{"id":"W4390615391","doi":"10.1038/s41559-023-02281-9","title":"Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data","year":2024,"lang":"en","type":"article","venue":"Nature Ecology & Evolution","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":32,"is_retracted":false,"has_abstract":false,"ca_institutions":"","funders":"Natural Sciences and Engineering Research Council of Canada; Government of Canada; Gruber Foundation","keywords":"Biology; Phylogenetic tree; Phylogenetics; Evolutionary biology; Clade; Cell type; Computational biology; Cell; Gene; Genetics","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.000302921,0.0002599746,0.0002604794,0.00007885259,0.0001796751,0.00003838752,0.0003914951,0.001066437,0.00003757188],"category_scores_gemma":[0.00008440005,0.0002636794,0.0001229335,0.0003109174,0.0002754373,0.00004861706,0.000174807,0.000542935,0.00002474905],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002927649,"about_ca_system_score_gemma":0.000324056,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00007716188,"about_ca_topic_score_gemma":0.0003785631,"domain_scores_codex":[0.998174,0.0001179811,0.0003927845,0.0007356872,0.0001667685,0.0004127747],"domain_scores_gemma":[0.9989064,0.00004540579,0.0001663758,0.0006048171,0.0002278801,0.00004908028],"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":[0.0001207273,0.0001185332,0.005144664,0.0001951312,0.00004226492,0.000003813783,0.0001704017,0.0002362753,0.9898112,0.0001375625,0.003778076,0.0002413864],"study_design_scores_gemma":[0.0006997365,0.0007281887,0.005878072,0.00005561271,0.0001359435,0.00006634746,0.000695365,0.001555636,0.9776021,0.0006680741,0.01150333,0.0004115545],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9691925,0.01723824,0.005371607,0.00007776147,0.004282488,0.0002331178,0.0002330985,0.00006269008,0.003308516],"genre_scores_gemma":[0.994446,0.0004656633,0.002319111,0.00005833149,0.0007664212,0.000005296683,0.0006836118,0.00003945391,0.001216072],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02525356,"threshold_uncertainty_score":0.9999815,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02360358273972969,"score_gpt":0.2580067490718485,"score_spread":0.2344031663321188,"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."}}