{"id":"W2030114807","doi":"10.1038/nature02601","title":"Positive selection at sites of multiple amino acid replacements since rat–mouse divergence","year":2004,"lang":"en","type":"article","venue":"Nature","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":78,"is_retracted":false,"has_abstract":false,"ca_institutions":"","funders":"Wellcome Trust; Medical Research Council; Genome Canada","keywords":"Lineage (genetic); Biology; Negative selection; Genetics; Positive selection; Gene; Amino acid; Selection (genetic algorithm); Genome; Mutation; Silent mutation; Evolutionary biology; Synonymous substitution; Divergence (linguistics); Gene conversion; Codon usage bias","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":[0.00004998367,0.000110337,0.00009833279,0.00001905483,0.00009909488,0.000004709935,0.000100152,0.0004005764,0.000006022601],"category_scores_gemma":[0.00007392347,0.0001034771,0.00005599804,0.00006713699,0.00004569063,8.297891e-7,0.0001372756,0.0001900025,0.000004291992],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003074896,"about_ca_system_score_gemma":0.00002726562,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00002061739,"about_ca_topic_score_gemma":0.0001742403,"domain_scores_codex":[0.9993742,0.0000162974,0.0001105907,0.0002533561,0.0001057414,0.0001397961],"domain_scores_gemma":[0.9995941,0.000006438504,0.00007591919,0.0001520865,0.0001394413,0.00003202159],"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":[0.0001169898,0.00004296317,0.04262248,0.000008150636,0.0000565234,6.991414e-7,0.00007654796,0.0002275958,0.9561748,0.00004434257,0.0005563105,0.00007258961],"study_design_scores_gemma":[0.000490293,0.0002176839,0.03056818,0.000006055943,0.00001430289,0.000004922057,0.00002528113,0.000006549233,0.9651641,0.00003402241,0.003360048,0.0001086074],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9966438,0.002577972,0.00009477733,0.00008852215,0.0001508882,0.0001281547,0.0000697655,0.000003207098,0.0002429302],"genre_scores_gemma":[0.9976237,0.0003000051,0.0009984588,0.0002309679,0.00007739358,0.000006063761,0.00008356404,0.000008651634,0.0006712312],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.0120543,"threshold_uncertainty_score":0.4219675,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005645573258702886,"score_gpt":0.2309633589091548,"score_spread":0.2253177856504519,"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."}}