{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001117861,0.0008789096,0.0008454964,0.0008801806,0.000905714,0.001384406,0.000939352,0.0009451088,0.003258222],"category_scores_gemma":[0.002244052,0.000637835,0.0008141067,0.001108216,0.0005753351,0.0007473276,0.001469092,0.002014108,0.002266668],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004811275,"about_ca_system_score_gemma":0.0009277027,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001296753,"about_ca_topic_score_gemma":0.005356046,"domain_scores_codex":[0.9990399,0.0001272481,0.00006009117,0.0004080638,0.0002855112,0.00007911244],"domain_scores_gemma":[0.9986498,0.0004363284,0.0002007141,0.0002433946,0.0003105136,0.0001593228],"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":[0.0004756423,0.0001342586,0.006264112,0.0008339412,0.0003161766,0.0003000059,0.0005215123,0.003057586,0.9198527,0.002994298,0.01172252,0.0535273],"study_design_scores_gemma":[0.0001345496,0.0005715081,0.02833593,0.0001874474,0.0002604952,0.001179588,0.0005064551,0.05702705,0.800128,0.01049432,0.1009108,0.0002637801],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.2097906,0.00344794,0.6863957,0.0007505492,0.0009328949,0.001174368,0.06670463,0.01353645,0.0172669],"genre_scores_gemma":[0.2425591,0.001975501,0.681326,0.001973484,0.0002757402,0.001831297,0.0580496,0.002800653,0.009208752],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.003258222,"threshold_uncertainty_score":0.01089984,"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."}}