{"id":"W2810995872","doi":"10.1093/molbev/msy131","title":"Evolution on the Biophysical Fitness Landscape of an RNA Virus","year":2018,"lang":"en","type":"article","venue":"Molecular Biology and Evolution","topic":"Evolution and Genetic Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":71,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal","funders":"Materials Research Science and Engineering Center, Harvard University; National Institute of General Medical Sciences; National Natural Science Foundation of China; National Institutes of Health; National Science Foundation","keywords":"Fitness landscape; Biology; Epistasis; Viral evolution; Capsid; Evolutionary biology; Evolutionary dynamics; Population; Molecular evolution; Genetic Fitness; Folding (DSP implementation); Selection (genetic algorithm); Experimental evolution; Viral entry; RNA; Virus; Computational biology; Genetics; Viral replication; Biological evolution; Genome; 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":[0.0002065081,0.0001372692,0.0001178439,0.00005106874,0.0001531732,0.00000687788,0.0001512529,0.0002265385,0.0000187264],"category_scores_gemma":[0.00007297155,0.0001028181,0.00006044596,0.0001194327,0.0005181751,0.00000360347,0.00007518283,0.00008536837,0.00001479479],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001323038,"about_ca_system_score_gemma":0.00004289753,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003952112,"about_ca_topic_score_gemma":0.00006078027,"domain_scores_codex":[0.9990561,0.0001865805,0.0001609188,0.0003206356,0.00007567666,0.0002000881],"domain_scores_gemma":[0.9993889,0.00001135072,0.00007880989,0.0003519513,0.0001107036,0.00005825088],"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":[0.0001476906,0.00008070582,0.001520372,0.000004183079,0.00002776424,4.526184e-7,0.00001786773,0.00008009058,0.9566635,0.04084035,0.0002456794,0.00037126],"study_design_scores_gemma":[0.001775912,0.007004187,0.1893092,0.00003752364,0.0001079291,0.00005520954,0.0002622977,0.03500369,0.734521,0.02768634,0.003473539,0.0007631989],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9532776,0.0003083768,0.04504085,0.0002016608,0.0001506067,0.0001265692,0.00002812363,0.000012695,0.0008534607],"genre_scores_gemma":[0.9990052,0.00002737053,0.0002875195,0.0002394704,0.0002146821,0.00001172023,0.0001233631,0.00001139789,0.00007930274],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.2221426,"threshold_uncertainty_score":0.41928,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.005157655913066714,"score_gpt":0.2537515167730834,"score_spread":0.2485938608600167,"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."}}