{"id":"W4386071185","doi":"10.1016/j.celrep.2023.112997","title":"Paired microbiome and metabolome analyses associate bile acid changes with colorectal cancer progression","year":2023,"lang":"en","type":"article","venue":"Cell Reports","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":78,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia Hospital","funders":"National Institute of Diabetes and Digestive and Kidney Diseases; National Center for Complementary and Integrative Health; National Institute of Allergy and Infectious Diseases; National Heart, Lung, and Blood Institute; Chiba University; University of California, San Diego; NOMIS Stiftung; National Cancer Institute; National Institutes of Health; Crohn's and Colitis Foundation of America; March of Dimes Foundation; David C. Copley Foundation; Samuel Waxman Cancer Research Foundation","keywords":"Metabolome; Microbiome; Metabolomics; Colorectal cancer; Biology; Bile acid; Ruminococcus; Cancer; Omics; Disease; Cholic acid; Bioinformatics; Computational biology; Internal medicine; Genetics; Biochemistry; Medicine","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001990117,0.0001450654,0.000194142,0.00007002868,0.0001157156,0.00002502041,0.00004486797,0.0001313909,0.00001782396],"category_scores_gemma":[0.00001439918,0.0001077621,0.00004077911,0.0002236907,0.00006748075,0.000002809478,0.00008621375,0.00005979176,0.000003898881],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001320927,"about_ca_system_score_gemma":0.0001151807,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005048353,"about_ca_topic_score_gemma":0.0002720724,"domain_scores_codex":[0.9990348,0.00003824061,0.0001427079,0.0004007209,0.00008286984,0.0003006365],"domain_scores_gemma":[0.9994687,0.000004800206,0.0001935636,0.0001733665,0.0000671137,0.00009248444],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00003138911,0.00002733686,0.01951469,0.00005175447,0.00004934303,0.00010416,0.00006428667,0.000002272114,0.9754889,1.39411e-7,0.003760216,0.0009055444],"study_design_scores_gemma":[0.0002079207,0.0002097781,0.03666948,0.00002539382,0.00004764493,0.00008038113,0.00005052659,0.00000319187,0.9353827,0.000002961913,0.02716188,0.0001580957],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9950724,0.004028975,0.000003732079,0.0002514676,0.0001562345,0.000231124,0.00002628832,0.00004238934,0.0001873514],"genre_scores_gemma":[0.9963362,0.00111252,0.0001626633,0.0001024329,0.00009872222,0.00005958406,0.0002892257,0.00002459611,0.001814116],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04010613,"threshold_uncertainty_score":0.439441,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0219227712800128,"score_gpt":0.3181297968698472,"score_spread":0.2962070255898344,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}