{"id":"W3139316222","doi":"10.1186/s12866-021-02158-6","title":"Human cell-dependent, directional, time-dependent changes in the mono- and oligonucleotide compositions of SARS-CoV-2 genomes","year":2021,"lang":"en","type":"article","venue":"BMC Microbiology","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":19,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Japan Society for the Promotion of Science; Research Organization of Information and Systems; Core Research for Evolutional Science and Technology; Institute of Genetics; Japan Agency for Medical Research and Development","keywords":"Biology; Genome; Clade; Population; Coronavirus; Host adaptation; Adaptation (eye); Virus; Oligonucleotide; Host (biology); Coronaviridae; Virology; Gene; Genetics; Evolutionary biology; Coronavirus disease 2019 (COVID-19); Phylogenetics; Disease; Infectious disease (medical specialty)","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":[0.0003314024,0.0001508702,0.0003442792,0.0001926153,0.0001112705,0.00001895432,0.0001662017,0.0001340103,0.00004445918],"category_scores_gemma":[0.00003248841,0.0001187574,0.00007592462,0.0002001678,0.0002072813,0.00002564288,0.0001461195,0.0002501528,0.00006989722],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005992226,"about_ca_system_score_gemma":0.0001405501,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002700042,"about_ca_topic_score_gemma":0.00216265,"domain_scores_codex":[0.9987136,0.0002853525,0.0002590743,0.0003518877,0.00009338488,0.0002967554],"domain_scores_gemma":[0.9992698,0.0002048831,0.00007425225,0.00032273,0.0001128154,0.00001547265],"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":[0.00005801615,0.0003053335,0.023032,0.00009758212,0.00004295624,0.00006380707,0.0003517823,7.141859e-7,0.9750091,0.00007155603,0.0008694693,0.00009766873],"study_design_scores_gemma":[0.001300784,0.0001964936,0.007675166,0.00003517628,0.00004742124,0.000591305,0.0003381653,0.00001381323,0.9731084,0.00008274271,0.01649276,0.0001178099],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.993361,0.002517237,0.00002474295,0.0005611596,0.00006274472,0.00033538,0.00007335323,0.00002545599,0.003038917],"genre_scores_gemma":[0.9895625,0.00005494886,0.0002639384,0.00965136,0.0001010314,0.00004321701,0.00005561829,0.0000209464,0.000246461],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01562329,"threshold_uncertainty_score":0.4842788,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04896130018538487,"score_gpt":0.3334713145669643,"score_spread":0.2845100143815795,"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."}}