{"id":"W2007567771","doi":"10.1142/s0219720009004199","title":"GENE LOSS UNDER NEIGHBORHOOD SELECTION FOLLOWING WHOLE GENOME DUPLICATION AND THE RECONSTRUCTION OF THE ANCESTRAL POPULUS GENOME","year":2009,"lang":"en","type":"article","venue":"Journal of Bioinformatics and Computational Biology","topic":"Genome Rearrangement Algorithms","field":"Biochemistry, Genetics and Molecular Biology","cited_by":18,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Ottawa","funders":"","keywords":"Genome; Gene duplication; Biology; Populus trichocarpa; Genetics; Gene; Chromosome; Genome evolution; Segmental duplication; Phylogenomics; Gene family; Computational biology; Phylogenetic tree","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":[0.0002993459,0.0000821992,0.0001453585,0.00004963332,0.00010797,0.00002109826,0.0001026009,0.00007149722,0.000001308269],"category_scores_gemma":[0.00001904371,0.0000455591,0.00008362134,0.00008924319,0.0001269205,0.00001583448,0.0000315611,0.00008258767,3.168813e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001333886,"about_ca_system_score_gemma":0.00005526756,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000001716958,"about_ca_topic_score_gemma":8.322947e-7,"domain_scores_codex":[0.9992998,0.00004725809,0.000397909,0.00006959643,0.00009005405,0.00009541136],"domain_scores_gemma":[0.9993176,0.00001870879,0.0004370863,0.00006668035,0.0001293642,0.00003050935],"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":[0.0008065637,0.0002183641,0.0333946,0.00009856813,0.001245824,0.000001470284,0.001486976,0.06332263,0.7182212,0.01011325,0.00005762447,0.1710329],"study_design_scores_gemma":[0.01092726,0.003005509,0.79907,0.00006699454,0.0003931373,0.003360506,0.001045845,0.0635705,0.007932851,0.1080419,0.001942162,0.0006433253],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9556701,0.0008711602,0.04170215,0.001408343,0.0001236307,0.0001423149,0.00001116425,0.000001750622,0.00006939858],"genre_scores_gemma":[0.9931951,0.0002295239,0.006205643,0.0002160627,0.0001093871,0.000001135934,0.00002956909,0.000003002204,0.00001059059],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.7656754,"threshold_uncertainty_score":0.1857846,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.006985693473040731,"score_gpt":0.2295840473966514,"score_spread":0.2225983539236106,"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."}}