{"id":"W2130640131","doi":"10.1101/gr.5383506","title":"Reconstructing contiguous regions of an ancestral genome","year":2006,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":302,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"National Cancer Institute; National Institutes of Health; Howard Hughes Medical Institute; U.S. Public Health Service; Broad Institute; National Human Genome Research Institute","keywords":"Biology; Genome; Breakpoint; Human genome; Lineage (genetic); Chromosome; Genetics; Evolutionary biology; Ancestor; Most recent common ancestor; Sequence (biology); Computational biology; 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":[0.0006015977,0.0001136041,0.0001703691,0.0001015105,0.0001966748,0.00002430025,0.0002980239,0.000100048,0.00002263994],"category_scores_gemma":[0.00003974445,0.0001141005,0.00007119622,0.0001710905,0.0003408814,9.618826e-7,0.0001644182,0.0001312921,0.000006098955],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001761954,"about_ca_system_score_gemma":0.0001182601,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000337405,"about_ca_topic_score_gemma":0.0001368014,"domain_scores_codex":[0.9985879,0.0001239441,0.0002565242,0.0003650511,0.0001996905,0.0004668578],"domain_scores_gemma":[0.9991333,0.00002070694,0.00006705595,0.0004304892,0.000266865,0.00008159984],"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":[0.0000339413,0.00004920039,0.004384228,0.00001717578,0.00003289205,0.000004363681,0.00005063688,0.0001698237,0.9937826,0.000468416,0.00005349894,0.0009532209],"study_design_scores_gemma":[0.002635283,0.00328938,0.372637,0.00003419393,0.00004745001,0.000259883,0.002832082,0.0001404119,0.408162,0.01285184,0.1958924,0.001218099],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9903558,0.002858074,0.00007616435,0.00007134736,0.00005970282,0.000199627,0.00008016919,0.000002658007,0.006296402],"genre_scores_gemma":[0.9960406,0.000350564,0.00237845,0.00001019462,0.0004544331,0.00002020628,0.00007730741,0.00002059592,0.0006476268],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5856206,"threshold_uncertainty_score":0.4652884,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06058883880245984,"score_gpt":0.3356076091649754,"score_spread":0.2750187703625155,"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."}}