{"id":"W2915269011","doi":"10.1101/558130","title":"Pooled CRISPR Inverse PCR sequencing (PCIP-seq): simultaneous sequencing of retroviral insertion points and the associated provirus in thousands of cells with long reads","year":2019,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"T-cell and Retrovirus Studies","field":"Immunology and Microbiology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan","funders":"Vlaamse regering; Amis de l'Institut Bordet; Université de Liège; Fonds Wetenschappelijk Onderzoek","keywords":"Minion; Provirus; CRISPR; Nanopore sequencing; Inverse polymerase chain reaction; Endogenous retrovirus; DNA sequencing; Deep sequencing; Genome; Identification (biology)","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":[0.0009133327,0.000514583,0.0006865505,0.0004608846,0.0003504254,0.0007369017,0.0005250889,0.0006305421,0.00218468],"category_scores_gemma":[0.001212747,0.0004075086,0.0004590302,0.0003811159,0.0004239496,0.0004059057,0.0009630714,0.001025986,0.001164791],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0003116098,"about_ca_system_score_gemma":0.0003959734,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0006623571,"about_ca_topic_score_gemma":0.002114076,"domain_scores_codex":[0.9992529,0.00008904284,0.00005224504,0.0003287597,0.0002216727,0.0000553539],"domain_scores_gemma":[0.9991233,0.0002987334,0.000138411,0.0001952116,0.0001391456,0.0001052683],"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":[0.0001318662,0.00002829836,0.002098312,0.0001532851,0.00007982699,0.00009864559,0.00007864532,0.001329757,0.977479,0.0004097183,0.001080959,0.01703162],"study_design_scores_gemma":[0.00003065727,0.0002214834,0.009696258,0.00002645487,0.00007035483,0.0005497169,0.0000874712,0.01788479,0.9565065,0.001264184,0.01361488,0.0000472353],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.4773974,0.001546308,0.4949637,0.0004723339,0.0003230817,0.0003337509,0.01298446,0.006904433,0.0050744],"genre_scores_gemma":[0.5607627,0.0006480968,0.4206405,0.0006821565,0.0001067784,0.0004828968,0.01064448,0.00116569,0.004866838],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.00218468,"threshold_uncertainty_score":0.007308543,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01079683934733902,"score_gpt":0.200142631234738,"score_spread":0.189345791887399,"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."}}