{"id":"https://openalex.org/W7164933701","doi":"https://doi.org/10.1093/bib/bbag316","title":"From association to causation: a decision-aware framework for reproducible biomarker discovery and precision intervention design in the human gut microbiome","display_name":"From association to causation: a decision-aware framework for reproducible biomarker discovery and precision intervention design in the human gut microbiome","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7164933701","doi":"https://doi.org/10.1093/bib/bbag316","pmid":"https://pubmed.ncbi.nlm.nih.gov/42302279"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag316","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag316","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-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://doi.org/10.1093/bib/bbag316","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5092404803","display_name":"AbdulAziz Ascandari","orcid":null},"institutions":[{"id":"https://openalex.org/I4210131560","display_name":"Universit\u00e9 Mohammed VI Polytechnique","ror":"https://ror.org/03xc55g68","country_code":"MA","type":"education","lineage":["https://openalex.org/I4210131560"]}],"countries":["MA"],"is_corresponding":true,"raw_author_name":"AbdulAziz Ascandari","raw_affiliation_strings":["College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical Sciences (CBS), Mohammed VI Polytechnic University (UM6P) , Lot 660, Hay Moulay Rachid, Ben Guerir, 43150 ,"],"raw_orcid":"https://orcid.org/0009-0005-4320-5609","affiliations":[{"raw_affiliation_string":"College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical Sciences (CBS), Mohammed VI Polytechnic University (UM6P) , Lot 660, Hay Moulay Rachid, Ben Guerir, 43150 ,","institution_ids":["https://openalex.org/I4210131560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000971514","display_name":"Suleiman Aminu","orcid":"https://orcid.org/0000-0002-6520-8596"},"institutions":[{"id":"https://openalex.org/I12789410","display_name":"Ahmadu Bello University","ror":"https://ror.org/019apvn83","country_code":"NG","type":"education","lineage":["https://openalex.org/I12789410"]},{"id":"https://openalex.org/I4210131560","display_name":"Universit\u00e9 Mohammed VI Polytechnique","ror":"https://ror.org/03xc55g68","country_code":"MA","type":"education","lineage":["https://openalex.org/I4210131560"]}],"countries":["MA","NG"],"is_corresponding":false,"raw_author_name":"Suleiman Aminu","raw_affiliation_strings":["College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical Sciences (CBS), Mohammed VI Polytechnic University (UM6P) , Lot 660, Hay Moulay Rachid, Ben Guerir, 43150 ,","Department of Biochemistry, Ahmadu Bello University , Zaria, Kaduna, 1096 ,"],"raw_orcid":"https://orcid.org/0000-0002-6520-8596","affiliations":[{"raw_affiliation_string":"College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical Sciences (CBS), Mohammed VI Polytechnic University (UM6P) , Lot 660, Hay Moulay Rachid, Ben Guerir, 43150 ,","institution_ids":["https://openalex.org/I4210131560"]},{"raw_affiliation_string":"Department of Biochemistry, Ahmadu Bello University , Zaria, Kaduna, 1096 ,","institution_ids":["https://openalex.org/I12789410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054373904","display_name":"Rachid Benhida","orcid":"https://orcid.org/0000-0003-3419-5697"},"institutions":[{"id":"https://openalex.org/I4210086528","display_name":"Institut de Chimie de Nice","ror":"https://ror.org/000pvc513","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I201841394","https://openalex.org/I4210086528","https://openalex.org/I4210128300"]},{"id":"https://openalex.org/I4210131560","display_name":"Universit\u00e9 Mohammed VI Polytechnique","ror":"https://ror.org/03xc55g68","country_code":"MA","type":"education","lineage":["https://openalex.org/I4210131560"]}],"countries":["FR","MA"],"is_corresponding":false,"raw_author_name":"Rachid Benhida","raw_affiliation_strings":["College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical Sciences (CBS), Mohammed VI Polytechnic University (UM6P) , Lot 660, Hay Moulay Rachid, Ben Guerir, 43150 ,","Institut de Chimie de Nice, CNRS UMR7272, Universit\u00e9 C\u00f4te d\u2019Azur , 28 Avenue Valrose, Nice, Provence-Alpes-C\u00f4te d'Azur, 06108 ,"],"raw_orcid":"https://orcid.org/0000-0003-3419-5697","affiliations":[{"raw_affiliation_string":"College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical Sciences (CBS), Mohammed VI Polytechnic University (UM6P) , Lot 660, Hay Moulay Rachid, Ben Guerir, 43150 ,","institution_ids":["https://openalex.org/I4210131560"]},{"raw_affiliation_string":"Institut de Chimie de Nice, CNRS UMR7272, Universit\u00e9 C\u00f4te d\u2019Azur , 28 Avenue Valrose, Nice, Provence-Alpes-C\u00f4te d'Azur, 06108 ,","institution_ids":["https://openalex.org/I4210086528"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5126317478","display_name":"Daoud Rachid","orcid":null},"institutions":[{"id":"https://openalex.org/I4210131560","display_name":"Universit\u00e9 Mohammed VI