{"id":"W4225688524","doi":"10.1038/s41592-022-01436-z","title":"Antigen identification and high-throughput interaction mapping by reprogramming viral entry","year":2022,"lang":"en","type":"article","venue":"Nature Methods","topic":"Virus-based gene therapy research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":119,"is_retracted":false,"has_abstract":false,"ca_institutions":"","funders":"National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; National Institute on Drug Abuse; National Research Foundation Singapore; National Cancer Institute; National Research Foundation; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; National Heart, Lung, and Blood Institute; Michelson Prize and Grants; Schmidt Futures; Pfizer; Ludwig Center for Molecular Oncology; Cancer Research Foundation; Canadian Institutes of Health Research; National Science Foundation; Damon Runyon Cancer Research Foundation; Cancer Research Institute; National Institutes of Health; Pew Charitable Trusts; U.S. Department of Health and Human Services; Ludwig Center at Harvard; Government of Canada; David and Lucile Packard Foundation; U.S. Department of Defense","keywords":"Biology; Computational biology; Reprogramming; Antigen; DECIPHER; Chimeric antigen receptor; Virology; Cell biology; Immune system; Genetics; T cell; Cell","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":[],"consensus_categories":[],"category_scores_codex":[0.00158828,0.0001124541,0.0001088432,0.00007000086,0.0002572176,0.00005223106,0.0001814158,0.0001665128,0.0000548859],"category_scores_gemma":[0.0001475998,0.0001214261,0.00005179256,0.00017037,0.00004275883,0.000007710899,0.0002351573,0.0005487448,0.000001574007],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004446803,"about_ca_system_score_gemma":0.00003149385,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001985213,"about_ca_topic_score_gemma":0.000004914709,"domain_scores_codex":[0.9982256,0.0007224667,0.0001775288,0.0004726715,0.0001946958,0.0002070903],"domain_scores_gemma":[0.999405,0.00003352003,0.00009693596,0.000364902,0.00005211278,0.00004758326],"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":[0.0002777689,0.00003081855,0.0002575807,0.000007163727,0.00004143161,0.000001265405,0.00006498618,0.00001446677,0.803902,0.00002018248,0.002246576,0.1931357],"study_design_scores_gemma":[0.0002699526,0.0003663231,0.0004451285,0.000002628799,0.000005055947,0.00001661032,0.0002010545,0.0001425247,0.7494456,0.000188434,0.2487931,0.0001235985],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9536713,0.009677254,0.03507519,0.0005178901,0.0005832583,0.0002669921,0.00002317239,0.00002808816,0.0001568322],"genre_scores_gemma":[0.9649537,0.0005559306,0.0322901,0.0004285578,0.0002348176,0.00008566002,0.0004126079,0.00003065218,0.001008019],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2465465,"threshold_uncertainty_score":0.4951612,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01837693257654908,"score_gpt":0.393387570340835,"score_spread":0.3750106377642859,"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."}}