{"id":"W2166123725","doi":"10.1038/nature12352","title":"Insights into the phylogeny and coding potential of microbial dark matter","year":2013,"lang":"en","type":"article","venue":"Nature","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2445,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"Office of International Science and Engineering; British Columbia Knowledge Development Fund; Australian Research Council; Joint Genome Institute; Tula Foundation; Canadian Institute for Advanced Research; Bundesministerium für Bildung und Forschung; University of Nevada, Las Vegas; Woods Hole Oceanographic Institution; Natural Sciences and Engineering Research Council of Canada; Alfred P. Sloan Foundation; Office of Science; National Aeronautics and Space Administration; U.S. Department of Energy; National Science Foundation","keywords":"Tree of life (biology); Biology; Metagenomics; Genome; Phylogenetics; Genomics; Organism; Evolutionary biology; Archaea; Phylum; Computational biology; Comparative genomics; Phylogenomics; Ecology; Genetics; Gene; Clade","routes":{"ca_aff":true,"ca_fund":true,"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":[0.0003386924,0.0004568676,0.0004465886,0.001749804,0.0006416463,0.0008840414,0.0004015151,0.0006611317,0.0009649796],"category_scores_gemma":[0.001248849,0.0003501138,0.0003612154,0.001885836,0.000412533,0.0008575595,0.0006531355,0.0008422839,0.0006180692],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004776812,"about_ca_system_score_gemma":0.0004163518,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0012078,"about_ca_topic_score_gemma":0.001743551,"domain_scores_codex":[0.9997547,0.00002973271,0.00001475167,0.0001041056,0.0000464013,0.00005031811],"domain_scores_gemma":[0.9989733,0.0003993126,0.0002226434,0.0001309678,0.0001442315,0.0001295663],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.000322107,0.00004850043,0.04541593,0.0003131329,0.00004052657,0.0002845653,0.0007523968,0.001393196,0.9002677,0.003273908,0.0001883326,0.0476997],"study_design_scores_gemma":[0.00004985965,0.0004892884,0.6926581,0.0003306917,0.0003254298,0.002254091,0.00157525,0.03372039,0.1951963,0.02208325,0.05115553,0.0001617727],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9811218,0.004131949,0.009932891,0.0002665905,0.00002547756,0.00001227574,0.002050124,0.0001073489,0.002351526],"genre_scores_gemma":[0.9806131,0.002937362,0.01212173,0.0001827019,0.00004711031,0.00001991282,0.003170271,0.00006286723,0.0008448464],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.001749804,"threshold_uncertainty_score":0.003465891,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.002829595861393096,"score_gpt":0.1979417628366231,"score_spread":0.19511216697523,"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."}}