{"id":"https://openalex.org/W4414934084","doi":"https://doi.org/10.1093/bib/bbaf502","title":"Multi-omics time-series analysis in microbiome research: a systematic review","display_name":"Multi-omics time-series analysis in microbiome research: a systematic review","publication_year":2025,"publication_date":"2025-08-31","ids":{"openalex":"https://openalex.org/W4414934084","doi":"https://doi.org/10.1093/bib/bbaf502","pmid":"https://pubmed.ncbi.nlm.nih.gov/41052276"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf502","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf502","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":"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://doi.org/10.1093/bib/bbaf502","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045581473","display_name":"Moiz Khan Sherwani","orcid":"https://orcid.org/0000-0001-6061-6753"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Moiz Khan Sherwani","raw_affiliation_strings":["Center for Evolutionary Hologenomics , GLOBE Institute, University of Copenhagen, \u00d8ster Farimagsgade 5, 1353 Copenhagen K,","Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, \u00d8ster Farimagsgade 5, 1353 Copenhagen K, Denmark"],"raw_orcid":"https://orcid.org/0000-0001-6061-6753","affiliations":[{"raw_affiliation_string":"Center for Evolutionary Hologenomics , GLOBE Institute, University of Copenhagen, \u00d8ster Farimagsgade 5, 1353 Copenhagen K,","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, \u00d8ster Farimagsgade 5, 1353 Copenhagen K, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011112541","display_name":"Matti O. Ruuskanen","orcid":"https://orcid.org/0000-0003-4221-2880"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I16231767","display_name":"Turku University of Applied Sciences","ror":"https://ror.org/04s0yt949","country_code":"FI","type":"education","lineage":["https://openalex.org/I16231767"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Matti O Ruuskanen","raw_affiliation_strings":["Department of Computing , University of Turku, 20014, Turku,","Department of Computing, University of Turku, 20014, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computing , University of Turku, 20014, Turku,","institution_ids":["https://openalex.org/I155660961","https://openalex.org/I16231767"]},{"raw_affiliation_string":"Department of Computing, University of Turku, 20014, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052888170","display_name":"Dylan Feldner-Busztin","orcid":"https://orcid.org/0000-0002-3984-0125"},"institutions":[{"id":"https://openalex.org/I113358080","display_name":"Champalimaud Foundation","ror":"https://ror.org/03g001n57","country_code":"PT","type":"facility","lineage":["https://openalex.org/I113358080"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Dylan Feldner-Busztin","raw_affiliation_strings":["Champalimaud Research , Champalimaud Centre for the Unknown, Av. Bras\u00edlia, 1400-038 Lisbon,","Champalimaud Research, Champalimaud Centre for the Unknown, Av. Bras\u00edlia, 1400-038 Lisbon, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Champalimaud Research , Champalimaud Centre for the Unknown, Av. Bras\u00edlia, 1400-038 Lisbon,","institution_ids":["https://openalex.org/I113358080"]},{"raw_affiliation_string":"Champalimaud Research, Champalimaud Centre for the Unknown, Av. Bras\u00edlia, 1400-038 Lisbon, Portugal","institution_ids":["https://openalex.org/I113358080"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023185271","display_name":"Panos Firbas","orcid":null},"institutions":[{"id":"https://openalex.org/I113358080","display_name":"Champalimaud Foundation","ror":"https://ror.org/03g001n57","country_code":"PT","type":"facility","lineage":["https://openalex.org/I113358080"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Panos Nisantzis Firbas","raw_affiliation_strings":["Champalimaud Research , Champalimaud Centre for the Unknown, Av. Bras\u00edlia, 1400-038 Lisbon,","Champalimaud Research, Champalimaud Centre for the Unknown, Av. Bras\u00edlia, 1400-038 Lisbon, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Champalimaud Research , Champalimaud Centre for the Unknown, Av. Bras\u00edlia, 1400-038 Lisbon,","institution_ids":["https://openalex.org/I113358080"]},{"raw_affiliation_string":"Champalimaud Research, Champalimaud Centre for the Unknown, Av. Bras\u00edlia, 1400-038 Lisbon, Portugal","institution_ids":["https://openalex.org/I113358080"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053170394","display_name":"Gergely Boza","orcid":"https://orcid.org/0000-0001-6453-8254"},"institutions":[{"id":"https://openalex.org/I4210125010","display_name":"Institute