{"id":"W4409302720","doi":"10.1038/s41596-025-01157-5","title":"Transcriptomic profiling of individual bacteria by MATQ-seq","year":2025,"lang":"en","type":"review","venue":"Nature Protocols","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":8,"is_retracted":false,"has_abstract":false,"ca_institutions":"University of Toronto","funders":"Deutsche Forschungsgemeinschaft","keywords":"Computational biology; Transcriptome; Profiling (computer programming); Biology; RNA-Seq; Bioinformatics; Computer science; Genetics; Gene expression; Gene","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":["metaepi_narrow","research_integrity"],"consensus_categories":[],"category_scores_codex":[0.0002560265,0.0004453456,0.001118896,0.00008303491,0.00005369474,0.0000335861,0.0006855021,0.00132864,0.00001011808],"category_scores_gemma":[0.00006234912,0.0003684741,0.0004602657,0.0001495353,0.00006810367,5.571047e-7,0.0002244478,0.0005168555,0.000002341868],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001616225,"about_ca_system_score_gemma":0.0004263652,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001235586,"about_ca_topic_score_gemma":0.000001900916,"domain_scores_codex":[0.9982896,0.000122336,0.0005785855,0.0005545926,0.0001766954,0.0002781702],"domain_scores_gemma":[0.9989946,0.0000264178,0.0003307994,0.000500439,0.00009702391,0.00005067037],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001155559,0.0002471941,0.000058838,0.08224477,0.001847135,0.000002595692,0.00004476236,3.91938e-7,0.08488924,0.0002805436,0.02326164,0.8070073],"study_design_scores_gemma":[0.0003074128,0.0001549713,0.000006670335,0.003691631,0.0002733963,0.000005062107,0.000004102511,5.600898e-8,0.0186559,0.00003665712,0.976548,0.0003161656],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.00004725624,0.9442882,0.00001922795,0.000008668848,0.0001622744,0.05341522,0.001456049,0.000004949086,0.0005981577],"genre_scores_gemma":[0.0000337095,0.9200374,0.001490281,0.00007334099,0.000207529,0.07671777,0.0008553397,0.00005122073,0.0005334145],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.9532863,"threshold_uncertainty_score":0.9999679,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02092539386099688,"score_gpt":0.3489943328005433,"score_spread":0.3280689389395464,"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."}}