{"id":"W4362521601","doi":"10.1038/s41564-023-01348-4","title":"Probe-based bacterial single-cell RNA sequencing predicts toxin regulation","year":2023,"lang":"en","type":"article","venue":"Nature Microbiology","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":117,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institute of General Medical Sciences; National Heart, Lung, and Blood Institute; Natural Sciences and Engineering Research Council of Canada; Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada; U.S. Department of Health and Human Services; National Institutes of Health; Harvard University","keywords":"Biology; Bacillus subtilis; Transcriptome; Escherichia coli; Clostridium perfringens; RNA; Context (archaeology); RNA-Seq; Gene; Computational biology; Bacterial genetics; Bacterial cell structure; Cell; Genetics; Gene expression; Bacteria","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002133581,0.0002132796,0.0002024292,0.0001199577,0.0001039577,0.00002057399,0.0002003645,0.001065046,0.00005519093],"category_scores_gemma":[0.00003378197,0.0002041438,0.00008956777,0.0002139944,0.00008912152,0.000003766252,0.00007665085,0.0003312366,0.00008263882],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008074832,"about_ca_system_score_gemma":0.0002368563,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00000502652,"about_ca_topic_score_gemma":0.00004643111,"domain_scores_codex":[0.9986651,0.0001098202,0.0002588092,0.0004589861,0.00003903985,0.0004682594],"domain_scores_gemma":[0.9993979,0.00001850245,0.00009513331,0.0003234386,0.00008956482,0.00007544016],"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":[0.00008537964,0.00002865456,0.0001206755,0.00006104232,0.00001421556,0.000004007072,0.00002664988,0.0000678707,0.9704416,0.00002201605,0.02883632,0.0002915543],"study_design_scores_gemma":[0.0008584058,0.0002969368,0.0007513334,0.0000197916,0.00001152878,0.00002852222,0.0000100764,0.00003506528,0.9079796,0.00004440447,0.08975498,0.0002093658],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9958274,0.0005206282,0.0003663463,0.000524057,0.001195112,0.0003652436,0.0001613482,0.0001296805,0.0009101949],"genre_scores_gemma":[0.9914109,0.00003765629,0.001432836,0.0009386077,0.0005865034,0.00001439438,0.004658807,0.00004026236,0.0008800427],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.06246203,"threshold_uncertainty_score":0.8324745,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01054032399567986,"score_gpt":0.2357461131808092,"score_spread":0.2252057891851293,"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."}}