{"id":"W4400457746","doi":"10.1128/msphere.00360-24","title":"PUPpy: a primer design pipeline for substrain-level microbial detection and absolute quantification","year":2024,"lang":"en","type":"article","venue":"mSphere","topic":"Microbial Community Ecology and Physiology","field":"Environmental Science","cited_by":8,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canadian Institute for Advanced Research; University of British Columbia","funders":"Michael Smith Health Research BC; Canada Foundation for Innovation; BC Children's Hospital; Natural Sciences and Engineering Research Council of Canada; Canadian Institute for Advanced Research","keywords":"Puppy; Biology; Computational biology; Metagenomics; Primer (cosmetics); Microbiome; Genetics; Gene; Ecology; Chemistry","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.005235902,0.004376497,0.002508745,0.002384083,0.001065915,0.00210967,0.003018645,0.002115292,0.02477506],"category_scores_gemma":[0.009780846,0.00326655,0.002727539,0.001134315,0.001240998,0.001880259,0.00300752,0.005302448,0.0190513],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000889331,"about_ca_system_score_gemma":0.00347716,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001051997,"about_ca_topic_score_gemma":0.001476623,"domain_scores_codex":[0.9959881,0.0008518446,0.0003897313,0.001186957,0.001216,0.000367369],"domain_scores_gemma":[0.9969835,0.001434021,0.0005059122,0.0003737994,0.0005248347,0.0001779778],"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":[0.002297478,0.000628181,0.005414732,0.005728101,0.0008270653,0.001777598,0.001166567,0.01410029,0.531476,0.009102219,0.1426837,0.2847981],"study_design_scores_gemma":[0.000635515,0.0009451661,0.00438107,0.0005877766,0.0002932479,0.002316532,0.0001443394,0.1114695,0.5833074,0.01624854,0.2789888,0.0006821462],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.004921892,0.0008235919,0.8589567,0.0002379419,0.000279513,0.0006916485,0.00828416,0.1241324,0.001672206],"genre_scores_gemma":[0.01895979,0.0006051005,0.9467534,0.0009501067,0.00006305124,0.004332298,0.01167097,0.01284989,0.003815465],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.02477506,"threshold_uncertainty_score":0.08288085,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04823156810349982,"score_gpt":0.2626261053436916,"score_spread":0.2143945372401918,"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."}}