{"id":"W4404838925","doi":"10.1016/j.cels.2024.11.001","title":"Tracking the gene expression programs and clonal relationships that underlie mast, myeloid, and T lineage specification from stem cells","year":2024,"lang":"en","type":"article","venue":"Cell Systems","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":11,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre; Université de Montréal; Institute for Research in Immunology and Cancer; University of British Columbia; University of Manitoba; Research Institute in Oncology and Hematology; CancerCare Manitoba","funders":"Wellcome Leap; Royal Commission for the Exhibition of 1851; Michael Smith Health Research BC; Allen Institute; European Molecular Biology Organization","keywords":"Stem cell; Biology; Lineage (genetic); Myeloid; Gene; Cell lineage; Gene expression; Gene expression profiling; Mast (botany); Genetics; Mast cell; Cell biology; Cellular differentiation; Immunology","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":[0.000235516,0.0001376851,0.000109849,0.00002095289,0.0001675884,0.0002619593,0.0000945542,0.0001647544,0.0000020032],"category_scores_gemma":[0.000002145788,0.00009943156,0.00004086812,0.00004781524,0.00006445746,0.00000910912,0.00003293944,0.0001532913,0.000006228739],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001198936,"about_ca_system_score_gemma":0.00002094765,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003855625,"about_ca_topic_score_gemma":0.00001440077,"domain_scores_codex":[0.9990789,0.0001170498,0.0001914532,0.0003606903,0.0001147954,0.0001371257],"domain_scores_gemma":[0.9995895,0.00005352788,0.00005423467,0.0002167678,0.0000240346,0.00006195523],"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":[0.00001964865,0.00001978077,0.004994768,0.00008918792,0.00001931705,0.000003989974,0.0003501409,0.00005092244,0.9906814,0.00004526225,0.0002546097,0.003470963],"study_design_scores_gemma":[0.0003314197,0.00007659617,0.001944405,0.0001699683,0.00004817553,0.00001892616,0.001006503,0.003374854,0.9454805,0.00003345907,0.04728005,0.0002351952],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9644415,0.01909189,0.01497451,0.00005818014,0.0006397748,0.0003825582,0.00002529214,0.0000325848,0.0003536611],"genre_scores_gemma":[0.997186,0.0007518116,0.000276604,0.00001207747,0.0006004827,0.0000258845,0.0001394955,0.00002746211,0.0009801788],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.04702545,"threshold_uncertainty_score":0.4054701,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05850306888950981,"score_gpt":0.2196282022808357,"score_spread":0.1611251333913259,"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."}}