{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002503206,0.0002048799,0.000165872,0.0002361284,0.0003104568,0.0006561493,0.0001954107,0.0004040317,0.0005076803],"category_scores_gemma":[0.001320704,0.0001569842,0.0002442955,0.0001272358,0.0004207433,0.0005834042,0.0002711096,0.0003742115,0.0001132482],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008600909,"about_ca_system_score_gemma":0.0003245302,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001695681,"about_ca_topic_score_gemma":0.001342596,"domain_scores_codex":[0.9999239,0.00002342491,0.000003011111,0.00002157526,0.00001620354,0.00001180255],"domain_scores_gemma":[0.9997562,0.0001440492,0.00003410545,0.00002425379,0.00002172989,0.00001972692],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0001133554,0.00006562939,0.03233402,0.00004993278,0.00007619157,0.0003100709,0.0001741649,0.6965491,0.2138612,0.04010881,0.0003081136,0.01604944],"study_design_scores_gemma":[0.000005647729,0.00004395741,0.006531497,0.000003230266,0.00001031415,0.00007160356,0.00003042797,0.980391,0.005143839,0.007422877,0.0003312498,0.00001433108],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9586796,0.00006627949,0.03959701,0.0001666565,0.000005316195,0.000006641772,0.00003302306,0.00003637786,0.001408964],"genre_scores_gemma":[0.9948461,0.00007616314,0.00472307,0.00002103462,0.000002330696,0.000008551961,0.00002166036,0.00001203024,0.0002890497],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001695681,"threshold_uncertainty_score":0.006240427,"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."}}