{"id":"W2903633084","doi":"10.1101/488676","title":"Codon usage and amino acid identity are major determinants of mRNA stability in humans","year":2018,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"RNA and protein synthesis mechanisms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":8,"is_retracted":false,"has_abstract":true,"ca_institutions":"SickKids Foundation; Hospital for Sick Children; University of Toronto","funders":"Canadian Institutes of Health Research; National Institutes of Health","keywords":"Open reading frame; Messenger RNA; Codon usage bias; Biology; Translation (biology); Untranslated region; Amino acid; Genetics; Gene; Peptide sequence; Protein biosynthesis; Start codon; Computational biology; Genome","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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002269773,0.0001528375,0.0003261906,0.0003464214,0.0001677657,0.000356235,0.00005679964,0.0001911874,0.001039592],"category_scores_gemma":[0.0003891182,0.0001122661,0.0001681157,0.00039707,0.0002104743,0.0001171581,0.0001261467,0.0001816442,0.0003222103],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001195248,"about_ca_system_score_gemma":0.0001009319,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003952303,"about_ca_topic_score_gemma":0.0006262404,"domain_scores_codex":[0.9997833,0.00003726302,0.0000203145,0.00009126408,0.00004743938,0.0000204116],"domain_scores_gemma":[0.9998024,0.00004853141,0.00008918354,0.00001814784,0.00002109974,0.00002065],"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":[0.0009126097,0.00002391583,0.1057519,0.0001293728,0.000120792,0.000498505,0.0002224648,0.0004035626,0.8654065,0.0004498367,0.0004488195,0.02563176],"study_design_scores_gemma":[0.00001870563,0.0002596028,0.8394966,0.00003091942,0.0001313089,0.003288597,0.0001772309,0.001326176,0.1475427,0.001134133,0.006559989,0.00003395788],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9933636,0.00266403,0.002105293,0.00005691804,0.000009141065,0.00000370745,0.0007888483,0.00004170234,0.000966707],"genre_scores_gemma":[0.9960127,0.0006562307,0.002052437,0.00007636176,0.00001505371,0.000006223795,0.000653267,0.00003823701,0.000489514],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001039592,"threshold_uncertainty_score":0.003477812,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01801776733825018,"score_gpt":0.2416999440843481,"score_spread":0.2236821767460979,"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."}}