{"id":"W2108147510","doi":"10.1101/gr.170753.113","title":"T-cell receptor repertoires share a restricted set of public and abundant CDR3 sequences that are associated with self-related immunity","year":2014,"lang":"en","type":"article","venue":"Genome Research","topic":"T-cell and B-cell Immunology","field":"Immunology and Microbiology","cited_by":196,"is_retracted":false,"has_abstract":true,"ca_institutions":"Institute of Infection and Immunity","funders":"Planning and Budgeting Committee of the Council for Higher Education of Israel; Israeli Centers for Research Excellence; Israel Science Foundation; Minerva Foundation","keywords":"Biology; T-cell receptor; Genetics; Repertoire; Major histocompatibility complex; Complementarity determining region; V(D)J recombination; Gene; T cell; Recombination; Immune system; Peptide sequence","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":"codex-gemma-dda1882f352a","candidate_categories":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.002240612,0.000293645,0.0006029903,0.0005430066,0.0007880698,0.00006937627,0.0007324487,0.000647646,0.0009462428],"category_scores_gemma":[0.0007692789,0.0002237508,0.00007997792,0.0009867118,0.001314246,0.0001611679,0.0004588801,0.001396872,0.0002884784],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000155431,"about_ca_system_score_gemma":0.0003093896,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0008095336,"about_ca_topic_score_gemma":0.0001685669,"domain_scores_codex":[0.9945135,0.003119434,0.0004670444,0.0006065227,0.0002117671,0.001081775],"domain_scores_gemma":[0.9970745,0.001129132,0.000347594,0.0006735612,0.0006871246,0.0000880958],"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":[0.0001793995,0.0003305679,0.01669349,0.00007872283,0.0004814791,0.00001248969,0.001322546,0.00000122209,0.9788155,0.0001371914,0.001323174,0.0006242432],"study_design_scores_gemma":[0.01544053,0.007515776,0.158924,0.0007418675,0.0002472048,0.0003089086,0.01422552,0.00005465001,0.6431005,0.001068231,0.156385,0.001987829],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9875153,0.008518069,0.000004243047,0.0007875708,0.0001244305,0.0004886166,0.000159426,0.0001619177,0.002240481],"genre_scores_gemma":[0.9921779,0.001378956,0.00005033292,0.00002089317,0.00001709704,0.00005066909,0.0006542309,0.000038195,0.005611751],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.335715,"threshold_uncertainty_score":0.999967,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.05526368847924804,"score_gpt":0.2734957500293038,"score_spread":0.2182320615500557,"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."}}