Polytechnique","ror":"https://ror.org/03xc55g68","country_code":"MA","type":"education","lineage":["https://openalex.org/I4210131560"]}],"countries":["MA"],"is_corresponding":true,"raw_author_name":"Daoud Rachid","raw_affiliation_strings":["College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical Sciences (CBS), Mohammed VI Polytechnic University (UM6P) , Lot 660, Hay Moulay Rachid, Ben Guerir, 43150 ,"],"raw_orcid":"https://orcid.org/0000-0003-0212-988X","affiliations":[{"raw_affiliation_string":"College of Chemical Sciences and Engineering (CCSE), Chemical and Biochemical Sciences (CBS), Mohammed VI Polytechnic University (UM6P) , Lot 660, Hay Moulay Rachid, Ben Guerir, 43150 ,","institution_ids":["https://openalex.org/I4210131560"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5092404803","https://openalex.org/A5126317478"],"corresponding_institution_ids":["https://openalex.org/I4210131560"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":{"value":3885,"currency":"USD","value_usd":3885},"fwci":3.209,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.9328413,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"27","issue":"3","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":0.28450000286102295,"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":0.28450000286102295,"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/T10845","display_name":"Advanced Causal Inference Techniques","score":0.2768000066280365,"subfield":{"id":"https://openalex.org/subfields/2613","display_name":"Statistics and Probability"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11303","display_name":"Bayesian Modeling and Causal Inference","score":0.10109999775886536,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/causal-inference","display_name":"Causal inference","score":0.7527999877929688},{"id":"https://openalex.org/keywords/observational-study","display_name":"Observational study","score":0.6504999995231628},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.5817999839782715},{"id":"https://openalex.org/keywords/confounding","display_name":"Confounding","score":0.5073000192642212},{"id":"https://openalex.org/keywords/causality","display_name":"Causality (physics)","score":0.4731000065803528},{"id":"https://openalex.org/keywords/mendelian-randomization","display_name":"Mendelian randomization","score":0.47099998593330383},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.43209999799728394},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.412200003862381},{"id":"https://openalex.org/keywords/causation","display_name":"Causation","score":0.3806000053882599},{"id":"https://openalex.org/keywords/gut-microbiome","display_name":"Gut microbiome","score":0.37610000371932983}],"concepts":[{"id":"https://openalex.org/C158600405","wikidata":"https://www.wikidata.org/wiki/Q5054566","display_name":"Causal inference","level":2,"score":0.7527999877929688},{"id":"https://openalex.org/C23131810","wikidata":"https://www.wikidata.org/wiki/Q818574","display_name":"Observational study","level":2,"score":0.6504999995231628},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5879999995231628},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.5817999839782715},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5429999828338623},{"id":"https://openalex.org/C77350462","wikidata":"https://www.wikidata.org/wiki/Q1125472","display_name":"Confounding","level":2,"score":0.5073000192642212},{"id":"https://openalex.org/C64357122","wikidata":"https://www.wikidata.org/wiki/Q1149766","display_name":"Causality (physics)","level":2,"score":0.4731000065803528},{"id":"https://openalex.org/C2779901538","wikidata":"https://www.wikidata.org/wiki/Q6816584","display_name":"Mendelian randomization","level":5,"score":0.47099998593330383},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.43209999799728394},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.412200003862381},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3813000023365021},{"id":"https://openalex.org/C166151441","wikidata":"https://www.wikidata.org/wiki/Q4923601","display_name":"Causation","level":2,"score":0.3806000053882599},{"id":"https://openalex.org/C3019978661","wikidata":"https://www.wikidata.org/wiki/Q739734","display_name":"Gut microbiome","level":3,"score":0.37610000371932983},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3603000044822693},{"id":"https://openalex.org/C179420905","wikidata":"https://www.wikidata.org/wiki/Q223871","display_name":"Mediation","level":2,"score":0.3465000092983246},{"id":"https://openalex.org/C2781197716","wikidata":"https://www.wikidata.org/wiki/Q864574","display_name":"Biomarker","level":2,"score":0.3449000120162964},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.34450000524520874},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.33660000562667847},{"id":"https://openalex.org/C186413461","wikidata":"https://www.wikidata.org/wiki/Q744727","display_name":"Genetic association","level":5,"score":0.3352999985218048},{"id":"https://openalex.org/C106208931","wikidata":"https://www.wikidata.org/wiki/Q1098876","display_name":"Genome-wide