{"id":"https://openalex.org/W4412103261","doi":"https://doi.org/10.1093/bib/bbaf323","title":"Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions","display_name":"Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions","publication_year":2025,"publication_date":"2025-06-18","ids":{"openalex":"https://openalex.org/W4412103261","doi":"https://doi.org/10.1093/bib/bbaf323","pmid":"https://pubmed.ncbi.nlm.nih.gov/40619813"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf323","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf323","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbaf323","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030665506","display_name":"Shamsur Rehman","orcid":"https://orcid.org/0000-0001-8755-3780"},"institutions":[{"id":"https://openalex.org/I176601375","display_name":"Khalifa University of Science and Technology","ror":"https://ror.org/05hffr360","country_code":"AE","type":"education","lineage":["https://openalex.org/I176601375"]},{"id":"https://openalex.org/I2801466683","display_name":"Shaikh Khalifa Medical City","ror":"https://ror.org/03gd1jf50","country_code":"AE","type":"healthcare","lineage":["https://openalex.org/I2801466683"]}],"countries":["AE"],"is_corresponding":true,"raw_author_name":"Syed Sabih Ur Rehman","raw_affiliation_strings":["Department of Biology, United Arab Emirates University , Sheik Khalifa Bin Zayed St, Asharij, P.O. Box 15551, Al Ain, Abu Dhabi ,"],"affiliations":[{"raw_affiliation_string":"Department of Biology, United Arab Emirates University , Sheik Khalifa Bin Zayed St, Asharij, P.O. Box 15551, Al Ain, Abu Dhabi ,","institution_ids":["https://openalex.org/I2801466683","https://openalex.org/I176601375"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044054346","display_name":"Muhammad Ibtisam Nasar","orcid":"https://orcid.org/0009-0009-9057-334X"},"institutions":[{"id":"https://openalex.org/I176601375","display_name":"Khalifa University of Science and Technology","ror":"https://ror.org/05hffr360","country_code":"AE","type":"education","lineage":["https://openalex.org/I176601375"]},{"id":"https://openalex.org/I2801466683","display_name":"Shaikh Khalifa Medical City","ror":"https://ror.org/03gd1jf50","country_code":"AE","type":"healthcare","lineage":["https://openalex.org/I2801466683"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Muhammad Ibtisam Nasar","raw_affiliation_strings":["Department of Biology, United Arab Emirates University , Sheik Khalifa Bin Zayed St, Asharij, P.O. Box 15551, Al Ain, Abu Dhabi ,"],"affiliations":[{"raw_affiliation_string":"Department of Biology, United Arab Emirates University , Sheik Khalifa Bin Zayed St, Asharij, P.O. Box 15551, Al Ain, Abu Dhabi ,","institution_ids":["https://openalex.org/I2801466683","https://openalex.org/I176601375"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017728922","display_name":"Cristina Sousa Mesquita","orcid":null},"institutions":[{"id":"https://openalex.org/I39555362","display_name":"University of Warwick","ror":"https://ror.org/01a77tt86","country_code":"GB","type":"education","lineage":["https://openalex.org/I39555362"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Cristina S Mesquita","raw_affiliation_strings":["Bioinformatics & Digital Health Services (RTP), University of Warwick , CV4 7AL, Coventry ,"],"affiliations":[{"raw_affiliation_string":"Bioinformatics & Digital Health Services (RTP), University of Warwick , CV4 7AL, Coventry ,","institution_ids":["https://openalex.org/I39555362"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025308944","display_name":"Souhaila Al Khodor","orcid":"https://orcid.org/0000-0003-4858-7130"},"institutions":[{"id":"https://openalex.org/I1301390666","display_name":"Qatar Airways (Qatar)","ror":"https://ror.org/01hx00y13","country_code":"QA","type":"company","lineage":["https://openalex.org/I1301390666"]}],"countries":["QA"],"is_corresponding":false,"raw_author_name":"Souhaila Al Khodor","raw_affiliation_strings":["Reproductive and Perinatal Health Division, Research Department, Sidra Medicine , Doha ,"],"affiliations":[{"raw_affiliation_string":"Reproductive and Perinatal Health Division, Research Department, Sidra Medicine , Doha ,","institution_ids":["https://openalex.org/I1301390666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069868522","display_name":"Richard A. Notebaart","orcid":"https://orcid.org/0000-0003-3469-1893"},"institutions":[{"id":"https://openalex.org/I913481162","display_name":"Wageningen University & Research","ror":"https://ror.org/04qw24q55","country_code":"NL","type":"education","lineage":["https://openalex.org/I913481162"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Richard A Notebaart","raw_affiliation_strings":["Food Microbiology, Wageningen University and Research , 6700 AA, Wageningen ,"],"affiliations":[{"raw_affiliation_string":"Food Microbiology, Wageningen University and Research , 6700 AA, Wageningen ,","institution_ids":["https://openalex.org/I913481162"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026718378","display_name":"Sascha Ott","orcid":null},"institutions":[{"id":"https://openalex.org/I39555362","display_name":"University of Warwick","ror":"https://ror.org/01a77tt86","country_code":"GB","type":"education","lineage":["https://openalex.org/I39555362"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Sascha Ott","raw_affiliation_strings":["Bioinformatics & Digital Health Services (RTP), University of Warwick , CV4 7AL, Coventry ,","Warwick Medical School, University of Warwick , CV4 7AL, Coventry ,"],"affiliations":[{"raw_affiliation_string":"Bioinformatics & Digital Health Services (RTP), University of Warwick , CV4 7AL, Coventry ,","institution_ids":["https://openalex.org/I39555362"]},{"raw_affiliation_string":"Warwick Medical School, University of Warwick , CV4 7AL, Coventry ,","institution_ids":["https://openalex.org/I39555362"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002072203","display_name":"Sunil Mundra","orcid":"https://orcid.org/0000-0002-0535-118X"},"institutions":[{"id":"https://openalex.org/I176601375","display_name":"Khalifa University of Science and Technology","ror":"https://ror.org/05hffr360","country_code":"AE","type":"education","lineage":["https://openalex.org/I176601375"]},{"id":"https://openalex.org/I2801466683","display_name":"Shaikh Khalifa Medical City","ror":"https://ror.org/03gd1jf50","country_code":"AE","type":"healthcare","lineage":["https://openalex.org/I2801466683"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Sunil Mundra","raw_affiliation_strings":["Department of Biology, United Arab Emirates University , Sheik Khalifa Bin Zayed St, Asharij, P.O. Box 15551, Al Ain, Abu Dhabi ,","Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Khalifa Bin Zayed Street, P.O. Box 15551, Al Ain , Abu Dhabi ,"],"affiliations":[{"raw_affiliation_string":"Department of Biology, United Arab Emirates University , Sheik Khalifa Bin Zayed St, Asharij, P.O. Box 15551, Al Ain, Abu Dhabi ,","institution_ids":["https://openalex.org/I2801466683","https://openalex.org/I176601375"]},{"raw_affiliation_string":"Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Khalifa Bin Zayed Street, P.O. Box 15551, Al Ain , Abu Dhabi ,","institution_ids":["https://openalex.org/I176601375"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5118854879","display_name":"Ramesh P Arasardanam","orcid":null},"institutions":[{"id":"https://openalex.org/I153648349","display_name":"University of Leicester","ror":"https://ror.org/04h699437","country_code":"GB","type":"education","lineage":["https://openalex.org/I153648349"]},{"id":"https://openalex.org/I2802705189","display_name":"University Hospitals Coventry and Warwickshire NHS Trust","ror":"https://ror.org/025n38288","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2802705189"]},{"id":"https://openalex.org/I39555362","display_name":"University of Warwick","ror":"https://ror.org/01a77tt86","country_code":"GB","type":"education","lineage":["https://openalex.org/I39555362"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ramesh P Arasardanam","raw_affiliation_strings":["Institute of Precision Diagnostics & Translational Medicine, University Hospitals Coventry & Warwickshire NHS Trust , Clifford Bridge Road, Coventry CV2 2DX ,","Leicester Cancer Research Centre, University of Leicester , LE1 7RH , Leicester,","Warwick Medical School, University of Warwick , CV4 7AL, Coventry ,"],"affiliations":[{"raw_affiliation_string":"Institute of Precision Diagnostics & Translational Medicine, University Hospitals Coventry & Warwickshire NHS Trust , Clifford Bridge Road, Coventry CV2 2DX ,","institution_ids":["https://openalex.org/I2802705189"]},{"raw_affiliation_string":"Leicester Cancer Research Centre, University of Leicester , LE1 7RH , Leicester,","institution_ids":["https://openalex.org/I153648349"]},{"raw_affiliation_string":"Warwick Medical School, University of Warwick , CV4 7AL, Coventry ,","institution_ids":["https://openalex.org/I39555362"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078830156","display_name":"Khalid