{"id":"W4280542175","doi":"10.1093/genetics/iyac074","title":"Reconstruction of full-length LINE-1 progenitors from ancestral genomes","year":2022,"lang":"en","type":"article","venue":"Genetics","topic":"Chromosomal and Genetic Variations","field":"Agricultural and Biological Sciences","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; University of British Columbia; University of Toronto","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institutes of Health Research","keywords":"Biology; Retrotransposon; Subfamily; ORFS; Genome; Genetics; Human genome; Zinc finger; Evolutionary biology; Gene; Transposable element; Computational biology; Peptide sequence; Open reading frame; Transcription factor","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":"codex-gemma-dda1882f352a","candidate_categories":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.00004769885,0.00006748363,0.00009047206,0.000007069153,0.0001785291,0.00001065723,0.0001525982,0.00002964464,0.00138582],"category_scores_gemma":[0.00000531967,0.00003253531,0.00005802223,0.0001927095,0.00003349242,0.00001540827,0.00008143641,0.0000666035,0.000006474785],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001509788,"about_ca_system_score_gemma":0.00001417724,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005811502,"about_ca_topic_score_gemma":0.0002645053,"domain_scores_codex":[0.9993438,0.00004507353,0.0001758234,0.000160506,0.0001524176,0.0001223886],"domain_scores_gemma":[0.9997522,0.0000385983,0.00008721307,0.0000468053,0.00003318776,0.00004201302],"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":[0.00001647657,0.00008635577,0.05980472,0.00000198248,0.00002481446,0.000001088742,0.0001636212,0.0006386906,0.659284,0.00005511643,0.00007166639,0.2798514],"study_design_scores_gemma":[0.0008206858,0.003300166,0.6905829,0.00001608533,0.0001568001,0.000159884,0.004391236,0.00429637,0.1571736,0.01549671,0.1226812,0.0009243279],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9980334,0.00070335,0.000003510279,0.0002979474,0.0003472231,0.0001118765,0.0003351828,0.00002112376,0.0001463667],"genre_scores_gemma":[0.9975015,0.00008389973,0.001838207,0.0000254422,0.0003758852,0.00001933311,0.00009966396,6.666293e-7,0.00005541746],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6307782,"threshold_uncertainty_score":0.999527,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02342164936196258,"score_gpt":0.2123254933578992,"score_spread":0.1889038439959366,"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."}}