomics and Phylogenetic Studies","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"}}],"keywords":[{"id":"https://openalex.org/keywords/probiotic","display_name":"Probiotic","score":0.9356484413146973},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.7548797130584717},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.535474419593811},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46519505977630615},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.24461808800697327},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.191640704870224},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.15251371264457703}],"concepts":[{"id":"https://openalex.org/C2780255968","wikidata":"https://www.wikidata.org/wiki/Q1816730","display_name":"Probiotic","level":3,"score":0.9356484413146973},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.7548797130584717},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.535474419593811},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46519505977630615},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.24461808800697327},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.191640704870224},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.15251371264457703}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":false},{"descriptor_ui":"D007802","descriptor_name":"Language","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":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019936","descriptor_name":"Probiotics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019936","descriptor_name":"Probiotics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019936","descriptor_name":"Probiotics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019936","descriptor_name":"Probiotics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054892","descriptor_name":"Metagenome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae085","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae085","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae085/56968598/bbae085.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":"pmid:38487846","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38487846","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:pubmedcentral.nih.gov:10940841","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10940841","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10940841/pdf/bbae085.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/bbae085","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae085","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae085/56968598/bbae085.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":[{"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities","score":0.6600000262260437}],"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/G1824455562","display_name":null,"funder_award_id":"81925026","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/G2495752485","display_name":null,"funder_award_id":"2022YFA","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program 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/G498353558","display_name":null,"funder_award_id":"82302610","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5836273602","display_name":null,"funder_award_id":"2022YFA0806400","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G5966715558","display_name":null,"funder_award_id":"82104625","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/G8398211057","display_name":null,"funder_award_id":"81925026","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G8636708979","display_name":null,"funder_award_id":"82102508","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4392870889.pdf"},"referenced_works_count":97,"referenced_works":["https://openalex.org/W1501531009","https://openalex.org/W1878521557","https://openalex.org/W1964027278","https://openalex.org/W1966327575","https://openalex.org/W1981761407","https://openalex.org/W2007227593","https://openalex.org/W2046657386","https://openalex.org/W2071841602","https://openalex.org/W2096128575","https://openalex.org/W2103901746","https://openalex.org/W2109848222","https://openalex.org/W2112364185","https://openalex.org/W2113679889","https://openalex.org/W2136500114","https://openalex.org/W2141920662","https://openalex.org/W2143485490","https://openalex.org/W2148652658","https://openalex.org/W2149074973","https://openalex.org/W2155860422","https://openalex.org/W2167419149","https://openalex.org/W2170747616","https://openalex.org/W2228687373","https://openalex.org/W2328023807","https://openalex.org/W2430356171","https://openalex.org/W2527237309","https://openalex.org/W2565336925","https://openalex.org/W2572263783","https://openalex.org/W2582377823","https://openalex.org/W2592811885","https://openalex.org/W2599417231","https://openalex.org/W2608502548","https://openalex.org/W2737522029","https://openalex.org/W2758908936","https://openalex.org/W2775651351","https://openalex.org/W2803787045","https://openalex.org/W2887711510","https://openalex.org/W2896461368","https://openalex.org/W2912030896","https://openalex.org/W2912990896","https://openalex.org/W2932049125","https://openalex.org/W2938868597","https://openalex.org/W2943320595","https://openalex.org/W2949831026","https://openalex.org/W2950464960","https://openalex.org/W2950657048","https://openalex.org/W2950868848","https