{"id":"W3141950101","doi":"10.1186/s13059-021-02307-0","title":"PCIP-seq: simultaneous sequencing of integrated viral genomes and their insertion sites with long reads","year":2021,"lang":"en","type":"article","venue":"Genome biology","topic":"T-cell and Retrovirus Studies","field":"Immunology and Microbiology","cited_by":41,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan","funders":"Amis de l'Institut Bordet; Fonds Wetenschappelijk Onderzoek; Vlaamse regering; Fonds De La Recherche Scientifique - FNRS","keywords":"Biology; Genome; Endogenous retrovirus; Computational biology; Genetics; Structural variation; Sequence (biology); Human genome; Whole genome sequencing; Reference genome; Long terminal repeat; Virology; 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":[0.0001070253,0.0002157969,0.0004448296,0.00009109521,0.0001691004,0.000006580473,0.0001044193,0.0002679205,0.0001417402],"category_scores_gemma":[0.00006511403,0.0001357416,0.00005326133,0.0001322015,0.0005540387,0.00003064849,0.0001342959,0.0002125191,0.00003274522],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005922752,"about_ca_system_score_gemma":0.000113595,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0001825731,"about_ca_topic_score_gemma":0.0003146006,"domain_scores_codex":[0.998836,0.0001922177,0.0002650276,0.0003562053,0.00001303004,0.0003375431],"domain_scores_gemma":[0.9993057,0.0001920766,0.0001250808,0.000197858,0.0001594328,0.00001990133],"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":[0.0001777587,0.00003595043,0.02826265,0.00002919772,0.0003581084,0.0000258138,0.001169064,0.00001900738,0.9641718,0.0002352908,0.000009874347,0.005505476],"study_design_scores_gemma":[0.002341423,0.002391322,0.02264496,0.00006393086,0.0001623586,0.0009413165,0.005475903,0.00002949254,0.934402,0.0008846281,0.02993065,0.0007319378],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9607271,0.03810101,0.000247129,0.0000938858,0.0001776033,0.0001096352,0.0001058517,0.00004905416,0.0003887148],"genre_scores_gemma":[0.9964671,0.001369314,0.0001315771,0.000110355,0.00003322764,0.000007636614,0.0004268395,0.0000141963,0.001439743],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03673169,"threshold_uncertainty_score":0.5535381,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01316663498700975,"score_gpt":0.2109361431785297,"score_spread":0.1977695081915199,"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."}}