of Aquatic Ecology","ror":"https://ror.org/02xywr964","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4210125010","https://openalex.org/I4210134135","https://openalex.org/I4387152226"]},{"id":"https://openalex.org/I4210134135","display_name":"HUN-REN Centre for Ecological Research","ror":"https://ror.org/04bhfmv97","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4210134135","https://openalex.org/I4387152226"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Gergely Boza","raw_affiliation_strings":["HUN-REN , Institute of Evolution, Centre for Ecological Research, H-1113 Budapest, Karolina Road 29,","HUN-REN, Institute of Evolution, Centre for Ecological Research, H-1113 Budapest, Karolina Road 29, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HUN-REN , Institute of Evolution, Centre for Ecological Research, H-1113 Budapest, Karolina Road 29,","institution_ids":["https://openalex.org/I4210134135"]},{"raw_affiliation_string":"HUN-REN, Institute of Evolution, Centre for Ecological Research, H-1113 Budapest, Karolina Road 29, Hungary","institution_ids":["https://openalex.org/I4210125010","https://openalex.org/I4210134135"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048953420","display_name":"\u00c1gnes M\u00f3r\u00e9h","orcid":"https://orcid.org/0000-0003-0948-9781"},"institutions":[{"id":"https://openalex.org/I4210125010","display_name":"Institute of Aquatic Ecology","ror":"https://ror.org/02xywr964","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4210125010","https://openalex.org/I4210134135","https://openalex.org/I4387152226"]},{"id":"https://openalex.org/I4210134135","display_name":"HUN-REN Centre for Ecological Research","ror":"https://ror.org/04bhfmv97","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4210134135","https://openalex.org/I4387152226"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"\u00c1gnes M\u00f3r\u00e9h","raw_affiliation_strings":["HUN-REN , Institute of Evolution, Centre for Ecological Research, H-1113 Budapest, Karolina Road 29,","HUN-REN, Institute of Evolution, Centre for Ecological Research, H-1113 Budapest, Karolina Road 29, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HUN-REN , Institute of Evolution, Centre for Ecological Research, H-1113 Budapest, Karolina Road 29,","institution_ids":["https://openalex.org/I4210134135"]},{"raw_affiliation_string":"HUN-REN, Institute of Evolution, Centre for Ecological Research, H-1113 Budapest, Karolina Road 29, Hungary","institution_ids":["https://openalex.org/I4210125010","https://openalex.org/I4210134135"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026860301","display_name":"Tuomas Borman","orcid":"https://orcid.org/0000-0002-8563-8884"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I16231767","display_name":"Turku University of Applied Sciences","ror":"https://ror.org/04s0yt949","country_code":"FI","type":"education","lineage":["https://openalex.org/I16231767"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Tuomas Borman","raw_affiliation_strings":["Department of Computing , University of Turku, 20014, Turku,","Department of Computing, University of Turku, 20014, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computing , University of Turku, 20014, Turku,","institution_ids":["https://openalex.org/I155660961","https://openalex.org/I16231767"]},{"raw_affiliation_string":"Department of Computing, University of Turku, 20014, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032078231","display_name":"Pande Putu Erawijantari","orcid":"https://orcid.org/0000-0002-5173-6347"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I16231767","display_name":"Turku University of Applied Sciences","ror":"https://ror.org/04s0yt949","country_code":"FI","type":"education","lineage":["https://openalex.org/I16231767"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Pande Putu Erawijantari","raw_affiliation_strings":["Department of Computing , University of Turku, 20014, Turku,","Department of Computing, University of Turku, 20014, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computing , University of Turku, 20014, Turku,","institution_ids":["https://openalex.org/I155660961","https://openalex.org/I16231767"]},{"raw_affiliation_string":"Department of Computing, University of Turku, 20014, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066422792","display_name":"Istv\u00e1n Scheuring","orcid":"https://orcid.org/0000-0002-8108-8897"},"institutions":[{"id":"https://openalex.org/I4210125010","display_name":"Institute of Aquatic