{"id":"W3128667856","doi":"10.1101/2021.02.04.429819","title":"Codon arrangement modulates MHC-I peptides presentation: implications for a SARS-CoV-2 peptide-based vaccine","year":2021,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"vaccines and immunoinformatics approaches","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; Institute for Research in Immunology and Cancer; HEC Montréal","funders":"","keywords":"Context (archaeology); Peptide vaccine; Computational biology; Identification (biology); Codon usage bias; Antigen presentation; Epitope; Biology; Peptide; Population; Virus; Major histocompatibility complex; Genetics; Virology; Genome; Antigen; Gene; T cell; Immune system; Medicine","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0004382499,0.0005613267,0.0004987224,0.0001363482,0.000225879,0.000340658,0.0005653282,0.0004600859,0.000007550446],"category_scores_gemma":[0.0002145982,0.000601268,0.0003487132,0.0002223384,0.00004023087,0.00002166853,0.000443955,0.0002534161,0.000006443538],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008721262,"about_ca_system_score_gemma":0.0004966258,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003934925,"about_ca_topic_score_gemma":0.00001373534,"domain_scores_codex":[0.9976694,0.00007850671,0.0007086153,0.0008673719,0.0001803801,0.0004957331],"domain_scores_gemma":[0.9969185,0.0000383344,0.0004944191,0.0015927,0.0008479427,0.0001080777],"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":[0.00009183981,0.0001883636,0.003262328,0.0006085734,0.0003196495,9.98268e-7,0.0000106292,0.0007177,0.9912523,0.0001052947,0.003436904,0.000005428496],"study_design_scores_gemma":[0.001238579,0.0001473287,0.04934413,0.0001733294,0.0001871259,3.930917e-8,0.00001570694,0.002582223,0.9358546,0.000003931496,0.009718593,0.0007344059],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9641733,0.002065084,0.03018552,0.0009646301,0.0004010268,0.001641409,0.0004574903,0.00009799474,0.00001359315],"genre_scores_gemma":[0.9762685,0.0003166107,0.02094445,0.0005015471,0.0004670424,0.001292765,0.00006669556,0.0001292578,0.00001313814],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.05539769,"threshold_uncertainty_score":0.9996439,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02714596623770584,"score_gpt":0.25997425574493,"score_spread":0.2328282895072242,"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."}}