Muhammad","orcid":"https://orcid.org/0000-0001-6488-1722"},"institutions":[{"id":"https://openalex.org/I176601375","display_name":"Khalifa University of Science and Technology","ror":"https://ror.org/05hffr360","country_code":"AE","type":"education","lineage":["https://openalex.org/I176601375"]},{"id":"https://openalex.org/I2801466683","display_name":"Shaikh Khalifa Medical City","ror":"https://ror.org/03gd1jf50","country_code":"AE","type":"healthcare","lineage":["https://openalex.org/I2801466683"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Khalid Muhammad","raw_affiliation_strings":["Department of Biology, United Arab Emirates University , Sheik Khalifa Bin Zayed St, Asharij, P.O. Box 15551, Al Ain, Abu Dhabi ,"],"affiliations":[{"raw_affiliation_string":"Department of Biology, United Arab Emirates University , Sheik Khalifa Bin Zayed St, Asharij, P.O. Box 15551, Al Ain, Abu Dhabi ,","institution_ids":["https://openalex.org/I2801466683","https://openalex.org/I176601375"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051158497","display_name":"Mohammad Tauqeer Alam","orcid":"https://orcid.org/0000-0002-6872-0691"},"institutions":[{"id":"https://openalex.org/I176601375","display_name":"Khalifa University of Science and Technology","ror":"https://ror.org/05hffr360","country_code":"AE","type":"education","lineage":["https://openalex.org/I176601375"]},{"id":"https://openalex.org/I2801466683","display_name":"Shaikh Khalifa Medical City","ror":"https://ror.org/03gd1jf50","country_code":"AE","type":"healthcare","lineage":["https://openalex.org/I2801466683"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Mohammad Tauqeer Alam","raw_affiliation_strings":["Department of Biology, United Arab Emirates University , Sheik Khalifa Bin Zayed St, Asharij, P.O. Box 15551, Al Ain, Abu Dhabi ,"],"affiliations":[{"raw_affiliation_string":"Department of Biology, United Arab Emirates University , Sheik Khalifa Bin Zayed St, Asharij, P.O. Box 15551, Al Ain, Abu Dhabi ,","institution_ids":["https://openalex.org/I2801466683","https://openalex.org/I176601375"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5030665506"],"corresponding_institution_ids":["https://openalex.org/I176601375","https://openalex.org/I2801466683"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":7.581,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.97699272,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"26","issue":"4","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":0.9990000128746033,"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"}},"topics":[{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9983999729156494,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9968000054359436,"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":0.864926815032959},{"id":"https://openalex.org/keywords/dysbiosis","display_name":"Dysbiosis","score":0.8389118909835815},{"id":"https://openalex.org/keywords/metaproteomics","display_name":"Metaproteomics","score":0.7163048386573792},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6499015688896179},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.6241125464439392},{"id":"https://openalex.org/keywords/human-microbiome-project","display_name":"Human Microbiome Project","score":0.6101758480072021},{"id":"https://openalex.org/keywords/human-microbiome","display_name":"Human microbiome","score":0.5812269449234009},{"id":"https://openalex.org/keywords/metabolomics","display_name":"Metabolomics","score":0.5490069389343262},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.534051775932312},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4918832778930664},{"id":"https://openalex.org/keywords/fecal-bacteriotherapy","display_name":"Fecal bacteriotherapy","score":0.43298590183258057},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3436662554740906},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.33079221844673157},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.265114426612854},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1090421974658966}],"concepts":[{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.864926815032959},{"id":"https://openalex.org/C2777165150","wikidata":"https://www.wikidata.org/wiki/Q269334","display_name":"Dysbiosis","level":3,"score":0.8389118909835815},{"id":"https://openalex.org/C199465337","wikidata":"https://www.wikidata.org/wiki/Q6823168","display_name":"Metaproteomics","level":4,"score":0.7163048386573792},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6499015688896179},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.6241125464439392},{"id":"https://openalex.org/C190944805","wikidata":"https://www.wikidata.org/wiki/Q3922751","display_name":"Human