Ecology","ror":"https://ror.org/02xywr964","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4210125010","https://openalex.org/I4210134135","https://openalex.org/I4387152226"]},{"id":"https://openalex.org/I4210134135","display_name":"HUN-REN Centre for Ecological Research","ror":"https://ror.org/04bhfmv97","country_code":"HU","type":"facility","lineage":["https://openalex.org/I4210134135","https://openalex.org/I4387152226"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Istv\u00e1n Scheuring","raw_affiliation_strings":["HUN-REN , Institute of Evolution, Centre for Ecological Research, H-1113 Budapest, Karolina Road 29,","HUN-REN, Institute of Evolution, Centre for Ecological Research, H-1113 Budapest, Karolina Road 29, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"HUN-REN , Institute of Evolution, Centre for Ecological Research, H-1113 Budapest, Karolina Road 29,","institution_ids":["https://openalex.org/I4210134135"]},{"raw_affiliation_string":"HUN-REN, Institute of Evolution, Centre for Ecological Research, H-1113 Budapest, Karolina Road 29, Hungary","institution_ids":["https://openalex.org/I4210125010","https://openalex.org/I4210134135"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009328156","display_name":"Shyam Gopalakrishnan","orcid":"https://orcid.org/0000-0002-2004-6810"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Shyam Gopalakrishnan","raw_affiliation_strings":["Center for Evolutionary Hologenomics , GLOBE Institute, University of Copenhagen, \u00d8ster Farimagsgade 5, 1353 Copenhagen K,","Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, \u00d8ster Farimagsgade 5, 1353 Copenhagen K, Denmark"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Evolutionary Hologenomics , GLOBE Institute, University of Copenhagen, \u00d8ster Farimagsgade 5, 1353 Copenhagen K,","institution_ids":["https://openalex.org/I124055696"]},{"raw_affiliation_string":"Center for Evolutionary Hologenomics, GLOBE Institute, University of Copenhagen, \u00d8ster Farimagsgade 5, 1353 Copenhagen K, Denmark","institution_ids":["https://openalex.org/I124055696"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082648063","display_name":"Leo Lahti","orcid":"https://orcid.org/0000-0001-5537-637X"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]},{"id":"https://openalex.org/I16231767","display_name":"Turku University of Applied Sciences","ror":"https://ror.org/04s0yt949","country_code":"FI","type":"education","lineage":["https://openalex.org/I16231767"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Leo Lahti","raw_affiliation_strings":["Department of Computing , University of Turku, 20014, Turku,","Department of Computing, University of Turku, 20014, Turku, Finland"],"raw_orcid":"https://orcid.org/0000-0001-5537-637X","affiliations":[{"raw_affiliation_string":"Department of Computing , University of Turku, 20014, Turku,","institution_ids":["https://openalex.org/I155660961","https://openalex.org/I16231767"]},{"raw_affiliation_string":"Department of Computing, University of Turku, 20014, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]}],"institutions":[],"countries_distinct_count":4,"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":12.3347,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.99097309,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"26","issue":"5","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":0.6338000297546387,"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":0.6338000297546387,"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":0.5440000295639038,"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/microbiome","display_name":"Microbiome","score":0.6389999985694885},{"id":"https://openalex.org/keywords/scope","display_name":"Scope (computer science)","score":0.4205999970436096},{"id":"https://openalex.org/keywords/systematic-review","display_name":"Systematic review","score":0.3465999960899353},{"id":"https://openalex.org/keywords/host","display_name":"Host (biology)","score":0.3359000086784363},{"id":"https://openalex.org/keywords/variation","display_name":"Variation (astronomy)","score":0.3199999928474426},{"id":"https://openalex.org/keywords/longitudinal-data","display_name":"Longitudinal data","score":0.313400000333786},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.3091000020503998},{"id":"https://openalex.org/keywords/thematic-analysis","display_name":"Thematic analysis","score":0.30469998717308044}],"concepts":[{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.7228000164031982},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.6389999985694885},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5666000247001648},{"id":"https://openalex.org/C2778012447","wikidata":"https://www.wikidata.org/wiki/Q1034415","display_name":"Scope (computer science)","level":2,"score":0.4205999970436096},{"id":"https://openalex.org/C189708586","wikidata":"https://www.wikidata.org/wiki/Q1504425","display_name":"Systematic review","level":3,"score":0.3465999960899353},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.3359000086784363},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.322299987077713},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.3199999928474426},{"id":"https://openalex.org/C3020672099","wikidata":"https://www.wikidata.org/wiki/Q857354","display_name":"Longitudinal data","level":2,"score":0.313400000333786},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.3091000020503998},{"id":"https://openalex.org/C74196892","wikidata":"https://www.wikidata.org/wiki/Q7781188","display_name":"Thematic analysis","level":3,"score":0.30469998717308044},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.28949999809265137},{"id":"https://openalex.org/C63882131","wikidata":"https://www.wikidata.org/wiki/Q17122954","display_name":"Strengths and weaknesses","level":2,"score":0.2806999981403351},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.2721000015735626},{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.2680000066757202},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.2637999951839447},{"id":"https://openalex.org/C112930515","wikidata":"https://www.wikidata.org/wiki/Q4389547","display_name":"Risk analysis (engineering)","level":1,"score":0.25769999623298645},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.25459998846054077},{"id":"https://openalex.org/C91478284","wikidata":"https://www.wikidata.org/wiki/Q6623796","display_name":"Human microbiome","level":3,"score":0.2508000135421753},{"id":"https://openalex.org/C14224292","wikidata":"https://www.wikidata.org/wiki/Q13600188","display_name":"Conceptual framework","level":2,"score":0.25029999017715454}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1093/bib/bbaf502","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf502","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":"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:41052276","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41052276","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:11307961","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12499790","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12499790","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12499790/","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/c508d472-acd2-45d8-995d-e71ffff5b4f3","is_oa":true,"landing_page_url":"https://researchprofiles.ku.dk/da/publications/c508d472-acd2-45d8-995d-e71ffff5b4f3","pdf_url":null,"source":{"id":"https://openalex.org/S4306401983","display_name":"Research at the University of Copenhagen (University of Copenhagen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I124055696","host_organization_name":"University of Copenhagen","host_organization_lineage":["https://openalex.org/I124055696"],"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":"Sherwani , M K , Ruuskanen , M O , Feldner-Busztin , D , Firbas , P N , Boza , G , M\u00f3r\u00e9h , \u00c1 , Borman , T , Erawijantari , P P , Scheuring , I , Gopalakrishnan , S & Lahti , L 2025 , ' Multi-omics time-series analysis in microbiome research : a systematic review ' , Briefings in Bioinformatics , vol. 26 , no. 5 , bbaf502 . https://doi.org/10.1093/bib/bbaf502","raw_type":"article"},{"id":"pmh:oai:www.utupub.fi:10024/195869","is_oa":false,"landing_page_url":"https://www.utupub.fi/handle/10024/195869","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf502","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf502","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":"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":[],"awards":[{"id":"https://openalex.org/G4855324266","display_name":"Unified computational solutions to disentangle biological interactions in multi-omics data","funder_award_id":"952914","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7842005466","display_name":null,"funder_award_id":"Horizon 