{"id":"W4321482703","doi":"10.1038/s41467-023-36202-y","title":"Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics","year":2023,"lang":"en","type":"article","venue":"Nature Communications","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":22,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Cancer Agency; University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada; Knut och Alice Wallenbergs Stiftelse; Uppsala Multidisciplinary Center for Advanced Computational Science; Linköpings Universitet; Uppsala Universitet; Vetenskapsrådet; Stiftelsen för Strategisk Forskning; Science for Life Laboratory; Michael Smith Health Research BC","keywords":"Biology; Computational biology; Somatic evolution in cancer; Transcriptome; Phenotype; Cancer; Genomics; Genetics; Genome; Gene; Gene expression","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001368761,0.0001274957,0.0001556768,0.00008183633,0.0001934452,0.00001806332,0.000471384,0.0003154559,0.000004090026],"category_scores_gemma":[0.00004779658,0.0001401803,0.0001265168,0.0002604813,0.0001068023,0.000008419735,0.00006214068,0.0002288374,7.264085e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002540311,"about_ca_system_score_gemma":0.00009908391,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002103944,"about_ca_topic_score_gemma":0.0002455024,"domain_scores_codex":[0.9992034,0.00005180635,0.000282136,0.0002035704,0.00007890791,0.0001801161],"domain_scores_gemma":[0.9989393,0.00004658594,0.0001582358,0.0006145905,0.0002021944,0.0000390417],"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":[0.00005064928,0.00008360695,0.006663797,0.00004060006,0.00003791723,4.501056e-8,0.0001063979,0.00004702388,0.9880599,0.0002261701,0.00006603033,0.004617867],"study_design_scores_gemma":[0.001089569,0.0001106604,0.003942913,0.00006389226,0.0001153257,0.000003047631,0.0001250591,0.01393142,0.9451202,0.0001197993,0.03505739,0.0003206984],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9938303,0.001282221,0.003058591,0.0003674614,0.0004442588,0.0002994538,0.0004232553,0.00003294804,0.0002615729],"genre_scores_gemma":[0.9882055,0.0007078613,0.009084022,0.0001406306,0.0001590345,0.00003817805,0.001507886,0.00003629303,0.0001206108],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04293967,"threshold_uncertainty_score":0.5716389,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04548634780047518,"score_gpt":0.3016584610781879,"score_spread":0.2561721132777128,"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."}}