{"id":"W4415293309","doi":"10.1371/journal.pcbi.1013574","title":"Stabilized marker gene identification and functional annotation from single-cell transcriptomic data","year":2025,"lang":"en","type":"article","venue":"PLoS Computational Biology","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Hotchkiss Brain Institute; Alberta Children's Hospital; University of Calgary","funders":"New York Stem Cell Foundation","keywords":"Transcriptome; Gene; Annotation; Identification (biology); Lasso (programming language); Consistency (knowledge bases); Gene expression; Gene expression profiling","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001258917,0.0008431022,0.0007559108,0.001047317,0.0003636937,0.001043838,0.0006416496,0.0004646292,0.001357941],"category_scores_gemma":[0.00283542,0.0002702642,0.001042224,0.001117941,0.0003571778,0.0006200824,0.000732378,0.0008332522,0.0009572265],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003173656,"about_ca_system_score_gemma":0.000812439,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0007039282,"about_ca_topic_score_gemma":0.001645446,"domain_scores_codex":[0.999371,0.0001185022,0.00004571736,0.000257189,0.0001615648,0.00004605897],"domain_scores_gemma":[0.9987612,0.0005848617,0.0001810519,0.0002263842,0.0001919102,0.00005461111],"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":[0.0009590386,0.0001381399,0.02322988,0.0009694268,0.0003727681,0.0004902063,0.0002801493,0.03107087,0.8346099,0.00333885,0.006203506,0.09833722],"study_design_scores_gemma":[0.0001056387,0.0003317575,0.04701523,0.00009559228,0.000185125,0.0004673763,0.0002769573,0.5162786,0.4037175,0.01042282,0.02099234,0.0001110151],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.2616282,0.0005939076,0.7003364,0.0002036075,0.00009115318,0.0001816295,0.02237691,0.01284102,0.001747218],"genre_scores_gemma":[0.4157361,0.0005520845,0.5236011,0.0002212676,0.00004763233,0.0005999755,0.05612226,0.001621267,0.001498392],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.001357941,"threshold_uncertainty_score":0.006657839,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03514057272229207,"score_gpt":0.248038691313765,"score_spread":0.2128981185914729,"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."}}