Microbiome Project","level":4,"score":0.6101758480072021},{"id":"https://openalex.org/C91478284","wikidata":"https://www.wikidata.org/wiki/Q6623796","display_name":"Human microbiome","level":3,"score":0.5812269449234009},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.5490069389343262},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.534051775932312},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4918832778930664},{"id":"https://openalex.org/C137923570","wikidata":"https://www.wikidata.org/wiki/Q2121103","display_name":"Fecal bacteriotherapy","level":4,"score":0.43298590183258057},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3436662554740906},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33079221844673157},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.265114426612854},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1090421974658966},{"id":"https://openalex.org/C2994496256","wikidata":"https://www.wikidata.org/wiki/Q27031090","display_name":"Clostridium difficile","level":3,"score":0.0},{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"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":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056186","descriptor_name":"Metagenomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D064806","descriptor_name":"Dysbiosis","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"descriptor_ui":"D064806","descriptor_name":"Dysbiosis","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"descriptor_ui":"D064806","descriptor_name":"Dysbiosis","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbaf323","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf323","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40619813","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40619813","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:library.wur.nl:wurpubs/648897","is_oa":true,"landing_page_url":"https://research.wur.nl/en/publications/integrative-systems-biology-approaches-for-analyzing-microbiome-d","pdf_url":"https://edepot.wur.nl/698502","source":{"id":"https://openalex.org/S4210201231","display_name":"Socio-Environmental Systems Modeling","issn_l":"2663-3027","issn":["2663-3027"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1467-5463","raw_type":"Article/Letter to editor"},{"id":"pmh:oai:europepmc.org:11038381","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12229991","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf323","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf323","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4102448147","display_name":null,"funder_award_id":"G00004152","funder_id":"https://openalex.org/F4320323593","funder_display_name":"United Arab Emirates University"}],"funders":[{"id":"https://openalex.org/F4320323593","display_name":"United Arab Emirates University","ror":"https://ror.org/01km6p862"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":340,"referenced_works":["https://openalex.org/W125869453","https://openalex.org/W642521510","https://openalex.org/W1703384511","https://openalex.org/W1864161604","https://openalex.org/W1964010911","https://openalex.org/W1966388533","https://openalex.org/W1971061059","https://openalex.org/W1978709058","https://openalex.org/W1982185581","https://openalex.org/W2002703043","https://openalex.org/W2011312755","https://openalex.org/W2025944550","https://openalex.org/W2044712133","https://openalex.org/W2062373556","https://openalex.org/W2064034649","https://openalex.org/W2080752012","https://openalex.org/W2082382448","https://openalex.org/W2082578477","https://openalex.org/W2083717261","https://openalex.org/W2085993965","https://openalex.org/W2088209062","https://openalex.org/W2100318643","https://openalex.org/W2108718991","https://openalex.org/W2109113634","https://openalex.org/W2110768797","https://openalex.org/W2112364185","https://openalex.org/W2113679889","https://openalex.org/W2114104545","https://openalex.org/W2114165700","https://openalex.org/W2116846792","https://openalex.org/W2122093325","https://openalex.org/W2126452774","https://openalex.org/W2131536322","https://openalex.org/W2169330513","https://openalex.org/W2169527381","https://openalex.org/W2172560158","https://openalex.org/W2175526948","https://openalex.org/W2178518