{"id":"W2768144926","doi":"10.1101/gr.226050.117","title":"Discovery of noncanonical translation initiation sites through mass spectrometric analysis of protein N termini","year":2017,"lang":"en","type":"article","venue":"Genome Research","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":101,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"Edgewood Chemical Biological Center; National Cancer Institute; National Institutes of Health; Fonds Wetenschappelijk Onderzoek; National Institute on Aging; National Research Foundation; Johns Hopkins University; Vlaamse regering; National Research Foundation of Korea","keywords":"Ribosome profiling; Biology; Eukaryotic translation; Start codon; Translation (biology); Open reading frame; Five prime untranslated region; Initiation factor; Shine-Dalgarno sequence; Stop codon; Internal ribosome entry site; Genetics; Protein biosynthesis; Translational regulation; Ribosome; Computational biology; Untranslated region; Cell biology; Amino acid; Messenger RNA; Peptide sequence; RNA; Gene","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":[],"consensus_categories":[],"category_scores_codex":[0.0010118,0.00008227048,0.0002323418,0.0003291148,0.0001390224,0.00005153783,0.0004037326,0.0001294933,0.00004679441],"category_scores_gemma":[0.0003327606,0.00007553901,0.0001612225,0.0004646826,0.0001595115,0.00002035353,0.00008635469,0.00008618007,0.00000349211],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001611352,"about_ca_system_score_gemma":0.000116566,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006442418,"about_ca_topic_score_gemma":0.00002743595,"domain_scores_codex":[0.9986496,0.000194344,0.0002611746,0.0002659799,0.0004024723,0.0002264226],"domain_scores_gemma":[0.9988918,0.00004754403,0.00018384,0.000674071,0.0001726788,0.00003008112],"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":[0.0001066803,0.00004972405,0.001345782,0.00004438215,0.0002369042,0.000001426025,0.00005386045,0.00001046118,0.9959001,0.0003527231,0.000002083387,0.001895849],"study_design_scores_gemma":[0.0002001826,0.0003756532,0.02294177,0.00001017354,0.00007296046,3.737514e-7,0.00003372454,0.00003956683,0.9749974,0.0009548941,0.0002929151,0.00008039505],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9844154,0.0008222962,0.01111116,0.0001087317,0.00001246812,0.0003521638,0.00006881256,0.000002086457,0.003106888],"genre_scores_gemma":[0.9957352,0.0002579241,0.00349066,0.000002767847,0.00007282676,0.00003610012,0.0001029049,0.00001108316,0.0002905345],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02159598,"threshold_uncertainty_score":0.3080392,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1103920258246406,"score_gpt":0.3859582026845067,"score_spread":0.2755661768598661,"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."}}