{"id":"https://openalex.org/W4399512891","doi":"https://doi.org/10.1093/bib/bbae264","title":"Multi-omic analysis tools for microbial metabolites prediction","display_name":"Multi-omic analysis tools for microbial metabolites prediction","publication_year":2024,"publication_date":"2024-05-23","ids":{"openalex":"https://openalex.org/W4399512891","doi":"https://doi.org/10.1093/bib/bbae264","pmid":"https://pubmed.ncbi.nlm.nih.gov/38859767"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae264","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae264","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae264/58185828/bbae264.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/25/4/bbae264/58185828/bbae264.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040092895","display_name":"Shengbo Wu","orcid":"https://orcid.org/0000-0001-7497-2935"},"institutions":[{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]},{"id":"https://openalex.org/I192209268","display_name":"Shaoxing University","ror":"https://ror.org/0435tej63","country_code":"CN","type":"education","lineage":["https://openalex.org/I192209268"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shengbo Wu","raw_affiliation_strings":["School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China","Zhejiang Institute of Tianjin University, Shaoxing , Shaoxing 312300 , China"],"raw_orcid":"https://orcid.org/0000-0001-7497-2935","affiliations":[{"raw_affiliation_string":"School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China","institution_ids":["https://openalex.org/I162868743"]},{"raw_affiliation_string":"Zhejiang Institute of Tianjin University, Shaoxing , Shaoxing 312300 , China","institution_ids":["https://openalex.org/I192209268","https://openalex.org/I162868743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075504252","display_name":"Haonan Zhou","orcid":"https://orcid.org/0000-0003-2056-6514"},"institutions":[{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haonan Zhou","raw_affiliation_strings":["School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China","institution_ids":["https://openalex.org/I162868743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048715626","display_name":"Danlei Chen","orcid":"https://orcid.org/0000-0003-4903-1222"},"institutions":[{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]},{"id":"https://openalex.org/I192209268","display_name":"Shaoxing University","ror":"https://ror.org/0435tej63","country_code":"CN","type":"education","lineage":["https://openalex.org/I192209268"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Danlei Chen","raw_affiliation_strings":["School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China","Zhejiang Institute of Tianjin University, Shaoxing , Shaoxing 312300 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China","institution_ids":["https://openalex.org/I162868743"]},{"raw_affiliation_string":"Zhejiang Institute of Tianjin University, Shaoxing , Shaoxing 312300 , China","institution_ids":["https://openalex.org/I192209268","https://openalex.org/I162868743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108647097","display_name":"Yutong Lu","orcid":null},"institutions":[{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]},{"id":"https://openalex.org/I192209268","display_name":"Shaoxing University","ror":"https://ror.org/0435tej63","country_code":"CN","type":"education","lineage":["https://openalex.org/I192209268"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yutong Lu","raw_affiliation_strings":["Zhejiang Institute of Tianjin University, Shaoxing , Shaoxing 312300 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zhejiang Institute of Tianjin University, Shaoxing , Shaoxing 312300 , China","institution_ids":["https://openalex.org/I192209268","https://openalex.org/I162868743"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100747558","display_name":"Yanni Li","orcid":"https://orcid.org/0000-0001-9184-5786"},"institutions":[{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanni Li","raw_affiliation_strings":["Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University) , Tianjin 300072 , China","School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University) , Tianjin 300072 , China","institution_ids":["https://openalex.org/I162868743"]},{"raw_affiliation_string":"School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China","institution_ids":["https://openalex.org/I162868743"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5114175306","display_name":"Jianjun Qiao","orcid":"https://orcid.org/0000-0002-8126-2074"},"institutions":[{"id":"https://openalex.org/I162868743","display_name":"Tianjin University","ror":"https://ror.org/012tb2g32","country_code":"CN","type":"education","lineage":["https://openalex.org/I162868743"]},{"id":"https://openalex.org/I192209268","display_name":"Shaoxing University","ror":"https://ror.org/0435tej63","country_code":"CN","type":"education","lineage":["https://openalex.org/I192209268"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianjun Qiao","raw_affiliation_strings":["Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University , Tianjin 300072 , China","Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University) , Tianjin 300072 , China","School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China","Zhejiang Institute of Tianjin University, Shaoxing , Shaoxing 312300 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University , Tianjin 300072 , China","institution_ids":["https://openalex.org/I162868743"]},{"raw_affiliation_string":"Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University) , Tianjin 300072 , China","institution_ids":["https://openalex.org/I162868743"]},{"raw_affiliation_string":"School of Chemical Engineering and Technology, Tianjin University , Tianjin 