272","https://openalex.org/W2179438025","https://openalex.org/W2254642444","https://openalex.org/W2272096331","https://openalex.org/W2285468881","https://openalex.org/W2323326409","https://openalex.org/W2338416429","https://openalex.org/W2401404581","https://openalex.org/W2461051021","https://openalex.org/W2463195069","https://openalex.org/W2472167991","https://openalex.org/W2473139211","https://openalex.org/W2504691963","https://openalex.org/W2510675082","https://openalex.org/W2539530515","https://openalex.org/W2558041282","https://openalex.org/W2559394418","https://openalex.org/W2559597060","https://openalex.org/W2568184332","https://openalex.org/W2587285770","https://openalex.org/W2587959748","https://openalex.org/W2592811885","https://openalex.org/W2597385024","https://openalex.org/W2597532406","https://openalex.org/W2599417231","https://openalex.org/W2605479728","https://openalex.org/W2606228938","https://openalex.org/W2607310450","https://openalex.org/W2611418622","https://openalex.org/W2617940752","https://openalex.org/W2734372941","https://openalex.org/W2736839127","https://openalex.org/W2740149173","https://openalex.org/W2742147437","https://openalex.org/W2743073899","https://openalex.org/W2754797405","https://openalex.org/W2760023427","https://openalex.org/W2761489767","https://openalex.org/W2762019694","https://openalex.org/W2765314233","https://openalex.org/W2769145826","https://openalex.org/W2769542288","https://openalex.org/W2773368689","https://openalex.org/W2775040279","https://openalex.org/W2775850469","https://openalex.org/W2778916763","https://openalex.org/W2784164089","https://openalex.org/W2785692071","https://openalex.org/W2790132182","https://openalex.org/W2791926234","https://openalex.org/W2794904294","https://openalex.org/W2795021885","https://openalex.org/W2803457956","https://openalex.org/W2807572295","https://openalex.org/W2808386728","https://openalex.org/W2810052012","https://openalex.org/W2859249641","https://openalex.org/W2885949449","https://openalex.org/W2887136521","https://openalex.org/W2891160423","https://openalex.org/W2900697674","https://openalex.org/W2901825094","https://openalex.org/W2910615673","https://openalex.org/W2913429571","https://openalex.org/W2913620138","https://openalex.org/W2913914265","https://openalex.org/W2938868597","https://openalex.org/W2948003108","https://openalex.org/W2949418748","https://openalex.org/W2950985821","https://openalex.org/W2952117162","https://openalex.org/W2953569287","https://openalex.org/W2963276645","https://openalex.org/W2966520335","https://openalex.org/W2967074377","https://openalex.org/W2967843340","https://openalex.org/W2972348732","https://openalex.org/W2972533507","https://openalex.org/W2973520306","https://openalex.org/W2976139609","https://openalex.org/W2980426566","https://openalex.org/W2980691057","https://openalex.org/W2982566732","https://openalex.org/W2990618091","https://openalex.org/W2991106430","https://openalex.org/W2993476941","https://openalex.org/W2993480649","https://openalex.org/W2995154691","https://openalex.org/W2996060321","https://openalex.org/W2996576365","https://openalex.org/W2998285518","https://openalex.org/W2998499873","https://openalex.org/W3001416095","https://openalex.org/W3001550815","https://openalex.org/W3006380141","https://openalex.org/W3008278285","https://openalex.org/W3009443760","https://openalex.org/W3010629926","https://openalex.org/W3011576831","https://openalex.org/W3013557327","https://openalex.org/W3025278547","https://openalex.org/W3025731895","https://openalex.org/W3027051073","https://openalex.org/W3028922180","https://openalex.org/W3040245690","https://openalex.org/W3043062835","https://openalex.org/W3048272826","https://openalex.org/W3048611368","https://openalex.org/W3087930045","https://openalex.org/W3088992294","https://openalex.org/W3090689814","https://openalex.org/W3091506611","https://openalex.org/W3092327810","https://openalex.org/W3092621787","https://openalex.org/W3093405588","https://openalex.org/W3107153021","https://openalex.org/W3112482983","https://openalex.org/W3112951959","https://openalex.org/W3117714294","https://openalex.org/W3118382168","https://openalex.org/W3118724893","https://openalex.org/W3127151710","https://openalex.org/W3128710215","https://openalex.org/W3132502413","https://openalex.org/W3134142139","https://openalex.org/W3134750680","https://openalex.org/W3135350989","https://openalex.org/W3138215020","https://openalex.org/W3143381592","https://openalex.org/W3147481189","https://openalex.