://openalex.org/W2951254987","https://openalex.org/W2951912016","https://openalex.org/W2952668074","https://openalex.org/W2952926828","https://openalex.org/W2955541898","https://openalex.org/W2983483109","https://openalex.org/W2983698537","https://openalex.org/W2986476597","https://openalex.org/W2991815166","https://openalex.org/W3016016792","https://openalex.org/W3093220132","https://openalex.org/W3093451665","https://openalex.org/W3115540694","https://openalex.org/W3122309590","https://openalex.org/W3174714560","https://openalex.org/W3174867515","https://openalex.org/W3175752499","https://openalex.org/W3177468406","https://openalex.org/W3184180527","https://openalex.org/W3186698701","https://openalex.org/W3195289809","https://openalex.org/W3203343200","https://openalex.org/W3205913984","https://openalex.org/W3217216416","https://openalex.org/W3217463608","https://openalex.org/W3217466685","https://openalex.org/W4212796599","https://openalex.org/W4214943162","https://openalex.org/W4220680270","https://openalex.org/W4223444461","https://openalex.org/W4282022128","https://openalex.org/W4283321006","https://openalex.org/W4285741166","https://openalex.org/W4291017722","https://openalex.org/W4298006192","https://openalex.org/W4313557165","https://openalex.org/W4320486508","https://openalex.org/W4323351135","https://openalex.org/W4324311480","https://openalex.org/W4368362991","https://openalex.org/W4377220192","https://openalex.org/W4382137637","https://openalex.org/W4385406776","https://openalex.org/W4389438665","https://openalex.org/W6784203530","https://openalex.org/W6797786779","https://openalex.org/W6802733608","https://openalex.org/W6808461364","https://openalex.org/W6808503445","https://openalex.org/W6810778144","https://openalex.org/W6859248369"],"related_works":["https://openalex.org/W2210738511","https://openalex.org/W2474302342","https://openalex.org/W1910109602","https://openalex.org/W2080583581","https://openalex.org/W4297131566","https://openalex.org/W2017364432","https://openalex.org/W3156493549","https://openalex.org/W3195915274","https://openalex.org/W3158976456","https://openalex.org/W4285082713"],"abstract_inverted_index":{"Beneficial":[0],"bacteria":[1],"remain":[2],"largely":[3],"unexplored.":[4],"Lacking":[5],"systematic":[6,233],"methods,":[7],"understanding":[8],"probiotic":[9,20,33,78,84,102,134,154,174,190,225,237],"community":[10,191],"traits":[11],"becomes":[12],"challenging,":[13],"leading":[14],"to":[15,30,130],"various":[16,77,179],"conclusions":[17],"about":[18],"their":[19,101],"effects":[21,177],"among":[22],"different":[23,89,165,168],"publications.":[24],"We":[25,181,213],"developed":[26],"language":[27,218],"model-based":[28,219],"metaProbiotics":[29,129,220,240],"rapidly":[31],"detect":[32],"bins":[34,58,62,75,93,115],"from":[35,48,137],"metagenomes,":[36],"demonstrating":[37],"superior":[38],"performance":[39],"in":[40,97,195],"simulated":[41],"benchmark":[42],"datasets.":[43],"Testing":[44],"on":[45,109,171,178,235],"gut":[46,139,197],"metagenomes":[47],"probiotic-treated":[49],"individuals,":[50,99],"it":[51],"revealed":[52,76],"the":[53,64,110,122,161,172,189,216],"probioticity":[54],"of":[55,73,113,125,144,160,188],"intervention":[56],"strains-derived":[57],"and":[59,80,205,231],"other":[60],"probiotic-associated":[61],"beyond":[63],"training":[65],"data,":[66],"such":[67],"as":[68,83],"a":[69,132],"plasmid-like":[70],"bin.":[71],"Analyses":[72],"these":[74,92,114],"mechanisms":[79],"bai":[81],"operon":[82],"Ruminococcaceae's":[85],"potential":[86],"marker.":[87],"In":[88],"health-disease":[90],"cohorts,":[91],"were":[94],"more":[95,193],"common":[96],"healthy":[98],"signifying":[100],"role,":[103],"but":[104],"relevant":[105],"health":[106],"predictions":[107],"based":[108],"abundance":[111],"profiles":[112],"faced":[116],"cross-disease":[117],"challenges.":[118],"To":[119],"better":[120],"understand":[121],"heterogeneous":[123,176],"nature":[124],"probiotics,":[126],"we":[127],"used":[128],"construct":[131],"comprehensive":[133],"genome":[135],"set":[136,146],"global":[138],"metagenomic":[140,229],"data.":[141],"Module":[142],"analysis":[143],"this":[145],"shows":[147],"that":[148,184,215],"diseased":[149],"individuals":[150],"often":[151],"lack":[152],"certain":[153],"gene":[155,169,185,203],"modules,":[156],"with":[157],"significant":[158],"variation":[159],"missing":[162],"modules":[163,170],"across":[164],"diseases.":[166,180],"Additionally,":[167],"same":[173],"have":[175],"thus":[182],"believe":[183],"function":[186],"integrity":[187],"is":[192],"crucial":[194],"maintaining":[196],"homeostasis":[198],"than":[199],"merely":[200],"increasing":[201],"specific":[202],"abundance,":[204],"adding":[206],"probiotics":[207],"indiscriminately":[208],"might":[209],"not":[210],"boost":[211],"health.":[212],"expect":[214],"innovative":[217],"tool":[221],"will":[222],"promote":[223],"novel":[224],"discovery":[226],"using":[227],"large-scale":[228],"data":[230],"facilitate":[232],"research":[234],"bacterial":[236],"effects.":[238],"The":[239],"program":[241],"can":[242],"be":[243],"freely":[244],"downloaded":[245],"at":[246],"https://github.com/zhenchengfang/metaProbiotics.":[247]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":21},{"year":2024,"cited_by_count":2}],"updated_date":"2026-04-15T08:11:43.952461","created_date":"2025-10-10T00:00:00"}