2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":190,"referenced_works":["https://openalex.org/W1513100667","https://openalex.org/W1978221234","https://openalex.org/W1978656070","https://openalex.org/W1987219048","https://openalex.org/W1987321525","https://openalex.org/W2014426403","https://openalex.org/W2054286320","https://openalex.org/W2083618510","https://openalex.org/W2098192588","https://openalex.org/W2151277589","https://openalex.org/W2171176373","https://openalex.org/W2208222770","https://openalex.org/W2235823035","https://openalex.org/W2287591593","https://openalex.org/W2559454592","https://openalex.org/W2591216002","https://openalex.org/W2593643932","https://openalex.org/W2624850887","https://openalex.org/W2657063209","https://openalex.org/W2738650962","https://openalex.org/W2767108658","https://openalex.org/W2775077703","https://openalex.org/W2784691731","https://openalex.org/W2790671088","https://openalex.org/W2807934525","https://openalex.org/W2808845633","https://openalex.org/W2860509233","https://openalex.org/W2884186750","https://openalex.org/W2903552683","https://openalex.org/W2907574677","https://openalex.org/W2910532619","https://openalex.org/W2912260118","https://openalex.org/W2918073486","https://openalex.org/W2921144944","https://openalex.org/W2922472044","https://openalex.org/W2932741476","https://openalex.org/W2947189704","https://openalex.org/W2948018512","https://openalex.org/W2952076809","https://openalex.org/W2952904999","https://openalex.org/W2953251770","https://openalex.org/W2953583829","https://openalex.org/W2971277259","https://openalex.org/W2971887687","https://openalex.org/W2971999614","https://openalex.org/W2974361058","https://openalex.org/W2979316703","https://openalex.org/W2987866500","https://openalex.org/W2989807288","https://openalex.org/W3003192283","https://openalex.org/W3010909871","https://openalex.org/W3011252329","https://openalex.org/W3011493793","https://openalex.org/W3029460150","https://openalex.org/W3029490310","https://openalex.org/W3037286204","https://openalex.org/W3038063066","https://openalex.org/W3042408668","https://openalex.org/W3044437943","https://openalex.org/W3046849576","https://openalex.org/W3080957951","https://openalex.org/W3081717401","https://openalex.org/W3082784190","https://openalex.org/W3084404023","https://openalex.org/W3085241016","https://openalex.org/W3086205341","https://openalex.org/W3087101817","https://openalex.org/W3088455929","https://openalex.org/W3091852264","https://openalex.org/W3093335133","https://openalex.org/W3101088963","https://openalex.org/W3106739077","https://openalex.org/W3108714922","https://openalex.org/W3109541743","https://openalex.org/W3110332441","https://openalex.org/W3111955104","https://openalex.org/W3118085634","https://openalex.org/W3118379911","https://openalex.org/W3118615836","https://openalex.org/W3125442646","https://openalex.org/W3126460810","https://openalex.org/W3127271359","https://openalex.org/W3128396492","https://openalex.org/W3129083536","https://openalex.org/W3133408889","https://openalex.org/W3134830631","https://openalex.org/W3134979737","https://openalex.org/W3141185229","https://openalex.org/W3152171186","https://openalex.org/W3159459899","https://openalex.org/W3167308207","https://openalex.org/W3169276553","https://openalex.org/W3169837827","https://openalex.org/W3170515317","https://openalex.org/W3171380437","https://openalex.org/W3171715282","https://openalex.org/W3173339746","https://openalex.org/W3173669269","https://openalex.org/W3177080725","https://openalex.org/W3180860571","https://openalex.org/W3182795721","https://openalex.org/W3186924370","https://openalex.org/W3191104078","https://openalex.org/W3191661929","https://openalex.org/W3193439709","https://openalex.org/W3193838886","https://openalex.org/W3197197951","https://openalex.org/W3199498600","https://openalex.org/W3199739642","https://openalex.org/W3201501887","https://openalex.org/W3201792477","https://openalex.org/W3202222059","https://openalex.org/W3206417922","https://openalex.org/W3206480417","https://openalex.org/W3207270823","https://openalex.org/W3211779138","https://openalex.org/W3214112664","https://openalex.org/W3216247689","https://openalex.org/W3217102738","https://openalex.org/W4200090677","https://openalex.org/W4200602277","https://openalex.org/W4205219984","https://openalex.org/W4205764570","https://openalex.org/W4205838693","https://openalex.org/W4206896921","https://openalex.org/W4207060592","https://openalex.org/W4210619028","https://openalex.org/W4210979106","https://openalex.org/W4212763698","https://openalex.org/W4213211303","https://openalex.org/W4213330983","https://openalex.org/W4214758482","https://openalex.org/W4220684263","https://openalex.org/W4220855574","https://openalex.org/W4220979272","https://openalex.org/W4221015681","https://openalex.org/W4221016109","https://openalex.org/W4221130426","https://openalex.org/W4224089448","https://openalex.org/W4225333916","https://openalex.org/W4225388682","https://openalex.org/W4225626778","https://openalex.org/W4226006837","https://openalex.org/W4252676770","https://openalex.org