association study","level":5,"score":0.3310000002384186},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.33059999346733093},{"id":"https://openalex.org/C74197172","wikidata":"https://www.wikidata.org/wiki/Q1195339","display_name":"Directed acyclic graph","level":2,"score":0.32440000772476196},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.3224000036716461},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.32170000672340393},{"id":"https://openalex.org/C108650721","wikidata":"https://www.wikidata.org/wiki/Q1783253","display_name":"Counterfactual thinking","level":2,"score":0.31619998812675476},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3125},{"id":"https://openalex.org/C91478284","wikidata":"https://www.wikidata.org/wiki/Q6623796","display_name":"Human microbiome","level":3,"score":0.3122999966144562},{"id":"https://openalex.org/C124535831","wikidata":"https://www.wikidata.org/wiki/Q4915074","display_name":"Biomarker discovery","level":4,"score":0.3109999895095825},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.3100999891757965},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.30329999327659607},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.29600000381469727},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2953000068664551},{"id":"https://openalex.org/C11671645","wikidata":"https://www.wikidata.org/wiki/Q5054567","display_name":"Causal model","level":2,"score":0.2896000146865845},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2896000146865845},{"id":"https://openalex.org/C2779318504","wikidata":"https://www.wikidata.org/wiki/Q1438035","display_name":"Research design","level":2,"score":0.28600001335144043},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27079999446868896},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26969999074935913},{"id":"https://openalex.org/C148482608","wikidata":"https://www.wikidata.org/wiki/Q17007018","display_name":"Clinical study design","level":3,"score":0.2563000023365021},{"id":"https://openalex.org/C7952369","wikidata":"https://www.wikidata.org/wiki/Q844116","display_name":"Phenome","level":4,"score":0.2558000087738037},{"id":"https://openalex.org/C2776459999","wikidata":"https://www.wikidata.org/wiki/Q2119376","display_name":"Fidelity","level":2,"score":0.2538999915122986}],"mesh":[{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069196","descriptor_name":"Gastrointestinal Microbiome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015984","descriptor_name":"Causality","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015984","descriptor_name":"Causality","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015984","descriptor_name":"Causality","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":"D057182","descriptor_name":"Mendelian Randomization Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057182","descriptor_name":"Mendelian Randomization Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057182","descriptor_name":"Mendelian Randomization Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag316","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag316","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-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:42302279","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42302279","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13271389","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13271389/","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag316","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag316","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-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":0.4149133265018463,"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16"},{"score":0.41142764687538147,"display_name":"Gender equality","id":"https://metadata.un.org/sdg/5"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":107,"referenced_works":["https://openalex.org/W1875396108","https://openalex.org/W1931590386","https://openalex.org/W2096139589","https://openalex.org/W2130725058","https://openalex.org/W2131415145","https://openalex.org/W2133814768","https://openalex.org/W2161511352","https://openalex.org/W2367851449","https://openalex.org/W2396961413","https://openalex.org/W2576536258","https://openalex.org/W2605341613","https://openalex.org/W2624135745","https://openalex.org/W2768799378","https://openalex.org/W2771045365","https://openalex.org/W2787902098","https://openalex.org/W2803072880","https://openalex.org/W2804672877","https://openalex.org/W2883668303","https://openalex.org/W2927453907","https://openalex.org/W2946564000","https://openalex.org/W2949004447","https://openalex.org/W2952076147","https://openalex.org/W2955161809","https://openalex.org/W2963699930","https://openalex.org/W2964204760","https://openalex.org/W2975952731","https://openalex.org/W3010580090","https://openalex.org/W3081341328","https://openalex.org/W3111771007","https://openalex.org/W3114319529","https://openalex.org/W3118848834","https://openalex.org/W3121407008","https://openalex.org/W3