org/W3154612714","https://openalex.org/W3159504416","https://openalex.org/W3160604189","https://openalex.org/W3163959579","https://openalex.org/W3164037342","https://openalex.org/W3164037858","https://openalex.org/W3164378295","https://openalex.org/W3165063555","https://openalex.org/W3167821832","https://openalex.org/W3170890035","https://openalex.org/W3173777885","https://openalex.org/W3179726909","https://openalex.org/W3183807981","https://openalex.org/W3196342511","https://openalex.org/W3200941727","https://openalex.org/W3203565491","https://openalex.org/W3207744615","https://openalex.org/W4200001874","https://openalex.org/W4200108718","https://openalex.org/W4200288189","https://openalex.org/W4200415024","https://openalex.org/W4205364647","https://openalex.org/W4205375560","https://openalex.org/W4205841525","https://openalex.org/W4205968426","https://openalex.org/W4206717829","https://openalex.org/W4210377299","https://openalex.org/W4210759055","https://openalex.org/W4211148844","https://openalex.org/W4212769682","https://openalex.org/W4213163295","https://openalex.org/W4214523762","https://openalex.org/W4220889742","https://openalex.org/W4220986765","https://openalex.org/W4223958058","https://openalex.org/W4225366109","https://openalex.org/W4226296560","https://openalex.org/W4229074162","https://openalex.org/W4245901258","https://openalex.org/W4280615884","https://openalex.org/W4281557603","https://openalex.org/W4281649950","https://openalex.org/W4281760779","https://openalex.org/W4282838866","https://openalex.org/W4283731082","https://openalex.org/W4286510420","https://openalex.org/W4290244583","https://openalex.org/W4290673832","https://openalex.org/W4294051685","https://openalex.org/W4298146555","https://openalex.org/W4306828792","https://openalex.org/W4306898301","https://openalex.org/W4307250618","https://openalex.org/W4307564313","https://openalex.org/W4308916361","https://openalex.org/W4313509441","https://openalex.org/W4313557733","https://openalex.org/W4313560729","https://openalex.org/W4313645415","https://openalex.org/W4317499868","https://openalex.org/W4317660914","https://openalex.org/W4319057789","https://openalex.org/W4319862254","https://openalex.org/W4321794491","https://openalex.org/W4322739219","https://openalex.org/W4323543731","https://openalex.org/W4366816962","https://openalex.org/W4378549390","https://openalex.org/W4380153151","https://openalex.org/W4380153583","https://openalex.org/W4380876696","https://openalex.org/W4381430266","https://openalex.org/W4383313822","https://openalex.org/W4383711104","https://openalex.org/W4385269948","https://openalex.org/W4385448317","https://openalex.org/W4385576614","https://openalex.org/W4385948318","https://openalex.org/W4386070166","https://openalex.org/W4386739120","https://openalex.org/W4387252500","https://openalex.org/W4387332224","https://openalex.org/W4387359984","https://openalex.org/W4387605428","https://openalex.org/W4387782576","https://openalex.org/W4388017975","https://openalex.org/W4388125607","https://openalex.org/W4388342205","https://openalex.org/W4388408162","https://openalex.org/W4388592776","https://openalex.org/W4388651667","https://openalex.org/W4388894222","https://openalex.org/W4388939078","https://openalex.org/W4389265247","https://openalex.org/W4389266183","https://openalex.org/W4389315477","https://openalex.org/W4389389425","https://openalex.org/W4390273582","https://openalex.org/W4390475387","https://openalex.org/W4390501111","https://openalex.org/W4390542770","https://openalex.org/W4390929150","https://openalex.org/W4390947582","https://openalex.org/W4391404600","https://openalex.org/W4391448422","https://openalex.org/W4391617630","https://openalex.org/W4391884376","https://openalex.org/W4391925517","https://openalex.org/W4392129283","https://openalex.org/W4392135492","https://openalex.org/W4392699695","https://openalex.org/W4392783067","https://openalex.org/W4392796828","https://openalex.org/W4392895531","https://openalex.org/W4392974592","https://openalex.org/W4392984046","https://openalex.org/W4392985440","https://openalex.org/W4393224953","https://openalex.org/W4393854569","https://openalex.org/W4394933497","https://openalex.org/W4394997309","https://openalex.org/W4395034790","https://openalex.org/W4396508654","https://openalex.org/W4398184645","https://openalex.org/W4398475265","https://openalex.org/W4399046512","https://openalex.org/W4399075652","https://openalex.org/W4399368521","https://openalex.org/W4399578574","https://openalex.org/W4400006710","https://