300072 , China","institution_ids":["https://openalex.org/I162868743"]},{"raw_affiliation_string":"Zhejiang Institute of Tianjin University, Shaoxing , Shaoxing 312300 , China","institution_ids":["https://openalex.org/I192209268","https://openalex.org/I162868743"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"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":3.2658,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.92644683,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9995999932289124,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9995999932289124,"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":0.9991000294685364,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9990000128746033,"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/metabolomics","display_name":"Metabolomics","score":0.6938537359237671},{"id":"https://openalex.org/keywords/omics","display_name":"Omics","score":0.6718364953994751},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5353171825408936},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.48290443420410156},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48006758093833923},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.477128267288208},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4346574544906616},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4288950562477112},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3269287943840027},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3092890977859497},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.10026615858078003},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.06734806299209595}],"concepts":[{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.6938537359237671},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.6718364953994751},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5353171825408936},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.48290443420410156},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48006758093833923},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.477128267288208},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4346574544906616},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4288950562477112},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3269287943840027},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3092890977859497},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.10026615858078003},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.06734806299209595},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","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":"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":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055442","descriptor_name":"Metabolome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae264","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae264","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae264/58185828/bbae264.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38859767","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38859767","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:11165163","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11165163","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11165163/pdf/bbae264.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae264","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae264","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae264/58185828/bbae264.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4300000071525574,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G4702043860","display_name":null,"funder_award_id":"2019YFA0904104","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G4819182094","display_name":null,"funder_award_id":"2019YFA0904104","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7271732890","display_name":null,"funder_award_id":"2023\u00a0M732599","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G7327463176","display_name":null,"funder_award_id":"2019YFA0905603","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8405865949","display_name":null,"funder_award_id":"32300022","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8762687678","display_name":null,"funder_award_id":"2019YFA0905603","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program 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/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"},{"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/W4399512891.pdf"},"referenced_works_count":126,"referenced_works":["https://openalex.org/W1535893202","https://openalex.org/W1898263885","https://openalex.org/W1965985248","https://openalex.org/W1982185581","https://openalex.org/W1990935073","https://openalex.org/W2013455629","https://openalex.org/W2020541351","https://openalex.org/W2031893281","https://openalex.org/W2059327215","https://openalex.org/W2065416213","https://openalex.org/W2075320162","https://openalex.org/W2088822458","https://openalex.org/W2107158607","https://openalex.org/W2118258530","https://openalex.org/W2132341951","https://openalex.org/W2137652007","https://openalex.org/W2139119508","https://openalex.org/W2145241604","https://openalex.org/W2150827955","https://openalex.org/W2151831732","https://openalex.org/W2159675211","https://openalex.org/W2162854463","https://openalex.org/W2168546553","https://openalex.org/W2170591794","https://openalex.org/W2187341651","https://openalex.org/W2229450847","https://openalex.org/W2252545027","https://openalex.org/W2256742438","https://openalex.org/W2410975458","https://openalex.org/W2559588208","https://openalex.org/W2608736608","https://openalex.org/W2615786037","https://openalex.org/W2749464300","https://openalex.org/W2756996412","https://openalex.org/W2765371419","https://openalex.org/W2794743485","https://openalex.org/W2802486069","https://openalex.org/W2807572295","https://openalex.org/W2808731431","https://openalex.org/W2808845633","https://openalex.org/W2809439583","https://openalex.org/W2899153547","https://openalex.org/W2922522932","https://openalex.org/W2950173838","https://openalex.org/W2950468843","https://openalex.org/W2950570200","https://openalex.org/W2951891306","https://openalex.org/W2958564218","https://openalex.org/W2978901899","https://openalex.org/W2980285196","https://openalex.org/W2982582384","https://openalex.org/W2987653794","https://openalex.org/W2989934249","https://openalex.org/W2990471452","https://openalex.org/W2993166334","https://openalex.org/W2997003451","https://openalex.org/W2997918501","https://openalex.org/W3000669201","https://openalex.org/W3006796998","https://openalex.org/W3037719963","https://openalex.org/W3081850759","https://openalex.org/W3088203083","https://openalex.org/W3091334475","https://openalex.org/W3091539089","https://openalex.org/W3091901779","https://openalex.org/W3094967361","https://openalex.org/W3095554357","https://openalex.org/W3105895642","https://openalex.org/W3107629351","https://openalex.org/W3112376646","https://openalex.org/W3113079090","https://openalex.org/W3121081543","https://openalex.org/W3123151863","https://openalex.org/W3134163041","https://openalex.org/W3136154691","https://openalex.org/W3138215020","https://openalex.org/W3153641190","https://openalex.org/W3159995035","https://openalex.org/W3160890790","https://openalex.org/W3161544633","https://openalex.org/W3161596995","https://openalex.org/W3162905226","https://openalex.org/W3163271454","https://openalex.org/W3167554945","https://openalex.org/W3173652646","https://openalex.org/W3200941727","https://openalex.org/W3210489033","https://openalex.org/W3212063608","https://openalex.org/W3216071587","https://openalex.org/W4206145266","https://openalex.org/W4206517007","https://openalex.org/W4206947476","https://openalex.org/W4210832235","https://openalex.org/W4212916956","https://openalex.org/W4213345389","https://openalex.org/W4214943162","https://openalex.org/W4220753051","https://openalex.org/W4225363104","https://openalex.org/W4225612076","https://openalex.org/W4281681342","https://openalex.org/W4282939468","https://openalex.org/W4286512419","https://openalex.org/W4290052546","https://openalex.org/W4293081069","https://openalex.org/W4294012193","https://openalex.org/W4295458983","https://openalex.org/W4297457250","https://openalex.org/W4306411778","https://openalex.org/W4306412223","https://openalex.org/W4307412745","https://openalex.org/W4307847181","https://openalex.org/W4308449887","https://openalex.org/W4309506674","https://openalex.org/W4315784590","https://openalex.org/W4317390278","https://openalex.org/W4320486508","https://openalex.org/W4327947056","https://openalex.org/W4362471278","https://openalex.org/W4366442044","https://openalex.org/W4388721902","https://openalex.org/W4388735079","https://openalex.org/W4388933225","https://openalex.org/W4391262585","https://openalex.org/W6689111526","https://openalex.org/W6770111283","https://openalex.org/W6784570739"],"related_works":["https://openalex.org/W3208879153","https://openalex.org/W2208562635","https://openalex.org/W2166430819","https://openalex.org/W2184120357","https://openalex.org/W2126088744","https://openalex.org/W2366576702","https://openalex.org/W1605828363","https://openalex.org/W2062993691","https://openalex.org/W3149361930","https://openalex.org/W2115386182"],"abstract_inverted_index":{"How":[0],"to":[1,25,40,96,145,193],"resolve":[2],"the":[3,27,42,57,92,99,103,106,114,137,140,158],"metabolic":[4,107],"dark":[5],"matter":[6],"of":[7,31,50,59,72,105,109,142,148,160],"microorganisms":[8],"has":[9],"long":[10],"been":[11,23],"a":[12,69],"challenging":[13],"problem":[14],"in":[15,91,178],"discovering":[16],"active":[17],"molecules.":[18],"Diverse":[19],"omics":[20,67],"tools":[21,53,86,182],"have":[22],"developed":[24],"guide":[26],"discovery":[28],"and":[29,81,131,152,168,176,196],"characterization":[30],"various":[32],"microbial":[33,88,150,189],"metabolites,":[34],"which":[35],"make":[36],"it":[37],"gradually":[38],"possible":[39],"predict":[41,146],"overall":[43],"metabolites":[44,89,147,190],"for":[45,56,87,98,183],"individual":[46],"strains.":[47],"The":[48],"combinations":[49],"multi-omic":[51,100,180],"analysis":[52,85,181],"effectively":[54],"compensates":[55],"shortcomings":[58],"current":[60],"studies":[61],"that":[62,125,191],"focus":[63],"only":[64],"on":[65,102,117,127,139,187],"single":[66],"or":[68,123],"broad":[70],"class":[71],"metabolites.":[73],"In":[74],"this":[75],"review,":[76],"we":[77,112,135,172],"systematically":[78],"update,":[79],"categorize":[80],"sort":[82],"out":[83],"different":[84,118,149],"prediction":[90,120,186],"last":[93],"five":[94],"years":[95],"appeal":[97],"combination":[101,159],"understanding":[104],"nature":[108],"microbes.":[110],"First,":[111],"provide":[113],"general":[115],"survey":[116],"updated":[119],"databases,":[121],"webservers,":[122],"software":[124],"based":[126],"genomics,":[128],"transcriptomics,":[129],"proteomics,":[130],"metabolomics,":[132],"respectively.":[133],"Then,":[134],"discuss":[136],"essentiality":[138],"integration":[141],"multi-omics":[143],"data":[144],"strains":[151],"communities,":[153],"as":[154,156,164],"well":[155],"stressing":[157],"other":[161],"techniques,":[162],"such":[163],"systems":[165],"biology":[166],"methods":[167],"data-driven":[169],"algorithms.":[170],"Finally,":[171],"identify":[173],"key":[174],"challenges":[175],"trends":[177],"developing":[179],"more":[184],"comprehensive":[185],"diverse":[188],"contribute":[192],"human":[194],"health":[195],"disease":[197],"treatment.":[198]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