122818329","https://openalex.org/W3123436326","https://openalex.org/W3134163041","https://openalex.org/W3134208348","https://openalex.org/W3141185229","https://openalex.org/W3146002984","https://openalex.org/W3168174218","https://openalex.org/W3190897300","https://openalex.org/W3191796027","https://openalex.org/W3193974615","https://openalex.org/W3194189363","https://openalex.org/W3205642313","https://openalex.org/W3217360279","https://openalex.org/W4200175876","https://openalex.org/W4212956995","https://openalex.org/W4223955556","https://openalex.org/W4284689492","https://openalex.org/W4293567165","https://openalex.org/W4294782938","https://openalex.org/W4307250618","https://openalex.org/W4311837847","https://openalex.org/W4319655953","https://openalex.org/W4321002266","https://openalex.org/W4321610956","https://openalex.org/W4362451010","https://openalex.org/W4377969036","https://openalex.org/W4382281637","https://openalex.org/W4383225068","https://openalex.org/W4385596139","https://openalex.org/W4385841574","https://openalex.org/W4386726284","https://openalex.org/W4386758008","https://openalex.org/W4387675472","https://openalex.org/W4388409610","https://openalex.org/W4388796965","https://openalex.org/W4388997323","https://openalex.org/W4389327220","https://openalex.org/W4390580041","https://openalex.org/W4390919901","https://openalex.org/W4391132258","https://openalex.org/W4392674481","https://openalex.org/W4392679676","https://openalex.org/W4394776230","https://openalex.org/W4400064765","https://openalex.org/W4400746144","https://openalex.org/W4400809046","https://openalex.org/W4400975015","https://openalex.org/W4401994297","https://openalex.org/W4402284905","https://openalex.org/W4402311999","https://openalex.org/W4403305444","https://openalex.org/W4403785309","https://openalex.org/W4403921078","https://openalex.org/W4405438719","https://openalex.org/W4405497072","https://openalex.org/W4405665911","https://openalex.org/W4406039804","https://openalex.org/W4406924440","https://openalex.org/W4407966201","https://openalex.org/W4408099174","https://openalex.org/W4408162031","https://openalex.org/W4408320656","https://openalex.org/W4408649802","https://openalex.org/W4409371275","https://openalex.org/W4409923106","https://openalex.org/W4410334260","https://openalex.org/W4410974032","https://openalex.org/W4411077624","https://openalex.org/W4412015485","https://openalex.org/W4412630731","https://openalex.org/W4412795152","https://openalex.org/W4414778166","https://openalex.org/W4414808686","https://openalex.org/W4414874646","https://openalex.org/W4415256503"],"related_works":[],"abstract_inverted_index":{"Human":[0],"gut":[1],"microbiome":[2,171],"research":[3,172],"has":[4],"generated":[5],"many":[6],"disease":[7],"associations,":[8],"yet":[9],"few":[10],"translate":[11],"into":[12,68,131,145],"clinical":[13],"applications.":[14],"A":[15],"central":[16],"obstacle":[17],"is":[18,137],"not":[19],"a":[20,46,69,110,146,163],"lack":[21],"of":[22,28,65,76,106,154],"data,":[23,118],"but":[24],"the":[25,122,152],"limited":[26],"integration":[27],"causal":[29,48,66,87],"reasoning,":[30],"as":[31],"most":[32],"studies":[33],"report":[34],"correlations":[35],"without":[36],"establishing":[37],"directionality,":[38],"confounding":[39],"control,":[40],"or":[41],"mechanistic":[42,92],"evidence.":[43],"We":[44],"propose":[45],"unified":[47],"inference":[49],"framework":[50,82,123],"that":[51,97,140,150],"integrates":[52],"directed":[53],"acyclic":[54],"graphs,":[55],"Mendelian":[56],"randomization,":[57],"double":[58],"machine":[59],"learning,":[60],"mediation":[61],"analysis,":[62],"and":[63,91,103,173],"tests":[64],"reversibility":[67],"single":[70],"decision-aware":[71],"workflow.":[72],"Unlike":[73],"prior":[74],"applications":[75],"these":[77],"tools":[78,144],"in":[79,139,170],"isolation,":[80],"our":[81],"explicitly":[83],"separates":[84],"assumption":[85],"mapping,":[86],"identification,":[88],"effect":[89],"estimation,":[90],"interpretation,":[93],"introducing":[94],"\"assumption":[95],"guardrails\"":[96],"constrain":[98],"interpretation":[99],"at":[100,156],"each":[101,157],"stage":[102],"prevent":[104],"overinterpretation":[105],"observational":[107,129],"findings.":[108],"Using":[109],"colorectal":[111],"cancer":[112],"case":[113],"study":[114],"with":[115],"public":[116],"metagenomic":[117],"we":[119],"demonstrate":[120],"how":[121],"operates":[124],"under":[125],"real-world":[126],"constraints,":[127],"transforming":[128],"associations":[130],"testable,":[132],"mechanism-based":[133],"hypotheses.":[134],"The":[135],"contribution":[136],"architectural":[138],"it":[141],"organizes":[142],"existing":[143],"disciplined,":[147],"integrated":[148],"pipeline":[149],"clarifies":[151],"strength":[153],"evidence":[155],"stage.":[158],"This":[159],"operational":[160],"blueprint":[161],"provides":[162],"reproducible":[164],"path":[165],"from":[166],"correlation":[167],"to":[168],"causation":[169],"toward":[174],"precision":[175],"interventions.":[176]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2026-06-17T00:00:00"}