/W4280580007","https://openalex.org/W4281555558","https://openalex.org/W4282035552","https://openalex.org/W4283017342","https://openalex.org/W4303946191","https://openalex.org/W4306775982","https://openalex.org/W4309771113","https://openalex.org/W4313455000","https://openalex.org/W4315928722","https://openalex.org/W4317498917","https://openalex.org/W4324020371","https://openalex.org/W4327639828","https://openalex.org/W4362596377","https://openalex.org/W4365454296","https://openalex.org/W4366087654","https://openalex.org/W4366601981","https://openalex.org/W4367313099","https://openalex.org/W4376223669","https://openalex.org/W4379376577","https://openalex.org/W4382245237","https://openalex.org/W4382459409","https://openalex.org/W4383710649","https://openalex.org/W4384920706","https://openalex.org/W4386452933","https://openalex.org/W4386615105","https://openalex.org/W4387400300","https://openalex.org/W4388098928","https://openalex.org/W4388126752","https://openalex.org/W4388626021","https://openalex.org/W4389146527","https://openalex.org/W4390229775","https://openalex.org/W4390661914","https://openalex.org/W4390729418","https://openalex.org/W4390811928","https://openalex.org/W4391386649","https://openalex.org/W4391567532","https://openalex.org/W4391688626","https://openalex.org/W4392626938","https://openalex.org/W4392953781","https://openalex.org/W4399075652","https://openalex.org/W4402223484","https://openalex.org/W4403052529","https://openalex.org/W4403349079","https://openalex.org/W4404234503","https://openalex.org/W4407318930","https://openalex.org/W4410105994"],"related_works":[],"abstract_inverted_index":{"Recent":[0],"developments":[1],"in":[2,76,217],"data":[3,55,73,210],"generation":[4],"have":[5,89],"opened":[6],"up":[7,82],"unprecedented":[8],"insights":[9],"into":[10,177],"living":[11],"systems.":[12],"It":[13],"has":[14,60],"been":[15,92],"recognized":[16],"that":[17,63,108],"integrating":[18],"and":[19,40,83,95,112,132,144,158,161,168,187,198,212],"characterizing":[20],"temporal":[21],"variation":[22],"simultaneously":[23],"across":[24,165],"multiple":[25],"scales,":[26],"from":[27],"specific":[28],"molecular":[29],"interactions":[30],"to":[31],"entire":[32],"ecosystems,":[33],"is":[34],"crucial":[35],"for":[36,68,116,195,206],"uncovering":[37],"biological":[38],"mechanisms":[39],"understanding":[41],"the":[42,48,86,103,128],"emergence":[43],"of":[44,51,85,127,170],"complex":[45],"phenotypes.":[46],"With":[47],"increasing":[49],"number":[50],"studies":[52],"incorporating":[53],"multi-omics":[54,78,118],"sampled":[56],"over":[57],"time,":[58],"it":[59],"become":[61],"clear":[62,193],"integrated":[64],"approaches":[65],"are":[66,79],"pivotal":[67],"these":[69,175],"efforts.":[70],"However,":[71],"standard":[72],"analytical":[74],"practices":[75],"longitudinal":[77,117,209],"still":[80],"shaping":[81],"many":[84],"available":[87],"methods":[88,115,176],"not":[90],"yet":[91],"widely":[93,156],"evaluated":[94],"adopted.":[96],"To":[97],"address":[98],"this":[99,218],"gap,":[100],"we":[101],"performed":[102],"first":[104],"systematic":[105],"literature":[106],"review":[107,150],"comprehensively":[109],"categorizes,":[110],"compares,":[111],"evaluates":[113],"computational":[114],"integration,":[119],"with":[120],"a":[121,192,203],"particular":[122],"emphasis":[123],"on":[124],"four":[125],"categories":[126],"studies:":[129],"(i)":[130],"host":[131,138],"host-associated":[133],"microbiome":[134,142],"studies,":[135,139,143],"(ii)":[136],"microbiome-free":[137],"(iii)":[140],"host-free":[141],"(iv)":[145],"methodological":[146,153],"framework":[147],"studies.":[148],"Our":[149],"highlights":[151],"current":[152],"trends,":[154],"identifies":[155],"used":[157],"high-performing":[159],"frameworks,":[160],"assesses":[162],"each":[163],"method":[164],"performance,":[166],"interpretability,":[167],"ease":[169],"use.":[171],"We":[172],"further":[173],"organize":[174],"thematic":[178],"groups-such":[179],"as":[180],"statistical":[181],"modeling,":[182],"machine":[183],"learning,":[184],"dimensionality":[185],"reduction,":[186],"latent":[188],"factor":[189],"approaches-to":[190],"provide":[191],"roadmap":[194],"future":[196],"research":[197],"application.":[199],"This":[200],"work":[201],"offers":[202],"critical":[204],"foundation":[205],"advancing":[207],"integrative":[208],"science":[211],"supporting":[213],"reproducible,":[214],"scalable":[215],"analysis":[216],"rapidly":[219],"evolving":[220],"field.":[221]},"counts_by_year":[{"year":2026,"cited_by_count":20},{"year":2025,"cited_by_count":3}],"updated_date":"2026-06-29T08:53:18.405633","created_date":"2025-10-10T00:00:00"}