openalex.org/W4400019207","https://openalex.org/W4400090893","https://openalex.org/W4400145995","https://openalex.org/W4400220867","https://openalex.org/W4400248548","https://openalex.org/W4400539833","https://openalex.org/W4400648627","https://openalex.org/W4400770059","https://openalex.org/W4400975015","https://openalex.org/W4402585762","https://openalex.org/W4402592537","https://openalex.org/W4402644419","https://openalex.org/W4402718468","https://openalex.org/W4402718470","https://openalex.org/W4403210115","https://openalex.org/W4403891484","https://openalex.org/W4404061463","https://openalex.org/W4404349959","https://openalex.org/W4404487676","https://openalex.org/W4404825033","https://openalex.org/W4405269061","https://openalex.org/W4406100850","https://openalex.org/W4406114912","https://openalex.org/W4406232165","https://openalex.org/W4406232750","https://openalex.org/W4406771940","https://openalex.org/W4406956834","https://openalex.org/W4407138601","https://openalex.org/W4407150795","https://openalex.org/W4407298345","https://openalex.org/W4407610550","https://openalex.org/W4408099174","https://openalex.org/W4408225827","https://openalex.org/W4408245606","https://openalex.org/W4408301706","https://openalex.org/W4408695444","https://openalex.org/W4408929067","https://openalex.org/W4408957800","https://openalex.org/W4409485749","https://openalex.org/W4410034945","https://openalex.org/W4410334260","https://openalex.org/W6779930276","https://openalex.org/W6838718623"],"related_works":["https://openalex.org/W2915830746","https://openalex.org/W1968369492","https://openalex.org/W4399273096","https://openalex.org/W2890512197","https://openalex.org/W4323565149","https://openalex.org/W4285794994","https://openalex.org/W2043102924","https://openalex.org/W1577826155","https://openalex.org/W3149998985","https://openalex.org/W2159255279"],"abstract_inverted_index":{"Microbiomes":[0],"are":[1,144],"crucial":[2,145],"for":[3,74,146],"human":[4,48],"health":[5],"and":[6,21,44,50,69,88,105,114,126,157,201],"well-being,":[7],"with":[8,28,66,123,139,192],"microbial":[9,67,197],"dysbiosis":[10,68],"being":[11],"linked":[12],"to":[13,59,92,180,195],"various":[14,71],"complex":[15],"diseases.":[16,60],"Therefore,":[17],"understanding":[18],"the":[19,25,29,42,128,169],"structural":[20],"functional":[22],"changes":[23,53],"in":[24,32,54,168,204],"microbiome,":[26,78],"along":[27],"underlying":[30],"mechanisms":[31],"disease":[33],"conditions,":[34],"is":[35],"essential.":[36],"In":[37],"this":[38],"review,":[39],"we":[40,97,161],"outline":[41,119],"structure":[43],"function":[45],"of":[46,130,171],"different":[47],"microbiomes":[49],"examine":[51],"how":[52],"their":[55,202],"composition":[56],"may":[57],"contribute":[58],"We":[61,118],"highlight":[62],"critical":[63],"information":[64],"associated":[65,122],"explore":[70],"therapeutic":[72],"strategies":[73],"restoring":[75],"a":[76,177,185],"healthy":[77],"including":[79,101],"microbiota":[80],"transplantation,":[81],"phage":[82],"therapy,":[83],"probiotics,":[84],"prebiotics,":[85],"dietary":[86],"interventions,":[87],"drug-based":[89],"approaches.":[90],"Further,":[91],"better":[93],"understand":[94],"microbiome":[95,149,158,172,181,199],"dysbiosis,":[96,200],"discuss":[98],"multi-omics":[99,124,137,190],"approaches":[100,110,134,143],"metagenomics,":[102],"metatranscriptomics,":[103],"metaproteomics,":[104],"meta-metabolomics,":[106],"alongside":[107],"computational":[108,140],"modeling":[109,194],"such":[111],"as":[112],"ecological":[113],"metabolic":[115],"network":[116],"analysis.":[117],"key":[120],"challenges":[121],"techniques":[125],"emphasize":[127],"importance":[129],"integrative":[131],"systems":[132],"biology":[133],"that":[135,188],"combine":[136],"data":[138,191],"modeling.":[141],"These":[142],"effectively":[147],"analyzing":[148],"data,":[150],"providing":[151],"deeper":[152],"insights":[153,163],"into":[154,164],"species":[155],"interactions":[156],"dynamics.":[159],"Finally,":[160],"offer":[162],"future":[165],"research":[166,182],"directions":[167],"field":[170],"research.":[173],"This":[174],"review":[175],"makes":[176],"unique":[178],"contribution":[179],"by":[183],"presenting":[184],"holistic":[186],"framework":[187],"integrates":[189],"multi-scale":[193],"elucidate":[196],"interactions,":[198],"modulation":[203],"disease-associated":[205],"contexts.":[206]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":7}],"updated_date":"2026-04-11T08:14:18.477133","created_date":"2025-10-10T00:00:00"}
